From 5daaab4ed750b7fe11df892a58d99c23e914e618 Mon Sep 17 00:00:00 2001 From: Christos Kopanos Date: Sun, 29 Mar 2026 12:50:00 +0300 Subject: [PATCH 1/6] refactor(DEV-1896)!: complete rewrite of varsome-api-client-python v1 BREAKING CHANGE: models/elements/* consolidated into models/annotation.py; CLI moved from scripts/ to varsome_api/cli/ package; client and VCF interfaces rewritten. - Migrate build tooling from setup.py/tox.ini to Poetry - Rewrite client.py with improved async/sync support via _sync.py - Rewrite vcf.py with expanded VCF annotation handling - Consolidate all fragmented models/elements/* into models/annotation.py - Add models/slim/ for lightweight annotation models - Restructure CLI into varsome_api/cli/ package (varsome_api_run, varsome_api_annotate_vcf, utils) - Expand exception hierarchy in exceptions.py - Add GitHub Actions workflows for tests and Docker release - Add Dockerfile, .dockerignore, and Docker documentation - Add parquet annotation example under examples/parquet/ - Expand test suite: test_cli, test_models, test_vcf, test_sync, test_exception with fixtures - Rewrite README and add docs/developer-guide.md, docs/docker.md - Add .editorconfig, .flake8, updated .pre-commit-config.yaml --- .cz.toml | 5 +- .dockerignore | 173 + .editorconfig | 37 + .flake8 | 2 + .github/workflows/docker-release.yml | 72 + .github/workflows/python-tests.yml | 65 + .gitignore | 97 +- .pre-commit-config.yaml | 35 +- CHANGELOG.md | 2 +- Dockerfile | 37 + MANIFEST.in | 8 - README.md | 551 +- docs/developer-guide.md | 613 + docs/docker.md | 199 + examples/README.md | 80 + examples/parquet/annotate_to_parquet.py | 184 + examples/parquet/models.py | 54 + examples/parquet/requirements.txt | 6 + examples/parquet/variants.csv | 25000 ++++++++++++++++ examples/parquet/writer.py | 53 + poetry.lock | 2939 ++ pyproject.toml | 87 +- requirements-dev.txt | 1040 + requirements.txt | 1245 + scripts/varsome_api_annotate_vcf.py | 92 - scripts/varsome_api_run.py | 190 - setup.py | 48 - tests/conftest.py | 46 + tests/fixtures/example_response_amp.json | 1 + tests/fixtures/example_response_germline.json | 1 + tests/fixtures/variants.vcf | 67 + tests/test_cli.py | 451 + tests/test_client.py | 655 +- tests/test_exception.py | 31 + tests/test_models.py | 483 + tests/test_sync.py | 87 + tests/test_vcf.py | 549 + tests/variants.csv | 3000 -- tests/variants.vcf | 156 - tox.ini | 9 - varsome_api/__init__.py | 1 + varsome_api/_sync.py | 54 + varsome_api/cli/__init__.py | 0 varsome_api/cli/utils.py | 248 + varsome_api/cli/varsome_api_annotate_vcf.py | 101 + varsome_api/cli/varsome_api_run.py | 267 + varsome_api/client.py | 628 +- varsome_api/constants.py | 5 + varsome_api/exceptions.py | 73 + varsome_api/log.py | 4 + varsome_api/models/__init__.py | 9 +- varsome_api/models/annotation.py | 2629 ++ varsome_api/models/elements/__init__.py | 16 - varsome_api/models/elements/acmg.py | 56 - varsome_api/models/elements/broad.py | 194 - varsome_api/models/elements/dann.py | 22 - varsome_api/models/elements/dbnsfp.py | 223 - varsome_api/models/elements/gerp.py | 31 - varsome_api/models/elements/gnomad.py | 177 - varsome_api/models/elements/gwas.py | 62 - varsome_api/models/elements/iarc.py | 77 - varsome_api/models/elements/icgc.py | 40 - varsome_api/models/elements/isb.py | 26 - varsome_api/models/elements/ncbi.py | 59 - varsome_api/models/elements/sanger.py | 215 - .../models/elements/thousand_genomes.py | 67 - varsome_api/models/elements/transcript.py | 49 - varsome_api/models/elements/uniprot.py | 50 - varsome_api/models/elements/wustl.py | 74 - varsome_api/models/fields.py | 45 - varsome_api/models/slim/__init__.py | 21 + varsome_api/models/slim/annotation.py | 73 + varsome_api/models/variant.py | 276 +- varsome_api/vcf.py | 627 +- version.py | 3 - 75 files changed, 38809 insertions(+), 6143 deletions(-) create mode 100644 .dockerignore create mode 100644 .editorconfig create mode 100644 .flake8 create mode 100644 .github/workflows/docker-release.yml create mode 100644 .github/workflows/python-tests.yml create mode 100644 Dockerfile delete mode 100644 MANIFEST.in create mode 100644 docs/developer-guide.md create mode 100644 docs/docker.md create mode 100644 examples/README.md create mode 100644 examples/parquet/annotate_to_parquet.py create mode 100644 examples/parquet/models.py create mode 100644 examples/parquet/requirements.txt create mode 100644 examples/parquet/variants.csv create mode 100644 examples/parquet/writer.py create mode 100644 poetry.lock create mode 100644 requirements-dev.txt create mode 100644 requirements.txt delete mode 100755 scripts/varsome_api_annotate_vcf.py delete mode 100755 scripts/varsome_api_run.py delete mode 100755 setup.py create mode 100644 tests/conftest.py create mode 100644 tests/fixtures/example_response_amp.json create mode 100644 tests/fixtures/example_response_germline.json create mode 100644 tests/fixtures/variants.vcf create mode 100644 tests/test_cli.py create mode 100644 tests/test_exception.py create mode 100644 tests/test_models.py create mode 100644 tests/test_sync.py create mode 100644 tests/test_vcf.py delete mode 100644 tests/variants.csv delete mode 100644 tests/variants.vcf delete mode 100644 tox.ini create mode 100644 varsome_api/_sync.py create mode 100644 varsome_api/cli/__init__.py create mode 100644 varsome_api/cli/utils.py create mode 100755 varsome_api/cli/varsome_api_annotate_vcf.py create mode 100755 varsome_api/cli/varsome_api_run.py create mode 100644 varsome_api/constants.py create mode 100644 varsome_api/exceptions.py create mode 100644 varsome_api/log.py create mode 100644 varsome_api/models/annotation.py delete mode 100755 varsome_api/models/elements/__init__.py delete mode 100644 varsome_api/models/elements/acmg.py delete mode 100755 varsome_api/models/elements/broad.py delete mode 100755 varsome_api/models/elements/dann.py delete mode 100755 varsome_api/models/elements/dbnsfp.py delete mode 100755 varsome_api/models/elements/gerp.py delete mode 100755 varsome_api/models/elements/gnomad.py delete mode 100755 varsome_api/models/elements/gwas.py delete mode 100755 varsome_api/models/elements/iarc.py delete mode 100755 varsome_api/models/elements/icgc.py delete mode 100755 varsome_api/models/elements/isb.py delete mode 100755 varsome_api/models/elements/ncbi.py delete mode 100755 varsome_api/models/elements/sanger.py delete mode 100755 varsome_api/models/elements/thousand_genomes.py delete mode 100755 varsome_api/models/elements/transcript.py delete mode 100755 varsome_api/models/elements/uniprot.py delete mode 100755 varsome_api/models/elements/wustl.py delete mode 100755 varsome_api/models/fields.py create mode 100644 varsome_api/models/slim/__init__.py create mode 100644 varsome_api/models/slim/annotation.py delete mode 100644 version.py diff --git a/.cz.toml b/.cz.toml index 43de6d1..c513397 100644 --- a/.cz.toml +++ b/.cz.toml @@ -1,10 +1,9 @@ - [tool.commitizen] name = "cz_github_jira_conventional" tag_format = "v$major.$minor.$patch$prerelease" -version = "0.0.2" +version = "0.0.3" version_files = [ - "version.py" + "varsome_api/__init__.py:__version__", ] jira_base_url = "https://saphetor.atlassian.net" github_repo = "saphetor/varsome-api-client-python" diff --git a/.dockerignore b/.dockerignore new file mode 100644 index 0000000..4788b2c --- /dev/null +++ b/.dockerignore @@ -0,0 +1,173 @@ +### Python template +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +share/python-wheels/ +*.egg-info/ +.installed.cfg +*.egg +MANIFEST + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.nox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*.cover +*.py,cover +.hypothesis/ +.pytest_cache/ +cover/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py +db.sqlite3 +db.sqlite3-journal + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +.pybuilder/ +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# IPython +profile_default/ +ipython_config.py + +# pyenv +# For a library or package, you might want to ignore these files since the code is +# intended to run in multiple environments; otherwise, check them in: +# .python-version + +# pipenv +# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. +# However, in case of collaboration, if having platform-specific dependencies or dependencies +# having no cross-platform support, pipenv may install dependencies that don't work, or not +# install all needed dependencies. +#Pipfile.lock + +# poetry +# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control. +# This is especially recommended for binary packages to ensure reproducibility, and is more +# commonly ignored for libraries. +# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control +#poetry.lock + +# pdm +# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control. +#pdm.lock +# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it +# in version control. +# https://pdm.fming.dev/latest/usage/project/#working-with-version-control +.pdm.toml +.pdm-python +.pdm-build/ + +# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm +__pypackages__/ + +# Celery stuff +celerybeat-schedule +celerybeat.pid + +# SageMath parsed files +*.sage.py + +# Environments +.env +.venv +env/ +venv/ +ENV/ +env.bak/ +venv.bak/ + +# Spyder project settings +.spyderproject +.spyproject + +# Rope project settings +.ropeproject + +# mkdocs documentation +/site + +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json + +# Pyre type checker +.pyre/ + +# pytype static type analyzer +.pytype/ + +# Cython debug symbols +cython_debug/ + +#jetbrains ide + +.idea +.envrc + +# Test files +tests/ + +# Documentation files +docs/ + +# Example files +examples/ + +# Github Actions +.github/ diff --git a/.editorconfig b/.editorconfig new file mode 100644 index 0000000..30706b5 --- /dev/null +++ b/.editorconfig @@ -0,0 +1,37 @@ +root = true + +[*] +charset = utf-8 +end_of_line = lf +indent_size = 4 +indent_style = space +insert_final_newline = true +max_line_length = 120 +tab_width = 4 +trim_trailing_whitespace = true + +[] +indent_size = 2 + +[*.cjs] +indent_size = 2 +max_line_length = 80 +tab_width = 2 + +[*.less] +indent_size = 2 + +[*.sass] +indent_size = 2 + +[*.scss] +indent_size = 2 + +[{*.har,*.jsb2,*.jsb3,*.json,.babelrc,.eslintrc,.prettierrc,.stylelintrc,bowerrc,jest.config}] +indent_size = 2 + +[{*.htm,*.html,*.ng,*.sht,*.shtm,*.shtml}] +max_line_length = 500 + +[{*.py,*.pyw,audit_trail}] +max_line_length = 88 diff --git a/.flake8 b/.flake8 new file mode 100644 index 0000000..2bcd70e --- /dev/null +++ b/.flake8 @@ -0,0 +1,2 @@ +[flake8] +max-line-length = 88 diff --git a/.github/workflows/docker-release.yml b/.github/workflows/docker-release.yml new file mode 100644 index 0000000..b63f0ba --- /dev/null +++ b/.github/workflows/docker-release.yml @@ -0,0 +1,72 @@ +name: Build and publish multi-arch image to GHCR on release + +on: + release: + types: [published] + workflow_dispatch: + inputs: + tag: + description: 'Docker image tag for manual build (e.g. 1.2.3 or latest)' + required: true + default: 'latest' + +permissions: + contents: read + packages: write + +env: + REGISTRY: ghcr.io + IMAGE_NAME: ${{ github.repository }} + +jobs: + build-and-push: + name: Build and push Docker image + runs-on: ubuntu-latest + steps: + - name: Checkout repository + uses: actions/checkout@v4 + + - name: Resolve image tag + id: vars + run: | + if [[ "${{ github.event_name }}" == "release" ]]; then + echo "tag=${{ github.event.release.tag_name }}" >> "$GITHUB_OUTPUT" + else + echo "tag=${{ inputs.tag }}" >> "$GITHUB_OUTPUT" + fi + + - name: Set up QEMU (for multi-arch) + uses: docker/setup-qemu-action@v3 + + - name: Set up Docker Buildx + uses: docker/setup-buildx-action@v3 + + - name: Log in to GHCR + uses: docker/login-action@v3 + with: + registry: ${{ env.REGISTRY }} + username: ${{ github.actor }} + password: ${{ secrets.GITHUB_TOKEN }} + + - name: Extract Docker metadata (tags, labels) + id: meta + uses: docker/metadata-action@v5 + with: + images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }} + tags: | + # Semver tags (patch, minor, major) — only when tag looks like a version + type=semver,pattern={{version}},value=${{ steps.vars.outputs.tag }},enable=${{ startsWith(steps.vars.outputs.tag, 'v') || contains(steps.vars.outputs.tag, '.') }} + type=semver,pattern={{major}}.{{minor}},value=${{ steps.vars.outputs.tag }},enable=${{ startsWith(steps.vars.outputs.tag, 'v') || contains(steps.vars.outputs.tag, '.') }} + type=semver,pattern={{major}},value=${{ steps.vars.outputs.tag }},enable=${{ startsWith(steps.vars.outputs.tag, 'v') || contains(steps.vars.outputs.tag, '.') }} + # Always tag with the exact resolved value (e.g. v1.2.3 or 'latest') + type=raw,value=${{ steps.vars.outputs.tag }} + + - name: Build and push (multi-arch) + uses: docker/build-push-action@v6 + with: + context: . + file: ./Dockerfile + push: true + platforms: linux/amd64,linux/arm64 + tags: ${{ steps.meta.outputs.tags }} + labels: ${{ steps.meta.outputs.labels }} diff --git a/.github/workflows/python-tests.yml b/.github/workflows/python-tests.yml new file mode 100644 index 0000000..a8a320e --- /dev/null +++ b/.github/workflows/python-tests.yml @@ -0,0 +1,65 @@ +name: Python Tests + +on: + push: + branches: [ main ] + pull_request: + branches: [ main ] + +jobs: + test: + runs-on: ubuntu-latest + permissions: + checks: write + pull-requests: write + contents: read + issues: read + + strategy: + fail-fast: false + matrix: + python-version: ["3.11", "3.12", "3.13", "3.14"] + + steps: + - uses: actions/checkout@v4 + + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v5 + with: + python-version: ${{ matrix.python-version }} + + - name: Install system build dependencies + run: | + sudo apt-get update -qq + sudo apt-get install -y --no-install-recommends \ + build-essential \ + zlib1g-dev \ + libbz2-dev \ + liblzma-dev \ + libcurl4-openssl-dev \ + libssl-dev \ + libdeflate-dev + + - name: Load cached dependencies + uses: actions/cache@v4 + id: cache-dependencies + with: + path: ~/.cache/pip + key: pip-${{ runner.os }}-${{ matrix.python-version }}-${{ hashFiles('**/requirements.txt') }}-${{ hashFiles('**/requirements-dev.txt') }} + + - name: Install dependencies + run: | + python -m pip install --upgrade pip + pip install -r requirements.txt + pip install -r requirements-dev.txt + + - name: Run tests + run: | + pytest -v --junitxml=pytest-report.xml + + - name: Publish Test Results + uses: EnricoMi/publish-unit-test-result-action@v2 + if: always() + with: + files: pytest-report.xml + check_name: "Python Test Results" diff --git a/.gitignore b/.gitignore index 427ea41..98d1c70 100644 --- a/.gitignore +++ b/.gitignore @@ -1,16 +1,3 @@ -# Created by .ignore support plugin (hsz.mobi) -### VirtualEnv template -# Virtualenv -# http://iamzed.com/2009/05/07/a-primer-on-virtualenv/ -.Python -[Bb]in -[Ii]nclude -[Ll]ib -[Ll]ib64 -[Ll]ocal -pyvenv.cfg -.venv -pip-selfcheck.json ### Python template # Byte-compiled / optimized / DLL files __pycache__/ @@ -22,7 +9,6 @@ __pycache__/ # Distribution / packaging .Python -env/ build/ develop-eggs/ dist/ @@ -34,9 +20,12 @@ lib64/ parts/ sdist/ var/ +wheels/ +share/python-wheels/ *.egg-info/ .installed.cfg *.egg +MANIFEST # PyInstaller # Usually these files are written by a python script from a template @@ -51,13 +40,17 @@ pip-delete-this-directory.txt # Unit test / coverage reports htmlcov/ .tox/ +.nox/ .coverage .coverage.* .cache nosetests.xml coverage.xml -*,cover +*.cover +*.py,cover .hypothesis/ +.pytest_cache/ +cover/ # Translations *.mo @@ -66,6 +59,8 @@ coverage.xml # Django stuff: *.log local_settings.py +db.sqlite3 +db.sqlite3-journal # Flask stuff: instance/ @@ -78,30 +73,88 @@ instance/ docs/_build/ # PyBuilder +.pybuilder/ target/ -# IPython Notebook +# Jupyter Notebook .ipynb_checkpoints -# pyenv -.python-version +# IPython +profile_default/ +ipython_config.py -# celery beat schedule file +# pyenv +# For a library or package, you might want to ignore these files since the code is +# intended to run in multiple environments; otherwise, check them in: +# .python-version + +# pipenv +# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. +# However, in case of collaboration, if having platform-specific dependencies or dependencies +# having no cross-platform support, pipenv may install dependencies that don't work, or not +# install all needed dependencies. +#Pipfile.lock + +# poetry +# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control. +# This is especially recommended for binary packages to ensure reproducibility, and is more +# commonly ignored for libraries. +# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control +#poetry.lock + +# pdm +# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control. +#pdm.lock +# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it +# in version control. +# https://pdm.fming.dev/latest/usage/project/#working-with-version-control +.pdm.toml +.pdm-python +.pdm-build/ + +# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm +__pypackages__/ + +# Celery stuff celerybeat-schedule +celerybeat.pid -# dotenv -.env +# SageMath parsed files +*.sage.py -# virtualenv +# Environments +.env +.venv +env/ venv/ ENV/ +env.bak/ +venv.bak/ # Spyder project settings .spyderproject +.spyproject # Rope project settings .ropeproject +# mkdocs documentation +/site + +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json + +# Pyre type checker +.pyre/ + +# pytype static type analyzer +.pytype/ + +# Cython debug symbols +cython_debug/ + #jetbrains ide .idea diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 6b0137c..5745743 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,22 +1,45 @@ default_install_hook_types: [pre-commit, commit-msg] repos: - repo: https://github.com/psf/black - rev: 23.3.0 + rev: 26.3.0 hooks: - id: black - language_version: python3.10 + language_version: python3.11 - repo: https://github.com/PyCQA/isort - rev: 5.12.0 + rev: 8.0.1 hooks: - id: isort - repo: https://github.com/PyCQA/flake8 - rev: 6.0.0 + rev: 7.3.0 hooks: - id: flake8 fail_fast: true - repo: https://github.com/commitizen-tools/commitizen - rev: v3.7.0 + rev: 4.13.9 hooks: - id: commitizen stages: [commit-msg] - additional_dependencies: [cz-github-jira-conventional==2.0.0] \ No newline at end of file + additional_dependencies: [cz-github-jira-conventional==3.0.2] + - repo: local + hooks: + - id: poetry-lock + name: poetry lock + entry: poetry lock --no-update + language: system + files: ^pyproject\.toml$ + pass_filenames: false + require_serial: true + - id: poetry-export + name: poetry export + entry: bash -c 'poetry export -f requirements.txt -o requirements.txt' + language: system + files: ^poetry\.lock$ + pass_filenames: false + require_serial: true + - id: poetry-export-dev + name: poetry export dev dependencies + entry: bash -c 'poetry export -f requirements.txt --only dev -o requirements-dev.txt' + language: system + files: ^poetry\.lock$ + pass_filenames: false + require_serial: true diff --git a/CHANGELOG.md b/CHANGELOG.md index 268a01b..8b13789 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1 +1 @@ -## Unreleased + diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 0000000..a2da007 --- /dev/null +++ b/Dockerfile @@ -0,0 +1,37 @@ +FROM python:3.14.3-slim-trixie AS base + +RUN apt-get update && apt-get install -y --no-install-recommends \ + build-essential \ + zlib1g-dev \ + libbz2-dev \ + liblzma-dev \ + libcurl4-openssl-dev \ + libssl-dev \ + libdeflate-dev \ + && rm -rf /var/lib/apt/lists/* + + +COPY . . +RUN pip install --no-cache-dir ".[vcf]" + +FROM python:3.14.3-slim-trixie AS final + +RUN apt-get update && apt-get install -y --no-install-recommends \ + libbz2-1.0 \ + liblzma5 \ + zlib1g \ + libcurl4 \ + libdeflate0 \ + && rm -rf /var/lib/apt/lists/* + +COPY --from=base /usr/local/lib/python3.14/site-packages /usr/local/lib/python3.14/site-packages +COPY --from=base /usr/local/bin /usr/local/bin + +RUN groupadd -r appuser && useradd -r -g appuser appuser && \ + mkdir -p /app && chown appuser:appuser /app + +WORKDIR /app +USER appuser + + +CMD ["varsome_api_run", "--help"] diff --git a/MANIFEST.in b/MANIFEST.in deleted file mode 100644 index 9a07580..0000000 --- a/MANIFEST.in +++ /dev/null @@ -1,8 +0,0 @@ -include LICENSE -include MANIFEST.in -include README.md -include setup.py -recursive-include variantapi/test *.csv -recursive-include variantapi/test *.vcf -recursive-exclude * __pycache__ -recursive-exclude * *.py[co] \ No newline at end of file diff --git a/README.md b/README.md index dde483e..d32a201 100644 --- a/README.md +++ b/README.md @@ -1,457 +1,270 @@ # VarSome API Client -## A basic API client implementation for [api.varsome.com](https://api.varsome.com) +A Python client for the [VarSome API](https://api.varsome.com) — annotate genetic variants +against gnomAD, ClinVar, and many other databases via a simple +command-line interface or a Python library. -This tool contains examples for the Varsome API usage. It can be used against the production server ([api.varsome.com](https://api.varsome.com)), the staging server ([staging-api.varsome.com](https://staging-api.varsome.com)) or the stable api server ([stable-api.varsome.com](https://stable-api.varsome.com)) +--- -### Staging-api environment +## ⚠️ Legacy version notice -The staging-api.varsome.com environment is a free usage test environment for subscribers. It is the perfect environment for evaluating the performance of the API. It is updated on an adhoc basis at our discretion, either together with live or possibly ahead of live in order to test upcoming new features. +This is a **new major version** (`1.x`) that requires **Python ≥ 3.11**. -It contains a substantial, but partial, data-set. Additionally it is throttled and is limited in the types of queries you can run. For example, it allows for only a limited number of samples and a limited size of data. +If you need compatibility with Python 3.10 or earlier, use the previous release: -**Please note: For this reason API queries performed against the staging environment within the client may not always run correctly or may produce different results to the production environment.** +> **[v0.0.3 — Python ≤ 3.10 compatible](https://github.com/saphetor/varsome-api-client-python/tree/v0.0.3)** -### Python versions +--- -Supports Python 3.3 to 3.10, you can download the latest version from [www.python.org](http://www.python.org) +## What this library provides -### Installation +- **`varsome_api_run`** — look up one or more variants and receive the full JSON + annotation response. +- **`varsome_api_annotate_vcf`** — read a VCF file, annotate every variant via the + VarSome API, and write an annotated output VCF. +- **`VarSomeAPIClient`** — a Python class for integrating variant annotation + directly into your own code (synchronous and async interfaces). +- **`VCFAnnotator`** — a customisable VCF annotation pipeline class for use in + your own Python projects. -We suggest that you create a python virtual environment instead of globally installing the library. +--- -There are several ways to create a virtual environment, but you can refer to [pip installation](https://pip.pypa.io/en/stable/installation/) and -[virtualenv installation](https://virtualenv.pypa.io/en/latest/installation.html) to first install these 2 tools if you don't -have them already installed via a package manager (Linux) or HomeBrew (MacOS), etc. -Remember to use "sudo -H" when installing on Mac. +## Installation -To create a virtual environment, you can follow the [user guide](https://virtualenv.pypa.io/en/latest/user_guide.html) or simply run: +### End users — CLI tools - virtualenv -p path_to/python3 venv_dir_name +If you only want to run `varsome_api_run` or `varsome_api_annotate_vcf`, +**the Docker image is the recommended approach** — it ships with all system +dependencies pre-installed and requires no local build toolchain: -Activate the virtual environment: - - source venv_dir_name/bin/activate +```bash +docker pull ghcr.io/saphetor/varsome-api-client-python:1 +``` -Finally, to use the client, either download or clone the repository from github and place the `varsome_api` -folder inside your project's directory, or run: +See the [Docker Guide](docs/docker.md) for full usage instructions. - pip install https://github.com/saphetor/varsome-api-client-python/archive/master.zip +--- -The client will be installed within your virtual environment. Also, 2 scripts called `varsome_api_run.py` and -`varsome_api_annotate_vcf.py` will be available within your virtual environment's `$PATH`. +### Python install — core library (no VCF support) -### Using the scripts to directly annotate a list of variants or a VCF file +If you only need `VarSomeAPIClient` for variant lookup in your own code and +**do not** require VCF reading/writing, install without extras: -#### Annotating a variant or list of variants +```bash +pip install git+https://github.com/saphetor/varsome-api-client-python.git +``` -Try the following query to annotate a single variant: +Or with [Poetry](https://python-poetry.org/): - varsome_api_run.py -g hg19 -k api_key -q 'chr7-140453136-A-T' -p add-all-data=1 +```bash +poetry add git+https://github.com/saphetor/varsome-api-client-python.git +``` -The script should complete without errors and display aproximately 6,700 lines of data from `dann`, `dbnsfp`, `ensembl_transcripts`, `gerp`, `gnomad_exomes`, `gnomad_exomes_coverage`, `icgc_somatic`, `ncbi_clinvar2`, `pub_med_articles`, `refseq_transcripts`, `sanger_cosmic_public`, `uniprot_variants`, `wustl_civic` etc. -The script can also accept a text file with variants (one per line) and an optional output file to store the -annotations in. We suggest that you don't use this script for a large number of variants, but use -the client within your code instead. +--- - varsome_api_run.py -g hg19 -k api_key -i variants.txt -o annotations.txt -p add-all-data=1 +### Python install — with VCF support (`[vcf]` extra) -The command above will read variants from `variants.txt` and dump the annotations to `annotations.txt`. -For any number of variants you will need to [register](mailto:support@saphetor.com) for an API key. +`varsome_api_annotate_vcf` and `VCFAnnotator` depend on +[pysam](https://pysam.readthedocs.io/), which requires several C build +libraries. Install the `vcf` extra to include pysam: -### Example to query CNVs +```bash +pip install "varsome_api[vcf] @ git+https://github.com/saphetor/varsome-api-client-python.git" +``` - varsome_api_run.py -g hg19 -k api-key -q 'cnv/chr2:83300000:106000000:dup' -p add-all-data=1 +Or with Poetry: -The query parameter specifies the CNV's details such as chromosome, start and end positions, and CNV type (deletion or duplication). In this example we have chr2, 83300000 and 106000000 and dup accordingly (for deletion use del). +```bash +poetry add "git+https://github.com/saphetor/varsome-api-client-python.git[vcf]" +``` -### Example to query Genes +> **Build requirements for pysam** — the following system libraries must be +> present before `pip` can compile pysam: +> +> | Library | Ubuntu/Debian | macOS (Homebrew) | +> |---------|---------------|-----------------| +> | zlib | `zlib1g-dev` | `zlib` | +> | bzip2 | `libbz2-dev` | `bzip2` | +> | lzma | `liblzma-dev` | `xz` | +> | libcurl | `libcurl4-openssl-dev` | `curl` | +> | OpenSSL | `libssl-dev` | `openssl` | +> | libdeflate | `libdeflate-dev` | `libdeflate` | +> | build tools | `build-essential` | Xcode CLT | +> +> If installing these is inconvenient, **use the Docker image instead** — +> it handles all of this for you. - varsome_api_run.py -g hg19 -k api-key -q 'gene/EGFR' -p add-all-data=1 +After installation, the `varsome_api_run` and `varsome_api_annotate_vcf` commands +will be available in your `PATH`. -The single gene lookup endpoint allows users to retrieve gene data associated with a specific gene symbol, specifying optional parameters such as reference genome and source databases. +Requires **Python ≥ 3.11, < 3.15**. -## Example to query Transcripts +--- -Try the following query to retrieve transcript-related data: +## API servers - varsome_api_run.py -g hg19 -k api-key -q 'transcript/NM_001276760' -p add-all-data=1 +| Server | URL | Notes | +|---------|-----|----------------------------------------------| +| Live | `https://api.varsome.com` | Default | +| Stable | `https://stable-api.varsome.com` | Kept frozen according to schedule | +| Staging | `https://staging-api.varsome.com` | Test environment, throttled | -### Example to query Single Reads +For more information on the different servers, [read here](https://docs.varsome.com/en/varsome-api-environments). -Try the following to retrieve data relevant to a single read: +Use the `-u` flag to select a non-default server. - varsome_api_run.py -g hg19 -k api-key -q 'single-read/AGTCCRAGTTGTAAATGGTACACTCGGCGTAAGCCTGAAAAGATAAAATCAAAGATGTAAAGGTGAGCACAGTCTAAGTTCTCTCTGAAGTGTCAATGGGAATGCAGATTGGATTAAATAAATGCTGCCCAAGTGCATACTCAAAGAGGC' -p add-all-data=1 +> **Note:** The staging environment is intended for evaluation only. It may contain a +> partial dataset, is throttled, and may produce different results from production. -#### Annotating a VCF file +--- -To annotate a VCF file, use: +## Quick-start: command-line tools - varsome_api_annotate_vcf.py -g hg19 -k api_key -i input.vcf -o annotated_vcf.vcf -p add-all-data=1 +### Annotate a single variant +```bash +varsome_api_run -g hg19 -k YOUR_API_KEY -q 'chr7-140453136-A-T' -p add-all-data=1 +``` -Notice, however, that not all available annotations will be present in the `annotated_vcf.vcf` file. Only a subset -of the returned annotations will be available when running this script. See the "Using the client in your code" -section below for how to annotate a VCF file with the annotations that are of interest to you. +### Annotate multiple variants in one call -*Warning*: varsome_api_annotate_vcf.py can only deal with: +```bash +varsome_api_run -g hg19 -k YOUR_API_KEY \ + -q 'chr7-140453136-A-T' 'chr19:20082943:1:G' \ + -p add-source-databases=gnomad-exomes,refseq-transcripts +``` -- SNPs -- small indels (up to 200bp) +### Annotate variants from a text file (one variant per line) -If you want to use this script please remove any variant from your VCF that does not meet the above criteria. +```bash +varsome_api_run -g hg19 -k YOUR_API_KEY -i variants.txt -o annotations.json -p add-all-data=1 +``` -### Using the client in your code +Output defaults to stdout. Use `-o` to write to a file. +The output is always written in [JSON Lines](https://jsonlines.org) format — +one JSON object per line — regardless of whether you write to a file or stdout. +See [Output format: JSON Lines](#output-format-json-lines-breaking-change-from-v0x) +for details and migration guidance. -Using the API client is quite straightforward. Just install the API client package and use the following in your code: +### Annotate a VCF file -```python -from varsome_api.client import VarSomeAPIClient -# API key is not required for single variant lookups -api_key = 'Your token' -api = VarSomeAPIClient(api_key, api_url="https://stable-api.varsome.com") -# fetch information about a variant into a dictionary -result = api.lookup('chr7-140453136-A-T', params={'add-source-databases': 'gnomad-exomes,refseq-transcripts'}, ref_genome='hg19') -# access results e.g. the transcripts of the variant -transcripts = result['refseq_transcripts'] -# fetch information for multiple variants -variants = ['chr19:20082943:1:G','chr22:39777823::CAA'] -# Results will be an array of dictionaries. An API key will be required for this request -results = api.batch_lookup(variants, params={'add-source-databases': 'gnomad-exomes,gnomad-genomes'}, ref_genome='hg19') -# look at the python doc for batch_lookup method for additional parameters +```bash +varsome_api_annotate_vcf -g hg19 -k YOUR_API_KEY -i input.vcf -o annotated.vcf -p add-all-data=1 ``` -If errors occur while using the client, an exception will be thrown. -You may wish to catch this exception and proceed with your own code logic: +> **VCF annotation limitation:** `varsome_api_annotate_vcf` supports SNPs and small +> indels (up to 200 bp). Remove any variants outside these criteria before running. -```python -from varsome_api.client import VarSomeAPIClient, VarSomeAPIException -api_key = 'Your token' -api = VarSomeAPIClient(api_key) -try: - result = api.lookup('chr19:20082943:1:G', ref_genome='hg64') -except VarSomeAPIException as e: - # proceed with your code flow e.g. - print(e) # 404 (invalid reference genome) -``` +### Common CLI flags -To view available request parameters (used by the `params` method parameter), refer to an example at [api.varsome.com](https://api.varsome.com). +| Flag | Description | Default | +|------|-------------|---------| +| `-k` | API key (required) | — | +| `-g` | Reference genome: `hg19` or `hg38` | `hg19` | +| `-p` | Request parameters as `key=value` pairs | `add-ACMG-annotation=1` | +| `-u` | API server URL | `https://api.varsome.com` | +| `-t` | Max concurrent requests (1–20) | `5` | +| `-m` | Max variants per batch request (1–200) | `100` | +| `-v` / `--verbose` | Enable debug-level logging | off | -To understand how annotation properties are included in the JSON response, please refer to the relevant [schema](https://api.varsome.com/docs/variants/). +Run any tool with `--help` for the full option reference. -#### JSON response wrapper +--- -If you don't want to read through each attribute in the JSON response, you can wrap the result into a Python -[JSON model](http://jsonmodels.readthedocs.io/en/latest/readme.html): +## Output format: JSON Lines (breaking change from v0.x) -```python -from varsome_api.client import VarSomeAPIClient -from varsome_api.models.variant import AnnotatedVariant -# API key is not required for single variant lookups -api_key = 'Your token' -api = VarSomeAPIClient(api_key) -# fetch information about a variant into a dictionary -result = api.lookup('chr7-140453136-A-T', params={'add-source-databases': 'gnomad-exomes,refseq-transcripts'}, ref_genome='hg19') -annotated_variant = AnnotatedVariant(**result) -``` +`varsome_api_run` v1.x writes all output — to a file or to stdout — in +**[JSON Lines](https://jsonlines.org)** (JSONL) format: one self-contained JSON +object per line, with no surrounding array wrapper. -You now have access to a set of shortcut attributes (these will be updated over time in the code base): +This is a **breaking change** from v0.x, which wrote the output file as a single +JSON array. -```python -annotated_variant.chromosome -annotated_variant.alt -annotated_variant.genes # directly get the genes related to the variant -annotated_variant.gnomad_exomes_af # etc -``` +### v0.x — old format (JSON array) -Or you may access other inner properties of other available properties: +The old output file looked like this: -```python -# get gnomad exomes allele number -allele_number = [gnomad_exome.an for gnomad_exome in annotated_variant.gnomad_exomes] +```json +[ + {"chromosome": "7", "pos": 140453136, "ref": "A", "alt": "T", ...}, + {"chromosome": "19", "pos": 20082943, "ref": "1", "alt": "G", ...} +] ``` -JSON model-type objects that contain a `version` property, like `annotated_variant.gnomad_exomes`, are -always returned as lists of objects. This is because the API has the ability to return multiple versions of -annotation databases (although this is not currently publicly available). For consistency, therefore, -these are always lists, though it is safe to assume that they will only include a single item. So it is safe -to rewrite as: +Users would load the entire file at once and iterate the resulting list: ```python -try: - allele_number = [gnomad_exome.an for gnomad_exome in annotated_variant.gnomad_exomes][0] -except IndexError: - pass # no gnomad exomes annotation for the variant +# v0.x — old approach +import json + +with open("annotations.json") as f: + annotations = json.load(f) # parses the whole file as a JSON array + +for annotation in annotations: + print(annotation["chromosome"], annotation["pos"]) ``` -#### Complete examples to try yourself +### v1.x — new format (JSON Lines) -Below there are examples utilizing cancer, tissue type and phenotypes, diseases options. +The new output file looks like this: -```python -from varsome_api.client import VarSomeAPIClient, VarSomeAPIException -from varsome_api.models.variant import AnnotatedVariant - - -api_key = 'Your token' -api = VarSomeAPIClient(api_key, api_url="https://stable-api.varsome.com") - -try: - result = api.lookup( - "chr22-29091857-G-", - params={ - "add-source-databases": "gnomad-exomes,refseq-transcripts", - "annotation-mode": "somatic", - "cancer-type": "Prostate Adenocarcinoma", - "tissue-type": "Prostate", - }, - ref_genome="hg19", - ) -except VarSomeAPIException as e: - print(e) - -annotated_variant = AnnotatedVariant(**result) -print( - annotated_variant.chromosome, - annotated_variant.genes, - annotated_variant.gnomad_exomes_af, -) -try: - allele_number = [ - gnomad_exome.an for gnomad_exome in annotated_variant.gnomad_exomes - ] -except IndexError: - pass -print(allele_number) +```jsonl +{"alt": "T", "chromosome": "7", "pos": 140453136, "ref": "A", ...} +{"alt": "G", "chromosome": "19", "pos": 20082943, "ref": "1", ...} ``` +Each line is an independent, complete JSON object. Read the file **line by line** +and parse each line separately: + ```python -from varsome_api.client import VarSomeAPIClient, VarSomeAPIException -from varsome_api.models.variant import AnnotatedVariant - -api_key = 'Your token' -api = VarSomeAPIClient(api_key, api_url="https://stable-api.varsome.com") - -try: - result = api.lookup( - "15:68500735:C:T", - params={ - "add-source-databases": "gnomad-exomes,refseq-transcripts", - "annotation-mode": "germline", - "patient-phenotypes": "Progressive Visual Loss", - "diseases": "Neuronal Ceroid Lipofuscinosis 4A", - }, - ref_genome="hg19", - ) -except VarSomeAPIException as e: - print(e) - -annotated_variant = AnnotatedVariant(**result) -print( - annotated_variant.chromosome, - annotated_variant.alt, - annotated_variant.genes, - annotated_variant.gnomad_exomes_af, -) -try: - allele_number = [ - gnomad_exome.an for gnomad_exome in annotated_variant.gnomad_exomes - ] -except IndexError: - pass -print(allele_number) +# v1.x — new approach +import json + +with open("annotations.jsonl") as f: + for line in f: + annotation = json.loads(line) # parse one object at a time + print(annotation["chromosome"], annotation["pos"]) ``` -#### Annotating a VCF using the client +> ⚠️ **`json.load(f)` will fail** on a JSONL file because the file as a whole is +> not valid JSON. Always use `json.loads(line)` inside a loop. -To annotate a VCF you can base your code on the VCFAnnotator object. This provides a basic implementation that -will annotate a VCF file using a set of the available annotations. It uses [PyVCF](https://pyvcf.readthedocs.io/en/latest/) to read and write to VCF files. +### Why the change? -```python -from varsome_api.vcf import VCFAnnotator -api_key = 'Your token' -vcf_annotator = VCFAnnotator(api_key=api_key, ref_genome='hg19', get_parameters={'add-all-data': 1, 'expand-pubmed-articles': 0}) -vcf_file = 'input.vcf' -output_vcf_file = 'annotated.vcf' -vcf_annotator.annotate(vcf_file, output_vcf_file) -``` +The JSONL format allows results to be streamed and written **as they arrive** from +the API, keeping memory usage constant regardless of how many variants are +annotated. The old array format required buffering all results in memory before +writing, which was impractical for large variant sets. -To annotate the VCF file with the annotations that you are interested in, you need only override 2 methods -(`annotate_record` and `add_vcf_header_info`) in the VCFAnnotator class: +--- -```python -from varsome_api.vcf import VCFAnnotator -from vcf.parser import _Info, _encode_type -class MyVCFAnnotator(VCFAnnotator): - - - def annotate_record(self, record, variant_result, original_variant): - """ - :param record: vcf record object - :param variant_result: AnnotatedVariant object - :param original_variant: The variant that was looked up - :return: annotated record object - """ - record.INFO["gnomad_exomes_AN"] = variant_result.gnomad_exomes_an - # if you wish to also include the default annotations - # return super().annotate_record(record, variant_result, original_variant) - return record - - def add_vcf_header_info(self, vcf_template): - """ - Adds vcf INFO headers for the annotated values provided - :param vcf_template: vcf reader object - :return: - """ - vcf_template.infos["gnomad_exomes_AN"] = _Info( - "gnomad_exomes_AN", - 1, - "Integer", - "GnomAD exomes allele number value", - None, - None, - _encode_type("Integer"), - ) - # if you wish to also include the default headers - # super().add_vcf_header_info(vcf_template) - -api_key = 'Your token' -vcf_annotator = MyVCFAnnotator(api_key=api_key, ref_genome='hg19', get_parameters={'add-all-data': 1, 'expand-pubmed-articles': 0}) -vcf_file = 'input.vcf' -output_vcf_file = 'annotated.vcf' -vcf_annotator.annotate(vcf_file, output_vcf_file) -``` +## Documentation -#### Complete examples to try yourself +| Document | Description | +|----------|-------------| +| [Developer Guide](docs/developer-guide.md) | Using `VarSomeAPIClient` and `VCFAnnotator` in your Python code | +| [Docker Guide](docs/docker.md) | Running the tools via the pre-built Docker image or building your own | -Below there are examples utilizing cancer, tissue type and phenotypes, diseases options. -Keep in mind that these options are subjective to your vcf file. +--- -```python -from varsome_api.vcf import VCFAnnotator -from vcf.parser import _Info, _encode_type - - -class MyVCFAnnotator(VCFAnnotator): - def annotate_record(self, record, variant_result, original_variant): - """ - :param record: vcf record object - :param variant_result: AnnotatedVariant object - :param original_variant: The variant that was looked up - :return: annotated record object - """ - record.INFO["gnomad_exomes_AN"] = variant_result.gnomad_exomes_an - # if you wish to also include the default annotations - # return super().annotate_record(record, variant_result, original_variant) - return record - - def add_vcf_header_info(self, vcf_template): - """ - Adds vcf INFO headers for the annotated values provided - :param vcf_template: vcf reader object - :return: - """ - vcf_template.infos["gnomad_exomes_AN"] = _Info( - "gnomad_exomes_AN", - 1, - "Integer", - "GnomAD exomes allele number value", - None, - None, - _encode_type("Integer"), - ) - # if you wish to also include the default headers - # super().add_vcf_header_info(vcf_template) - - -api_key = 'Your token' -vcf_annotator = MyVCFAnnotator( - api_key=api_key, - ref_genome="hg38", - get_parameters={ - "add-source-databases": "gnomad-exomes,refseq-transcripts", - "expand-pubmed-articles": 0, - "annotation-mode": "somatic", - "cancer-type": "Prostate Adenocarcinoma", - "tissue-type": "Prostate", - }, -) -vcf_file = "input.vcf" -output_vcf_file = "annotated.vcf" -vcf_annotator.annotate(vcf_file, output_vcf_file) -``` - -```python -from varsome_api.vcf import VCFAnnotator -from vcf.parser import _Info, _encode_type - - -class MyVCFAnnotator(VCFAnnotator): - def annotate_record(self, record, variant_result, original_variant): - """ - :param record: vcf record object - :param variant_result: AnnotatedVariant object - :param original_variant: The variant that was looked up - :return: annotated record object - """ - record.INFO["gnomad_exomes_AN"] = variant_result.gnomad_exomes_an - # if you wish to also include the default annotations - # return super().annotate_record(record, variant_result, original_variant) - return record - - def add_vcf_header_info(self, vcf_template): - """ - Adds vcf INFO headers for the annotated values provided - :param vcf_template: vcf reader object - :return: - """ - vcf_template.infos["gnomad_exomes_AN"] = _Info( - "gnomad_exomes_AN", - 1, - "Integer", - "GnomAD exomes allele number value", - None, - None, - _encode_type("Integer"), - ) - # if you wish to also include the default headers - # super().add_vcf_header_info(vcf_template) - - -api_key = 'Your token' -vcf_annotator = MyVCFAnnotator( - api_key=api_key, - ref_genome="hg19", - get_parameters={ - "add-source-databases": "gnomad-exomes,refseq-transcripts", - "expand-pubmed-articles": 0, - "annotation-mode": "germline", - "patient-phenotypes": "Progressive Visual Loss", - "diseases": "Neuronal Ceroid Lipofuscinosis 4A", - }, -) -vcf_file = "input.vcf" -output_vcf_file = "annotated.vcf" -vcf_annotator.annotate(vcf_file, output_vcf_file) -``` +## How to get an API key -### API Documentation +[Contact support](mailto:support@saphetor.com) to register for an API key. -See [API documentation](https://api.varsome.com) for information on how to use the API and -what values the API provides as a response to lookup requests. +An API key is required for all CLI operations and for batch lookups. +Single-variant lookups via `VarSomeAPIClient` do not require a key, but will be throttled. -### How to get an API key +--- -To obtain an API key please [contact us](mailto:support@saphetor.com). +## API documentation -### How to run the tests +See [api.varsome.com](https://api.varsome.com) for available request parameters and +the full response schema. The OpenAPI specification is available at +`https://api.varsome.com/openapi/variants/`. -Clone the repository, after creating a virtual environment, and run: +--- - pip install tox - tox +## Contributing & running the tests -To run the tests, set the `VARSOME_API_KEY` environment variable to your API token. Otherwise, -tests will fail because the API will return a 401 (not authenticated) error. -Be advised as well that running the tests will count towards your account request limit depending on the -API package you are subscribed to. +See the [Developer Guide](docs/developer-guide.md) for instructions on cloning +the repository, setting up a development environment, and running the test suite. diff --git a/docs/developer-guide.md b/docs/developer-guide.md new file mode 100644 index 0000000..25ecab3 --- /dev/null +++ b/docs/developer-guide.md @@ -0,0 +1,613 @@ +# Developer Guide + +This guide covers using `VarSomeAPIClient` and `VCFAnnotator` inside your own Python code. + +For CLI usage see the [root README](../README.md). +For Docker usage see [docker.md](docker.md). + +--- + +## Installation + +### Core library (no VCF support) + +If you only need `VarSomeAPIClient` for programmatic variant lookup and **do not** +require `VCFAnnotator`, install without extras — no C compiler or system libraries +are needed: + +```bash +pip install git+https://github.com/saphetor/varsome-api-client-python.git +``` + +With [Poetry](https://python-poetry.org/): + +```bash +poetry add git+https://github.com/saphetor/varsome-api-client-python.git +``` + +### With VCF support (`[vcf]` extra) + +`VCFAnnotator` and `varsome_api_annotate_vcf` depend on +[pysam](https://pysam.readthedocs.io/), a C extension that wraps htslib. +Install the `vcf` extra to include it: + +```bash +pip install "varsome_api[vcf] @ git+https://github.com/saphetor/varsome-api-client-python.git" +``` + +With Poetry: + +```bash +poetry add "git+https://github.com/saphetor/varsome-api-client-python.git[vcf]" +``` + +#### Build dependencies for pysam + +pysam requires the following system libraries to compile. Install them before +running `pip install`: + +**Ubuntu / Debian** + +```bash +sudo apt-get update && sudo apt-get install -y \ + build-essential \ + zlib1g-dev \ + libbz2-dev \ + liblzma-dev \ + libcurl4-openssl-dev \ + libssl-dev \ + libdeflate-dev +``` + +**macOS (Homebrew)** + +```bash +brew install bzip2 xz curl openssl libdeflate +``` + +> **Tip:** If managing these libraries is inconvenient, use the pre-built +> Docker image instead — it ships with all dependencies pre-compiled. +> See [docker.md](docker.md) for details. + +### Cloning the repository (development) + +Clone the repository and install all dependencies, including dev tooling: + +```bash +git clone https://github.com/saphetor/varsome-api-client-python.git +cd varsome-api-client-python +poetry install --all-extras +``` + +`--all-extras` ensures pysam is installed alongside the regular dev dependencies. +Without it, tests that import `pysam` will fail with an `ImportError`. + +--- + +## Running the tests + +The test suite uses [pytest](https://docs.pytest.org/) with +[pytest-asyncio](https://pytest-asyncio.readthedocs.io/) and +[pytest-cov](https://pytest-cov.readthedocs.io/). + +### Run the full suite + +```bash +poetry run pytest +``` + +Coverage is measured automatically. The suite must reach **80 % total coverage** +or pytest exits with a non-zero status. + +### Run a specific test file + +```bash +poetry run pytest tests/test_vcf.py +``` + +### Run a specific test class or function + +```bash +poetry run pytest tests/test_vcf.py::TestReadHeaderFromVcf +poetry run pytest tests/test_vcf.py::TestReadHeaderFromVcf::test_returns_header_object +``` + +### Run with verbose output + +```bash +poetry run pytest -v +``` + +--- +Requires **Python ≥ 3.11, < 3.15**. + +--- + +## VarSomeAPIClient + +### Single variant lookup (synchronous) + +`lookup` is a synchronous convenience wrapper around the underlying async method. +It returns a plain `dict` containing the full API JSON response. + +```python +from varsome_api.client import VarSomeAPIClient + +api = VarSomeAPIClient(api_key="YOUR_API_KEY") + +result = api.lookup( + "chr7-140453136-A-T", + params={"add-source-databases": "gnomad-exomes,refseq-transcripts"}, + ref_genome="hg19", +) + +# Access any field from the raw JSON response +print(result["chromosome"]) +print(result["gnomad_exomes"]) +``` + +`api_key` is optional for single-variant lookups against public data. It is +required for batch lookups. + +To target a specific API server, pass `api_url`: + +```python +api = VarSomeAPIClient( + api_key="YOUR_API_KEY", + api_url="https://stable-api.varsome.com", +) +``` + +### Batch lookup (synchronous) + +`batch_lookup` sends variants in batches and returns a `list[BatchResult]`. +Each `BatchResult` pairs the submitted variant strings with the corresponding +API response list, aligned by index. + +```python +from varsome_api.client import VarSomeAPIClient + +api = VarSomeAPIClient(api_key="YOUR_API_KEY") + +variants = ["chr7-140453136-A-T", "chr19:20082943:1:G", "chr22:39777823::CAA"] + +batch_results = api.batch_lookup( + variants, + params={"add-source-databases": "gnomad-exomes,gnomad-genomes"}, + ref_genome="hg19", +) + +for batch in batch_results: + for i, variant_str in enumerate(batch.variants): + annotation = batch.response[i] + if "error" in annotation: + print(f"{variant_str}: error — {annotation['error']}") + elif "filtered_out" in annotation: + print(f"{variant_str}: filtered out — {annotation['filtered_out']}") + else: + print(f"{variant_str}: gnomad_exomes = {annotation.get('gnomad_exomes')}") +``` + +`max_variants_per_batch` (default `200`) controls how many variants are sent per +POST request. `max_requests` (default `5`) controls the maximum number of +concurrent HTTP requests: + +```python +api = VarSomeAPIClient(api_key="YOUR_API_KEY", max_variants_per_batch=50) +results = api.batch_lookup(variants, max_requests=10, ref_genome="hg38") +``` + +### Exception handling + +All API errors raise `VarSomeAPIException`: + +```python +from varsome_api.client import VarSomeAPIClient +from varsome_api.exceptions import VarSomeAPIException + +api = VarSomeAPIClient(api_key="YOUR_API_KEY") + +try: + result = api.lookup("chr19:20082943:1:G", ref_genome="hg64") +except VarSomeAPIException as e: + print(e) # e.g. "404 — invalid reference genome" +``` + +--- + +## Async interface + +The client is async-native. The synchronous `lookup` / `batch_lookup` methods are +thin wrappers. Use the async interface directly for better performance in async code. + +### Single lookup + +```python +import asyncio +from varsome_api.client import VarSomeAPIClient + +async def main(): + async with VarSomeAPIClient(api_key="YOUR_API_KEY") as api: + result = await api.alookup( + "chr7-140453136-A-T", + params={"add-source-databases": "gnomad-exomes"}, + ref_genome="hg19", + ) + print(result["chromosome"]) + +asyncio.run(main()) +``` + +Using `async with` keeps a single HTTP session alive for all requests inside the +block, avoiding per-request connection overhead. Without the context manager, each +call creates and closes its own session automatically. + +### Batch lookup (async generator) + +`abatch_lookup` is an async generator that yields `BatchResult` objects as each +batch completes: + +```python +import asyncio +from varsome_api.client import VarSomeAPIClient + +async def main(): + variants = ["chr7-140453136-A-T", "chr19:20082943:1:G", "chr22:39777823::CAA"] + + async with VarSomeAPIClient(api_key="YOUR_API_KEY") as api: + async for batch in api.abatch_lookup( + variants, + params={"add-source-databases": "gnomad-exomes,gnomad-genomes"}, + ref_genome="hg19", + max_requests=5, + ): + for i, variant_str in enumerate(batch.variants): + annotation = batch.response[i] + print(variant_str, annotation.get("gnomad_exomes")) + +asyncio.run(main()) +``` + +--- + +## Working with response models + +The raw API response is a `dict`. You can wrap it in `AnnotatedVariant` for typed +attribute access and convenience properties. + +### Full model + +```python +from varsome_api.client import VarSomeAPIClient +from varsome_api.models.variant import AnnotatedVariant + +api = VarSomeAPIClient(api_key="YOUR_API_KEY") + +result = api.lookup( + "chr7-140453136-A-T", + params={"add-source-databases": "gnomad-exomes,refseq-transcripts"}, + ref_genome="hg19", +) + +variant = AnnotatedVariant(**result) + +print(variant.chromosome) # e.g. "7" +print(variant.pos) # e.g. 140453136 +print(variant.ref) # e.g. "A" +print(variant.alt) # e.g. "T" +print(variant.genes) # deduplicated list of gene symbols +print(variant.gnomad_exomes_af) # allele frequency float or None +print(variant.gnomad_genomes_af) # allele frequency float or None +print(variant.acmg_verdict) # e.g. "Pathogenic" or None +print(variant.acmg_rules) # list of ACMG rule names +print(variant.rs_ids) # e.g. ["rs113488022"] +``` + +`AnnotatedVariant` (from `varsome_api.models.variant`) validates **every** field +the API returns. For performance-sensitive pipelines processing many variants, see +the slim model section below. + +### Accessing versioned database entries + +Some annotation databases (e.g. gnomAD) are returned as lists because the API may in the future +return multiple database versions. Each list item is a typed object: + +```python +try: + allele_number = [entry.an for entry in variant.gnomad_exomes][0] +except IndexError: + allele_number = None # no gnomAD exomes annotation for this variant +``` + +It is safe to assume only one item is present currently. + +### Somatic and germline annotation modes + +Pass annotation-mode parameters via the `params` argument: + +```python +from varsome_api.client import VarSomeAPIClient +from varsome_api.models.variant import AnnotatedVariant +from varsome_api.exceptions import VarSomeAPIException + +api = VarSomeAPIClient(api_key="YOUR_API_KEY", api_url="https://stable-api.varsome.com") + +try: + result = api.lookup( + "chr22-29091857-G-", + params={ + "add-source-databases": "gnomad-exomes,refseq-transcripts", + "annotation-mode": "somatic", + "cancer-type": "Prostate Adenocarcinoma", + "tissue-type": "Prostate", + }, + ref_genome="hg19", + ) +except VarSomeAPIException as e: + print(e) +else: + variant = AnnotatedVariant(**result) + print(variant.chromosome, variant.gnomad_exomes_af, variant.amp_annotation) +``` + +```python +try: + result = api.lookup( + "15:68500735:C:T", + params={ + "add-source-databases": "gnomad-exomes,refseq-transcripts", + "annotation-mode": "germline", # default + "patient-phenotypes": "Progressive Visual Loss", + }, + ref_genome="hg19", + ) +except VarSomeAPIException as e: + print(e) +else: + variant = AnnotatedVariant(**result) + print(variant.chromosome, variant.alt, variant.gnomad_exomes_af) +``` + +--- + +## VCF annotation + +### Basic usage + +`VCFAnnotator` reads an input VCF, sends variants in batches to the API, and +writes an annotated output VCF. It subclasses `VarSomeAPIClient` so all client +parameters apply. + +```python +from varsome_api.vcf import VCFAnnotator + +annotator = VCFAnnotator( + api_key="YOUR_API_KEY", + ref_genome="hg19", + request_parameters={"add-all-data": "1"}, +) +annotator.annotate("input.vcf", "annotated.vcf") +``` + +The default annotator writes the following INFO fields to the output VCF: +`gnomad_exomes_AF`, `gnomad_genomes_AF`, `acmg_verdict`, `acmg_rules`, `genes`, +`original_variant`. + +> **Limitation:** VCF annotation supports SNPs and small indels (up to 200 bp) only. + +### Async annotation + +`VCFAnnotator` also exposes an async method and supports `async with`: + +```python +import asyncio +from varsome_api.vcf import VCFAnnotator + +async def main(): + annotator = VCFAnnotator( + api_key="YOUR_API_KEY", + ref_genome="hg19", + request_parameters={"add-all-data": "1"}, + max_requests=5, + ) + async with annotator: + result = await annotator.aannotate("input.vcf", "annotated.vcf") + + print(f"Annotated {result.total_variants} variant(s)") + for variant, info in result.filtered_out_variants: + print(f"Filtered: {variant} — {info.get('filtered_out')}") + for variant, info in result.variants_with_errors: + print(f"Error: {variant} — {info.get('error')}") + +asyncio.run(main()) +``` + +### Customising what gets written to the VCF + +Override `annotate_record` and `add_vcf_header_info` to control which fields +appear in the output VCF: + +```python +import pysam +from varsome_api.vcf import VCFAnnotator +from varsome_api.models.variant import AnnotatedVariant + + +class MyVCFAnnotator(VCFAnnotator): + # Switch to the full model to access gnomad_exomes_an, + # which is not present on the default slim model. + variant_model = AnnotatedVariant + + def annotate_record(self, record, variant_result, original_variant): + an = variant_result.gnomad_exomes_an + if an is not None: + record.info["gnomad_exomes_AN"] = an + # Optionally include the default annotations too: + # super().annotate_record(record, variant_result, original_variant) + + def add_vcf_header_info(self, header): + header.info.add( + "gnomad_exomes_AN", "1", "Integer", + "gnomAD exomes allele number", + ) + # super().add_vcf_header_info(header) + + +annotator = MyVCFAnnotator( + api_key="YOUR_API_KEY", + ref_genome="hg38", + request_parameters={ + "add-source-databases": "gnomad-exomes,refseq-transcripts", + "annotation-mode": "somatic", + "cancer-type": "Prostate Adenocarcinoma", + "tissue-type": "Prostate", + }, +) +annotator.annotate("input.vcf", "annotated.vcf") +``` + +--- + +## Slim vs full `AnnotatedVariant` + +| Model | Location | Fields validated | Use when | +|-------|----------|-----------------|----------| +| Slim (default) | `varsome_api.models.slim.annotation` | ~12 fields used by `annotate_record` | VCF annotation pipelines where you only need the defaults | +| Full | `varsome_api.models.variant` | Every field the API returns | You need access to any field beyond the slim defaults | + +The slim model uses `extra="ignore"` so unknown fields are silently discarded +before Pydantic validates — significantly faster for large VCFs. + +### Custom slim model + +If you need a handful of fields beyond the defaults without the overhead of +the full model, define your own: + +```python +from pydantic import BaseModel, ConfigDict +from varsome_api.models.annotation import AcmgAnnotation, GnomadExome, DbnsfpItem +from varsome_api.models.variant import AnnotatedVariantPropertiesMixin +from varsome_api.vcf import VCFAnnotator + + +class MySlimVariant(BaseModel, AnnotatedVariantPropertiesMixin): + """Slim model with dbnsfp added on top of the basics.""" + + model_config = ConfigDict(extra="ignore") + + original_variant: str | None = None + chromosome: str | None = None + pos: int | None = None + ref: str | None = None + alt: str | None = None + gnomad_exomes: list[GnomadExome] | None = None + acmg_annotation: AcmgAnnotation | None = None + dbnsfp: list[DbnsfpItem] | None = None + + +class MyAnnotator(VCFAnnotator): + variant_model = MySlimVariant + + def annotate_record(self, record, variant_result, original_variant): + if variant_result.dbnsfp: + sift_values = variant_result.dbnsfp[0].sift_pred + if sift_values: + record.info["sift_pred"] = ",".join(s for s in sift_values if s) + record.info["original_variant"] = original_variant + + def add_vcf_header_info(self, header): + header.info.add("sift_pred", ".", "String", "SIFT predictions") + header.info.add("original_variant", "1", "String", "Original variant string") +``` + +> **Tip:** `AnnotatedVariantPropertiesMixin` provides the convenience properties +> (`genes`, `gnomad_exomes_af`, `acmg_verdict`, etc.) on any model that declares +> the expected attribute names. Mix-and-match slim and full nested types freely. + +--- + +## Model generation + +`varsome_api/models/annotation.py` was **code-generated** from the OpenAPI schema +published at [`https://api.varsome.com/openapi/variants/`](https://api.varsome.com/openapi/variants/) +using [`datamodel-code-generator`](https://github.com/koxudaxi/datamodel-code-generator): + +```bash +pip install datamodel-code-generator + +datamodel-codegen \ + --url https://api.varsome.com/openapi/variants/ \ + --output varsome_api/models/annotation.py \ + --output-model-type pydantic_v2.BaseModel \ + --target-python-version 3.11 \ + --use-standard-collections \ + --use-union-operator +``` + +The raw output was then customised in two ways: + +1. **Shared base class.** A `_GeneratedBase` class was introduced at the top of + `annotation.py`. Every generated model was rebased onto it (replacing + `BaseModel`) so that configuration changes — currently `extra="allow"` to + absorb undocumented fields — apply uniformly: + + ```python + class _GeneratedBase(BaseModel): + model_config = ConfigDict(extra="allow") + + class UniprotRegionItem(_GeneratedBase): # was: BaseModel + ... + ``` + +2. **Readability pass.** Field names, ordering, and minor type annotations were + adjusted to match the rest of the codebase style; no semantic changes were + made. + +### Regenerating after an API schema change + +1. Re-run `datamodel-codegen` with the command above to produce a fresh + `annotation.py`. +2. Restore the `_GeneratedBase` class at the top of the file and rebase all + generated models onto it (search-replace `(BaseModel)` → `(_GeneratedBase)`). +3. Re-apply any readability edits that are worth keeping. +4. Run the test suite — `poetry run pytest` — to catch any field renames or + structural changes introduced by the updated schema. + +--- + +## Using the library for custom output formats + +`VarSomeAPIClient` and the Pydantic annotation models are not tied to VCF. +Any Python project can use the batch API, parse responses with the slim (or full) +`AnnotatedVariant` model, and write the results in whatever format is most +appropriate for the downstream workflow — Parquet, CSV, JSON-lines, a database, +a message queue, etc. + +The general pattern is always the same: + +```python +from varsome_api.client import VarSomeAPIClient +from varsome_api.models.slim.annotation import AnnotatedVariant + +api = VarSomeAPIClient(api_key="YOUR_API_KEY") + +for batch in api.batch_lookup(my_variants, params={...}, ref_genome="hg19"): + for i, variant_str in enumerate(batch.variants): + raw = batch.response[i] + if "error" not in raw and "filtered_out" not in raw: + variant = AnnotatedVariant(**raw) + # … transform `variant` and write to your target format +``` + +### Working example — CSV → Parquet + +See [`examples/README.md`](../examples/README.md) for a +self-contained, runnable example that demonstrates this pattern end-to-end. + +--- + +## Available request parameters + +Refer to [api.varsome.com](https://api.varsome.com) and the +[API documentation](https://api.varsome.com/docs/variants/) for the full list of +query parameters and response fields. diff --git a/docs/docker.md b/docs/docker.md new file mode 100644 index 0000000..2c9a4e0 --- /dev/null +++ b/docs/docker.md @@ -0,0 +1,199 @@ +# Docker Guide + +This guide covers running the VarSome API CLI tools via Docker — either using the +pre-built image from the GitHub Container Registry (GHCR) or building your own image +from source. + +For CLI flag reference see the [root README](../README.md). +For using the library in Python code see the [Developer Guide](developer-guide.md). + +--- + +## Pre-built image from GHCR + +Images are built automatically on every release and pushed to the GitHub Container +Registry at: + +``` +ghcr.io/saphetor/varsome-api-client-python +``` + +### Available tags + +| Tag | Description | +|-----|-------------| +| `1` | Latest `1.x` release (major) | +| `1.3` | Latest `1.3.x` patch (major.minor) | +| `1.3.0` | Exact release version | + +Replace the version number with the release you want. See the +[GitHub releases page](https://github.com/saphetor/varsome-api-client-python/releases) +for all available versions. + +### Pull the image + +```bash +docker pull ghcr.io/saphetor/varsome-api-client-python:1 +``` + +--- + +## Running `varsome_api_run` via Docker + +### Annotate a single variant + +```bash +docker run --rm \ + ghcr.io/saphetor/varsome-api-client-python:1 \ + varsome_api_run \ + -k YOUR_API_KEY \ + -g hg19 \ + -q 'chr7-140453136-A-T' \ + -p add-all-data=1 +``` + +### Annotate multiple variants + +```bash +docker run --rm \ + ghcr.io/saphetor/varsome-api-client-python:1 \ + varsome_api_run \ + -k YOUR_API_KEY \ + -g hg19 \ + -q 'chr7-140453136-A-T' 'chr19:20082943:1:G' \ + -p add-source-databases=gnomad-exomes,refseq-transcripts +``` + +### Read variants from a file, write output to a file + +Mount the directory containing your input file and write output to the same mount: + +```bash +docker run --rm \ + -v /path/to/your/data:/data \ + ghcr.io/saphetor/varsome-api-client-python:1 \ + varsome_api_run \ + -k YOUR_API_KEY \ + -g hg19 \ + -i /data/variants.txt \ + -o /data/annotations.json \ + -p add-all-data=1 +``` + +Replace `/path/to/your/data` with the absolute path to the directory on your host +that contains `variants.txt`. The output file `annotations.json` will be written +to the same directory. + +--- + +## Running `varsome_api_annotate_vcf` via Docker + +Mount the directory containing your VCF and write the annotated output to the same +mount: + +```bash +docker run --rm \ + -v /path/to/your/data:/data \ + ghcr.io/saphetor/varsome-api-client-python:1 \ + varsome_api_annotate_vcf \ + -k YOUR_API_KEY \ + -g hg19 \ + -i /data/input.vcf \ + -o /data/annotated.vcf \ + -p add-all-data=1 +``` + +> **VCF limitation:** Only SNPs and small indels (≤ 200 bp) are supported. +> Remove other variant types from your VCF before running. + +### Tune concurrency and batch size + +Use `-t` to control how many API requests run in parallel and `-m` to set the +number of variants per batch: + +```bash +docker run --rm \ + -v /path/to/your/data:/data \ + ghcr.io/saphetor/varsome-api-client-python:1 \ + varsome_api_annotate_vcf \ + -k YOUR_API_KEY \ + -g hg19 \ + -i /data/input.vcf \ + -o /data/annotated.vcf \ + -t 10 \ + -m 100 \ + -p add-source-databases=gnomad-exomes,refseq-transcripts +``` + +### Use the stable API server + +Pass `-u` to target a different API server: + +```bash +docker run --rm \ + -v /path/to/your/data:/data \ + ghcr.io/saphetor/varsome-api-client-python:1 \ + varsome_api_annotate_vcf \ + -k YOUR_API_KEY \ + -g hg19 \ + -u https://stable-api.varsome.com \ + -i /data/input.vcf \ + -o /data/annotated.vcf \ + -p add-all-data=1 +``` + +--- + +## Building the image from source + +Clone the repository and build locally: + +```bash +git clone https://github.com/saphetor/varsome-api-client-python.git +cd varsome-api-client-python +docker build -t varsome-api-client-python . +``` + +Run using your locally built image — the usage is identical to the GHCR image: + +```bash +docker run --rm \ + -v /path/to/your/data:/data \ + varsome-api-client-python \ + varsome_api_run \ + -k YOUR_API_KEY \ + -g hg19 \ + -q 'chr7-140453136-A-T' \ + -p add-all-data=1 +``` + +### Multi-platform build (amd64 + arm64) + +The official release workflow builds for both `linux/amd64` and `linux/arm64`. +To replicate this locally with Docker Buildx: + +```bash +docker buildx build \ + --platform linux/amd64,linux/arm64 \ + -t varsome-api-client-python:local \ + --load \ + . +``` + +> **Note:** `--load` only works for single-platform builds. For multi-platform, +> use `--push` to push to a registry instead. + +--- + +## Container notes + +- The container runs as a non-root user (`appuser`) for security. +- The working directory inside the container is `/app`. +- The default command (`CMD`) is `varsome_api_run --help`, so running the image + without arguments prints the help text. +- Input and output files must be mounted via `-v` — the container has no access + to your host filesystem by default. +- The image is built with the `[vcf]` extra, so **pysam and its htslib runtime + libraries are pre-installed**. No local build toolchain or system libraries + are required on the host — this is why Docker is the recommended way for end + users to run `varsome_api_annotate_vcf`. diff --git a/examples/README.md b/examples/README.md new file mode 100644 index 0000000..c87251f --- /dev/null +++ b/examples/README.md @@ -0,0 +1,80 @@ +# Examples + +This directory contains self-contained examples that demonstrate how the +`varsome_api` library can be used for custom annotation pipelines beyond +the built-in VCF workflow. + +Each sub-directory is a standalone project with its own `requirements.txt`. + +--- + +## Available examples + +### [`parquet/`](parquet/) + +**Annotate variants from a CSV file and write results to Parquet.** + +This example shows how to: + +- Read variant strings from a plain CSV file. +- Annotate them in batches using `VarSomeAPIClient`. +- Parse each API response with the lightweight **slim** Pydantic model + (`varsome_api.models.slim.annotation.AnnotatedVariant`) — the same model + used internally by `VCFAnnotator`. +- Flatten the nested annotation into a plain `dict` using `to_parquet_row()`. +- Write all rows to a [Parquet](https://parquet.apache.org/) file via + [PyArrow](https://arrow.apache.org/docs/python/). + +#### Quick start + +```bash +# 1. Clone the repository and enter the example directory +git clone https://github.com/saphetor/varsome-api-client-python.git +cd varsome-api-client-python/examples/parquet + +# 2. Create and activate a virtual environment +python -m venv .venv +source .venv/bin/activate # Windows: .venv\Scripts\activate + +# 3. Install dependencies (varsome_api from the local clone + pyarrow) +pip install -r requirements.txt + +# 4. Run the annotation script +# Set VARSOME_API_KEY if you have one; batch lookups require one. +VARSOME_API_KEY=your_key_here python annotate_to_parquet.py + +# Optional flags +python annotate_to_parquet.py \ + --api-key your_key_here \ + --input variants.csv \ + --output annotated_variants.parquet \ + --genome hg19 + +# 5. Inspect the output (pyarrow is already installed) +python - <<'EOF' +import pyarrow.parquet as pq +table = pq.read_table("annotated_variants.parquet") +print(table.schema) +print(table.slice(0, 5).to_pydict()) +EOF +``` + +The script writes `annotated_variants.parquet` in the same directory. +Each row corresponds to one annotated variant and contains the following +columns: + +| Column | Type | Description | +|--------|------|-------------| +| `original_variant` | `string` | Variant string as submitted to the API | +| `chromosome` | `string` | Chromosome identifier | +| `pos` | `int64` | Genomic position | +| `ref` | `string` | Reference allele | +| `alt` | `string` | Alternate allele | +| `gnomad_exomes_af` | `double` | gnomAD exomes allele frequency | +| `gnomad_exomes_an` | `int64` | gnomAD exomes allele number | +| `gnomad_genomes_af` | `double` | gnomAD genomes allele frequency | +| `gnomad_genomes_an` | `int64` | gnomAD genomes allele number | +| `acmg_verdict` | `string` | ACMG classification verdict | +| `acmg_rules` | `list` | Active ACMG rule names | +| `genes` | `list` | Deduplicated gene symbols | +| `rs_ids` | `list` | dbSNP RS identifiers (`rs…`) | diff --git a/examples/parquet/annotate_to_parquet.py b/examples/parquet/annotate_to_parquet.py new file mode 100644 index 0000000..3bc5674 --- /dev/null +++ b/examples/parquet/annotate_to_parquet.py @@ -0,0 +1,184 @@ +import argparse +import logging +import os +import sys +import time +from pathlib import Path + +from varsome_api.client import VarSomeAPIClient +from varsome_api.constants import DEFAULT_REF_GENOME, REFERENCE_GENOMES, RefGenome +from varsome_api.exceptions import VarSomeAPIException +from varsome_api.log import logger +from varsome_api.models.slim.annotation import AnnotatedVariant + +from writer import ParquetWriter + +DEFAULT_INPUT = Path(__file__).parent / "variants.csv" +DEFAULT_OUTPUT = Path(__file__).parent / "annotated_variants.parquet" + + + +def _build_arg_parser() -> argparse.ArgumentParser: + parser = argparse.ArgumentParser( + description="Annotate variants from a CSV file and write to Parquet.", + formatter_class=argparse.ArgumentDefaultsHelpFormatter, + ) + parser.add_argument( + "--api-key", + default=os.environ.get("VARSOME_API_KEY"), + help=( + "VarSome API key. Falls back to the VARSOME_API_KEY environment " + "variable." + ), + ) + parser.add_argument( + "--input", + type=Path, + default=DEFAULT_INPUT, + help="Path to the input CSV file (one variant per line, no header).", + ) + parser.add_argument( + "--output", + type=Path, + default=DEFAULT_OUTPUT, + help="Path for the output Parquet file.", + ) + parser.add_argument( + "--genome", + choices=REFERENCE_GENOMES, + default=DEFAULT_REF_GENOME, + help="Reference genome assembly.", + ) + parser.add_argument( + "--batch-size", + type=int, + default=100, + help="Maximum number of variants per API batch request.", + ) + parser.add_argument( + "--max-requests", + type=int, + default=10, + help="Maximum number of concurrent HTTP requests.", + ) + return parser + + +def load_variants(path: Path) -> list[str]: + with path.open() as fh: + return [line.strip() for line in fh] + + +def annotate_and_write( + variants: list[str], + *, + api_key: str | None, + ref_genome: RefGenome, + batch_size: int, + max_requests: int, + output_path: Path, +) -> tuple[int, int, int]: + api = VarSomeAPIClient( + api_key=api_key, + max_variants_per_batch=batch_size, + ) + + written = 0 + filtered = 0 + errors = 0 + + with ParquetWriter(str(output_path)) as pw: + batch_results = api.batch_lookup( + variants, + params={"add-ACMG-annotation": "1"}, + ref_genome=ref_genome, + max_requests=max_requests, + ) + + for batch in batch_results: + for i, variant_str in enumerate(batch.variants): + raw: dict = batch.response[i] + + if "error" in raw: + logger.error( + "API error for variant %s: %s", + variant_str, + raw["error"], + ) + errors += 1 + continue + + if "filtered_out" in raw: + logger.warning( + "Variant filtered: %s — %s", + variant_str, + raw["filtered_out"], + ) + filtered += 1 + continue + + annotated = AnnotatedVariant(**raw) + pw.add(annotated) + written += 1 + + return written, filtered, errors + + +def _configure_logging() -> None: + handler = logging.StreamHandler() + handler.setLevel(logging.DEBUG) + formatter = logging.Formatter( + "%(asctime)s — %(name)s — %(levelname)s — %(message)s" + ) + handler.setFormatter(formatter) + logger.addHandler(handler) + logger.setLevel(logging.DEBUG) + + +def main() -> None: + _configure_logging() + + parser = _build_arg_parser() + args = parser.parse_args() + + logger.info("Loading variants from %s …", args.input) + variants = load_variants(args.input) + + logger.info("%d variant(s) loaded", len(variants)) + + logger.info( + "Annotating against %s (batch size=%d, concurrency=%d) …", + args.genome, + args.batch_size, + args.max_requests, + ) + + start_time = time.monotonic() + + try: + written, filtered, errors = annotate_and_write( + variants, + api_key=args.api_key, + ref_genome=args.genome, + batch_size=args.batch_size, + max_requests=args.max_requests, + output_path=args.output, + ) + except VarSomeAPIException as exc: + logger.exception("API error: %s", exc) + sys.exit(1) + + elapsed_time = time.monotonic() - start_time + + logger.info( + "Done. Written: %d row(s) → %s, Filtered: %d variant(s), Errors: %d variant(s)", + written, + args.output, + filtered, + errors, + ) + logger.info("Total time: %.2f seconds", elapsed_time) + + +if __name__ == "__main__": + main() diff --git a/examples/parquet/models.py b/examples/parquet/models.py new file mode 100644 index 0000000..7ed26bd --- /dev/null +++ b/examples/parquet/models.py @@ -0,0 +1,54 @@ +from typing import Any + +import pyarrow as pa + +from varsome_api.models.slim.annotation import AnnotatedVariant + + +PARQUET_SCHEMA: pa.Schema = pa.schema( + [ + pa.field("original_variant", pa.string(), nullable=True), + pa.field("chromosome", pa.string(), nullable=True), + pa.field("pos", pa.int64(), nullable=True), + pa.field("ref", pa.string(), nullable=True), + pa.field("alt", pa.string(), nullable=True), + pa.field("gnomad_exomes_af", pa.float64(), nullable=True), + pa.field("gnomad_exomes_an", pa.int64(), nullable=True), + pa.field("gnomad_genomes_af", pa.float64(), nullable=True), + pa.field("gnomad_genomes_an", pa.int64(), nullable=True), + pa.field("acmg_verdict", pa.string(), nullable=True), + pa.field("acmg_rules", pa.list_(pa.string()), nullable=True), + pa.field("genes", pa.list_(pa.string()), nullable=True), + pa.field("rs_ids", pa.list_(pa.string()), nullable=True), + ] +) + + +def _coerce_float(value: float | str | None) -> float | None: + if value is None: + return None + try: + return float(value) + except (TypeError, ValueError): + return None + +def to_parquet_row(variant: AnnotatedVariant) -> dict[str, Any]: + clean_acmg_rules: list[str] = [ + r for r in (variant.acmg_rules or []) if r is not None + ] + + return { + "original_variant": variant.original_variant, + "chromosome": variant.chromosome, + "pos": variant.pos, + "ref": variant.ref, + "alt": variant.alt, + "gnomad_exomes_af": _coerce_float(variant.gnomad_exomes_af), + "gnomad_exomes_an": variant.gnomad_exomes_an, + "gnomad_genomes_af": _coerce_float(variant.gnomad_genomes_af), + "gnomad_genomes_an": variant.gnomad_genomes_an, + "acmg_verdict": variant.acmg_verdict, + "acmg_rules": clean_acmg_rules or None, + "genes": variant.genes or None, + "rs_ids": variant.rs_ids or None, + } diff --git a/examples/parquet/requirements.txt b/examples/parquet/requirements.txt new file mode 100644 index 0000000..89b09e4 --- /dev/null +++ b/examples/parquet/requirements.txt @@ -0,0 +1,6 @@ +# varsome_api from the local clone (no [vcf] extra — no pysam / C build deps) +# Run from examples/parquet/ so the relative path resolves correctly. +../../ + +# Columnar storage +pyarrow diff --git a/examples/parquet/variants.csv b/examples/parquet/variants.csv new file mode 100644 index 0000000..d274a87 --- /dev/null +++ b/examples/parquet/variants.csv @@ -0,0 +1,25000 @@ +chr1:126113:C:A +chr1:535131:T:G +chr1:567239:CG:C +chr1:570254:A:G +chr1:592368:A:G +chr1:610426:A:G +chr1:628140:T:C +chr1:645605:T:A +chr1:649192:A:T +chr1:662414:C:T +chr1:662622:G:A +chr1:662857:G:A +chr1:663097:G:C 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self._build_table() + pq.write_table(table, self._output_path, compression="lz4") + return len(self._rows) + + def __enter__(self) -> "ParquetWriter": + return self + + def __exit__( + self, + exc_type: type[BaseException] | None, + exc_val: BaseException | None, + exc_tb: TracebackType | None, + ) -> None: + if exc_type is None: + self.write() + + + def _build_table(self) -> pa.Table: + columns: dict[str, list] = {field.name: [] for field in self._schema} + + for row in self._rows: + for field in self._schema: + columns[field.name].append(row.get(field.name)) + + arrays: list[pa.Array] = [ + pa.array(columns[field.name], type=field.type) + for field in self._schema + ] + return pa.Table.from_arrays(arrays, schema=self._schema) diff --git a/poetry.lock b/poetry.lock new file mode 100644 index 0000000..227c8fc --- /dev/null +++ b/poetry.lock @@ -0,0 +1,2939 @@ +# This file is automatically @generated by Poetry 1.8.5 and should not be changed by hand. + +[[package]] +name = "aiodns" 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"] +readme = "README.md" +license = "Apache License, Version 2.0" +classifiers=[ + "Development Status :: 4 - Beta", + "Intended Audience :: Developers", + "Intended Audience :: Science/Research", + "Operating System :: OS Independent", + "License :: OSI Approved :: Apache License", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", + "Programming Language :: Python :: 3.13", + "Programming Language :: Python :: 3.14", + "Topic :: Scientific/Engineering :: Bio-Informatics", + ] +repository = "https://github.com/saphetor/varsome-api-client-python" + +[tool.poetry.scripts] +varsome_api_run = "varsome_api.cli.varsome_api_run:main" +varsome_api_annotate_vcf = "varsome_api.cli.varsome_api_annotate_vcf:main" + +[tool.poetry.dependencies] +python = ">=3.11, <3.15" +aiohttp = {version = "^3.13", extras = ["speedups"]} +pydantic = "^2.0" +pysam = {version = "^0.23", optional = true} + +[tool.poetry.extras] +vcf = ["pysam"] + +[tool.poetry.dev-dependencies] 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Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. - -import argparse - -from varsome_api.vcf import VCFAnnotator - - -def annotate_vcf(): - parser = argparse.ArgumentParser(description="VCF Annotator command line") - parser.add_argument( - "-k", help="Your key to the API", type=str, metavar="API Key", required=True - ) - parser.add_argument( - "-g", - help="Reference genome either hg19 or hg38", - type=str, - metavar="Reference Genome", - required=False, - default="hg19", - ) - parser.add_argument( - "-i", help="Path to vcf file", type=str, metavar="Input VCF File", required=True - ) - parser.add_argument( - "-o", - help="Path to output vcf file", - type=str, - metavar="Output VCF File", - required=False, - ) - parser.add_argument( - "-p", - help="Request parameters e.g. add-all-data=1 add-ACMG-annotation=1", - type=str, - metavar="Request Params", - required=False, - nargs="+", - ) - parser.add_argument( - "-t", - help="Run vcf annotator using x threads", - type=int, - default=3, - required=False, - metavar="Number of threads", - ) - parser.add_argument( - "-u", - help="Use specific VarSome API host url " - "(e.g. https://api.varsome.com or https://stable-api.varsome.com", - type=str, - required=False, - metavar="VarSome API host url", - ) - args = parser.parse_args() - api_key = args.k - vcf_file = args.i - output_vcf_file = args.o - ref_genome = args.g - num_threads = args.t - api_url = args.u - request_parameters = None - if args.p: - request_parameters = { - param[0]: param[1] for param in [param.split("=") for param in args.p] - } - vcf_annotator = VCFAnnotator( - api_key=api_key, - api_url=api_url, - ref_genome=ref_genome, - get_parameters=request_parameters, - max_threads=num_threads, - ) - vcf_annotator.annotate(vcf_file, output_vcf_file) - - -if __name__ == "__main__": - annotate_vcf() diff --git a/scripts/varsome_api_run.py b/scripts/varsome_api_run.py deleted file mode 100755 index eef0abf..0000000 --- a/scripts/varsome_api_run.py +++ /dev/null @@ -1,190 +0,0 @@ -#!/usr/bin/env python3 - -# Copyright 2018 Saphetor S.A. -# -# Licensed under the Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.apache.org/licenses/LICENSE-2.0 -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. - -import argparse -import json -import os -import sys - -from varsome_api.client import VarSomeAPIClient - - -def annotate_variant(): - parser = argparse.ArgumentParser(description="Sample VarSome API calls") - parser.add_argument( - "-k", help="Your key to the API", type=str, metavar="API Key", required=False - ) - parser.add_argument( - "-g", - help="Reference genome either hg19 or hg38", - type=str, - metavar="Reference Genome", - required=False, - default="hg19", - ) - parser.add_argument( - "-q", - help="Query to lookup in the API e.g. " - "chr19:20082943:1:G or in case of batch request " - "e.g. chr15-73027478-T-C rs113488022. " - "Don't use it together with the -i option", - type=str, - metavar="Query", - required=False, - nargs="+", - ) - parser.add_argument( - "-p", - help="Request parameters e.g. add-all-data=1 expand-pubmed-articles=0", - type=str, - metavar="Request Params", - required=False, - nargs="+", - ) - parser.add_argument( - "-i", - help="Path to text file with variants. " - "It should include one variant per line. Don't use it " - "together with the -q option", - type=str, - metavar="Text/CSV File one line per variant", - required=False, - ) - parser.add_argument( - "-o", - help="Path to output file to store variant annotations", - type=str, - metavar="Output File with json entries", - required=False, - ) - parser.add_argument( - "-u", - help="Use specific VarSome API host url " - "(e.g. https://api.varsome.com or https://stable-api.varsome.com", - type=str, - required=False, - metavar="VarSome API host url", - ) - args = parser.parse_args() - api_key = args.k - query = args.q - ref_genome = args.g - input_file = args.i - output_file = args.o - api_url = args.u - if query and input_file: - sys.stderr.write( - "Don't specify -i and -q options together. Use only one of them\n" - ) - sys.exit(1) - if not query and not input_file: - sys.stderr.write("Please either specify -i or -q options\n") - sys.exit(1) - if input_file and not os.path.exists(input_file): - sys.stderr.write("File %s does not exist\n" % input_file) - sys.exit(1) - if output_file and os.path.exists(output_file): - sys.stderr.write("File %s already exists\n" % output_file) - sys.exit(1) - request_parameters = None - if args.p: - request_parameters = { - param[0]: param[1] for param in [param.split("=") for param in args.p] - } - api = VarSomeAPIClient(api_key, api_url=api_url) - if query: - if len(query) == 1: - result = api.lookup( - query[0], params=request_parameters, ref_genome=ref_genome - ) - else: - if api_key is None: - sys.exit("You need to pass an api key to perform batch requests") - result = api.batch_lookup( - query, params=request_parameters, ref_genome=ref_genome - ) - result = list(result) - if output_file: - with open(output_file, "w") as fp: - json.dump(result, fp, indent=4, sort_keys=True) - else: - sys.stdout.write( - json.dumps(result, indent=4, sort_keys=True) if result else "No result" - ) - sys.stdout.write("\n") - sys.exit(0) - with open(input_file) as f: - variants = f.read().splitlines() - if variants: - if len(variants) > 1000: - sys.stdout.write( - "Too many variants.. Consider using annotate_vcf instead\n" - ) - sys.stdout.flush() - try: - if api_key is None: - sys.stdout.write( - "Without an API key, variants will be annotated one a time, " - "causing a 429 too many requests error after some time\n" - ) - sys.stdout.flush() - results = [] - for variant in variants: - result = api.lookup( - variant, params=request_parameters, ref_genome=ref_genome - ) - if not result: - result = { - "error": "Could not fetch annotations for %s" % variant - } - results.append(result) - if output_file: - with open(output_file, "w") as fp: - json.dump(results, fp, indent=4, sort_keys=True) - else: - sys.stdout.write( - json.dumps(results, indent=4, sort_keys=True) - if results - else "No result" - ) - sys.stdout.write("\n") - else: - result = api.batch_lookup( - variants, params=request_parameters, ref_genome=ref_genome - ) - result = list(result) - if output_file: - with open(output_file, "w") as fp: - json.dump(result, fp, indent=4, sort_keys=True) - else: - sys.stdout.write( - json.dumps(result, indent=4, sort_keys=True) - if result - else "No result" - ) - sys.stdout.write("\n") - except Exception as e: - # several things might occur. This is too broad, - sys.stderr.write(str(e)) - sys.stderr.write("\n") - sys.exit(1) - else: - sys.stderr.write("No variants found in file %s\n" % input_file) - sys.exit(1) - - -if __name__ == "__main__": - annotate_variant() diff --git a/setup.py b/setup.py deleted file mode 100755 index d983987..0000000 --- a/setup.py +++ /dev/null @@ -1,48 +0,0 @@ -import sys -from os import path - -from setuptools import setup, find_packages - -VERSION = (1, 2, "0b1") -__version__ = VERSION -__versionstr__ = ".".join(map(str, VERSION)) - -here = path.abspath(path.dirname(__file__)) -installation_requirements = [ - "requests>=2.0.0, <3.0.0", - "PyVCF3>=1.0.1", - "jsonmodels>=2.2", -] -if sys.version_info < (3, 4): - installation_requirements.extend(["asyncio", "unittest2"]) -setup( - name="varsome_api_client", - version=__versionstr__, - packages=find_packages( - ".", - ), - scripts=["scripts/varsome_api_run.py", "scripts/varsome_api_annotate_vcf.py"], - url="https://github.com/saphetor/varsome-api-client-python", - license="Apache License, Version 2.0", - author="Saphetor S.A.", - author_email="support@saphetor.com", - description="A basic python api client implementation for https://api.varsome.com", - classifiers=[ - "Development Status :: 4 - Beta", - "Intended Audience :: Developers", - "Intended Audience :: Science/Research", - "Operating System :: OS Independent", - "License :: OSI Approved :: Apache License", - "Programming Language :: Python :: 3.3", - "Programming Language :: Python :: 3.4", - "Programming Language :: Python :: 3.5", - "Programming Language :: Python :: 3.6", - "Programming Language :: Python :: 3.7", - "Programming Language :: Python :: 3.8", - "Programming Language :: Python :: 3.9", - "Programming Language :: Python :: 3.10", - "Topic :: Scientific/Engineering :: Bio-Informatics", - ], - install_requires=installation_requirements, - python_requires=">=3.3,<3.11", -) diff --git a/tests/conftest.py b/tests/conftest.py new file mode 100644 index 0000000..b55d182 --- /dev/null +++ b/tests/conftest.py @@ -0,0 +1,46 @@ +from collections.abc import Callable +from typing import Any + +import pytest + +from varsome_api.client import VarSomeAPIClient + + +@pytest.fixture() +def api_client() -> VarSomeAPIClient: + """A ``VarSomeAPIClient`` pre-configured with a test API key.""" + return VarSomeAPIClient(api_key="test") + + +@pytest.fixture() +def make_fake_request() -> Callable[ + [Callable[[list[str]], list[dict[str, Any]]]], + Callable[..., Any], +]: + """Factory that builds an async ``_make_request`` replacement. + + Call with a *response_builder* — a function that receives the + variant list extracted from the POST JSON body and returns the + mock API response list. + + Example:: + + fake = make_fake_request(lambda batch: [{"id": v} for v in batch]) + """ + + def _factory( + response_builder: Callable[[list[str]], list[dict[str, Any]]], + ) -> Callable[..., Any]: + async def _fake( + _session: Any, + *, + path: str, + method: str = "GET", + **kwargs: Any, + ) -> list[dict[str, Any]]: + batch = kwargs.get("json", {}).get("variants", []) + return response_builder(batch) + + return _fake + + return _factory diff --git a/tests/fixtures/example_response_amp.json b/tests/fixtures/example_response_amp.json new file mode 100644 index 0000000..fbe5eb0 --- /dev/null +++ b/tests/fixtures/example_response_amp.json @@ -0,0 +1 @@ +{"chromosome":"chr7","alt":"T","ref":"A","pos":140453136,"variant_id":"10190071404531360004","regions":{"uniprot_regions":{"version":"07-Feb-2026","items":[{"absolute_positon":2611797646,"amino_acid":"M1-E46,V47-E80,A81-V168,V169-G203,G203-F237,V238-D287,D287-G327,G327-D380,D381-G393,G393-M438,K439-G478,G478-R506,R506-D565,D565-N581,N581-M620,A621-Q664,I665-Q709,I710-H766","chromo":"chr7","colour":"255,0,0","description":null,"length":194265,"position":140430465,"protein":"BRAF_HUMAN","type":"homo_sapiens proteome 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Tumour",1],"tissue_freq":["Stomach",1]},{"drug_name":"Cetuximab","somatic_status":null,"zygosity":null,"gene":"BRAF","transcript":"ENST00000288602.6","census_gene":"Yes","pub_med_references":[24553385],"histology_freq":["Carcinoma",1],"tissue_freq":["Large Intestine",1]}]}]}],"ncbi_clinvar2":[{"version":"07-Feb-2026","review_status":"criteria provided, conflicting classifications","review_stars":1,"variation_id":13961,"num_submitters":21,"pub_med_references":[12068308,12198537,12447372,12619120,12644542,12670889,12794760,12960123,14513361,14602780,15001635,15126572,15181070,15342696,15356022,15386408,15687339,15998781,16015629,16174717,16187918,16772349,17374713,17488796,17785355,18398503,19571295,20818844,20823850,21107320,21107323,22039425,22113612,22281684,23302800,23685455,24512911,24670642,24717435,25079330,25950823,28854169,29925953,31891627,34476331],"clinical_significance":["Conflicting Classifications Of Pathogenicity"],"last_evaluation":"20260201","origin":null,"accessions":[{"submissions":[{"submission_description":["This sequence change replaces valine, which is neutral and non-polar, with glutamic acid, which is acidic and polar, at codon 600 of the BRAF protein (p.Val600Glu). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has been reported as a known somatic variant in various cancers but has not been reported in the literature in individuals affected with germline BRAF-related conditions. ClinVar contains an entry for this variant (Variation ID: 13961). Invitae Evidence Modeling incorporating data from in vitro experimental studies (internal data) indicates that this missense variant is expected to disrupt BRAF function with a positive predictive value of 95%. This variant disrupts the p.Val600 amino acid residue in BRAF. Other variant(s) that disrupt this residue have been determined to be pathogenic (internal data). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance."],"submitter_name":"Labcorp Genetics (formerly Invitae), Labcorp","review_date":20250123,"origin":"germline","method":"clinical testing","submitter_date":20250207,"diseases":[{"symbols":{"medgen":"CN166718"}}],"review_description":"Uncertain significance","date_updated":20250225,"clinical_significance":["Uncertain significance"],"review_status":"criteria provided, single submitter","accession_id":"SCV005812663"}],"variation_id":13961,"submission_description":[],"title":"NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) AND RASopathy","review_date":20250123,"diseases":[{"symbols":{"medgen":"C5555857","mondo":"MONDO:0021060"},"normalized_disease":["Rasopathy"],"names":["Rasopathy","Rasopathies","Noonan Spectrum Disorder"]}],"date_created":20250225,"variant_id":10190071404531360004,"review_description":"Uncertain significance","clinical_significance":["Uncertain significance"],"allele_id":29000,"accession_id":"RCV005089260"},{"submissions":[{"submission_description":["The BRAF c.1799T>A (p.Val600Glu) variant was identified at an allelic fraction consistent with somatic origin. This variant is absent from the general population (gnomAD v.3.1.2), indicating it is not a common variant. This variant occurs in a highly conserved residue within the CR3 activation segment, amino acids 594-627, of BRAF that is defined as a critical functional domain (Wellbrock C, et al., PMID: 15520807; Gelb BD, et al., PMID: 29493581). The BRAF c.1799T>A (p.Val600Glu) variant in a somatic state has been reported in multiple individuals affected with sporadic vascular malformations, brain arteriovenous malformation (BAVM) and spinal arteriovenous malformation (SAVM) (Hong T, et al., PMID: 30544177; Al-Olabi L, et al., PMID: 29461977; Goss JA, et al., PMID: 31891627; Li H, et al., PMID: 34530633). The BRAF c.1799T>A (p.Val600Glu) variant has been reported in the ClinVar database as pathogenic by numerous submitters (ClinVar ID: 13961). Computational predictors indicate that the variant is damaging, evidence that correlates with impact to BRAF function. In support of this prediction, functional studies show constitutively active kinase activity (Rodriguez-Viciana P, et al., PMID: 16439621; Sarkozy A, et al., PMID:19206169; Al-Olabi L, et al., PMID: 29461977). Based on an internally developed protocol informed by the ACMG/AMP guidelines (Richards S et al., PMID: 25741868) and gene-specific practices from the ClinGen Criteria Specification Registry, this variant is classified as pathogenic."],"submitter_name":"Clinical Genomics Laboratory, Washington University in St. Louis","review_date":20231022,"origin":"somatic","method":"clinical testing","submitter_date":20231212,"diseases":[{"normalized_disease":["Vascular Malformation"],"names":["Vascular Malformation"]}],"review_description":"Pathogenic","date_updated":20231224,"clinical_significance":["Pathogenic"],"review_status":"criteria provided, single submitter","accession_id":"SCV004176942"}],"variation_id":13961,"submission_description":[],"title":"NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) AND Vascular malformation","review_date":20231022,"diseases":[{"symbols":{"medgen":"C0158570","mondo":"MONDO:0024291"},"normalized_disease":["Vascular Malformation"],"names":["Vascular Malformation","Vascular Malformations"]}],"date_created":20231224,"variant_id":10190071404531360004,"review_description":"Pathogenic","clinical_significance":["Pathogenic"],"allele_id":29000,"accession_id":"RCV003458334"},{"submissions":[{"submitter_date":20240424,"submission_description":["ASSESSED FOR SOMATIC SAMPLE ONLY. FOR ANY GERMLINE INDICATION, PLEASE REASSESS."],"submitter_name":"Ambry Genetics","review_date":20220523,"origin":"germline","method":"clinical testing","finding":[{"symbols":{"medgen":"CN230736"}}],"review_description":"Likely pathogenic","date_updated":20240501,"clinical_significance":["Likely pathogenic"],"review_status":"criteria provided, single submitter","accession_id":"SCV005022010"}],"variation_id":13961,"submission_description":[],"title":"NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) AND Cardiovascular phenotype","review_date":20220523,"diseases":[{"symbols":{"medgen":"CN230736"},"names":["Cardiovascular Phenotype"]}],"date_created":20240501,"variant_id":10190071404531360004,"review_description":"Likely pathogenic","clinical_significance":["Likely pathogenic"],"allele_id":29000,"accession_id":"RCV004018627"},{"submissions":[{"submission_description":["The Val600Glu variant in BRAF was observed at very low levels (VAF 0.3-2%) in lymphatic malformation tissue from three unrelated individuals using high depth NGS (VANseq), confirmatory digital droplet PCR, and BRAF V600E immunohistochemistry."],"submitter_name":"James Bennett Lab, Seattle Childrens Research Institute","review_date":20220209,"origin":"somatic","method":"research","finding":[{"symbols":{"hp":"HP:0100766"},"normalized_phenotype":["Abnormal Lymphatic Vessel Morphology"]}],"submitter_date":20220325,"diseases":[{"symbols":{"hp":"HP:0100764"}}],"review_description":"Pathogenic","date_updated":20250803,"clinical_significance":["Pathogenic"],"review_status":"no assertion criteria provided","accession_id":"SCV002318371"}],"variation_id":13961,"submission_description":[],"title":"NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) AND Lymphangioma","review_date":20220209,"diseases":[{"symbols":{"medgen":"C0024221","mondo":"MONDO:0002013","human_phenotype_ontology":"HP:0100764"},"normalized_disease":["Lymphangioma"],"names":["Lymphangioma"]}],"date_created":20220328,"variant_id":10190071404531360004,"review_description":"Pathogenic","clinical_significance":["Pathogenic"],"allele_id":29000,"accession_id":"RCV002051586"},{"submissions":[{"submission_description":[],"submitter_name":"Xiao lab, Department of Pathology, Memorial Sloan Kettering Cancer Center","review_date":20190831,"origin":"somatic","method":"clinical testing","submitter_date":20190912,"diseases":[{"normalized_cancer":["Plasma Cell Myeloma"],"symbols":{"orphanet":"ORPHA29073"},"normalized_disease":["Plasma Cell Myeloma"],"names":["Plasma Cell Myeloma"]}],"review_description":"Likely pathogenic","date_updated":20191223,"clinical_significance":["Likely pathogenic"],"review_status":"no assertion criteria provided","accession_id":"SCV001132084"}],"variation_id":13961,"submission_description":[],"title":"NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) AND Multiple myeloma","review_date":20190831,"diseases":[{"symbols":{"omim":"254500","medgen":"C0026764","orphanet":"85443","mesh":"D009101","mondo":"MONDO:0009693","human_phenotype_ontology":"HP:0006775"},"normalized_disease":["Plasma Cell Myeloma"],"names":["Plasma Cell Myeloma","Plasma Cell Myeloma","Multiple Myeloma, Somatic"],"normalized_cancer":["Plasma Cell Myeloma"],"keyword":"Hereditary cancer syndrome"}],"date_created":20170308,"variant_id":10190071404531360004,"review_description":"Likely pathogenic","clinical_significance":["Likely pathogenic"],"allele_id":29000,"accession_id":"RCV000430562"},{"submissions":[{"submission_description":[],"submitter_name":"Pediatric Oncology, Johns Hopkins University","review_date":20190215,"origin":"somatic","method":"clinical testing","submitter_date":20200116,"diseases":[{"normalized_cancer":["Wilms' Tumor"],"normalized_disease":["Kidney Wilms Tumor"],"names":["Kidney Wilms Tumor"]}],"review_description":"Pathogenic","date_updated":20250413,"clinical_significance":["Pathogenic"],"review_status":"no assertion criteria provided","accession_id":"SCV001147031"}],"variation_id":13961,"submission_description":[],"title":"NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) AND Nephroblastoma","review_date":20190215,"diseases":[{"normalized_cancer":["Wilms' Tumor"],"symbols":{"medgen":"C0027708","mesh":"D009396","mondo":"MONDO:0006058","human_phenotype_ontology":"HP:0000115"},"normalized_disease":["Kidney Wilms Tumor"],"names":["Kidney Wilms Tumor","Kidney Wilms Tumor","Kidney Wilms Tumor"]}],"date_created":20200719,"variant_id":10190071404531360004,"review_description":"Pathogenic","clinical_significance":["Pathogenic"],"allele_id":29000,"accession_id":"RCV001248834"},{"submissions":[{"submission_description":[],"submitter_name":"Yale Center for Mendelian Genomics, Yale University","review_date":20150507,"origin":"somatic","method":"literature only","submitter_date":20171127,"diseases":[{"names":["Cystic Epithelial Invagination Containing Papillae Lined By Columnar Epithelium"]}],"review_description":"Pathogenic","date_updated":20180714,"clinical_significance":["Pathogenic"],"review_status":"no assertion criteria provided","accession_id":"SCV000784606"},{"submission_description":[],"submitter_name":"Yale Center for Mendelian Genomics, Yale University","review_date":20150507,"origin":"somatic","method":"literature only","submitter_date":20220321,"diseases":[{"names":["Cystic Epithelial Invagination Containing Papillae Lined By Columnar Epithelium"]}],"review_description":"Pathogenic","date_updated":20220328,"clinical_significance":["Pathogenic"],"review_status":"no assertion criteria provided","accession_id":"SCV002106413"}],"variation_id":13961,"submission_description":[],"title":"NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) AND Cystic epithelial invagination containing papillae lined by columnar epithelium","review_date":20150507,"diseases":[{"names":["Cystic Epithelial Invagination Containing Papillae Lined By Columnar Epithelium"]}],"date_created":20180714,"variant_id":10190071404531360004,"review_description":"Pathogenic","clinical_significance":["Pathogenic"],"allele_id":29000,"accession_id":"RCV000662278"},{"submissions":[{"submission_description":["Variant has Tier I (strong) clinical significance as a diagnostic inclusion criterion in thyroid gland papillary carcinoma, based on the following evidence: 1) Documented in one or more cancer databases (e.g., St. Jude Pecan, COSMIC, CIViC, OncoKB). 2) Appears in one or more well-established professional guidelines (e.g., World Health Organization [WHO]; National Comprehensive Cancer Network [NCCN]) as providing diagnostic, prognostic, or therapeutic information. 3) Information in the literature supports potential biologic effect of variant. 4) Diagnostic for a specific tumor type/classification based on well-powered studies with expert-level consensus (Evidence Level B; PMIDs: 25417114, 12970315, 14508525, 21878896)."],"submitter_name":"Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital","review_date":20241218,"origin":"somatic","method":"clinical testing","submitter_date":20251120,"diseases":[{"symbols":{"mondo":"MONDO:0005075"}}],"date_updated":20251122,"clinical_significance":[],"review_status":"criteria provided, single submitter","accession_id":"SCV007105546"},{"pub_med_references":[12068308,12198537,12447372,12619120,12644542,12670889,12794760,12960123,14513361,14602780,15001635,15126572,15181070,15342696,15356022,15386408,15687339,15998781,16015629,16174717,16187918,16772349,17374713,17488796,17785355,18398503,19571295,20818844,20823850,21107320,21107323,22113612,22281684,23302800,23685455,24512911,24670642,24717435,25079330,28854169,29925953],"submission_description":["The val600-to-glu (V600E) mutation caused by a 1799T-A transversion in the BRAF gene was previously designated VAL599GLU (1796T-A). Kumar et al. (2003) noted that an earlier version of the BRAF sequence showed a discrepancy of 3 nucleotides in exon 1; based on the corrected sequence, they proposed a change in nucleotide numbering after nucleotide 94 (the ATG codon) by +3 and a corresponding codon change of +1.","Malignant Melanoma","Davies et al. (2002) identified a 1799T-A transversion in exon 15 of the BRAF gene that leads to a val600-to-glu (V600E) substitution. This mutation accounted for 92% of BRAF mutations in malignant melanoma (see 155600). The V600E mutation is an activating mutation resulting in constitutive activation of BRAF and downstream signal transduction in the MAP kinase pathway.","To evaluate the timing of mutations in BRAF during melanocyte neoplasia, Pollock et al. (2003) carried out mutation analysis on microdissected melanoma and nevi samples. They observed mutations resulting in the V600E amino acid substitution in 41 (68%) of 60 melanoma metastases, 4 (80%) of 5 primary melanomas, and, unexpectedly, in 63 (82%) of 77 nevi. The data suggested that mutational activation of the RAS/RAF/MAPK pathway in nevi is a critical step in the initiation of melanocytic neoplasia but alone is insufficient for melanoma tumorigenesis.","Lang et al. (2003) failed to find the V600E mutation as a germline mutation in 42 cases of familial melanoma studied. Their collection of families included 15 with and 24 without detected mutations in CDKN2A (600160). They did, however, find the V600E mutation in 6 (27%) of 22 samples of secondary (metastatic) melanomas studied. Meyer et al. (2003) found no V600E mutation in 172 melanoma patients comprising 46 familial cases, 21 multiple melanoma patients, and 106 cases with at least 1 first-degree relative suffering from other cancers. They concluded, therefore, that the common somatic BRAF mutation V600E does not contribute to polygenic or familial melanoma predisposition.","Kim et al. (2003) stated that V600E, the most common of BRAF mutations, had not been identified in tumors with mutations of the KRAS gene (190070). This mutually exclusive relationship supports the hypothesis that BRAF (V600E) and KRAS mutations exert equivalent effects in tumorigenesis (Rajagopalan et al., 2002; Singer et al., 2003).","Flaherty et al. (2010) reported complete or partial regression of V600E-associated metastatic melanoma in 81% of patients treated with an inhibitor (PLX4032) specific to the V600E mutation. Among 16 patients in a dose-escalation cohort, 10 had a partial response, and 1 had a complete response. Among 32 patients in an extension cohort, 24 had a partial response, and 2 had a complete response. The estimated median progression-free survival among all patients was more than 7 months. Responses were observed at all sites of disease, including bone, liver, and small bowel. Tumor biopsy specimens from 7 patients showed markedly reduced levels of phosphorylated ERK (600997), cyclin D1 (168461), and Ki67 (MKI67; 176741) at day 15 compared to baseline, indicating inhibition of the MAP kinase pathway. Three additional patients with V600E-associated papillary thyroid also showed a partial or complete response.","Bollag et al. (2010) described the structure-guided discovery of PLX4032 (RG7204), a potent inhibitor of oncogenic BRAF kinase activity. PLX4032 was cocrystallized with a protein construct that contained the kinase domain of BRAF(V600E). In a clinical trial, patients exposed to higher plasma levels of PLX4032 experienced tumor regression; in patients with tumor regressions, pathway analysis typically showed greater than 80% inhibition of cytoplasmic ERK phosphorylation. Bollag et al. (2010) concluded that their data demonstrated that BRAF-mutant melanomas are highly dependent on BRAF kinase activity.","Patients with BRAF(V600E)-positive melanomas exhibit an initial antitumor response to the RAF kinase inhibitor PLX4032, but acquired drug resistance almost invariably develops. Johannessen et al. (2010) identified MAP3K8 (191195), encoding COT (cancer Osaka thyroid oncogene) as a MAPK pathway agonist that drives resistance to RAF inhibition in BRAF(V600E) cell lines. COT activates ERK primarily through MARK/ERK (MEK)-dependent mechanisms that do not require RAF signaling. Moreover, COT expression is associated with de novo resistance in BRAF(V600E) cultured cell lines and acquired resistance in melanoma cells and tissue obtained from relapsing patients following treatment with MEK or RAF inhibitors. Johannessen et al. (2010) further identified combinatorial MAPK pathway inhibition or targeting of COT kinase activity as possible therapeutic strategies for reducing MAPK pathway activation in this setting.","Nazarian et al. (2010) showed that acquired resistance to PLX4032, a novel class I RAF-selective inhibitor, develops by mutually exclusive PDGFRB (173410) upregulation or NRAS (164790) mutations but not through secondary mutations in BRAF(V600E). Nazarian et al. (2010) used PLX4032-resistant sublines artificially derived from BRAF (V600E)-positive melanoma cell lines and validated key findings in PLX4032-resistant tumors and tumor-matched, short-term cultures from clinical trial patients. Induction of PDGFRB RNA, protein and tyrosine phosphorylation emerged as a dominant feature of acquired PLX4032 resistance in a subset of melanoma sublines, patient-derived biopsies, and short-term cultures. PDGFRB upregulated tumor cells have low activated RAS levels and, when treated with PLX4032, do not reactivate the MAPK pathway significantly. In another subset, high levels of activated N-RAS resulting from mutations lead to significant MAPK pathway reactivation upon PLX4032 treatment. Knockdown of PDGFRB or NRAS reduced growth of the respective PLX4032-resistant subsets. Overexpression of PDGFRB or NRAS(Q61K) conferred PLX4032 resistance to PLX4032-sensitive parental cell lines. Importantly, Nazarian et al. (2010) showed that MAPK reactivation predicts MEK inhibitor sensitivity. Thus, Nazarian et al. (2010) concluded that melanomas escape BRAF(V600E) targeting not through secondary BRAF(V600E) mutations but via receptor tyrosine kinase (RTK)-mediated activation of alternative survival pathway(s) or activated RAS-mediated reactivation of the MAPK pathway, suggesting additional therapeutic strategies.","Poulikakos et al. (2011) identified a novel resistance mechanism for melanomas with BRAF(V600E) treated with RAF inhibitors. The authors found that a subset of cells resistant to vemurafenib (PLX4032, RG7204) express a 61-kD variant form of BRAF(V600E), p61BRAF(V600E), that lacks exons 4 through 8, a region that encompasses the RAS-binding domain. p61BRAF(V600E) showed enhanced dimerization in cells with low levels of RAS activation, as compared to full-length BRAF(V600E). In cells in which p61BRAF(V600E) was expressed endogenously or ectopically, ERK signaling was resistant to the RAF inhibitor. Moreover, a mutation that abolished the dimerization of p61BRAF(V600E) restored its sensitivity to vemurafenib. Finally, Poulikakos et al. (2011) identified BRAF(V600E) splicing variants lacking the RAS-binding domain in the tumors of 6 of 19 patients with acquired resistance to vemurafenib. Poulikakos et al. (2011) concluded that their data supported the model that inhibition of ERK signaling by RAF inhibitors is dependent on levels of RAS-GTP too low to support RAF dimerization and identified a novel mechanism of acquired resistance in patients: expression of splicing isoforms of BRAF(V600E) that dimerize in a RAS-independent manner.","Thakur et al. (2013) investigated the cause and consequences of vemurafenib resistance using 2 independently-derived primary human melanoma xenograft models in which drug resistance is selected by continuous vemurafenib administration. In one of these models, resistant tumors showed continued dependency on BRAF(V600E)-MEK-ERK signaling owing to elevated BRAF(V600E) expression. Thakur et al. (2013) showed that vemurafenib-resistant melanomas become drug-dependent for their continued proliferation, such that cessation of drug administration leads to regression of established drug-resistant tumors. Thakur et al. (2013) further demonstrated that a discontinuous dosing strategy, which exploits the fitness disadvantage displayed by drug-resistant cells in the absence of the drug, forestalls the onset of lethal drug-resistant disease. Thakur et al. (2013) concluded that their data highlighted the concept that drug-resistant cells may also display drug dependency, such that altered dosing may prevent the emergence of lethal drug resistance. These observations may contribute to sustaining the durability of vemurafenib response with the ultimate goal of curative therapy for the subset of melanoma patients with BRAF mutations.","Using metabolic profiling and functional perturbations, Kaplon et al. (2013) showed that the mitochondrial gatekeeper pyruvate dehydrogenase (PDH; 300502) is a crucial mediator of senescence induced by BRAF(V600E), an oncogene commonly mutated in melanoma and other cancers. BRAF(V600E)-induced senescence is accompanied by simultaneous suppression of the PDH-inhibitory enzyme pyruvate dehydrogenase kinase-1 (PDK1; 602524) and induction of the PDH-activating enzyme pyruvate dehydrogenase phosphatase-2 (PDP2; 615499). The resulting combined activation of PDH enhanced the use of pyruvate in the tricarboxylic acid cycle, causing increased respiration and redox stress. Abrogation of oncogene-induced senescence (OIS), a rate-limiting step towards oncogenic transformation, coincided with reversion of these processes. Further supporting a crucial role of PDH in OIS, enforced normalization of either PDK1 or PDP2 expression levels inhibited PDH and abrogated OIS, thereby licensing BRAF(V600E)-driven melanoma development. Finally, depletion of PDK1 eradicated melanoma subpopulations resistant to targeted BRAF inhibition, and caused regression of established melanomas.","Sun et al. (2014) showed that 6 out of 16 BRAF(V600E)-positive melanoma tumors analyzed acquired EGFR (131550) expression after the development of resistance to inhibitors of BRAF or MEK (176872). Using a chromatin regulator-focused short hairpin RNA (shRNA) library, Sun et al. (2014) found that suppression of SRY-box 10 (SOX10; 602229) in melanoma causes activation of TGF-beta (190180) signaling, thus leading to upregulation of EGFR and platelet-derived growth factor receptor-beta (PDGFRB; 173410), which confer resistance to BRAF and MEK inhibitors. Expression of EGFR in melanoma or treatment with TGF-beta results in a slow-growth phenotype with cells displaying hallmarks of oncogene-induced senescence. However, EGFR expression or exposure to TGF-beta becomes beneficial for proliferation in the presence of BRAF or MEK inhibitors. In a heterogeneous population of melanoma cells that have varying levels of SOX10 suppression, cells with low SOX10 and consequently high EGFR expression are rapidly enriched in the presence of drug treatment, but this is reversed when the treatment is discontinued. Sun et al. (2014) found evidence for SOX10 loss and/or activation of TGF-beta signaling in 4 of the 6 EGFR-positive drug-resistant melanoma patient samples. Sun et al. (2014) concluded that their findings provided a rationale for why some BRAF or MEK inhibitor-resistant melanoma patients may regain sensitivity to these drugs after a 'drug holiday' and identified patients with EGFR-positive melanoma as a group that may benefit from retreatment after a drug holiday.","Boussemart et al. (2014) demonstrated that the persistent formation of the eIF4F complex, comprising the eIF4E (133440) cap-binding protein, the eIF4G (600495) scaffolding protein, and the eIF4A (602641) RNA helicase, is associated with resistance to anti-BRAF (164757), anti-MEK, and anti-BRAF plus anti-MEK drug combinations in BRAF(V600)-mutant melanoma, colon, and thyroid cancer cell lines. Resistance to treatment and maintenance of eIF4F complex formation is associated with 1 of 3 mechanisms: reactivation of MAPK (see 176948) signaling; persistent ERK-independent phosphorylation of the inhibitory eIF4E-binding protein 4EBP1 (602223); or increased proapoptotic BMF (606266)-dependent degradation of eIF4G. The development of an in situ method to detect the eIF4E-eIF4G interactions showed that eIF4F complex formation is decreased in tumors that respond to anti-BRAF therapy and increased in resistant metastases compared to tumors before treatment. Strikingly, inhibiting the eIF4F complex, either by blocking the eIF4E-eIF4G interaction or by targeting eIF4A, synergized with inhibiting BRAF(V600) to kill the cancer cells. eIF4F appeared not only to be an indicator of both innate and acquired resistance, but also a therapeutic target. Boussemart et al. (2014) concluded that combinations of drugs targeting BRAF (and/or MEK) and eIF4F may overcome most of the resistance mechanisms in BRAF(V600)-mutant cancers.","Colorectal Carcinoma","Rajagopalan et al. (2002) identified the V600E mutation in 28 of 330 colorectal tumors (see 114500) screened for BRAF mutations. In all cases the mutation was heterozygous and occurred somatically.","Domingo et al. (2004) pointed out that the V600E hotspot mutation had been found in colorectal tumors that showed inherited mutation in a DNA mismatch repair (MMR) gene, such as MLH1 (120436) or MSH2 (609309). These mutations had been shown to occur almost exclusively in tumors located in the proximal colon and with hypermethylation of MLH1, the gene involved in the initial steps of development of these tumors; however, BRAF mutations were not detected in those cases with or presumed to have germline mutation in either MLH1 or MSH2. Domingo et al. (2004) studied mutation analysis of the BRAF hotspot as a possible low-cost effective strategy for genetic testing for hereditary nonpolyposis colorectal cancer (HNPCC; 120435). The V600E mutation was found in 82 (40%) of 206 sporadic tumors with high microsatellite instability (MSI-H) but in none of 111 tested HNPCC tumors or in 45 cases showing abnormal MSH2 immunostaining. Domingo et al. (2004) concluded that detection of the V600E mutation in a colorectal MSI-H tumor argues against the presence of germline mutation in either MLH1 or MSH2, and that screening of these MMR genes can be avoided in cases positive for V600E.","Lubomierski et al. (2005) analyzed 45 colorectal carcinomas with MSI and 37 colorectal tumors without MSI but with similar clinical characteristics and found that BRAF was mutated more often in tumors with MSI than without (27% vs 5%, p = 0.016). The most prevalent BRAF alteration, V600E, occurred only in tumors with MSI and was associated with more frequent MLH1 promoter methylation and loss of MLH1. The median age of patients with BRAF V600E was older than that of those without V600E (78 vs 49 years, p = 0.001). There were no BRAF alterations in patients with germline mutations of mismatch repair genes. Lubomierski et al. (2005) concluded that tumors with MSI caused by epigenetic MLH1 silencing have a mutational background distinct from that of tumors with genetic loss of mismatch repair, and suggested that there are 2 genetically distinct entities of microsatellite unstable tumors.","Tol et al. (2009) detected a somatic V600E mutation in 45 (8.7%) of 519 metastatic colorectal tumors. Patients with BRAF-mutated tumors had significantly shorter median progression-free and median overall survival compared to patients with wildtype BRAF tumors, regardless of the use of cetuximab. Tol et al. (2009) suggested that the BRAF mutation may be a negative prognostic factor in these patients.","Inhibition of the BRAF(V600E) oncoprotein by the small-molecule drug PLX4032 (vemurafenib) is highly effective in the treatment of melanoma. However, colon cancer patients harboring the same BRAF(V600E) oncogenic lesion have poor prognosis and show only a very limited response to this drug. To investigate the cause of this limited therapeutic effect in BRAF(V600E) mutant colon cancer, Prahallad et al. (2012) performed an RNA interference-based genetic screen in human cells to search for kinases whose knockdown synergizes with BRAF(V600E) inhibition. They reported that blockade of the epidermal growth factor receptor (EGFR; 131550) shows strong synergy with BRAF(V600E) inhibition. Prahallad et al. (2012) found in multiple BRAF(V600E) mutant colon cancers that inhibition of EGFR by the antibody drug cetuximab or the small-molecule drugs gefitinib or erlotinib is strongly synergistic with BRAF(V600E) inhibition, both in vitro and in vivo. Mechanistically, Prahallad et al. (2012) found that BRAF(V600E) inhibition causes a rapid feedback activation of EGFR, which supports continued proliferation in the presence of BRAF(V600E) inhibition. Melanoma cells express low levels of EGFR and are therefore not subject to this feedback activation. Consistent with this, Prahallad et al. (2012) found that ectopic expression of EGFR in melanoma cells is sufficient to cause resistance to PLX4032. Prahallad et al. (2012) concluded that BRAF(V600E) mutant colon cancers (approximately 8 to 10% of all colon cancers) might benefit from combination therapy consisting of BRAF and EGFR inhibitors.","Gala et al. (2014) identified the BRAF V600E mutation in 18 of 19 sessile serrated adenomas from 19 unrelated patients with sessile serrated polyposis cancer syndrome (SSPCS; 617108).","Papillary Thyroid Carcinoma","Kimura et al. (2003) identified the V600E mutation in 28 (35.8%) of 78 papillary thyroid cancers (PTC; see 188550); it was not found in any of the other types of differentiated follicular neoplasms arising from the same cell type (0 of 46). RET (see 164761)/PTC mutations and RAS (see 190020) mutations were each identified in 16.4% of PTCs, but there was no overlap in the 3 mutations. Kimura et al. (2003) concluded that thyroid cell transformation to papillary cancer takes place through constitutive activation of effectors along the RET/PTC-RAS-BRAF signaling pathway.","Xing et al. (2004) studied various thyroid tumor types for the most common BRAF mutation, 1799T-A, by DNA sequencing. They found a high and similar frequency (45%) of the 1799T-A mutation in 2 geographically distinct papillary thyroid cancer patient populations, 1 composed of sporadic cases from North America, and the other from Kiev, Ukraine, that included individuals who were exposed to the Chernobyl nuclear accident. In contrast, Xing et al. (2004) found BRAF mutations in only 20% of anaplastic thyroid cancers and in no medullary thyroid cancers or benign thyroid hyperplasia. They also confirmed previous reports that the BRAF 1799T-A mutation did not occur in benign thyroid adenomas or follicular thyroid cancers. They concluded that frequent occurrence of BRAF mutation is associated with PTC, irrespective of geographic origin, and is apparently not a radiation-susceptible mutation.","Nikiforova et al. (2003) analyzed 320 thyroid tumors and 6 anaplastic carcinoma cell lines and detected BRAF mutations in 45 papillary carcinomas (38%), 2 poorly differentiated carcinomas (13%), 3 (10%) anaplastic carcinomas (10%), and 5 thyroid anaplastic carcinoma cell lines (83%) but not in follicular, Hurthle cell, and medullary carcinomas, follicular and Hurthle cell adenomas, or benign hyperplastic nodules. All mutations involved a T-to-A transversion at nucleotide 1799. All BRAF-positive poorly differentiated and anaplastic carcinomas contained areas of preexisting papillary carcinoma, and mutation was present in both the well differentiated and dedifferentiated components. The authors concluded that BRAF mutations are restricted to papillary carcinomas and poorly differentiated and anaplastic carcinomas arising from papillary carcinomas, and that they are associated with distinct phenotypic and biologic properties of papillary carcinomas and may participate in progression to poorly differentiated and anaplastic carcinomas.","Hypothesizing that childhood thyroid carcinomas may be associated with a different prevalence of the BRAF 1799T-A mutation compared with adult cases, Kumagai et al. (2004) examined 31 cases of Japanese childhood thyroid carcinoma and an additional 48 cases of PTC from Ukraine, all of whom were less than 17 years of age at the time of the Chernobyl accident. The BRAF 1799T-A mutation was found in only 1 of 31 Japanese cases (3.4%) and in none of the 15 Ukrainian cases operated on before the age of 15 years, although it was found in 8 of 33 Ukrainian young adult cases (24.2%). Kumagai et al. (2004) concluded that the BRAF 1799T-A mutation is uncommon in childhood thyroid carcinomas.","Puxeddu et al. (2004) found the V600E substitution in 24 of 60 PTCs (40%) but in none of 6 follicular adenomas, 5 follicular carcinomas, or 1 anaplastic carcinoma. Nine of the 60 PTCs (15%) presented expression of a RET/PTC rearrangement. A genetico-clinical association analysis showed a statistically significant correlation between BRAF mutation and development of PTCs of the classic papillary histotype (P = 0.038). No link could be detected between expression of BRAF V600E and age at diagnosis, gender, dimension, local invasiveness of the primary cancer, presence of lymph node metastases, tumor stage, or multifocality of the disease. The authors concluded that these data clearly confirmed that BRAF V600E was the most common genetic alteration found to that time in adult sporadic PTCs, that it is unique for this thyroid cancer histotype, and that it might drive the development of PTCs of the classic papillary subtype.","Xing et al. (2004) demonstrated detection of the 1799T-A mutation on thyroid cytologic specimens from fine needle aspiration biopsy (FNAB). Prospective analysis showed that 50% of the nodules that proved to be PTCs on surgical histopathology were correctly diagnosed by BRAF mutation analysis on FNAB specimens; there were no false positive findings.","Xing et al. (2005) studied the relationships between the BRAF V600E mutation and clinicopathologic outcomes, including recurrence, in 219 PTC patients. The authors concluded that in patients with PTC, BRAF mutation is associated with poorer clinicopathologic outcomes and independently predicts recurrence. Therefore, BRAF mutation may be a useful molecular marker to assist in risk stratification for patients with PTC.","In a series of 52 classic PTCs, Porra et al. (2005) found that low SLC5A8 (608044) expression was highly significantly associated with the presence of the BRAF 1799T-A mutation. SLC5A8 expression was selectively downregulated (40-fold) in PTCs of classical form; methylation-specific PCR analyses showed that SLC5A8 was methylated in 90% of classic PTCs and in about 20% of other PTCs. Porra et al. (2005) concluded that their data identified a relationship between the methylation-associated silencing of the tumor-suppressor gene SLC5A8 and the 1799T-A point mutation of the BRAF gene in the classic PTC subtype of thyroid carcinomas.","Vasko et al. (2005) studied the relationship between the BRAF 1799T-A mutation and lymph node metastasis of PTC by examining the mutation in both the primary tumors and their paired lymph node metastases. Their findings indicated that the high prevalence of BRAF mutation in lymph node-metastasized PTC tissues from BRAF mutation-positive primary tumors and the possible de novo formation of BRAF mutation in lymph node-metastasized PTC were consistent with a role of BRAF mutation in facilitating the metastasis and progression of PTC in lymph nodes.","In a patient with congenital hypothyroidism and long-standing goiter due to mutation in the thyroglobulin gene (see TG, 188540; and TDH3, 274700), who was also found to have multifocal follicular carcinoma of the thyroid, Hishinuma et al. (2005) identified somatic heterozygosity for the V600E mutation in the BRAF gene in the cancerous thyroid tissue.","Liu et al. (2007) used BRAF siRNA to transfect stably several BRAF mutation-harboring PTC cell lines, isolated clones with stable suppression of BRAF, and assessed their ability to proliferate, transform, and grow xenograft tumors in nude mice. They found that the V600E mutation not only initiates PTC but also maintains the proliferation, transformation, and tumorigenicity of PTC cells harboring the BRAF mutation, and that the growth of tumors derived from such cells continues to depend on the V600E mutation.","Jo et al. (2006) found that of 161 PTC patients, 102 (63.4%) had the BRAF V600E mutation and that these patients had significantly larger tumor sizes and significantly higher expression of vascular endothelial growth factor (VEGF; 192240) compared to patients without this mutation. The level of VEGF expression was closely correlated with tumor size, extrathyroidal invasion, and stage. Jo et al. (2006) concluded that the relatively high levels of VEGF expression may be related to poorer clinical outcomes and recurrences in BRAF V600E(+) PTC.","Durante et al. (2007) found that the BRAF V600E mutation in PTCs is associated with reduced expression of key genes involved in iodine metabolism. They noted that this effect may alter the effectiveness of diagnostic and/or therapeutic use of radioiodine in BRAF-mutation PTCs.","Lupi et al. (2007) found a BRAF mutation in 219 of 500 cases (43.8%) of PTC. The most common BRAF mutation, V600E, was found in 214 cases (42.8%). BRAF V600E was associated with extrathyroidal invasion (p less than 0.0001), multicentricity (p = 0.0026), presence of nodal metastases (p = 0.0009), class III versus classes I and II (p less than 0.00000006), and absence of tumor capsule (p less than 0.0001), in particular, in follicular- and micro-PTC variants. By multivariate analysis, the absence of tumor capsule remained the only parameter associated (p = 0.0005) with the BRAF V600E mutation. The authors concluded that the BRAF V600E mutation is associated with high-risk PTC and, in particular, in follicular variant with invasive tumor growth.","Flaherty et al. (2010) reported complete or partial regression of V600E-associated papillary thyroid cancer in 3 patients treated with an inhibitor (PLX4032) specific to the V600E mutation.","Nonseminomatous Germ Cell Tumors","In 3 (9%) of 32 nonseminomatous germ cell tumors (see 273300) with a mixture of embryonal carcinoma, yolk sac tumor, choriocarcinoma, and mature teratoma, Sommerer et al. (2005) identified the activating 1796T-A mutation in the BRAF gene; the mutation was present within the embryonic carcinoma component.","Astrocytoma","Pfister et al. (2008) identified a somatic V600E mutation in 4 (6%) of 66 pediatric low-grade astrocytomas (see 137800). Thirty (45%) of the 66 tumors had a copy number gain spanning the BRAF locus, indicating a novel mechanism of MAPK (176948) pathway activation in these tumors.","Role in Neurodegeneration","Mass et al. (2017) hypothesized that a somatic BRAF(V600E) mutation in the erythromyeloid lineage may cause neurodegeneration. Mass et al. (2017) showed that mosaic expression of BRAF(V600E) in mouse erythromyeloid progenitors results in clonal expansion of tissue-resident macrophages and a severe late-onset neurodegenerative disorder. This is associated with accumulation of ERK-activated amoeboid microglia in mice, and is also observed in human patients with histiocytoses. In the mouse model, neurobehavioral signs, astrogliosis, deposition of amyloid precursor protein, synaptic loss, and neuronal death were driven by ERK-activated microglia and were preventable by BRAF inhibition. Mass et al. (2017) suggested that the results identified the fetal precursors of tissue-resident macrophages as a potential cell of origin for histiocytoses and demonstrated that a somatic mutation in the erythromyeloid progenitor lineage in mice can drive late-onset neurodegeneration.","Variant Function","Brady et al. (2014) showed that decreasing the levels of CTR1 (603085), or mutations in MEK1 (176872) that disrupt copper binding, decreased BRAF(V600E)-driven signaling and tumorigenesis in mice and human cell settings. Conversely, a MEK1-MEK5 (602520) chimera that phosphorylated ERK1/2 independently of copper or an active ERK2 restored the tumor growth of murine cells lacking Ctr1. Copper chelators used in the treatment of Wilson disease (277900) decreased tumor growth of human or murine cells that were either transformed by BRAF(V600E) or engineered to be resistant to BRAF inhibition. Brady et al. (2014) concluded that copper chelation therapy could be repurposed to treat cancers containing the BRAF(V600E) mutation.","Rapino et al. (2018) showed in humans that the enzymes that catalyze modifications of wobble uridine-34 (U34) tRNA are key players of the protein synthesis rewiring that is induced by the transformation driven by the BRAF V600E oncogene and by resistance to targeted therapy in melanoma. Rapino et al. (2018) showed that BRAF V600E-expressing melanoma cells are dependent on U34 enzymes for survival, and that concurrent inhibition of MAPK signaling and ELP3 (612722) or CTU1 (612694) and/or CTU2 (617057) synergizes to kill melanoma cells. Activation of the PI3K signaling pathway, one of the most common mechanisms of acquired resistance to MAPK therapeutic agents, markedly increases the expression of U34 enzymes. Mechanistically, U34 enzymes promote glycolysis in melanoma cells through the direct, codon-dependent, regulation of the translation of HIF1A (603348) mRNA and the maintenance of high levels of HIF1-alpha protein. Therefore, the acquired resistance to anti-BRAF therapy is associated with high levels of U34 enzymes and HIF1-alpha. Rapino et al. (2018) concluded that U34 enzymes promote the survival and resistance to therapy of melanoma cells by regulating specific mRNA translation."],"submitter_name":"OMIM","review_date":20140904,"origin":"somatic","method":"literature only","submitter_date":20220317,"diseases":[{"normalized_cancer":["Papillary Thyroid Cancer"],"names":["Thyroid Carcinoma, Papillary, Somatic"]}],"review_description":"Pathogenic","date_updated":20220328,"clinical_significance":["Pathogenic"],"review_status":"no assertion criteria provided","accession_id":"SCV000035249"}],"variation_id":13961,"submission_description":[],"title":"NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) AND Papillary thyroid carcinoma","review_date":20140904,"diseases":[{"pub_med":[26389271,26389258],"normalized_cancer":["Papillary Thyroid Cancer"],"symbols":{"medgen":"C0238463","orphanet":"146","mesh":"D000077273","mondo":"MONDO:0005075","human_phenotype_ontology":"HP:0002895"},"normalized_disease":["Thyroid Gland Papillary Carcinoma"],"names":["Thyroid Gland Papillary Carcinoma","Nonmedullary Thyroid Carcinoma, Papillary","Thyroid Carcinoma, Papillary, Somatic","Thyroid Gland Papillary Carcinoma"]}],"pub_med_references":[12068308,12198537,12447372,12619120,12644542,12670889,12794760,12960123,14513361,14602780,15001635,15126572,15181070,15342696,15356022,15386408,15687339,15998781,16015629,16174717,16187918,16772349,17374713,17488796,17785355,18398503,19571295,20818844,20823850,21107320,21107323,22113612,22281684,23302800,23685455,24512911,24670642,24717435,25079330,28854169,29925953],"date_created":20130404,"variant_id":10190071404531360004,"review_description":"Pathogenic","clinical_significance":["Pathogenic"],"allele_id":29000,"accession_id":"RCV000014993"},{"submissions":[{"submission_description":["Vemurafenib and cobimetinib combination is an FDA approved first line treatment for BRAF V600E mutant metastatic melanoma based on clinical data including the Phase III coBRIM trial. The cobas 4800 BRAF V600 Mutation Test is approved as an FDA companion test for Cotellic (cobimetinib) in combination with Zelboraf (vemurafenib)."],"submitter_name":"Wagner Lab, Nationwide Children's Hospital","review_date":20181101,"origin":"somatic","method":"curation","submitter_date":20250226,"diseases":[{"normalized_cancer":["Melanoma"],"normalized_disease":["Melanoma"],"names":["Melanoma"]}],"date_updated":20250304,"clinical_significance":[],"review_status":"criteria provided, single submitter","accession_id":"SCV005870910"},{"submission_description":["Combination treatment of BRAF inhibitor dabrafenib and MEK inhibitor trametinib is recommended for adjuvant treatment of stage III or recurrent melanoma with BRAF V600E mutation detected by the approved THxID kit, as well as first line treatment for metastatic melanoma. The treatments are FDA approved based on studies including the Phase III COMBI-V, COMBI-D and COMBI-AD Trials. Combination therapy is now recommended above BRAF inhibitor monotherapy. Cutaneous squamous-cell carcinoma and keratoacanthoma occur at lower rates with combination therapy than with BRAF inhibitor alone."],"submitter_name":"CIViC knowledgebase, Washington University School of Medicine","review_date":20180515,"origin":"somatic","method":"curation","submitter_date":20240216,"diseases":[{"normalized_cancer":["Melanoma"],"normalized_disease":["Melanoma"],"names":["Melanoma"]}],"date_updated":20240220,"clinical_significance":[],"review_status":"criteria provided, single submitter","accession_id":"SCV004565360"},{"pub_med_references":[12068308,12198537,12447372,12619120,12644542,12670889,12794760,12960123,14513361,14602780,15001635,15126572,15181070,15342696,15356022,15386408,15687339,15998781,16015629,16174717,16187918,16772349,17374713,17488796,17785355,18398503,19571295,20818844,20823850,21107320,21107323,22113612,22281684,23302800,23685455,24512911,24670642,24717435,25079330,28854169,29925953],"submission_description":["The val600-to-glu (V600E) mutation caused by a 1799T-A transversion in the BRAF gene was previously designated VAL599GLU (1796T-A). Kumar et al. (2003) noted that an earlier version of the BRAF sequence showed a discrepancy of 3 nucleotides in exon 1; based on the corrected sequence, they proposed a change in nucleotide numbering after nucleotide 94 (the ATG codon) by +3 and a corresponding codon change of +1.","Malignant Melanoma","Davies et al. (2002) identified a 1799T-A transversion in exon 15 of the BRAF gene that leads to a val600-to-glu (V600E) substitution. This mutation accounted for 92% of BRAF mutations in malignant melanoma (see 155600). The V600E mutation is an activating mutation resulting in constitutive activation of BRAF and downstream signal transduction in the MAP kinase pathway.","To evaluate the timing of mutations in BRAF during melanocyte neoplasia, Pollock et al. (2003) carried out mutation analysis on microdissected melanoma and nevi samples. They observed mutations resulting in the V600E amino acid substitution in 41 (68%) of 60 melanoma metastases, 4 (80%) of 5 primary melanomas, and, unexpectedly, in 63 (82%) of 77 nevi. The data suggested that mutational activation of the RAS/RAF/MAPK pathway in nevi is a critical step in the initiation of melanocytic neoplasia but alone is insufficient for melanoma tumorigenesis.","Lang et al. (2003) failed to find the V600E mutation as a germline mutation in 42 cases of familial melanoma studied. Their collection of families included 15 with and 24 without detected mutations in CDKN2A (600160). They did, however, find the V600E mutation in 6 (27%) of 22 samples of secondary (metastatic) melanomas studied. Meyer et al. (2003) found no V600E mutation in 172 melanoma patients comprising 46 familial cases, 21 multiple melanoma patients, and 106 cases with at least 1 first-degree relative suffering from other cancers. They concluded, therefore, that the common somatic BRAF mutation V600E does not contribute to polygenic or familial melanoma predisposition.","Kim et al. (2003) stated that V600E, the most common of BRAF mutations, had not been identified in tumors with mutations of the KRAS gene (190070). This mutually exclusive relationship supports the hypothesis that BRAF (V600E) and KRAS mutations exert equivalent effects in tumorigenesis (Rajagopalan et al., 2002; Singer et al., 2003).","Flaherty et al. (2010) reported complete or partial regression of V600E-associated metastatic melanoma in 81% of patients treated with an inhibitor (PLX4032) specific to the V600E mutation. Among 16 patients in a dose-escalation cohort, 10 had a partial response, and 1 had a complete response. Among 32 patients in an extension cohort, 24 had a partial response, and 2 had a complete response. The estimated median progression-free survival among all patients was more than 7 months. Responses were observed at all sites of disease, including bone, liver, and small bowel. Tumor biopsy specimens from 7 patients showed markedly reduced levels of phosphorylated ERK (600997), cyclin D1 (168461), and Ki67 (MKI67; 176741) at day 15 compared to baseline, indicating inhibition of the MAP kinase pathway. Three additional patients with V600E-associated papillary thyroid also showed a partial or complete response.","Bollag et al. (2010) described the structure-guided discovery of PLX4032 (RG7204), a potent inhibitor of oncogenic BRAF kinase activity. PLX4032 was cocrystallized with a protein construct that contained the kinase domain of BRAF(V600E). In a clinical trial, patients exposed to higher plasma levels of PLX4032 experienced tumor regression; in patients with tumor regressions, pathway analysis typically showed greater than 80% inhibition of cytoplasmic ERK phosphorylation. Bollag et al. (2010) concluded that their data demonstrated that BRAF-mutant melanomas are highly dependent on BRAF kinase activity.","Patients with BRAF(V600E)-positive melanomas exhibit an initial antitumor response to the RAF kinase inhibitor PLX4032, but acquired drug resistance almost invariably develops. Johannessen et al. (2010) identified MAP3K8 (191195), encoding COT (cancer Osaka thyroid oncogene) as a MAPK pathway agonist that drives resistance to RAF inhibition in BRAF(V600E) cell lines. COT activates ERK primarily through MARK/ERK (MEK)-dependent mechanisms that do not require RAF signaling. Moreover, COT expression is associated with de novo resistance in BRAF(V600E) cultured cell lines and acquired resistance in melanoma cells and tissue obtained from relapsing patients following treatment with MEK or RAF inhibitors. Johannessen et al. (2010) further identified combinatorial MAPK pathway inhibition or targeting of COT kinase activity as possible therapeutic strategies for reducing MAPK pathway activation in this setting.","Nazarian et al. (2010) showed that acquired resistance to PLX4032, a novel class I RAF-selective inhibitor, develops by mutually exclusive PDGFRB (173410) upregulation or NRAS (164790) mutations but not through secondary mutations in BRAF(V600E). Nazarian et al. (2010) used PLX4032-resistant sublines artificially derived from BRAF (V600E)-positive melanoma cell lines and validated key findings in PLX4032-resistant tumors and tumor-matched, short-term cultures from clinical trial patients. Induction of PDGFRB RNA, protein and tyrosine phosphorylation emerged as a dominant feature of acquired PLX4032 resistance in a subset of melanoma sublines, patient-derived biopsies, and short-term cultures. PDGFRB upregulated tumor cells have low activated RAS levels and, when treated with PLX4032, do not reactivate the MAPK pathway significantly. In another subset, high levels of activated N-RAS resulting from mutations lead to significant MAPK pathway reactivation upon PLX4032 treatment. Knockdown of PDGFRB or NRAS reduced growth of the respective PLX4032-resistant subsets. Overexpression of PDGFRB or NRAS(Q61K) conferred PLX4032 resistance to PLX4032-sensitive parental cell lines. Importantly, Nazarian et al. (2010) showed that MAPK reactivation predicts MEK inhibitor sensitivity. Thus, Nazarian et al. (2010) concluded that melanomas escape BRAF(V600E) targeting not through secondary BRAF(V600E) mutations but via receptor tyrosine kinase (RTK)-mediated activation of alternative survival pathway(s) or activated RAS-mediated reactivation of the MAPK pathway, suggesting additional therapeutic strategies.","Poulikakos et al. (2011) identified a novel resistance mechanism for melanomas with BRAF(V600E) treated with RAF inhibitors. The authors found that a subset of cells resistant to vemurafenib (PLX4032, RG7204) express a 61-kD variant form of BRAF(V600E), p61BRAF(V600E), that lacks exons 4 through 8, a region that encompasses the RAS-binding domain. p61BRAF(V600E) showed enhanced dimerization in cells with low levels of RAS activation, as compared to full-length BRAF(V600E). In cells in which p61BRAF(V600E) was expressed endogenously or ectopically, ERK signaling was resistant to the RAF inhibitor. Moreover, a mutation that abolished the dimerization of p61BRAF(V600E) restored its sensitivity to vemurafenib. Finally, Poulikakos et al. (2011) identified BRAF(V600E) splicing variants lacking the RAS-binding domain in the tumors of 6 of 19 patients with acquired resistance to vemurafenib. Poulikakos et al. (2011) concluded that their data supported the model that inhibition of ERK signaling by RAF inhibitors is dependent on levels of RAS-GTP too low to support RAF dimerization and identified a novel mechanism of acquired resistance in patients: expression of splicing isoforms of BRAF(V600E) that dimerize in a RAS-independent manner.","Thakur et al. (2013) investigated the cause and consequences of vemurafenib resistance using 2 independently-derived primary human melanoma xenograft models in which drug resistance is selected by continuous vemurafenib administration. In one of these models, resistant tumors showed continued dependency on BRAF(V600E)-MEK-ERK signaling owing to elevated BRAF(V600E) expression. Thakur et al. (2013) showed that vemurafenib-resistant melanomas become drug-dependent for their continued proliferation, such that cessation of drug administration leads to regression of established drug-resistant tumors. Thakur et al. (2013) further demonstrated that a discontinuous dosing strategy, which exploits the fitness disadvantage displayed by drug-resistant cells in the absence of the drug, forestalls the onset of lethal drug-resistant disease. Thakur et al. (2013) concluded that their data highlighted the concept that drug-resistant cells may also display drug dependency, such that altered dosing may prevent the emergence of lethal drug resistance. These observations may contribute to sustaining the durability of vemurafenib response with the ultimate goal of curative therapy for the subset of melanoma patients with BRAF mutations.","Using metabolic profiling and functional perturbations, Kaplon et al. (2013) showed that the mitochondrial gatekeeper pyruvate dehydrogenase (PDH; 300502) is a crucial mediator of senescence induced by BRAF(V600E), an oncogene commonly mutated in melanoma and other cancers. BRAF(V600E)-induced senescence is accompanied by simultaneous suppression of the PDH-inhibitory enzyme pyruvate dehydrogenase kinase-1 (PDK1; 602524) and induction of the PDH-activating enzyme pyruvate dehydrogenase phosphatase-2 (PDP2; 615499). The resulting combined activation of PDH enhanced the use of pyruvate in the tricarboxylic acid cycle, causing increased respiration and redox stress. Abrogation of oncogene-induced senescence (OIS), a rate-limiting step towards oncogenic transformation, coincided with reversion of these processes. Further supporting a crucial role of PDH in OIS, enforced normalization of either PDK1 or PDP2 expression levels inhibited PDH and abrogated OIS, thereby licensing BRAF(V600E)-driven melanoma development. Finally, depletion of PDK1 eradicated melanoma subpopulations resistant to targeted BRAF inhibition, and caused regression of established melanomas.","Sun et al. (2014) showed that 6 out of 16 BRAF(V600E)-positive melanoma tumors analyzed acquired EGFR (131550) expression after the development of resistance to inhibitors of BRAF or MEK (176872). Using a chromatin regulator-focused short hairpin RNA (shRNA) library, Sun et al. (2014) found that suppression of SRY-box 10 (SOX10; 602229) in melanoma causes activation of TGF-beta (190180) signaling, thus leading to upregulation of EGFR and platelet-derived growth factor receptor-beta (PDGFRB; 173410), which confer resistance to BRAF and MEK inhibitors. Expression of EGFR in melanoma or treatment with TGF-beta results in a slow-growth phenotype with cells displaying hallmarks of oncogene-induced senescence. However, EGFR expression or exposure to TGF-beta becomes beneficial for proliferation in the presence of BRAF or MEK inhibitors. In a heterogeneous population of melanoma cells that have varying levels of SOX10 suppression, cells with low SOX10 and consequently high EGFR expression are rapidly enriched in the presence of drug treatment, but this is reversed when the treatment is discontinued. Sun et al. (2014) found evidence for SOX10 loss and/or activation of TGF-beta signaling in 4 of the 6 EGFR-positive drug-resistant melanoma patient samples. Sun et al. (2014) concluded that their findings provided a rationale for why some BRAF or MEK inhibitor-resistant melanoma patients may regain sensitivity to these drugs after a 'drug holiday' and identified patients with EGFR-positive melanoma as a group that may benefit from retreatment after a drug holiday.","Boussemart et al. (2014) demonstrated that the persistent formation of the eIF4F complex, comprising the eIF4E (133440) cap-binding protein, the eIF4G (600495) scaffolding protein, and the eIF4A (602641) RNA helicase, is associated with resistance to anti-BRAF (164757), anti-MEK, and anti-BRAF plus anti-MEK drug combinations in BRAF(V600)-mutant melanoma, colon, and thyroid cancer cell lines. Resistance to treatment and maintenance of eIF4F complex formation is associated with 1 of 3 mechanisms: reactivation of MAPK (see 176948) signaling; persistent ERK-independent phosphorylation of the inhibitory eIF4E-binding protein 4EBP1 (602223); or increased proapoptotic BMF (606266)-dependent degradation of eIF4G. The development of an in situ method to detect the eIF4E-eIF4G interactions showed that eIF4F complex formation is decreased in tumors that respond to anti-BRAF therapy and increased in resistant metastases compared to tumors before treatment. Strikingly, inhibiting the eIF4F complex, either by blocking the eIF4E-eIF4G interaction or by targeting eIF4A, synergized with inhibiting BRAF(V600) to kill the cancer cells. eIF4F appeared not only to be an indicator of both innate and acquired resistance, but also a therapeutic target. Boussemart et al. (2014) concluded that combinations of drugs targeting BRAF (and/or MEK) and eIF4F may overcome most of the resistance mechanisms in BRAF(V600)-mutant cancers.","Colorectal Carcinoma","Rajagopalan et al. (2002) identified the V600E mutation in 28 of 330 colorectal tumors (see 114500) screened for BRAF mutations. In all cases the mutation was heterozygous and occurred somatically.","Domingo et al. (2004) pointed out that the V600E hotspot mutation had been found in colorectal tumors that showed inherited mutation in a DNA mismatch repair (MMR) gene, such as MLH1 (120436) or MSH2 (609309). These mutations had been shown to occur almost exclusively in tumors located in the proximal colon and with hypermethylation of MLH1, the gene involved in the initial steps of development of these tumors; however, BRAF mutations were not detected in those cases with or presumed to have germline mutation in either MLH1 or MSH2. Domingo et al. (2004) studied mutation analysis of the BRAF hotspot as a possible low-cost effective strategy for genetic testing for hereditary nonpolyposis colorectal cancer (HNPCC; 120435). The V600E mutation was found in 82 (40%) of 206 sporadic tumors with high microsatellite instability (MSI-H) but in none of 111 tested HNPCC tumors or in 45 cases showing abnormal MSH2 immunostaining. Domingo et al. (2004) concluded that detection of the V600E mutation in a colorectal MSI-H tumor argues against the presence of germline mutation in either MLH1 or MSH2, and that screening of these MMR genes can be avoided in cases positive for V600E.","Lubomierski et al. (2005) analyzed 45 colorectal carcinomas with MSI and 37 colorectal tumors without MSI but with similar clinical characteristics and found that BRAF was mutated more often in tumors with MSI than without (27% vs 5%, p = 0.016). The most prevalent BRAF alteration, V600E, occurred only in tumors with MSI and was associated with more frequent MLH1 promoter methylation and loss of MLH1. The median age of patients with BRAF V600E was older than that of those without V600E (78 vs 49 years, p = 0.001). There were no BRAF alterations in patients with germline mutations of mismatch repair genes. Lubomierski et al. (2005) concluded that tumors with MSI caused by epigenetic MLH1 silencing have a mutational background distinct from that of tumors with genetic loss of mismatch repair, and suggested that there are 2 genetically distinct entities of microsatellite unstable tumors.","Tol et al. (2009) detected a somatic V600E mutation in 45 (8.7%) of 519 metastatic colorectal tumors. Patients with BRAF-mutated tumors had significantly shorter median progression-free and median overall survival compared to patients with wildtype BRAF tumors, regardless of the use of cetuximab. Tol et al. (2009) suggested that the BRAF mutation may be a negative prognostic factor in these patients.","Inhibition of the BRAF(V600E) oncoprotein by the small-molecule drug PLX4032 (vemurafenib) is highly effective in the treatment of melanoma. However, colon cancer patients harboring the same BRAF(V600E) oncogenic lesion have poor prognosis and show only a very limited response to this drug. To investigate the cause of this limited therapeutic effect in BRAF(V600E) mutant colon cancer, Prahallad et al. (2012) performed an RNA interference-based genetic screen in human cells to search for kinases whose knockdown synergizes with BRAF(V600E) inhibition. They reported that blockade of the epidermal growth factor receptor (EGFR; 131550) shows strong synergy with BRAF(V600E) inhibition. Prahallad et al. (2012) found in multiple BRAF(V600E) mutant colon cancers that inhibition of EGFR by the antibody drug cetuximab or the small-molecule drugs gefitinib or erlotinib is strongly synergistic with BRAF(V600E) inhibition, both in vitro and in vivo. Mechanistically, Prahallad et al. (2012) found that BRAF(V600E) inhibition causes a rapid feedback activation of EGFR, which supports continued proliferation in the presence of BRAF(V600E) inhibition. Melanoma cells express low levels of EGFR and are therefore not subject to this feedback activation. Consistent with this, Prahallad et al. (2012) found that ectopic expression of EGFR in melanoma cells is sufficient to cause resistance to PLX4032. Prahallad et al. (2012) concluded that BRAF(V600E) mutant colon cancers (approximately 8 to 10% of all colon cancers) might benefit from combination therapy consisting of BRAF and EGFR inhibitors.","Gala et al. (2014) identified the BRAF V600E mutation in 18 of 19 sessile serrated adenomas from 19 unrelated patients with sessile serrated polyposis cancer syndrome (SSPCS; 617108).","Papillary Thyroid Carcinoma","Kimura et al. (2003) identified the V600E mutation in 28 (35.8%) of 78 papillary thyroid cancers (PTC; see 188550); it was not found in any of the other types of differentiated follicular neoplasms arising from the same cell type (0 of 46). RET (see 164761)/PTC mutations and RAS (see 190020) mutations were each identified in 16.4% of PTCs, but there was no overlap in the 3 mutations. Kimura et al. (2003) concluded that thyroid cell transformation to papillary cancer takes place through constitutive activation of effectors along the RET/PTC-RAS-BRAF signaling pathway.","Xing et al. (2004) studied various thyroid tumor types for the most common BRAF mutation, 1799T-A, by DNA sequencing. They found a high and similar frequency (45%) of the 1799T-A mutation in 2 geographically distinct papillary thyroid cancer patient populations, 1 composed of sporadic cases from North America, and the other from Kiev, Ukraine, that included individuals who were exposed to the Chernobyl nuclear accident. In contrast, Xing et al. (2004) found BRAF mutations in only 20% of anaplastic thyroid cancers and in no medullary thyroid cancers or benign thyroid hyperplasia. They also confirmed previous reports that the BRAF 1799T-A mutation did not occur in benign thyroid adenomas or follicular thyroid cancers. They concluded that frequent occurrence of BRAF mutation is associated with PTC, irrespective of geographic origin, and is apparently not a radiation-susceptible mutation.","Nikiforova et al. (2003) analyzed 320 thyroid tumors and 6 anaplastic carcinoma cell lines and detected BRAF mutations in 45 papillary carcinomas (38%), 2 poorly differentiated carcinomas (13%), 3 (10%) anaplastic carcinomas (10%), and 5 thyroid anaplastic carcinoma cell lines (83%) but not in follicular, Hurthle cell, and medullary carcinomas, follicular and Hurthle cell adenomas, or benign hyperplastic nodules. All mutations involved a T-to-A transversion at nucleotide 1799. All BRAF-positive poorly differentiated and anaplastic carcinomas contained areas of preexisting papillary carcinoma, and mutation was present in both the well differentiated and dedifferentiated components. The authors concluded that BRAF mutations are restricted to papillary carcinomas and poorly differentiated and anaplastic carcinomas arising from papillary carcinomas, and that they are associated with distinct phenotypic and biologic properties of papillary carcinomas and may participate in progression to poorly differentiated and anaplastic carcinomas.","Hypothesizing that childhood thyroid carcinomas may be associated with a different prevalence of the BRAF 1799T-A mutation compared with adult cases, Kumagai et al. (2004) examined 31 cases of Japanese childhood thyroid carcinoma and an additional 48 cases of PTC from Ukraine, all of whom were less than 17 years of age at the time of the Chernobyl accident. The BRAF 1799T-A mutation was found in only 1 of 31 Japanese cases (3.4%) and in none of the 15 Ukrainian cases operated on before the age of 15 years, although it was found in 8 of 33 Ukrainian young adult cases (24.2%). Kumagai et al. (2004) concluded that the BRAF 1799T-A mutation is uncommon in childhood thyroid carcinomas.","Puxeddu et al. (2004) found the V600E substitution in 24 of 60 PTCs (40%) but in none of 6 follicular adenomas, 5 follicular carcinomas, or 1 anaplastic carcinoma. Nine of the 60 PTCs (15%) presented expression of a RET/PTC rearrangement. A genetico-clinical association analysis showed a statistically significant correlation between BRAF mutation and development of PTCs of the classic papillary histotype (P = 0.038). No link could be detected between expression of BRAF V600E and age at diagnosis, gender, dimension, local invasiveness of the primary cancer, presence of lymph node metastases, tumor stage, or multifocality of the disease. The authors concluded that these data clearly confirmed that BRAF V600E was the most common genetic alteration found to that time in adult sporadic PTCs, that it is unique for this thyroid cancer histotype, and that it might drive the development of PTCs of the classic papillary subtype.","Xing et al. (2004) demonstrated detection of the 1799T-A mutation on thyroid cytologic specimens from fine needle aspiration biopsy (FNAB). Prospective analysis showed that 50% of the nodules that proved to be PTCs on surgical histopathology were correctly diagnosed by BRAF mutation analysis on FNAB specimens; there were no false positive findings.","Xing et al. (2005) studied the relationships between the BRAF V600E mutation and clinicopathologic outcomes, including recurrence, in 219 PTC patients. The authors concluded that in patients with PTC, BRAF mutation is associated with poorer clinicopathologic outcomes and independently predicts recurrence. Therefore, BRAF mutation may be a useful molecular marker to assist in risk stratification for patients with PTC.","In a series of 52 classic PTCs, Porra et al. (2005) found that low SLC5A8 (608044) expression was highly significantly associated with the presence of the BRAF 1799T-A mutation. SLC5A8 expression was selectively downregulated (40-fold) in PTCs of classical form; methylation-specific PCR analyses showed that SLC5A8 was methylated in 90% of classic PTCs and in about 20% of other PTCs. Porra et al. (2005) concluded that their data identified a relationship between the methylation-associated silencing of the tumor-suppressor gene SLC5A8 and the 1799T-A point mutation of the BRAF gene in the classic PTC subtype of thyroid carcinomas.","Vasko et al. (2005) studied the relationship between the BRAF 1799T-A mutation and lymph node metastasis of PTC by examining the mutation in both the primary tumors and their paired lymph node metastases. Their findings indicated that the high prevalence of BRAF mutation in lymph node-metastasized PTC tissues from BRAF mutation-positive primary tumors and the possible de novo formation of BRAF mutation in lymph node-metastasized PTC were consistent with a role of BRAF mutation in facilitating the metastasis and progression of PTC in lymph nodes.","In a patient with congenital hypothyroidism and long-standing goiter due to mutation in the thyroglobulin gene (see TG, 188540; and TDH3, 274700), who was also found to have multifocal follicular carcinoma of the thyroid, Hishinuma et al. (2005) identified somatic heterozygosity for the V600E mutation in the BRAF gene in the cancerous thyroid tissue.","Liu et al. (2007) used BRAF siRNA to transfect stably several BRAF mutation-harboring PTC cell lines, isolated clones with stable suppression of BRAF, and assessed their ability to proliferate, transform, and grow xenograft tumors in nude mice. They found that the V600E mutation not only initiates PTC but also maintains the proliferation, transformation, and tumorigenicity of PTC cells harboring the BRAF mutation, and that the growth of tumors derived from such cells continues to depend on the V600E mutation.","Jo et al. (2006) found that of 161 PTC patients, 102 (63.4%) had the BRAF V600E mutation and that these patients had significantly larger tumor sizes and significantly higher expression of vascular endothelial growth factor (VEGF; 192240) compared to patients without this mutation. The level of VEGF expression was closely correlated with tumor size, extrathyroidal invasion, and stage. Jo et al. (2006) concluded that the relatively high levels of VEGF expression may be related to poorer clinical outcomes and recurrences in BRAF V600E(+) PTC.","Durante et al. (2007) found that the BRAF V600E mutation in PTCs is associated with reduced expression of key genes involved in iodine metabolism. They noted that this effect may alter the effectiveness of diagnostic and/or therapeutic use of radioiodine in BRAF-mutation PTCs.","Lupi et al. (2007) found a BRAF mutation in 219 of 500 cases (43.8%) of PTC. The most common BRAF mutation, V600E, was found in 214 cases (42.8%). BRAF V600E was associated with extrathyroidal invasion (p less than 0.0001), multicentricity (p = 0.0026), presence of nodal metastases (p = 0.0009), class III versus classes I and II (p less than 0.00000006), and absence of tumor capsule (p less than 0.0001), in particular, in follicular- and micro-PTC variants. By multivariate analysis, the absence of tumor capsule remained the only parameter associated (p = 0.0005) with the BRAF V600E mutation. The authors concluded that the BRAF V600E mutation is associated with high-risk PTC and, in particular, in follicular variant with invasive tumor growth.","Flaherty et al. (2010) reported complete or partial regression of V600E-associated papillary thyroid cancer in 3 patients treated with an inhibitor (PLX4032) specific to the V600E mutation.","Nonseminomatous Germ Cell Tumors","In 3 (9%) of 32 nonseminomatous germ cell tumors (see 273300) with a mixture of embryonal carcinoma, yolk sac tumor, choriocarcinoma, and mature teratoma, Sommerer et al. (2005) identified the activating 1796T-A mutation in the BRAF gene; the mutation was present within the embryonic carcinoma component.","Astrocytoma","Pfister et al. (2008) identified a somatic V600E mutation in 4 (6%) of 66 pediatric low-grade astrocytomas (see 137800). Thirty (45%) of the 66 tumors had a copy number gain spanning the BRAF locus, indicating a novel mechanism of MAPK (176948) pathway activation in these tumors.","Role in Neurodegeneration","Mass et al. (2017) hypothesized that a somatic BRAF(V600E) mutation in the erythromyeloid lineage may cause neurodegeneration. Mass et al. (2017) showed that mosaic expression of BRAF(V600E) in mouse erythromyeloid progenitors results in clonal expansion of tissue-resident macrophages and a severe late-onset neurodegenerative disorder. This is associated with accumulation of ERK-activated amoeboid microglia in mice, and is also observed in human patients with histiocytoses. In the mouse model, neurobehavioral signs, astrogliosis, deposition of amyloid precursor protein, synaptic loss, and neuronal death were driven by ERK-activated microglia and were preventable by BRAF inhibition. Mass et al. (2017) suggested that the results identified the fetal precursors of tissue-resident macrophages as a potential cell of origin for histiocytoses and demonstrated that a somatic mutation in the erythromyeloid progenitor lineage in mice can drive late-onset neurodegeneration.","Variant Function","Brady et al. (2014) showed that decreasing the levels of CTR1 (603085), or mutations in MEK1 (176872) that disrupt copper binding, decreased BRAF(V600E)-driven signaling and tumorigenesis in mice and human cell settings. Conversely, a MEK1-MEK5 (602520) chimera that phosphorylated ERK1/2 independently of copper or an active ERK2 restored the tumor growth of murine cells lacking Ctr1. Copper chelators used in the treatment of Wilson disease (277900) decreased tumor growth of human or murine cells that were either transformed by BRAF(V600E) or engineered to be resistant to BRAF inhibition. Brady et al. (2014) concluded that copper chelation therapy could be repurposed to treat cancers containing the BRAF(V600E) mutation.","Rapino et al. (2018) showed in humans that the enzymes that catalyze modifications of wobble uridine-34 (U34) tRNA are key players of the protein synthesis rewiring that is induced by the transformation driven by the BRAF V600E oncogene and by resistance to targeted therapy in melanoma. Rapino et al. (2018) showed that BRAF V600E-expressing melanoma cells are dependent on U34 enzymes for survival, and that concurrent inhibition of MAPK signaling and ELP3 (612722) or CTU1 (612694) and/or CTU2 (617057) synergizes to kill melanoma cells. Activation of the PI3K signaling pathway, one of the most common mechanisms of acquired resistance to MAPK therapeutic agents, markedly increases the expression of U34 enzymes. Mechanistically, U34 enzymes promote glycolysis in melanoma cells through the direct, codon-dependent, regulation of the translation of HIF1A (603348) mRNA and the maintenance of high levels of HIF1-alpha protein. Therefore, the acquired resistance to anti-BRAF therapy is associated with high levels of U34 enzymes and HIF1-alpha. Rapino et al. (2018) concluded that U34 enzymes promote the survival and resistance to therapy of melanoma cells by regulating specific mRNA translation."],"submitter_name":"OMIM","review_date":20140904,"origin":"somatic","method":"literature only","submitter_date":20220317,"diseases":[{"normalized_cancer":["MELANOMA, MALIGNANT, SOMATIC"],"normalized_disease":["Melanoma, Cutaneous Malignant, Susceptibility to, 1"],"names":["Melanoma, Cutaneous Malignant, Susceptibility to, 1"]}],"review_description":"Pathogenic","date_updated":20220328,"clinical_significance":["Pathogenic"],"review_status":"no assertion criteria provided","accession_id":"SCV000035247"}],"variation_id":13961,"submission_description":[],"title":"NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) AND Melanoma","review_date":20140904,"diseases":[{"pub_med":[26389333,26389258],"symbols":{"medgen":"C0025202","mesh":"D008545","mondo":"MONDO:0005105","human_phenotype_ontology":"HP:0007474"},"normalized_disease":["Melanoma"],"names":["Melanoma"],"normalized_cancer":["Melanoma"],"keyword":"Neoplasm"}],"pub_med_references":[12068308,12198537,12447372,12619120,12644542,12670889,12794760,12960123,14513361,14602780,15001635,15126572,15181070,15342696,15356022,15386408,15687339,15998781,16015629,16174717,16187918,16772349,17374713,17488796,17785355,18398503,19571295,20818844,20823850,21107320,21107323,22113612,22281684,23302800,23685455,24512911,24670642,24717435,25079330,28854169,29925953],"date_created":20131031,"variant_id":10190071404531360004,"review_description":"Pathogenic","clinical_significance":["Pathogenic"],"allele_id":29000,"accession_id":"RCV000067669"},{"submissions":[{"pub_med_references":[12068308,12198537,12447372,12619120,12644542,12670889,12794760,12960123,14513361,14602780,15001635,15126572,15181070,15342696,15356022,15386408,15687339,15998781,16015629,16174717,16187918,16772349,17374713,17488796,17785355,18398503,19571295,20818844,20823850,21107320,21107323,22113612,22281684,23302800,23685455,24512911,24670642,24717435,25079330,28854169,29925953],"submission_description":["The val600-to-glu (V600E) mutation caused by a 1799T-A transversion in the BRAF gene was previously designated VAL599GLU (1796T-A). Kumar et al. (2003) noted that an earlier version of the BRAF sequence showed a discrepancy of 3 nucleotides in exon 1; based on the corrected sequence, they proposed a change in nucleotide numbering after nucleotide 94 (the ATG codon) by +3 and a corresponding codon change of +1.","Malignant Melanoma","Davies et al. (2002) identified a 1799T-A transversion in exon 15 of the BRAF gene that leads to a val600-to-glu (V600E) substitution. This mutation accounted for 92% of BRAF mutations in malignant melanoma (see 155600). The V600E mutation is an activating mutation resulting in constitutive activation of BRAF and downstream signal transduction in the MAP kinase pathway.","To evaluate the timing of mutations in BRAF during melanocyte neoplasia, Pollock et al. (2003) carried out mutation analysis on microdissected melanoma and nevi samples. They observed mutations resulting in the V600E amino acid substitution in 41 (68%) of 60 melanoma metastases, 4 (80%) of 5 primary melanomas, and, unexpectedly, in 63 (82%) of 77 nevi. The data suggested that mutational activation of the RAS/RAF/MAPK pathway in nevi is a critical step in the initiation of melanocytic neoplasia but alone is insufficient for melanoma tumorigenesis.","Lang et al. (2003) failed to find the V600E mutation as a germline mutation in 42 cases of familial melanoma studied. Their collection of families included 15 with and 24 without detected mutations in CDKN2A (600160). They did, however, find the V600E mutation in 6 (27%) of 22 samples of secondary (metastatic) melanomas studied. Meyer et al. (2003) found no V600E mutation in 172 melanoma patients comprising 46 familial cases, 21 multiple melanoma patients, and 106 cases with at least 1 first-degree relative suffering from other cancers. They concluded, therefore, that the common somatic BRAF mutation V600E does not contribute to polygenic or familial melanoma predisposition.","Kim et al. (2003) stated that V600E, the most common of BRAF mutations, had not been identified in tumors with mutations of the KRAS gene (190070). This mutually exclusive relationship supports the hypothesis that BRAF (V600E) and KRAS mutations exert equivalent effects in tumorigenesis (Rajagopalan et al., 2002; Singer et al., 2003).","Flaherty et al. (2010) reported complete or partial regression of V600E-associated metastatic melanoma in 81% of patients treated with an inhibitor (PLX4032) specific to the V600E mutation. Among 16 patients in a dose-escalation cohort, 10 had a partial response, and 1 had a complete response. Among 32 patients in an extension cohort, 24 had a partial response, and 2 had a complete response. The estimated median progression-free survival among all patients was more than 7 months. Responses were observed at all sites of disease, including bone, liver, and small bowel. Tumor biopsy specimens from 7 patients showed markedly reduced levels of phosphorylated ERK (600997), cyclin D1 (168461), and Ki67 (MKI67; 176741) at day 15 compared to baseline, indicating inhibition of the MAP kinase pathway. Three additional patients with V600E-associated papillary thyroid also showed a partial or complete response.","Bollag et al. (2010) described the structure-guided discovery of PLX4032 (RG7204), a potent inhibitor of oncogenic BRAF kinase activity. PLX4032 was cocrystallized with a protein construct that contained the kinase domain of BRAF(V600E). In a clinical trial, patients exposed to higher plasma levels of PLX4032 experienced tumor regression; in patients with tumor regressions, pathway analysis typically showed greater than 80% inhibition of cytoplasmic ERK phosphorylation. Bollag et al. (2010) concluded that their data demonstrated that BRAF-mutant melanomas are highly dependent on BRAF kinase activity.","Patients with BRAF(V600E)-positive melanomas exhibit an initial antitumor response to the RAF kinase inhibitor PLX4032, but acquired drug resistance almost invariably develops. Johannessen et al. (2010) identified MAP3K8 (191195), encoding COT (cancer Osaka thyroid oncogene) as a MAPK pathway agonist that drives resistance to RAF inhibition in BRAF(V600E) cell lines. COT activates ERK primarily through MARK/ERK (MEK)-dependent mechanisms that do not require RAF signaling. Moreover, COT expression is associated with de novo resistance in BRAF(V600E) cultured cell lines and acquired resistance in melanoma cells and tissue obtained from relapsing patients following treatment with MEK or RAF inhibitors. Johannessen et al. (2010) further identified combinatorial MAPK pathway inhibition or targeting of COT kinase activity as possible therapeutic strategies for reducing MAPK pathway activation in this setting.","Nazarian et al. (2010) showed that acquired resistance to PLX4032, a novel class I RAF-selective inhibitor, develops by mutually exclusive PDGFRB (173410) upregulation or NRAS (164790) mutations but not through secondary mutations in BRAF(V600E). Nazarian et al. (2010) used PLX4032-resistant sublines artificially derived from BRAF (V600E)-positive melanoma cell lines and validated key findings in PLX4032-resistant tumors and tumor-matched, short-term cultures from clinical trial patients. Induction of PDGFRB RNA, protein and tyrosine phosphorylation emerged as a dominant feature of acquired PLX4032 resistance in a subset of melanoma sublines, patient-derived biopsies, and short-term cultures. PDGFRB upregulated tumor cells have low activated RAS levels and, when treated with PLX4032, do not reactivate the MAPK pathway significantly. In another subset, high levels of activated N-RAS resulting from mutations lead to significant MAPK pathway reactivation upon PLX4032 treatment. Knockdown of PDGFRB or NRAS reduced growth of the respective PLX4032-resistant subsets. Overexpression of PDGFRB or NRAS(Q61K) conferred PLX4032 resistance to PLX4032-sensitive parental cell lines. Importantly, Nazarian et al. (2010) showed that MAPK reactivation predicts MEK inhibitor sensitivity. Thus, Nazarian et al. (2010) concluded that melanomas escape BRAF(V600E) targeting not through secondary BRAF(V600E) mutations but via receptor tyrosine kinase (RTK)-mediated activation of alternative survival pathway(s) or activated RAS-mediated reactivation of the MAPK pathway, suggesting additional therapeutic strategies.","Poulikakos et al. (2011) identified a novel resistance mechanism for melanomas with BRAF(V600E) treated with RAF inhibitors. The authors found that a subset of cells resistant to vemurafenib (PLX4032, RG7204) express a 61-kD variant form of BRAF(V600E), p61BRAF(V600E), that lacks exons 4 through 8, a region that encompasses the RAS-binding domain. p61BRAF(V600E) showed enhanced dimerization in cells with low levels of RAS activation, as compared to full-length BRAF(V600E). In cells in which p61BRAF(V600E) was expressed endogenously or ectopically, ERK signaling was resistant to the RAF inhibitor. Moreover, a mutation that abolished the dimerization of p61BRAF(V600E) restored its sensitivity to vemurafenib. Finally, Poulikakos et al. (2011) identified BRAF(V600E) splicing variants lacking the RAS-binding domain in the tumors of 6 of 19 patients with acquired resistance to vemurafenib. Poulikakos et al. (2011) concluded that their data supported the model that inhibition of ERK signaling by RAF inhibitors is dependent on levels of RAS-GTP too low to support RAF dimerization and identified a novel mechanism of acquired resistance in patients: expression of splicing isoforms of BRAF(V600E) that dimerize in a RAS-independent manner.","Thakur et al. (2013) investigated the cause and consequences of vemurafenib resistance using 2 independently-derived primary human melanoma xenograft models in which drug resistance is selected by continuous vemurafenib administration. In one of these models, resistant tumors showed continued dependency on BRAF(V600E)-MEK-ERK signaling owing to elevated BRAF(V600E) expression. Thakur et al. (2013) showed that vemurafenib-resistant melanomas become drug-dependent for their continued proliferation, such that cessation of drug administration leads to regression of established drug-resistant tumors. Thakur et al. (2013) further demonstrated that a discontinuous dosing strategy, which exploits the fitness disadvantage displayed by drug-resistant cells in the absence of the drug, forestalls the onset of lethal drug-resistant disease. Thakur et al. (2013) concluded that their data highlighted the concept that drug-resistant cells may also display drug dependency, such that altered dosing may prevent the emergence of lethal drug resistance. These observations may contribute to sustaining the durability of vemurafenib response with the ultimate goal of curative therapy for the subset of melanoma patients with BRAF mutations.","Using metabolic profiling and functional perturbations, Kaplon et al. (2013) showed that the mitochondrial gatekeeper pyruvate dehydrogenase (PDH; 300502) is a crucial mediator of senescence induced by BRAF(V600E), an oncogene commonly mutated in melanoma and other cancers. BRAF(V600E)-induced senescence is accompanied by simultaneous suppression of the PDH-inhibitory enzyme pyruvate dehydrogenase kinase-1 (PDK1; 602524) and induction of the PDH-activating enzyme pyruvate dehydrogenase phosphatase-2 (PDP2; 615499). The resulting combined activation of PDH enhanced the use of pyruvate in the tricarboxylic acid cycle, causing increased respiration and redox stress. Abrogation of oncogene-induced senescence (OIS), a rate-limiting step towards oncogenic transformation, coincided with reversion of these processes. Further supporting a crucial role of PDH in OIS, enforced normalization of either PDK1 or PDP2 expression levels inhibited PDH and abrogated OIS, thereby licensing BRAF(V600E)-driven melanoma development. Finally, depletion of PDK1 eradicated melanoma subpopulations resistant to targeted BRAF inhibition, and caused regression of established melanomas.","Sun et al. (2014) showed that 6 out of 16 BRAF(V600E)-positive melanoma tumors analyzed acquired EGFR (131550) expression after the development of resistance to inhibitors of BRAF or MEK (176872). Using a chromatin regulator-focused short hairpin RNA (shRNA) library, Sun et al. (2014) found that suppression of SRY-box 10 (SOX10; 602229) in melanoma causes activation of TGF-beta (190180) signaling, thus leading to upregulation of EGFR and platelet-derived growth factor receptor-beta (PDGFRB; 173410), which confer resistance to BRAF and MEK inhibitors. Expression of EGFR in melanoma or treatment with TGF-beta results in a slow-growth phenotype with cells displaying hallmarks of oncogene-induced senescence. However, EGFR expression or exposure to TGF-beta becomes beneficial for proliferation in the presence of BRAF or MEK inhibitors. In a heterogeneous population of melanoma cells that have varying levels of SOX10 suppression, cells with low SOX10 and consequently high EGFR expression are rapidly enriched in the presence of drug treatment, but this is reversed when the treatment is discontinued. Sun et al. (2014) found evidence for SOX10 loss and/or activation of TGF-beta signaling in 4 of the 6 EGFR-positive drug-resistant melanoma patient samples. Sun et al. (2014) concluded that their findings provided a rationale for why some BRAF or MEK inhibitor-resistant melanoma patients may regain sensitivity to these drugs after a 'drug holiday' and identified patients with EGFR-positive melanoma as a group that may benefit from retreatment after a drug holiday.","Boussemart et al. (2014) demonstrated that the persistent formation of the eIF4F complex, comprising the eIF4E (133440) cap-binding protein, the eIF4G (600495) scaffolding protein, and the eIF4A (602641) RNA helicase, is associated with resistance to anti-BRAF (164757), anti-MEK, and anti-BRAF plus anti-MEK drug combinations in BRAF(V600)-mutant melanoma, colon, and thyroid cancer cell lines. Resistance to treatment and maintenance of eIF4F complex formation is associated with 1 of 3 mechanisms: reactivation of MAPK (see 176948) signaling; persistent ERK-independent phosphorylation of the inhibitory eIF4E-binding protein 4EBP1 (602223); or increased proapoptotic BMF (606266)-dependent degradation of eIF4G. The development of an in situ method to detect the eIF4E-eIF4G interactions showed that eIF4F complex formation is decreased in tumors that respond to anti-BRAF therapy and increased in resistant metastases compared to tumors before treatment. Strikingly, inhibiting the eIF4F complex, either by blocking the eIF4E-eIF4G interaction or by targeting eIF4A, synergized with inhibiting BRAF(V600) to kill the cancer cells. eIF4F appeared not only to be an indicator of both innate and acquired resistance, but also a therapeutic target. Boussemart et al. (2014) concluded that combinations of drugs targeting BRAF (and/or MEK) and eIF4F may overcome most of the resistance mechanisms in BRAF(V600)-mutant cancers.","Colorectal Carcinoma","Rajagopalan et al. (2002) identified the V600E mutation in 28 of 330 colorectal tumors (see 114500) screened for BRAF mutations. In all cases the mutation was heterozygous and occurred somatically.","Domingo et al. (2004) pointed out that the V600E hotspot mutation had been found in colorectal tumors that showed inherited mutation in a DNA mismatch repair (MMR) gene, such as MLH1 (120436) or MSH2 (609309). These mutations had been shown to occur almost exclusively in tumors located in the proximal colon and with hypermethylation of MLH1, the gene involved in the initial steps of development of these tumors; however, BRAF mutations were not detected in those cases with or presumed to have germline mutation in either MLH1 or MSH2. Domingo et al. (2004) studied mutation analysis of the BRAF hotspot as a possible low-cost effective strategy for genetic testing for hereditary nonpolyposis colorectal cancer (HNPCC; 120435). The V600E mutation was found in 82 (40%) of 206 sporadic tumors with high microsatellite instability (MSI-H) but in none of 111 tested HNPCC tumors or in 45 cases showing abnormal MSH2 immunostaining. Domingo et al. (2004) concluded that detection of the V600E mutation in a colorectal MSI-H tumor argues against the presence of germline mutation in either MLH1 or MSH2, and that screening of these MMR genes can be avoided in cases positive for V600E.","Lubomierski et al. (2005) analyzed 45 colorectal carcinomas with MSI and 37 colorectal tumors without MSI but with similar clinical characteristics and found that BRAF was mutated more often in tumors with MSI than without (27% vs 5%, p = 0.016). The most prevalent BRAF alteration, V600E, occurred only in tumors with MSI and was associated with more frequent MLH1 promoter methylation and loss of MLH1. The median age of patients with BRAF V600E was older than that of those without V600E (78 vs 49 years, p = 0.001). There were no BRAF alterations in patients with germline mutations of mismatch repair genes. Lubomierski et al. (2005) concluded that tumors with MSI caused by epigenetic MLH1 silencing have a mutational background distinct from that of tumors with genetic loss of mismatch repair, and suggested that there are 2 genetically distinct entities of microsatellite unstable tumors.","Tol et al. (2009) detected a somatic V600E mutation in 45 (8.7%) of 519 metastatic colorectal tumors. Patients with BRAF-mutated tumors had significantly shorter median progression-free and median overall survival compared to patients with wildtype BRAF tumors, regardless of the use of cetuximab. Tol et al. (2009) suggested that the BRAF mutation may be a negative prognostic factor in these patients.","Inhibition of the BRAF(V600E) oncoprotein by the small-molecule drug PLX4032 (vemurafenib) is highly effective in the treatment of melanoma. However, colon cancer patients harboring the same BRAF(V600E) oncogenic lesion have poor prognosis and show only a very limited response to this drug. To investigate the cause of this limited therapeutic effect in BRAF(V600E) mutant colon cancer, Prahallad et al. (2012) performed an RNA interference-based genetic screen in human cells to search for kinases whose knockdown synergizes with BRAF(V600E) inhibition. They reported that blockade of the epidermal growth factor receptor (EGFR; 131550) shows strong synergy with BRAF(V600E) inhibition. Prahallad et al. (2012) found in multiple BRAF(V600E) mutant colon cancers that inhibition of EGFR by the antibody drug cetuximab or the small-molecule drugs gefitinib or erlotinib is strongly synergistic with BRAF(V600E) inhibition, both in vitro and in vivo. Mechanistically, Prahallad et al. (2012) found that BRAF(V600E) inhibition causes a rapid feedback activation of EGFR, which supports continued proliferation in the presence of BRAF(V600E) inhibition. Melanoma cells express low levels of EGFR and are therefore not subject to this feedback activation. Consistent with this, Prahallad et al. (2012) found that ectopic expression of EGFR in melanoma cells is sufficient to cause resistance to PLX4032. Prahallad et al. (2012) concluded that BRAF(V600E) mutant colon cancers (approximately 8 to 10% of all colon cancers) might benefit from combination therapy consisting of BRAF and EGFR inhibitors.","Gala et al. (2014) identified the BRAF V600E mutation in 18 of 19 sessile serrated adenomas from 19 unrelated patients with sessile serrated polyposis cancer syndrome (SSPCS; 617108).","Papillary Thyroid Carcinoma","Kimura et al. (2003) identified the V600E mutation in 28 (35.8%) of 78 papillary thyroid cancers (PTC; see 188550); it was not found in any of the other types of differentiated follicular neoplasms arising from the same cell type (0 of 46). RET (see 164761)/PTC mutations and RAS (see 190020) mutations were each identified in 16.4% of PTCs, but there was no overlap in the 3 mutations. Kimura et al. (2003) concluded that thyroid cell transformation to papillary cancer takes place through constitutive activation of effectors along the RET/PTC-RAS-BRAF signaling pathway.","Xing et al. (2004) studied various thyroid tumor types for the most common BRAF mutation, 1799T-A, by DNA sequencing. They found a high and similar frequency (45%) of the 1799T-A mutation in 2 geographically distinct papillary thyroid cancer patient populations, 1 composed of sporadic cases from North America, and the other from Kiev, Ukraine, that included individuals who were exposed to the Chernobyl nuclear accident. In contrast, Xing et al. (2004) found BRAF mutations in only 20% of anaplastic thyroid cancers and in no medullary thyroid cancers or benign thyroid hyperplasia. They also confirmed previous reports that the BRAF 1799T-A mutation did not occur in benign thyroid adenomas or follicular thyroid cancers. They concluded that frequent occurrence of BRAF mutation is associated with PTC, irrespective of geographic origin, and is apparently not a radiation-susceptible mutation.","Nikiforova et al. (2003) analyzed 320 thyroid tumors and 6 anaplastic carcinoma cell lines and detected BRAF mutations in 45 papillary carcinomas (38%), 2 poorly differentiated carcinomas (13%), 3 (10%) anaplastic carcinomas (10%), and 5 thyroid anaplastic carcinoma cell lines (83%) but not in follicular, Hurthle cell, and medullary carcinomas, follicular and Hurthle cell adenomas, or benign hyperplastic nodules. All mutations involved a T-to-A transversion at nucleotide 1799. All BRAF-positive poorly differentiated and anaplastic carcinomas contained areas of preexisting papillary carcinoma, and mutation was present in both the well differentiated and dedifferentiated components. The authors concluded that BRAF mutations are restricted to papillary carcinomas and poorly differentiated and anaplastic carcinomas arising from papillary carcinomas, and that they are associated with distinct phenotypic and biologic properties of papillary carcinomas and may participate in progression to poorly differentiated and anaplastic carcinomas.","Hypothesizing that childhood thyroid carcinomas may be associated with a different prevalence of the BRAF 1799T-A mutation compared with adult cases, Kumagai et al. (2004) examined 31 cases of Japanese childhood thyroid carcinoma and an additional 48 cases of PTC from Ukraine, all of whom were less than 17 years of age at the time of the Chernobyl accident. The BRAF 1799T-A mutation was found in only 1 of 31 Japanese cases (3.4%) and in none of the 15 Ukrainian cases operated on before the age of 15 years, although it was found in 8 of 33 Ukrainian young adult cases (24.2%). Kumagai et al. (2004) concluded that the BRAF 1799T-A mutation is uncommon in childhood thyroid carcinomas.","Puxeddu et al. (2004) found the V600E substitution in 24 of 60 PTCs (40%) but in none of 6 follicular adenomas, 5 follicular carcinomas, or 1 anaplastic carcinoma. Nine of the 60 PTCs (15%) presented expression of a RET/PTC rearrangement. A genetico-clinical association analysis showed a statistically significant correlation between BRAF mutation and development of PTCs of the classic papillary histotype (P = 0.038). No link could be detected between expression of BRAF V600E and age at diagnosis, gender, dimension, local invasiveness of the primary cancer, presence of lymph node metastases, tumor stage, or multifocality of the disease. The authors concluded that these data clearly confirmed that BRAF V600E was the most common genetic alteration found to that time in adult sporadic PTCs, that it is unique for this thyroid cancer histotype, and that it might drive the development of PTCs of the classic papillary subtype.","Xing et al. (2004) demonstrated detection of the 1799T-A mutation on thyroid cytologic specimens from fine needle aspiration biopsy (FNAB). Prospective analysis showed that 50% of the nodules that proved to be PTCs on surgical histopathology were correctly diagnosed by BRAF mutation analysis on FNAB specimens; there were no false positive findings.","Xing et al. (2005) studied the relationships between the BRAF V600E mutation and clinicopathologic outcomes, including recurrence, in 219 PTC patients. The authors concluded that in patients with PTC, BRAF mutation is associated with poorer clinicopathologic outcomes and independently predicts recurrence. Therefore, BRAF mutation may be a useful molecular marker to assist in risk stratification for patients with PTC.","In a series of 52 classic PTCs, Porra et al. (2005) found that low SLC5A8 (608044) expression was highly significantly associated with the presence of the BRAF 1799T-A mutation. SLC5A8 expression was selectively downregulated (40-fold) in PTCs of classical form; methylation-specific PCR analyses showed that SLC5A8 was methylated in 90% of classic PTCs and in about 20% of other PTCs. Porra et al. (2005) concluded that their data identified a relationship between the methylation-associated silencing of the tumor-suppressor gene SLC5A8 and the 1799T-A point mutation of the BRAF gene in the classic PTC subtype of thyroid carcinomas.","Vasko et al. (2005) studied the relationship between the BRAF 1799T-A mutation and lymph node metastasis of PTC by examining the mutation in both the primary tumors and their paired lymph node metastases. Their findings indicated that the high prevalence of BRAF mutation in lymph node-metastasized PTC tissues from BRAF mutation-positive primary tumors and the possible de novo formation of BRAF mutation in lymph node-metastasized PTC were consistent with a role of BRAF mutation in facilitating the metastasis and progression of PTC in lymph nodes.","In a patient with congenital hypothyroidism and long-standing goiter due to mutation in the thyroglobulin gene (see TG, 188540; and TDH3, 274700), who was also found to have multifocal follicular carcinoma of the thyroid, Hishinuma et al. (2005) identified somatic heterozygosity for the V600E mutation in the BRAF gene in the cancerous thyroid tissue.","Liu et al. (2007) used BRAF siRNA to transfect stably several BRAF mutation-harboring PTC cell lines, isolated clones with stable suppression of BRAF, and assessed their ability to proliferate, transform, and grow xenograft tumors in nude mice. They found that the V600E mutation not only initiates PTC but also maintains the proliferation, transformation, and tumorigenicity of PTC cells harboring the BRAF mutation, and that the growth of tumors derived from such cells continues to depend on the V600E mutation.","Jo et al. (2006) found that of 161 PTC patients, 102 (63.4%) had the BRAF V600E mutation and that these patients had significantly larger tumor sizes and significantly higher expression of vascular endothelial growth factor (VEGF; 192240) compared to patients without this mutation. The level of VEGF expression was closely correlated with tumor size, extrathyroidal invasion, and stage. Jo et al. (2006) concluded that the relatively high levels of VEGF expression may be related to poorer clinical outcomes and recurrences in BRAF V600E(+) PTC.","Durante et al. (2007) found that the BRAF V600E mutation in PTCs is associated with reduced expression of key genes involved in iodine metabolism. They noted that this effect may alter the effectiveness of diagnostic and/or therapeutic use of radioiodine in BRAF-mutation PTCs.","Lupi et al. (2007) found a BRAF mutation in 219 of 500 cases (43.8%) of PTC. The most common BRAF mutation, V600E, was found in 214 cases (42.8%). BRAF V600E was associated with extrathyroidal invasion (p less than 0.0001), multicentricity (p = 0.0026), presence of nodal metastases (p = 0.0009), class III versus classes I and II (p less than 0.00000006), and absence of tumor capsule (p less than 0.0001), in particular, in follicular- and micro-PTC variants. By multivariate analysis, the absence of tumor capsule remained the only parameter associated (p = 0.0005) with the BRAF V600E mutation. The authors concluded that the BRAF V600E mutation is associated with high-risk PTC and, in particular, in follicular variant with invasive tumor growth.","Flaherty et al. (2010) reported complete or partial regression of V600E-associated papillary thyroid cancer in 3 patients treated with an inhibitor (PLX4032) specific to the V600E mutation.","Nonseminomatous Germ Cell Tumors","In 3 (9%) of 32 nonseminomatous germ cell tumors (see 273300) with a mixture of embryonal carcinoma, yolk sac tumor, choriocarcinoma, and mature teratoma, Sommerer et al. (2005) identified the activating 1796T-A mutation in the BRAF gene; the mutation was present within the embryonic carcinoma component.","Astrocytoma","Pfister et al. (2008) identified a somatic V600E mutation in 4 (6%) of 66 pediatric low-grade astrocytomas (see 137800). Thirty (45%) of the 66 tumors had a copy number gain spanning the BRAF locus, indicating a novel mechanism of MAPK (176948) pathway activation in these tumors.","Role in Neurodegeneration","Mass et al. (2017) hypothesized that a somatic BRAF(V600E) mutation in the erythromyeloid lineage may cause neurodegeneration. Mass et al. (2017) showed that mosaic expression of BRAF(V600E) in mouse erythromyeloid progenitors results in clonal expansion of tissue-resident macrophages and a severe late-onset neurodegenerative disorder. This is associated with accumulation of ERK-activated amoeboid microglia in mice, and is also observed in human patients with histiocytoses. In the mouse model, neurobehavioral signs, astrogliosis, deposition of amyloid precursor protein, synaptic loss, and neuronal death were driven by ERK-activated microglia and were preventable by BRAF inhibition. Mass et al. (2017) suggested that the results identified the fetal precursors of tissue-resident macrophages as a potential cell of origin for histiocytoses and demonstrated that a somatic mutation in the erythromyeloid progenitor lineage in mice can drive late-onset neurodegeneration.","Variant Function","Brady et al. (2014) showed that decreasing the levels of CTR1 (603085), or mutations in MEK1 (176872) that disrupt copper binding, decreased BRAF(V600E)-driven signaling and tumorigenesis in mice and human cell settings. Conversely, a MEK1-MEK5 (602520) chimera that phosphorylated ERK1/2 independently of copper or an active ERK2 restored the tumor growth of murine cells lacking Ctr1. Copper chelators used in the treatment of Wilson disease (277900) decreased tumor growth of human or murine cells that were either transformed by BRAF(V600E) or engineered to be resistant to BRAF inhibition. Brady et al. (2014) concluded that copper chelation therapy could be repurposed to treat cancers containing the BRAF(V600E) mutation.","Rapino et al. (2018) showed in humans that the enzymes that catalyze modifications of wobble uridine-34 (U34) tRNA are key players of the protein synthesis rewiring that is induced by the transformation driven by the BRAF V600E oncogene and by resistance to targeted therapy in melanoma. Rapino et al. (2018) showed that BRAF V600E-expressing melanoma cells are dependent on U34 enzymes for survival, and that concurrent inhibition of MAPK signaling and ELP3 (612722) or CTU1 (612694) and/or CTU2 (617057) synergizes to kill melanoma cells. Activation of the PI3K signaling pathway, one of the most common mechanisms of acquired resistance to MAPK therapeutic agents, markedly increases the expression of U34 enzymes. Mechanistically, U34 enzymes promote glycolysis in melanoma cells through the direct, codon-dependent, regulation of the translation of HIF1A (603348) mRNA and the maintenance of high levels of HIF1-alpha protein. Therefore, the acquired resistance to anti-BRAF therapy is associated with high levels of U34 enzymes and HIF1-alpha. Rapino et al. (2018) concluded that U34 enzymes promote the survival and resistance to therapy of melanoma cells by regulating specific mRNA translation."],"submitter_name":"OMIM","review_date":20140904,"origin":"somatic","method":"literature only","submitter_date":20220317,"diseases":[{"normalized_cancer":["NONSEMINOMATOUS GERM CELL TUMORS, SOMATIC"],"names":["Nonseminomatous Germ Cell Tumors, Somatic"]}],"review_description":"Pathogenic","date_updated":20220328,"clinical_significance":["Pathogenic"],"review_status":"no assertion criteria provided","accession_id":"SCV000043966"}],"variation_id":13961,"submission_description":["The val600-to-glu (V600E) mutation caused by a 1799T-A transversion in the BRAF gene was previously designated VAL599GLU (1796T-A). Kumar et al. (2003) noted that an earlier version of the BRAF sequence showed a discrepancy of 3 nucleotides in exon 1; based on the corrected sequence, they proposed a change in nucleotide numbering after nucleotide 94 (the ATG codon) by +3 and a corresponding codon change of +1.","Malignant Melanoma","Davies et al. (2002) identified a 1799T-A transversion in exon 15 of the BRAF gene that leads to a val600-to-glu (V600E) substitution. This mutation accounted for 92% of BRAF mutations in malignant melanoma (see 155600). The V600E mutation is an activating mutation resulting in constitutive activation of BRAF and downstream signal transduction in the MAP kinase pathway.","To evaluate the timing of mutations in BRAF during melanocyte neoplasia, Pollock et al. (2003) carried out mutation analysis on microdissected melanoma and nevi samples. They observed mutations resulting in the V600E amino acid substitution in 41 (68%) of 60 melanoma metastases, 4 (80%) of 5 primary melanomas, and, unexpectedly, in 63 (82%) of 77 nevi. The data suggested that mutational activation of the RAS/RAF/MAPK pathway in nevi is a critical step in the initiation of melanocytic neoplasia but alone is insufficient for melanoma tumorigenesis.","Lang et al. (2003) failed to find the V600E mutation as a germline mutation in 42 cases of familial melanoma studied. Their collection of families included 15 with and 24 without detected mutations in CDKN2A (600160). They did, however, find the V600E mutation in 6 (27%) of 22 samples of secondary (metastatic) melanomas studied. Meyer et al. (2003) found no V600E mutation in 172 melanoma patients comprising 46 familial cases, 21 multiple melanoma patients, and 106 cases with at least 1 first-degree relative suffering from other cancers. They concluded, therefore, that the common somatic BRAF mutation V600E does not contribute to polygenic or familial melanoma predisposition.","Kim et al. (2003) stated that V600E, the most common of BRAF mutations, had not been identified in tumors with mutations of the KRAS gene (190070). This mutually exclusive relationship supports the hypothesis that BRAF (V600E) and KRAS mutations exert equivalent effects in tumorigenesis (Rajagopalan et al., 2002; Singer et al., 2003).","Flaherty et al. (2010) reported complete or partial regression of V600E-associated metastatic melanoma in 81% of patients treated with an inhibitor (PLX4032) specific to the V600E mutation. Among 16 patients in a dose-escalation cohort, 10 had a partial response, and 1 had a complete response. Among 32 patients in an extension cohort, 24 had a partial response, and 2 had a complete response. The estimated median progression-free survival among all patients was more than 7 months. Responses were observed at all sites of disease, including bone, liver, and small bowel. Tumor biopsy specimens from 7 patients showed markedly reduced levels of phosphorylated ERK (600997), cyclin D1 (168461), and Ki67 (MKI67; 176741) at day 15 compared to baseline, indicating inhibition of the MAP kinase pathway. Three additional patients with V600E-associated papillary thyroid also showed a partial or complete response.","Bollag et al. (2010) described the structure-guided discovery of PLX4032 (RG7204), a potent inhibitor of oncogenic BRAF kinase activity. PLX4032 was cocrystallized with a protein construct that contained the kinase domain of BRAF(V600E). In a clinical trial, patients exposed to higher plasma levels of PLX4032 experienced tumor regression; in patients with tumor regressions, pathway analysis typically showed greater than 80% inhibition of cytoplasmic ERK phosphorylation. Bollag et al. (2010) concluded that their data demonstrated that BRAF-mutant melanomas are highly dependent on BRAF kinase activity.","Patients with BRAF(V600E)-positive melanomas exhibit an initial antitumor response to the RAF kinase inhibitor PLX4032, but acquired drug resistance almost invariably develops. Johannessen et al. (2010) identified MAP3K8 (191195), encoding COT (cancer Osaka thyroid oncogene) as a MAPK pathway agonist that drives resistance to RAF inhibition in BRAF(V600E) cell lines. COT activates ERK primarily through MARK/ERK (MEK)-dependent mechanisms that do not require RAF signaling. Moreover, COT expression is associated with de novo resistance in BRAF(V600E) cultured cell lines and acquired resistance in melanoma cells and tissue obtained from relapsing patients following treatment with MEK or RAF inhibitors. Johannessen et al. (2010) further identified combinatorial MAPK pathway inhibition or targeting of COT kinase activity as possible therapeutic strategies for reducing MAPK pathway activation in this setting.","Nazarian et al. (2010) showed that acquired resistance to PLX4032, a novel class I RAF-selective inhibitor, develops by mutually exclusive PDGFRB (173410) upregulation or NRAS (164790) mutations but not through secondary mutations in BRAF(V600E). Nazarian et al. (2010) used PLX4032-resistant sublines artificially derived from BRAF (V600E)-positive melanoma cell lines and validated key findings in PLX4032-resistant tumors and tumor-matched, short-term cultures from clinical trial patients. Induction of PDGFRB RNA, protein and tyrosine phosphorylation emerged as a dominant feature of acquired PLX4032 resistance in a subset of melanoma sublines, patient-derived biopsies, and short-term cultures. PDGFRB upregulated tumor cells have low activated RAS levels and, when treated with PLX4032, do not reactivate the MAPK pathway significantly. In another subset, high levels of activated N-RAS resulting from mutations lead to significant MAPK pathway reactivation upon PLX4032 treatment. Knockdown of PDGFRB or NRAS reduced growth of the respective PLX4032-resistant subsets. Overexpression of PDGFRB or NRAS(Q61K) conferred PLX4032 resistance to PLX4032-sensitive parental cell lines. Importantly, Nazarian et al. (2010) showed that MAPK reactivation predicts MEK inhibitor sensitivity. Thus, Nazarian et al. (2010) concluded that melanomas escape BRAF(V600E) targeting not through secondary BRAF(V600E) mutations but via receptor tyrosine kinase (RTK)-mediated activation of alternative survival pathway(s) or activated RAS-mediated reactivation of the MAPK pathway, suggesting additional therapeutic strategies.","Poulikakos et al. (2011) identified a novel resistance mechanism for melanomas with BRAF(V600E) treated with RAF inhibitors. The authors found that a subset of cells resistant to vemurafenib (PLX4032, RG7204) express a 61-kD variant form of BRAF(V600E), p61BRAF(V600E), that lacks exons 4 through 8, a region that encompasses the RAS-binding domain. p61BRAF(V600E) showed enhanced dimerization in cells with low levels of RAS activation, as compared to full-length BRAF(V600E). In cells in which p61BRAF(V600E) was expressed endogenously or ectopically, ERK signaling was resistant to the RAF inhibitor. Moreover, a mutation that abolished the dimerization of p61BRAF(V600E) restored its sensitivity to vemurafenib. Finally, Poulikakos et al. (2011) identified BRAF(V600E) splicing variants lacking the RAS-binding domain in the tumors of 6 of 19 patients with acquired resistance to vemurafenib. Poulikakos et al. (2011) concluded that their data supported the model that inhibition of ERK signaling by RAF inhibitors is dependent on levels of RAS-GTP too low to support RAF dimerization and identified a novel mechanism of acquired resistance in patients: expression of splicing isoforms of BRAF(V600E) that dimerize in a RAS-independent manner.","Thakur et al. (2013) investigated the cause and consequences of vemurafenib resistance using 2 independently-derived primary human melanoma xenograft models in which drug resistance is selected by continuous vemurafenib administration. In one of these models, resistant tumors showed continued dependency on BRAF(V600E)-MEK-ERK signaling owing to elevated BRAF(V600E) expression. Thakur et al. (2013) showed that vemurafenib-resistant melanomas become drug-dependent for their continued proliferation, such that cessation of drug administration leads to regression of established drug-resistant tumors. Thakur et al. (2013) further demonstrated that a discontinuous dosing strategy, which exploits the fitness disadvantage displayed by drug-resistant cells in the absence of the drug, forestalls the onset of lethal drug-resistant disease. Thakur et al. (2013) concluded that their data highlighted the concept that drug-resistant cells may also display drug dependency, such that altered dosing may prevent the emergence of lethal drug resistance. These observations may contribute to sustaining the durability of vemurafenib response with the ultimate goal of curative therapy for the subset of melanoma patients with BRAF mutations.","Using metabolic profiling and functional perturbations, Kaplon et al. (2013) showed that the mitochondrial gatekeeper pyruvate dehydrogenase (PDH; 300502) is a crucial mediator of senescence induced by BRAF(V600E), an oncogene commonly mutated in melanoma and other cancers. BRAF(V600E)-induced senescence is accompanied by simultaneous suppression of the PDH-inhibitory enzyme pyruvate dehydrogenase kinase-1 (PDK1; 602524) and induction of the PDH-activating enzyme pyruvate dehydrogenase phosphatase-2 (PDP2; 615499). The resulting combined activation of PDH enhanced the use of pyruvate in the tricarboxylic acid cycle, causing increased respiration and redox stress. Abrogation of oncogene-induced senescence (OIS), a rate-limiting step towards oncogenic transformation, coincided with reversion of these processes. Further supporting a crucial role of PDH in OIS, enforced normalization of either PDK1 or PDP2 expression levels inhibited PDH and abrogated OIS, thereby licensing BRAF(V600E)-driven melanoma development. Finally, depletion of PDK1 eradicated melanoma subpopulations resistant to targeted BRAF inhibition, and caused regression of established melanomas.","Sun et al. (2014) showed that 6 out of 16 BRAF(V600E)-positive melanoma tumors analyzed acquired EGFR (131550) expression after the development of resistance to inhibitors of BRAF or MEK (176872). Using a chromatin regulator-focused short hairpin RNA (shRNA) library, Sun et al. (2014) found that suppression of SRY-box 10 (SOX10; 602229) in melanoma causes activation of TGF-beta (190180) signaling, thus leading to upregulation of EGFR and platelet-derived growth factor receptor-beta (PDGFRB; 173410), which confer resistance to BRAF and MEK inhibitors. Expression of EGFR in melanoma or treatment with TGF-beta results in a slow-growth phenotype with cells displaying hallmarks of oncogene-induced senescence. However, EGFR expression or exposure to TGF-beta becomes beneficial for proliferation in the presence of BRAF or MEK inhibitors. In a heterogeneous population of melanoma cells that have varying levels of SOX10 suppression, cells with low SOX10 and consequently high EGFR expression are rapidly enriched in the presence of drug treatment, but this is reversed when the treatment is discontinued. Sun et al. (2014) found evidence for SOX10 loss and/or activation of TGF-beta signaling in 4 of the 6 EGFR-positive drug-resistant melanoma patient samples. Sun et al. (2014) concluded that their findings provided a rationale for why some BRAF or MEK inhibitor-resistant melanoma patients may regain sensitivity to these drugs after a 'drug holiday' and identified patients with EGFR-positive melanoma as a group that may benefit from retreatment after a drug holiday.","Boussemart et al. (2014) demonstrated that the persistent formation of the eIF4F complex, comprising the eIF4E (133440) cap-binding protein, the eIF4G (600495) scaffolding protein, and the eIF4A (602641) RNA helicase, is associated with resistance to anti-BRAF (164757), anti-MEK, and anti-BRAF plus anti-MEK drug combinations in BRAF(V600)-mutant melanoma, colon, and thyroid cancer cell lines. Resistance to treatment and maintenance of eIF4F complex formation is associated with 1 of 3 mechanisms: reactivation of MAPK (see 176948) signaling; persistent ERK-independent phosphorylation of the inhibitory eIF4E-binding protein 4EBP1 (602223); or increased proapoptotic BMF (606266)-dependent degradation of eIF4G. The development of an in situ method to detect the eIF4E-eIF4G interactions showed that eIF4F complex formation is decreased in tumors that respond to anti-BRAF therapy and increased in resistant metastases compared to tumors before treatment. Strikingly, inhibiting the eIF4F complex, either by blocking the eIF4E-eIF4G interaction or by targeting eIF4A, synergized with inhibiting BRAF(V600) to kill the cancer cells. eIF4F appeared not only to be an indicator of both innate and acquired resistance, but also a therapeutic target. Boussemart et al. (2014) concluded that combinations of drugs targeting BRAF (and/or MEK) and eIF4F may overcome most of the resistance mechanisms in BRAF(V600)-mutant cancers.","Colorectal Carcinoma","Rajagopalan et al. (2002) identified the V600E mutation in 28 of 330 colorectal tumors (see 114500) screened for BRAF mutations. In all cases the mutation was heterozygous and occurred somatically.","Domingo et al. (2004) pointed out that the V600E hotspot mutation had been found in colorectal tumors that showed inherited mutation in a DNA mismatch repair (MMR) gene, such as MLH1 (120436) or MSH2 (609309). These mutations had been shown to occur almost exclusively in tumors located in the proximal colon and with hypermethylation of MLH1, the gene involved in the initial steps of development of these tumors; however, BRAF mutations were not detected in those cases with or presumed to have germline mutation in either MLH1 or MSH2. Domingo et al. (2004) studied mutation analysis of the BRAF hotspot as a possible low-cost effective strategy for genetic testing for hereditary nonpolyposis colorectal cancer (HNPCC; 120435). The V600E mutation was found in 82 (40%) of 206 sporadic tumors with high microsatellite instability (MSI-H) but in none of 111 tested HNPCC tumors or in 45 cases showing abnormal MSH2 immunostaining. Domingo et al. (2004) concluded that detection of the V600E mutation in a colorectal MSI-H tumor argues against the presence of germline mutation in either MLH1 or MSH2, and that screening of these MMR genes can be avoided in cases positive for V600E.","Lubomierski et al. (2005) analyzed 45 colorectal carcinomas with MSI and 37 colorectal tumors without MSI but with similar clinical characteristics and found that BRAF was mutated more often in tumors with MSI than without (27% vs 5%, p = 0.016). The most prevalent BRAF alteration, V600E, occurred only in tumors with MSI and was associated with more frequent MLH1 promoter methylation and loss of MLH1. The median age of patients with BRAF V600E was older than that of those without V600E (78 vs 49 years, p = 0.001). There were no BRAF alterations in patients with germline mutations of mismatch repair genes. Lubomierski et al. (2005) concluded that tumors with MSI caused by epigenetic MLH1 silencing have a mutational background distinct from that of tumors with genetic loss of mismatch repair, and suggested that there are 2 genetically distinct entities of microsatellite unstable tumors.","Tol et al. (2009) detected a somatic V600E mutation in 45 (8.7%) of 519 metastatic colorectal tumors. Patients with BRAF-mutated tumors had significantly shorter median progression-free and median overall survival compared to patients with wildtype BRAF tumors, regardless of the use of cetuximab. Tol et al. (2009) suggested that the BRAF mutation may be a negative prognostic factor in these patients.","Inhibition of the BRAF(V600E) oncoprotein by the small-molecule drug PLX4032 (vemurafenib) is highly effective in the treatment of melanoma. However, colon cancer patients harboring the same BRAF(V600E) oncogenic lesion have poor prognosis and show only a very limited response to this drug. To investigate the cause of this limited therapeutic effect in BRAF(V600E) mutant colon cancer, Prahallad et al. (2012) performed an RNA interference-based genetic screen in human cells to search for kinases whose knockdown synergizes with BRAF(V600E) inhibition. They reported that blockade of the epidermal growth factor receptor (EGFR; 131550) shows strong synergy with BRAF(V600E) inhibition. Prahallad et al. (2012) found in multiple BRAF(V600E) mutant colon cancers that inhibition of EGFR by the antibody drug cetuximab or the small-molecule drugs gefitinib or erlotinib is strongly synergistic with BRAF(V600E) inhibition, both in vitro and in vivo. Mechanistically, Prahallad et al. (2012) found that BRAF(V600E) inhibition causes a rapid feedback activation of EGFR, which supports continued proliferation in the presence of BRAF(V600E) inhibition. Melanoma cells express low levels of EGFR and are therefore not subject to this feedback activation. Consistent with this, Prahallad et al. (2012) found that ectopic expression of EGFR in melanoma cells is sufficient to cause resistance to PLX4032. Prahallad et al. (2012) concluded that BRAF(V600E) mutant colon cancers (approximately 8 to 10% of all colon cancers) might benefit from combination therapy consisting of BRAF and EGFR inhibitors.","Gala et al. (2014) identified the BRAF V600E mutation in 18 of 19 sessile serrated adenomas from 19 unrelated patients with sessile serrated polyposis cancer syndrome (SSPCS; 617108).","Papillary Thyroid Carcinoma","Kimura et al. (2003) identified the V600E mutation in 28 (35.8%) of 78 papillary thyroid cancers (PTC; see 188550); it was not found in any of the other types of differentiated follicular neoplasms arising from the same cell type (0 of 46). RET (see 164761)/PTC mutations and RAS (see 190020) mutations were each identified in 16.4% of PTCs, but there was no overlap in the 3 mutations. Kimura et al. (2003) concluded that thyroid cell transformation to papillary cancer takes place through constitutive activation of effectors along the RET/PTC-RAS-BRAF signaling pathway.","Xing et al. (2004) studied various thyroid tumor types for the most common BRAF mutation, 1799T-A, by DNA sequencing. They found a high and similar frequency (45%) of the 1799T-A mutation in 2 geographically distinct papillary thyroid cancer patient populations, 1 composed of sporadic cases from North America, and the other from Kiev, Ukraine, that included individuals who were exposed to the Chernobyl nuclear accident. In contrast, Xing et al. (2004) found BRAF mutations in only 20% of anaplastic thyroid cancers and in no medullary thyroid cancers or benign thyroid hyperplasia. They also confirmed previous reports that the BRAF 1799T-A mutation did not occur in benign thyroid adenomas or follicular thyroid cancers. They concluded that frequent occurrence of BRAF mutation is associated with PTC, irrespective of geographic origin, and is apparently not a radiation-susceptible mutation.","Nikiforova et al. (2003) analyzed 320 thyroid tumors and 6 anaplastic carcinoma cell lines and detected BRAF mutations in 45 papillary carcinomas (38%), 2 poorly differentiated carcinomas (13%), 3 (10%) anaplastic carcinomas (10%), and 5 thyroid anaplastic carcinoma cell lines (83%) but not in follicular, Hurthle cell, and medullary carcinomas, follicular and Hurthle cell adenomas, or benign hyperplastic nodules. All mutations involved a T-to-A transversion at nucleotide 1799. All BRAF-positive poorly differentiated and anaplastic carcinomas contained areas of preexisting papillary carcinoma, and mutation was present in both the well differentiated and dedifferentiated components. The authors concluded that BRAF mutations are restricted to papillary carcinomas and poorly differentiated and anaplastic carcinomas arising from papillary carcinomas, and that they are associated with distinct phenotypic and biologic properties of papillary carcinomas and may participate in progression to poorly differentiated and anaplastic carcinomas.","Hypothesizing that childhood thyroid carcinomas may be associated with a different prevalence of the BRAF 1799T-A mutation compared with adult cases, Kumagai et al. (2004) examined 31 cases of Japanese childhood thyroid carcinoma and an additional 48 cases of PTC from Ukraine, all of whom were less than 17 years of age at the time of the Chernobyl accident. The BRAF 1799T-A mutation was found in only 1 of 31 Japanese cases (3.4%) and in none of the 15 Ukrainian cases operated on before the age of 15 years, although it was found in 8 of 33 Ukrainian young adult cases (24.2%). Kumagai et al. (2004) concluded that the BRAF 1799T-A mutation is uncommon in childhood thyroid carcinomas.","Puxeddu et al. (2004) found the V600E substitution in 24 of 60 PTCs (40%) but in none of 6 follicular adenomas, 5 follicular carcinomas, or 1 anaplastic carcinoma. Nine of the 60 PTCs (15%) presented expression of a RET/PTC rearrangement. A genetico-clinical association analysis showed a statistically significant correlation between BRAF mutation and development of PTCs of the classic papillary histotype (P = 0.038). No link could be detected between expression of BRAF V600E and age at diagnosis, gender, dimension, local invasiveness of the primary cancer, presence of lymph node metastases, tumor stage, or multifocality of the disease. The authors concluded that these data clearly confirmed that BRAF V600E was the most common genetic alteration found to that time in adult sporadic PTCs, that it is unique for this thyroid cancer histotype, and that it might drive the development of PTCs of the classic papillary subtype.","Xing et al. (2004) demonstrated detection of the 1799T-A mutation on thyroid cytologic specimens from fine needle aspiration biopsy (FNAB). Prospective analysis showed that 50% of the nodules that proved to be PTCs on surgical histopathology were correctly diagnosed by BRAF mutation analysis on FNAB specimens; there were no false positive findings.","Xing et al. (2005) studied the relationships between the BRAF V600E mutation and clinicopathologic outcomes, including recurrence, in 219 PTC patients. The authors concluded that in patients with PTC, BRAF mutation is associated with poorer clinicopathologic outcomes and independently predicts recurrence. Therefore, BRAF mutation may be a useful molecular marker to assist in risk stratification for patients with PTC.","In a series of 52 classic PTCs, Porra et al. (2005) found that low SLC5A8 (608044) expression was highly significantly associated with the presence of the BRAF 1799T-A mutation. SLC5A8 expression was selectively downregulated (40-fold) in PTCs of classical form; methylation-specific PCR analyses showed that SLC5A8 was methylated in 90% of classic PTCs and in about 20% of other PTCs. Porra et al. (2005) concluded that their data identified a relationship between the methylation-associated silencing of the tumor-suppressor gene SLC5A8 and the 1799T-A point mutation of the BRAF gene in the classic PTC subtype of thyroid carcinomas.","Vasko et al. (2005) studied the relationship between the BRAF 1799T-A mutation and lymph node metastasis of PTC by examining the mutation in both the primary tumors and their paired lymph node metastases. Their findings indicated that the high prevalence of BRAF mutation in lymph node-metastasized PTC tissues from BRAF mutation-positive primary tumors and the possible de novo formation of BRAF mutation in lymph node-metastasized PTC were consistent with a role of BRAF mutation in facilitating the metastasis and progression of PTC in lymph nodes.","In a patient with congenital hypothyroidism and long-standing goiter due to mutation in the thyroglobulin gene (see TG, 188540; and TDH3, 274700), who was also found to have multifocal follicular carcinoma of the thyroid, Hishinuma et al. (2005) identified somatic heterozygosity for the V600E mutation in the BRAF gene in the cancerous thyroid tissue.","Liu et al. (2007) used BRAF siRNA to transfect stably several BRAF mutation-harboring PTC cell lines, isolated clones with stable suppression of BRAF, and assessed their ability to proliferate, transform, and grow xenograft tumors in nude mice. They found that the V600E mutation not only initiates PTC but also maintains the proliferation, transformation, and tumorigenicity of PTC cells harboring the BRAF mutation, and that the growth of tumors derived from such cells continues to depend on the V600E mutation.","Jo et al. (2006) found that of 161 PTC patients, 102 (63.4%) had the BRAF V600E mutation and that these patients had significantly larger tumor sizes and significantly higher expression of vascular endothelial growth factor (VEGF; 192240) compared to patients without this mutation. The level of VEGF expression was closely correlated with tumor size, extrathyroidal invasion, and stage. Jo et al. (2006) concluded that the relatively high levels of VEGF expression may be related to poorer clinical outcomes and recurrences in BRAF V600E(+) PTC.","Durante et al. (2007) found that the BRAF V600E mutation in PTCs is associated with reduced expression of key genes involved in iodine metabolism. They noted that this effect may alter the effectiveness of diagnostic and/or therapeutic use of radioiodine in BRAF-mutation PTCs.","Lupi et al. (2007) found a BRAF mutation in 219 of 500 cases (43.8%) of PTC. The most common BRAF mutation, V600E, was found in 214 cases (42.8%). BRAF V600E was associated with extrathyroidal invasion (p less than 0.0001), multicentricity (p = 0.0026), presence of nodal metastases (p = 0.0009), class III versus classes I and II (p less than 0.00000006), and absence of tumor capsule (p less than 0.0001), in particular, in follicular- and micro-PTC variants. By multivariate analysis, the absence of tumor capsule remained the only parameter associated (p = 0.0005) with the BRAF V600E mutation. The authors concluded that the BRAF V600E mutation is associated with high-risk PTC and, in particular, in follicular variant with invasive tumor growth.","Flaherty et al. (2010) reported complete or partial regression of V600E-associated papillary thyroid cancer in 3 patients treated with an inhibitor (PLX4032) specific to the V600E mutation.","Nonseminomatous Germ Cell Tumors","In 3 (9%) of 32 nonseminomatous germ cell tumors (see 273300) with a mixture of embryonal carcinoma, yolk sac tumor, choriocarcinoma, and mature teratoma, Sommerer et al. (2005) identified the activating 1796T-A mutation in the BRAF gene; the mutation was present within the embryonic carcinoma component.","Astrocytoma","Pfister et al. (2008) identified a somatic V600E mutation in 4 (6%) of 66 pediatric low-grade astrocytomas (see 137800). Thirty (45%) of the 66 tumors had a copy number gain spanning the BRAF locus, indicating a novel mechanism of MAPK (176948) pathway activation in these tumors.","Role in Neurodegeneration","Mass et al. (2017) hypothesized that a somatic BRAF(V600E) mutation in the erythromyeloid lineage may cause neurodegeneration. Mass et al. (2017) showed that mosaic expression of BRAF(V600E) in mouse erythromyeloid progenitors results in clonal expansion of tissue-resident macrophages and a severe late-onset neurodegenerative disorder. This is associated with accumulation of ERK-activated amoeboid microglia in mice, and is also observed in human patients with histiocytoses. In the mouse model, neurobehavioral signs, astrogliosis, deposition of amyloid precursor protein, synaptic loss, and neuronal death were driven by ERK-activated microglia and were preventable by BRAF inhibition. Mass et al. (2017) suggested that the results identified the fetal precursors of tissue-resident macrophages as a potential cell of origin for histiocytoses and demonstrated that a somatic mutation in the erythromyeloid progenitor lineage in mice can drive late-onset neurodegeneration.","Variant Function","Brady et al. (2014) showed that decreasing the levels of CTR1 (603085), or mutations in MEK1 (176872) that disrupt copper binding, decreased BRAF(V600E)-driven signaling and tumorigenesis in mice and human cell settings. Conversely, a MEK1-MEK5 (602520) chimera that phosphorylated ERK1/2 independently of copper or an active ERK2 restored the tumor growth of murine cells lacking Ctr1. Copper chelators used in the treatment of Wilson disease (277900) decreased tumor growth of human or murine cells that were either transformed by BRAF(V600E) or engineered to be resistant to BRAF inhibition. Brady et al. (2014) concluded that copper chelation therapy could be repurposed to treat cancers containing the BRAF(V600E) mutation.","Rapino et al. (2018) showed in humans that the enzymes that catalyze modifications of wobble uridine-34 (U34) tRNA are key players of the protein synthesis rewiring that is induced by the transformation driven by the BRAF V600E oncogene and by resistance to targeted therapy in melanoma. Rapino et al. (2018) showed that BRAF V600E-expressing melanoma cells are dependent on U34 enzymes for survival, and that concurrent inhibition of MAPK signaling and ELP3 (612722) or CTU1 (612694) and/or CTU2 (617057) synergizes to kill melanoma cells. Activation of the PI3K signaling pathway, one of the most common mechanisms of acquired resistance to MAPK therapeutic agents, markedly increases the expression of U34 enzymes. Mechanistically, U34 enzymes promote glycolysis in melanoma cells through the direct, codon-dependent, regulation of the translation of HIF1A (603348) mRNA and the maintenance of high levels of HIF1-alpha protein. Therefore, the acquired resistance to anti-BRAF therapy is associated with high levels of U34 enzymes and HIF1-alpha. Rapino et al. (2018) concluded that U34 enzymes promote the survival and resistance to therapy of melanoma cells by regulating specific mRNA translation."],"title":"NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) AND Nongerminomatous germ cell tumor","review_date":20140904,"diseases":[{"symbols":{"medgen":"C1266158","mondo":"MONDO:0021656"},"normalized_disease":["Nongerminomatous Germ Cell Tumor"],"names":["Nongerminomatous Germ Cell Tumor","Nonseminomatous Germ Cell Tumors, Somatic","Nongerminomatous Germ Cell Tumor","Non-Seminomatous Germ-Cell Tumors"],"normalized_cancer":["Nongerminomatous germ cell tumor","NONSEMINOMATOUS GERM CELL TUMORS, SOMATIC","Germ cell tumor, nonseminomatous","Non-seminomatous germ-cell tumors"],"keyword":"Neoplasm"}],"pub_med_references":[12068308,12198537,12447372,12619120,12644542,12670889,12794760,12960123,14513361,14602780,15001635,15126572,15181070,15342696,15356022,15386408,15687339,15998781,16015629,16174717,16187918,16772349,17374713,17488796,17785355,18398503,19571295,20818844,20823850,21107320,21107323,22113612,22281684,23302800,23685455,24512911,24670642,24717435,25079330,28854169,29925953],"date_created":20130404,"variant_id":10190071404531360004,"review_description":"Pathogenic","clinical_significance":["Pathogenic"],"allele_id":29000,"accession_id":"RCV000022677"},{"submissions":[{"pub_med_references":[12068308,12198537,12447372,12619120,12644542,12670889,12794760,12960123,14513361,14602780,15001635,15126572,15181070,15342696,15356022,15386408,15687339,15998781,16015629,16174717,16187918,16772349,17374713,17488796,17785355,18398503,19571295,20818844,20823850,21107320,21107323,22113612,22281684,23302800,23685455,24512911,24670642,24717435,25079330,28854169,29925953],"submission_description":["The val600-to-glu (V600E) mutation caused by a 1799T-A transversion in the BRAF gene was previously designated VAL599GLU (1796T-A). Kumar et al. (2003) noted that an earlier version of the BRAF sequence showed a discrepancy of 3 nucleotides in exon 1; based on the corrected sequence, they proposed a change in nucleotide numbering after nucleotide 94 (the ATG codon) by +3 and a corresponding codon change of +1.","Malignant Melanoma","Davies et al. (2002) identified a 1799T-A transversion in exon 15 of the BRAF gene that leads to a val600-to-glu (V600E) substitution. This mutation accounted for 92% of BRAF mutations in malignant melanoma (see 155600). The V600E mutation is an activating mutation resulting in constitutive activation of BRAF and downstream signal transduction in the MAP kinase pathway.","To evaluate the timing of mutations in BRAF during melanocyte neoplasia, Pollock et al. (2003) carried out mutation analysis on microdissected melanoma and nevi samples. They observed mutations resulting in the V600E amino acid substitution in 41 (68%) of 60 melanoma metastases, 4 (80%) of 5 primary melanomas, and, unexpectedly, in 63 (82%) of 77 nevi. The data suggested that mutational activation of the RAS/RAF/MAPK pathway in nevi is a critical step in the initiation of melanocytic neoplasia but alone is insufficient for melanoma tumorigenesis.","Lang et al. (2003) failed to find the V600E mutation as a germline mutation in 42 cases of familial melanoma studied. Their collection of families included 15 with and 24 without detected mutations in CDKN2A (600160). They did, however, find the V600E mutation in 6 (27%) of 22 samples of secondary (metastatic) melanomas studied. Meyer et al. (2003) found no V600E mutation in 172 melanoma patients comprising 46 familial cases, 21 multiple melanoma patients, and 106 cases with at least 1 first-degree relative suffering from other cancers. They concluded, therefore, that the common somatic BRAF mutation V600E does not contribute to polygenic or familial melanoma predisposition.","Kim et al. (2003) stated that V600E, the most common of BRAF mutations, had not been identified in tumors with mutations of the KRAS gene (190070). This mutually exclusive relationship supports the hypothesis that BRAF (V600E) and KRAS mutations exert equivalent effects in tumorigenesis (Rajagopalan et al., 2002; Singer et al., 2003).","Flaherty et al. (2010) reported complete or partial regression of V600E-associated metastatic melanoma in 81% of patients treated with an inhibitor (PLX4032) specific to the V600E mutation. Among 16 patients in a dose-escalation cohort, 10 had a partial response, and 1 had a complete response. Among 32 patients in an extension cohort, 24 had a partial response, and 2 had a complete response. The estimated median progression-free survival among all patients was more than 7 months. Responses were observed at all sites of disease, including bone, liver, and small bowel. Tumor biopsy specimens from 7 patients showed markedly reduced levels of phosphorylated ERK (600997), cyclin D1 (168461), and Ki67 (MKI67; 176741) at day 15 compared to baseline, indicating inhibition of the MAP kinase pathway. Three additional patients with V600E-associated papillary thyroid also showed a partial or complete response.","Bollag et al. (2010) described the structure-guided discovery of PLX4032 (RG7204), a potent inhibitor of oncogenic BRAF kinase activity. PLX4032 was cocrystallized with a protein construct that contained the kinase domain of BRAF(V600E). In a clinical trial, patients exposed to higher plasma levels of PLX4032 experienced tumor regression; in patients with tumor regressions, pathway analysis typically showed greater than 80% inhibition of cytoplasmic ERK phosphorylation. Bollag et al. (2010) concluded that their data demonstrated that BRAF-mutant melanomas are highly dependent on BRAF kinase activity.","Patients with BRAF(V600E)-positive melanomas exhibit an initial antitumor response to the RAF kinase inhibitor PLX4032, but acquired drug resistance almost invariably develops. Johannessen et al. (2010) identified MAP3K8 (191195), encoding COT (cancer Osaka thyroid oncogene) as a MAPK pathway agonist that drives resistance to RAF inhibition in BRAF(V600E) cell lines. COT activates ERK primarily through MARK/ERK (MEK)-dependent mechanisms that do not require RAF signaling. Moreover, COT expression is associated with de novo resistance in BRAF(V600E) cultured cell lines and acquired resistance in melanoma cells and tissue obtained from relapsing patients following treatment with MEK or RAF inhibitors. Johannessen et al. (2010) further identified combinatorial MAPK pathway inhibition or targeting of COT kinase activity as possible therapeutic strategies for reducing MAPK pathway activation in this setting.","Nazarian et al. (2010) showed that acquired resistance to PLX4032, a novel class I RAF-selective inhibitor, develops by mutually exclusive PDGFRB (173410) upregulation or NRAS (164790) mutations but not through secondary mutations in BRAF(V600E). Nazarian et al. (2010) used PLX4032-resistant sublines artificially derived from BRAF (V600E)-positive melanoma cell lines and validated key findings in PLX4032-resistant tumors and tumor-matched, short-term cultures from clinical trial patients. Induction of PDGFRB RNA, protein and tyrosine phosphorylation emerged as a dominant feature of acquired PLX4032 resistance in a subset of melanoma sublines, patient-derived biopsies, and short-term cultures. PDGFRB upregulated tumor cells have low activated RAS levels and, when treated with PLX4032, do not reactivate the MAPK pathway significantly. In another subset, high levels of activated N-RAS resulting from mutations lead to significant MAPK pathway reactivation upon PLX4032 treatment. Knockdown of PDGFRB or NRAS reduced growth of the respective PLX4032-resistant subsets. Overexpression of PDGFRB or NRAS(Q61K) conferred PLX4032 resistance to PLX4032-sensitive parental cell lines. Importantly, Nazarian et al. (2010) showed that MAPK reactivation predicts MEK inhibitor sensitivity. Thus, Nazarian et al. (2010) concluded that melanomas escape BRAF(V600E) targeting not through secondary BRAF(V600E) mutations but via receptor tyrosine kinase (RTK)-mediated activation of alternative survival pathway(s) or activated RAS-mediated reactivation of the MAPK pathway, suggesting additional therapeutic strategies.","Poulikakos et al. (2011) identified a novel resistance mechanism for melanomas with BRAF(V600E) treated with RAF inhibitors. The authors found that a subset of cells resistant to vemurafenib (PLX4032, RG7204) express a 61-kD variant form of BRAF(V600E), p61BRAF(V600E), that lacks exons 4 through 8, a region that encompasses the RAS-binding domain. p61BRAF(V600E) showed enhanced dimerization in cells with low levels of RAS activation, as compared to full-length BRAF(V600E). In cells in which p61BRAF(V600E) was expressed endogenously or ectopically, ERK signaling was resistant to the RAF inhibitor. Moreover, a mutation that abolished the dimerization of p61BRAF(V600E) restored its sensitivity to vemurafenib. Finally, Poulikakos et al. (2011) identified BRAF(V600E) splicing variants lacking the RAS-binding domain in the tumors of 6 of 19 patients with acquired resistance to vemurafenib. Poulikakos et al. (2011) concluded that their data supported the model that inhibition of ERK signaling by RAF inhibitors is dependent on levels of RAS-GTP too low to support RAF dimerization and identified a novel mechanism of acquired resistance in patients: expression of splicing isoforms of BRAF(V600E) that dimerize in a RAS-independent manner.","Thakur et al. (2013) investigated the cause and consequences of vemurafenib resistance using 2 independently-derived primary human melanoma xenograft models in which drug resistance is selected by continuous vemurafenib administration. In one of these models, resistant tumors showed continued dependency on BRAF(V600E)-MEK-ERK signaling owing to elevated BRAF(V600E) expression. Thakur et al. (2013) showed that vemurafenib-resistant melanomas become drug-dependent for their continued proliferation, such that cessation of drug administration leads to regression of established drug-resistant tumors. Thakur et al. (2013) further demonstrated that a discontinuous dosing strategy, which exploits the fitness disadvantage displayed by drug-resistant cells in the absence of the drug, forestalls the onset of lethal drug-resistant disease. Thakur et al. (2013) concluded that their data highlighted the concept that drug-resistant cells may also display drug dependency, such that altered dosing may prevent the emergence of lethal drug resistance. These observations may contribute to sustaining the durability of vemurafenib response with the ultimate goal of curative therapy for the subset of melanoma patients with BRAF mutations.","Using metabolic profiling and functional perturbations, Kaplon et al. (2013) showed that the mitochondrial gatekeeper pyruvate dehydrogenase (PDH; 300502) is a crucial mediator of senescence induced by BRAF(V600E), an oncogene commonly mutated in melanoma and other cancers. BRAF(V600E)-induced senescence is accompanied by simultaneous suppression of the PDH-inhibitory enzyme pyruvate dehydrogenase kinase-1 (PDK1; 602524) and induction of the PDH-activating enzyme pyruvate dehydrogenase phosphatase-2 (PDP2; 615499). The resulting combined activation of PDH enhanced the use of pyruvate in the tricarboxylic acid cycle, causing increased respiration and redox stress. Abrogation of oncogene-induced senescence (OIS), a rate-limiting step towards oncogenic transformation, coincided with reversion of these processes. Further supporting a crucial role of PDH in OIS, enforced normalization of either PDK1 or PDP2 expression levels inhibited PDH and abrogated OIS, thereby licensing BRAF(V600E)-driven melanoma development. Finally, depletion of PDK1 eradicated melanoma subpopulations resistant to targeted BRAF inhibition, and caused regression of established melanomas.","Sun et al. (2014) showed that 6 out of 16 BRAF(V600E)-positive melanoma tumors analyzed acquired EGFR (131550) expression after the development of resistance to inhibitors of BRAF or MEK (176872). Using a chromatin regulator-focused short hairpin RNA (shRNA) library, Sun et al. (2014) found that suppression of SRY-box 10 (SOX10; 602229) in melanoma causes activation of TGF-beta (190180) signaling, thus leading to upregulation of EGFR and platelet-derived growth factor receptor-beta (PDGFRB; 173410), which confer resistance to BRAF and MEK inhibitors. Expression of EGFR in melanoma or treatment with TGF-beta results in a slow-growth phenotype with cells displaying hallmarks of oncogene-induced senescence. However, EGFR expression or exposure to TGF-beta becomes beneficial for proliferation in the presence of BRAF or MEK inhibitors. In a heterogeneous population of melanoma cells that have varying levels of SOX10 suppression, cells with low SOX10 and consequently high EGFR expression are rapidly enriched in the presence of drug treatment, but this is reversed when the treatment is discontinued. Sun et al. (2014) found evidence for SOX10 loss and/or activation of TGF-beta signaling in 4 of the 6 EGFR-positive drug-resistant melanoma patient samples. Sun et al. (2014) concluded that their findings provided a rationale for why some BRAF or MEK inhibitor-resistant melanoma patients may regain sensitivity to these drugs after a 'drug holiday' and identified patients with EGFR-positive melanoma as a group that may benefit from retreatment after a drug holiday.","Boussemart et al. (2014) demonstrated that the persistent formation of the eIF4F complex, comprising the eIF4E (133440) cap-binding protein, the eIF4G (600495) scaffolding protein, and the eIF4A (602641) RNA helicase, is associated with resistance to anti-BRAF (164757), anti-MEK, and anti-BRAF plus anti-MEK drug combinations in BRAF(V600)-mutant melanoma, colon, and thyroid cancer cell lines. Resistance to treatment and maintenance of eIF4F complex formation is associated with 1 of 3 mechanisms: reactivation of MAPK (see 176948) signaling; persistent ERK-independent phosphorylation of the inhibitory eIF4E-binding protein 4EBP1 (602223); or increased proapoptotic BMF (606266)-dependent degradation of eIF4G. The development of an in situ method to detect the eIF4E-eIF4G interactions showed that eIF4F complex formation is decreased in tumors that respond to anti-BRAF therapy and increased in resistant metastases compared to tumors before treatment. Strikingly, inhibiting the eIF4F complex, either by blocking the eIF4E-eIF4G interaction or by targeting eIF4A, synergized with inhibiting BRAF(V600) to kill the cancer cells. eIF4F appeared not only to be an indicator of both innate and acquired resistance, but also a therapeutic target. Boussemart et al. (2014) concluded that combinations of drugs targeting BRAF (and/or MEK) and eIF4F may overcome most of the resistance mechanisms in BRAF(V600)-mutant cancers.","Colorectal Carcinoma","Rajagopalan et al. (2002) identified the V600E mutation in 28 of 330 colorectal tumors (see 114500) screened for BRAF mutations. In all cases the mutation was heterozygous and occurred somatically.","Domingo et al. (2004) pointed out that the V600E hotspot mutation had been found in colorectal tumors that showed inherited mutation in a DNA mismatch repair (MMR) gene, such as MLH1 (120436) or MSH2 (609309). These mutations had been shown to occur almost exclusively in tumors located in the proximal colon and with hypermethylation of MLH1, the gene involved in the initial steps of development of these tumors; however, BRAF mutations were not detected in those cases with or presumed to have germline mutation in either MLH1 or MSH2. Domingo et al. (2004) studied mutation analysis of the BRAF hotspot as a possible low-cost effective strategy for genetic testing for hereditary nonpolyposis colorectal cancer (HNPCC; 120435). The V600E mutation was found in 82 (40%) of 206 sporadic tumors with high microsatellite instability (MSI-H) but in none of 111 tested HNPCC tumors or in 45 cases showing abnormal MSH2 immunostaining. Domingo et al. (2004) concluded that detection of the V600E mutation in a colorectal MSI-H tumor argues against the presence of germline mutation in either MLH1 or MSH2, and that screening of these MMR genes can be avoided in cases positive for V600E.","Lubomierski et al. (2005) analyzed 45 colorectal carcinomas with MSI and 37 colorectal tumors without MSI but with similar clinical characteristics and found that BRAF was mutated more often in tumors with MSI than without (27% vs 5%, p = 0.016). The most prevalent BRAF alteration, V600E, occurred only in tumors with MSI and was associated with more frequent MLH1 promoter methylation and loss of MLH1. The median age of patients with BRAF V600E was older than that of those without V600E (78 vs 49 years, p = 0.001). There were no BRAF alterations in patients with germline mutations of mismatch repair genes. Lubomierski et al. (2005) concluded that tumors with MSI caused by epigenetic MLH1 silencing have a mutational background distinct from that of tumors with genetic loss of mismatch repair, and suggested that there are 2 genetically distinct entities of microsatellite unstable tumors.","Tol et al. (2009) detected a somatic V600E mutation in 45 (8.7%) of 519 metastatic colorectal tumors. Patients with BRAF-mutated tumors had significantly shorter median progression-free and median overall survival compared to patients with wildtype BRAF tumors, regardless of the use of cetuximab. Tol et al. (2009) suggested that the BRAF mutation may be a negative prognostic factor in these patients.","Inhibition of the BRAF(V600E) oncoprotein by the small-molecule drug PLX4032 (vemurafenib) is highly effective in the treatment of melanoma. However, colon cancer patients harboring the same BRAF(V600E) oncogenic lesion have poor prognosis and show only a very limited response to this drug. To investigate the cause of this limited therapeutic effect in BRAF(V600E) mutant colon cancer, Prahallad et al. (2012) performed an RNA interference-based genetic screen in human cells to search for kinases whose knockdown synergizes with BRAF(V600E) inhibition. They reported that blockade of the epidermal growth factor receptor (EGFR; 131550) shows strong synergy with BRAF(V600E) inhibition. Prahallad et al. (2012) found in multiple BRAF(V600E) mutant colon cancers that inhibition of EGFR by the antibody drug cetuximab or the small-molecule drugs gefitinib or erlotinib is strongly synergistic with BRAF(V600E) inhibition, both in vitro and in vivo. Mechanistically, Prahallad et al. (2012) found that BRAF(V600E) inhibition causes a rapid feedback activation of EGFR, which supports continued proliferation in the presence of BRAF(V600E) inhibition. Melanoma cells express low levels of EGFR and are therefore not subject to this feedback activation. Consistent with this, Prahallad et al. (2012) found that ectopic expression of EGFR in melanoma cells is sufficient to cause resistance to PLX4032. Prahallad et al. (2012) concluded that BRAF(V600E) mutant colon cancers (approximately 8 to 10% of all colon cancers) might benefit from combination therapy consisting of BRAF and EGFR inhibitors.","Gala et al. (2014) identified the BRAF V600E mutation in 18 of 19 sessile serrated adenomas from 19 unrelated patients with sessile serrated polyposis cancer syndrome (SSPCS; 617108).","Papillary Thyroid Carcinoma","Kimura et al. (2003) identified the V600E mutation in 28 (35.8%) of 78 papillary thyroid cancers (PTC; see 188550); it was not found in any of the other types of differentiated follicular neoplasms arising from the same cell type (0 of 46). RET (see 164761)/PTC mutations and RAS (see 190020) mutations were each identified in 16.4% of PTCs, but there was no overlap in the 3 mutations. Kimura et al. (2003) concluded that thyroid cell transformation to papillary cancer takes place through constitutive activation of effectors along the RET/PTC-RAS-BRAF signaling pathway.","Xing et al. (2004) studied various thyroid tumor types for the most common BRAF mutation, 1799T-A, by DNA sequencing. They found a high and similar frequency (45%) of the 1799T-A mutation in 2 geographically distinct papillary thyroid cancer patient populations, 1 composed of sporadic cases from North America, and the other from Kiev, Ukraine, that included individuals who were exposed to the Chernobyl nuclear accident. In contrast, Xing et al. (2004) found BRAF mutations in only 20% of anaplastic thyroid cancers and in no medullary thyroid cancers or benign thyroid hyperplasia. They also confirmed previous reports that the BRAF 1799T-A mutation did not occur in benign thyroid adenomas or follicular thyroid cancers. They concluded that frequent occurrence of BRAF mutation is associated with PTC, irrespective of geographic origin, and is apparently not a radiation-susceptible mutation.","Nikiforova et al. (2003) analyzed 320 thyroid tumors and 6 anaplastic carcinoma cell lines and detected BRAF mutations in 45 papillary carcinomas (38%), 2 poorly differentiated carcinomas (13%), 3 (10%) anaplastic carcinomas (10%), and 5 thyroid anaplastic carcinoma cell lines (83%) but not in follicular, Hurthle cell, and medullary carcinomas, follicular and Hurthle cell adenomas, or benign hyperplastic nodules. All mutations involved a T-to-A transversion at nucleotide 1799. All BRAF-positive poorly differentiated and anaplastic carcinomas contained areas of preexisting papillary carcinoma, and mutation was present in both the well differentiated and dedifferentiated components. The authors concluded that BRAF mutations are restricted to papillary carcinomas and poorly differentiated and anaplastic carcinomas arising from papillary carcinomas, and that they are associated with distinct phenotypic and biologic properties of papillary carcinomas and may participate in progression to poorly differentiated and anaplastic carcinomas.","Hypothesizing that childhood thyroid carcinomas may be associated with a different prevalence of the BRAF 1799T-A mutation compared with adult cases, Kumagai et al. (2004) examined 31 cases of Japanese childhood thyroid carcinoma and an additional 48 cases of PTC from Ukraine, all of whom were less than 17 years of age at the time of the Chernobyl accident. The BRAF 1799T-A mutation was found in only 1 of 31 Japanese cases (3.4%) and in none of the 15 Ukrainian cases operated on before the age of 15 years, although it was found in 8 of 33 Ukrainian young adult cases (24.2%). Kumagai et al. (2004) concluded that the BRAF 1799T-A mutation is uncommon in childhood thyroid carcinomas.","Puxeddu et al. (2004) found the V600E substitution in 24 of 60 PTCs (40%) but in none of 6 follicular adenomas, 5 follicular carcinomas, or 1 anaplastic carcinoma. Nine of the 60 PTCs (15%) presented expression of a RET/PTC rearrangement. A genetico-clinical association analysis showed a statistically significant correlation between BRAF mutation and development of PTCs of the classic papillary histotype (P = 0.038). No link could be detected between expression of BRAF V600E and age at diagnosis, gender, dimension, local invasiveness of the primary cancer, presence of lymph node metastases, tumor stage, or multifocality of the disease. The authors concluded that these data clearly confirmed that BRAF V600E was the most common genetic alteration found to that time in adult sporadic PTCs, that it is unique for this thyroid cancer histotype, and that it might drive the development of PTCs of the classic papillary subtype.","Xing et al. (2004) demonstrated detection of the 1799T-A mutation on thyroid cytologic specimens from fine needle aspiration biopsy (FNAB). Prospective analysis showed that 50% of the nodules that proved to be PTCs on surgical histopathology were correctly diagnosed by BRAF mutation analysis on FNAB specimens; there were no false positive findings.","Xing et al. (2005) studied the relationships between the BRAF V600E mutation and clinicopathologic outcomes, including recurrence, in 219 PTC patients. The authors concluded that in patients with PTC, BRAF mutation is associated with poorer clinicopathologic outcomes and independently predicts recurrence. Therefore, BRAF mutation may be a useful molecular marker to assist in risk stratification for patients with PTC.","In a series of 52 classic PTCs, Porra et al. (2005) found that low SLC5A8 (608044) expression was highly significantly associated with the presence of the BRAF 1799T-A mutation. SLC5A8 expression was selectively downregulated (40-fold) in PTCs of classical form; methylation-specific PCR analyses showed that SLC5A8 was methylated in 90% of classic PTCs and in about 20% of other PTCs. Porra et al. (2005) concluded that their data identified a relationship between the methylation-associated silencing of the tumor-suppressor gene SLC5A8 and the 1799T-A point mutation of the BRAF gene in the classic PTC subtype of thyroid carcinomas.","Vasko et al. (2005) studied the relationship between the BRAF 1799T-A mutation and lymph node metastasis of PTC by examining the mutation in both the primary tumors and their paired lymph node metastases. Their findings indicated that the high prevalence of BRAF mutation in lymph node-metastasized PTC tissues from BRAF mutation-positive primary tumors and the possible de novo formation of BRAF mutation in lymph node-metastasized PTC were consistent with a role of BRAF mutation in facilitating the metastasis and progression of PTC in lymph nodes.","In a patient with congenital hypothyroidism and long-standing goiter due to mutation in the thyroglobulin gene (see TG, 188540; and TDH3, 274700), who was also found to have multifocal follicular carcinoma of the thyroid, Hishinuma et al. (2005) identified somatic heterozygosity for the V600E mutation in the BRAF gene in the cancerous thyroid tissue.","Liu et al. (2007) used BRAF siRNA to transfect stably several BRAF mutation-harboring PTC cell lines, isolated clones with stable suppression of BRAF, and assessed their ability to proliferate, transform, and grow xenograft tumors in nude mice. They found that the V600E mutation not only initiates PTC but also maintains the proliferation, transformation, and tumorigenicity of PTC cells harboring the BRAF mutation, and that the growth of tumors derived from such cells continues to depend on the V600E mutation.","Jo et al. (2006) found that of 161 PTC patients, 102 (63.4%) had the BRAF V600E mutation and that these patients had significantly larger tumor sizes and significantly higher expression of vascular endothelial growth factor (VEGF; 192240) compared to patients without this mutation. The level of VEGF expression was closely correlated with tumor size, extrathyroidal invasion, and stage. Jo et al. (2006) concluded that the relatively high levels of VEGF expression may be related to poorer clinical outcomes and recurrences in BRAF V600E(+) PTC.","Durante et al. (2007) found that the BRAF V600E mutation in PTCs is associated with reduced expression of key genes involved in iodine metabolism. They noted that this effect may alter the effectiveness of diagnostic and/or therapeutic use of radioiodine in BRAF-mutation PTCs.","Lupi et al. (2007) found a BRAF mutation in 219 of 500 cases (43.8%) of PTC. The most common BRAF mutation, V600E, was found in 214 cases (42.8%). BRAF V600E was associated with extrathyroidal invasion (p less than 0.0001), multicentricity (p = 0.0026), presence of nodal metastases (p = 0.0009), class III versus classes I and II (p less than 0.00000006), and absence of tumor capsule (p less than 0.0001), in particular, in follicular- and micro-PTC variants. By multivariate analysis, the absence of tumor capsule remained the only parameter associated (p = 0.0005) with the BRAF V600E mutation. The authors concluded that the BRAF V600E mutation is associated with high-risk PTC and, in particular, in follicular variant with invasive tumor growth.","Flaherty et al. (2010) reported complete or partial regression of V600E-associated papillary thyroid cancer in 3 patients treated with an inhibitor (PLX4032) specific to the V600E mutation.","Nonseminomatous Germ Cell Tumors","In 3 (9%) of 32 nonseminomatous germ cell tumors (see 273300) with a mixture of embryonal carcinoma, yolk sac tumor, choriocarcinoma, and mature teratoma, Sommerer et al. (2005) identified the activating 1796T-A mutation in the BRAF gene; the mutation was present within the embryonic carcinoma component.","Astrocytoma","Pfister et al. (2008) identified a somatic V600E mutation in 4 (6%) of 66 pediatric low-grade astrocytomas (see 137800). Thirty (45%) of the 66 tumors had a copy number gain spanning the BRAF locus, indicating a novel mechanism of MAPK (176948) pathway activation in these tumors.","Role in Neurodegeneration","Mass et al. (2017) hypothesized that a somatic BRAF(V600E) mutation in the erythromyeloid lineage may cause neurodegeneration. Mass et al. (2017) showed that mosaic expression of BRAF(V600E) in mouse erythromyeloid progenitors results in clonal expansion of tissue-resident macrophages and a severe late-onset neurodegenerative disorder. This is associated with accumulation of ERK-activated amoeboid microglia in mice, and is also observed in human patients with histiocytoses. In the mouse model, neurobehavioral signs, astrogliosis, deposition of amyloid precursor protein, synaptic loss, and neuronal death were driven by ERK-activated microglia and were preventable by BRAF inhibition. Mass et al. (2017) suggested that the results identified the fetal precursors of tissue-resident macrophages as a potential cell of origin for histiocytoses and demonstrated that a somatic mutation in the erythromyeloid progenitor lineage in mice can drive late-onset neurodegeneration.","Variant Function","Brady et al. (2014) showed that decreasing the levels of CTR1 (603085), or mutations in MEK1 (176872) that disrupt copper binding, decreased BRAF(V600E)-driven signaling and tumorigenesis in mice and human cell settings. Conversely, a MEK1-MEK5 (602520) chimera that phosphorylated ERK1/2 independently of copper or an active ERK2 restored the tumor growth of murine cells lacking Ctr1. Copper chelators used in the treatment of Wilson disease (277900) decreased tumor growth of human or murine cells that were either transformed by BRAF(V600E) or engineered to be resistant to BRAF inhibition. Brady et al. (2014) concluded that copper chelation therapy could be repurposed to treat cancers containing the BRAF(V600E) mutation.","Rapino et al. (2018) showed in humans that the enzymes that catalyze modifications of wobble uridine-34 (U34) tRNA are key players of the protein synthesis rewiring that is induced by the transformation driven by the BRAF V600E oncogene and by resistance to targeted therapy in melanoma. Rapino et al. (2018) showed that BRAF V600E-expressing melanoma cells are dependent on U34 enzymes for survival, and that concurrent inhibition of MAPK signaling and ELP3 (612722) or CTU1 (612694) and/or CTU2 (617057) synergizes to kill melanoma cells. Activation of the PI3K signaling pathway, one of the most common mechanisms of acquired resistance to MAPK therapeutic agents, markedly increases the expression of U34 enzymes. Mechanistically, U34 enzymes promote glycolysis in melanoma cells through the direct, codon-dependent, regulation of the translation of HIF1A (603348) mRNA and the maintenance of high levels of HIF1-alpha protein. Therefore, the acquired resistance to anti-BRAF therapy is associated with high levels of U34 enzymes and HIF1-alpha. Rapino et al. (2018) concluded that U34 enzymes promote the survival and resistance to therapy of melanoma cells by regulating specific mRNA translation."],"submitter_name":"OMIM","review_date":20140904,"origin":"somatic","method":"literature only","submitter_date":20220317,"diseases":[{"normalized_cancer":["ASTROCYTOMA, LOW-GRADE, SOMATIC"],"names":["Astrocytoma, Low-Grade, Somatic"]}],"review_description":"Pathogenic","date_updated":20220328,"clinical_significance":["Pathogenic"],"review_status":"no assertion criteria provided","accession_id":"SCV000035250"}],"variation_id":13961,"submission_description":["The val600-to-glu (V600E) mutation caused by a 1799T-A transversion in the BRAF gene was previously designated VAL599GLU (1796T-A). Kumar et al. (2003) noted that an earlier version of the BRAF sequence showed a discrepancy of 3 nucleotides in exon 1; based on the corrected sequence, they proposed a change in nucleotide numbering after nucleotide 94 (the ATG codon) by +3 and a corresponding codon change of +1.","Malignant Melanoma","Davies et al. (2002) identified a 1799T-A transversion in exon 15 of the BRAF gene that leads to a val600-to-glu (V600E) substitution. This mutation accounted for 92% of BRAF mutations in malignant melanoma (see 155600). The V600E mutation is an activating mutation resulting in constitutive activation of BRAF and downstream signal transduction in the MAP kinase pathway.","To evaluate the timing of mutations in BRAF during melanocyte neoplasia, Pollock et al. (2003) carried out mutation analysis on microdissected melanoma and nevi samples. They observed mutations resulting in the V600E amino acid substitution in 41 (68%) of 60 melanoma metastases, 4 (80%) of 5 primary melanomas, and, unexpectedly, in 63 (82%) of 77 nevi. The data suggested that mutational activation of the RAS/RAF/MAPK pathway in nevi is a critical step in the initiation of melanocytic neoplasia but alone is insufficient for melanoma tumorigenesis.","Lang et al. (2003) failed to find the V600E mutation as a germline mutation in 42 cases of familial melanoma studied. Their collection of families included 15 with and 24 without detected mutations in CDKN2A (600160). They did, however, find the V600E mutation in 6 (27%) of 22 samples of secondary (metastatic) melanomas studied. Meyer et al. (2003) found no V600E mutation in 172 melanoma patients comprising 46 familial cases, 21 multiple melanoma patients, and 106 cases with at least 1 first-degree relative suffering from other cancers. They concluded, therefore, that the common somatic BRAF mutation V600E does not contribute to polygenic or familial melanoma predisposition.","Kim et al. (2003) stated that V600E, the most common of BRAF mutations, had not been identified in tumors with mutations of the KRAS gene (190070). This mutually exclusive relationship supports the hypothesis that BRAF (V600E) and KRAS mutations exert equivalent effects in tumorigenesis (Rajagopalan et al., 2002; Singer et al., 2003).","Flaherty et al. (2010) reported complete or partial regression of V600E-associated metastatic melanoma in 81% of patients treated with an inhibitor (PLX4032) specific to the V600E mutation. Among 16 patients in a dose-escalation cohort, 10 had a partial response, and 1 had a complete response. Among 32 patients in an extension cohort, 24 had a partial response, and 2 had a complete response. The estimated median progression-free survival among all patients was more than 7 months. Responses were observed at all sites of disease, including bone, liver, and small bowel. Tumor biopsy specimens from 7 patients showed markedly reduced levels of phosphorylated ERK (600997), cyclin D1 (168461), and Ki67 (MKI67; 176741) at day 15 compared to baseline, indicating inhibition of the MAP kinase pathway. Three additional patients with V600E-associated papillary thyroid also showed a partial or complete response.","Bollag et al. (2010) described the structure-guided discovery of PLX4032 (RG7204), a potent inhibitor of oncogenic BRAF kinase activity. PLX4032 was cocrystallized with a protein construct that contained the kinase domain of BRAF(V600E). In a clinical trial, patients exposed to higher plasma levels of PLX4032 experienced tumor regression; in patients with tumor regressions, pathway analysis typically showed greater than 80% inhibition of cytoplasmic ERK phosphorylation. Bollag et al. (2010) concluded that their data demonstrated that BRAF-mutant melanomas are highly dependent on BRAF kinase activity.","Patients with BRAF(V600E)-positive melanomas exhibit an initial antitumor response to the RAF kinase inhibitor PLX4032, but acquired drug resistance almost invariably develops. Johannessen et al. (2010) identified MAP3K8 (191195), encoding COT (cancer Osaka thyroid oncogene) as a MAPK pathway agonist that drives resistance to RAF inhibition in BRAF(V600E) cell lines. COT activates ERK primarily through MARK/ERK (MEK)-dependent mechanisms that do not require RAF signaling. Moreover, COT expression is associated with de novo resistance in BRAF(V600E) cultured cell lines and acquired resistance in melanoma cells and tissue obtained from relapsing patients following treatment with MEK or RAF inhibitors. Johannessen et al. (2010) further identified combinatorial MAPK pathway inhibition or targeting of COT kinase activity as possible therapeutic strategies for reducing MAPK pathway activation in this setting.","Nazarian et al. (2010) showed that acquired resistance to PLX4032, a novel class I RAF-selective inhibitor, develops by mutually exclusive PDGFRB (173410) upregulation or NRAS (164790) mutations but not through secondary mutations in BRAF(V600E). Nazarian et al. (2010) used PLX4032-resistant sublines artificially derived from BRAF (V600E)-positive melanoma cell lines and validated key findings in PLX4032-resistant tumors and tumor-matched, short-term cultures from clinical trial patients. Induction of PDGFRB RNA, protein and tyrosine phosphorylation emerged as a dominant feature of acquired PLX4032 resistance in a subset of melanoma sublines, patient-derived biopsies, and short-term cultures. PDGFRB upregulated tumor cells have low activated RAS levels and, when treated with PLX4032, do not reactivate the MAPK pathway significantly. In another subset, high levels of activated N-RAS resulting from mutations lead to significant MAPK pathway reactivation upon PLX4032 treatment. Knockdown of PDGFRB or NRAS reduced growth of the respective PLX4032-resistant subsets. Overexpression of PDGFRB or NRAS(Q61K) conferred PLX4032 resistance to PLX4032-sensitive parental cell lines. Importantly, Nazarian et al. (2010) showed that MAPK reactivation predicts MEK inhibitor sensitivity. Thus, Nazarian et al. (2010) concluded that melanomas escape BRAF(V600E) targeting not through secondary BRAF(V600E) mutations but via receptor tyrosine kinase (RTK)-mediated activation of alternative survival pathway(s) or activated RAS-mediated reactivation of the MAPK pathway, suggesting additional therapeutic strategies.","Poulikakos et al. (2011) identified a novel resistance mechanism for melanomas with BRAF(V600E) treated with RAF inhibitors. The authors found that a subset of cells resistant to vemurafenib (PLX4032, RG7204) express a 61-kD variant form of BRAF(V600E), p61BRAF(V600E), that lacks exons 4 through 8, a region that encompasses the RAS-binding domain. p61BRAF(V600E) showed enhanced dimerization in cells with low levels of RAS activation, as compared to full-length BRAF(V600E). In cells in which p61BRAF(V600E) was expressed endogenously or ectopically, ERK signaling was resistant to the RAF inhibitor. Moreover, a mutation that abolished the dimerization of p61BRAF(V600E) restored its sensitivity to vemurafenib. Finally, Poulikakos et al. (2011) identified BRAF(V600E) splicing variants lacking the RAS-binding domain in the tumors of 6 of 19 patients with acquired resistance to vemurafenib. Poulikakos et al. (2011) concluded that their data supported the model that inhibition of ERK signaling by RAF inhibitors is dependent on levels of RAS-GTP too low to support RAF dimerization and identified a novel mechanism of acquired resistance in patients: expression of splicing isoforms of BRAF(V600E) that dimerize in a RAS-independent manner.","Thakur et al. (2013) investigated the cause and consequences of vemurafenib resistance using 2 independently-derived primary human melanoma xenograft models in which drug resistance is selected by continuous vemurafenib administration. In one of these models, resistant tumors showed continued dependency on BRAF(V600E)-MEK-ERK signaling owing to elevated BRAF(V600E) expression. Thakur et al. (2013) showed that vemurafenib-resistant melanomas become drug-dependent for their continued proliferation, such that cessation of drug administration leads to regression of established drug-resistant tumors. Thakur et al. (2013) further demonstrated that a discontinuous dosing strategy, which exploits the fitness disadvantage displayed by drug-resistant cells in the absence of the drug, forestalls the onset of lethal drug-resistant disease. Thakur et al. (2013) concluded that their data highlighted the concept that drug-resistant cells may also display drug dependency, such that altered dosing may prevent the emergence of lethal drug resistance. These observations may contribute to sustaining the durability of vemurafenib response with the ultimate goal of curative therapy for the subset of melanoma patients with BRAF mutations.","Using metabolic profiling and functional perturbations, Kaplon et al. (2013) showed that the mitochondrial gatekeeper pyruvate dehydrogenase (PDH; 300502) is a crucial mediator of senescence induced by BRAF(V600E), an oncogene commonly mutated in melanoma and other cancers. BRAF(V600E)-induced senescence is accompanied by simultaneous suppression of the PDH-inhibitory enzyme pyruvate dehydrogenase kinase-1 (PDK1; 602524) and induction of the PDH-activating enzyme pyruvate dehydrogenase phosphatase-2 (PDP2; 615499). The resulting combined activation of PDH enhanced the use of pyruvate in the tricarboxylic acid cycle, causing increased respiration and redox stress. Abrogation of oncogene-induced senescence (OIS), a rate-limiting step towards oncogenic transformation, coincided with reversion of these processes. Further supporting a crucial role of PDH in OIS, enforced normalization of either PDK1 or PDP2 expression levels inhibited PDH and abrogated OIS, thereby licensing BRAF(V600E)-driven melanoma development. Finally, depletion of PDK1 eradicated melanoma subpopulations resistant to targeted BRAF inhibition, and caused regression of established melanomas.","Sun et al. (2014) showed that 6 out of 16 BRAF(V600E)-positive melanoma tumors analyzed acquired EGFR (131550) expression after the development of resistance to inhibitors of BRAF or MEK (176872). Using a chromatin regulator-focused short hairpin RNA (shRNA) library, Sun et al. (2014) found that suppression of SRY-box 10 (SOX10; 602229) in melanoma causes activation of TGF-beta (190180) signaling, thus leading to upregulation of EGFR and platelet-derived growth factor receptor-beta (PDGFRB; 173410), which confer resistance to BRAF and MEK inhibitors. Expression of EGFR in melanoma or treatment with TGF-beta results in a slow-growth phenotype with cells displaying hallmarks of oncogene-induced senescence. However, EGFR expression or exposure to TGF-beta becomes beneficial for proliferation in the presence of BRAF or MEK inhibitors. In a heterogeneous population of melanoma cells that have varying levels of SOX10 suppression, cells with low SOX10 and consequently high EGFR expression are rapidly enriched in the presence of drug treatment, but this is reversed when the treatment is discontinued. Sun et al. (2014) found evidence for SOX10 loss and/or activation of TGF-beta signaling in 4 of the 6 EGFR-positive drug-resistant melanoma patient samples. Sun et al. (2014) concluded that their findings provided a rationale for why some BRAF or MEK inhibitor-resistant melanoma patients may regain sensitivity to these drugs after a 'drug holiday' and identified patients with EGFR-positive melanoma as a group that may benefit from retreatment after a drug holiday.","Boussemart et al. (2014) demonstrated that the persistent formation of the eIF4F complex, comprising the eIF4E (133440) cap-binding protein, the eIF4G (600495) scaffolding protein, and the eIF4A (602641) RNA helicase, is associated with resistance to anti-BRAF (164757), anti-MEK, and anti-BRAF plus anti-MEK drug combinations in BRAF(V600)-mutant melanoma, colon, and thyroid cancer cell lines. Resistance to treatment and maintenance of eIF4F complex formation is associated with 1 of 3 mechanisms: reactivation of MAPK (see 176948) signaling; persistent ERK-independent phosphorylation of the inhibitory eIF4E-binding protein 4EBP1 (602223); or increased proapoptotic BMF (606266)-dependent degradation of eIF4G. The development of an in situ method to detect the eIF4E-eIF4G interactions showed that eIF4F complex formation is decreased in tumors that respond to anti-BRAF therapy and increased in resistant metastases compared to tumors before treatment. Strikingly, inhibiting the eIF4F complex, either by blocking the eIF4E-eIF4G interaction or by targeting eIF4A, synergized with inhibiting BRAF(V600) to kill the cancer cells. eIF4F appeared not only to be an indicator of both innate and acquired resistance, but also a therapeutic target. Boussemart et al. (2014) concluded that combinations of drugs targeting BRAF (and/or MEK) and eIF4F may overcome most of the resistance mechanisms in BRAF(V600)-mutant cancers.","Colorectal Carcinoma","Rajagopalan et al. (2002) identified the V600E mutation in 28 of 330 colorectal tumors (see 114500) screened for BRAF mutations. In all cases the mutation was heterozygous and occurred somatically.","Domingo et al. (2004) pointed out that the V600E hotspot mutation had been found in colorectal tumors that showed inherited mutation in a DNA mismatch repair (MMR) gene, such as MLH1 (120436) or MSH2 (609309). These mutations had been shown to occur almost exclusively in tumors located in the proximal colon and with hypermethylation of MLH1, the gene involved in the initial steps of development of these tumors; however, BRAF mutations were not detected in those cases with or presumed to have germline mutation in either MLH1 or MSH2. Domingo et al. (2004) studied mutation analysis of the BRAF hotspot as a possible low-cost effective strategy for genetic testing for hereditary nonpolyposis colorectal cancer (HNPCC; 120435). The V600E mutation was found in 82 (40%) of 206 sporadic tumors with high microsatellite instability (MSI-H) but in none of 111 tested HNPCC tumors or in 45 cases showing abnormal MSH2 immunostaining. Domingo et al. (2004) concluded that detection of the V600E mutation in a colorectal MSI-H tumor argues against the presence of germline mutation in either MLH1 or MSH2, and that screening of these MMR genes can be avoided in cases positive for V600E.","Lubomierski et al. (2005) analyzed 45 colorectal carcinomas with MSI and 37 colorectal tumors without MSI but with similar clinical characteristics and found that BRAF was mutated more often in tumors with MSI than without (27% vs 5%, p = 0.016). The most prevalent BRAF alteration, V600E, occurred only in tumors with MSI and was associated with more frequent MLH1 promoter methylation and loss of MLH1. The median age of patients with BRAF V600E was older than that of those without V600E (78 vs 49 years, p = 0.001). There were no BRAF alterations in patients with germline mutations of mismatch repair genes. Lubomierski et al. (2005) concluded that tumors with MSI caused by epigenetic MLH1 silencing have a mutational background distinct from that of tumors with genetic loss of mismatch repair, and suggested that there are 2 genetically distinct entities of microsatellite unstable tumors.","Tol et al. (2009) detected a somatic V600E mutation in 45 (8.7%) of 519 metastatic colorectal tumors. Patients with BRAF-mutated tumors had significantly shorter median progression-free and median overall survival compared to patients with wildtype BRAF tumors, regardless of the use of cetuximab. Tol et al. (2009) suggested that the BRAF mutation may be a negative prognostic factor in these patients.","Inhibition of the BRAF(V600E) oncoprotein by the small-molecule drug PLX4032 (vemurafenib) is highly effective in the treatment of melanoma. However, colon cancer patients harboring the same BRAF(V600E) oncogenic lesion have poor prognosis and show only a very limited response to this drug. To investigate the cause of this limited therapeutic effect in BRAF(V600E) mutant colon cancer, Prahallad et al. (2012) performed an RNA interference-based genetic screen in human cells to search for kinases whose knockdown synergizes with BRAF(V600E) inhibition. They reported that blockade of the epidermal growth factor receptor (EGFR; 131550) shows strong synergy with BRAF(V600E) inhibition. Prahallad et al. (2012) found in multiple BRAF(V600E) mutant colon cancers that inhibition of EGFR by the antibody drug cetuximab or the small-molecule drugs gefitinib or erlotinib is strongly synergistic with BRAF(V600E) inhibition, both in vitro and in vivo. Mechanistically, Prahallad et al. (2012) found that BRAF(V600E) inhibition causes a rapid feedback activation of EGFR, which supports continued proliferation in the presence of BRAF(V600E) inhibition. Melanoma cells express low levels of EGFR and are therefore not subject to this feedback activation. Consistent with this, Prahallad et al. (2012) found that ectopic expression of EGFR in melanoma cells is sufficient to cause resistance to PLX4032. Prahallad et al. (2012) concluded that BRAF(V600E) mutant colon cancers (approximately 8 to 10% of all colon cancers) might benefit from combination therapy consisting of BRAF and EGFR inhibitors.","Gala et al. (2014) identified the BRAF V600E mutation in 18 of 19 sessile serrated adenomas from 19 unrelated patients with sessile serrated polyposis cancer syndrome (SSPCS; 617108).","Papillary Thyroid Carcinoma","Kimura et al. (2003) identified the V600E mutation in 28 (35.8%) of 78 papillary thyroid cancers (PTC; see 188550); it was not found in any of the other types of differentiated follicular neoplasms arising from the same cell type (0 of 46). RET (see 164761)/PTC mutations and RAS (see 190020) mutations were each identified in 16.4% of PTCs, but there was no overlap in the 3 mutations. Kimura et al. (2003) concluded that thyroid cell transformation to papillary cancer takes place through constitutive activation of effectors along the RET/PTC-RAS-BRAF signaling pathway.","Xing et al. (2004) studied various thyroid tumor types for the most common BRAF mutation, 1799T-A, by DNA sequencing. They found a high and similar frequency (45%) of the 1799T-A mutation in 2 geographically distinct papillary thyroid cancer patient populations, 1 composed of sporadic cases from North America, and the other from Kiev, Ukraine, that included individuals who were exposed to the Chernobyl nuclear accident. In contrast, Xing et al. (2004) found BRAF mutations in only 20% of anaplastic thyroid cancers and in no medullary thyroid cancers or benign thyroid hyperplasia. They also confirmed previous reports that the BRAF 1799T-A mutation did not occur in benign thyroid adenomas or follicular thyroid cancers. They concluded that frequent occurrence of BRAF mutation is associated with PTC, irrespective of geographic origin, and is apparently not a radiation-susceptible mutation.","Nikiforova et al. (2003) analyzed 320 thyroid tumors and 6 anaplastic carcinoma cell lines and detected BRAF mutations in 45 papillary carcinomas (38%), 2 poorly differentiated carcinomas (13%), 3 (10%) anaplastic carcinomas (10%), and 5 thyroid anaplastic carcinoma cell lines (83%) but not in follicular, Hurthle cell, and medullary carcinomas, follicular and Hurthle cell adenomas, or benign hyperplastic nodules. All mutations involved a T-to-A transversion at nucleotide 1799. All BRAF-positive poorly differentiated and anaplastic carcinomas contained areas of preexisting papillary carcinoma, and mutation was present in both the well differentiated and dedifferentiated components. The authors concluded that BRAF mutations are restricted to papillary carcinomas and poorly differentiated and anaplastic carcinomas arising from papillary carcinomas, and that they are associated with distinct phenotypic and biologic properties of papillary carcinomas and may participate in progression to poorly differentiated and anaplastic carcinomas.","Hypothesizing that childhood thyroid carcinomas may be associated with a different prevalence of the BRAF 1799T-A mutation compared with adult cases, Kumagai et al. (2004) examined 31 cases of Japanese childhood thyroid carcinoma and an additional 48 cases of PTC from Ukraine, all of whom were less than 17 years of age at the time of the Chernobyl accident. The BRAF 1799T-A mutation was found in only 1 of 31 Japanese cases (3.4%) and in none of the 15 Ukrainian cases operated on before the age of 15 years, although it was found in 8 of 33 Ukrainian young adult cases (24.2%). Kumagai et al. (2004) concluded that the BRAF 1799T-A mutation is uncommon in childhood thyroid carcinomas.","Puxeddu et al. (2004) found the V600E substitution in 24 of 60 PTCs (40%) but in none of 6 follicular adenomas, 5 follicular carcinomas, or 1 anaplastic carcinoma. Nine of the 60 PTCs (15%) presented expression of a RET/PTC rearrangement. A genetico-clinical association analysis showed a statistically significant correlation between BRAF mutation and development of PTCs of the classic papillary histotype (P = 0.038). No link could be detected between expression of BRAF V600E and age at diagnosis, gender, dimension, local invasiveness of the primary cancer, presence of lymph node metastases, tumor stage, or multifocality of the disease. The authors concluded that these data clearly confirmed that BRAF V600E was the most common genetic alteration found to that time in adult sporadic PTCs, that it is unique for this thyroid cancer histotype, and that it might drive the development of PTCs of the classic papillary subtype.","Xing et al. (2004) demonstrated detection of the 1799T-A mutation on thyroid cytologic specimens from fine needle aspiration biopsy (FNAB). Prospective analysis showed that 50% of the nodules that proved to be PTCs on surgical histopathology were correctly diagnosed by BRAF mutation analysis on FNAB specimens; there were no false positive findings.","Xing et al. (2005) studied the relationships between the BRAF V600E mutation and clinicopathologic outcomes, including recurrence, in 219 PTC patients. The authors concluded that in patients with PTC, BRAF mutation is associated with poorer clinicopathologic outcomes and independently predicts recurrence. Therefore, BRAF mutation may be a useful molecular marker to assist in risk stratification for patients with PTC.","In a series of 52 classic PTCs, Porra et al. (2005) found that low SLC5A8 (608044) expression was highly significantly associated with the presence of the BRAF 1799T-A mutation. SLC5A8 expression was selectively downregulated (40-fold) in PTCs of classical form; methylation-specific PCR analyses showed that SLC5A8 was methylated in 90% of classic PTCs and in about 20% of other PTCs. Porra et al. (2005) concluded that their data identified a relationship between the methylation-associated silencing of the tumor-suppressor gene SLC5A8 and the 1799T-A point mutation of the BRAF gene in the classic PTC subtype of thyroid carcinomas.","Vasko et al. (2005) studied the relationship between the BRAF 1799T-A mutation and lymph node metastasis of PTC by examining the mutation in both the primary tumors and their paired lymph node metastases. Their findings indicated that the high prevalence of BRAF mutation in lymph node-metastasized PTC tissues from BRAF mutation-positive primary tumors and the possible de novo formation of BRAF mutation in lymph node-metastasized PTC were consistent with a role of BRAF mutation in facilitating the metastasis and progression of PTC in lymph nodes.","In a patient with congenital hypothyroidism and long-standing goiter due to mutation in the thyroglobulin gene (see TG, 188540; and TDH3, 274700), who was also found to have multifocal follicular carcinoma of the thyroid, Hishinuma et al. (2005) identified somatic heterozygosity for the V600E mutation in the BRAF gene in the cancerous thyroid tissue.","Liu et al. (2007) used BRAF siRNA to transfect stably several BRAF mutation-harboring PTC cell lines, isolated clones with stable suppression of BRAF, and assessed their ability to proliferate, transform, and grow xenograft tumors in nude mice. They found that the V600E mutation not only initiates PTC but also maintains the proliferation, transformation, and tumorigenicity of PTC cells harboring the BRAF mutation, and that the growth of tumors derived from such cells continues to depend on the V600E mutation.","Jo et al. (2006) found that of 161 PTC patients, 102 (63.4%) had the BRAF V600E mutation and that these patients had significantly larger tumor sizes and significantly higher expression of vascular endothelial growth factor (VEGF; 192240) compared to patients without this mutation. The level of VEGF expression was closely correlated with tumor size, extrathyroidal invasion, and stage. Jo et al. (2006) concluded that the relatively high levels of VEGF expression may be related to poorer clinical outcomes and recurrences in BRAF V600E(+) PTC.","Durante et al. (2007) found that the BRAF V600E mutation in PTCs is associated with reduced expression of key genes involved in iodine metabolism. They noted that this effect may alter the effectiveness of diagnostic and/or therapeutic use of radioiodine in BRAF-mutation PTCs.","Lupi et al. (2007) found a BRAF mutation in 219 of 500 cases (43.8%) of PTC. The most common BRAF mutation, V600E, was found in 214 cases (42.8%). BRAF V600E was associated with extrathyroidal invasion (p less than 0.0001), multicentricity (p = 0.0026), presence of nodal metastases (p = 0.0009), class III versus classes I and II (p less than 0.00000006), and absence of tumor capsule (p less than 0.0001), in particular, in follicular- and micro-PTC variants. By multivariate analysis, the absence of tumor capsule remained the only parameter associated (p = 0.0005) with the BRAF V600E mutation. The authors concluded that the BRAF V600E mutation is associated with high-risk PTC and, in particular, in follicular variant with invasive tumor growth.","Flaherty et al. (2010) reported complete or partial regression of V600E-associated papillary thyroid cancer in 3 patients treated with an inhibitor (PLX4032) specific to the V600E mutation.","Nonseminomatous Germ Cell Tumors","In 3 (9%) of 32 nonseminomatous germ cell tumors (see 273300) with a mixture of embryonal carcinoma, yolk sac tumor, choriocarcinoma, and mature teratoma, Sommerer et al. (2005) identified the activating 1796T-A mutation in the BRAF gene; the mutation was present within the embryonic carcinoma component.","Astrocytoma","Pfister et al. (2008) identified a somatic V600E mutation in 4 (6%) of 66 pediatric low-grade astrocytomas (see 137800). Thirty (45%) of the 66 tumors had a copy number gain spanning the BRAF locus, indicating a novel mechanism of MAPK (176948) pathway activation in these tumors.","Role in Neurodegeneration","Mass et al. (2017) hypothesized that a somatic BRAF(V600E) mutation in the erythromyeloid lineage may cause neurodegeneration. Mass et al. (2017) showed that mosaic expression of BRAF(V600E) in mouse erythromyeloid progenitors results in clonal expansion of tissue-resident macrophages and a severe late-onset neurodegenerative disorder. This is associated with accumulation of ERK-activated amoeboid microglia in mice, and is also observed in human patients with histiocytoses. In the mouse model, neurobehavioral signs, astrogliosis, deposition of amyloid precursor protein, synaptic loss, and neuronal death were driven by ERK-activated microglia and were preventable by BRAF inhibition. Mass et al. (2017) suggested that the results identified the fetal precursors of tissue-resident macrophages as a potential cell of origin for histiocytoses and demonstrated that a somatic mutation in the erythromyeloid progenitor lineage in mice can drive late-onset neurodegeneration.","Variant Function","Brady et al. (2014) showed that decreasing the levels of CTR1 (603085), or mutations in MEK1 (176872) that disrupt copper binding, decreased BRAF(V600E)-driven signaling and tumorigenesis in mice and human cell settings. Conversely, a MEK1-MEK5 (602520) chimera that phosphorylated ERK1/2 independently of copper or an active ERK2 restored the tumor growth of murine cells lacking Ctr1. Copper chelators used in the treatment of Wilson disease (277900) decreased tumor growth of human or murine cells that were either transformed by BRAF(V600E) or engineered to be resistant to BRAF inhibition. Brady et al. (2014) concluded that copper chelation therapy could be repurposed to treat cancers containing the BRAF(V600E) mutation.","Rapino et al. (2018) showed in humans that the enzymes that catalyze modifications of wobble uridine-34 (U34) tRNA are key players of the protein synthesis rewiring that is induced by the transformation driven by the BRAF V600E oncogene and by resistance to targeted therapy in melanoma. Rapino et al. (2018) showed that BRAF V600E-expressing melanoma cells are dependent on U34 enzymes for survival, and that concurrent inhibition of MAPK signaling and ELP3 (612722) or CTU1 (612694) and/or CTU2 (617057) synergizes to kill melanoma cells. Activation of the PI3K signaling pathway, one of the most common mechanisms of acquired resistance to MAPK therapeutic agents, markedly increases the expression of U34 enzymes. Mechanistically, U34 enzymes promote glycolysis in melanoma cells through the direct, codon-dependent, regulation of the translation of HIF1A (603348) mRNA and the maintenance of high levels of HIF1-alpha protein. Therefore, the acquired resistance to anti-BRAF therapy is associated with high levels of U34 enzymes and HIF1-alpha. Rapino et al. (2018) concluded that U34 enzymes promote the survival and resistance to therapy of melanoma cells by regulating specific mRNA translation."],"title":"NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) AND Astrocytoma, low-grade, somatic","review_date":20140904,"diseases":[{"normalized_cancer":["Astrocytoma, low-grade, somatic"],"symbols":{"medgen":"C2674727"},"names":["Astrocytoma, Low-Grade, Somatic"]}],"pub_med_references":[12068308,12198537,12447372,12619120,12644542,12670889,12794760,12960123,14513361,14602780,15001635,15126572,15181070,15342696,15356022,15386408,15687339,15998781,16015629,16174717,16187918,16772349,17374713,17488796,17785355,18398503,19571295,20818844,20823850,21107320,21107323,22113612,22281684,23302800,23685455,24512911,24670642,24717435,25079330,28854169,29925953],"date_created":20130404,"variant_id":10190071404531360004,"review_description":"Pathogenic","clinical_significance":["Pathogenic"],"allele_id":29000,"accession_id":"RCV000014994"},{"submissions":[{"pub_med_references":[12068308,12198537,12447372,12619120,12644542,12670889,12794760,12960123,14513361,14602780,15001635,15126572,15181070,15342696,15356022,15386408,15687339,15998781,16015629,16174717,16187918,16772349,17374713,17488796,17785355,18398503,19571295,20818844,20823850,21107320,21107323,22113612,22281684,23302800,23685455,24512911,24670642,24717435,25079330,28854169,29925953],"submission_description":["The val600-to-glu (V600E) mutation caused by a 1799T-A transversion in the BRAF gene was previously designated VAL599GLU (1796T-A). Kumar et al. (2003) noted that an earlier version of the BRAF sequence showed a discrepancy of 3 nucleotides in exon 1; based on the corrected sequence, they proposed a change in nucleotide numbering after nucleotide 94 (the ATG codon) by +3 and a corresponding codon change of +1.","Malignant Melanoma","Davies et al. (2002) identified a 1799T-A transversion in exon 15 of the BRAF gene that leads to a val600-to-glu (V600E) substitution. This mutation accounted for 92% of BRAF mutations in malignant melanoma (see 155600). The V600E mutation is an activating mutation resulting in constitutive activation of BRAF and downstream signal transduction in the MAP kinase pathway.","To evaluate the timing of mutations in BRAF during melanocyte neoplasia, Pollock et al. (2003) carried out mutation analysis on microdissected melanoma and nevi samples. They observed mutations resulting in the V600E amino acid substitution in 41 (68%) of 60 melanoma metastases, 4 (80%) of 5 primary melanomas, and, unexpectedly, in 63 (82%) of 77 nevi. The data suggested that mutational activation of the RAS/RAF/MAPK pathway in nevi is a critical step in the initiation of melanocytic neoplasia but alone is insufficient for melanoma tumorigenesis.","Lang et al. (2003) failed to find the V600E mutation as a germline mutation in 42 cases of familial melanoma studied. Their collection of families included 15 with and 24 without detected mutations in CDKN2A (600160). They did, however, find the V600E mutation in 6 (27%) of 22 samples of secondary (metastatic) melanomas studied. Meyer et al. (2003) found no V600E mutation in 172 melanoma patients comprising 46 familial cases, 21 multiple melanoma patients, and 106 cases with at least 1 first-degree relative suffering from other cancers. They concluded, therefore, that the common somatic BRAF mutation V600E does not contribute to polygenic or familial melanoma predisposition.","Kim et al. (2003) stated that V600E, the most common of BRAF mutations, had not been identified in tumors with mutations of the KRAS gene (190070). This mutually exclusive relationship supports the hypothesis that BRAF (V600E) and KRAS mutations exert equivalent effects in tumorigenesis (Rajagopalan et al., 2002; Singer et al., 2003).","Flaherty et al. (2010) reported complete or partial regression of V600E-associated metastatic melanoma in 81% of patients treated with an inhibitor (PLX4032) specific to the V600E mutation. Among 16 patients in a dose-escalation cohort, 10 had a partial response, and 1 had a complete response. Among 32 patients in an extension cohort, 24 had a partial response, and 2 had a complete response. The estimated median progression-free survival among all patients was more than 7 months. Responses were observed at all sites of disease, including bone, liver, and small bowel. Tumor biopsy specimens from 7 patients showed markedly reduced levels of phosphorylated ERK (600997), cyclin D1 (168461), and Ki67 (MKI67; 176741) at day 15 compared to baseline, indicating inhibition of the MAP kinase pathway. Three additional patients with V600E-associated papillary thyroid also showed a partial or complete response.","Bollag et al. (2010) described the structure-guided discovery of PLX4032 (RG7204), a potent inhibitor of oncogenic BRAF kinase activity. PLX4032 was cocrystallized with a protein construct that contained the kinase domain of BRAF(V600E). In a clinical trial, patients exposed to higher plasma levels of PLX4032 experienced tumor regression; in patients with tumor regressions, pathway analysis typically showed greater than 80% inhibition of cytoplasmic ERK phosphorylation. Bollag et al. (2010) concluded that their data demonstrated that BRAF-mutant melanomas are highly dependent on BRAF kinase activity.","Patients with BRAF(V600E)-positive melanomas exhibit an initial antitumor response to the RAF kinase inhibitor PLX4032, but acquired drug resistance almost invariably develops. Johannessen et al. (2010) identified MAP3K8 (191195), encoding COT (cancer Osaka thyroid oncogene) as a MAPK pathway agonist that drives resistance to RAF inhibition in BRAF(V600E) cell lines. COT activates ERK primarily through MARK/ERK (MEK)-dependent mechanisms that do not require RAF signaling. Moreover, COT expression is associated with de novo resistance in BRAF(V600E) cultured cell lines and acquired resistance in melanoma cells and tissue obtained from relapsing patients following treatment with MEK or RAF inhibitors. Johannessen et al. (2010) further identified combinatorial MAPK pathway inhibition or targeting of COT kinase activity as possible therapeutic strategies for reducing MAPK pathway activation in this setting.","Nazarian et al. (2010) showed that acquired resistance to PLX4032, a novel class I RAF-selective inhibitor, develops by mutually exclusive PDGFRB (173410) upregulation or NRAS (164790) mutations but not through secondary mutations in BRAF(V600E). Nazarian et al. (2010) used PLX4032-resistant sublines artificially derived from BRAF (V600E)-positive melanoma cell lines and validated key findings in PLX4032-resistant tumors and tumor-matched, short-term cultures from clinical trial patients. Induction of PDGFRB RNA, protein and tyrosine phosphorylation emerged as a dominant feature of acquired PLX4032 resistance in a subset of melanoma sublines, patient-derived biopsies, and short-term cultures. PDGFRB upregulated tumor cells have low activated RAS levels and, when treated with PLX4032, do not reactivate the MAPK pathway significantly. In another subset, high levels of activated N-RAS resulting from mutations lead to significant MAPK pathway reactivation upon PLX4032 treatment. Knockdown of PDGFRB or NRAS reduced growth of the respective PLX4032-resistant subsets. Overexpression of PDGFRB or NRAS(Q61K) conferred PLX4032 resistance to PLX4032-sensitive parental cell lines. Importantly, Nazarian et al. (2010) showed that MAPK reactivation predicts MEK inhibitor sensitivity. Thus, Nazarian et al. (2010) concluded that melanomas escape BRAF(V600E) targeting not through secondary BRAF(V600E) mutations but via receptor tyrosine kinase (RTK)-mediated activation of alternative survival pathway(s) or activated RAS-mediated reactivation of the MAPK pathway, suggesting additional therapeutic strategies.","Poulikakos et al. (2011) identified a novel resistance mechanism for melanomas with BRAF(V600E) treated with RAF inhibitors. The authors found that a subset of cells resistant to vemurafenib (PLX4032, RG7204) express a 61-kD variant form of BRAF(V600E), p61BRAF(V600E), that lacks exons 4 through 8, a region that encompasses the RAS-binding domain. p61BRAF(V600E) showed enhanced dimerization in cells with low levels of RAS activation, as compared to full-length BRAF(V600E). In cells in which p61BRAF(V600E) was expressed endogenously or ectopically, ERK signaling was resistant to the RAF inhibitor. Moreover, a mutation that abolished the dimerization of p61BRAF(V600E) restored its sensitivity to vemurafenib. Finally, Poulikakos et al. (2011) identified BRAF(V600E) splicing variants lacking the RAS-binding domain in the tumors of 6 of 19 patients with acquired resistance to vemurafenib. Poulikakos et al. (2011) concluded that their data supported the model that inhibition of ERK signaling by RAF inhibitors is dependent on levels of RAS-GTP too low to support RAF dimerization and identified a novel mechanism of acquired resistance in patients: expression of splicing isoforms of BRAF(V600E) that dimerize in a RAS-independent manner.","Thakur et al. (2013) investigated the cause and consequences of vemurafenib resistance using 2 independently-derived primary human melanoma xenograft models in which drug resistance is selected by continuous vemurafenib administration. In one of these models, resistant tumors showed continued dependency on BRAF(V600E)-MEK-ERK signaling owing to elevated BRAF(V600E) expression. Thakur et al. (2013) showed that vemurafenib-resistant melanomas become drug-dependent for their continued proliferation, such that cessation of drug administration leads to regression of established drug-resistant tumors. Thakur et al. (2013) further demonstrated that a discontinuous dosing strategy, which exploits the fitness disadvantage displayed by drug-resistant cells in the absence of the drug, forestalls the onset of lethal drug-resistant disease. Thakur et al. (2013) concluded that their data highlighted the concept that drug-resistant cells may also display drug dependency, such that altered dosing may prevent the emergence of lethal drug resistance. These observations may contribute to sustaining the durability of vemurafenib response with the ultimate goal of curative therapy for the subset of melanoma patients with BRAF mutations.","Using metabolic profiling and functional perturbations, Kaplon et al. (2013) showed that the mitochondrial gatekeeper pyruvate dehydrogenase (PDH; 300502) is a crucial mediator of senescence induced by BRAF(V600E), an oncogene commonly mutated in melanoma and other cancers. BRAF(V600E)-induced senescence is accompanied by simultaneous suppression of the PDH-inhibitory enzyme pyruvate dehydrogenase kinase-1 (PDK1; 602524) and induction of the PDH-activating enzyme pyruvate dehydrogenase phosphatase-2 (PDP2; 615499). The resulting combined activation of PDH enhanced the use of pyruvate in the tricarboxylic acid cycle, causing increased respiration and redox stress. Abrogation of oncogene-induced senescence (OIS), a rate-limiting step towards oncogenic transformation, coincided with reversion of these processes. Further supporting a crucial role of PDH in OIS, enforced normalization of either PDK1 or PDP2 expression levels inhibited PDH and abrogated OIS, thereby licensing BRAF(V600E)-driven melanoma development. Finally, depletion of PDK1 eradicated melanoma subpopulations resistant to targeted BRAF inhibition, and caused regression of established melanomas.","Sun et al. (2014) showed that 6 out of 16 BRAF(V600E)-positive melanoma tumors analyzed acquired EGFR (131550) expression after the development of resistance to inhibitors of BRAF or MEK (176872). Using a chromatin regulator-focused short hairpin RNA (shRNA) library, Sun et al. (2014) found that suppression of SRY-box 10 (SOX10; 602229) in melanoma causes activation of TGF-beta (190180) signaling, thus leading to upregulation of EGFR and platelet-derived growth factor receptor-beta (PDGFRB; 173410), which confer resistance to BRAF and MEK inhibitors. Expression of EGFR in melanoma or treatment with TGF-beta results in a slow-growth phenotype with cells displaying hallmarks of oncogene-induced senescence. However, EGFR expression or exposure to TGF-beta becomes beneficial for proliferation in the presence of BRAF or MEK inhibitors. In a heterogeneous population of melanoma cells that have varying levels of SOX10 suppression, cells with low SOX10 and consequently high EGFR expression are rapidly enriched in the presence of drug treatment, but this is reversed when the treatment is discontinued. Sun et al. (2014) found evidence for SOX10 loss and/or activation of TGF-beta signaling in 4 of the 6 EGFR-positive drug-resistant melanoma patient samples. Sun et al. (2014) concluded that their findings provided a rationale for why some BRAF or MEK inhibitor-resistant melanoma patients may regain sensitivity to these drugs after a 'drug holiday' and identified patients with EGFR-positive melanoma as a group that may benefit from retreatment after a drug holiday.","Boussemart et al. (2014) demonstrated that the persistent formation of the eIF4F complex, comprising the eIF4E (133440) cap-binding protein, the eIF4G (600495) scaffolding protein, and the eIF4A (602641) RNA helicase, is associated with resistance to anti-BRAF (164757), anti-MEK, and anti-BRAF plus anti-MEK drug combinations in BRAF(V600)-mutant melanoma, colon, and thyroid cancer cell lines. Resistance to treatment and maintenance of eIF4F complex formation is associated with 1 of 3 mechanisms: reactivation of MAPK (see 176948) signaling; persistent ERK-independent phosphorylation of the inhibitory eIF4E-binding protein 4EBP1 (602223); or increased proapoptotic BMF (606266)-dependent degradation of eIF4G. The development of an in situ method to detect the eIF4E-eIF4G interactions showed that eIF4F complex formation is decreased in tumors that respond to anti-BRAF therapy and increased in resistant metastases compared to tumors before treatment. Strikingly, inhibiting the eIF4F complex, either by blocking the eIF4E-eIF4G interaction or by targeting eIF4A, synergized with inhibiting BRAF(V600) to kill the cancer cells. eIF4F appeared not only to be an indicator of both innate and acquired resistance, but also a therapeutic target. Boussemart et al. (2014) concluded that combinations of drugs targeting BRAF (and/or MEK) and eIF4F may overcome most of the resistance mechanisms in BRAF(V600)-mutant cancers.","Colorectal Carcinoma","Rajagopalan et al. (2002) identified the V600E mutation in 28 of 330 colorectal tumors (see 114500) screened for BRAF mutations. In all cases the mutation was heterozygous and occurred somatically.","Domingo et al. (2004) pointed out that the V600E hotspot mutation had been found in colorectal tumors that showed inherited mutation in a DNA mismatch repair (MMR) gene, such as MLH1 (120436) or MSH2 (609309). These mutations had been shown to occur almost exclusively in tumors located in the proximal colon and with hypermethylation of MLH1, the gene involved in the initial steps of development of these tumors; however, BRAF mutations were not detected in those cases with or presumed to have germline mutation in either MLH1 or MSH2. Domingo et al. (2004) studied mutation analysis of the BRAF hotspot as a possible low-cost effective strategy for genetic testing for hereditary nonpolyposis colorectal cancer (HNPCC; 120435). The V600E mutation was found in 82 (40%) of 206 sporadic tumors with high microsatellite instability (MSI-H) but in none of 111 tested HNPCC tumors or in 45 cases showing abnormal MSH2 immunostaining. Domingo et al. (2004) concluded that detection of the V600E mutation in a colorectal MSI-H tumor argues against the presence of germline mutation in either MLH1 or MSH2, and that screening of these MMR genes can be avoided in cases positive for V600E.","Lubomierski et al. (2005) analyzed 45 colorectal carcinomas with MSI and 37 colorectal tumors without MSI but with similar clinical characteristics and found that BRAF was mutated more often in tumors with MSI than without (27% vs 5%, p = 0.016). The most prevalent BRAF alteration, V600E, occurred only in tumors with MSI and was associated with more frequent MLH1 promoter methylation and loss of MLH1. The median age of patients with BRAF V600E was older than that of those without V600E (78 vs 49 years, p = 0.001). There were no BRAF alterations in patients with germline mutations of mismatch repair genes. Lubomierski et al. (2005) concluded that tumors with MSI caused by epigenetic MLH1 silencing have a mutational background distinct from that of tumors with genetic loss of mismatch repair, and suggested that there are 2 genetically distinct entities of microsatellite unstable tumors.","Tol et al. (2009) detected a somatic V600E mutation in 45 (8.7%) of 519 metastatic colorectal tumors. Patients with BRAF-mutated tumors had significantly shorter median progression-free and median overall survival compared to patients with wildtype BRAF tumors, regardless of the use of cetuximab. Tol et al. (2009) suggested that the BRAF mutation may be a negative prognostic factor in these patients.","Inhibition of the BRAF(V600E) oncoprotein by the small-molecule drug PLX4032 (vemurafenib) is highly effective in the treatment of melanoma. However, colon cancer patients harboring the same BRAF(V600E) oncogenic lesion have poor prognosis and show only a very limited response to this drug. To investigate the cause of this limited therapeutic effect in BRAF(V600E) mutant colon cancer, Prahallad et al. (2012) performed an RNA interference-based genetic screen in human cells to search for kinases whose knockdown synergizes with BRAF(V600E) inhibition. They reported that blockade of the epidermal growth factor receptor (EGFR; 131550) shows strong synergy with BRAF(V600E) inhibition. Prahallad et al. (2012) found in multiple BRAF(V600E) mutant colon cancers that inhibition of EGFR by the antibody drug cetuximab or the small-molecule drugs gefitinib or erlotinib is strongly synergistic with BRAF(V600E) inhibition, both in vitro and in vivo. Mechanistically, Prahallad et al. (2012) found that BRAF(V600E) inhibition causes a rapid feedback activation of EGFR, which supports continued proliferation in the presence of BRAF(V600E) inhibition. Melanoma cells express low levels of EGFR and are therefore not subject to this feedback activation. Consistent with this, Prahallad et al. (2012) found that ectopic expression of EGFR in melanoma cells is sufficient to cause resistance to PLX4032. Prahallad et al. (2012) concluded that BRAF(V600E) mutant colon cancers (approximately 8 to 10% of all colon cancers) might benefit from combination therapy consisting of BRAF and EGFR inhibitors.","Gala et al. (2014) identified the BRAF V600E mutation in 18 of 19 sessile serrated adenomas from 19 unrelated patients with sessile serrated polyposis cancer syndrome (SSPCS; 617108).","Papillary Thyroid Carcinoma","Kimura et al. (2003) identified the V600E mutation in 28 (35.8%) of 78 papillary thyroid cancers (PTC; see 188550); it was not found in any of the other types of differentiated follicular neoplasms arising from the same cell type (0 of 46). RET (see 164761)/PTC mutations and RAS (see 190020) mutations were each identified in 16.4% of PTCs, but there was no overlap in the 3 mutations. Kimura et al. (2003) concluded that thyroid cell transformation to papillary cancer takes place through constitutive activation of effectors along the RET/PTC-RAS-BRAF signaling pathway.","Xing et al. (2004) studied various thyroid tumor types for the most common BRAF mutation, 1799T-A, by DNA sequencing. They found a high and similar frequency (45%) of the 1799T-A mutation in 2 geographically distinct papillary thyroid cancer patient populations, 1 composed of sporadic cases from North America, and the other from Kiev, Ukraine, that included individuals who were exposed to the Chernobyl nuclear accident. In contrast, Xing et al. (2004) found BRAF mutations in only 20% of anaplastic thyroid cancers and in no medullary thyroid cancers or benign thyroid hyperplasia. They also confirmed previous reports that the BRAF 1799T-A mutation did not occur in benign thyroid adenomas or follicular thyroid cancers. They concluded that frequent occurrence of BRAF mutation is associated with PTC, irrespective of geographic origin, and is apparently not a radiation-susceptible mutation.","Nikiforova et al. (2003) analyzed 320 thyroid tumors and 6 anaplastic carcinoma cell lines and detected BRAF mutations in 45 papillary carcinomas (38%), 2 poorly differentiated carcinomas (13%), 3 (10%) anaplastic carcinomas (10%), and 5 thyroid anaplastic carcinoma cell lines (83%) but not in follicular, Hurthle cell, and medullary carcinomas, follicular and Hurthle cell adenomas, or benign hyperplastic nodules. All mutations involved a T-to-A transversion at nucleotide 1799. All BRAF-positive poorly differentiated and anaplastic carcinomas contained areas of preexisting papillary carcinoma, and mutation was present in both the well differentiated and dedifferentiated components. The authors concluded that BRAF mutations are restricted to papillary carcinomas and poorly differentiated and anaplastic carcinomas arising from papillary carcinomas, and that they are associated with distinct phenotypic and biologic properties of papillary carcinomas and may participate in progression to poorly differentiated and anaplastic carcinomas.","Hypothesizing that childhood thyroid carcinomas may be associated with a different prevalence of the BRAF 1799T-A mutation compared with adult cases, Kumagai et al. (2004) examined 31 cases of Japanese childhood thyroid carcinoma and an additional 48 cases of PTC from Ukraine, all of whom were less than 17 years of age at the time of the Chernobyl accident. The BRAF 1799T-A mutation was found in only 1 of 31 Japanese cases (3.4%) and in none of the 15 Ukrainian cases operated on before the age of 15 years, although it was found in 8 of 33 Ukrainian young adult cases (24.2%). Kumagai et al. (2004) concluded that the BRAF 1799T-A mutation is uncommon in childhood thyroid carcinomas.","Puxeddu et al. (2004) found the V600E substitution in 24 of 60 PTCs (40%) but in none of 6 follicular adenomas, 5 follicular carcinomas, or 1 anaplastic carcinoma. Nine of the 60 PTCs (15%) presented expression of a RET/PTC rearrangement. A genetico-clinical association analysis showed a statistically significant correlation between BRAF mutation and development of PTCs of the classic papillary histotype (P = 0.038). No link could be detected between expression of BRAF V600E and age at diagnosis, gender, dimension, local invasiveness of the primary cancer, presence of lymph node metastases, tumor stage, or multifocality of the disease. The authors concluded that these data clearly confirmed that BRAF V600E was the most common genetic alteration found to that time in adult sporadic PTCs, that it is unique for this thyroid cancer histotype, and that it might drive the development of PTCs of the classic papillary subtype.","Xing et al. (2004) demonstrated detection of the 1799T-A mutation on thyroid cytologic specimens from fine needle aspiration biopsy (FNAB). Prospective analysis showed that 50% of the nodules that proved to be PTCs on surgical histopathology were correctly diagnosed by BRAF mutation analysis on FNAB specimens; there were no false positive findings.","Xing et al. (2005) studied the relationships between the BRAF V600E mutation and clinicopathologic outcomes, including recurrence, in 219 PTC patients. The authors concluded that in patients with PTC, BRAF mutation is associated with poorer clinicopathologic outcomes and independently predicts recurrence. Therefore, BRAF mutation may be a useful molecular marker to assist in risk stratification for patients with PTC.","In a series of 52 classic PTCs, Porra et al. (2005) found that low SLC5A8 (608044) expression was highly significantly associated with the presence of the BRAF 1799T-A mutation. SLC5A8 expression was selectively downregulated (40-fold) in PTCs of classical form; methylation-specific PCR analyses showed that SLC5A8 was methylated in 90% of classic PTCs and in about 20% of other PTCs. Porra et al. (2005) concluded that their data identified a relationship between the methylation-associated silencing of the tumor-suppressor gene SLC5A8 and the 1799T-A point mutation of the BRAF gene in the classic PTC subtype of thyroid carcinomas.","Vasko et al. (2005) studied the relationship between the BRAF 1799T-A mutation and lymph node metastasis of PTC by examining the mutation in both the primary tumors and their paired lymph node metastases. Their findings indicated that the high prevalence of BRAF mutation in lymph node-metastasized PTC tissues from BRAF mutation-positive primary tumors and the possible de novo formation of BRAF mutation in lymph node-metastasized PTC were consistent with a role of BRAF mutation in facilitating the metastasis and progression of PTC in lymph nodes.","In a patient with congenital hypothyroidism and long-standing goiter due to mutation in the thyroglobulin gene (see TG, 188540; and TDH3, 274700), who was also found to have multifocal follicular carcinoma of the thyroid, Hishinuma et al. (2005) identified somatic heterozygosity for the V600E mutation in the BRAF gene in the cancerous thyroid tissue.","Liu et al. (2007) used BRAF siRNA to transfect stably several BRAF mutation-harboring PTC cell lines, isolated clones with stable suppression of BRAF, and assessed their ability to proliferate, transform, and grow xenograft tumors in nude mice. They found that the V600E mutation not only initiates PTC but also maintains the proliferation, transformation, and tumorigenicity of PTC cells harboring the BRAF mutation, and that the growth of tumors derived from such cells continues to depend on the V600E mutation.","Jo et al. (2006) found that of 161 PTC patients, 102 (63.4%) had the BRAF V600E mutation and that these patients had significantly larger tumor sizes and significantly higher expression of vascular endothelial growth factor (VEGF; 192240) compared to patients without this mutation. The level of VEGF expression was closely correlated with tumor size, extrathyroidal invasion, and stage. Jo et al. (2006) concluded that the relatively high levels of VEGF expression may be related to poorer clinical outcomes and recurrences in BRAF V600E(+) PTC.","Durante et al. (2007) found that the BRAF V600E mutation in PTCs is associated with reduced expression of key genes involved in iodine metabolism. They noted that this effect may alter the effectiveness of diagnostic and/or therapeutic use of radioiodine in BRAF-mutation PTCs.","Lupi et al. (2007) found a BRAF mutation in 219 of 500 cases (43.8%) of PTC. The most common BRAF mutation, V600E, was found in 214 cases (42.8%). BRAF V600E was associated with extrathyroidal invasion (p less than 0.0001), multicentricity (p = 0.0026), presence of nodal metastases (p = 0.0009), class III versus classes I and II (p less than 0.00000006), and absence of tumor capsule (p less than 0.0001), in particular, in follicular- and micro-PTC variants. By multivariate analysis, the absence of tumor capsule remained the only parameter associated (p = 0.0005) with the BRAF V600E mutation. The authors concluded that the BRAF V600E mutation is associated with high-risk PTC and, in particular, in follicular variant with invasive tumor growth.","Flaherty et al. (2010) reported complete or partial regression of V600E-associated papillary thyroid cancer in 3 patients treated with an inhibitor (PLX4032) specific to the V600E mutation.","Nonseminomatous Germ Cell Tumors","In 3 (9%) of 32 nonseminomatous germ cell tumors (see 273300) with a mixture of embryonal carcinoma, yolk sac tumor, choriocarcinoma, and mature teratoma, Sommerer et al. (2005) identified the activating 1796T-A mutation in the BRAF gene; the mutation was present within the embryonic carcinoma component.","Astrocytoma","Pfister et al. (2008) identified a somatic V600E mutation in 4 (6%) of 66 pediatric low-grade astrocytomas (see 137800). Thirty (45%) of the 66 tumors had a copy number gain spanning the BRAF locus, indicating a novel mechanism of MAPK (176948) pathway activation in these tumors.","Role in Neurodegeneration","Mass et al. (2017) hypothesized that a somatic BRAF(V600E) mutation in the erythromyeloid lineage may cause neurodegeneration. Mass et al. (2017) showed that mosaic expression of BRAF(V600E) in mouse erythromyeloid progenitors results in clonal expansion of tissue-resident macrophages and a severe late-onset neurodegenerative disorder. This is associated with accumulation of ERK-activated amoeboid microglia in mice, and is also observed in human patients with histiocytoses. In the mouse model, neurobehavioral signs, astrogliosis, deposition of amyloid precursor protein, synaptic loss, and neuronal death were driven by ERK-activated microglia and were preventable by BRAF inhibition. Mass et al. (2017) suggested that the results identified the fetal precursors of tissue-resident macrophages as a potential cell of origin for histiocytoses and demonstrated that a somatic mutation in the erythromyeloid progenitor lineage in mice can drive late-onset neurodegeneration.","Variant Function","Brady et al. (2014) showed that decreasing the levels of CTR1 (603085), or mutations in MEK1 (176872) that disrupt copper binding, decreased BRAF(V600E)-driven signaling and tumorigenesis in mice and human cell settings. Conversely, a MEK1-MEK5 (602520) chimera that phosphorylated ERK1/2 independently of copper or an active ERK2 restored the tumor growth of murine cells lacking Ctr1. Copper chelators used in the treatment of Wilson disease (277900) decreased tumor growth of human or murine cells that were either transformed by BRAF(V600E) or engineered to be resistant to BRAF inhibition. Brady et al. (2014) concluded that copper chelation therapy could be repurposed to treat cancers containing the BRAF(V600E) mutation.","Rapino et al. (2018) showed in humans that the enzymes that catalyze modifications of wobble uridine-34 (U34) tRNA are key players of the protein synthesis rewiring that is induced by the transformation driven by the BRAF V600E oncogene and by resistance to targeted therapy in melanoma. Rapino et al. (2018) showed that BRAF V600E-expressing melanoma cells are dependent on U34 enzymes for survival, and that concurrent inhibition of MAPK signaling and ELP3 (612722) or CTU1 (612694) and/or CTU2 (617057) synergizes to kill melanoma cells. Activation of the PI3K signaling pathway, one of the most common mechanisms of acquired resistance to MAPK therapeutic agents, markedly increases the expression of U34 enzymes. Mechanistically, U34 enzymes promote glycolysis in melanoma cells through the direct, codon-dependent, regulation of the translation of HIF1A (603348) mRNA and the maintenance of high levels of HIF1-alpha protein. Therefore, the acquired resistance to anti-BRAF therapy is associated with high levels of U34 enzymes and HIF1-alpha. Rapino et al. (2018) concluded that U34 enzymes promote the survival and resistance to therapy of melanoma cells by regulating specific mRNA translation."],"submitter_name":"OMIM","review_date":20140904,"origin":"somatic","method":"literature only","submitter_date":20220317,"diseases":[{"normalized_cancer":["COLORECTAL CANCER, SOMATIC"],"normalized_disease":["Colorectal Cancer"],"names":["Colorectal Cancer"]}],"review_description":"Pathogenic","date_updated":20220328,"clinical_significance":["Pathogenic"],"review_status":"no assertion criteria provided","accession_id":"SCV000035248"}],"variation_id":13961,"submission_description":["The val600-to-glu (V600E) mutation caused by a 1799T-A transversion in the BRAF gene was previously designated VAL599GLU (1796T-A). Kumar et al. (2003) noted that an earlier version of the BRAF sequence showed a discrepancy of 3 nucleotides in exon 1; based on the corrected sequence, they proposed a change in nucleotide numbering after nucleotide 94 (the ATG codon) by +3 and a corresponding codon change of +1.","Malignant Melanoma","Davies et al. (2002) identified a 1799T-A transversion in exon 15 of the BRAF gene that leads to a val600-to-glu (V600E) substitution. This mutation accounted for 92% of BRAF mutations in malignant melanoma (see 155600). The V600E mutation is an activating mutation resulting in constitutive activation of BRAF and downstream signal transduction in the MAP kinase pathway.","To evaluate the timing of mutations in BRAF during melanocyte neoplasia, Pollock et al. (2003) carried out mutation analysis on microdissected melanoma and nevi samples. They observed mutations resulting in the V600E amino acid substitution in 41 (68%) of 60 melanoma metastases, 4 (80%) of 5 primary melanomas, and, unexpectedly, in 63 (82%) of 77 nevi. The data suggested that mutational activation of the RAS/RAF/MAPK pathway in nevi is a critical step in the initiation of melanocytic neoplasia but alone is insufficient for melanoma tumorigenesis.","Lang et al. (2003) failed to find the V600E mutation as a germline mutation in 42 cases of familial melanoma studied. Their collection of families included 15 with and 24 without detected mutations in CDKN2A (600160). They did, however, find the V600E mutation in 6 (27%) of 22 samples of secondary (metastatic) melanomas studied. Meyer et al. (2003) found no V600E mutation in 172 melanoma patients comprising 46 familial cases, 21 multiple melanoma patients, and 106 cases with at least 1 first-degree relative suffering from other cancers. They concluded, therefore, that the common somatic BRAF mutation V600E does not contribute to polygenic or familial melanoma predisposition.","Kim et al. (2003) stated that V600E, the most common of BRAF mutations, had not been identified in tumors with mutations of the KRAS gene (190070). This mutually exclusive relationship supports the hypothesis that BRAF (V600E) and KRAS mutations exert equivalent effects in tumorigenesis (Rajagopalan et al., 2002; Singer et al., 2003).","Flaherty et al. (2010) reported complete or partial regression of V600E-associated metastatic melanoma in 81% of patients treated with an inhibitor (PLX4032) specific to the V600E mutation. Among 16 patients in a dose-escalation cohort, 10 had a partial response, and 1 had a complete response. Among 32 patients in an extension cohort, 24 had a partial response, and 2 had a complete response. The estimated median progression-free survival among all patients was more than 7 months. Responses were observed at all sites of disease, including bone, liver, and small bowel. Tumor biopsy specimens from 7 patients showed markedly reduced levels of phosphorylated ERK (600997), cyclin D1 (168461), and Ki67 (MKI67; 176741) at day 15 compared to baseline, indicating inhibition of the MAP kinase pathway. Three additional patients with V600E-associated papillary thyroid also showed a partial or complete response.","Bollag et al. (2010) described the structure-guided discovery of PLX4032 (RG7204), a potent inhibitor of oncogenic BRAF kinase activity. PLX4032 was cocrystallized with a protein construct that contained the kinase domain of BRAF(V600E). In a clinical trial, patients exposed to higher plasma levels of PLX4032 experienced tumor regression; in patients with tumor regressions, pathway analysis typically showed greater than 80% inhibition of cytoplasmic ERK phosphorylation. Bollag et al. (2010) concluded that their data demonstrated that BRAF-mutant melanomas are highly dependent on BRAF kinase activity.","Patients with BRAF(V600E)-positive melanomas exhibit an initial antitumor response to the RAF kinase inhibitor PLX4032, but acquired drug resistance almost invariably develops. Johannessen et al. (2010) identified MAP3K8 (191195), encoding COT (cancer Osaka thyroid oncogene) as a MAPK pathway agonist that drives resistance to RAF inhibition in BRAF(V600E) cell lines. COT activates ERK primarily through MARK/ERK (MEK)-dependent mechanisms that do not require RAF signaling. Moreover, COT expression is associated with de novo resistance in BRAF(V600E) cultured cell lines and acquired resistance in melanoma cells and tissue obtained from relapsing patients following treatment with MEK or RAF inhibitors. Johannessen et al. (2010) further identified combinatorial MAPK pathway inhibition or targeting of COT kinase activity as possible therapeutic strategies for reducing MAPK pathway activation in this setting.","Nazarian et al. (2010) showed that acquired resistance to PLX4032, a novel class I RAF-selective inhibitor, develops by mutually exclusive PDGFRB (173410) upregulation or NRAS (164790) mutations but not through secondary mutations in BRAF(V600E). Nazarian et al. (2010) used PLX4032-resistant sublines artificially derived from BRAF (V600E)-positive melanoma cell lines and validated key findings in PLX4032-resistant tumors and tumor-matched, short-term cultures from clinical trial patients. Induction of PDGFRB RNA, protein and tyrosine phosphorylation emerged as a dominant feature of acquired PLX4032 resistance in a subset of melanoma sublines, patient-derived biopsies, and short-term cultures. PDGFRB upregulated tumor cells have low activated RAS levels and, when treated with PLX4032, do not reactivate the MAPK pathway significantly. In another subset, high levels of activated N-RAS resulting from mutations lead to significant MAPK pathway reactivation upon PLX4032 treatment. Knockdown of PDGFRB or NRAS reduced growth of the respective PLX4032-resistant subsets. Overexpression of PDGFRB or NRAS(Q61K) conferred PLX4032 resistance to PLX4032-sensitive parental cell lines. Importantly, Nazarian et al. (2010) showed that MAPK reactivation predicts MEK inhibitor sensitivity. Thus, Nazarian et al. (2010) concluded that melanomas escape BRAF(V600E) targeting not through secondary BRAF(V600E) mutations but via receptor tyrosine kinase (RTK)-mediated activation of alternative survival pathway(s) or activated RAS-mediated reactivation of the MAPK pathway, suggesting additional therapeutic strategies.","Poulikakos et al. (2011) identified a novel resistance mechanism for melanomas with BRAF(V600E) treated with RAF inhibitors. The authors found that a subset of cells resistant to vemurafenib (PLX4032, RG7204) express a 61-kD variant form of BRAF(V600E), p61BRAF(V600E), that lacks exons 4 through 8, a region that encompasses the RAS-binding domain. p61BRAF(V600E) showed enhanced dimerization in cells with low levels of RAS activation, as compared to full-length BRAF(V600E). In cells in which p61BRAF(V600E) was expressed endogenously or ectopically, ERK signaling was resistant to the RAF inhibitor. Moreover, a mutation that abolished the dimerization of p61BRAF(V600E) restored its sensitivity to vemurafenib. Finally, Poulikakos et al. (2011) identified BRAF(V600E) splicing variants lacking the RAS-binding domain in the tumors of 6 of 19 patients with acquired resistance to vemurafenib. Poulikakos et al. (2011) concluded that their data supported the model that inhibition of ERK signaling by RAF inhibitors is dependent on levels of RAS-GTP too low to support RAF dimerization and identified a novel mechanism of acquired resistance in patients: expression of splicing isoforms of BRAF(V600E) that dimerize in a RAS-independent manner.","Thakur et al. (2013) investigated the cause and consequences of vemurafenib resistance using 2 independently-derived primary human melanoma xenograft models in which drug resistance is selected by continuous vemurafenib administration. In one of these models, resistant tumors showed continued dependency on BRAF(V600E)-MEK-ERK signaling owing to elevated BRAF(V600E) expression. Thakur et al. (2013) showed that vemurafenib-resistant melanomas become drug-dependent for their continued proliferation, such that cessation of drug administration leads to regression of established drug-resistant tumors. Thakur et al. (2013) further demonstrated that a discontinuous dosing strategy, which exploits the fitness disadvantage displayed by drug-resistant cells in the absence of the drug, forestalls the onset of lethal drug-resistant disease. Thakur et al. (2013) concluded that their data highlighted the concept that drug-resistant cells may also display drug dependency, such that altered dosing may prevent the emergence of lethal drug resistance. These observations may contribute to sustaining the durability of vemurafenib response with the ultimate goal of curative therapy for the subset of melanoma patients with BRAF mutations.","Using metabolic profiling and functional perturbations, Kaplon et al. (2013) showed that the mitochondrial gatekeeper pyruvate dehydrogenase (PDH; 300502) is a crucial mediator of senescence induced by BRAF(V600E), an oncogene commonly mutated in melanoma and other cancers. BRAF(V600E)-induced senescence is accompanied by simultaneous suppression of the PDH-inhibitory enzyme pyruvate dehydrogenase kinase-1 (PDK1; 602524) and induction of the PDH-activating enzyme pyruvate dehydrogenase phosphatase-2 (PDP2; 615499). The resulting combined activation of PDH enhanced the use of pyruvate in the tricarboxylic acid cycle, causing increased respiration and redox stress. Abrogation of oncogene-induced senescence (OIS), a rate-limiting step towards oncogenic transformation, coincided with reversion of these processes. Further supporting a crucial role of PDH in OIS, enforced normalization of either PDK1 or PDP2 expression levels inhibited PDH and abrogated OIS, thereby licensing BRAF(V600E)-driven melanoma development. Finally, depletion of PDK1 eradicated melanoma subpopulations resistant to targeted BRAF inhibition, and caused regression of established melanomas.","Sun et al. (2014) showed that 6 out of 16 BRAF(V600E)-positive melanoma tumors analyzed acquired EGFR (131550) expression after the development of resistance to inhibitors of BRAF or MEK (176872). Using a chromatin regulator-focused short hairpin RNA (shRNA) library, Sun et al. (2014) found that suppression of SRY-box 10 (SOX10; 602229) in melanoma causes activation of TGF-beta (190180) signaling, thus leading to upregulation of EGFR and platelet-derived growth factor receptor-beta (PDGFRB; 173410), which confer resistance to BRAF and MEK inhibitors. Expression of EGFR in melanoma or treatment with TGF-beta results in a slow-growth phenotype with cells displaying hallmarks of oncogene-induced senescence. However, EGFR expression or exposure to TGF-beta becomes beneficial for proliferation in the presence of BRAF or MEK inhibitors. In a heterogeneous population of melanoma cells that have varying levels of SOX10 suppression, cells with low SOX10 and consequently high EGFR expression are rapidly enriched in the presence of drug treatment, but this is reversed when the treatment is discontinued. Sun et al. (2014) found evidence for SOX10 loss and/or activation of TGF-beta signaling in 4 of the 6 EGFR-positive drug-resistant melanoma patient samples. Sun et al. (2014) concluded that their findings provided a rationale for why some BRAF or MEK inhibitor-resistant melanoma patients may regain sensitivity to these drugs after a 'drug holiday' and identified patients with EGFR-positive melanoma as a group that may benefit from retreatment after a drug holiday.","Boussemart et al. (2014) demonstrated that the persistent formation of the eIF4F complex, comprising the eIF4E (133440) cap-binding protein, the eIF4G (600495) scaffolding protein, and the eIF4A (602641) RNA helicase, is associated with resistance to anti-BRAF (164757), anti-MEK, and anti-BRAF plus anti-MEK drug combinations in BRAF(V600)-mutant melanoma, colon, and thyroid cancer cell lines. Resistance to treatment and maintenance of eIF4F complex formation is associated with 1 of 3 mechanisms: reactivation of MAPK (see 176948) signaling; persistent ERK-independent phosphorylation of the inhibitory eIF4E-binding protein 4EBP1 (602223); or increased proapoptotic BMF (606266)-dependent degradation of eIF4G. The development of an in situ method to detect the eIF4E-eIF4G interactions showed that eIF4F complex formation is decreased in tumors that respond to anti-BRAF therapy and increased in resistant metastases compared to tumors before treatment. Strikingly, inhibiting the eIF4F complex, either by blocking the eIF4E-eIF4G interaction or by targeting eIF4A, synergized with inhibiting BRAF(V600) to kill the cancer cells. eIF4F appeared not only to be an indicator of both innate and acquired resistance, but also a therapeutic target. Boussemart et al. (2014) concluded that combinations of drugs targeting BRAF (and/or MEK) and eIF4F may overcome most of the resistance mechanisms in BRAF(V600)-mutant cancers.","Colorectal Carcinoma","Rajagopalan et al. (2002) identified the V600E mutation in 28 of 330 colorectal tumors (see 114500) screened for BRAF mutations. In all cases the mutation was heterozygous and occurred somatically.","Domingo et al. (2004) pointed out that the V600E hotspot mutation had been found in colorectal tumors that showed inherited mutation in a DNA mismatch repair (MMR) gene, such as MLH1 (120436) or MSH2 (609309). These mutations had been shown to occur almost exclusively in tumors located in the proximal colon and with hypermethylation of MLH1, the gene involved in the initial steps of development of these tumors; however, BRAF mutations were not detected in those cases with or presumed to have germline mutation in either MLH1 or MSH2. Domingo et al. (2004) studied mutation analysis of the BRAF hotspot as a possible low-cost effective strategy for genetic testing for hereditary nonpolyposis colorectal cancer (HNPCC; 120435). The V600E mutation was found in 82 (40%) of 206 sporadic tumors with high microsatellite instability (MSI-H) but in none of 111 tested HNPCC tumors or in 45 cases showing abnormal MSH2 immunostaining. Domingo et al. (2004) concluded that detection of the V600E mutation in a colorectal MSI-H tumor argues against the presence of germline mutation in either MLH1 or MSH2, and that screening of these MMR genes can be avoided in cases positive for V600E.","Lubomierski et al. (2005) analyzed 45 colorectal carcinomas with MSI and 37 colorectal tumors without MSI but with similar clinical characteristics and found that BRAF was mutated more often in tumors with MSI than without (27% vs 5%, p = 0.016). The most prevalent BRAF alteration, V600E, occurred only in tumors with MSI and was associated with more frequent MLH1 promoter methylation and loss of MLH1. The median age of patients with BRAF V600E was older than that of those without V600E (78 vs 49 years, p = 0.001). There were no BRAF alterations in patients with germline mutations of mismatch repair genes. Lubomierski et al. (2005) concluded that tumors with MSI caused by epigenetic MLH1 silencing have a mutational background distinct from that of tumors with genetic loss of mismatch repair, and suggested that there are 2 genetically distinct entities of microsatellite unstable tumors.","Tol et al. (2009) detected a somatic V600E mutation in 45 (8.7%) of 519 metastatic colorectal tumors. Patients with BRAF-mutated tumors had significantly shorter median progression-free and median overall survival compared to patients with wildtype BRAF tumors, regardless of the use of cetuximab. Tol et al. (2009) suggested that the BRAF mutation may be a negative prognostic factor in these patients.","Inhibition of the BRAF(V600E) oncoprotein by the small-molecule drug PLX4032 (vemurafenib) is highly effective in the treatment of melanoma. However, colon cancer patients harboring the same BRAF(V600E) oncogenic lesion have poor prognosis and show only a very limited response to this drug. To investigate the cause of this limited therapeutic effect in BRAF(V600E) mutant colon cancer, Prahallad et al. (2012) performed an RNA interference-based genetic screen in human cells to search for kinases whose knockdown synergizes with BRAF(V600E) inhibition. They reported that blockade of the epidermal growth factor receptor (EGFR; 131550) shows strong synergy with BRAF(V600E) inhibition. Prahallad et al. (2012) found in multiple BRAF(V600E) mutant colon cancers that inhibition of EGFR by the antibody drug cetuximab or the small-molecule drugs gefitinib or erlotinib is strongly synergistic with BRAF(V600E) inhibition, both in vitro and in vivo. Mechanistically, Prahallad et al. (2012) found that BRAF(V600E) inhibition causes a rapid feedback activation of EGFR, which supports continued proliferation in the presence of BRAF(V600E) inhibition. Melanoma cells express low levels of EGFR and are therefore not subject to this feedback activation. Consistent with this, Prahallad et al. (2012) found that ectopic expression of EGFR in melanoma cells is sufficient to cause resistance to PLX4032. Prahallad et al. (2012) concluded that BRAF(V600E) mutant colon cancers (approximately 8 to 10% of all colon cancers) might benefit from combination therapy consisting of BRAF and EGFR inhibitors.","Gala et al. (2014) identified the BRAF V600E mutation in 18 of 19 sessile serrated adenomas from 19 unrelated patients with sessile serrated polyposis cancer syndrome (SSPCS; 617108).","Papillary Thyroid Carcinoma","Kimura et al. (2003) identified the V600E mutation in 28 (35.8%) of 78 papillary thyroid cancers (PTC; see 188550); it was not found in any of the other types of differentiated follicular neoplasms arising from the same cell type (0 of 46). RET (see 164761)/PTC mutations and RAS (see 190020) mutations were each identified in 16.4% of PTCs, but there was no overlap in the 3 mutations. Kimura et al. (2003) concluded that thyroid cell transformation to papillary cancer takes place through constitutive activation of effectors along the RET/PTC-RAS-BRAF signaling pathway.","Xing et al. (2004) studied various thyroid tumor types for the most common BRAF mutation, 1799T-A, by DNA sequencing. They found a high and similar frequency (45%) of the 1799T-A mutation in 2 geographically distinct papillary thyroid cancer patient populations, 1 composed of sporadic cases from North America, and the other from Kiev, Ukraine, that included individuals who were exposed to the Chernobyl nuclear accident. In contrast, Xing et al. (2004) found BRAF mutations in only 20% of anaplastic thyroid cancers and in no medullary thyroid cancers or benign thyroid hyperplasia. They also confirmed previous reports that the BRAF 1799T-A mutation did not occur in benign thyroid adenomas or follicular thyroid cancers. They concluded that frequent occurrence of BRAF mutation is associated with PTC, irrespective of geographic origin, and is apparently not a radiation-susceptible mutation.","Nikiforova et al. (2003) analyzed 320 thyroid tumors and 6 anaplastic carcinoma cell lines and detected BRAF mutations in 45 papillary carcinomas (38%), 2 poorly differentiated carcinomas (13%), 3 (10%) anaplastic carcinomas (10%), and 5 thyroid anaplastic carcinoma cell lines (83%) but not in follicular, Hurthle cell, and medullary carcinomas, follicular and Hurthle cell adenomas, or benign hyperplastic nodules. All mutations involved a T-to-A transversion at nucleotide 1799. All BRAF-positive poorly differentiated and anaplastic carcinomas contained areas of preexisting papillary carcinoma, and mutation was present in both the well differentiated and dedifferentiated components. The authors concluded that BRAF mutations are restricted to papillary carcinomas and poorly differentiated and anaplastic carcinomas arising from papillary carcinomas, and that they are associated with distinct phenotypic and biologic properties of papillary carcinomas and may participate in progression to poorly differentiated and anaplastic carcinomas.","Hypothesizing that childhood thyroid carcinomas may be associated with a different prevalence of the BRAF 1799T-A mutation compared with adult cases, Kumagai et al. (2004) examined 31 cases of Japanese childhood thyroid carcinoma and an additional 48 cases of PTC from Ukraine, all of whom were less than 17 years of age at the time of the Chernobyl accident. The BRAF 1799T-A mutation was found in only 1 of 31 Japanese cases (3.4%) and in none of the 15 Ukrainian cases operated on before the age of 15 years, although it was found in 8 of 33 Ukrainian young adult cases (24.2%). Kumagai et al. (2004) concluded that the BRAF 1799T-A mutation is uncommon in childhood thyroid carcinomas.","Puxeddu et al. (2004) found the V600E substitution in 24 of 60 PTCs (40%) but in none of 6 follicular adenomas, 5 follicular carcinomas, or 1 anaplastic carcinoma. Nine of the 60 PTCs (15%) presented expression of a RET/PTC rearrangement. A genetico-clinical association analysis showed a statistically significant correlation between BRAF mutation and development of PTCs of the classic papillary histotype (P = 0.038). No link could be detected between expression of BRAF V600E and age at diagnosis, gender, dimension, local invasiveness of the primary cancer, presence of lymph node metastases, tumor stage, or multifocality of the disease. The authors concluded that these data clearly confirmed that BRAF V600E was the most common genetic alteration found to that time in adult sporadic PTCs, that it is unique for this thyroid cancer histotype, and that it might drive the development of PTCs of the classic papillary subtype.","Xing et al. (2004) demonstrated detection of the 1799T-A mutation on thyroid cytologic specimens from fine needle aspiration biopsy (FNAB). Prospective analysis showed that 50% of the nodules that proved to be PTCs on surgical histopathology were correctly diagnosed by BRAF mutation analysis on FNAB specimens; there were no false positive findings.","Xing et al. (2005) studied the relationships between the BRAF V600E mutation and clinicopathologic outcomes, including recurrence, in 219 PTC patients. The authors concluded that in patients with PTC, BRAF mutation is associated with poorer clinicopathologic outcomes and independently predicts recurrence. Therefore, BRAF mutation may be a useful molecular marker to assist in risk stratification for patients with PTC.","In a series of 52 classic PTCs, Porra et al. (2005) found that low SLC5A8 (608044) expression was highly significantly associated with the presence of the BRAF 1799T-A mutation. SLC5A8 expression was selectively downregulated (40-fold) in PTCs of classical form; methylation-specific PCR analyses showed that SLC5A8 was methylated in 90% of classic PTCs and in about 20% of other PTCs. Porra et al. (2005) concluded that their data identified a relationship between the methylation-associated silencing of the tumor-suppressor gene SLC5A8 and the 1799T-A point mutation of the BRAF gene in the classic PTC subtype of thyroid carcinomas.","Vasko et al. (2005) studied the relationship between the BRAF 1799T-A mutation and lymph node metastasis of PTC by examining the mutation in both the primary tumors and their paired lymph node metastases. Their findings indicated that the high prevalence of BRAF mutation in lymph node-metastasized PTC tissues from BRAF mutation-positive primary tumors and the possible de novo formation of BRAF mutation in lymph node-metastasized PTC were consistent with a role of BRAF mutation in facilitating the metastasis and progression of PTC in lymph nodes.","In a patient with congenital hypothyroidism and long-standing goiter due to mutation in the thyroglobulin gene (see TG, 188540; and TDH3, 274700), who was also found to have multifocal follicular carcinoma of the thyroid, Hishinuma et al. (2005) identified somatic heterozygosity for the V600E mutation in the BRAF gene in the cancerous thyroid tissue.","Liu et al. (2007) used BRAF siRNA to transfect stably several BRAF mutation-harboring PTC cell lines, isolated clones with stable suppression of BRAF, and assessed their ability to proliferate, transform, and grow xenograft tumors in nude mice. They found that the V600E mutation not only initiates PTC but also maintains the proliferation, transformation, and tumorigenicity of PTC cells harboring the BRAF mutation, and that the growth of tumors derived from such cells continues to depend on the V600E mutation.","Jo et al. (2006) found that of 161 PTC patients, 102 (63.4%) had the BRAF V600E mutation and that these patients had significantly larger tumor sizes and significantly higher expression of vascular endothelial growth factor (VEGF; 192240) compared to patients without this mutation. The level of VEGF expression was closely correlated with tumor size, extrathyroidal invasion, and stage. Jo et al. (2006) concluded that the relatively high levels of VEGF expression may be related to poorer clinical outcomes and recurrences in BRAF V600E(+) PTC.","Durante et al. (2007) found that the BRAF V600E mutation in PTCs is associated with reduced expression of key genes involved in iodine metabolism. They noted that this effect may alter the effectiveness of diagnostic and/or therapeutic use of radioiodine in BRAF-mutation PTCs.","Lupi et al. (2007) found a BRAF mutation in 219 of 500 cases (43.8%) of PTC. The most common BRAF mutation, V600E, was found in 214 cases (42.8%). BRAF V600E was associated with extrathyroidal invasion (p less than 0.0001), multicentricity (p = 0.0026), presence of nodal metastases (p = 0.0009), class III versus classes I and II (p less than 0.00000006), and absence of tumor capsule (p less than 0.0001), in particular, in follicular- and micro-PTC variants. By multivariate analysis, the absence of tumor capsule remained the only parameter associated (p = 0.0005) with the BRAF V600E mutation. The authors concluded that the BRAF V600E mutation is associated with high-risk PTC and, in particular, in follicular variant with invasive tumor growth.","Flaherty et al. (2010) reported complete or partial regression of V600E-associated papillary thyroid cancer in 3 patients treated with an inhibitor (PLX4032) specific to the V600E mutation.","Nonseminomatous Germ Cell Tumors","In 3 (9%) of 32 nonseminomatous germ cell tumors (see 273300) with a mixture of embryonal carcinoma, yolk sac tumor, choriocarcinoma, and mature teratoma, Sommerer et al. (2005) identified the activating 1796T-A mutation in the BRAF gene; the mutation was present within the embryonic carcinoma component.","Astrocytoma","Pfister et al. (2008) identified a somatic V600E mutation in 4 (6%) of 66 pediatric low-grade astrocytomas (see 137800). Thirty (45%) of the 66 tumors had a copy number gain spanning the BRAF locus, indicating a novel mechanism of MAPK (176948) pathway activation in these tumors.","Role in Neurodegeneration","Mass et al. (2017) hypothesized that a somatic BRAF(V600E) mutation in the erythromyeloid lineage may cause neurodegeneration. Mass et al. (2017) showed that mosaic expression of BRAF(V600E) in mouse erythromyeloid progenitors results in clonal expansion of tissue-resident macrophages and a severe late-onset neurodegenerative disorder. This is associated with accumulation of ERK-activated amoeboid microglia in mice, and is also observed in human patients with histiocytoses. In the mouse model, neurobehavioral signs, astrogliosis, deposition of amyloid precursor protein, synaptic loss, and neuronal death were driven by ERK-activated microglia and were preventable by BRAF inhibition. Mass et al. (2017) suggested that the results identified the fetal precursors of tissue-resident macrophages as a potential cell of origin for histiocytoses and demonstrated that a somatic mutation in the erythromyeloid progenitor lineage in mice can drive late-onset neurodegeneration.","Variant Function","Brady et al. (2014) showed that decreasing the levels of CTR1 (603085), or mutations in MEK1 (176872) that disrupt copper binding, decreased BRAF(V600E)-driven signaling and tumorigenesis in mice and human cell settings. Conversely, a MEK1-MEK5 (602520) chimera that phosphorylated ERK1/2 independently of copper or an active ERK2 restored the tumor growth of murine cells lacking Ctr1. Copper chelators used in the treatment of Wilson disease (277900) decreased tumor growth of human or murine cells that were either transformed by BRAF(V600E) or engineered to be resistant to BRAF inhibition. Brady et al. (2014) concluded that copper chelation therapy could be repurposed to treat cancers containing the BRAF(V600E) mutation.","Rapino et al. (2018) showed in humans that the enzymes that catalyze modifications of wobble uridine-34 (U34) tRNA are key players of the protein synthesis rewiring that is induced by the transformation driven by the BRAF V600E oncogene and by resistance to targeted therapy in melanoma. Rapino et al. (2018) showed that BRAF V600E-expressing melanoma cells are dependent on U34 enzymes for survival, and that concurrent inhibition of MAPK signaling and ELP3 (612722) or CTU1 (612694) and/or CTU2 (617057) synergizes to kill melanoma cells. Activation of the PI3K signaling pathway, one of the most common mechanisms of acquired resistance to MAPK therapeutic agents, markedly increases the expression of U34 enzymes. Mechanistically, U34 enzymes promote glycolysis in melanoma cells through the direct, codon-dependent, regulation of the translation of HIF1A (603348) mRNA and the maintenance of high levels of HIF1-alpha protein. Therefore, the acquired resistance to anti-BRAF therapy is associated with high levels of U34 enzymes and HIF1-alpha. Rapino et al. (2018) concluded that U34 enzymes promote the survival and resistance to therapy of melanoma cells by regulating specific mRNA translation."],"title":"NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) AND Carcinoma of colon","review_date":20140904,"diseases":[{"pub_med":[19042984,25006736,17060676,22138009,24996433,22855150,23012255,25373533,23852704,23429431,34043773],"symbols":{"medgen":"C0699790","mondo":"MONDO:0002032"},"normalized_disease":["Malignant Colon Neoplasm"],"names":["Malignant Colon Neoplasm","Malignant Colon Neoplasm","Malignant Colon Neoplasm"],"normalized_cancer":["Bowel"],"keyword":"Hereditary cancer syndrome"}],"pub_med_references":[12068308,12198537,12447372,12619120,12644542,12670889,12794760,12960123,14513361,14602780,15001635,15126572,15181070,15342696,15356022,15386408,15687339,15998781,16015629,16174717,16187918,16772349,17374713,17488796,17785355,18398503,19571295,20818844,20823850,21107320,21107323,22113612,22281684,23302800,23685455,24512911,24670642,24717435,25079330,28854169,29925953],"date_created":20130404,"variant_id":10190071404531360004,"review_description":"Pathogenic","clinical_significance":["Pathogenic"],"allele_id":29000,"accession_id":"RCV000014992"},{"submissions":[{"submission_description":[],"submitter_name":"Clinical Genetics and Genomics, Karolinska University Hospital","review_date":20140711,"origin":"germline","method":"clinical testing","submitter_date":20201126,"diseases":[{"names":["Not Provided"]}],"review_description":"Pathogenic","date_updated":20201212,"clinical_significance":["Pathogenic"],"review_status":"criteria provided, single submitter","accession_id":"SCV001450230"},{"submission_description":[],"submitter_name":"Eurofins Ntd Llc (ga)","review_date":20131008,"origin":"germline","method":"clinical testing","submitter_date":20180919,"diseases":[{"names":["Not Provided"]}],"review_description":"Pathogenic","date_updated":20250413,"clinical_significance":["Pathogenic"],"review_status":"criteria provided, single submitter","accession_id":"SCV000112810"},{"submitter_name":"Department of Pathology and Laboratory Medicine, Sinai Health System","submission_description":[],"origin":"unknown","method":"clinical testing","submitter_date":20210331,"diseases":[{"names":["Not Provided"]}],"review_description":"Uncertain significance","date_updated":20210413,"clinical_significance":["Uncertain significance"],"review_status":"no assertion criteria provided","accession_id":"SCV001550994"},{"submitter_name":"Sylvester Comprehensive Cancer Center, University of Miami","submission_description":["BRAF V600E variant is involved in encoding cytoplasmic serine/threonine kinases within the MAPK pathway. The NCCN Guidelines state that BRAF mutations are an indicative prognostic marker with poor clinical outcome. It it recommended to do baseline genomic genotyping of the patient's primary or metastatic tumor tissue at diagnosis if the patient is stage IV. BRAF V600E is mutated in about 15% of all cancers (El-Osta et. al, 2011). Frequency of all RAF mutations is 2.2% within pancreatic cancer, where BRAF V600E is one of the more common variants, and is actionable (Hendifar et al., 2021)"],"origin":"somatic","method":"clinical testing","submitter_date":20211006,"diseases":[{"symbols":{"medgen":"CN517202"}}],"review_description":"Pathogenic","date_updated":20250803,"clinical_significance":["Pathogenic"],"review_status":"no assertion criteria provided","accession_id":"SCV001962698"}],"variation_id":13961,"submission_description":[],"title":"NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) AND not provided","review_date":20140711,"diseases":[{"symbols":{"medgen":"C3661900"},"names":["Not Provided","None Provided"]}],"date_created":20140117,"variant_id":10190071404531360004,"review_description":"Pathogenic","clinical_significance":["Pathogenic"],"allele_id":29000,"accession_id":"RCV000080903"},{"submissions":[{"submission_description":[],"submitter_name":"Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine","review_date":20090529,"origin":"somatic","method":"clinical testing","submitter_date":20190321,"diseases":[{"symbols":{"mesh":"D002289"}}],"review_description":"Pathogenic","date_updated":20150131,"clinical_significance":["Pathogenic"],"review_status":"no assertion criteria provided","accession_id":"SCV000061601"}],"variation_id":13961,"submission_description":[],"title":"NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) AND Non-small cell lung carcinoma","review_date":20090529,"diseases":[{"pub_med":[24868098,24673736,24627688,23667368,30813707],"normalized_cancer":["Non-Small Cell Lung Cancer"],"symbols":{"medgen":"C0007131","mesh":"D002289","mondo":"MONDO:0005233","human_phenotype_ontology":"HP:0030358"},"normalized_disease":["Non-Small Cell Lung Carcinoma"],"names":["Non-Small Cell Lung Carcinoma","Non-Small Cell Lung Carcinoma"],"disease_mechanism":"Other"}],"date_created":20130503,"variant_id":10190071404531360004,"review_description":"Pathogenic","clinical_significance":["Pathogenic"],"allele_id":29000,"accession_id":"RCV000037936"},{"title":"NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) AND Ganglioglioma","submissions":[{"submission_description":["Variant has Tier I (strong) clinical significance as a diagnostic inclusion criterion in ganglioglioma, based on the following evidence: 1) Documented in one or more cancer databases (e.g., St. Jude Pecan, COSMIC, CIViC, OncoKB). 2) Appears in one or more well-established professional guidelines (e.g., World Health Organization [WHO]; National Comprehensive Cancer Network [NCCN]) as providing diagnostic, prognostic, or therapeutic information. 3) Information in the literature supports potential biologic effect of variant (PMID: 17496922). 4) Diagnostic for a specific tumor type/classification according to professional guidelines (Evidence Level A; PMIDs: 34185076, 20156809, 21274720, 29880043, 32289278, 24238153)."],"submitter_name":"Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital","review_date":20241226,"origin":"somatic","method":"clinical testing","submitter_date":20251120,"diseases":[{"symbols":{"mondo":"MONDO:0016733"}}],"date_updated":20251122,"clinical_significance":[],"review_status":"criteria provided, single submitter","accession_id":"SCV007105544"}],"variation_id":13961,"submission_description":[],"diseases":[{"normalized_cancer":["Mixed cell tumors containing both neural ganglionic cells and neural glial cell components"],"symbols":{"medgen":"C0206716","mondo":"MONDO:0016733","human_phenotype_ontology":"HP:0033664"},"normalized_disease":["Ganglioglioma"],"names":["Ganglioglioma","Mixed Cell Tumors Containing Both Neural Ganglionic Cells Neural Glial Cell Components"]}],"date_created":20251122,"variant_id":10190071404531360004,"clinical_significance":[],"allele_id":29000,"accession_id":"RCV006253603"},{"title":"NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) AND Pilocytic astrocytoma","submissions":[{"submission_description":["Variant has Tier I (strong) clinical significance as a diagnostic inclusion criterion in pilocytic astrocytoma, based on the following evidence: 1) Documented in one or more cancer databases (e.g., St. Jude Pecan, COSMIC, CIViC, OncoKB). 2) Appears in one or more well-established professional guidelines (e.g., World Health Organization [WHO]; National Comprehensive Cancer Network [NCCN]) as providing diagnostic, prognostic, or therapeutic information. 3) Information in the literature supports potential biologic effect of variant (PMID: 17496922). 4) Diagnostic for a specific tumor type/classification based on well-powered studies with expert-level consensus (Evidence Level B; PMIDs: 23583981, 23817572, 32289278, 34718782)."],"submitter_name":"Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital","review_date":20241030,"origin":"somatic","method":"clinical testing","submitter_date":20251120,"diseases":[{"symbols":{"mondo":"MONDO:0016691"}}],"date_updated":20251122,"clinical_significance":[],"review_status":"criteria provided, single submitter","accession_id":"SCV007105549"}],"variation_id":13961,"submission_description":[],"diseases":[{"normalized_cancer":["Pilocytic Astrocytoma"],"symbols":{"medgen":"C0334583","mondo":"MONDO:0016691","human_phenotype_ontology":"HP:0033680"},"normalized_disease":["Pilocytic Astrocytoma"],"names":["Pilocytic Astrocytoma","Pilocytic Astrocytoma, Somatic"]}],"date_created":20251122,"variant_id":10190071404531360004,"clinical_significance":[],"allele_id":29000,"accession_id":"RCV006253599"},{"title":"NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) AND Malignant glioma","submissions":[{"submission_description":["Variant has Tier I (strong) clinical significance as a diagnostic inclusion criterion in malignant glioma, based on the following evidence: 1) Documented in one or more cancer databases (e.g., St. Jude Pecan, COSMIC, CIViC, OncoKB). 2) Appears in one or more well-established professional guidelines (e.g., World Health Organization [WHO]; National Comprehensive Cancer Network [NCCN]) as providing diagnostic, prognostic, or therapeutic information. 3) Information in the literature supports potential biologic effect of variant (PMID: 17496922). 4) Diagnostic for a specific tumor type/classification based on well-powered studies with expert-level consensus (Evidence Level B; PMIDs: 23583981, 28912153, 28966033, 25752754, 23552385, 29763623)."],"submitter_name":"Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital","review_date":20250603,"origin":"somatic","method":"clinical testing","submitter_date":20251120,"diseases":[{"symbols":{"mondo":"MONDO:0100342"}}],"date_updated":20251122,"clinical_significance":[],"review_status":"criteria provided, single submitter","accession_id":"SCV007105131"}],"variation_id":13961,"submission_description":[],"diseases":[{"normalized_cancer":["Malignant glioma"],"symbols":{"medgen":"C0555198","mondo":"MONDO:0100342"},"normalized_disease":["Malignant Glioma"],"names":["Malignant Glioma"]}],"date_created":20251122,"variant_id":10190071404531360004,"clinical_significance":[],"allele_id":29000,"accession_id":"RCV006253604"},{"title":"NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) AND Diffuse midline glioma, H3 K27M-mutant","submissions":[{"submission_description":["Variant has Tier I (strong) clinical significance as a diagnostic inclusion criterion in diffuse midline glioma, H3 K27M-mutant, based on the following evidence: 1) Documented in one or more cancer databases (e.g., St. Jude Pecan, COSMIC, CIViC, OncoKB). 2) Appears in one or more well-established professional guidelines (e.g., World Health Organization [WHO]; National Comprehensive Cancer Network [NCCN]) as providing diagnostic, prognostic, or therapeutic information. 3) Information in the literature supports potential biologic effect of variant. 4) Diagnostic for a specific tumor type/classification based on well-powered studies with expert-level consensus (Evidence Level B)."],"submitter_name":"Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital","review_date":20221226,"origin":"somatic","method":"clinical testing","submitter_date":20251120,"diseases":[{"symbols":{"mondo":"MONDO:0957196"}}],"date_updated":20251122,"clinical_significance":[],"review_status":"criteria provided, single submitter","accession_id":"SCV007105098"}],"variation_id":13961,"submission_description":[],"diseases":[{"normalized_cancer":["Diffuse Glioma"],"symbols":{"medgen":"C4289688","mondo":"MONDO:0957196"},"normalized_disease":["Diffuse Midline Glioma, H3 K27M-Mutant"],"names":["Diffuse Midline Glioma, H3 K27M-Mutant"]}],"date_created":20251122,"variant_id":10190071404531360004,"clinical_significance":[],"allele_id":29000,"accession_id":"RCV006253605"},{"title":"NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) AND Malignant peripheral nerve sheath tumor","submissions":[{"submission_description":["Variant has Tier I (strong) clinical significance as a diagnostic inclusion criterion in malignant peripheral nerve sheath tumor, based on the following evidence: 1) Documented in one or more cancer databases (e.g., St. Jude Pecan, COSMIC, CIViC, OncoKB). 2) Information in the literature supports potential biologic effect of variant. 3) Diagnostic for a specific tumor type/classification based on well-powered studies with expert-level consensus (Evidence Level B; PMIDs: 36067829, 24366910, 30099373)."],"submitter_name":"Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital","review_date":20250606,"origin":"somatic","method":"clinical testing","submitter_date":20251120,"diseases":[{"symbols":{"mondo":"MONDO:0017827"}}],"date_updated":20251122,"clinical_significance":[],"review_status":"criteria provided, single submitter","accession_id":"SCV007105134"}],"variation_id":13961,"submission_description":[],"diseases":[{"normalized_cancer":["Malignant Peripheral Nerve Sheath Tumor"],"symbols":{"medgen":"C0751690","mondo":"MONDO:0017827"},"normalized_disease":["Malignant Peripheral Nerve Sheath Tumor"],"names":["Malignant Peripheral Nerve Sheath Tumor"]}],"date_created":20251122,"variant_id":10190071404531360004,"clinical_significance":[],"allele_id":29000,"accession_id":"RCV006253606"},{"title":"NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) AND IDH-wildtype glioblastoma","submissions":[{"submission_description":["Variant has Tier I (strong) clinical significance as a diagnostic inclusion criterion in IDH-wildtype glioblastoma, based on the following evidence: 1) Documented in one or more cancer databases (e.g., St. Jude Pecan, COSMIC, CIViC, OncoKB). 2) Appears in one or more well-established professional guidelines (e.g., World Health Organization [WHO]; National Comprehensive Cancer Network [NCCN]) as providing diagnostic, prognostic, or therapeutic information. 3) Information in the literature supports potential biologic effect of variant (PMID: 17496922). 4) Diagnostic for a specific tumor type/classification based on well-powered studies with expert-level consensus (Evidence Level B; PMIDs: 28990704, 23552385, 29105198, 29532523, 24127995)."],"submitter_name":"Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital","review_date":20241119,"origin":"somatic","method":"clinical testing","submitter_date":20251120,"diseases":[{"symbols":{"mondo":"MONDO:0850335"}}],"date_updated":20251122,"clinical_significance":[],"review_status":"criteria provided, single submitter","accession_id":"SCV007105125"}],"variation_id":13961,"submission_description":[],"diseases":[{"symbols":{"medgen":"CN372125","mondo":"MONDO:0850335"},"normalized_disease":["Idh-Wildtype Glioblastoma"],"names":["Idh-Wildtype Glioblastoma"]}],"date_created":20251122,"variant_id":10190071404531360004,"clinical_significance":[],"allele_id":29000,"accession_id":"RCV006253607"},{"title":"NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) AND Diffuse leptomeningeal glioneuronal tumor","submissions":[{"submission_description":["Variant has Tier I (strong) clinical significance as a diagnostic inclusion criterion in diffuse leptomeningeal glioneuronal tumor, based on the following evidence: 1) Documented in one or more cancer databases (e.g., St. Jude Pecan, COSMIC, CIViC, OncoKB). 2) Appears in one or more well-established professional guidelines (e.g., World Health Organization [WHO]; National Comprehensive Cancer Network [NCCN]) as providing diagnostic, prognostic, or therapeutic information. 3) Information in the literature supports potential biologic effect of variant (PMID: 17496922). 4) Diagnostic for a specific tumor type/classification according to professional guidelines (Evidence Level A; PMIDs: 26994902, 32605662, 36382112)."],"submitter_name":"Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital","review_date":20231207,"origin":"somatic","method":"clinical testing","submitter_date":20251120,"diseases":[{"symbols":{"mondo":"MONDO:0858956"}}],"date_updated":20251122,"clinical_significance":[],"review_status":"criteria provided, single submitter","accession_id":"SCV007105110"}],"variation_id":13961,"submission_description":[],"diseases":[{"normalized_cancer":["Diffuse leptomeningeal glioneuronal tumor"],"symbols":{"medgen":"C4329735","mondo":"MONDO:0858956"},"normalized_disease":["Diffuse Leptomeningeal Glioneuronal Tumor"],"names":["Diffuse Leptomeningeal Glioneuronal Tumor"]}],"date_created":20251122,"variant_id":10190071404531360004,"clinical_significance":[],"allele_id":29000,"accession_id":"RCV006253608"},{"title":"NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) AND Nodular ganglioneuroblastoma","submissions":[{"submission_description":["Variant has Tier II (potential) clinical significance as a diagnostic inclusion criterion in nodular ganglioneuroblastoma, based on the following evidence: 1) Documented in one or more cancer databases (e.g., St. Jude Pecan, COSMIC, CIViC, OncoKB). 2) Information in the literature supports potential biologic effect of variant (PMID: 17496922). 3) Diagnostic significance based on multiple small studies (Evidence Level C; PMIDs: 22142829, 26121087, 34331515)."],"submitter_name":"Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital","review_date":20240320,"origin":"somatic","method":"clinical testing","submitter_date":20251120,"diseases":[{"symbols":{"mondo":"MONDO:0003325"}}],"date_updated":20251122,"clinical_significance":[],"review_status":"criteria provided, single submitter","accession_id":"SCV007105113"}],"variation_id":13961,"submission_description":[],"diseases":[{"symbols":{"medgen":"C1517445","mondo":"MONDO:0003325"},"normalized_disease":["Nodular Ganglioneuroblastoma"],"names":["Nodular Ganglioneuroblastoma"]}],"date_created":20251122,"variant_id":10190071404531360004,"clinical_significance":[],"allele_id":29000,"accession_id":"RCV006253609"},{"title":"NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) AND Polymorphous low grade neuroepithelial tumor of the young","submissions":[{"submission_description":["Variant has Tier I (strong) clinical significance as a diagnostic inclusion criterion in polymorphous low grade neuroepithelial tumor of the young, based on the following evidence: 1) Documented in one or more cancer databases (e.g., St. Jude Pecan, COSMIC, CIViC, OncoKB). 2) Appears in one or more well-established professional guidelines (e.g., World Health Organization [WHO]; National Comprehensive Cancer Network [NCCN]) as providing diagnostic, prognostic, or therapeutic information. 3) Information in the literature supports potential biologic effect of variant (PMID: 17496922). 4) Diagnostic for a specific tumor type/classification according to professional guidelines (Evidence Level A; PMIDs: 27812792, 29701169, 30926558, 31520766, 31617914)."],"submitter_name":"Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital","review_date":20240531,"origin":"somatic","method":"clinical testing","submitter_date":20251120,"diseases":[{"symbols":{"mondo":"MONDO:0858959"}}],"date_updated":20251122,"clinical_significance":[],"review_status":"criteria provided, single submitter","accession_id":"SCV007105118"}],"variation_id":13961,"submission_description":[],"diseases":[{"normalized_cancer":["Low-Grade Neuroepithelial Tumor"],"symbols":{"medgen":"C5556330","mondo":"MONDO:0858959"},"normalized_disease":["Polymorphous Low Grade Neuroepithelial Tumor The Young"],"names":["Polymorphous Low Grade Neuroepithelial Tumor The Young","Polymorphous Low Grade Neuroepithelial Tumour The Young"]}],"date_created":20251122,"variant_id":10190071404531360004,"clinical_significance":[],"allele_id":29000,"accession_id":"RCV006253610"},{"title":"NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) AND Diffuse low-grade glioma, MAPK pathway–altered","submissions":[{"submission_description":["Variant has Tier I (strong) clinical significance as a diagnostic inclusion criterion in diffuse low-grade glioma, MAPK pathway–altered, based on the following evidence: 1) Documented in one or more cancer databases (e.g., St. Jude Pecan, COSMIC, CIViC, OncoKB). 2) Appears in one or more well-established professional guidelines (e.g., World Health Organization [WHO]; National Comprehensive Cancer Network [NCCN]) as providing diagnostic, prognostic, or therapeutic information. 3) Diagnostic for a specific tumor type/classification according to professional guidelines (Evidence Level A)."],"submitter_name":"Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital","review_date":20240904,"origin":"somatic","method":"clinical testing","submitter_date":20251120,"diseases":[{"symbols":{"mondo":"MONDO:0859614"}}],"date_updated":20251122,"clinical_significance":[],"review_status":"criteria provided, single submitter","accession_id":"SCV007105121"}],"variation_id":13961,"submission_description":[],"diseases":[{"normalized_cancer":["Low-Grade Glioma, NOS"],"symbols":{"medgen":"CN372173","mondo":"MONDO:0859614"},"normalized_disease":["Diffuse Low-Grade Glioma, Mapk Pathway???Altered"],"names":["Diffuse Low-Grade Glioma, Mapk Pathway???Altered"]}],"date_created":20251122,"variant_id":10190071404531360004,"clinical_significance":[],"allele_id":29000,"accession_id":"RCV006253611"},{"title":"NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) AND Benign metanephric tumor","submissions":[{"submission_description":["Variant has Tier I (strong) clinical significance as a diagnostic inclusion criterion in benign metanephric tumor, based on the following evidence: 1) Documented in one or more cancer databases (e.g., St. Jude Pecan, COSMIC, CIViC, OncoKB). 2) Appears in one or more well-established professional guidelines (e.g., World Health Organization [WHO]; National Comprehensive Cancer Network [NCCN]) as providing diagnostic, prognostic, or therapeutic information. 3) Information in the literature supports potential biologic effect of variant (PMID: 17496922). 4) Diagnostic for a specific tumor type/classification according to professional guidelines (Evidence Level A; PMIDs: 26796506, 26014474, 27769870, 32371339)."],"submitter_name":"Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital","review_date":20250130,"origin":"somatic","method":"clinical testing","submitter_date":20251120,"diseases":[{"symbols":{"mondo":"MONDO:0018738"}}],"date_updated":20251122,"clinical_significance":[],"review_status":"criteria provided, single submitter","accession_id":"SCV007105133"}],"variation_id":13961,"submission_description":[],"diseases":[{"normalized_cancer":["Benign metanephric tumor","Benign metanephric tumour"],"symbols":{"medgen":"C5681098","mondo":"MONDO:0018738"},"normalized_disease":["Benign Metanephric Tumor"],"names":["Benign Metanephric Tumor","Benign Metanephric Tumour"]}],"date_created":20251122,"variant_id":10190071404531360004,"clinical_significance":[],"allele_id":29000,"accession_id":"RCV006253612"},{"title":"NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) AND Dysembryoplastic neuroepithelial tumor","submissions":[{"submission_description":["Variant has Tier I (strong) clinical significance as a diagnostic inclusion criterion in dysembryoplastic neuroepithelial tumor, based on the following evidence: 1) Documented in one or more cancer databases (e.g., St. Jude Pecan, COSMIC, CIViC, OncoKB). 2) Appears in one or more well-established professional guidelines (e.g., World Health Organization [WHO]; National Comprehensive Cancer Network [NCCN]) as providing diagnostic, prognostic, or therapeutic information. 3) Information in the literature supports potential biologic effect of variant (PMID: 17496922). 4) Diagnostic for a specific tumor type/classification based on well-powered studies with expert-level consensus (Evidence Level B; PMIDs: 25346165, 26810070, 23442159, 31617914, 32164789)."],"submitter_name":"Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital","review_date":20251105,"origin":"somatic","method":"clinical testing","submitter_date":20251120,"diseases":[{"symbols":{"mondo":"MONDO:0005505"}}],"date_updated":20251122,"clinical_significance":[],"review_status":"criteria provided, single submitter","accession_id":"SCV007105140"}],"variation_id":13961,"submission_description":[],"diseases":[{"normalized_cancer":["Dysembryoplastic Neuroepithelial Tumor"],"symbols":{"medgen":"C1266177","mondo":"MONDO:0005505","human_phenotype_ontology":"HP:0033703"},"normalized_disease":["Dysembryoplastic Neuroepithelial Tumor"],"names":["Dysembryoplastic Neuroepithelial Tumor"]}],"date_created":20251122,"variant_id":10190071404531360004,"clinical_significance":[],"allele_id":29000,"accession_id":"RCV006253613"},{"title":"NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) AND Pleomorphic xanthoastrocytoma","submissions":[{"submission_description":["Variant has Tier I (strong) clinical significance as a diagnostic inclusion criterion in pleomorphic xanthoastrocytoma, based on the following evidence: 1) Documented in one or more cancer databases (e.g., St. Jude Pecan, COSMIC, CIViC, OncoKB). 2) Appears in one or more well-established professional guidelines (e.g., World Health Organization [WHO]; National Comprehensive Cancer Network [NCCN]) as providing diagnostic, prognostic, or therapeutic information. 3) Information in the literature supports potential biologic effect of variant (PMIDs: 15035987, 12068308, 19251651, 26343582). 4) Diagnostic for a specific tumor type/classification according to professional guidelines (Evidence Level A; PMIDs: 21274720, 21479234, 30051528, 32619305, 32289278)."],"submitter_name":"Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital","review_date":20250512,"origin":"somatic","method":"clinical testing","submitter_date":20251120,"diseases":[{"symbols":{"mondo":"MONDO:0016690"}}],"date_updated":20251122,"clinical_significance":[],"review_status":"criteria provided, single submitter","accession_id":"SCV007105547"}],"variation_id":13961,"submission_description":[],"diseases":[{"normalized_cancer":["Pleomorphic Xanthoastrocytoma"],"symbols":{"medgen":"C0334586","mondo":"MONDO:0016690","human_phenotype_ontology":"HP:0033682"},"normalized_disease":["Pleomorphic Xanthoastrocytoma"],"names":["Pleomorphic Xanthoastrocytoma"]}],"date_created":20251122,"variant_id":10190071404531360004,"clinical_significance":[],"allele_id":29000,"accession_id":"RCV006253602"},{"title":"NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) AND Alveolar rhabdomyosarcoma","submissions":[{"submission_description":["Variant has Tier II (potential) clinical significance as a diagnostic inclusion criterion in alveolar rhabdomyosarcoma, based on the following evidence: 1) Documented in one or more cancer databases (e.g., St. Jude Pecan, COSMIC, CIViC, OncoKB). 2) Information in the literature supports potential biologic effect of variant (PMID: 17496922). 3) Diagnostic significance based on multiple small studies (Evidence Level C; 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malformation","disease_description":null,"disease_symbol":null,"disease_alt_symbol":null,"evidences":{}}],"siftscore":null,"siftprediction":null,"polyphenscore":null,"polyphenprediction":null,"evidences":{"pub_med_references":[12068308,12198537,12447372,12619120,12644542,12670889,12794760,12960123,14500344,14513361,14602780,15001635,15126572,15181070,15342696,15356022,15386408,15687339,15998781,16015629,16174717,16187918,16772349,17374713,17488796,17785355,18398503,19571295,20818844,20823850,21107320,21107323,21917714,22113612,22281684,23263490,23302800,23685455,24455489,24512911,24670642,24717435,25079330,28854169,29925953],"cosmic_study":[]},"xrefs":{"cosmicmutationid":["COSV56056643","COSV56059110"],"clinvaraccession":[]},"variant_type":"Disease","disease":"Adenomas and Adenocarcinomas","disease_symbol":null,"disease_alt_symbol":null,"bed_comments":null,"pub_med_references":[12068308,12198537,12447372,12619120,12644542,12670889,12794760,12960123,14500344,14513361,14602780,15001635,15126572,15181070,15342696,15356022,15386408,15687339,15998781,16015629,16174717,16187918,16772349,17374713,17488796,17785355,18398503,19571295,20818844,20823850,21107320,21107323,21917714,22113612,22281684,23263490,23302800,23685455,24455489,24512911,24670642,24717435,25079330,28854169,29925953]}]}],"weill_cornell_medicine_pmkb":[{"version":"08-Nov-2024","items":[{"tier":1,"definition":["BRAF V600E","BRAF codon(s) 600 any"],"interpretations":"Eighty percent of all thyroid cancers are papillary thyroid carcinomas (PTCs). BRAF is part of the mitogen-activated protein kinase (MAPK) signaling pathway and V600E is an activating mutation of BRAF. The BRAF V600E mutation has been reported in 45% of patients with papillary thyroid carcinoma. The BRAF V600E-like PTC's (BVL) and the RAS-like PTC (RL-PTC) are fundamentally different in their genomic, epigenomic, and proteomic profiles. Presence of a BRAF p.Val600Glu (V600E) mutation is highly specific for papillary thyroid carcinoma and is only rarely associated with the follicular variant PTC , other well-differentiated thyroid neoplasms or nodular goiters. The possible prognostic impact of BRAF V600E mutations in papillary carcinoma of the thyroid continues to be studied. \nFDA approved dabrafenib and trametinib administered together for the treatment of BRAF V600E mutation-positive anaplastic thyroid cancer. ","tissues":["Thyroid"],"tumour_types":["Papillary Carcinoma"],"disease_or_trait":null,"pub_med_references":[12068308,25417114,25422487],"variants":[{"definition":"BRAF V600E","type":"variantId","coding_impact":"any","variants":["10190071404531360004","10380071407533360004"],"gene_id":2273},{"aa_positions":[600],"definition":"BRAF codon(s) 600 any","type":"codon","coding_impact":"any","gene_id":2273}]},{"tier":1,"definition":["BRAF V600E","BRAF codon(s) 600 any","BRAF V600D","BRAF V600K","BRAF V600R","BRAF V600M","BRAF V600G"],"interpretations":"Presence of a BRAF c.1799T>A, p.Val600Glu (V600E) mutation in a microsatellite unstable colorectal carcinoma indicates that the tumor is probably sporadic and not associated with Lynch syndrome (HNPCC). However, if a BRAF mutation is not detected, the tumor may either be sporadic or Lynch syndrome associated. Detection of BRAF mutations may also be useful in determining patient eligibility for anti-EGFR treatment. Approximately 8--15% of colorectal cancer (CRC) tumors harbor BRAF mutations. The presence of BRAF mutation is significantly associated with right-sided colon cancers and is associated with decreased overall survival. Some studies have reported that patients with metastatic CRC (mCRC) that harbor BRAF mutations do not respond to anti-EGFR antibody agents cetuximab or panitumumab in the chemotherapy-refractory setting. BRAF V600-mutated CRCs may not be sensitive to V600E targeted TKIs.\n\nDrug: Vemurafenib + Panitumumab,\nEncorafenib + Binimetinib + Cetuximab,\nRadiation + Trametinib + Fluorouracil","tissues":["Colon","Rectum"],"tumour_types":["Adenocarcinoma"],"disease_or_trait":null,"pub_med_references":[12068308,17195912,19001320,19571295,19616446,19884556,22281684,23438367],"variants":[{"definition":"BRAF V600E","type":"variantId","coding_impact":"any","variants":["10190071404531360004","10380071407533360004"],"gene_id":2273},{"aa_positions":[600],"definition":"BRAF codon(s) 600 any","type":"codon","coding_impact":"any","gene_id":2273}]},{"tier":1,"definition":["BRAF V600E","BRAF codon(s) 600 any","BRAF V600D","BRAF V600K","BRAF V600R","BRAF V600M","BRAF V600G"],"interpretations":"B-RAF is a member of the RAF-family of kinases which plays an important role in the RAS-RAF-MEK-ERK mitotic signaling pathway. BRAF mutations are present in approximately 50% to 60% of cutaneous melanomas and are also present at lower frequencies in other melanoma subtypes. The hotspot for mutations in BRAF is at codon Val600 and the most common one is p.Val600Glu (V600E). Various B-Raf inhibitors(Vemurafenib, Dabrafenib) have been FDA approved for melanoma therapy in certain settings.\nDrug: \nVemurafenib\nDabrafenib\nDabrafenib + Trametinib\nVemurafenib + Cobimetinib\nTrametinib","tissues":["Skin"],"tumour_types":["Melanoma"],"disease_or_trait":null,"pub_med_references":[12068308,22157295,23415641,23770823,24331719],"variants":[{"definition":"BRAF V600E","type":"variantId","coding_impact":"any","variants":["10190071404531360004","10380071407533360004"],"gene_id":2273},{"aa_positions":[600],"definition":"BRAF codon(s) 600 any","type":"codon","coding_impact":"any","gene_id":2273}]},{"tier":1,"definition":["BRAF V600E","BRAF codon(s) 600 any"],"interpretations":"BRAF alterations have been described in a wide spectrum of brain tumors, including in gliomas and glioneuronal tumors. BRAFV600E mutations have been found in approximately 10--15% of pilocytic astrocytoma and in approximately 5--10% of pediatric diffusely infiltrating gliomas, including diffuse astrocytomas (WHO grade II), anaplastic astrocytomas (WHO grade III) and glioblastomas (WHO grade IV), but in less than 2% of comparable adult gliomas. This mutation is potentially targetable.","tissues":["Spinal Cord","Brain","Supratentorial","Infratentorial"],"tumour_types":["Glioblastoma","Pleomorphic Xanthoastrocytoma","Ganglioglioma","Neuroepithelial Neoplasm","NOS","Neuroepithelial neoplasm","high grade","Astrocytoma","Pilocytic"],"disease_or_trait":null,"pub_med_references":[21274720,23547069,24725538],"variants":[{"definition":"BRAF V600E","type":"variantId","coding_impact":"any","variants":["10190071404531360004","10380071407533360004"],"gene_id":2273},{"aa_positions":[600],"definition":"BRAF codon(s) 600 any","type":"codon","coding_impact":"any","gene_id":2273}]},{"tier":1,"definition":["BRAF V600E","BRAF codon(s) 600 any"],"interpretations":"B-RAF is a member of the RAF-family of kinases which plays an important role in the RAS-RAF-MEK-ERK mitotic signaling pathway. Mutations of B-RAF have been described in up to 40-70% of Langerhans cell histiocytosis and approximately 50% of Erdheim-Chester disease. The hotspot for mutations in BRAF is at codon Val600 and these are activating mutations. The most common activating mutation is p.Val600Glu(V600E). Various B-Raf inhibitors(Vemurafenib, Dabrafenib) have been FDA approved for therapy for some tumor types in certain settings, and clinical trials for advanced BRAF V600 mutation-positive tumors using targeted therapy (often in combination with other therapy) may be available (clinical trials.gov).\n","tissues":["Bone","Lung","Bone Marrow","Lymph Node","Skin"],"tumour_types":["Langerhans Cell Histiocytosis","Histiocytic and Dendritic Cell Neoplasms"],"disease_or_trait":null,"pub_med_references":null,"variants":[{"definition":"BRAF V600E","type":"variantId","coding_impact":"any","variants":["10190071404531360004","10380071407533360004"],"gene_id":2273},{"aa_positions":[600],"definition":"BRAF codon(s) 600 any","type":"codon","coding_impact":"any","gene_id":2273}]},{"tier":1,"definition":["BRAF V600E"],"interpretations":"Mutations in beta catenin (CTNNB1) are seen in about 90% of adamantinomatous craniopharyngiomas and mutations in BRAF (V600E) in papillary craniopharyngiomas. Adamantinomatous and papillary craniopharyngiomas have been shown to carry clonal mutations that are typically mutually exclusive but may occasionally coexist. These findings indicate that the adamantinomatous and papillary subtypes have distinct molecular underpinnings, each principally driven by mutations in a single well-established oncogene - CTNNB1 in the adamantinomatous form and BRAF in the papillary form, independent of age. This may have implications for the diagnosis and treatment of these tumors. Treatment with the BRAF inhibitor vemurafenib has been reported to result in disease stabilization in a patient with a papillary craniopharyngioma with a BRAF V600E mutation.","tissues":["Brain"],"tumour_types":["Craniopharyngioma"],"disease_or_trait":null,"pub_med_references":[24715106],"variants":[{"definition":"BRAF V600E","type":"variantId","coding_impact":"any","variants":["10190071404531360004","10380071407533360004"],"gene_id":2273}]},{"tier":1,"definition":["BRAF V600E"],"interpretations":"BRAF is part of the mitogen-activated protein kinase (MAPK) signaling pathway and V600E is an activating mutation of BRAF. The BRAF V600E mutation has been reported in 45% of patients with papillary thyroid carcinoma, which comprise 80 % of all thyroid cancers. Presence of a BRAF p.Val600Glu (V600E) mutation is highly specific for papillary thyroid carcinoma and is only rarely associated with the follicular variant PTC, other thyroid neoplasms, or nodular goiters. Anaplastic thyroid carcinomas are rare, highly aggressive, undifferentiated tumors that comprise 1% to 2% of all thyroid cancers in the United States. Well-differentiated papillary thyroid cancer, in which BRAF V600 mutations are an early and common driver mutation, precedes or coexists with approximately 50% of anaplastic thyroid carcinomas. Between 20% and 50% of anaplastic thyroid carcinomas harbor activating BRAF V600 mutations, with unknown prognostic significance. The possible prognostic impact of BRAF V600E mutations in carcinoma of the thyroid continues to be studied. ","tissues":["Thyroid"],"tumour_types":["Carcinoma"],"disease_or_trait":null,"pub_med_references":null,"variants":[{"definition":"BRAF V600E","type":"variantId","coding_impact":"any","variants":["10190071404531360004","10380071407533360004"],"gene_id":2273}]},{"tier":1,"definition":["BRAF V600D","BRAF codon(s) 600 any"],"interpretations":"Drug\nVemurafenib\nDabrafenib\nDabrafenib + Trametinib\nVemurafenib + Cobimetinib","tissues":null,"tumour_types":["Melanoma"],"disease_or_trait":null,"pub_med_references":null,"variants":[{"aa_positions":[600],"definition":"BRAF codon(s) 600 any","type":"codon","coding_impact":"any","gene_id":2273}]},{"tier":1,"definition":["BRAF codon(s) 600 any","BRAF V600G"],"interpretations":"Vemurafenib","tissues":null,"tumour_types":["Langerhans Cell Histiocytosis"],"disease_or_trait":null,"pub_med_references":null,"variants":[{"aa_positions":[600],"definition":"BRAF codon(s) 600 any","type":"codon","coding_impact":"any","gene_id":2273}]},{"tier":1,"definition":["BRAF codon(s) 600 any","BRAF V600M"],"interpretations":"Vemurafenib\nDabrafenib\nDabrafenib + Trametinib\nVemurafenib + Cobimetinib\nVemurafenib + Panitumumab\nEncorafenib + Binimetinib + Cetuximab\nRadiation + Trametinib + Fluorouracil","tissues":["Colon","Lung"],"tumour_types":["Melanoma","Langerhans Cell Histiocytosis","Non-Small Cell Lung Carcinoma"],"disease_or_trait":null,"pub_med_references":[19884556,23438367,27080216],"variants":[{"aa_positions":[600],"definition":"BRAF codon(s) 600 any","type":"codon","coding_impact":"any","gene_id":2273}]},{"tier":1,"definition":["BRAF V600D","BRAF V600E","BRAF V600K","BRAF V600R","BRAF codon(s) 600 any"],"interpretations":"B-RAF is a member of the RAF-family of kinases which plays an important role in the RAS-RAF-MEK-ERK mitotic signaling pathway. Mutations of B-RAF have been described in up to 100% of Hairy cell leukemia, 40-70% of Langerhans cell histiocytosis, approximately 50% of Erdheim-Chester disease, approximately 5% of diffuse large B cell lymphoma and plasma cell neoplasms and less than 5% of chronic lymphocytic leukemia. Some types of Hairy Cell Leukemia (eg, Hairy Cell Leukemia-Variant, Hairy Cell Leukemia with IgHV4-34 rearrangement) are negative for BRAF V600E mutation and may have MAP2K1 mutations. While some reports have found that 10-20% of cases of acute leukemias (ALL or AML) may have BRAF mutations, other reports have described no BRAF in those diseases or in myeloid diseases such as MDS or CML. The hotspot for mutations in BRAF is at codon Val600 and these are activating mutations. The most common activating mutation is p.Val600Glu(V600E). B-Raf inhibitors(eg, Vemurafenib) have been FDA approved for therapy for various tumor types and have been used in Hairy Cell Leukemia in some clinical settings, including in combination with other therapy.","tissues":["Blood","Bone Marrow"],"tumour_types":["Hairy Cell Leukemia"],"disease_or_trait":null,"pub_med_references":[22230299,22639828,23009221,23088640,24428489,24495477],"variants":[{"definition":"BRAF V600E","type":"variantId","coding_impact":"any","variants":["10190071404531360004","10380071407533360004"],"gene_id":2273},{"aa_positions":[600],"definition":"BRAF codon(s) 600 any","type":"codon","coding_impact":"any","gene_id":2273}]},{"tier":2,"definition":["BRAF V600E"],"interpretations":"B-RAF is a member of the RAF-family of kinases which plays an important role in the RAS-RAF-MEK-ERK mitotic signaling pathway. Mutations of B-RAF have been described in <2% of head and neck squamous cell carcinomas. The hotspot for mutations in BRAF is at codon Val600 and the most common one is p.Val600Glu (V600E). Various B-RAF inhibitors have been FDA approved for cancer therapy in certain settings. ","tissues":["Larynx","Oral Cavity"],"tumour_types":["Squamous Cell Carcinoma"],"disease_or_trait":null,"pub_med_references":[12068308],"variants":[{"definition":"BRAF V600E","type":"variantId","coding_impact":"any","variants":["10190071404531360004","10380071407533360004"],"gene_id":2273}]},{"tier":2,"definition":["BRAF V600D","BRAF V600E","BRAF V600K","BRAF V600R","BRAF codon(s) 600 any","BRAF any mutation"],"interpretations":"B-RAF is a member of the RAF-family of kinases which plays an important role in the RAS-RAF-MEK-ERK mitotic signaling pathway. Mutations of B-RAF have been described in up to 100% of Hairy cell leukemia, 40-70% of Langerhans cell histiocytosis, approximately 50% of Erdheim-Chester disease, approximately 5% of diffuse large B cell lymphoma and plasma cell neoplasms and less than 5% of chronic lymphocytic leukemia. While some reports have found that 10-20% of cases of acute leukemias (ALL or AML) may have BRAF mutations, other reports have described no BRAF in those diseases or in myeloid diseases such as MDS or CML. The hotspot for mutations in BRAF is at codon Val600 and these are activating mutations. The most common activating mutation is p.Val600Glu(V600E). Various B-Raf inhibitors(Vemurafenib, Dabrafenib) have been FDA approved for therapy for some tumor types in certain clinical settings. ","tissues":["Blood","Bone Marrow"],"tumour_types":["Acute Leukemia of Unspecified Cell Type","Acute Myeloid Leukemia","Anemia","Unspecified","Atypical Chronic Myeloid Leukemia","B Lymphoblastic Leukemia/Lymphoma","Chronic Myeloid Leukemia","Chronic Myelomonocytic Leukemia","Chronic Neutrophilic Leukemia","Cytopenia","Eosinophilia","Essential Thrombocythemia","Leukocytosis","Leukopenia","Mast Cell Neoplasm","MDS with Ring Sideroblasts","Monocytosis","Myelodysplastic Syndrome","Myelodysplastic/Myeloproliferative Neoplasm","Myeloproliferative Neoplasm","Myeloid Neoplasm","Other Acute Leukemia","Polycythemia Vera","Polycythemia","Primary Myelofibrosis","T Lymphoblastic Leukemia/Lymphoma","Thrombocytopenia","Thrombocytosis","Chronic Lymphocytic Leukemia","Diffuse Large B Cell Lymphoma"],"disease_or_trait":null,"pub_med_references":[22230299,22639828,23009221,23088640,24428489,24495477],"variants":[{"definition":"BRAF V600E","type":"variantId","coding_impact":"any","variants":["10190071404531360004","10380071407533360004"],"gene_id":2273},{"aa_positions":[600],"definition":"BRAF codon(s) 600 any","type":"codon","coding_impact":"any","gene_id":2273}]},{"tier":2,"definition":["BRAF V600E"],"interpretations":"BRAF is a member of the RAF-family of kinases which plays an important role in the RAS-RAF-MEK-ERK mitotic signaling pathway. The hotspot for mutations in BRAF is at codon Val600 and these are activating mutations. The most common activating mutation is p.Val600Glu(V600E). Activating BRAF(V600E) (Val600Glu) mutations have been identified in approximately 1-2% of lung adenocarcinomas. Various BRAF inhibitors (Vemurafenib, Dabrafenib, and Trametinib) have been FDA approved for therapy for some tumor types in certain clinical settings. Of note, Dabrafenib and Trametinib are approved for metastatic non-small cell lung cancer (NSCLC) harboring BRAF V600E mutations.","tissues":["Lung"],"tumour_types":["Adenocarcinoma"],"disease_or_trait":null,"pub_med_references":[22663011,27080216],"variants":[{"definition":"BRAF V600E","type":"variantId","coding_impact":"any","variants":["10190071404531360004","10380071407533360004"],"gene_id":2273}]},{"tier":2,"definition":["BRAF V600E"],"interpretations":"B-RAF is a member of the RAF-family of kinases which plays an important role in the RAS-RAF-MEK-ERK mitotic signaling pathway. The hotspot for mutations in BRAF is at codon Val600 and these are activating mutations. The most common activating mutation is p.Val600Glu(V600E). Various B-Raf inhibitors(Vemurafenib, Dabrafenib) have been FDA approved for therapy for some tumor types in certain settings, and clinical trials for advanced BRAF V600 mutation-positive tumors using targeted therapy (often in combination with other therapy) may be available (clinical trials.gov). It has been found that BRAF V600E has a mutation frequency of 2% in pancreatic cancer. A small study showed that no BRAF mutations were present in cases without KRAS mutations and in the few cases with BRAF mutations, a KRAS mutation was also present. ","tissues":["Pancreas"],"tumour_types":["Adenocarcinoma"],"disease_or_trait":null,"pub_med_references":null,"variants":[{"definition":"BRAF V600E","type":"variantId","coding_impact":"any","variants":["10190071404531360004","10380071407533360004"],"gene_id":2273}]},{"tier":2,"definition":["BRAF V600E"],"interpretations":"BRAF is a member of the RAF-family of kinases which plays an important role in the RAS-RAF-MEK-ERK mitotic signaling pathway. The hotspot for mutations in BRAF is at codon Val600 and these are activating mutations. The most common activating mutation is p.Val600Glu(V600E). BRAF mutation frequencies are highly controversial in biliary tract cancers ranging from 0 to 33% for BRAF V600E. As most studies with high BRAF mutation rates were performed on European cohorts, this has raised the question of whether these discordant results represent a regional difference in the genetics of biliary tract cancer. In large cohort of biliary tract cancers including intrahepatic cholangiocarcinomas, extrahepatic cholangiocarcinomas, and adenocarcinomas of the gallbladder, BRAF V600E mutations were only rarely found in intrahepatic cholangiocarcinomas and were not identified in any cases of gallbladder adenocarcinoma. The clinicopathologic significance of BRAF V600E remains to be further elucidated in adenocarcinoma of the gallbladder. Various BRAF inhibitors (Vemurafenib, Dabrafenib) have been FDA approved for therapy for some tumor types in certain settings. These results should be interpreted in the clinical and radiographic context. ","tissues":["Gall Bladder"],"tumour_types":["Adenocarcinoma"],"disease_or_trait":null,"pub_med_references":null,"variants":[{"definition":"BRAF V600E","type":"variantId","coding_impact":"any","variants":["10190071404531360004","10380071407533360004"],"gene_id":2273}]},{"tier":2,"definition":["BRAF V600E"],"interpretations":"BRAF is a member of the RAF-family of kinases which plays an important role in the RAS-RAF-MEK-ERK mitotic signaling pathway. BRAF V600E lies within the activation segment of the kinase domain of the BRAF protein and confers a gain of function. BRAF mutations are infrequent in urothelial carcinoma and are identified in 3-5% of cases. Various BRAF inhibitors (Vemurafenib, Dabrafenib) have been FDA approved for therapy for some tumor types in certain settings. The use of BRAF inhibitors in a number of other cancer types harboring BRAF V600E mutations are under investigation (clinicaltrials.gov). The clinicopathologic effects of BRAF in urothelial carcinoma remains to be fully elucidated.","tissues":["Kidney","Bladder","Ureter"],"tumour_types":["Urothelial Carcinoma"],"disease_or_trait":null,"pub_med_references":null,"variants":[{"definition":"BRAF V600E","type":"variantId","coding_impact":"any","variants":["10190071404531360004","10380071407533360004"],"gene_id":2273}]}]}],"wustl_civic":[{"version":"19-Jan-2026","items":[{"asco_entry":null,"clinical_significance":"Positive","disease":"Thyroid Cancer","doid":"1781","drug_interaction_type":null,"drugs":null,"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/79","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"BRAF V600E is shown to be associated with the tall-cell variant of papillary thyroid cancer.","evidence_status":"accepted","evidence_type":"Diagnostic","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:24 UTC","nct_ids":null,"normalized_drug":null,"phenotypes":null,"pub_med_references":[21594703],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":[{"amp_category":"Tier I - Level A","assertion_civic_url":"https://civicdb.org/links/assertions/7","assertion_description":"Combination treatment of BRAF inhibitor dabrafenib and MEK inhibitor trametinib is recommended for adjuvant treatment of stage III or recurrent melanoma with BRAF V600E mutation detected by the approved THxID kit, as well as first line treatment for metastatic melanoma. The treatments are FDA approved based on studies including the Phase III COMBI-V, COMBI-D and COMBI-AD Trials. Combination therapy is now recommended above BRAF inhibitor monotherapy. Cutaneous squamous-cell carcinoma and keratoacanthoma occur at lower rates with combination therapy than with BRAF inhibitor alone.","assertion_direction":"Supports","assertion_id":"7","assertion_summary":"BRAF V600E mutant melanoma is sensitive to dabrafenib and trametinib combination therapy","assertion_type":"Predictive","clinical_significance":"Sensitivity/Response","disease":"Melanoma","doid":"1909","drugs":["Trametinib","Dabrafenib"],"evidence_item_ids":["6940","6178","3758","6938"],"fda_companion_test":true,"gene":"BRAF","nccn_guideline":"Melanoma","nccn_guideline_version":"2.2018","normalized_drug":["Dabrafenib, Trametinib"],"regulatory_approval":true},{"amp_category":"Tier I - Level A","assertion_civic_url":"https://civicdb.org/links/assertions/10","assertion_description":"Vemurafenib and cobimetinib combination is an FDA approved first line treatment for BRAF V600E mutant metastatic melanoma based on clinical data including the Phase III coBRIM trial. The cobas 4800 BRAF V600 Mutation Test is approved as an FDA companion test for Cotellic (cobimetinib) in combination with Zelboraf (vemurafenib).","assertion_direction":"Supports","assertion_id":"10","assertion_summary":"BRAF V600E mutant melanoma is sensitive to vemurafenib and cobimetinib combination therapy","assertion_type":"Predictive","clinical_significance":"Sensitivity/Response","disease":"Melanoma","doid":"1909","drugs":["Vemurafenib","Cobimetinib"],"evidence_item_ids":["6044","6966","1421"],"fda_companion_test":true,"gene":"BRAF","nccn_guideline":"Melanoma","nccn_guideline_version":"2.2018","normalized_drug":["Cobimetinib, Vemurafenib"],"regulatory_approval":true},{"amp_category":"Tier I - Level A","assertion_civic_url":"https://civicdb.org/links/assertions/20","assertion_description":"BRAF V600E was associated with worse prognosis in Phase II and III colorectal cancer, with a stronger effect in MSI-Low or MSI-Stable tumors. In metastatic CRC, V600E was associated with worse prognosis, and meta-analysis showed BRAF mutation in CRC associated with multiple negative prognostic markers.","assertion_direction":"Supports","assertion_id":"20","assertion_summary":"BRAF V600E indicates poor prognosis in advanced colorectal cancer","assertion_type":"Prognostic","clinical_significance":"Poor Outcome","disease":"Colorectal Cancer","doid":"9256","drugs":null,"evidence_item_ids":["1552","7156","7157","7158","7159","103"],"fda_companion_test":false,"gene":"BRAF","nccn_guideline":"Colon Cancer","nccn_guideline_version":"2.2017","normalized_drug":null,"regulatory_approval":null}],"civic_variant_evidence_score":"CA123643","variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":[{"molecular_profile":{"evidence_item_ids":[73],"name":"BRAF V600E AND BRAF 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Triplet therapy resulted in better TGI and ILS compared to any agent in isolation or capecitabine + vemurafenib doublet therapy (p <0.05, p <0.0001, for all comparisons).","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":["Bevacizumab","Capecitabine","Vemurafenib"],"phenotypes":null,"pub_med_references":[22180495],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":null,"drugs":["Vemurafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/99","evidence_direction":"Supports","evidence_level":"D","evidence_statement":"This preclinical study examined vemurafenib efficacy on various colorectal cancer cell lines and in mouse xenograft experiments. Of the cell lines tested, six harbored BRAF V600E (and WT KRAS) and three harbored BRAF WT (but mutant KRAS). Of the six BRAF V600E expressing cell lines, four were sensitive to vemurafenib (IC50 ranging between 0.025 and 0.35 uM; HT29, Colo205, Colo741, LS411N). Cell lines expressing the BRAF V600E mutation responded better to vemurafenib treatment than cells wildtype for BRAF as measured by reduced cellular proliferation and inhibition of MET and ERK phosphorylation (none of the three BRAF wt cell lines had IC50s less than 10uM). Authors note that one of the vemurafenib-resistant cell lines harboring BRAF V600E (RKO) harbored a concurrent activating PIK3CA H1047R mutation. Nude, athymic mice with HT29 xenografts treated with vemurafenib experienced substantial tumor inhibition and increased lifespan at every dose tested, though authors found 75 mg/kg twice daily to be optimal (95% tumor growth inhibition, 90% increased lifespan compared to vehicle treated controls).","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":["Vemurafenib"],"phenotypes":null,"pub_med_references":[22180495],"rating":"2","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Poor Outcome","disease":"Papillary Thyroid Carcinoma","doid":"3969","drug_interaction_type":null,"drugs":null,"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/102","evidence_direction":"Does Not Support","evidence_level":"B","evidence_statement":"Unlike other studies that suggest a poorer outcome, BRAF mutation in this study was not correlated with poorer prognosis in papillary thyroid cancer.","evidence_status":"accepted","evidence_type":"Prognostic","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":null,"phenotypes":null,"pub_med_references":[24354346],"rating":"5","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Poor Outcome","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":null,"drugs":null,"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/103","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"V600E is associated with adverse pathological features of colorectal cancer. 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study of 691 cetuximab treated patients with metastatic, chemotherapy refractory colorectal cancer. Of those, 30 patients harbored BRAF V600E, were KRAS, NRAS and PIK3CA wt, and had individual response data. One patient (who harbored BRAF V600E in low copy number) responded, 11 had stable disease, and 18 progressed. Treatments included cetuximab + irinotecan (n=20), cetuximab monotherapy (n=5), cetuximab + FOLFIRI (n=4), and cetuximab + oxaliplatin + 5FU (n=1). Median PFS was 8 weeks (2-32 weeks), median OS was 25 weeks (4-237 weeks), and median number of previous chemotherapy lines was 2 (0-4). Median age was 61 years old (42-78) and there were 16 males and 14 females. Authors concluded that BRAF mutation (23/24 of mutants were BRAF V600E) was strongly associated with poor response to cetuximab and suggested that mutation status of BRAF is more informative than those of NRAS and PIK3CA exon 20 for predicting cetuximab response (second only to KRAS).","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":["Cetuximab"],"phenotypes":null,"pub_med_references":[20619739],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Poor Outcome","disease":"Multiple Myeloma","doid":"9538","drug_interaction_type":null,"drugs":null,"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/463","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"In patients with multiple myeloma, those with BRAF V600E had shorter overall survival than wild-type.","evidence_status":"accepted","evidence_type":"Prognostic","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:24 UTC","nct_ids":null,"normalized_drug":null,"phenotypes":null,"pub_med_references":[23612012],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Poor Outcome","disease":"Papillary Thyroid Carcinoma","doid":"3969","drug_interaction_type":null,"drugs":null,"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/656","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"In patients with papillary thyroid cancer harboring both BRAF V600E and the TERT promotor mutation C228T (N=35), recurrence-free survival is worse than in patients harboring one of these mutations (N=159 BRAF, N=26 TERT promoter mutated) or no mutations in either gene (N=287)(P<0.001).","evidence_status":"accepted","evidence_type":"Prognostic","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":null,"phenotypes":null,"pub_med_references":[25024077],"rating":"5","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Melanoma","doid":"1909","drug_interaction_type":null,"drugs":["Pictilisib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/757","evidence_direction":"Supports","evidence_level":"C","evidence_statement":"One patient with BRAF V600E mutated melanoma (with no detected PI3K pathway deregulation) had a partial response on treatment with pictilisib, a PI3K inhibitor, for 9.5 months. Study was a phase-1 with 60 patients enrolled.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:24 UTC","nct_ids":null,"normalized_drug":["Pictilisib"],"phenotypes":null,"pub_med_references":[25370471],"rating":"2","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Resistance","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":"Substitutes","drugs":["Cetuximab","Panitumumab"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/816","evidence_direction":"Does Not Support","evidence_level":"B","evidence_statement":"This meta-analysis of 7 randomized control trials evaluating overall survival (OS) (8 for progression free survival) could not definitely state that survival benefit of anti-EGFR monoclonal antibodies is limited to patients with wild type BRAF. In other words, the authors believe that there is insufficient data to justify the exclusion of anti-EGFR monoclonal antibody therapy for patients with mutant BRAF. In these studies, mutant BRAF specifically meant the V600E mutation.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:24 UTC","nct_ids":null,"normalized_drug":["Cetuximab, Panitumumab"],"phenotypes":null,"pub_med_references":[25989278],"rating":"4","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Resistance","disease":"Melanoma","doid":"1909","drug_interaction_type":null,"drugs":["MEK Inhibitor RO4987655"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/994","evidence_direction":"Does Not Support","evidence_level":"B","evidence_statement":"This was a phase I expansion and pharmacodynamic study of oral MEK inhibitor RO4987655 on advanced cancer. Of 17 patients with BRAF V600E melanoma, 4 achieved partial response, 5 experienced stable disease lasting longer than 16 weeks, and 8 experienced disease progression (including 2 with prior vemurafenib treatment). One of the partial responders had a concomitant EGFR mutation, and two of the stable disease patients had other concomitant mutations (in RET or MET). The median days on treatment was 113 (18-366) for BRAF V600E melanoma patients and 107 (17-323) for BRAF V600 wildtype patients (n=23). Patients with BRAF V600E mutant melanoma experienced similar response rates (24% vs 20%) and rates of metabolic response measured by decrease in FDG uptake assessed by FDG-PET (86% vs 75%) compared to non-BRAF mutant patients. Patients with melanoma, either BRAF wt or V600E, experienced significant decreases in Ki67 expression by day 15 of MEK inhibitor treatment (P<0.02). The authors conclude that RO4987655 has clinical activity in BRAF V600E and BRAF wt melanoma.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":null,"phenotypes":null,"pub_med_references":[24947927],"rating":"2","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Melanoma","doid":"1909","drug_interaction_type":"Combination","drugs":["Dactolisib","Selumetinib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/1005","evidence_direction":"Supports","evidence_level":"D","evidence_statement":"49 BRAF-mutant melanoma cell lines from patients not previously treated with BRAF inhibition were analyzed. 21 exhibited primary resistance to BRAF inhibition using PLX4720. Inhibition of MEK1/2 (AZD6244 [selumetinib]) and PI3K/mTOR (BEZ235 [dactolisib]) was the most effective approach to counteract resistance in comparison to inhibition with the PLX4720 (progenitor of vemurafenib)-BEZ235 (where response was assessed by apoptosis, viability, p-ERK, p-Akt inhibition).","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":["Dactolisib","Selumetinib"],"phenotypes":null,"pub_med_references":[26678033],"rating":"2","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Positive","disease":"Hairy Cell Leukemia","doid":"285","drug_interaction_type":null,"drugs":null,"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/1127","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"In 47 patients with Hairy Cell Leukemia, sequencing discovered a V600E mutation in all 47 of the sequenced patients.","evidence_status":"accepted","evidence_type":"Diagnostic","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:24 UTC","nct_ids":null,"normalized_drug":null,"phenotypes":null,"pub_med_references":[21663470],"rating":"4","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Cancer","doid":"162","drug_interaction_type":null,"drugs":["Cobimetinib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/1141","evidence_direction":"Supports","evidence_level":"D","evidence_statement":"Preclinical study analyzing the differential response to MEK inhibitors in KRAS and BRAF mutant cancer cell lines and mouse xenografts. Inhibition of active, phosphorylated MEK by GDC-0973 (cobimetinib) is required for strong inhibition of the MAPK pathway in BRAF-mutant tumours. This study provides mechanistic rationale for improved efficacy of cobimetinib in BRAF-mutant models compared to MEK inhibitors acting through an alternative mechanism (GDC-0623 and G-573).","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:24 UTC","nct_ids":null,"normalized_drug":["Cobimetinib"],"phenotypes":null,"pub_med_references":[23934108],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Melanoma","doid":"1909","drug_interaction_type":null,"drugs":["Vemurafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/1398","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"The BRIM-3 Phase III trial NCT01006980 assessed BRAF inhibitor vemurafenib versus dacarbazine in 598 patients with treatment naive metastatic melanoma and confirmed V600E mutation. Significant differences were seen in overall survival (13.3 months with vemurafenib vs. 10.0 months with dacarbazine) and median progression free survival (6.9 months with vemurafenib vs. 1.6 months with dacarbazine)","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:24 UTC","nct_ids":["NCT01006980"],"normalized_drug":["Vemurafenib"],"phenotypes":null,"pub_med_references":[24508103],"rating":"5","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":null,"drugs":["Vemurafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/1405","evidence_direction":"Does Not Support","evidence_level":"B","evidence_statement":"In this Phase II pilot study (NCT00405587) of BRAF V600 inhibitor vemurafenib in 21 metastatic colorectal cancer (CRC) patients with BRAF V600E, one patient had a durable 21 week partial response, and seven patients had 8 week stable disease as best response. Median progression free survival was 2.1 months and median overall survival was 7.7 months. The authors conclude that single agent vemurafenib did not show meaningful activity in V600E CRC, in contrast to the significant vemurafenib activity against V600 in melanoma.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:24 UTC","nct_ids":["NCT00405587"],"normalized_drug":["Vemurafenib"],"phenotypes":null,"pub_med_references":[26460303],"rating":"4","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Reduced Sensitivity","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":null,"drugs":["Dabrafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/1406","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"In trial NCT00880321, dabrafenib was tested in various solid tumor types harboring mutant BRAF after establishing dosage of 150 mg twice daily. In nine colorectal cancer patients with established V600E mutation, 1 confirmed response, 7 instances of stable disease, and 1 case of progressive disease was seen, which contrasted strongly with a 56% confirmed response rate seen in metastatic V600E melanoma patients similarly treated in the same study.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2025-12-17 19:06:25 UTC","nct_ids":["NCT00880321"],"normalized_drug":["Dabrafenib"],"phenotypes":null,"pub_med_references":[22608338],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":"Combination","drugs":["Vemurafenib","Cetuximab","Gefitinib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/1408","evidence_direction":"Supports","evidence_level":"D","evidence_statement":"5 of 7 colorectal cancer (CRC) cell lines with BRAF V600E mutation were resistant to treatment with the BRAF inhibitor vemurafenib. An RNAi screen in the WiDr cell line (a V600E CRC line) identified EGFR as an enhancer for survival when exposed to vemurafenib. Treatment with vemurafenib and EGFR inhibitor (cetuximab or gefitinib) in V600E CRC cells (WiDr, VACO432 and KM20) showed inhibited growth as well as induction of the cleaved PARP apoptotic marker. WiDr and VACO432 cells were injected into immunodeficient mice. Modest response was seen with vemurafenib treatment, while combination treatment showed considerable tumor growth inhibition as compared to control.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:24 UTC","nct_ids":null,"normalized_drug":["Cetuximab","Gefitinib","Vemurafenib"],"phenotypes":null,"pub_med_references":[22281684],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Skin Melanoma","doid":"8923","drug_interaction_type":null,"drugs":["Vemurafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/1409","evidence_direction":"Supports","evidence_level":"A","evidence_statement":"Phase 3 randomized clinical trial comparing vemurafenib with dacarbazine in 675 patients with previously untreated, metastatic melanoma with the BRAF V600E mutation. At 6 months, overall survival was 84% (95% confidence interval [CI], 78 to 89) in the vemurafenib group and 64% (95% CI, 56 to 73) in the dacarbazine group. A relative reduction of 63% in the risk of death and of 74% in the risk of either death or disease progression was observed with vemurafenib as compared with dacarbazine (P<0.001 for both comparisons).","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:24 UTC","nct_ids":["NCT01006980"],"normalized_drug":["Vemurafenib"],"phenotypes":null,"pub_med_references":[21639808],"rating":"5","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Skin Melanoma","doid":"8923","drug_interaction_type":null,"drugs":["Vemurafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/1410","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"Phase 2 trial in 132 patients with previously treated metastatic melanoma with BRAF V600E mutation. Confirmed overall response rate was 53% (95% confidence interval [CI], 44 to 62; 6% with a complete response and 47% with a partial response), median duration of response was 6.7 months (95% CI, 5.6 to 8.6), and median progression-free survival was 6.8 months (95% CI, 5.6 to 8.1). Median overall survival was 15.9 months (95% CI, 11.6 to 18.3).","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:24 UTC","nct_ids":["NCT00949702"],"normalized_drug":["Vemurafenib"],"phenotypes":null,"pub_med_references":[22356324],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":"Combination","drugs":["Panitumumab","Vemurafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/1413","evidence_direction":"Does Not Support","evidence_level":"B","evidence_statement":"Treatment response to mutant BRAF inhibitor vemurafenib and EGFR inhibitor panitumumab was assayed in 12 patients with metastatic colorectal cancer (CRC) who had progressed on chemotherapy. Two patients had confirmed partial responses, and 2 showed stable disease over 6 months. The authors conclude that although some efficacy is seen, only a small subset of patients respond to this treatment and the responses are not durable.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:24 UTC","nct_ids":null,"normalized_drug":["Panitumumab","Vemurafenib"],"phenotypes":null,"pub_med_references":[25589621],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Papillary Thyroid Carcinoma","doid":"3969","drug_interaction_type":null,"drugs":["Vemurafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/1414","evidence_direction":"Supports","evidence_level":"C","evidence_statement":"A 73 year old patient with prior history of breast cancer presented with metastatic papillary thyroid carcinoma. After two treatments of I-131 a comprehensive tumor profile revealed BRAF V600E as the only genetic alteration on a near diploid genome with trisomy 1q. Vemurafenib treatment resulted in improvement of symptoms and considerable reductions in tumor mass, and after 23 months the patient remained on therapy with well controlled disease.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:24 UTC","nct_ids":null,"normalized_drug":["Vemurafenib"],"phenotypes":null,"pub_med_references":[24987354],"rating":"4","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Melanoma","doid":"1909","drug_interaction_type":"Combination","drugs":["Vemurafenib","Cobimetinib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/1421","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"In this Phase III trial (coBRIM, NCT01689519) of 495 V600 mutant melanoma patients, 344 had V600E mutation. 174 patients were treated with vemurafenib and placebo, and 170 were treated with vemurafenib and cobimetinib and tested for progression free survival. 88 of 174 monotherapy group patients had an event with median progression free survival of 6.5 months. In the combination group 58 of 174 patients had an event with median progression-free survival not met, however, when in combination with other V600 mutations median progression-free survival was 9.9 months with combination treatment. Median time to followup for the whole cohort was 7.3 months. Hazard Ratio for progression or death was 0.57 (0.41-0.80).","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":["NCT01689519"],"normalized_drug":["Cobimetinib, Vemurafenib"],"phenotypes":null,"pub_med_references":[25265494],"rating":"4","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":"Combination","drugs":["GDC-0879","Dactolisib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/1428","evidence_direction":"Supports","evidence_level":"D","evidence_statement":"In a mouse model of BRAF V600E colorectal cancer, western blots from tumors in mice treated with BRAF inhibitor GDC-0879 and PI3K/mTOR inhibitor BEZ235 showed stronger reduction in phospho-Akt and phospho-S6 than PI3K/mTOR inhibitor alone, and combination inhibition also resulted in stronger phospho-ERK inhibition in tumors than did BRAF inhibition alone. Increased apoptosis in tumors was seen in dual treatment conditions with increased TUNEL-positive cells. In vehicle treated mice, area of colon covered by tumor increased, while treatment with single agent inhibitors caused growth inhibition resulting in no change in colon area covered by tumors. Administration of dual inhibitors induced tumor regression apparent in a decrease of colonic area covered by tumors over the course of treatment.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:24 UTC","nct_ids":null,"normalized_drug":["Dactolisib"],"phenotypes":null,"pub_med_references":[23549875],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Gastrointestinal Neuroendocrine Tumor","doid":"0050626","drug_interaction_type":"Combination","drugs":["Trametinib","Vemurafenib","Dabrafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/1430","evidence_direction":"Supports","evidence_level":"C","evidence_statement":"BRAF mutations were identified in 9% of 108 cases of high-grade colorectal neuroendocrine tumors (80% V600E). Two patients were treated with a combination of BRAF and MEK inhibition and exhibited durable response (beyond 7 and 9 months, respectively). Urinary BRAF V600E tumor DNA correlated with disease response in one of the patients. BRAF and MEK inhibition was either dabrafenib+trametinib (case 1) or vemurafenib+trametinib (case 2).","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:24 UTC","nct_ids":null,"normalized_drug":["Dabrafenib","Trametinib","Vemurafenib"],"phenotypes":null,"pub_med_references":[27048246],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Poor Outcome","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":null,"drugs":null,"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/1552","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"In a study of 908 patients with colorectal cancer, 45 patients had BRAF V600E mutations and 589 patients were BRAF wild type. BRAF V600E mutations were more likely to be proximal tumors (68.9%, 20.7%; p<0.0001), they were more likely to be poorly differentiated (17.7%, 1.9%; p<0.0001), they were more likely to be mucinous carcinoma type (20.0%, 4.2%; p=0.0003), they were more likely to have lymphatic invasion (77.6%, 49.9%; p=0.0003), and they had a shorter survival time (31.1 mo, 41.6 mo; p=0.001). The 3-year survival rate was significantly poorer in the V600E group when compared to the wild type group (63.8%, 87.9%; p<0.0001).","evidence_status":"accepted","evidence_type":"Prognostic","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:24 UTC","nct_ids":null,"normalized_drug":null,"phenotypes":null,"pub_med_references":[27404270],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Hairy Cell Leukemia","doid":"285","drug_interaction_type":null,"drugs":["Vemurafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/1579","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"Two clinical trials evaluated the effects of vemurafenib in 54 patients with BRAF (V600E) positive hairy-cell leukemia. The overall response rate was 98% with 19/54 having a complete response and 34/54 having a partial response. In the Italian study (n=25), the median relapse-free survival was 9 months and in the U.S. study (n=24), rate of progression-free survival was 73% with overall survival rate of 91%.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:24 UTC","nct_ids":["NCT01711632"],"normalized_drug":["Vemurafenib"],"phenotypes":null,"pub_med_references":[26352686],"rating":"2","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":"Combination","drugs":["Vemurafenib","Panitumumab"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/1589","evidence_direction":"Supports","evidence_level":"C","evidence_statement":"Case report of a patient with BRAF V600E mutant metastatic colorectal cancer. Combined EGFR and BRAF inhibition (panitumumab and vemurafenib) showed an initial partial response for 4 months with subsequent disease progression.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:24 UTC","nct_ids":null,"normalized_drug":["Panitumumab","Vemurafenib"],"phenotypes":null,"pub_med_references":[27325282],"rating":"2","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Papillary Thyroid Carcinoma","doid":"3969","drug_interaction_type":null,"drugs":["Vemurafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/1591","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"Open-label non-randomised phase 2 trial in patients with recurrent or metastatic BRAF V600E mutant papillary thyroid cancer refractory to radioactive iodine. Patients had (cohort 2) or had not (cohort 1) previously been treated with VEGFR inhibitors. 51 patients were enrolled (26 cohort 1, 25 cohort 2). In cohort 1, partial response was achieved in ten (38.5%) patients. Nine patients achieved stable disease for at least 6 months (35%). Median PFS was 18.2 months and median OS not reached after a median follow-up pf 18.8 months. In cohort 2, six patients (27.3%) achieved a partial response and another six patients achieved stable disease for at least six months. Median PFS was 8.9 months and median OS was 14.4. months.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:24 UTC","nct_ids":["NCT01286753"],"normalized_drug":["Vemurafenib"],"phenotypes":null,"pub_med_references":[27460442],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Multiple Myeloma","doid":"9538","drug_interaction_type":null,"drugs":["Vemurafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/1698","evidence_direction":"Supports","evidence_level":"C","evidence_statement":"A 65-year-old man presented with stage II myeloma. He was initially treated with chemotherapy and he received an autologous stem cell transplant. Sequencing of the recurrent tumor harbored BRAF V600E mutation and he was treated with vemurafenib. After 7 weeks of treatment, the patient relapsed and died.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:24 UTC","nct_ids":null,"normalized_drug":["Vemurafenib"],"phenotypes":null,"pub_med_references":[24997557],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Multiple Myeloma","doid":"9538","drug_interaction_type":null,"drugs":["Vemurafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/1699","evidence_direction":"Supports","evidence_level":"C","evidence_statement":"A 54-year-old man presented with stage II myeloma. He was initially treated with chemotherapy and received an autologous stem cell transplant. Genomic profiling of the bone biopsy revealed BRAF V600E activating mutation and the patient was treated with vemurafenib. At 4-months post treatment (time of case study report) the patient maintains near-resolution of hypermetabolic lesions.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:24 UTC","nct_ids":null,"normalized_drug":["Vemurafenib"],"phenotypes":null,"pub_med_references":[24997557],"rating":"2","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Melanoma","doid":"1909","drug_interaction_type":null,"drugs":["Vemurafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/1749","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"Multicenter, phase 1, dose-escalation trial of PLX4032 (Vemurafenib). Treatment of metastatic melanoma with PLX4032 in patients with tumors that carry the V600E BRAF mutation resulted in complete or partial tumor regression in the majority of patients (N=37/48). Patients without the V600E mutation had evidence of tumor regression.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":["Vemurafenib"],"phenotypes":null,"pub_med_references":[20818844],"rating":"4","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":"Combination","drugs":["Vemurafenib","Irinotecan","Cetuximab"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/1902","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"Phase 1b study of vemurafenib, cetuximab and irinotecan in 19 patients with colorectal cancer (1 with appendiceal cancer). Six of 17 evaluable patients achieved an objective response, 15 patients total had either stable disease or radiographic response (the patient with appendiceal cancer had disease progression). Estimated median PFS was 7.7 months. Effect of the combined treatment was also observed in xenograft and cell line studies.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:24 UTC","nct_ids":["NCT01787500"],"normalized_drug":["Cetuximab","Irinotecan","Vemurafenib"],"phenotypes":null,"pub_med_references":[27729313],"rating":"4","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Poor Outcome","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":null,"drugs":null,"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/1940","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"In a study of 468 colorectal cancer samples, 61 patients had micro-satellite instability and there was a statistically significantly better prognosis for BRAF WT patients relative to BRAF (V600E)-mutated patients (Log-rank P=0.0903).","evidence_status":"accepted","evidence_type":"Prognostic","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":null,"phenotypes":null,"pub_med_references":null,"rating":"4","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Resistance","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":"Substitutes","drugs":["Panitumumab","Cetuximab"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/2115","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"In metastatic colorectal cancer patients with wildtype KRAS status, those with a BRAF V600E mutation were less likely to respond to treatment with cetuximab or panitumumab than those with wildtype BRAF (0% vs. 32% , P=0.029). Regardless of KRAS status, patients with BRAF mutations had reduced progression-free and overall survival (P=0.0107 and P <0.0001, respectively). Transfection of the colorectal cancer cell line DiFi with a BRAF V600E expression vector conferred decreased sensitivity to cetuximab and panitumumab in comparison to cells transfected with empty vector.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:24 UTC","nct_ids":null,"normalized_drug":["Cetuximab, Panitumumab"],"phenotypes":null,"pub_med_references":[19001320],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Poor Outcome","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":null,"drugs":null,"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/2116","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"In a study of metastatic colorectal cancer patients who received 5-FU-based first-line chemotherapy, those with BRAF V600E mutations had reduced progression-free survival (4.3mo vs. 12.5mo, HR:4.9, 95%CI:2.7-9.0, P<0.0001, univariate analysis; HR:4.0, 95%CI:2.2-7.4, P<0.0001, multivariate analysis) and reduced overall survival (10.9mo vs. 40.5mo, HR:4.5, 95%CI:2.4-8.4, P<0.0001, univariate analysis; HR:4.1, 95%CI:2.1-8.0, P<0.0001, multivariate analysis) compared to those with wildtype BRAF.","evidence_status":"accepted","evidence_type":"Prognostic","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-12-03 08:11:19 UTC","nct_ids":null,"normalized_drug":null,"phenotypes":null,"pub_med_references":[19603024],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Resistance","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":null,"drugs":["Oxaliplatin"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/2117","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"Of 100 metastatic colorectal cancer patients treated with oxaliplatin-based first-line therapy, the 6 patients with either BRAF V600E or D594K had reduced progression-free survival compared to 94 patients with wildtype BRAF (5.0mo vs. 11.7mo, HR:6.4, 95%CI:2.6-15.6, P<0.0001).","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:24 UTC","nct_ids":null,"normalized_drug":["Oxaliplatin"],"phenotypes":null,"pub_med_references":[19603024],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Resistance","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":null,"drugs":["Irinotecan"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/2118","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"The presence of BRAF V600E or D594K was associated with reduced progression-free survival in 5 patients with metastatic colorectal cancer treated with irinotecan-based first line therapy (3.5mo vs. 12.8mo, HR:4.1, 95%CI:1.5-11.3, P=0.006) when compared to 39 patients with wildtype BRAF.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":["Irinotecan"],"phenotypes":null,"pub_med_references":[19603024],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Resistance","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":"Combination","drugs":["Oxaliplatin","Bevacizumab","Capecitabine"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/2121","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"In a study of metastatic colorectal cancer patients treated with capecitabine, oxaliplatin, and bevacizumab, those with BRAF V600E mutations had reduced progression-free survival (5.9mo vs. 12.2mo, P=0.003) and reduced overall survival (15.0mo vs. 24.6mo, P=0.002) compared to those with wildtype BRAF.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":["Bevacizumab, Capecitabine, Oxaliplatin"],"phenotypes":null,"pub_med_references":[19571295],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Melanoma","doid":"1909","drug_interaction_type":null,"drugs":["Trametinib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/2135","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"In a study of 322 advanced melanoma patients with BRAF-V600E (N=281), BRAF-V600K (N=40), or both mutations (N=1), treatment with trametinib was associated with improved progression-free survival (4.8mo vs. 1.5mo; HR: 0.45, 95% CI: 0.33-0.63, P<0.001) compared to chemotherapy control group. Additionally, treatment with trametinib was associated with increased 6-month overall survival (HR: 0.54, 95% CI: 0.32-0.92, P=0.01). The authors note similar outcomes for the primary efficacy population (V600E only) and the intention-to-treat population.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":["NCT01245062"],"normalized_drug":["Trametinib"],"phenotypes":null,"pub_med_references":[22663011],"rating":"4","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Poor Outcome","disease":"Papillary Thyroid Carcinoma","doid":"3969","drug_interaction_type":null,"drugs":null,"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/2137","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"In a study of 102 papillary thyroid cancer patients with a 15 year median follow-up time, those with BRAF V600E mutations had reduced overall survival compared to those with wildtype BRAF (P=0.015, log-rank test). The presence of BRAF V600E was associated with poorer outcome as defined by persistent disease or death (Odds ratio:14.63, 95%CI:1.28-167.29, P=0.03, multivariate analysis.","evidence_status":"accepted","evidence_type":"Prognostic","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:24 UTC","nct_ids":null,"normalized_drug":null,"phenotypes":null,"pub_med_references":[18682506],"rating":"4","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Poor Outcome","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":null,"drugs":null,"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/2362","evidence_direction":"Does Not Support","evidence_level":"C","evidence_statement":"This study examined outcomes of 240 rectum cancer patients treated with total mesorectal excision therapy. Tumor samples were obtained at the time of surgery and genotyped for BRAF exon 15 mutations. BRAF V600E was identified in 5 cases. The authors reported that no differences were found in overall survival between patients with and without BRAF mutations (P > 0.1).","evidence_status":"accepted","evidence_type":"Prognostic","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":null,"phenotypes":null,"pub_med_references":[19903786],"rating":"2","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Poor Outcome","disease":"Papillary Thyroid Carcinoma","doid":"3969","drug_interaction_type":null,"drugs":null,"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/2503","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"In a meta-analysis of 8 studies, papillary thyroid cancer patients with BRAF V600E mutation had a higher frequency of recurrence and persistent disease compared to those with wildtype BRAF (28.5% vs. 12.8% , Risk ratio:2.14, 95%CI:1.67-2.74, P<0.00001).","evidence_status":"accepted","evidence_type":"Prognostic","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":null,"phenotypes":null,"pub_med_references":[21882184],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Lung Non-small Cell Carcinoma","doid":"3908","drug_interaction_type":"Combination","drugs":["Trametinib","Dabrafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/3017","evidence_direction":"Supports","evidence_level":"A","evidence_statement":"Patients with BRAF V600E-mutant NSCLC (n=57) were enrolled into a phase 2, multicentre, non-randomised, open-label study, administering dabrafenib plus trametinib. The overall response rate was 36/57 (63.2%, [95% CI 49.3-75.6]) and the median progression-free survival was 9.7 months (95% CI 6.9-19.6). At data cutoff (11.6 months of follow-up), 18/36 (50%) confirmed responses were ongoing and 23/57 (40%) of patients had died.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":["NCT01336634"],"normalized_drug":["Dabrafenib, Trametinib"],"phenotypes":null,"pub_med_references":[27283860],"rating":"4","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Resistance","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":"Combination","drugs":["FOLFOX-4 Regimen","Cetuximab"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/3739","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"In a retrospective study of 148 treatment naive metastatic colorectal cancer patients, patients with BRAF V600E and wildtype NRAS/KRAS (n=14) mutation treated with FOLFOX4 plus cetuximab were associated with a decreased progression free survival (7.2mo vs. 9.7mo, HR:0.39, 95% CI:0.21-0.72, P=0.0017), and decreased overall survival (11.7mo vs. 28.5mo, HR:0.23, 95% CI:0.12-0.41, P<0.0001), as compared to patients with wildtype BRAF, NRAS and KRAS.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:24 UTC","nct_ids":null,"normalized_drug":["Cetuximab","Folfox"],"phenotypes":null,"pub_med_references":[25666295],"rating":"4","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Melanoma","doid":"1909","drug_interaction_type":null,"drugs":["Vemurafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/3750","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"In a phase 2 clinical trial (NCT00949702) of 132 BRAF mutation positive metastatic melanoma patients treated with vemurafenib monotherapy, patients harboring BRAF V600E (n=123) or V600K (n=9) mutations were associated with a favorable objective response rate (53% per RECIST v1.1 criteria, 70/132), with 6% (8/132) and 47% (62/132) of patients achieving complete response and partial response, respectively.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":["Vemurafenib"],"phenotypes":null,"pub_med_references":[23569304],"rating":"4","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Melanoma","doid":"1909","drug_interaction_type":null,"drugs":["Vemurafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/3755","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"In a clinical study (NCT01307397) of Polish, stage IIIC/IV, melanoma patients with metastases (n=75) harboring BRAF V600 mutation (as detected by cobas 4800 BRAF V600 Mutation Test), median overall survival was 61.9% (95% CI: 50.1-73.6) and median progression free survival was 7.4 months (95% CI: 5.5-9.2). Median duration of response was 7.4 months (95% CI: 5.7-9.2), with 3% (2/75) and 43% (29/75) of patients achieving a complete and partial response, respectively.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":["Vemurafenib"],"phenotypes":null,"pub_med_references":[26557775],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Melanoma","doid":"1909","drug_interaction_type":null,"drugs":["Vemurafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/3757","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"In a retrospective study of 300 stage IV melanoma patients, patients with BRAF V600E mutation (n=175) were associated with a 4.8% (8/167) complete response, a 58.1% (97/167) partial response and stable disease in 22.2% (37/167) of cases, while 15% (25/167) of patients harboring BRAF V600E experienced progressive disease.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":["Vemurafenib"],"phenotypes":null,"pub_med_references":[25524477],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Skin Melanoma","doid":"8923","drug_interaction_type":"Combination","drugs":["Trametinib","Dabrafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/3758","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"In a clinical trial (NCT01597908) of 704 metastatic melanoma patients, patients harboring a BRAF V600E mutation and treated with vemurafenib (n=317) were associated with a 51% response rate, as compared to a 64% response rate (p<0.001) in V600E mutation positive patients treated with dabrafenib and trametinib combination therapy (n=312). Median progression-free survival was 11.4 months in the combination-therapy group and 7.3 months in the vemurafenib group (hazard ratio, 0.56; 95% CI, 0.46 to 0.69; P<0.001).","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":["NCT01597908"],"normalized_drug":["Dabrafenib, Trametinib"],"phenotypes":null,"pub_med_references":[25399551],"rating":"4","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Childhood Pilocytic Astrocytoma","doid":"6812","drug_interaction_type":null,"drugs":["Vemurafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/3777","evidence_direction":"Supports","evidence_level":"C","evidence_statement":"In a case report, a 28 month old patient with a cervicomedullary low grade glioma compatible with pilocytic astrocytoma which was resected had a second lesion consistent with a ganglioglioma 3 years later. This mass progressed under treatment at which point PCR amplification of BRAF exon 15 and subsequent Sanger sequencing the initial biopsy revealed the tumor harbored a BRAF V600E mutation. Based on these results, vemurafenib monotherapy was started and radiological and clinical response was noted after 3 months of treatment, which was sustained after 6 months of therapy. Prior to vemurafenib treatment, the patient had undergone tracheotomy, was treated with standard chemotherapy and underwent another surgery, but had developed progressive disease.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":["Vemurafenib"],"phenotypes":null,"pub_med_references":[25524464],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Ovarian Serous Carcinoma","doid":"0050933","drug_interaction_type":null,"drugs":["Vemurafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/3787","evidence_direction":"Supports","evidence_level":"C","evidence_statement":"A stage 4B, low-grade papillary serous ovarian adenocarcinoma patient, harboring a BRAF V600E mutation was associated with response to vemurafenib monotherapy. The patient was treated with standard chemotherapy, hormone therapy and bevacizumab prior to the identification of the BRAF V600E mutation; next, the patient was treated with paclitaxel and an anti-HER3 antibody and finally with vemurafenib, obtaining a partial response of greater than 1 year.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":["Vemurafenib"],"phenotypes":null,"pub_med_references":[26490654],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Resistance","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":null,"drugs":["Panitumumab"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/3827","evidence_direction":"Supports","evidence_level":"C","evidence_statement":"One patient participating in a large retrospective study of EGFR monoclonal antibodies in metastatic colorectal cancer had a tumor which harbored BRAF V600E, was wildtype for NRAS, KRAS and PIK3CA, and had individual response data. This patient was was a male treated with panitumumab monotherapy as 1st line therapy who experienced progressive disease (PFS: 7 weeks; OS: 10 weeks).","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":["Panitumumab"],"phenotypes":null,"pub_med_references":[20619739],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Cholangiocarcinoma","doid":"4947","drug_interaction_type":"Combination","drugs":["Dabrafenib","Trametinib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/5902","evidence_direction":"Supports","evidence_level":"C","evidence_statement":"Chemotherapy-refractory, metastatic cholangiocarcinoma with CNS involvement and a BRAF V600E mutation had a partial response at 8 weeks to dabrafenib and trametinib combination with complete radiologic regression at 12 weeks. At 6 months the patient was still on treatment.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":["Dabrafenib, Trametinib"],"phenotypes":null,"pub_med_references":[28480077],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Intrahepatic Cholangiocarcinoma","doid":"4928","drug_interaction_type":"Combination","drugs":["Trametinib","Dabrafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/5903","evidence_direction":"Supports","evidence_level":"C","evidence_statement":"Two cases of patients with BRAF V600E positive, refractory intrahepatic cholangiocarcinoma showed excellent clinical and radiographic response to combination dabrafenib and trametinib treatment. One patient achieved complete remission at 6 months with progression at 9 months and the other partial remission at 2 months and no progression as of 5 months.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":["Dabrafenib, Trametinib"],"phenotypes":null,"pub_med_references":[28078132],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Intrahepatic Cholangiocarcinoma","doid":"4928","drug_interaction_type":"Combination","drugs":["Dabrafenib","Trametinib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/5904","evidence_direction":"Supports","evidence_level":"C","evidence_statement":"Dabrafenib and trametinib combination showed durable response for a patient with standard chemotherapy and radiation refractory, poorly differentiated, intrahepatic cholangiocarcinoma harboring BRAF V600E. At time of publication, 8.5 months, the patient was still on treatment.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":["Dabrafenib, Trametinib"],"phenotypes":null,"pub_med_references":[25435907],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Cholangiocarcinoma","doid":"4947","drug_interaction_type":"Combination","drugs":["Vemurafenib","Irinotecan","Panitumumab"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/5906","evidence_direction":"Supports","evidence_level":"C","evidence_statement":"A 31 year old patient with metastatic cholangiocarcinoma with BRAF V600E was treated with vemurafenib, panitumumab and irinotecan triplet therapy. By 2 months, 50% reduction of tumor volume was noted, including multiple lung metastases, complete clinical response was noted by CT 6 months post therapy and this treatment was continued.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":["Irinotecan","Panitumumab","Vemurafenib"],"phenotypes":null,"pub_med_references":[26687137],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Lung Non-small Cell Carcinoma","doid":"3908","drug_interaction_type":null,"drugs":["Vemurafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/5958","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"The phase 2a MyPathway study assigned patients with HER2, EGFR, BRAF or SHH alterations to treatment with pertuzumab plus trastuzumab, erlotinib, vemurafenib, or vismodegib, respectively. Within the BRAF mutant group, fourteen patients had refractory BRAF V600E-mutated NSCLC (adenocarcinoma, n = 13; sarcomatoid, n = 1). Six patients (43%; 95% CI, 18% to 71%) had objective responses (one CR, five PR), and two additional patients had SD > 120 days. The median DOR was 5 months (range, 4 to 14 months).","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":["NCT02091141"],"normalized_drug":["Vemurafenib"],"phenotypes":null,"pub_med_references":null,"rating":"4","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Ovarian Cancer","doid":"2394","drug_interaction_type":null,"drugs":["Vemurafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/5959","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"The phase 2a MyPathway study assigned patients with HER2, EGFR, BRAF or SHH alterations to treatment with pertuzumab plus trastuzumab, erlotinib, vemurafenib, or vismodegib, respectively. Among 4 patients with BRAF V600E mutant ovarian cancer, 2 had a partial response and one had stable disease > 120days.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":["NCT02091141"],"normalized_drug":["Vemurafenib"],"phenotypes":null,"pub_med_references":null,"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":null,"drugs":["Vemurafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/5960","evidence_direction":"Supports","evidence_level":"C","evidence_statement":"The phase 2a MyPathway study assigned patients with HER2, EGFR, BRAF or SHH alterations to treatment with pertuzumab plus trastuzumab, erlotinib, vemurafenib, or vismodegib, respectively. Among 2 patients with BRAF V600E mutant colorectal cancer, 1 had a partial response.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":["NCT02091141"],"normalized_drug":["Vemurafenib"],"phenotypes":null,"pub_med_references":null,"rating":"2","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Anaplastic Thyroid Carcinoma","doid":"0080522","drug_interaction_type":"Combination","drugs":["Vemurafenib","Pertuzumab"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/5961","evidence_direction":"Supports","evidence_level":"C","evidence_statement":"The phase 2a MyPathway study assigned patients with HER2, EGFR, BRAF or SHH alterations to treatment with pertuzumab plus trastuzumab, erlotinib, vemurafenib, or vismodegib, respectively. One patient with BRAF V600E mutant anaplastic thyroid cancer had a complete response.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":["NCT02091141"],"normalized_drug":["Pertuzumab","Vemurafenib"],"phenotypes":null,"pub_med_references":null,"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Laryngeal Squamous Cell Carcinoma","doid":"2876","drug_interaction_type":null,"drugs":["Vemurafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/5962","evidence_direction":"Supports","evidence_level":"C","evidence_statement":"The phase 2a MyPathway study assigned patients with HER2, EGFR, BRAF or SHH alterations to treatment with pertuzumab plus trastuzumab, erlotinib, vemurafenib, or vismodegib, respectively. One patient with BRAF V600E mutant laryngeal cancer had a partial response with vemurafenib.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":["NCT02091141"],"normalized_drug":["Vemurafenib"],"phenotypes":null,"pub_med_references":null,"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Anaplastic Thyroid Carcinoma","doid":"0080522","drug_interaction_type":null,"drugs":["Vemurafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/6045","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"In a phase 2 “basket” study of vemurafenib in BRAF V600-positive non-melanoma cancers, seven patients with anaplastic thyroid cancer were enrolled. All 7 patients had V600E mutations. One complete response and one partial response was observed, for a response rate of 29%.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":["NCT01524978"],"normalized_drug":["Vemurafenib"],"phenotypes":null,"pub_med_references":[26287849],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":"Combination","drugs":["Panitumumab","Trametinib","Dabrafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/6123","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"In this trial, 142 patients with metastatic, BRAF V600E mutant colorectal cancer were randomized to receive either BRAF inhibitor dabrafenib (D) + EGFR inhibitor panitumumab (P); or a triple therapy of D + P and MEK inhibition with trametinib (T) or T + P. Confirmed response rates for D+P (n=20), D+T+P (n=91), and T+P (n=31) were 10%, 21%, and 0%, respectively.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":["Dabrafenib","Panitumumab","Trametinib"],"phenotypes":null,"pub_med_references":[29431699],"rating":"4","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Colorectal Adenocarcinoma","doid":"0050861","drug_interaction_type":"Combination","drugs":["Panitumumab","Trametinib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/6124","evidence_direction":"Does Not Support","evidence_level":"B","evidence_statement":"In this trial, 142 patients with metastatic, BRAF V600E mutant colorectal cancer were randomized to receive either BRAF inhibitor dabrafenib (D) + EGFR inhibitor panitumumab (P); or a triple therapy of D + P and MEK inhibition with trametinib (T) or T + P. Confirmed response rates for D+P (n=20), D+T+P (n=91), and T+P (n=31) were 10%, 21%, and 0%, respectively.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":["Panitumumab","Trametinib"],"phenotypes":null,"pub_med_references":[29431699],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Melanoma","doid":"1909","drug_interaction_type":"Combination","drugs":["Dabrafenib","Trametinib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/6178","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"Adjuvant dual treatment with BRAF inhibitor dabrafenib and MEK inhibitor trametinib was administered to patients with stage III resected melenoma with V600E or V600K mutation in this stage III trial (COMBO-AD, NCT01682083). 792 (91%) patients had V600E, and were administered dabrafenib and trametinib or placebo for 12 months. In subsequent analysis, relapse or death occurred in 150/397 patients (38%) in the treatment group and 229/395 patients (58%) in the placebo group for a 95% CI Hazard Ratio of 0.48 (0.39-0.58).","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":["NCT01682083"],"normalized_drug":["Dabrafenib, Trametinib"],"phenotypes":null,"pub_med_references":[28891408],"rating":"5","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Melanoma","doid":"1909","drug_interaction_type":"Combination","drugs":["Dabrafenib","Trametinib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/6938","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"In this Phase III trial (NCT01584648 COMBI-d), previously untreated patients with unresectable stage IIIC or IV melanoma with BRAF V600E (359 patients) or V600K (61 patients) received dabrafenib and trametinib or dabrafenib alone with primary endpoint of progression free survival and secondary endpoints including disease response. The hazard ratio for progression or death in the V600E group was 0.81 for dabrafenib-trametinib vs dabrafenib-alone. Of 179 V600E patients in the dabrafenib-trametinib group, 68% of patients had a response, which was 15 percentage points higher than in the dabrafenib-alone group (95% CI, 4 to 24; P=0.006).","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":["NCT01584648"],"normalized_drug":["Dabrafenib, Trametinib"],"phenotypes":null,"pub_med_references":[25265492],"rating":"5","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Melanoma","doid":"1909","drug_interaction_type":"Combination","drugs":["Trametinib","Dabrafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/6940","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"In this Phase I and II study (NCT01072175) patients with metastatic melanoma were given dabrafenib and trametinib combination therapy vs. dabrafenib monotherapy. From V600E patients, 45 received monotherapy and 92 received combination therapy. Hazard ratio for progression or death was 0.43 (95% CI, 0.27-0.71). Both patients with the BRAF V600E and V600K mutation showed significant improvement in progression-free survival.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":["NCT01072175"],"normalized_drug":["Dabrafenib, Trametinib"],"phenotypes":null,"pub_med_references":[23020132],"rating":"4","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Anaplastic Thyroid Carcinoma","doid":"0080522","drug_interaction_type":"Combination","drugs":["Trametinib","Dabrafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/6975","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"Interim analysis of a basket trial evaluating the combination of dabrafenib (BRAF inhibitor) and trametinib (MEK inhibitor) in previously treated V600E-mutated patients showed 11/16 patients with anaplastic thyroid carcinoma responded to treatment (overall response rate 69%; 95% CI, 41% to 89%). Seven patients had ongoing responses. Median duration of response, progression-free survival, and overall survival were not reached after 120 weeks.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":["NCT02034110"],"normalized_drug":["Dabrafenib, Trametinib"],"phenotypes":null,"pub_med_references":[29072975],"rating":"4","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Poor Outcome","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":null,"drugs":null,"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/7156","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"Patients with completely resected colorectal adenocarcinoma (Stage II-III) were treated with fluorouracil and leucovorin +/- ironotecan. Of the 1,307 FFPE samples tested, V600E was observed in 31 Stage II samples (7.6%) and 72 Stage III samples (7.9%). V600E was prognostic for overall survival, but not for relapse-free survival, in patients with stages II and III combined, and in stage III alone. For all MSI low and stable tumors, BRAF V600E positive samples had a hazard ratio (HR) of 2.19 (95% CI, 1.43 to 3.37, P=0.00034). For all samples in the cohort (MSI-H and MSI-L) BRAF V600E positive samples had a 1.66 HR (95% CI, 1.15 to 2.40, P=0.0069). The authors note prognostic value for BRAF V600E, especially in non-MSI high tumors.","evidence_status":"accepted","evidence_type":"Prognostic","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":null,"phenotypes":null,"pub_med_references":[20008640],"rating":"4","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Poor Outcome","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":null,"drugs":null,"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/7157","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"The CRYSTAL Phase III Trial evaluated efficacy of irinotecan, fluorouracil, and leucovorin (FOLFIRI) with or without Cetuximab for colorectal cancer patients who presented with unresectable metastatic disease. BRAF mutation status (V600E) was analyzed via LightMix BRAF V600E Kit. V600E mutations were detected in 60/999 tumor samples (6%), 59 of which were wild-type for KRAS. When comparing patients with wildtype KRAS (n=625), BRAF V600E tumors had worse outcomes relative to BRAF wildtype. For patients with BRAF V600E tumors (n=566), median overall survival (OS) was 25.1 months with cetuximab and 21.6 months without cetuximab. For patients with wildtype BRAF (n=59), median OS was 14.1 months with cetuximab and 10.3 months without cetuximab.","evidence_status":"accepted","evidence_type":"Prognostic","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":null,"phenotypes":null,"pub_med_references":[21502544],"rating":"4","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Poor Outcome","disease":"Childhood Low-grade Glioma","doid":"0080830","drug_interaction_type":null,"drugs":null,"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/7191","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"Using Sanger sequencing, BRAFV600E mutations were identified in 21 of 285 patients with PLGGs (7.4%). This mutation was enriched in hemispheric tumors (p<0.007) and was associated with shorter progression-free survival (p=0.011) and overall survival (p=0.032) [mt (n=18) vs wt (n=166)].","evidence_status":"accepted","evidence_type":"Prognostic","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":null,"phenotypes":["Pediatric onset","Early young adult onset"],"pub_med_references":[29948154],"rating":"4","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":{"asco_citation_id":"168986","asco_abstract_id":"688"},"clinical_significance":"Sensitivity/Response","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":"Combination","drugs":["Cetuximab","Encorafenib","Binimetinib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/7260","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"In a phase III trial, patients with BRAF V600E mutated metastatic colorectal cancer received triplet combination with encorafenib + binimetinib + cetuximab in a second or third-line setting. In the safety-lead in part of this trial, 30 patients were given triplet therapy, of which 29 with V600E mutation were included in the efficacy analysis. The objective response rate was 48% [95%CI: 29.4 - 67.5], median PFS was 8.0 mo [95%CI: 5.6 - 9.3], and median OS was 15.3 mo [95%CI: 9.6 - not reached]. The author concluded that triplet therapy was well tolerated and PFS and OS were substantially improved over historical standard of care.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":["NCT02928224"],"normalized_drug":["Binimetinib","Cetuximab","Encorafenib"],"phenotypes":null,"pub_med_references":null,"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":{"asco_citation_id":"169315","asco_abstract_id":"187"},"clinical_significance":"Sensitivity/Response","disease":"Biliary Tract Cancer","doid":"4607","drug_interaction_type":"Combination","drugs":["Trametinib","Dabrafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/7264","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"In a phase II trial, 33 patients with advanced or metastatic biliary tract cancer (BTC) received dabrafenib (D) and trametinib (T) in a second or higher line therapeutic context. Of the 33 patients, 30 had BRAF V600E mutated tumors, and 32 were evaluable. Objective response rate was 41% (13/32; 95% CI, 24 - 59%). Median PFS was 7.2 months (95% CI, 4.6 - 10.1 months), and median OS was 11.3 months (95% CI, 7.3 - 17.6 months). The author concluded that D+T therapy should be considered for patients with BRAF V600E mutated BTC.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":["NCT02034110"],"normalized_drug":["Dabrafenib, Trametinib"],"phenotypes":null,"pub_med_references":null,"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Langerhans Cell Sarcoma","doid":"7146","drug_interaction_type":null,"drugs":["Vemurafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/7583","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"Off-label use of vemurafenib to treat BRAF V600E mutation-positive, refractory, childhood Langerhans cell histiocytosis (LCH) was evaluated. Fifty-four patients from 12 countries were treated with vemurafenib 20 mg/kg/day. Because LCH is a heterogeneous systemic disease, the quantitative Disease Activity Score (DAS), which reflects overall LCH extension, was used as an evaluation criterion. At 8 weeks, 38 patients had CRs (non-active disease) and 16 had PRs (active disease better). DAS decreased from a median value of 7 to 0 between VMF initiation and day 60 (P < 0.001).","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":["Vemurafenib"],"phenotypes":null,"pub_med_references":[31513482],"rating":"4","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":"Combination","drugs":["Encorafenib","Binimetinib","Cetuximab"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/7612","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"665 patients with BRAF V600E-mutated metastatic CRC were enrolled In this open-label, phase 3 trial. Patients were randomly assigned in a 1:1:1 ratio to receive encorafenib, binimetinib, and cetuximab (triplet-therapy group); encorafenib and cetuximab (doublet-therapy group); or the investigators’ choice of either cetuximab and irinotecan or cetuximab and FOLFIRI. The median overall survival was 9.0 months in the triplet-therapy group and 5.4 months in the control group (hazard ratio for death, 0.52; 95% confidence interval [CI], 0.39 to 0.70; P<0.001). The confirmed response rate was 26% (95% CI, 18 to 35) in the triplet-therapy group and 2% (95% CI, 0 to 7) in the control group (triplet group vs. control P<0.001). The median progression-free survival in the triplet-therapy group was 4.3 months (95% CI, 4.1 to 5.2) and 1.5 months (95% CI, 1.5 to 1.7) in the control group (hazard ratio for disease progression or death, 0.38; 95% CI, 0.29 to 0.49; P<0.001).","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":["NCT02928224"],"normalized_drug":["Binimetinib","Cetuximab","Encorafenib"],"phenotypes":null,"pub_med_references":[31566309],"rating":"5","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":"Combination","drugs":["Vemurafenib","Irinotecan","Cetuximab"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/8506","evidence_direction":"Supports","evidence_level":"D","evidence_statement":"This in vivo study examined the efficacy of various treatments on athymic nude mice xenografted with colorectal cancer HT29 cells, which harbor BRAF V600E. The authors sought to understand whether the addition of vemurafenib (a BRAF V600E inhibitor) to agents approved for the treatment of metastatic colorectal cancer increased therapeutic efficacy, and which combinations worked best. Irinotecan, cetuximab and vemurafenib combination therapy resulted in >100% tumor growth inhibition (TGI) and 250% increased lifespan (ILS) compared to vehicle treated controls. Of the ten treated mice, nine experienced partial response and one experienced a complete response. Compared to all doublet and single agent combinations of vemurafenib, irinotecan, and cetuximab, triplet therapy produced the best TGI and ILS (p<0.05, p <0.0001 for all comparisons).","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":["Cetuximab","Irinotecan","Vemurafenib"],"phenotypes":null,"pub_med_references":[22180495],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":"Combination","drugs":["Vemurafenib","Erlotinib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/8507","evidence_direction":"Supports","evidence_level":"D","evidence_statement":"This in vivo study examined the efficacy of various treatments on athymic nude mice xenografted with colorectal cancer HT29 cells, which harbor BRAF V600E. The authors sought to understand whether the addition of vemurafenib (a BRAF V600E inhibitor) to agents approved for the treatment of metastatic colorectal cancer increased therapeutic efficacy, and which combinations worked best. Erlotinib and vemurafenib combination therapy resulted in >100% tumor growth inhibition (TGI) and 142% increased lifespan (ILS) compared to vehicle treated controls. Of ten treated mice, 9 experienced partial response. Doublet therapy produced a greater increase in TGI and ILS than either agent in isolation.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":["Erlotinib","Vemurafenib"],"phenotypes":null,"pub_med_references":[22180495],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Papillary Thyroid Carcinoma","doid":"3969","drug_interaction_type":null,"drugs":["Vemurafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/9018","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"Open label phase 2 (Clinical Level B) trial including patients from across the globe (USA, Italy, and the Netherlands) investigating sensitivity to Vemurafenib in patients that have BRAF V600E-positive papillary thyroid cancer that have become resistant to radioactive iodine (the standard treatment). There were 116 patients identified for this trial, 51 of which met the conditions to be included. These 51 patients were split into two cohorts: 1) patients that had never been treated with a multikinase inhibitor targeting VEGFR and 2) patients that have previously been treated with a VEGFR multikinase inhibitor. In cohort 1, ten of 26 patients had best overall response. Best overall response was defined as the proportion of patients with a complete or partial response, however these ten patients were all partial response. In the same cohort 1, nine had achieved stable disease control for at least six months; therefore, 19 patients achieved disease control (73% of total cohort 1, 95% CI 52-88). In cohort 2, of 23 eligible patients, six had a partial response as best overall response and six had stable disease control for at least six months; therefore, 12 patients achieved disease control. (55% of total cohort 2, 95% CI 32-76). The authors conclude that vemurafenib is a potential treatment option for late-stage BRAF V600E-positive papillary thyroid cancer for treatment in patients naïve to a multikinase inhibitor (Cohort 1) and to patients that have been previously treated with a multikinase inhibitor (Cohort 2).","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":["NCT01286753"],"normalized_drug":["Vemurafenib"],"phenotypes":null,"pub_med_references":[27460442],"rating":"4","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Poor Outcome","disease":"Papillary Thyroid Carcinoma","doid":"3969","drug_interaction_type":null,"drugs":null,"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/9170","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"Clinical study including 219 patients with papillary thyroid cancer (PTC) to determine a correlation between the BRAF V600E mutation and poor oncological outcome. This study found that 107 of the 219 (49%) patients had this mutation signifying that the BRAF V600E mutation is one of the most commonly occurring among PTC patients. This cohort was split into two groups—BRAF+ and BRAF-. Of the 107 patients that were BRAF+, 25% had tumor reoccurrence compared with 9% in the BRAF- group (P=0.004). Multivariate analysis was performed to assess BRAF correlation independent of known contributing factors to cancer such as age, gender, and multifocality. The results showed that the BRAF mutation is indicative/contributes to lymph node metastasis, associated with tumor reoccurrence, stage, and that recurrent disease was more extensive and required more aggressive treatments in BRAF+ patients compared with BRAF- patients. The authors conclude that PTC patients with the BRAF V600E mutation have worse clinicopathological outcomes, and that the BRAF mutation can be used to assess risk stratification in patients with PTC.","evidence_status":"accepted","evidence_type":"Prognostic","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":null,"phenotypes":null,"pub_med_references":[16174717],"rating":"4","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":"Combination","drugs":["Cetuximab","Encorafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/9851","evidence_direction":"Supports","evidence_level":"A","evidence_statement":"The open-label phase 3 BEACON CRC trial included 665 patients with BRAF V600E-mutated metastatic CRC. Patients were randomly assigned in a 1:1:1 ratio to receive encorafenib, binimetinib, and cetuximab (triplet-therapy group); encorafenib and cetuximab (doublet-therapy group); or the investigators’ choice of either cetuximab and irinotecan or cetuximab and FOLFIRI. The median overall survival was 8.4 months (95% CI, 7.5 to 11.0) in the doublet-therapy group and 5.4 months (95% CI, 4.8 to 6.6) in the control group, with a significantly lower risk of death compared to the control group (hazard ratio for death doublet-group vs. control, 0.60; 95% CI, 0.45 to 0.79; P<0.001). The confirmed response rate was 26% (95% CI, 18 to 35) in the triplet-therapy group, 20% in the doublet-therapy group (95% CI 13 to 29) and 2% (95% CI, 0 to 7) in the control group (doublet group vs. control P<0.001). Median PFS was 4.2 months (95% CI, 3.7 to 5.4) in the doublet-therapy group, and 1.5 months (95% CI, 1.5 to 1.7) in the control group (hazard ratio for disease progression doublet-group vs control, 0.40; 95% CI, 0.31 to 0.52, P<0.001).","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":["NCT02928224"],"normalized_drug":["Cetuximab, Encorafenib"],"phenotypes":null,"pub_med_references":[31566309],"rating":"5","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Cancer","doid":"162","drug_interaction_type":"Combination","drugs":["Dabrafenib","Trametinib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/11672","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"This NCI-MATCH trial was conducted in 35 patients of which 29 were included in the primary efficacy analysis with tumors with BRAF V600E mutations, and treated with a combination of dabrafenib and trametinib. The ORR was 37.9% (90% CI, 22.9-54.9). The median PFS and median OS were 11.4 months (90% CI, 8.4-16.3) and 28.6 months respectively. Meaningful results were achieved with this treatment with an overall DCR of 75.9%.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2024-01-22 16:58:55 UTC","nct_ids":null,"normalized_drug":["Dabrafenib, Trametinib"],"phenotypes":null,"pub_med_references":[32758030],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Low Grade Glioma","doid":"0080829","drug_interaction_type":null,"drugs":["Vemurafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/11770","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"In this trial, 19 patients with pediatric brain tumours (1 patient with Astrocytoma, 1 with Fibrillary Astrocytoma, 10 with Pilocytic Astrocytoma, 5 with Ganglioglioma and 2 with Pleomorphic Xanthoastrocytoma) harbouring BRAF V600E were treated with vemurafenib. The study reported a positive response to the treatment, with 1 complete response, 5 partial responses, and 13 patients with stable disease.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2024-03-25 21:25:38 UTC","nct_ids":["NCT01748149"],"normalized_drug":["Vemurafenib"],"phenotypes":null,"pub_med_references":[32523649],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Solid Tumor","doid":null,"drug_interaction_type":"Combination","drugs":["Dabrafenib","Trametinib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/12161","evidence_direction":"Supports","evidence_level":"A","evidence_statement":"In this trial, patients with advanced rare tumours harbouring BRAF V600E mutations were treated with a combination of dabrafenib and trametinib. The study included eight distinct cohorts: anaplastic thyroid carcinoma (ATC) (n=36), biliary tract cancer (BTC)(n=43), gastrointestinal stromal tumour (GIST) (n=1), adenocarcinoma of the small intestine (ASI) (n=3), low-grade glioma (LGG) (n=13), high-grade glioma (HGG)(n=45), hairy cell leukemia(HCL) (n=55), and multiple myeloma (MM)(n=19). The overall response rates for these cohorts were 56%, 53%, 0%, 67%, 54%, 33%, 89%, and 50% respectively. The median duration of response varied, with 14.4 months for anaplastic thyroid carcinoma, 8.9 months for biliary tract cancer, 7.7 months for adenocarcinoma of the small intestine, 31.2 months for high-grade glioma, and 11.1 months in multiple myeloma. In the remaining cohorts, the duration of response was not reached. Progression-free survival was measured at 6.7 months for ATC, 9.0 months for BTC, 9.5 months for ASI, 5.5 months for HGG, and 6.3 months for MM. PFS could not be evaluated in the LGG and HCL groups due to small patient numbers. The overall survival was 14.5 months for ATC, 13.5 months for BTC, 17.6 months for HGG, 21.8 months for ASI, and 33.9 months for MM cohorts. OS could not be evaluated for the LGG and HCL groups due to a low number of deaths. Adverse events were reported in 97.6% of the patients (n=201), with 87.9% (n=181) of these being related to the study treatment. Serious adverse events occurred in 45.1% (n=93) of patients across all cohorts.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2025-01-24 17:19:02 UTC","nct_ids":["NCT02034110"],"normalized_drug":["Dabrafenib, Trametinib"],"phenotypes":null,"pub_med_references":[37059834],"rating":"4","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Low Grade Glioma","doid":"0080829","drug_interaction_type":"Combination","drugs":["Trametinib","Dabrafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/12162","evidence_direction":"Supports","evidence_level":"A","evidence_statement":"In this trial, patients with pediatric (age <18 years) low-grade gliomas harbouring BRAF V600E (n=49), were treated with either trametinib monotherapy (n=13) or dabrafenib + trametinib (n=36). In patients treated with trametinib monotherapy, 15% (95% CI, 1.9-45.4; n=2) had objective PRs, and 46% (n=6) had stable disease for 12 or more weeks after the first dose of therapy. The estimated 24-month duration of response (DOR) was 100%. The median PFS was 16.4 months (95% CI, 3.2 to NR). In patients treated with a combination of trametinib and dabrafenib 25% (95% CI, 12.1-42.2; n=9) had objective PRs and 64% (n=23) experienced stable disease. The median DOR was 33.6 months (95% CI, 11.2 - NR), while the 24-month DOR was 80% (95% CI, 30-100). The median PFS was 36.9 months (95% CI, 36.0 - NR).","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2025-01-13 16:55:37 UTC","nct_ids":["NCT02124772"],"normalized_drug":["Dabrafenib, Trametinib"],"phenotypes":null,"pub_med_references":[36375115],"rating":"4","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null}]}],"saphetor_known_pathogenicity":[{"version":"19-Mar-2026","items":[{"annotations":{"NCBI ClinVar2":[{"functions":["coding"],"coding_impact":"missense","acmg_confirmed":false,"acmg_class":"Uncertain Significance","acmg_reannotated":"Pathogenic","source":"NCBI 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07:13:43","id":1624,"saphetorClass":"pathogenic","user_id":261,"variant_id":10190071404531360004},{"functions":["coding"],"coding_impact":"missense","acmg_confirmed":true,"acmg_class":"Pathogenic","acmg_reannotated":"Pathogenic","source":"Saphetor VarSome Comment","codon":600,"gene_symbol":"BRAF","hgvs":"V600E","transcript":"NM_004333.6","comment":"","flagged_at_timestamp":"2018-02-06 10:26:11","id":1737,"saphetorClass":"pathogenic","user_id":2582,"variant_id":10190071404531360004},{"functions":["coding"],"coding_impact":"missense","acmg_confirmed":true,"acmg_class":"Pathogenic","acmg_reannotated":"Pathogenic","source":"Saphetor VarSome Comment","codon":600,"gene_symbol":"BRAF","hgvs":"V600E","transcript":"NM_004333.6","comment":"","flagged_at_timestamp":"2019-03-30 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Genotypes AT + TT is associated with increased progression-free survival when treated with selumetinib in people with Thyroid Neoplasms as compared to genotype AA.","annotation_id":1447017413,"drug_variant_relation":"Efficacy","pub_med_references":[22241789],"id":"PA166129529","name":"selumetinib","normalized_drug":["Selumetinib"],"association":"associated"},{"significant":true,"curator_notes":"\"\"\"BRAF V600E wild-type status correlated with better survival than BRAF V600E patients (HR = 0.28, 95% CI 0.087–0.909)\"\"\" Allele T is associated with decreased overall survival when treated with FOLFIRI, FOLFOX or XELOX in people with Colorectal Neoplasms as compared to genotype AA.","annotation_id":1452367960,"drug_variant_relation":"Efficacy","pub_med_references":[38248103],"id":"PA166182863","name":"FOLFIRI","normalized_drug":["Folfiri"],"association":"associated"},{"significant":true,"curator_notes":"\"\"\"BRAF V600E wild-type status correlated with better survival than BRAF V600E patients (HR = 0.28, 95% CI 0.087–0.909)\"\"\" Allele T is associated with decreased overall survival when treated with FOLFIRI, FOLFOX or XELOX in people with Colorectal Neoplasms as compared to genotype AA.","annotation_id":1452367960,"drug_variant_relation":"Efficacy","pub_med_references":[38248103],"id":"PA166182862","name":"FOLFOX","normalized_drug":["Folfox"],"association":"associated"},{"significant":true,"curator_notes":"\"\"\"BRAF V600E wild-type status correlated with better survival than BRAF V600E patients (HR = 0.28, 95% CI 0.087–0.909)\"\"\" Allele T is associated with decreased overall survival when treated with FOLFIRI, FOLFOX or XELOX in people with Colorectal Neoplasms as compared to genotype AA.","annotation_id":1452367960,"drug_variant_relation":"Efficacy","pub_med_references":[38248103],"id":"PA166182864","name":"XELOX","normalized_drug":["Xelox"],"association":"associated"},{"curator_notes":"Dabrafenib had IC50 of 3.2nM against wild-type human BRAF (A allele) and IC50 of 0.6nM against V600E BRAF. Allele T is associated with increased sensitivity to dabrafenib as compared to allele A.","annotation_id":1447521538,"drug_variant_relation":"Efficacy","pub_med_references":[23844038],"id":"PA166114911","name":"dabrafenib","normalized_drug":["Dabrafenib"],"association":"associated"},{"curator_notes":"Dabrafenib had IC50 of 3.2nM against wild-type human BRAF (A allele) and IC50 of 0.5nM against V600K BRAF. Allele G is associated with increased sensitivity to dabrafenib as compared to allele A.","annotation_id":1447521543,"drug_variant_relation":"Efficacy","pub_med_references":[23844038],"id":"PA166114911","name":"dabrafenib","normalized_drug":["Dabrafenib"],"association":"associated"}],"disease_relations":[{"pub_med_references":[22241789],"pharmacodynamic":false,"pharmacokinetic":false,"name":"Thyroid Neoplasms","association":"associated","id":"PA445857"},{"pub_med_references":[38248103],"pharmacodynamic":false,"pharmacokinetic":false,"name":"Overall survival","association":"associated","id":"PA166123207"},{"pub_med_references":[38248103],"pharmacodynamic":false,"pharmacokinetic":false,"name":"Colorectal Neoplasms","association":"associated","id":"PA446108"},{"pub_med_references":[22241789],"pharmacodynamic":false,"pharmacokinetic":false,"name":"Progression-free 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Pathogenic, citing %%PUBMED:37231247%%, Pathogenic, citing %%PUBMED:37296851%% and Pathogenic, citing %%PUBMED:36579983%%.","Moderate: LOVD classifies this variant as Pathogenic."],"strength":"Very Strong"},{"name":"PS3","met_criteria":true,"user_explain":["Combined evidence strength is Strong (score = 4). .","Moderate: ClinVar classifies this variant as Uncertain Significance but a number of high confidence submitters have classified as Likely Pathogenic and Pathogenic, 1 star (reviewed Feb '26, 45 submissions of which 2 are from high confidence submitters), backed by functional studies (requires user validation) mentioned in 2 articles (%%PUBMED:22281684%% and %%PUBMED:17374713%%), and also citing 11 articles (%%PUBMED:34476331%%, %%PUBMED:31891627%%, %%PUBMED:29925953%%, %%PUBMED:28854169%%, %%PUBMED:25950823%%, and 6 more).","Supporting: UniProt Variants classifies this variant as Pathogenic, backed by functional studies (requires user validation) mentioned in 3 articles (%%PUBMED:23263490%%, %%PUBMED:22281684%%, and %%PUBMED:17374713%%), and also citing 9 articles (%%PUBMED:29925953%%, %%PUBMED:28854169%%, %%PUBMED:25079330%%, %%PUBMED:24717435%%, %%PUBMED:24670642%%, and 4 more).","Supporting: a VarSome user has classified this variant as Pathogenic, confirmed by a functional study, mentioned in %%PUBMED:18287029%%."]},{"name":"PM1","met_criteria":true,"user_explain":["Hot-spot of length 17 amino-acids has 46 missense/in-frame variants (37 pathogenic variants, 9 uncertain variants, and no benign), which qualifies as strong pathogenic.","UniProt protein BRAF_HUMAN domain 'Protein kinase' has 293 missense/in-frame variants (132 pathogenic variants, 160 uncertain variants, and 1 benign variant), which qualifies as moderate pathogenic.","Limiting strength to Moderate due to co-occurrence with other predictive evidence."]},{"name":"PM5","met_criteria":true,"user_explain":["Alternative variant ##chr7:140453137 C⇒T## (Val600Met) is classified Likely Pathogenic, 1 star, by ClinVar (confirmed using the germline classifier).","Alternative variant ##chr7:140453137 C⇒G## (Val600Leu) is classified Pathogenic, 2 stars, by ClinVar (confirmed using the germline classifier).","Alternative variant ##chr7:140453137 C⇒A## (Val600Leu) is classified Likely Pathogenic, 1 star, by ClinVar (confirmed using the germline classifier).","Alternative variant ##chr7:140453136 A⇒C## (Val600Gly) is classified Pathogenic, 3 stars, by ClinVar (confirmed using the germline classifier).","4 pathogenic alternative variants identified.","Limiting strength to Moderate due to co-occurrence with other predictive evidence."]},{"name":"PP3","met_criteria":true,"user_explain":["MetaRNN = 0.883 is between 0.841 and 0.939 ⇒ moderate pathogenic."],"strength":"Moderate"},{"name":"PM2","met_criteria":true,"user_explain":["Variant not found in gnomAD genomes, good gnomAD genomes coverage = 30.6.","GnomAD exomes allele count = 1 is less than 5 for AD gene BRAF, good gnomAD exomes coverage = 82.5."],"strength":"Supporting"}],"gene_id":2273,"sample_findings":{"phenotypes":"No matching phenotype found for gene BRAF which is associated with Cardiofaciocutaneous Syndrome, Cardiofaciocutaneous Syndrome 1, Colorectal Cancer, Craniopharyngioma, and 16 more, according to CGD, ClinGen Disease Validity, GenCC, Mondo, OMIM, and gene2phenotype.","mode_of_inheritance":"AD, based on gene information from CGD, ClinGen Disease Validity, GenCC, Mondo, OMIM, and gene2phenotype."}},"amp_annotation":{"version_name":"13.15.0","verdict":{"tier":"Tier I","approx_score":3.355},"classifications":[{"name":"Crtd","tier":"Tier I","user_explain":{"Tier I":["Melanoma, Colorectal Cancer, Cutaneous Melanoma, Non-Small Cell Lung Cancer, and 40 more, 19 therapies (Dabrafenib + Trametinib, Vemurafenib, Cobimetinib + Vemurafenib, Dabrafenib, and 15 more), sensitive, actionable, diagnostic, prognostic, and resistant, guideline, FDA-approved, FDA or Standard Care, Clinical Evidence, and 2 more, from CKB, OncoKB, and CIViC, citing %%PUBMED:39864891%%, %%PUBMED:39863775%%, %%PUBMED:39615406%%, %%PUBMED:39550033%%, and 94 more. No patient information was provided to match the cancer."],"Tier II":["Melanoma, Colorectal Cancer, All Solid Tumors, Non-Small Cell Lung Cancer, and 79 more, 396 therapies (Dabrafenib + Trametinib, Vemurafenib, Dabrafenib, Trametinib, and 392 more), sensitive, resistant, actionable, decreased response, and 4 more, pre-clinical, case reports, phase I clinical trial, phase II clinical trial, and 3 more, from CKB and CIViC, citing %%PUBMED:41367868%%, %%PUBMED:41066726%%, %%PUBMED:40912045%%, %%PUBMED:40481178%%, and 458 more. No patient information was provided to match the cancer."],"Tier III":["Non-Small Cell Lung Cancer, Colorectal Cancer, Melanoma, Colon Adenocarcinoma, and 2 more, 10 therapies (Vemurafenib, PF-07799933, Atezolizumab, CC-91516, and 6 more), actionable, no benefit, sensitive, emerging, and unknown, pre-clinical, case reports, clinical study, Clinical Evidence, and phase III clinical trial, from CKB and CIViC, citing %%PUBMED:38691346%%, %%PUBMED:31367539%%, %%PUBMED:30268448%%, %%PUBMED:29723688%%, and 8 more. No patient information was provided to match the cancer."]},"approx_score":9.0},{"name":"Drug","tier":"Tier I","user_explain":{"Tier I":["19 therapies (Dabrafenib + Trametinib, Vemurafenib, Cobimetinib + Vemurafenib, Dabrafenib, and 15 more), Sensitive, Actionable, Diagnostic, Prognostic, and Resistant, guideline, FDA-approved, FDA or Standard Care, Clinical Evidence, and 2 more, from CKB, OncoKB, and CIViC. Citing %%PUBMED:39864891%%, %%PUBMED:39863775%%, %%PUBMED:39615406%%, %%PUBMED:39550033%%, and 94 more. Related to Melanoma, Colorectal Cancer, Cutaneous Melanoma, Non-Small Cell Lung Cancer, and 40 more. No patient information was provided to match the cancer."],"Tier II":["396 therapies (Dabrafenib + Trametinib, Vemurafenib, Dabrafenib, Trametinib, and 392 more), Sensitive, Resistant, Actionable, Decreased Response, and 4 more, pre-clinical, case reports, phase I clinical trial, phase II clinical trial, and 3 more, from CKB and CIViC. Citing %%PUBMED:41367868%%, %%PUBMED:41066726%%, %%PUBMED:40912045%%, %%PUBMED:40481178%%, and 458 more. Related to Melanoma, Colorectal Cancer, All Solid Tumors, Non-Small Cell Lung Cancer, and 79 more. No patient information was provided to match the cancer."],"Tier III":["Searches for drugs or clinical trials are disabled because there is Tier I curated drug evidence for this variant.","10 therapies (Vemurafenib, PF-07799933, Atezolizumab, CC-91516, and 6 more), Actionable, No Benefit, Sensitive, Emerging, and Unknown, pre-clinical, case reports, clinical study, Clinical Evidence, and phase III clinical trial, from CKB and CIViC. Citing %%PUBMED:38691346%%, %%PUBMED:31367539%%, %%PUBMED:30268448%%, %%PUBMED:29723688%%, and 8 more. Related to Non-Small Cell Lung Cancer, Colorectal Cancer, Melanoma, Colon Adenocarcinoma, and 2 more. No patient information was provided to match the cancer."]},"approx_score":8.0},{"name":"Germ","tier":"Tier I","user_explain":{"Tier I":["This missense variant is classified Pathogenic by the germline classifier, using rules PP5_Very Strong, PS3, PM1, PM5, PP3_Moderate, and PM2_Supporting."]},"approx_score":7.0},{"name":"Path","tier":"Tier II","user_explain":{"Tier II":["CKB Genes reports that BRAF, serine/threonine-protein kinase B-raf, is a member of the Raf family of serine/threonine protein kinases, which signals through the MAP kinase pathway to regulate cell proliferation and cell growth (%%PUBMED:24737949%%, %%PUBMED:29540830%%). BRAF mutations and fusions have been identified in a variety of cancers, including, colorectal (%%PUBMED:30122982%%), lung (%%PUBMED:29729495%%), thyroid (%%PUBMED:12970315%%), and melanoma (%%PUBMED:24737949%%), and a number of mutations have also been demonstrated to confer drug resistance (%%PUBMED:27478040%%). 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astrrocytoma harboring BRAF V600E, with 2 other patients achieved stable disease lasting 14.9, and 5.6 months, respectively (%%PUBMED:30351999%%; NCT01524978).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"colorectal cancer","therapy_id":14099,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Encorafenib + Ulixertinib","efficacy_evidence":"In an expanded access program (ULI-EAP-100), Ulixertinib (BVD-523), Braftovi (encorafenib), and Erbitux (cetuximab) combination therapy resulted in a complete response in a patient with colorectal cancer harboring BRAF V600E (J Clin Oncol 40, no. 16_suppl (June 01, 2022) e15101; NCT04566393).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Cobimetinib, Vemurafenib","indication":"anaplastic astrocytoma","therapy_id":1657,"normalized_cancer":"Astrocytoma, IDH-Mutant, Grade 3","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"Combination of Zelboraf (vemurafenib) and Cotellic (cobimetinib) is included in guidelines for patients with recurrent anaplastic gliomas harboring BRAF V600E, including anaplastic astrocytoma (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[24423321],"response_type":"sensitive","indication":"thyroid cancer","therapy_id":3502,"normalized_cancer":"Thyroid Cancer","evidence_type":"Actionable","therapy":"CLM3","efficacy_evidence":"In a preclinical study, CLM3 inhibited growth, Egfr signaling, and CCND1 expression in thyroid cancer cells harboring BRAF V600E in culture (%%PUBMED:24423321%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[37808191],"response_type":"sensitive","indication":"melanoma","therapy_id":9644,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Tunlametinib","efficacy_evidence":"In a preclinical study, Tunlametinib (HL-085) inhibited viability and induced cell cycle arrest in melanoma cell lines harboring BRAF V600E in culture, and inhibited tumor growth in a cell line xenograft model (%%PUBMED:37808191%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[26461489],"response_type":"sensitive","indication":"melanoma","therapy_id":3698,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Cediranib + PLX4720","efficacy_evidence":"In a preclinical study, PLX4720 and Cediranib (AZD-2171) worked synergistically to inhibit cell growth and induce apoptosis in PLX4720-resistant human melanoma cell lines harboring BRAF V600E in culture and to suppress tumor growth in xenograft models (%%PUBMED:26461489%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[36759733],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":15041,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Bosutinib + Vemurafenib","efficacy_evidence":"In a preclinical study, the combination of Zelboraf (vemurafenib) and Bosulif (bosutinib) synergistically inhibited viability in colorectal cancer cell lines harboring BRAF V600E in culture (%%PUBMED:36759733%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[30959471],"normalized_drug":"Binimetinib, Encorafenib","indication":"skin melanoma","therapy_id":1100,"normalized_cancer":"Cutaneous Melanoma","evidence_type":"Actionable","therapy":"Binimetinib + Encorafenib","efficacy_evidence":"Braftovi (encorafenib) in combination with Mektovi (binimetinib) is included in guidelines as first-line and second-line therapy for patients with metastatic or unresectable cutaneous melanoma harboring BRAF V600E or V600K mutations (%%PUBMED:30959471%%; NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[27523909],"response_type":"sensitive","indication":"melanoma","therapy_id":1093,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"AZ628","efficacy_evidence":"In a preclinical study, AZ628 inhibited proliferation of melanoma cell lines harboring either monomeric BRAF V600E or dimeric isoform of V600E which conferred Zelboraf (vemurafenib)-resistance in culture (%%PUBMED:27523909%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[25589621],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":1717,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Panitumumab + Vemurafenib","efficacy_evidence":"In a Phase I trial, 83% (10/12) of patients with colorectal cancer carrying a BRAF V600E mutation demonstrated tumor regression when treated with a combination of Zelboraf (vemurafenib) and Vectibix (panitumumab) (%%PUBMED:25589621%%).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase I","amp_tier":"II"},{"pub_med_references":[40481178],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":19129,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Dasatinib + Encorafenib","efficacy_evidence":"In a preclinical study, treatment with the combination of Braftovi (encorafenib) and Sprycel (dasatinib) induced apoptosis and cell cycle arrest, inhibited colony formation and migration, and synergistically inhibited viability in colorectal cancer cell lines harboring BRAF V600E in culture and increased tumor growth inhibition in cell line and patient-derived xenograft (PDX) models compared to either drug alone (%%PUBMED:40481178%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Pdx & cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[38096472],"normalized_drug":"Cobimetinib, Vemurafenib","indication":"pancreatic cancer","therapy_id":1657,"normalized_cancer":"Pancreatic Cancer","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"In a Phase II trial (TAPUR), Zelboraf (vemurafenib) and Cotellic (cobimetinib) combination therapy resulted in a partial response in 2 patients with pancreatic cancer harboring BRAF V600E (%%PUBMED:38096472%%; NCT02693535).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[31618628],"normalized_drug":"Lifirafenib","indication":"melanoma","therapy_id":4025,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Lifirafenib","efficacy_evidence":"In a preclinical study, Lifirafenib (BGB-283) treatment inhibited viability of a melanoma cell line harboring BRAF V600E in culture (%%PUBMED:31618628%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[26208524],"normalized_drug":"Lifirafenib","indication":"melanoma","therapy_id":4025,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Lifirafenib","efficacy_evidence":"In a preclinical study, Lifirafenib (BGB-283) inhibited Braf phosphorylation and cell proliferation in melanoma cell lines harboring BRAF V600E in culture (%%PUBMED:26208524%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Vemurafenib","indication":"oncocytic carcinoma of the thyroid","therapy_id":342,"normalized_cancer":"Hurthle Cell Thyroid Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"Zelboraf (vemurafenib) is included in guidelines for patients with recurrent, advanced, or metastatic thyroid Hurthle cell carcinoma harboring BRAF V600E for whom clinical trials are not available or appropriate (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[38691346],"response_type":"predicted - sensitive","indication":"pleomorphic xanthoastrocytoma","therapy_id":13602,"normalized_cancer":"Pleomorphic Xanthoastrocytoma","evidence_type":"Actionable","therapy":"PF-07799933","efficacy_evidence":"In a Phase I trial, PF-07799933 treatment resulted in a complete response in a patient with pleomorphic xanthoastrocytoma harboring BRAF V600E (%%PUBMED:38691346%%; NCT05355701).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"decreased response","pub_med_references":[30630828],"normalized_drug":"Pembrolizumab","indication":"melanoma","therapy_id":1447,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Pembrolizumab","efficacy_evidence":"In a retrospective analysis, patients with melanoma harboring BRAF V600E (n=84) had decreased response rates (29% vs. 53%, p=0.059), progression-free survival (2.7 vs. 19 months, p=0.049), and overall survival (11.7 vs. 20.4 months, p=0.081) relative to patients with BRAF V600K (n=19) when treated with Keytruda (pembrolizumab) (n=62 and 17 for BRAF V600E and V600K, respectively) or Opdivo (nivolumab) (n=22 and 2 for BRAF V600E and V600K, respectively) (%%PUBMED:30630828%%).","cap_asco_evidence_level":"NA","molecular_profile":"BRAF V600E","approval_status":"Clinical Study","amp_tier":"NA"},{"response_type":"decreased response","pub_med_references":[37403699],"normalized_drug":"Pembrolizumab","indication":"melanoma","therapy_id":1447,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Pembrolizumab","efficacy_evidence":"In a retrospective analysis, real-world treatment with either Keytruda (pembrolizumab) or Toripalimab (JS001) resulted in a median disease-free survival of 17 months in melanoma patients harboring BRAF V600E compared to 32 months in patients with wild-type BRAF, NRAS, and KIT (p=0.022) (%%PUBMED:37403699%%).","cap_asco_evidence_level":"NA","molecular_profile":"BRAF V600E","approval_status":"Clinical Study","amp_tier":"NA"},{"response_type":"sensitive","pub_med_references":[39018564],"normalized_drug":"Cetuximab, Encorafenib","indication":"pseudomyxoma peritonei","therapy_id":1916,"normalized_cancer":"Peritoneal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Encorafenib","efficacy_evidence":"In a preclinical study, treatment with the combination of Braftovi (encorafenib) and Erbitux (cetuximab) inhibited viability and induced apoptosis in a patient-derived pseudomyxoma peritonei cell line harboring BRAF V600E in culture and inhibited tumor growth and improved survival of a patient-derived xenograft (PDX) model (%%PUBMED:39018564%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Pdx & cell culture","amp_tier":"II"},{"pub_med_references":[26461489],"response_type":"sensitive","indication":"melanoma","therapy_id":3699,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Cediranib + PLX4720 + Selumetinib","efficacy_evidence":"In a preclinical study, PLX4720, Cediranib (AZD-2171) and Koselugo (selumetinib) worked synergistically to inhibit cell growth in PLX4720-resistant melanoma cell lines harboring BRAF V600E in culture (%%PUBMED:26461489%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","indication":"colon cancer","therapy_id":18195,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Encorafenib + Fluorouracil + Leucovorin + Oxaliplatin + Panitumumab","efficacy_evidence":"Braftovi (encorafenib) in combination with Vectibix (panitumumab) and FOLFOX is included in guidelines as initial (category 2A) or subsequent-line (category 2B) therapy for patients with advanced or metastatic colon cancer harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"predicted - sensitive","pub_med_references":[36847048],"normalized_drug":"Dabrafenib, Trametinib","indication":"large cell neuroendocrine carcinoma","therapy_id":1066,"normalized_cancer":"Large Cell Neuroendocrine Carcinoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, treatment with the combination of Mekinist (trametinib) and Tafinlar (dabrafenib) resulted in a partial response in one of the lesions and a complete response in other lesions after 1 month in a patient with large cell neuroendocrine carcinoma of unknown primary harboring BRAF V600E (%%PUBMED:36847048%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[28551618],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":15620,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Binimetinib + Trifluridine-tipiracil hydrochloride","efficacy_evidence":"In a preclinical study, the addition of Mektovi (binimetinib) enhanced the efficacy of Lonsurf (trifluridine/tipiracil hydrochloride) treatment and synergistically inhibited proliferation in colorectal cancer cells harboring BRAF V600E in culture (%%PUBMED:28551618%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[31085763],"normalized_drug":"Dabrafenib, Trametinib","indication":"papillary thyroid carcinoma","therapy_id":1066,"normalized_cancer":"Papillary Thyroid Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, a papillary thyroid carcinoma patient who progressed on Lenvima (lenvatinib) was found to harbor BRAF V600E and was treated with the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) on a clinical trial, resulting in partial response in the thyroid bed, cervical and intrathoracic lymph nodes, and pulmonary lesions, with a decrease in target lesion size of 67%, and the patient remained on treatment for 18 months before stopping due to progression (%%PUBMED:31085763%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"papillary thyroid carcinoma","therapy_id":1066,"normalized_cancer":"Papillary Thyroid Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"The combination of Tafinlar (dabrafenib) and Mekinist (trametinib) is included in guidelines for patients with papillary thyroid carcinoma harboring BRAF V600E who have progressed on therapy and have no further treatment options (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[26392102],"normalized_drug":"Dabrafenib, Trametinib","indication":"colorectal cancer","therapy_id":1066,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a Phase Ib/II trial, treatment with the combination of Mekinist (trametinib) and Tafinlar (dabrafenib) resulted in partial response or better in 12% (5/43), including 1 complete response, and stable disease in 51% (22/43) of patients with colorectal cancer harboring BRAF V600E (%%PUBMED:26392102%%).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase Ib/II","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[27312529],"normalized_drug":"Dabrafenib, Trametinib","indication":"colorectal cancer","therapy_id":1066,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a preclinical study, combination therapy consisting of Tafinlar (dabrafenib) and Mekinist (trametinib) inhibited survival of colorectal cancer cell lines harboring BRAF V600E in culture (%%PUBMED:27312529%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[26208524],"normalized_drug":"Lifirafenib","indication":"Advanced Solid Tumor","therapy_id":4025,"normalized_cancer":"All Solid Tumors","evidence_type":"Actionable","therapy":"Lifirafenib","efficacy_evidence":"In a preclinical study, Lifirafenib (BGB-283) inhibited viability of a variety of cancer cell lines harboring BRAF V600E in culture (%%PUBMED:26208524%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[27312529],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":4542,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Dabrafenib + SCH772984","efficacy_evidence":"In a preclinical study, combination therapy consisting of Erbitux (cetuximab), Tafinlar (dabrafenib), and SCH772984 inhibited survival of colorectal cancer cell lines harboring BRAF V600E in culture (%%PUBMED:27312529%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[27312529],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":4543,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + SCH772984","efficacy_evidence":"In a preclinical study, combination therapy consisting of Erbitux (cetuximab) and SCH772984 inhibited survival of colorectal cancer cell lines harboring BRAF V600E in culture (%%PUBMED:27312529%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[38992135],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":17518,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"MTX-531 + Trametinib","efficacy_evidence":"In a preclinical study, treatment with the combination of Mekinist (trametinib) and MTX-531 inhibited tumor growth with a 40% partial response rate and increased survival in a patient-derived xenograft (PDX) model of colorectal cancer harboring BRAF V600E (%%PUBMED:38992135%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"pub_med_references":[39574163],"response_type":"sensitive","indication":"melanoma","therapy_id":17922,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Roflumilast + Vemurafenib","efficacy_evidence":"In a preclinical study, treatment with the combination of Roflumilast and Zelboraf (vemurafenib) inhibited colony formation and resulted in decreased spheroid size of melanoma cells harboring BRAF V600E in culture, and led to greater inhibition of tumor growth in a cell line xenograft model compared to Zelboraf (vemurafenib) alone (%%PUBMED:39574163%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[38795180],"response_type":"sensitive","indication":"thyroid cancer","therapy_id":17199,"normalized_cancer":"Thyroid Cancer","evidence_type":"Actionable","therapy":"Lenvatinib + PLX4720","efficacy_evidence":"In a preclinical study, treatment with the combination of PLX4720 and Lenvima (lenvatinib) inhibited proliferation of thyroid cancer cell lines harboring BRAF V600E in culture and resulted in greater tumor growth inhibition than PLX4720 alone in a cell line xenograft model (%%PUBMED:38795180%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"predicted - sensitive","normalized_drug":"Binimetinib, Encorafenib","indication":"Advanced Solid Tumor","therapy_id":1100,"normalized_cancer":"All Solid Tumors","evidence_type":"Actionable","therapy":"Binimetinib + Encorafenib","efficacy_evidence":"In a Phase II trial (BELIEVE), treatment with the combination of Braftovi (encorafenib) and Mektovi (binimetinib) resulted in an objective response rate of 32.7%, median progression-free survival (PFS) of 4.8 months, and 6-month PFS rate of 37.5% in patients with advanced solid tumors harboring BRAF V600E (n=43), other BRAF mutation (n=5), or a BRAF fusion (n=1) (Ann Oncol (2024) 35 (Suppl_2): S497).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[32067683],"normalized_drug":"Vemurafenib","indication":"salivary gland carcinoma","therapy_id":342,"normalized_cancer":"Salivary Carcinoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase II (MyPathway) trial, Zelboraf (vemurafenib) treatment resulted in a partial response in a patient with advanced salivary gland carcinoma harboring BRAF V600E, with a progression-free survival of 18.5 months (%%PUBMED:32067683%%; NCT02091141).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[37808191],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":15985,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Tunlametinib + Vemurafenib","efficacy_evidence":"In a preclinical study, treatment with the combination of Tunlametinib (HL-085) and Zelboraf (vemurafenib) synergistically inhibited proliferation of a colorectal cancer cell line harboring BRAF V600E in culture (%%PUBMED:37808191%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[31217909],"normalized_drug":"Vemurafenib","indication":"glioblastoma","therapy_id":342,"normalized_cancer":"Glioblastoma, IDH-Wildtype","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a clinical case study, Zelboraf (vemurafenib) treatment resulted in tumor regression as confirmed by MRI after 3-weeks of treatment in a patient with epithelioid glioblastoma harboring BRAF V600E (%%PUBMED:31217909%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[31386052],"normalized_drug":"Vemurafenib","indication":"glioblastoma","therapy_id":342,"normalized_cancer":"Glioblastoma, IDH-Wildtype","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a clinical case study, Zelboraf (vemurafenib) treatment resulted in a partial response 1 week after treatment in a patient with epithelioid type glioblastoma harboring BRAF V600E, although the patient soon passed due to complications (%%PUBMED:31386052%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[30351999],"normalized_drug":"Vemurafenib","indication":"glioblastoma","therapy_id":342,"normalized_cancer":"Glioblastoma, IDH-Wildtype","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase II trial (VE-BASKET), Zelboraf (vemurafenib) treatment resulted in stable disease as best response in 3 of 6 patients with glioblastoma harboring BRAF V600E, with stable disease lasting 3.6, 3.7, and 12.9 months, respectively (%%PUBMED:30351999%%; NCT01524978).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[36759733],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":15039,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Saracatinib + Vemurafenib","efficacy_evidence":"In a preclinical study, the combination of Zelboraf (vemurafenib) and Saracatinib (AZD0530) synergistically inhibited viability in colorectal cancer cell lines harboring BRAF V600E in culture (%%PUBMED:36759733%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[38343359],"normalized_drug":"Binimetinib, Encorafenib","indication":"anaplastic thyroid carcinoma","therapy_id":1100,"normalized_cancer":"Anaplastic Thyroid Cancer","evidence_type":"Actionable","therapy":"Binimetinib + Encorafenib","efficacy_evidence":"In a Phase II trial, Mektovi (binimetinib) and Braftovi (encorafenib) combination therapy demonstrated safety and activity in patients with thyroid cancer harboring BRAF V600E, resulting in an objective response rate (ORR) of 54.5% (12/22, 12 partial responses (PR)), with an ORR of 80% (4/5, 4 PR) and a disease control rate of 100% (5/5) in patients with anaplastic thyroid cancer, and median duration of response, progression-free survival, and overall survival were not reached (%%PUBMED:38343359%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[33043759],"normalized_drug":"Dabrafenib, Trametinib","indication":"ovarian serous carcinoma","therapy_id":1066,"normalized_cancer":"Serous Ovarian Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, Tafinlar (dabrafenib) and Mekinist (trametinib) combination therapy resulted in a complete response after 8 months of treatment in a patient with low-grade serous ovarian carcinoma harboring BRAF V600E (%%PUBMED:33043759%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[35242981],"normalized_drug":"Dabrafenib, Trametinib","indication":"ovarian serous carcinoma","therapy_id":1066,"normalized_cancer":"Serous Ovarian Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, Tafinlar (dabrafenib) and Mekinist (trametinib) combination treatment resulted in a partial response lasting at least 2.5 years in one patient with low grade serous ovarian carcinoma harboring BRAF V600E, and resulted in a complete metabolic response after 4 months of treatment in a second patient (%%PUBMED:35242981%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[26916115],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":3712,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Afatinib + BI 882370","efficacy_evidence":"In a preclinical study, colorectal cancer cells harboring BRAF V600E were sensitive to the combination of BI 882370 and Gilotrif (afatinib) in xenograft models, resulting in tumor growth inhibition and partial tumor regression (%%PUBMED:26916115%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"Adenocarcinoma of Unknown Primary","therapy_id":1066,"normalized_cancer":"Adenocarcinoma, NOS","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"The combination of Tafinlar (dabrafenib) and Mekinist (trametinib) is included in guidelines for patients with adenocarcinoma of unknown primary harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[30104724],"response_type":"resistant","indication":"melanoma","therapy_id":7839,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"RMC-4550","efficacy_evidence":"In a preclinical study, RMC-4550 did not inhibit Erk phosphorylation or proliferation of melanoma cells harboring BRAF V600E in culture (%%PUBMED:30104724%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"conflicting","pub_med_references":[27523909],"normalized_drug":"Vemurafenib","indication":"thyroid cancer","therapy_id":342,"normalized_cancer":"Thyroid Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a preclinical study, thyroid cancer cells harboring BRAF V600E demonstrated decreased sensitivity to Zelboraf (vemurafenib) in culture (%%PUBMED:27523909%%).","cap_asco_evidence_level":"NA","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"NA"},{"response_type":"conflicting","normalized_drug":"Vemurafenib","indication":"thyroid cancer","therapy_id":342,"normalized_cancer":"Thyroid Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase II trial (MyPathway), Zelboraf (vemurafenib) treatment resulted in complete response in a patient with anaplastic thyroid cancer harboring BRAF V600E (%%PUBMED:29320312%%; NCT02091141).","cap_asco_evidence_level":"NA","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"NA"},{"response_type":"sensitive","normalized_drug":"Encorafenib","indication":"melanoma","therapy_id":796,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Encorafenib","efficacy_evidence":"In preclinical studies, Encorafenib (LGX818) treatment of human melanoma xenograft models with BRAF V600E significantly decreased Mek activation and resulted in tumor regression (Cancer Res: 72(8) Suppl 1, Abstract #3790).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[30559419],"normalized_drug":"Encorafenib","indication":"melanoma","therapy_id":796,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Encorafenib","efficacy_evidence":"In a preclinical study, Braftovi (encorafenib) treatment inhibited Erk phosphorylation and reduced proliferation of melanoma cells harboring monomeric BRAF V600E in culture (%%PUBMED:30559419%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[25285888],"normalized_drug":"Dabrafenib","indication":"thyroid gland carcinoma","therapy_id":3,"normalized_cancer":"Thyroid Cancer","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a Phase I trial, Tafinlar (dabrafenib) treatment resulted in a partial response in 29% (4/14) and stable disease in 43% (6/14) of patients with thyroid carcinoma harboring BRAF V600E, with 64% (9/14) of patients achieved at least a 10% decrease by RECIST, and a median progression-free survival of 11.3 months among responders (%%PUBMED:25285888%%; NCT00880321).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[33568355],"response_type":"sensitive","indication":"melanoma","therapy_id":11478,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + LXH 254 + Trametinib","efficacy_evidence":"In a preclinical study, combination treatment with LXH 254, Tafinlar (dabrafenib), and Mekinist (trametinib) in a melanoma cell line harboring BRAF V600E resulted in suppression of colony formation in culture (%%PUBMED:33568355%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"gastroesophageal junction adenocarcinoma","therapy_id":1066,"normalized_cancer":"Adenocarcinoma of the Gastroesophageal Junction","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Tafinlar (dabrafenib) and Mekinist (trametinib) combination therapy is included in guidelines as second-line or subsequent therapy for patients with locally advanced, recurrent, or metastatic gastroesophageal junction adenocarcinoma harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"resistant","pub_med_references":[22649091],"normalized_drug":"Dasatinib","indication":"lung carcinoma","therapy_id":717,"normalized_cancer":"Lung Cancer","evidence_type":"Actionable","therapy":"Dasatinib","efficacy_evidence":"In a preclinical study, Sprycel (dasatinib) failed to induce apoptosis in lung carcinoma cells expressing BRAF V600E (%%PUBMED:22649091%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"ovarian serous carcinoma","therapy_id":7465,"normalized_cancer":"Serous Ovarian Cancer","evidence_type":"Actionable","therapy":"BGB3245","efficacy_evidence":"In a Phase I trial, BGB3245 treatment demonstrated manageable safety and resulted in a disease control rate of 48% (16/33,1 complete response, 5 confirmed partial responses (PR), 2 unconfirmed PR, and 8 stable disease > 24 weeks) in patients with advanced solid tumors harboring MAPK pathway alterations, including a partial response in a patient with low grade serous ovarian carcinoma harboring BRAF V600E (Cancer Res (2023) 83 (8_Supplement): CT031).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[27523909],"response_type":"sensitive","indication":"thyroid cancer","therapy_id":3300,"normalized_cancer":"Thyroid Cancer","evidence_type":"Actionable","therapy":"TAK-632","efficacy_evidence":"In a preclinical study, TAK-632 inhibited proliferation of thyroid cancer cells harboring BRAF V600E in culture (%%PUBMED:27523909%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[26810733],"response_type":"sensitive","indication":"melanoma","therapy_id":6368,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"EBI-907","efficacy_evidence":"In a preclinical study, EBI-907 inhibited BRAF and ERK signaling, resulted in growth inhibition of melanoma cells harboring BRAF V600E in culture and in cell line xenograft models (%%PUBMED:26810733%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[27362227],"response_type":"resistant","indication":"colorectal cancer","therapy_id":4504,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"SHP099","efficacy_evidence":"In a preclincial study, colorectal cancer cell lines harboring BRAF V600E demonstrated resistance to SHP099 in culture (%%PUBMED:27362227%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[34956922],"normalized_drug":"Dabrafenib, Trametinib","indication":"thyroid gland carcinoma","therapy_id":1066,"normalized_cancer":"Thyroid Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, Mekinist (trametinib) and Tafinlar (dabrafenib) combination treatment resulted in a partial response after 3 months in a patient with metastatic squamous cell carcinoma of the thyroid harboring BRAF V600E (%%PUBMED:34956922%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[33568355],"response_type":"sensitive","indication":"melanoma","therapy_id":11479,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + RAF709 + Trametinib","efficacy_evidence":"In a preclinical study, combination treatment with RAF709, Tafinlar (dabrafenib), and Mekinist (trametinib) in melanoma cell line harboring BRAF V600E resulted in suppression of colony formation in culture (%%PUBMED:33568355%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[28784858],"normalized_drug":"Dabrafenib","indication":"pilocytic astrocytoma","therapy_id":3,"normalized_cancer":"Pilocytic Astrocytoma","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a clinical case study, Tafinlar (dabrafenib) treatment resulted in a near complete response and resolution of leptomeningeal dissemination in a patient with pilocytic astrocytoma harboring BRAF V600E (%%PUBMED:28784858%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[22180495],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":1331,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Irinotecan + Vemurafenib","efficacy_evidence":"In a preclinical study, Zelboraf (vemurafenib) treatment in combination with Erbitux (cetuximab) and Camptosar (irinotecan) enhanced tumor growth inhibition and increased survival in a cell line xenograft model of colorectal cancer harboring BRAF V600E (%%PUBMED:22180495%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[33356422],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":1331,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Irinotecan + Vemurafenib","efficacy_evidence":"In a Phase II trial (SWOG1406), addition of Zelboraf (vemurafenib) to Camptosar (irinotecan) plus Erbitux (cetuximab) improved progression-free survival (4.4 vs. 2.0 mo, HR 0.50, p=0.001), response rate (17% vs 4%, p=0.05), and disease control rate (67% vs. 22%, p<0.001) in patients with metastatic colorectal cancer harboring BRAF V600E (%%PUBMED:33356422%%; NCT02164916).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[32182156],"normalized_drug":"Lifirafenib","indication":"thyroid cancer","therapy_id":4025,"normalized_cancer":"Thyroid Cancer","evidence_type":"Actionable","therapy":"Lifirafenib","efficacy_evidence":"In a Phase I trial, Lifirafenib (BGB-283) treatment resulted in partial response in 15.1% (8/53) of solid tumor patients with BRAF mutations, including 2 thyroid cancer patients harboring BRAF V600E (1 in dose-escalation phase, 1 in the dose-expansion), and in the dose-expansion phase 1 of 3 thyroid cancer patients harboring a BRAF V600 mutation demonstrated a partial response and 2 demonstrated stable disease, resulting in a disease control rate of 100% (3/3) (%%PUBMED:32182156%%; NCT02610361).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[27424159],"normalized_drug":"Cobimetinib","indication":"melanoma","therapy_id":1004,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Cobimetinib","efficacy_evidence":"In a Phase I trial, Cotellic (cobimetinib) treatment resulted in a confirmed partial response in six melanoma patients harboring BRAF V600E (%%PUBMED:27424159%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[25665005],"response_type":"sensitive","indication":"melanoma","therapy_id":1386,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Navitoclax + Trametinib","efficacy_evidence":"In a preclinical study, Navitoclax (ABT-263) enhanced the inhibitory effect of Mekinist (trametinib) on human melanoma cells harboring BRAF V600E in culture (%%PUBMED:25665005%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[31848189],"response_type":"predicted - sensitive","indication":"colorectal cancer","therapy_id":2149,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Ravoxertinib","efficacy_evidence":"In a Phase I trial, two colorectal cancer patients harboring BRAF V600E achieved partial responses lasting 21 and 73 weeks following treatment with Ravoxertinib (GDC-0994) (%%PUBMED:31848189%%; NCT01875705).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[31566309],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":4886,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Binimetinib + Cetuximab + Encorafenib","efficacy_evidence":"In a Phase III (BEACON CRC) trial, Braftovi (encorafenib), Mektovi (binimetinib), and Erbitux (cetuximab) combination treatment (n=111) resulted in improved median overall survival (9.0 vs 5.4 months, HR=0.52, p<0.001), confirmed response rate (26% vs 2%, p<0.001), and median progression-free survival (4.3 vs 1.5 months, HR=0.38, p<0.001) compared to control (n=107) in patients with metastatic colorectal cancer harboring BRAF V600E (%%PUBMED:31566309%%; NCT02928224).","cap_asco_evidence_level":"B","molecular_profile":"BRAF V600E","approval_status":"Phase III","amp_tier":"I"},{"pub_med_references":[39255538],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":4886,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Binimetinib + Cetuximab + Encorafenib","efficacy_evidence":"In a retrospective analysis, real-world treatment with Erbitux (cetuximab) and Braftovi (encorafenib) with or without Mektovi (binimetinib) led to an objective response rate (ORR) of 32.2% (57/201, 2 complete responses (CR)), disease control rate of 71.2% (126/201), median progression-free survival of 4.5 months, and median overall survival of 9.2 months in metastatic colorectal cancer patients with BRAF V600E, with an ORR of 33.3% (7/21, 1 CR) in patients treated with triplet therapy (%%PUBMED:39255538%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Clinical Study","amp_tier":"II"},{"pub_med_references":[35696748],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":4886,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Binimetinib + Cetuximab + Encorafenib","efficacy_evidence":"In a retrospective study, combination treatment with Mektovi (binimetinib), Erbitux (cetuximab), and Braftovi (encorafenib) resulted in an objective response rate of 31%, a disease control rate of 78%, a median progression-free survival of 4.2 mo, and a median overall survival of 7.1 mo in patients with metastatic colorectal cancer harboring BRAF V600E (%%PUBMED:35696748%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Clinical Study","amp_tier":"II"},{"pub_med_references":[36763936],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":4886,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Binimetinib + Cetuximab + Encorafenib","efficacy_evidence":"In a Phase II (ANCHOR CRC) trial, Braftovi (encorafenib), Mektovi (binimetinib), and Erbitux (cetuximab) combination treatment (n=95) demonstrated an acceptable safety profile and resulted in a confirmed objective response rate of 47.8% (44/92), a disease control rate of 88% (81/92), a median progression-free survival of 5.8 months, and a median overall survival of 18.3 months in patients with metastatic colorectal cancer harboring BRAF V600E (%%PUBMED:36763936%%; NCT03693170).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Selumetinib","indication":"pilocytic astrocytoma","therapy_id":913,"normalized_cancer":"Pilocytic Astrocytoma","evidence_type":"Actionable","therapy":"Selumetinib","efficacy_evidence":"Koselugo (selumetinib) is included in guidelines for patients with recurrent or progressive pilocytic astrocytoma harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[36409971],"normalized_drug":"Cobimetinib, Vemurafenib","indication":"colorectal cancer","therapy_id":1657,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"In a Phase II trial (TAPUR), the combination of Cotellic (cobimetinib) and Zelboraf (vemurafenib) resulted in an objective response rate of 30% (8/27; all partial responses), a disease control rate of 52% (14/27), a median progression-free survival of 15.7 weeks, and a median overall survival of 38.9 weeks in patients with colorectal cancer harboring BRAF V600E (n=26) or K601E (n=1) (%%PUBMED:36409971%%; NCT02693535).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[28649441],"normalized_drug":"Cobimetinib, Vemurafenib","indication":"colorectal cancer","therapy_id":1657,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"In a preclinical study, the combination of Cotellic (cobimetinib) and Zelboraf (vemurafenib) inhibited tumor growth in a cell line xenograft model of colorectal cancer harboring BRAF V600E (%%PUBMED:28649441%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[33595872],"response_type":"sensitive","indication":"thyroid cancer","therapy_id":4544,"normalized_cancer":"Thyroid Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + SCH772984","efficacy_evidence":"In a preclinical study, combination treatment with Tafinlar (dabrafenib) and SCH772984 synergistically inhibited cell growth of thyroid cancer cell lines harboring BRAF V600E in culture, and inhibited tumor growth in a cell line xenograft model (%%PUBMED:33595872%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[26603897],"response_type":"sensitive","indication":"melanoma","therapy_id":3310,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"SBI-0640756 + Vemurafenib","efficacy_evidence":"In a preclinical study, Zelboraf (vemurafenib) in combination with SBI-0640756 inhibited the association of eIF4G1 and eIF4E in Zelboraf (vemurafenib) resistant human melanoma cell lines harboring BRAF V600E in culture and reduced tumor growth in xenograft models (%%PUBMED:26603897%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[33953400],"response_type":"predicted - sensitive","indication":"melanoma","therapy_id":7209,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Belvarafenib","efficacy_evidence":"In a preclinical study, Belvarafenib (HM95573) treatment led to inhibition of tumor growth in a melanoma cell line xenograft model harboring BRAF V600E (%%PUBMED:33953400%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[27312529],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":1711,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Vemurafenib","efficacy_evidence":"In a preclinical study, Zelboraf (vemurafenib) and Erbitux (cetuximab) combination treatment inhibited survival of colorectal cancer cell lines harboring BRAF V600E in culture (%%PUBMED:27312529%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[22180495],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":1711,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Vemurafenib","efficacy_evidence":"In a preclinical study, Zelboraf (vemurafenib) treatment in combination with Erbitux (cetuximab) enhanced tumor growth inhibition and increased survival in a cell line xenograft model of colorectal cancer harboring BRAF V600E (%%PUBMED:22180495%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[24523613],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":1711,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Vemurafenib","efficacy_evidence":"In a clinical case study, the combination of Zelboraf (vemurafenib) and Erbitux (cetuximab) was tolerated and showed clinical benefit in a patient with BRAF V600E mutant colorectal cancer (%%PUBMED:24523613%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[41066726],"normalized_drug":"Plx8394","indication":"histiocytosis","therapy_id":1041,"normalized_cancer":"Histiocytosis","evidence_type":"Actionable","therapy":"PLX8394","efficacy_evidence":"In a Phase I/II trial (PLX120-03), PLX8394 treatment resulted in clinical symptom improvement and stable disease ongoing for at least 6.5 years in a young adult patient with recurrent neurodegenerative Langerhans cell histiocytosis harboring BRAF V600E (%%PUBMED:41066726%%; NCT02428712).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[38096472],"normalized_drug":"Cobimetinib, Vemurafenib","indication":"clear cell sarcoma","therapy_id":1657,"normalized_cancer":"Clear Cell Sarcoma","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"In a Phase II trial (TAPUR), Zelboraf (vemurafenib) and Cotellic (cobimetinib) combination therapy resulted in a partial response in a patient with clear cell sarcoma harboring BRAF V600E (%%PUBMED:38096472%%; NCT02693535).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case 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combination of Tafinlar (dabrafenib) and Mekinist (trametinib) resulted in decreased tumor size lasting at least 9 months in an adolescent (18 years old) patient with malignant glomus tumor harboring BRAF V600E (%%PUBMED:30556047%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[35882450],"response_type":"sensitive","indication":"pleomorphic xanthoastrocytoma","therapy_id":14717,"normalized_cancer":"Pleomorphic Xanthoastrocytoma","evidence_type":"Actionable","therapy":"Ulixertinib + Vinblastine","efficacy_evidence":"In a preclinical study, the combination of Ulixertinib (BVD-523) and Velban (vinblastine) inhibited proliferation and had a synergistic effect on induction of apoptosis in a pleomorphic xanthoastrocytoma cell line harboring BRAF V600E in culture (%%PUBMED:35882450%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell 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(trametinib) is included in guidelines as subsequent-line therapy for patients with biliary tract cancer harboring BRAF V600E, including intrahepatic cholangiocarcinoma, extrahepatic cholangiocarcinoma, and gallbladder cancer (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[39864891],"normalized_drug":"Dabrafenib, Trametinib","indication":"biliary tract cancer","therapy_id":1066,"normalized_cancer":"Biliary Tract Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Tafinlar (dabrafenib) in combination with Mekinist (trametinib) is included in guidelines as second or later-line therapy for patients with biliary tract cancer harboring BRAF V600E (%%PUBMED:39864891%%; ESMO.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[32818466],"normalized_drug":"Dabrafenib, Trametinib","indication":"biliary tract cancer","therapy_id":1066,"normalized_cancer":"Biliary Tract Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a Phase II trial (ROAR), Tafinlar (dabrafenib) in combination with Mekinist (trametinib) demonstrated a manageable safety profile and resulted in an overall response rate of 51% (22/43, all partial responses) in patients with biliary tract cancer harboring BRAF V600E, with a median duration of response of 9 months, a median progression-free survival of 9 months, and a median overall survival of 14 months (%%PUBMED:32818466%%; NCT02034110).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase 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(%%PUBMED:32234759%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"pub_med_references":[26461489],"response_type":"sensitive","indication":"melanoma","therapy_id":3700,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"PLX4720 + Tivozanib","efficacy_evidence":"In a preclinical study, PLX4720 and Tivozanib (AV-951) worked synergistically to inhibit cell growth in PLX4720-resistant melanoma cell lines harboring BRAF V600E in culture (%%PUBMED:26461489%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[28645859],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":6241,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"INU-152","efficacy_evidence":"In a preclinical study, INU-152 inhibited growth of colorectal cancer cell lines harboring BRAF V600E in culture, and reduced tumor growth in BRAF V600E-mutant colorectal cancer cell line xenograft models (%%PUBMED:28645859%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Vemurafenib","indication":"Erdheim-Chester disease","therapy_id":342,"normalized_cancer":"Erdheim-Chester Disease","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"Zelboraf (vemurafenib) is included in guidelines as preferred first-line or subsequent-line therapy for patients with Erdheim-Chester disease harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"predicted - sensitive","pub_med_references":[39376796],"normalized_drug":"Dabrafenib, Trametinib","indication":"lung adenocarcinoma","therapy_id":1066,"normalized_cancer":"Lung 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lung adenocarcinoma harboring BRAF V600E and germline BRCA L1908Rfs*2, who had previously progressed on several lines of therapy (%%PUBMED:38715777%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[36531075],"normalized_drug":"Dabrafenib, Trametinib","indication":"Her2-receptor negative breast cancer","therapy_id":1066,"normalized_cancer":"Invasive Breast Carcinoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) resulted in a complete response in the liver and bone lesions with a progression-free survival of 9 months in a patient with metastatic ERBB2 (HER2)-negative, hormone receptor-positive breast cancer harboring BRAF V600E (%%PUBMED:36531075%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[32029534],"normalized_drug":"Vemurafenib","indication":"histiocytic and dendritic cell cancer","therapy_id":342,"normalized_cancer":"Histiocytic and Dendritic Cell Neoplasms","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase II trial (VE-BASKET), responses were seen in patients with histiocytic neoplasms harboring BRAF V600E (n=27) when treated with Zelboraf (vemurafenib), including 15 patients with a partial response and 2 patients with a complete response (%%PUBMED:32029534%%; NCT01524978).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[19706763],"normalized_drug":"Refametinib","indication":"colorectal cancer","therapy_id":888,"normalized_cancer":"Colorectal 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inhibited growth of melanoma cells harboring BRAF V600E in culture (%%PUBMED:22389471%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[28268064],"normalized_drug":"Dabrafenib, Trametinib","indication":"melanoma","therapy_id":1066,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a Phase II trial, BRAF V600E positive melanoma patients who progressed on treatment with BRAF inhibitors or the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) were treated again with the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) after 12 weeks off treatment, which resulted in a partial response in 35% (8/25) and stable disease in 40% (10/25) (%%PUBMED:28268064%%).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase 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Diagnostic","amp_tier":"I"},{"pub_med_references":[37838724],"response_type":"sensitive","indication":"melanoma","therapy_id":16290,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"ARCC4 + Dabrafenib","efficacy_evidence":"In a preclinical study, the addition of ARCC4 to Tafinlar (dabrafenib) treatment inhibited colony formation in melanoma cell lines harboring BRAF V600E in culture (%%PUBMED:37838724%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[34433654],"response_type":"predicted - sensitive","indication":"high grade glioma","therapy_id":7209,"normalized_cancer":"High-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"Belvarafenib","efficacy_evidence":"In a preclinical study, Belvarafenib (HM95573) treatment led to inhibition of cell viability in a patient-derived glioma cell line harboring BRAF V600E in culture (%%PUBMED:34433654%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"anaplastic astrocytoma","therapy_id":1066,"normalized_cancer":"Astrocytoma, IDH-Mutant, Grade 3","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Combination of Mekinist (trametinib) and Tafinlar (dabrafenib) is included in guidelines for patients with recurrent anaplastic gliomas harboring BRAF V600E, including anaplastic astrocytoma (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[25665005],"response_type":"sensitive","indication":"melanoma","therapy_id":3530,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Navitoclax + Vemurafenib","efficacy_evidence":"In a preclinical study, Navitoclax (ABT-263) enhanced the inhibitory effect of Zelboraf (vemurafenib) on human melanoma cells harboring BRAF V600E in culture (%%PUBMED:25665005%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[27312529],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":4536,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Selumetinib","efficacy_evidence":"In a preclinical study, Koselugo (selumetinib) and Erbitux (cetuximab) combination treatment inhibited survival of colorectal cancer cell lines harboring BRAF V600E in culture (%%PUBMED:27312529%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[34476331],"normalized_drug":"Dabrafenib, Trametinib","indication":"pancreatic cancer","therapy_id":1066,"normalized_cancer":"Pancreatic Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a retrospective analysis, treatment with the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) resulted in a partial response in two patients with pancreatic cancer harboring BRAF V600E, including one patient with a progression-free survival (PFS) of at least 2 years on third-line therapy and another patient with a PFS of 48 weeks on second-line therapy (%%PUBMED:34476331%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[33953400],"response_type":"predicted - sensitive","indication":"colorectal cancer","therapy_id":7209,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Belvarafenib","efficacy_evidence":"In a Phase I trial, Belvarafenib (HM95573) treatment in a colorectal cancer patient harboring BRAF V600E led to a tumor reduction of 39% after 8 weeks of treatment and a confirmed partial response at 12 weeks, and response to treatment was maintained for 8 weeks (%%PUBMED:33953400%%; NCT03118817).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[24398428],"normalized_drug":"Ganetespib","indication":"skin melanoma","therapy_id":745,"normalized_cancer":"Cutaneous Melanoma","evidence_type":"Actionable","therapy":"Ganetespib","efficacy_evidence":"In a preclinical study, the Hsp90 inhibitor Ganetespib destabilized BRAF, especially BRAF V600E, resulted in loss of cell viability in culture and antitumor effects in cell line xenograft models of melanoma (%%PUBMED:24398428%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line 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in guidelines as neoadjuvant or systemic treatment for thyroid gland anaplastic carcinoma patients harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[27697975],"normalized_drug":"Dabrafenib, Trametinib","indication":"anaplastic thyroid carcinoma","therapy_id":1066,"normalized_cancer":"Anaplastic Thyroid Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, Tafinlar (dabrafenib) and Mekinist (trametinib) combination treatment resulted in a clinical and radiologic response that lasted for 9 months in an anaplastic thyroid cancer patient harboring BRAF V600E (%%PUBMED:27697975%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case 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melanoma cell line harboring BRAF V600E in culture, and inhibited tumor growth in patient-derived xenograft (PDX) models, including a Zelboraf (vemurafenib)-resistant PDX model (%%PUBMED:34337566%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Pdx & cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[32029534],"normalized_drug":"Vemurafenib","indication":"salivary gland cancer","therapy_id":342,"normalized_cancer":"Salivary Gland Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase II trial (VE-BASKET), a patient with salivary ductal carcinoma harboring BRAF V600E demonstrated a partial response when treated with Zelboraf (vemurafenib) (%%PUBMED:32029534%%; NCT01524978).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[26267534],"response_type":"sensitive","indication":"melanoma","therapy_id":2618,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"SCH772984","efficacy_evidence":"In a preclinical study, SCH772984 inhibited growth of melanoma cell lines harboring BRAF V600E in culture (%%PUBMED:26267534%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[25665005],"response_type":"sensitive","indication":"melanoma","therapy_id":3532,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Trametinib + TW-37","efficacy_evidence":"In a preclinical study, TW-37 enhanced the inhibitory effect of Mekinist (trametinib) on human melanoma cells harboring BRAF V600E in culture (%%PUBMED:25665005%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"response_type":"predicted - 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Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase II trial (VE-BASKET), Zelboraf (vemurafenib) treatment resulted in a response in patients with anaplastic thyroid carcinoma harboring BRAF V600E (n=12), including 1 patient with a complete response and 2 patients with a partial response (%%PUBMED:32029534%%; NCT01524978).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","normalized_drug":"Vemurafenib","indication":"ovarian cancer","therapy_id":342,"normalized_cancer":"Ovarian Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase II trial (MyPathway), Zelboraf (vemurafenib) treatment resulted in an objective response of 50% (2/4, 2 partial response) in patients with ovarian cancer harboring BRAF V600E, and stable disease lasting more than 120 days in 1 patient (%%PUBMED:29320312%%; NCT02091141).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[32029534],"normalized_drug":"Vemurafenib","indication":"ovarian cancer","therapy_id":342,"normalized_cancer":"Ovarian Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase II trial (VE-BASKET), responses were seen in ovarian cancer patients harboring BRAF V600E (n=4) when treated with Zelboraf (vemurafenib), including 2 patients with a partial response (%%PUBMED:32029534%%; NCT01524978).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[25665005],"response_type":"sensitive","indication":"melanoma","therapy_id":3531,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"TW-37 + Vemurafenib","efficacy_evidence":"In a preclinical study, TW-37 enhanced the inhibitory effect of Zelboraf (vemurafenib) on human melanoma cells harboring BRAF V600E in culture (%%PUBMED:25665005%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"response_type":"resistant","pub_med_references":[19001320],"normalized_drug":"Panitumumab","indication":"colorectal cancer","therapy_id":845,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Panitumumab","efficacy_evidence":"In a retrospective analysis, metastatic colorectal cancer patients harboring BRAF V600E demonstrated shorter progression-free survival (p=0.0107) and overall survival (p<0.0001) compared to patients with wild-type BRAF following Vectibix (panitumumab) or Erbitux (cetuximab) therapy with or without chemotherapy, and in a preclinical study, colorectal cancer cell lines harboring BRAF V600E were resistant to Vectibix (panitumumab) in culture (%%PUBMED:19001320%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Clinical Study","amp_tier":"II"},{"response_type":"resistant","pub_med_references":[25673558],"normalized_drug":"Panitumumab","indication":"colorectal cancer","therapy_id":845,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Panitumumab","efficacy_evidence":"In a meta-analysis, the addition of Erbitux (cetuximab) or Vectibix (panitumumab) to standard of care treatment with chemotherapy did not result in improved progression-free survival (HR=0.88; 95% CI, 0.67-1.14; p=0.33), overall survival (HR=0.91; 95% CI, 0.62-1.34; p=0.63), or objective response rate (relative risk=1.31; 95% CI, 0.83-2.08; p=0.25) in patients with advanced colorectal cancer harboring BRAF V600E (%%PUBMED:25673558%%).","cap_asco_evidence_level":"B","molecular_profile":"BRAF V600E","approval_status":"Clinical Study - Meta-analysis","amp_tier":"I"},{"response_type":"resistant","pub_med_references":[36307056],"normalized_drug":"Panitumumab","indication":"colorectal cancer","therapy_id":845,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Panitumumab","efficacy_evidence":"Vectibix (panitumumab), as a monotherapy, is not indicated for use in metastatic colorectal cancer patients with BRAF V600E (%%PUBMED:36307056%%; ESMO.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[26573800],"response_type":"decreased response","indication":"glioblastoma","therapy_id":1060,"normalized_cancer":"Glioblastoma, IDH-Wildtype","evidence_type":"Actionable","therapy":"PLX4720","efficacy_evidence":"In a preclinical study, a glioblastoma cell line harboring BRAF V600E demonstrated a decreased response to treatment with PLX4720, demonstrating increased viability of CD133 positive cells in culture and in xenograft models (%%PUBMED:26573800%%).","cap_asco_evidence_level":"NA","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"NA"},{"response_type":"sensitive","normalized_drug":"Cobimetinib, Vemurafenib","indication":"low grade glioma","therapy_id":1657,"normalized_cancer":"Low-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"Combination of Zelboraf (vemurafenib) and Cotellic (cobimetinib) is included in guidelines for patients with recurrent or progressive low grade glioma harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[27048246],"normalized_drug":"Dabrafenib, Trametinib","indication":"neuroendocrine tumor","therapy_id":1066,"normalized_cancer":"Gastrointestinal Neuroendocrine Tumor","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, Mekinist (trametinib) and Tafinlar (dabrafenib) combination treatment resulted in a rapid and sustained clinical response in a patient with a rectal neuroendocrine tumor harboring a BRAF V600E mutation (%%PUBMED:27048246%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"neuroendocrine tumor","therapy_id":1066,"normalized_cancer":"Gastrointestinal Neuroendocrine Tumor","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Mekinist (trametinib) and Tafinlar (dabrafenib) combination therapy is included in guidelines for patients with unresectable or metastatic extrapulmonary poorly differentiated neuroendocrine carcinoma, large or small cell carcinoma, or mixed neuroendocrine/non-neuroendocrine neoplasms harboring BRAF V600E who have progressed on or following prior treatment (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[34330842],"response_type":"sensitive","indication":"melanoma","therapy_id":6971,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"ASTX029","efficacy_evidence":"In a preclinical study, ASTX029 treatment reduced Erk and Rsk phosphorylation, induced cell-cycle arrest, and inhibited growth of a melanoma cell line harboring BRAF V600E in culture and inhibited tumor growth in cell line xenograft models, and was also effective against cells with acquired resistance to Zelboraf (vemurafenib) or Koselugo (selumetinib) (%%PUBMED:34330842%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[39399174],"normalized_drug":"Trametinib","indication":"diffuse leptomeningeal glioneuronal tumor","therapy_id":2,"normalized_cancer":"Miscellaneous Neuroepithelial Tumor","evidence_type":"Actionable","therapy":"Trametinib","efficacy_evidence":"In a clinical case study, Mekinist (trametinib) treatment resulted in a partial response in the brain and stable disease in the spine in a pediatric patient with diffuse leptomeningeal glioneuronal tumor harboring BRAF V600E (%%PUBMED:39399174%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"not predictive","pub_med_references":[29723688],"normalized_drug":"Atezolizumab","indication":"lung non-small cell carcinoma","therapy_id":1201,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Atezolizumab","efficacy_evidence":"In a retrospective analysis, non-small cell lung cancer patients harboring BRAF V600E did not demonstrate a significantly different response to treatment with either Keytruda (pembrolizumab), Opdivo (nivolumab), or Tecentriq (atezolizumab) compared to patients with BRAF non-V600E mutations, demonstrating an objective response rate of 25% (3/12) vs 33% (3/9) (p=1.0) and median progression-free survival of 3.7 months vs 4.1 months (p=0.37) (%%PUBMED:29723688%%).","cap_asco_evidence_level":"NA","molecular_profile":"BRAF V600E","approval_status":"Clinical Study - Cohort","amp_tier":"NA"},{"response_type":"sensitive","normalized_drug":"Vemurafenib","indication":"high grade glioma","therapy_id":342,"normalized_cancer":"High-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"Zelboraf (vemurafenib) is included in guidelines as adjuvant therapy for pediatric patients with diffuse high-grade gliomas harboring BRAF V600E, or as a preferred regimen for patients with recurrent or progressive disease (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[32029534],"normalized_drug":"Vemurafenib","indication":"high grade glioma","therapy_id":342,"normalized_cancer":"High-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase II trial (VE-BASKET), responses were seen in glioma patients harboring BRAF V600E (n=24) when treated with Zelboraf (vemurafenib), including 1 patient with a complete response and 5 patients with a partial response (%%PUBMED:32029534%%; NCT01524978).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[30351999],"normalized_drug":"Vemurafenib","indication":"high grade glioma","therapy_id":342,"normalized_cancer":"High-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase II trial (VE-BASKET), Zelboraf (vemurafenib) treatment resulted in an objective response rate of 25% (6/24, 1 complete response, 5 partial responses) in patients with gliomas harboring BRAF V600E, with a median progression free survival of 5.5-months, a median overall survival of 28.2 months (%%PUBMED:30351999%%; NCT01524978).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[24859340],"normalized_drug":"Vemurafenib","indication":"ameloblastoma","therapy_id":342,"normalized_cancer":"Head and Neck Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a preclinical study, Zelboraf (vemurafenib) inhibited viability of an ameloblastoma cell line harboring BRAF V600E in culture (%%PUBMED:24859340%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[35689405],"normalized_drug":"Vemurafenib","indication":"ameloblastoma","therapy_id":342,"normalized_cancer":"Head and Neck Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a preclinical study, Zelboraf (vemurafenib) inhibited viability of ameloblastoma cell lines harboring BRAF V600E in culture (%%PUBMED:35689405%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Vemurafenib","indication":"skin melanoma","therapy_id":342,"normalized_cancer":"Cutaneous Melanoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"Zelboraf (vemurafenib) therapy is included in guidelines for cutaneous melanoma patients with unresectable or metastatic disease harboring BRAF V600 activating mutations, such as BRAF V600E, in cases where BRAF/MEK inhibitor combination therapy is contraindicated (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","normalized_drug":"Dabrafenib","indication":"skin melanoma","therapy_id":3,"normalized_cancer":"Cutaneous Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"Tafinlar (dabrafenib) therapy is included in guidelines for cutaneous melanoma patients with unresectable or metastatic disease harboring BRAF V600 activating mutations, such as BRAF V600E, in cases where BRAF/MEK inhibitor combination therapy is contraindicated (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[33568355],"response_type":"predicted - sensitive","indication":"colon adenocarcinoma","therapy_id":11477,"normalized_cancer":"Colon Adenocarcinoma","evidence_type":"Actionable","therapy":"Dabrafenib + Regorafenib + Trametinib","efficacy_evidence":"In a clinical case study, combination treatment with Stivarga (regorafenib), Tafinlar (dabrafenib), and Mekinist (trametinib) in a patient with colon adenocarcinoma harboring BRAF V600E led to stable disease, and treatment continued for eight months, at which time some disease progression was observed (%%PUBMED:33568355%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[34818649],"response_type":"predicted - sensitive","indication":"triple-receptor negative breast cancer","therapy_id":12792,"normalized_cancer":"Invasive Breast Carcinoma","evidence_type":"Actionable","therapy":"Nab-paclitaxel + Vemurafenib","efficacy_evidence":"In a clinical case study, Zelboraf (vemurafenib) and Abraxane (nab-paclitaxel) combination treatment resulted in regression of some metastatic pulmonary lesions and a progression-free survival of 4.4 months in a patient with triple-negative breast cancer harboring BRAF V600E, but a biopsy in lesions that progressed showed acquisition of additional mutations in PDGFRB, NF2, GRM3, MLH1, FOXA1, LRP1B, and AR amplification (%%PUBMED:34818649%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[27217440],"response_type":"predicted - sensitive","indication":"high grade glioma","therapy_id":4902,"normalized_cancer":"High-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"Everolimus + PLX4720","efficacy_evidence":"In a preclinical study, Afinitor (everolimus) and PLX4720 synergistically inhibited growth and induced apoptosis in glioma cell lines in culture (%%PUBMED:27217440%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[36343387],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":14549,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Trametinib + Valproic acid","efficacy_evidence":"In a preclinical study, the combination of Mekinist (trametinib) and Valproic acid resulted in greater apoptotic activity compared to either agent alone in a colorectal cancer cell line harboring BRAF V600E in culture (%%PUBMED:36343387%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[29343524],"response_type":"sensitive","indication":"melanoma","therapy_id":6995,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"RAF709","efficacy_evidence":"In a preclinical study, RAF709 inhibited Erk signaling and proliferation of melanoma cells harboring BRAF V600E in culture (%%PUBMED:29343524%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","normalized_drug":"Ulixertinib","indication":"central nervous system cancer","therapy_id":997,"normalized_cancer":"CNS/Brain Cancer","evidence_type":"Actionable","therapy":"Ulixertinib","efficacy_evidence":"In a Phase II trial (APEC1621J), Ulixertinib (BVD-523) treatment resulted in a 6-month progression-free survival rate of 37% but no objective response in pediatric and young adult patients with advanced solid tumors harboring MAPK pathway activation, however, a patient with glioneuronal tumor harboring a BRAF V600E achieved prolonged stable disease and remained on treatment for 9 cycles (J Clin Oncol 40, no. 16_suppl (June 01, 2022) 3009; NCT03698994).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Cobimetinib, Vemurafenib","indication":"anaplastic oligodendroglioma","therapy_id":1657,"normalized_cancer":"Oligodendroglioma, IDH-mutant, and 1p/19q-Codeleted","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"Combination of Zelboraf (vemurafenib) and Cotellic (cobimetinib) is included in guidelines for patients with recurrent anaplastic gliomas harboring BRAF V600E, including anaplastic oligodendroglioma (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[37326340],"response_type":"sensitive","indication":"colorectal carcinoma","therapy_id":4034,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Gedatolisib + Palbociclib","efficacy_evidence":"In a preclinical study, the combination of Ibrance (palbociclib) and Gedatolisib (PF-05212384) synergistically inhibited growth of a colorectal carcinoma cell line harboring BRAF V600E in culture (%%PUBMED:37326340%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[39087485],"response_type":"no benefit","indication":"melanoma","therapy_id":17373,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"RGT-018","efficacy_evidence":"In a preclinical study, RGT-018 did not inhibit proliferation of melanoma cells harboring BRAF V600E in 3D culture (%%PUBMED:39087485%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[36343387],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":14548,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Entinostat + Trametinib","efficacy_evidence":"In a preclinical study, the combination of Mekinist (trametinib) and Entinostat (MS-275) resulted in greater apoptotic activity compared to either agent alone in a colorectal cancer cell line harboring BRAF V600E in culture (%%PUBMED:36343387%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[33461766],"normalized_drug":"Dabrafenib, Trametinib","indication":"brain glioblastoma multiforme","therapy_id":1066,"normalized_cancer":"Glioblastoma, IDH-Wildtype","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, Tafinlar (dabrafenib) and Mekinist (trametinib) combination therapy resulted in tumor shrinkage after 2 months in a patient with epithelioid glioblastoma multiforme harboring BRAF V600E, who had progressed after resection, radiotherapy, and chemotherapy, and following an interruption in therapy due to toxicity demonstrated a partial response and remained progression-free for 19 months, prior to progressing 29 months after initiation of therapy (%%PUBMED:33461766%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[36638198],"response_type":"predicted - sensitive","indication":"Advanced Solid Tumor","therapy_id":1710,"normalized_cancer":"All Solid Tumors","evidence_type":"Actionable","therapy":"Erlotinib + Vemurafenib","efficacy_evidence":"In a Phase Ib/II trial (EVICT), the combination of Zelboraf (vemurafenib) and Tarceva (erlotinib) resulted in an overall response rate of 43% (3/7), a clinical benefit rate of 100%, and a median PFS of 5.5 months in patients with advanced solid tumors other tan colorectal cancer harboring BRAF V600E (%%PUBMED:36638198%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[22389471],"response_type":"sensitive","indication":"melanoma","therapy_id":3027,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"GSK2126458 + Trametinib","efficacy_evidence":"In a preclinical study, Mekinist (trametinib) in combination with Omipalisib (GSK2126458) inhibited growth of melanoma cell lines harboring BRAF V600E in culture (%%PUBMED:22389471%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"lung non-small cell carcinoma","therapy_id":6765,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"LTT462 + LXH 254","efficacy_evidence":"In a Phase Ib trial, LTT462 and LXH 254 combination therapy was well tolerated and resulted in an unconfirmed partial response (PR) in 4% (2/49) and stable disease (SD) in 33% (16/49) of patients with advanced or metastatic KRAS- or BRAF-mutant non-small cell lung cancer, with 1 patient harboring BRAF V600E achieving an unconfirmed PR and 1 achieving SD with over 25% tumor reduction (Ann Oncol 31 (suppl 4):S881-S882; NCT02974725).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[33824136],"response_type":"no benefit","indication":"melanoma","therapy_id":11754,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"RM-018","efficacy_evidence":"In a preclinical study, RM-018 did not inhibit growth of melanoma cells harboring BRAF V600E in culture (%%PUBMED:33824136%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"colon cancer","therapy_id":13708,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"ABM-1310 + Cetuximab","efficacy_evidence":"In a preclinical study, combination treatment with ABM-1310 and Erbitux (cetuximab) led to inhibition of tumor growth in a colon cancer cell line xenograft model harboring BRAF V600E (Cancer Res (2020) 80 (16_Supplement): 4038).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[26916115],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":3709,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"BI 882370 + Trametinib","efficacy_evidence":"In a preclinical study, colorectal cancer cells harboring BRAF V600E were sensitive to the combination of BI 882370 and Mekinist (trametinib) in xenograft models, resulting in tumor growth inhibition and partial tumor regression (%%PUBMED:26916115%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[37040395],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":11094,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Encorafenib + Fluorouracil + Leucovorin + Oxaliplatin","efficacy_evidence":"In a preclinical study, treatment with the combination of Erbitux (cetuximab), Braftovi (encorafenib), and FOLFOX resulted in increased tumor growth inhibition and survival compared to Erbitux (cetuximab) plus Braftovi (encorafenib) or FOLFOX alone in colorectal cancer cell line xenograft models harboring BRAF V600E (%%PUBMED:37040395%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[39863775],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":11094,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Encorafenib + Fluorouracil + Leucovorin + Oxaliplatin","efficacy_evidence":"In a Phase III trial (BREAKWATER) that supported FDA approval, Braftovi (encorafenib) in combination with Erbitux (cetuximab) and mFOLFOX6 significantly improved objective response rate (60.9%, 67/110 vs 40.0%, 44/110, OR 2.443, p=0.0008) compared to standard of care in patients with metastatic colorectal cancer harboring BRAF V600E, with median duration of response of 13.9 vs 11.1 mo, and overall survival was not estimable vs 14.6 mo (HR 0.47) (%%PUBMED:39863775%%; NCT04607421).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"FDA approved - On Companion Diagnostic","amp_tier":"I"},{"pub_med_references":[36759733],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":15050,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Gefitinib + PLX4720 + Saracatinib","efficacy_evidence":"In a preclinical study, the combination of PLX4720, Iressa (gefitinib), and Saracatinib (AZD0530) inhibited tumor growth in colorectal cancer cell line xenograft models harboring BRAF V600E to a greater degree than the combinations of PLX4720 and Iressa (gefitinib) or PLX4720 and Saracatinib (AZD0530) (%%PUBMED:36759733%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[27048246],"response_type":"predicted - sensitive","indication":"neuroendocrine tumor","therapy_id":4234,"normalized_cancer":"Gastrointestinal Neuroendocrine Tumor","evidence_type":"Actionable","therapy":"Trametinib + Vemurafenib","efficacy_evidence":"In a clinical case study, Mekinist (trametinib) and Zelboraf (vemurafenib) combination treatment resulted in a rapid and sustained clinical response in a patient with a rectal neuroendocrine tumor harboring a BRAF V600E mutation (%%PUBMED:27048246%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[32758030],"normalized_drug":"Trametinib","indication":"Advanced Solid Tumor","therapy_id":2,"normalized_cancer":"All Solid Tumors","evidence_type":"Actionable","therapy":"Trametinib","efficacy_evidence":"In a Phase II trial (NCI-MATCH), Mekinist (trametinib) treatment resulted in an objective response rate of 37.9% (11/29) in patients with BRAF V600E positive advanced solid tumors other than melanoma, thyroid cancer, or colorectal cancer, with a median duration of response of 25.1 months, and a disease control rate of 75.9% (22/29) (%%PUBMED:32758030%%; NCT02465060).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[23733758],"normalized_drug":"Vemurafenib","indication":"lung non-small cell carcinoma","therapy_id":342,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a clinical case study, a non-small cell lung cancer patient harboring a BRAF V600E mutation had a complete response after treatment with Zelboraf (vemurafenib) (%%PUBMED:23733758%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[26200454],"normalized_drug":"Vemurafenib","indication":"lung non-small cell carcinoma","therapy_id":342,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a retrospective analysis, non-small cell lung cancer patients harboring BRAF V600E achieved an overall response rate of 54% (13/24, 2 complete responses, 11 partial responses, and 10 with stable disease) and a disease control rate of 96% following treatment with Zelboraf (vemurafenib) (%%PUBMED:26200454%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Clinical Study","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Vemurafenib","indication":"lung non-small cell carcinoma","therapy_id":342,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase II trial (MyPathway), Zelboraf (vemurafenib) treatment resulted in an objective response of 43% (6/14, 1 complete response, 5 partial response) in patients with non-small cell lung cancer harboring BRAF V600E, and stable disease lasting more than 120 days in 2 patients (%%PUBMED:29320312%%; NCT02091141).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Vemurafenib","indication":"lung non-small cell carcinoma","therapy_id":342,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"Zelboraf (vemurafenib) is included in guidelines as a first-line therapy for advanced or metastatic non-small cell lung cancer patients harboring BRAF V600E mutations who can not tolerate the combination of Mekinist (trametinib) and Tafinlar (dabrafenib) (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[32029534],"normalized_drug":"Vemurafenib","indication":"lung non-small cell carcinoma","therapy_id":342,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase II trial (VE-BASKET), responses were seen in patients with non-small cell lung cancer harboring BRAF V600E (n=63) when treated with Zelboraf (vemurafenib), including 23 patients with a partial response (%%PUBMED:32029534%%; NCT01524978).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"gallbladder cancer","therapy_id":1066,"normalized_cancer":"Gallbladder Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Tafinlar (dabrafenib) in combination with Mekinist (trametinib) is included in guidelines as subsequent-line therapy for patients with biliary cancer harboring BRAF V600E, including gallbladder cancer (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[27488531],"response_type":"conflicting","indication":"melanoma","therapy_id":849,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Mirdametinib","efficacy_evidence":"In a preclinical study, a melanoma cell line xenograft model harboring BRAF V600E treated with Gomekli (mirdametinib) demonstrated stable tumor growth, but by day 44, growth ensued and thus, demonstrated no benefit (%%PUBMED:27488531%%).","cap_asco_evidence_level":"NA","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"NA"},{"pub_med_references":[26267534],"response_type":"conflicting","indication":"melanoma","therapy_id":849,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Mirdametinib","efficacy_evidence":"In a preclinical study, Gomekli (mirdametinib) inhibited growth of melanoma cell lines harboring BRAF V600E in culture (%%PUBMED:26267534%%).","cap_asco_evidence_level":"NA","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"NA"},{"pub_med_references":[25422890],"response_type":"conflicting","indication":"melanoma","therapy_id":849,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Mirdametinib","efficacy_evidence":"In a preclinical study, Gomekli (mirdametinib) treatment induced cell cycle arrest and inhibited growth of melanoma cells harboring BRAF V600E in culture (%%PUBMED:25422890%%).","cap_asco_evidence_level":"NA","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"NA"},{"response_type":"predicted - sensitive","pub_med_references":[32206360],"normalized_drug":"Dabrafenib, Trametinib","indication":"breast metaplastic carcinoma","therapy_id":1066,"normalized_cancer":"Metaplastic Breast Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, treatment with the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) resulted in a partial response in a patient with metaplastic breast cancer harboring BRAF V600E, however, progression occurred after 8 weeks (%%PUBMED:32206360%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[38728872],"response_type":"sensitive","indication":"melanoma","therapy_id":2149,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Ravoxertinib","efficacy_evidence":"In a preclinical study, Ravoxertinib (GDC-0994) inhibited viability and colony formation in melanoma cell lines harboring BRAF V600E in culture (%%PUBMED:38728872%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[36622773],"response_type":"sensitive","indication":"melanoma","therapy_id":14824,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + DS03090629","efficacy_evidence":"In a preclinical study, the combination of DS03090629 and Tafinlar (dabrafenib) inhibited Erk phosphorylation and proliferation in a melanoma cell line harboring BRAF V600E in culture and induced tumor regression in a cell line xenograft model (%%PUBMED:36622773%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[23629727],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":4657,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Pimasertib + Regorafenib","efficacy_evidence":"In a preclinical study, Pimasertib (MSC1936369B) and Stivarga (regorafenib) synergistically inhibited proliferation of colorectal cancer cells harboring BRAF V600E in culture (%%PUBMED:23629727%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[20538618],"response_type":"sensitive","indication":"Advanced Solid Tumor","therapy_id":884,"normalized_cancer":"All Solid Tumors","evidence_type":"Actionable","therapy":"RAF265","efficacy_evidence":"In a preclinical study, RAF265 inhibited Erk phosphorylation and cell proliferation in BRAF V600E expressing cells in culture (%%PUBMED:20538618%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[27080216,27283860,28919011],"normalized_drug":"Dabrafenib, Trametinib","indication":"lung non-small cell carcinoma","therapy_id":1066,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a Phase II trial that supported FDA approval, treatment with the combination of Mekinist (trametinib) and Tafinlar (dabrafenib) in patients with non-small cell lung cancer harboring BRAF V600E resulted in an overall response rate of 66.7% (38/57) in previously treated patients and 64% (23/36) in untreated patients, versus 33% (26/78) treated with Tafinlar (dabrafenib) alone (%%PUBMED:27080216%%, %%PUBMED:27283860%%, %%PUBMED:28919011%%; NCT01336634).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"FDA approved - On Companion Diagnostic","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[39615406],"normalized_drug":"Dabrafenib, Trametinib","indication":"lung non-small cell carcinoma","therapy_id":1066,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Combination of Mekinist (trametinib) and Tafinlar (dabrafenib) is included in the Pan-Asian Guidelines Adaptation (PAGA) for advanced and metastatic non-small cell lung cancer patients harboring BRAF V600E (%%PUBMED:39615406%%; ESMO.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"lung non-small cell carcinoma","therapy_id":1066,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Combination of Mekinist (trametinib) and Tafinlar (dabrafenib) is included in guidelines as a first-line or subsequent therapy for advanced or metastatic non-small cell lung cancer patients harboring BRAF V600E mutations (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","normalized_drug":"Cobimetinib, Vemurafenib","indication":"glioblastoma","therapy_id":1657,"normalized_cancer":"Glioblastoma, IDH-Wildtype","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"Combination of Zelboraf (vemurafenib) and Cotellic (cobimetinib) is included in guidelines for patients with recurrent glioblastoma harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[31217909],"normalized_drug":"Cobimetinib, Vemurafenib","indication":"glioblastoma","therapy_id":1657,"normalized_cancer":"Glioblastoma, IDH-Wildtype","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"In a clinical case study, a patient with epithelioid glioblastoma harboring BRAF V600E continued to response as Cotellic (cobimetinib) was added to Zelboraf (vemurafenib) treatment (%%PUBMED:31217909%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[36967525],"normalized_drug":"Vemurafenib","indication":"ovarian serous cystadenocarcinoma","therapy_id":342,"normalized_cancer":"Serous Ovarian Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a clinical case study, Zelboraf (vemurafenib) treatment resulted in a complete radiological response that lasted for 3 years in a patient with low-grade serous cystadenocarcinoma of the ovary harboring BRAF V600E (%%PUBMED:36967525%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[27669459],"response_type":"sensitive","indication":"papillary thyroid carcinoma","therapy_id":2011,"normalized_cancer":"Papillary Thyroid Cancer","evidence_type":"Actionable","therapy":"RO5126766","efficacy_evidence":"In a preclinical study, RO5126766 inhibited Mek signaling and increased radioiodide uptake and response in transgenic animal models of papillary thyroid carcinoma driven by BRAF V600E (%%PUBMED:27669459%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[33669326],"normalized_drug":"Cobimetinib, Vemurafenib","indication":"cholangiocarcinoma","therapy_id":1657,"normalized_cancer":"Cholangiocarcinoma","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"In a clinical case study, Zelboraf (vemurafenib) and Cotellic (cobimetinib) combination treatment resulted in reduction of the pulmonary nodules and hepatic lesions 6 months after treatment initiation in a patient with metastatic cholangiocarcinoma harboring BRAF V600E, who maintained a stable disease and remained on treatment at 20 months (%%PUBMED:33669326%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[38096472],"normalized_drug":"Cobimetinib, Vemurafenib","indication":"cholangiocarcinoma","therapy_id":1657,"normalized_cancer":"Cholangiocarcinoma","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"In a Phase II trial (TAPUR), Zelboraf (vemurafenib) and Cotellic (cobimetinib) combination therapy resulted in a partial response in a patient with cholangiocarcinoma harboring BRAF V600E (%%PUBMED:38096472%%; NCT02693535).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[32816843],"response_type":"predicted - resistant","indication":"colorectal cancer","therapy_id":8871,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"BI-3406","efficacy_evidence":"In a preclinical study, BI-3406 treatment failed to inhibit growth of colorectal cancer cells harboring BRAF V600E in culture (%%PUBMED:32816843%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[27924459],"response_type":"sensitive","indication":"melanoma","therapy_id":5122,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Doxorubicin + PLX4720","efficacy_evidence":"In a preclinical study, the combination of PLX4720 and Adriamycin (doxorubicin) resulted in antitumor efficacy in a melanoma cell line harboring BRAF V600E, demonstrating decreased cell survival and increased apoptotic activity in xenograft models, and inhibition of cell growth in culture (%%PUBMED:27924459%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[27222538],"normalized_drug":"Trametinib","indication":"thyroid cancer","therapy_id":2,"normalized_cancer":"Thyroid Cancer","evidence_type":"Actionable","therapy":"Trametinib","efficacy_evidence":"In a preclinical study, Mekinist (trametinib) inhibited growth of both parental thyroid cancer cell lines harboring BRAF V600E and those acquired Sprycel (dasatinib)-resistance in culture (%%PUBMED:27222538%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[34433654],"response_type":"predicted - sensitive","indication":"high grade glioma","therapy_id":12678,"normalized_cancer":"High-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"Vemurafenib + ZM336372","efficacy_evidence":"In a preclinical study, combination treatment with Zelboraf (vemurafenib) and ZM336372 treatment led to inhibition of cell growth in a patient-derived glioma cell line harboring BRAF V600E in culture (%%PUBMED:34433654%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Patient cell culture","amp_tier":"II"},{"pub_med_references":[37504287],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":15636,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"SJ-C1044","efficacy_evidence":"In a preclinical study, SJ-C1044 decreased growth in a colorectal cancer cell line harboring BRAF V600E in culture and inhibited tumor growth in a cell line xenograft model (%%PUBMED:37504287%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"pancreatic adenocarcinoma","therapy_id":1066,"normalized_cancer":"Pancreatic Adenocarcinoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Tafinlar (dabrafenib) and Mekinist (trametinib) combination therapy is included in guidelines as first-line therapy for pancreatic adenocarcinoma patients harboring BRAF V600E with locally advanced disease (category 2A) with good (ECOG 0-1) or intermediate (ECOG 2) performance status, as first-line therapy in patients metastatic disease (category 2B) disease, and as subsequent-line therapy for patients with locally advanced, recurrent, or metastatic disease (category 2A) (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[27222538],"response_type":"sensitive","indication":"thyroid cancer","therapy_id":4600,"normalized_cancer":"Thyroid Cancer","evidence_type":"Actionable","therapy":"Dasatinib + Selumetinib","efficacy_evidence":"In a preclinical study, Sprycel (dasatinib) and Koselugo (selumetinib) synergistically inhibited proliferation and induced apoptosis in both parental thyroid cancer cell lines harboring BRAF V600E and those acquired Sprycel (dasatinib)-resistance in culture (%%PUBMED:27222538%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"resistant","normalized_drug":"Cetuximab","indication":"rectum cancer","therapy_id":694,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab","efficacy_evidence":"Erbitux (cetuximab), as a monotherapy, is not indicated for use in rectum cancer patients with BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"unknown","indication":"lung non-small cell carcinoma","therapy_id":10383,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"unspecified immune checkpoint inhibitor","efficacy_evidence":"In a retrospective clinical study, patients with non-small cell lung cancer harboring rare targetable drivers (RTD) (BRAF, ERBB2/3, RET, MET, ROS1, NTRK) who received immune checkpoint inhibitors (ICI) achieved longer median overall survival (mOS) (32 vs 13 mo, p=0.01) compared to those who did not receive ICI, mOS was not reached in patients harboring BRAF V600E (n=5) mutations, although RTD type was not associated with OS in a univariate analysis (%%PUBMED:30268448%%).","cap_asco_evidence_level":"NA","molecular_profile":"BRAF V600E","approval_status":"Clinical Study - Cohort","amp_tier":"NA"},{"response_type":"predicted - sensitive","pub_med_references":[37981300],"normalized_drug":"Cetuximab, Encorafenib","indication":"colon neuroendocrine neoplasm","therapy_id":1916,"normalized_cancer":"Gastrointestinal Neuroendocrine Tumors","evidence_type":"Actionable","therapy":"Cetuximab + Encorafenib","efficacy_evidence":"In a clinical case study, treatment with the combination of Erbitux (cetuximab) and Braftovi (encorafenib) resulted in reduced liver metastasis and a progression-free survival of 14 months in a patient with colorectal neuroendocrine carcinoma harboring BRAF V600E (%%PUBMED:37981300%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[27523909],"response_type":"sensitive","indication":"melanoma","therapy_id":4281,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"SB590885","efficacy_evidence":"In a preclinical study, SB590885 inhibited proliferation of melanoma cell lines harboring either monomeric BRAF V600E or dimeric isoform of V600E which conferred Zelboraf (vemurafenib)-resistance in culture (%%PUBMED:27523909%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"no benefit","pub_med_references":[35363510],"normalized_drug":"Selumetinib","indication":"Advanced Solid Tumor","therapy_id":913,"normalized_cancer":"All Solid Tumors","evidence_type":"Actionable","therapy":"Selumetinib","efficacy_evidence":"In a Phase II trial (Pediatric MATCH), Koselugo (selumetinib) treatment was tolerated but did not result in an objective response in pediatric patients with advanced solid tumors including high-grade glioma (n=8) and rhabdomyosarcoma (n=7) harboring MAPK pathway alterations including BRAF V600E (n=2), activating KRAS (n=8)/HRAS (n=1)/NRAS (n=3) or inactivating NF1 (n=7) mutations, with a 6-month progression-free survival of 15% (3/20) and 3 stable disease as best response (%%PUBMED:35363510%%; NCT03213691).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[33537843],"normalized_drug":"Dabrafenib, Trametinib","indication":"basal cell carcinoma","therapy_id":1066,"normalized_cancer":"Basal Cell Carcinoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) resulted in stable disease after three months of treatment in a patient with basal cell carcinoma harboring BRAF V600E (%%PUBMED:33537843%%)","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[29632053],"normalized_drug":"Dabrafenib, Trametinib","indication":"glioblastoma","therapy_id":1066,"normalized_cancer":"Glioblastoma, IDH-Wildtype","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, an epithelioid glioblastoma patient harboring BRAF V600E treated with Mekinist (trametinib) and Tafinlar (dabrafenib) combination therapy resulted in stable disease, and the patient continued to demonstrate stable disease at least 16 months after initiation of therapy (%%PUBMED:29632053%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"glioblastoma","therapy_id":1066,"normalized_cancer":"Glioblastoma, IDH-Wildtype","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Combination of Mekinist (trametinib) and Tafinlar (dabrafenib) is included in guidelines for patients with recurrent glioblastoma harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[32923904],"normalized_drug":"Dabrafenib, Trametinib","indication":"glioblastoma","therapy_id":1066,"normalized_cancer":"Glioblastoma, IDH-Wildtype","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, Mekinist (trametinib) and Tafinlar (dabrafenib) combination treatment resulted in a complete resolution of symptoms and radiographic partial response after the first treatment in a patient with glioblastoma harboring BRAF V600E whose disease progressed on PLX8394 treatment, and a complete response after 11 months of treatment, CDKN2A/B loss and CHEK2 T367fs were also identified in the tumor (%%PUBMED:32923904%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[31345255],"normalized_drug":"Dabrafenib, Trametinib","indication":"glioblastoma","therapy_id":1066,"normalized_cancer":"Glioblastoma, IDH-Wildtype","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, combination therapy of Tafinlar (dabrafenib) and Mekinist (trametinib) resulted in improved clinical symptoms in a patient with epithelioid glioblastoma harboring BRAF V600E, and treatment of the patient's cells resulted in decreased cell viability, reduced phosphorylation of Mek and Erk, increased apoptotic activity compared to either agent alone, and cell cycle arrest in culture, and led to tumor growth suppression in the patient-derived xenograft (PDX) model (%%PUBMED:31345255%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[31217909],"normalized_drug":"Dabrafenib, Trametinib","indication":"glioblastoma","therapy_id":1066,"normalized_cancer":"Glioblastoma, IDH-Wildtype","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, Mekinist (trametinib) and Tafinlar (dabrafenib) combination treatment resulted in significant clinical improvement in a patient with epithelioid glioblastoma harboring BRAF V600E, however, her disease progressed after 3 months of therapy (%%PUBMED:31217909%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[34838156],"normalized_drug":"Dabrafenib, Trametinib","indication":"glioblastoma","therapy_id":1066,"normalized_cancer":"Glioblastoma, IDH-Wildtype","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a Phase II trial (ROAR), Tafinlar (dabrafenib) and Mekinist (trametinib) combination treatment resulted in an objective response in 32% (10/31, 2 complete responses, 8 partial responses) and stable disease in 19% (6/31) of patients with glioblastoma harboring BRAF V600E (%%PUBMED:34838156%%; NCT02034110).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"pub_med_references":[27312529],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":4541,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Dabrafenib + Trametinib","efficacy_evidence":"In a preclinical study, combination therapy consisting of Erbitux (cetuximab), Tafinlar (dabrafenib), and Mekinist (trametinib) inhibited survival of colorectal cancer cell lines harboring BRAF V600E in culture (%%PUBMED:27312529%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[20531415,26603897],"response_type":"sensitive","indication":"melanoma","therapy_id":3306,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"SBI-0640756","efficacy_evidence":"In a preclinical study, SBI-0640756 inhibited proliferation and Akt/mTOR signaling in human melanoma cell lines harboring BRAF V600E in culture (%%PUBMED:26603897%%, %%PUBMED:20531415%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[20531415,26603897],"response_type":"sensitive","indication":"melanoma","therapy_id":3308,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"BI-69A11","efficacy_evidence":"In a preclinical study, BI-69A11 inhibited proliferation and Akt/mTOR signaling in human melanoma cell lines harboring BRAF V600E in culture (%%PUBMED:26603897%%, %%PUBMED:20531415%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[28714990],"response_type":"decreased response","indication":"melanoma","therapy_id":6430,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + SCH772984 + Trametinib","efficacy_evidence":"In a preclinical study, combination of Tafinlar (dabrafenib), SCH772984, and Mekinist (trametinib) resulted in durable inhibition of Erk signaling and proliferation of melanoma cells overexpressing BRAF V600E in culture (%%PUBMED:28714990%%).","cap_asco_evidence_level":"NA","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"NA"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"pilocytic astrocytoma","therapy_id":1066,"normalized_cancer":"Pilocytic Astrocytoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Combination of Mekinist (trametinib) and Tafinlar (dabrafenib) is included in guidelines as an adjuvant treatment for patients with pilocytic astrocytoma harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[39399174],"normalized_drug":"Dabrafenib, Trametinib","indication":"pilocytic astrocytoma","therapy_id":1066,"normalized_cancer":"Pilocytic Astrocytoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, the addition of Mekinist (trametinib) to treatment with Tafinlar (dabrafenib) resulted in a partial response in 3 pediatric patients with suprasellar pilocytic astrocytoma harboring BRAF V600E who all previously progressed on Tafinlar (dabrafenib) treatment alone (%%PUBMED:39399174%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[33568355],"response_type":"sensitive","indication":"melanoma","therapy_id":11477,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + Regorafenib + Trametinib","efficacy_evidence":"In a preclinical study, combination treatment with Stivarga (regorafenib), Tafinlar (dabrafenib), and Mekinist (trametinib) in a melanoma cell line harboring BRAF V600E resulted in suppression of colony formation in culture, and suppressed tumor growth in patient-derived xenograft (PDX) models (%%PUBMED:33568355%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Pdx & cell culture","amp_tier":"II"},{"pub_med_references":[26810733],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":6368,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"EBI-907","efficacy_evidence":"In a preclinical study, EBI-907 inhibited BRAF and ERK signaling, resulted in growth inhibition of colorectal cancer cells harboring BRAF V600E in culture and in cell line xenograft models (%%PUBMED:26810733%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[37164118],"response_type":"sensitive","indication":"Advanced Solid Tumor","therapy_id":15389,"normalized_cancer":"All Solid Tumors","evidence_type":"Actionable","therapy":"IHMT-RAF-128","efficacy_evidence":"In a preclinical study, IHMT-RAF-128 inhibited proliferation of a cell line expressing BRAF V600E in culture (%%PUBMED:37164118%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[30036245],"normalized_drug":"Dabrafenib, Trametinib","indication":"colon neuroendocrine neoplasm","therapy_id":1066,"normalized_cancer":"Gastrointestinal Neuroendocrine Tumors","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, treatment with the combination of Mekinist (trametinib) and Tafinlar (dabrafenib) resulted in a clinical improvement and reduction of the primary tumor as well as the metastatic lesions in a cecal neuroendocrine carcinoma patient harboring BRAF V600E (%%PUBMED:30036245%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[38716076],"normalized_drug":"Dabrafenib, Trametinib","indication":"colon neuroendocrine neoplasm","therapy_id":1066,"normalized_cancer":"Gastrointestinal Neuroendocrine Tumors","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical study, second-line treatment with the combination of Mekinist (trametinib) and Tafinlar (dabrafenib) resulted in a partial response in two patients with a neuroendocrine carcinoma of the colon harboring BRAF V600E, with progression-free survival of 6 months in one patient and 4 months in the second patient (%%PUBMED:38716076%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[37808191],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":9644,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Tunlametinib","efficacy_evidence":"In a preclinical study, Tunlametinib (HL-085) inhibited viability of a colorectal cancer cell line harboring BRAF V600E in culture and inhibited tumor growth in a cell line xenograft model (%%PUBMED:37808191%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[30833748],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":11211,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Chloroquine + Trametinib","efficacy_evidence":"In a preclinical study, combination treatment with Mekinist (trametinib) and Chloroquine resulted in tumor regression in a colorectal cancer patient-derived xenograft (PDX) model harboring BRAF V600E (%%PUBMED:30833748%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[27480103],"normalized_drug":"Cobimetinib, Vemurafenib","indication":"melanoma","therapy_id":1657,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"In a Phase III trial (coBRIM) that supported FDA approval, treatment with the combination of Zelboraf (vemurafenib) and Cotellic (cobimetinib) resulted in an improved progression-free survival of 12.3 months, compared to 7.2 months with Zelboraf (vemurafenib) plus placebo, among patients with BRAF V600-mutated metastatic melanoma, and BRAF V600E and BRAF V600K are on the companion diagnostic (%%PUBMED:27480103%%; NCT01689519).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"FDA approved - On Companion Diagnostic","amp_tier":"I"},{"response_type":"sensitive","normalized_drug":"Dabrafenib","indication":"papillary thyroid carcinoma","therapy_id":3,"normalized_cancer":"Papillary Thyroid Cancer","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"Tafinlar (dabrafenib) is included in guidelines for patients with recurrent, advanced, or metastatic thyroid papillary carcinoma harboring BRAF V600E for whom clinical trials are not available or appropriate (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[25549723],"normalized_drug":"Dabrafenib","indication":"papillary thyroid carcinoma","therapy_id":3,"normalized_cancer":"Papillary Thyroid Cancer","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a clinical study, Tafinlar (dabrafenib) treatment stimulated radioiodine uptake in 60% (6/10) of patients with metastatic iodine-refractory papillary thyroid cancer harboring BRAF V600E (%%PUBMED:25549723%%; NCT01534897).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Clinical Study - Cohort","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"melanoma","therapy_id":17152,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Binimetinib + PLX8394","efficacy_evidence":"In a preclinical study, treatment with the combination of Mektovi (binimetinib) and PLX8394 inhibited viability of melanoma cells harboring BRAF V600E in culture (Cancer Res (2024) 84 (6_Supplement): 4609).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[39143272],"normalized_drug":"Dabrafenib, Trametinib","indication":"craniopharyngioma","therapy_id":1066,"normalized_cancer":"Sellar Tumor","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, treatment with the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) resulted in a partial response and progression-free survival of 1040 days in a patient with craniopharyngioma harboring BRAF V600E (%%PUBMED:39143272%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[38096472],"normalized_drug":"Cobimetinib, Vemurafenib","indication":"Advanced Solid Tumor","therapy_id":1657,"normalized_cancer":"All Solid Tumors","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"In a Phase II trial (TAPUR), treatment with the combination of Zelboraf (vemurafenib) and Cotellic (cobimetinib) resulted in an objective response rate of 57% (16/28, 2 complete responses (CR), 14 partial responses (PR)) and a disease control rate (CR + PR + stable disease at 16 wks (SD16+)) of 68% in patients with advanced solid tumors harboring BRAF mutations, with 2 CR, 13 PR, and 2 SD16+ in a total of 26 patients harboring BRAF V600E (%%PUBMED:38096472%%; NCT02693535).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"pub_med_references":[30264293],"response_type":"sensitive","indication":"melanoma","therapy_id":1011,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"E6201","efficacy_evidence":"In a Phase I trial, a patient with metastatic melanoma and brain metastasis harboring BRAF V600E demonstrated an ongoing near complete response with an overall survival of more than 8 years, and preclinical analysis of melanoma cell lines harboring homozygous or heterozygous BRAF V600E in culture were sensitive to treatment with E6201 (%%PUBMED:30264293%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[24448821],"response_type":"sensitive","indication":"melanoma","therapy_id":1011,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"E6201","efficacy_evidence":"In a preclinical study, E6201 inhibited Mapk pathway activation and proliferation of melanoma cell lines harboring BRAF V600E mutation in culture (%%PUBMED:24448821%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[27362227],"response_type":"no benefit","indication":"melanoma","therapy_id":4504,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"SHP099","efficacy_evidence":"In a preclinical study, SHP099 did not inhibit proliferation or ERK activation in a melanoma cell line harboring BRAF V600E in culture (%%PUBMED:27362227%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"stomach cancer","therapy_id":1066,"normalized_cancer":"Esophageal/Stomach Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Tafinlar (dabrafenib) and Mekinist (trametinib) combination therapy is included in guidelines as second-line or subsequent therapy for patients with unresectable locally advanced, recurrent, or metastatic gastric cancer harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[36343387],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":14547,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Mocetinostat + Trametinib","efficacy_evidence":"In a preclinical study, the combination of Mekinist (trametinib) and Mocetinostat (MGCD0103) resulted in greater apoptotic activity compared to either agent alone in a colorectal cancer cell line harboring BRAF V600E in culture (%%PUBMED:36343387%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[22319199],"response_type":"sensitive","indication":"melanoma","therapy_id":1002,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"RXDX-105","efficacy_evidence":"In preclinical studies, CEP-32496 (RXDX-105) reduced tumor volume and promoted tumor regression in xenograft models of a BRAF V600E mutant human melanoma cell line (%%PUBMED:22319199%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[23242808],"response_type":"sensitive","indication":"melanoma","therapy_id":3124,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"S3I-201","efficacy_evidence":"In a preclinical study, S3I-201 inhibited cell invasion and Stat3 signaling in human melanoma cell lines harboring BRAF V600E that are resistant to Braf inhibition in culture (%%PUBMED:23242808%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[27217440],"response_type":"predicted - sensitive","indication":"high grade glioma","therapy_id":1061,"normalized_cancer":"High-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"PLX4720 + Selumetinib","efficacy_evidence":"In a preclinical study, Koselugo (selumetinib) and PLX4720 synergistically inhibited growth and induced apoptosis in glioma cell lines in culture, resulted in prolonged survival in cell line xenograft models (%%PUBMED:27217440%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"sensitive","indication":"colon cancer","therapy_id":9562,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Encorafenib + Panitumumab","efficacy_evidence":"Braftovi (encorafenib) in combination with Vectibix (panitumumab) is included in guidelines as primary or subsequent therapy for patients with colon cancer harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[33318037],"response_type":"sensitive","indication":"melanoma","therapy_id":11345,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Lifirafenib + Trametinib","efficacy_evidence":"In a preclinical study, the combination treatment of Mekinist (trametinib) and Lifirafenib (BGB-283) led to greater inhibition of growth in melanoma cell lines harboring BRAF V600E in culture compared to either treatment alone (%%PUBMED:33318037%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[30351999],"normalized_drug":"Vemurafenib","indication":"pilocytic astrocytoma","therapy_id":342,"normalized_cancer":"Pilocytic Astrocytoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase II trial (VE-BASKET), Zelboraf (vemurafenib) treatment resulted in a partial response in a patient with pilocytic astrrocytoma harboring BRAF V600E who stayed on treatment for 15.3 months (%%PUBMED:30351999%%; NCT01524978).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[36622773],"response_type":"predicted - sensitive","indication":"melanoma","therapy_id":14819,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"DS03090629","efficacy_evidence":"In a preclinical study, DS03090629 inhibited Erk and Mek phosphorylation and proliferation in a melanoma cell line harboring BRAF V600E in culture and led to tumor stasis in a cell line xenograft model (%%PUBMED:36622773%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[32758030],"normalized_drug":"Trametinib","indication":"intrahepatic cholangiocarcinoma","therapy_id":2,"normalized_cancer":"Intrahepatic Cholangiocarcinoma","evidence_type":"Actionable","therapy":"Trametinib","efficacy_evidence":"In a Phase II trial (NCI-MATCH), Mekinist (trametinib) treatment resulted in an objective response rate of 37.9% (11/29) in patients with advanced solid tumors harboring BRAF V600E, of 4 patients with intrahepatic cholangiocarcinoma, 3 achieved a partial response, with individual progression-free survival of 12.8, 9.1, and 29.4 months (%%PUBMED:32758030%%; NCT02465060).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[34330842],"response_type":"sensitive","indication":"colorectal adenocarcinoma","therapy_id":6971,"normalized_cancer":"Colorectal Adenocarcinoma","evidence_type":"Actionable","therapy":"ASTX029","efficacy_evidence":"In a preclinical study, ASTX029 treatment reduced Erk and Rsk phosphorylation and inhibited growth of colorectal adenocarcinoma cell lines harboring BRAF V600E in culture, and inhibited tumor growth and induced tumor regression in cell line xenograft models (%%PUBMED:34330842%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[32758030],"normalized_drug":"Trametinib","indication":"pleomorphic xanthoastrocytoma","therapy_id":2,"normalized_cancer":"Pleomorphic Xanthoastrocytoma","evidence_type":"Actionable","therapy":"Trametinib","efficacy_evidence":"In a Phase II trial (NCI-MATCH), Mekinist (trametinib) treatment resulted in an objective response rate of 37.9% (11/29) in patients with advanced solid tumors harboring BRAF V600E, 1 patient with pleomorphic xanthoastrocytoma achieved a partial response lasting 7.2 months (%%PUBMED:32758030%%; NCT02465060).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib","indication":"lung non-small cell carcinoma","therapy_id":3,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"Tafinlar (dabrafenib) is in guidelines as a first-line therapy for patients with advanced or metastatic non-small cell lung cancer with BRAF V600E mutations who can not tolerate the combination of Mekinist (trametinib) and Tafinlar (dabrafenib) (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[27080216],"normalized_drug":"Dabrafenib","indication":"lung non-small cell carcinoma","therapy_id":3,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a Phase II trial, 33% (26/78) of previously treated non-small cell lung carcinoma patients harboring BRAF V600E demonstrated an overall response, which included all partial responses, when treated with Tafinlar (dabrafenib) while 67% (4/6) receiving Tafinlar (dabrafenib) as a first-line treatment achieved partial responses (%%PUBMED:27080216%%; NCT01336634).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"pub_med_references":[25665005],"response_type":"sensitive","indication":"lung non-small cell carcinoma","therapy_id":1386,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Navitoclax + Trametinib","efficacy_evidence":"In a preclinical study, Navitoclax (ABT-263) enhanced the inhibitory effect of Mekinist (trametinib) on human non-small cell lung cancer cells harboring BRAF V600E in culture (%%PUBMED:25665005%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[26916115],"response_type":"sensitive","indication":"melanoma","therapy_id":3709,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"BI 882370 + Trametinib","efficacy_evidence":"In a preclinical study, xenograft models of melanoma harboring BRAF V600E treated with the combination of BI 882370 and Mekinist (trametinib) demonstrated tumor regression with no regrowth during the 5 weeks of treatment (%%PUBMED:26916115%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"colorectal cancer","therapy_id":10113,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"JSI-1187","efficacy_evidence":"In a preclinical study, JSI-1187 treatment in a colorectal cancer cell line harboring BRAF V600E led to inhibition of cell proliferation in culture, and tumor regression and dose-dependent tumor growth inhibition in a cell line xenograft model (Cancer Res 2020;80(16 Suppl):Abstract nr 4188).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[22448344],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":1709,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Gefitinib + Vemurafenib","efficacy_evidence":"In a preclinical study, the combination of Zelboraf (vemurafenib) and Iressa (gefitinib) decreased the number of viable colorectal cancer cells harboring a BRAF V600E mutation in cell culture (%%PUBMED:22448344%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[25665005],"response_type":"sensitive","indication":"colon cancer","therapy_id":3530,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Navitoclax + Vemurafenib","efficacy_evidence":"In a preclinical study, Navitoclax (ABT-263) enhanced the inhibitory effect of Zelboraf (vemurafenib) on human colon cancer cells harboring BRAF V600E in culture (%%PUBMED:25665005%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[33917428],"response_type":"sensitive","indication":"melanoma","therapy_id":16090,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"SIJ777","efficacy_evidence":"In a preclinical study, SIJ777 inhibited Mek, Erk, and Akt phosphorylation, proliferation, migration, and invasion, and induced apoptosis in melanoma cell lines harboring BRAF V600E in culture (%%PUBMED:33917428%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"ampulla of Vater adenocarcinoma","therapy_id":1066,"normalized_cancer":"Ampullary Carcinoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Tafinlar (dabrafenib) and Mekinist (trametinib) combination therapy is included in guidelines as first-line therapy with good (ECOG 0-1; category 3) or poor (category 2B) performance status, or as subsequent therapy (category 2A), for metastatic ampullary adenocarcinoma patients harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[33355204],"response_type":"predicted - sensitive","indication":"melanoma","therapy_id":4442,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"LXH 254","efficacy_evidence":"In a preclinical study, a melanoma cell line harboring BRAF V600E was sensitive to treatment with LXH254, demonstrating inhibition of cell proliferation in culture, and inhibition of tumor growth and tumor regression in a cell line xenograft model of melanoma (%%PUBMED:33355204%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[23242808],"normalized_drug":"Saracatinib","indication":"melanoma","therapy_id":912,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Saracatinib","efficacy_evidence":"In a preclinical study, saracatinib inhibited proliferation of human melanoma cell lines harboring BRAF V600E that are resistant to Braf inhibition in culture (%%PUBMED:23242808%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[30559419],"response_type":"sensitive","indication":"melanoma","therapy_id":6245,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"BGB659","efficacy_evidence":"In a preclinical study, BGB659 treatment inhibited Erk phosphorylation and reduced proliferation of a melanoma cells harboring either monomeric BRAF V600E or dimeric isoform (p61) of V600E in culture (%%PUBMED:30559419%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[29247021],"normalized_drug":"Ulixertinib","indication":"lung cancer","therapy_id":997,"normalized_cancer":"Lung Cancer","evidence_type":"Actionable","therapy":"Ulixertinib","efficacy_evidence":"In a Phase I trial, treatment with Ulixertinib (BVD-523) resulted in a partial response in two patients with lung cancer each harboring BRAF V600E (%%PUBMED:29247021%%; NCT01781429).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[19706763],"normalized_drug":"Refametinib","indication":"melanoma","therapy_id":888,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Refametinib","efficacy_evidence":"In a preclinical study, Refametinib (BAY86-9766) inhibited growth of melanoma cell lines harboring BRAF V600E in culture and suppressed tumor growth in cell line xenograft models (%%PUBMED:19706763%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[27523909],"response_type":"sensitive","indication":"melanoma","therapy_id":3300,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"TAK-632","efficacy_evidence":"In a preclinical study, TAK-632 inhibited proliferation of melanoma cell lines harboring either monomeric BRAF V600E or dimeric isoform of V600E which conferred Zelboraf (vemurafenib)-resistance in culture (%%PUBMED:27523909%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell 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biliary cancer harboring BRAF V600E, including extrahepatic cholangiocarcinoma (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[20538618],"response_type":"sensitive","indication":"Advanced Solid Tumor","therapy_id":1060,"normalized_cancer":"All Solid Tumors","evidence_type":"Actionable","therapy":"PLX4720","efficacy_evidence":"In a preclinical study, PLX4720 inhibited Erk phosphorylation and cell proliferation of transformed cells expression BRAF V600E in culture (%%PUBMED:20538618%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[36759733],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":15044,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Celecoxib + Gefitinib + Trametinib + Vemurafenib","efficacy_evidence":"In a preclinical study, the addition of Celecoxib to the combination of Zelboraf (vemurafenib), Mekinist (trametinib), and Iressa (gefitinib) synergistically inhibited viability in colorectal cancer cell lines harboring BRAF V600E in culture (%%PUBMED:36759733%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[33537843],"response_type":"predicted - sensitive","indication":"endometrial adenocarcinoma","therapy_id":12031,"normalized_cancer":"Endometrial Carcinoma","evidence_type":"Actionable","therapy":"Dabrafenib + Rabeprazole + Rifampin + Trametinib","efficacy_evidence":"In a Phase I trial, the addition of Mekinist (trametinib) to combination treatment with Tafinlar (dabrafenib), Rabeprazole, and Rifampin resulted in a maintained radiographic response of lung metastases and stable pelvic mass size in a patient with metastatic endometrial adenocarcinoma harboring BRAF V600E, which lasted for 12 months (%%PUBMED:33537843%%; NCT01954043).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[31744895],"response_type":"sensitive","indication":"melanoma","therapy_id":4588,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"LY3214996","efficacy_evidence":"In a preclinical study, LY3214996 treatment in a melanoma cell line harboring BRAF V600E led to decreased cell proliferation in culture, and inhibition of tumor growth in a cell line xenograft model (%%PUBMED:31744895%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[31386052],"normalized_drug":"Vemurafenib","indication":"pleomorphic xanthoastrocytoma","therapy_id":342,"normalized_cancer":"Pleomorphic Xanthoastrocytoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a clinical case study, Zelboraf (vemurafenib) treatment resulted in a complete intracranial response 2 months after treatment in a patient with anaplastic pleomorphic xanthoastrocytoma harboring BRAF V600E, although the disease progressed 1 month later (%%PUBMED:31386052%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[30351999],"normalized_drug":"Vemurafenib","indication":"pleomorphic xanthoastrocytoma","therapy_id":342,"normalized_cancer":"Pleomorphic Xanthoastrocytoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase II trial (VE-BASKET), Zelboraf (vemurafenib) treatment resulted in an objective response rate of 42.9% (3/7, 1 complete response, 2 partial responses) and a clinical benefit rate of 57% in patients with pleomorphic xanthoastrocytoma harboring BRAF V600E, with a median progression-free survival of 5.7 months, and median overall survival not reached (%%PUBMED:30351999%%; NCT01524978).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[32523649],"normalized_drug":"Vemurafenib","indication":"pleomorphic xanthoastrocytoma","therapy_id":342,"normalized_cancer":"Pleomorphic Xanthoastrocytoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase I trial (PNOC-002), Zelboraf (vemurafenib) treatment was tolerable and resulted in 1 complete response, 5 partial responses, and 13 stable disease in 19 pediatric patients with recurrent low grade gliomas harboring BRAF V600E, including 1 complete response and 1 stable disease among 2 patients with pleomorphic xanthroastrocytoma (%%PUBMED:32523649%%; NCT01748149).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[25665005],"response_type":"sensitive","indication":"lung non-small cell carcinoma","therapy_id":3531,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"TW-37 + Vemurafenib","efficacy_evidence":"In a preclinical study, TW-37 enhanced the inhibitory effect of Zelboraf (vemurafenib) on human non-small cell lung cancer cells harboring BRAF V600E in culture (%%PUBMED:25665005%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[26466569],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":4606,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"PLX7904","efficacy_evidence":"In a preclinical study, PLX7904 inhibited survival of colorectal cancer cells harboring BRAF V600E in culture and demonstrated anti-tumor activity in cell line xenograft models (%%PUBMED:26466569%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[26490654],"normalized_drug":"Vemurafenib","indication":"ovary serous adenocarcinoma","therapy_id":342,"normalized_cancer":"Serous Ovarian Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a clinical case study, Zelboraf (vemurafenib) treatment resulted in a partial response lasting more than 21 months in a patient with low grade serous ovarian adenocarcinoma harboring BRAF V600E (%%PUBMED:26490654%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[27523909],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":4607,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"PLX4720 + TAK-632","efficacy_evidence":"In a preclinical study, PLX4720 and TAK-632 combination treatment resulted in durable inhibition of Erk signaling and tumor growth in xenograft models of colorectal cancer cells harboring BRAF V600E (%%PUBMED:27523909%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[27924459],"response_type":"sensitive","indication":"melanoma","therapy_id":5118,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Imatinib + PLX4720","efficacy_evidence":"In a preclinical study, the combination of Gleevec (imatinib) and PLX4720 enhanced antitumor efficacy of melanoma cells harboring BRAF V600E, demonstrating decreased cell survival in xenograft models, and decreased phosphorylation of Mapk1 in culture (%%PUBMED:27924459%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[37326340],"response_type":"no benefit","indication":"colorectal carcinoma","therapy_id":1823,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Mirdametinib + Palbociclib","efficacy_evidence":"In a preclinical study, the combination of Ibrance (palbociclib) and Gomekli (mirdametinib) demonstrated antagonism in a colorectal carcinoma cell line harboring BRAF V600E in culture (%%PUBMED:37326340%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[29621181],"normalized_drug":"Dabrafenib","indication":"glioblastoma","therapy_id":3,"normalized_cancer":"Glioblastoma, 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(%%PUBMED:36759733%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Encorafenib","indication":"colorectal cancer","therapy_id":796,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Encorafenib","efficacy_evidence":"In a Phase I trial, Encorafenib (LGX818) showed activity in patients with advanced metastatic colorectal cancer harboring a BRAF V600E mutation, resulting in a median progression-free survival of 4 months and a best response of stable disease in 66.7% (12/18) (Ann Oncol (2014) 25 (suppl 4): iv182-iv183).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase I","amp_tier":"II"},{"pub_med_references":[28719152],"response_type":"predicted - sensitive","indication":"melanoma","therapy_id":884,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"RAF265","efficacy_evidence":"In a Phase I trial, treatment with RAF265 in melanoma patients resulted in an objective response rate of 12.1% (8/66), including a partial response in four patients harboring BRAF V600E, two partial responses and one complete response in patients with wild-type BRAF, and one complete response in a patient with unknown mutational status (%%PUBMED:28719152%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[28939558],"normalized_drug":"Ulixertinib","indication":"melanoma","therapy_id":997,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Ulixertinib","efficacy_evidence":"In a preclinical study, Ulixertinib (BVD-523) inhibited Erk signaling in melanoma cells harboring BRAF V600E, resulted in cell cycle arrest in culture and tumor growth inhibition in cell line xenograft models (%%PUBMED:28939558%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[38820503],"normalized_drug":"Dabrafenib, Trametinib","indication":"acinar cell carcinoma","therapy_id":1066,"normalized_cancer":"Acinar Cell Carcinoma of the Pancreas","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, treatment with the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) resulted in near complete metabolic remission at 5 months and persistent complete metabolic remission at 12 months in a patient with metastatic acinar cell carcinoma of unknown primary harboring BRAF V600E (%%PUBMED:38820503%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - 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vemurafenib/PLX4720-resistant cells harboring distinct BRAF V600E splice variants (%%PUBMED:24422853%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[38593698],"response_type":"sensitive","indication":"papillary thyroid carcinoma","therapy_id":17831,"normalized_cancer":"Papillary Thyroid Cancer","evidence_type":"Actionable","therapy":"AZD1208 + Vemurafenib","efficacy_evidence":"In a preclinical study, treatment with the combination of Zelboraf (vemurafenib) and AZD1208 synergistically inhibited viability and colony formation of papillary thyroid carcinoma cell lines harboring BRAF V600E in culture (%%PUBMED:38593698%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[38565920],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":16825,"normalized_cancer":"Colorectal 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BRAF V600E in culture, and improved the partial response rate compared to either drug alone in a zebrafish xenograft model (%%PUBMED:35882450%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib","indication":"oncocytic carcinoma of the thyroid","therapy_id":3,"normalized_cancer":"Hurthle Cell Thyroid Cancer","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"Tafinlar (dabrafenib) is included in guidelines for patients with recurrent, advanced, or metastatic thyroid Hurthle cell carcinoma harboring BRAF V600E for whom clinical trials are not available or appropriate (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"predicted - sensitive","pub_med_references":[38814411],"normalized_drug":"Dabrafenib, 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or refractory hairy cell leukemia patients with BRAF V600E demonstrated safety, and led to complete response (CR) in 87% (26/30) of patients, including 17 (65%) with negative minimal residual disease, a progression-free survival rate of 78% at a median follow-up of 37 months, and a relapse-free survival rate of 85% in the 26 patients with a CR at a median follow-up of 34 months (%%PUBMED:33979489%%).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"melanoma","therapy_id":7465,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"BGB3245","efficacy_evidence":"In a Phase I trial, BGB3245 treatment demonstrated manageable safety and resulted in a disease control rate of 48% (16/33,1 complete response, 5 confirmed partial responses (PR), 2 unconfirmed PR, and 8 stable disease > 24 weeks) in patients with advanced solid tumors harboring MAPK pathway alterations, including 1 complete response and 1 confirmed partial response in patients with melanoma harboring BRAF V600E (Cancer Res (2023) 83 (8_Supplement): CT031).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[32758030],"normalized_drug":"Trametinib","indication":"ovarian serous carcinoma","therapy_id":2,"normalized_cancer":"Serous Ovarian Cancer","evidence_type":"Actionable","therapy":"Trametinib","efficacy_evidence":"In a Phase II trial (NCI-MATCH), Mekinist (trametinib) treatment resulted in an objective response rate of 37.9% (11/29) in patients with advanced solid tumors harboring BRAF V600E, of 5 patients with low grade serous ovarian carcinoma, 4 achieved a partial response (PR), 1 had stable disease, 3 of the PRs lasted over 12 months (%%PUBMED:32758030%%; NCT02465060).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[37808191],"response_type":"sensitive","indication":"melanoma","therapy_id":15985,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Tunlametinib + Vemurafenib","efficacy_evidence":"In a preclinical study, treatment with the combination of Tunlametinib (HL-085) and Zelboraf (vemurafenib) synergistically inhibited proliferation of a melanoma cell line harboring BRAF V600E in culture, and synergistically inhibited tumor growth in a cell line xenograft model (%%PUBMED:37808191%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[26573800],"response_type":"sensitive","indication":"glioblastoma","therapy_id":676,"normalized_cancer":"Glioblastoma, IDH-Wildtype","evidence_type":"Actionable","therapy":"BI2536","efficacy_evidence":"In a preclinical study, a glioblastoma cell line harboring BRAF V600E demonstrated sensitivity to BI2536 in culture (%%PUBMED:26573800%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[36702949],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":6023,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Spartalizumab + Trametinib","efficacy_evidence":"In a Phase II trial, the combination of Spartalizumab (PDR001), Tafinlar (dabrafenib), and Mekinist (trametinib) was well tolerated and resulted in a confirmed objective response rate of 24.3% (9/37, 2 complete responses), disease control rate of 70.3% (26/37), median progression-free survival of 4.3 months, median duration of response of 7.4 months, and median overall survival of 13.6 months in patients with metastatic colorectal cancer harboring BRAF V600E (%%PUBMED:36702949%%; NCT03668431).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"pub_med_references":[31937621],"response_type":"sensitive","indication":"thyroid cancer","therapy_id":10186,"normalized_cancer":"Thyroid Cancer","evidence_type":"Actionable","therapy":"Ponatinib + Vemurafenib","efficacy_evidence":"In a preclinical study, Iclusig (ponatinib) and Zelboraf (vemurafenib) treatment synergistically inhibited proliferation of thyroid cancer cells harboring BRAF V600E in culture (%%PUBMED:31937621%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[33976643],"normalized_drug":"Vemurafenib","indication":"triple-receptor negative breast cancer","therapy_id":342,"normalized_cancer":"Invasive Breast Carcinoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a clinical case study, Zelboraf (vemurafenib) treatment resulted in a partial response in the lung lesion lasting at least 19 months in a patient with metastatic triple-negative breast cancer harboring BRAF V600E (%%PUBMED:33976643%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[33318037],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":11345,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Lifirafenib + Trametinib","efficacy_evidence":"In a preclinical study, the combination treatment of Mekinist (trametinib) and Lifirafenib (BGB-283) led to greater inhibition of growth in a colorectal cancer cell line harboring BRAF V600E in culture compared to either treatment alone (%%PUBMED:33318037%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[23629727],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":1659,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Pimasertib + Sorafenib","efficacy_evidence":"In a preclinical study, Pimasertib (MSC1936369B) and Nexavar (sorafenib) synergistically inhibited proliferation of colorectal cancer cells harboring BRAF V600E in culture (%%PUBMED:23629727%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[27924459],"response_type":"sensitive","indication":"melanoma","therapy_id":5121,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"PLX4720 + Vorinostat","efficacy_evidence":"In a preclinical study, the combination of PLX4720 and Zolinza (vorinostat) resulted in antitumor efficacy in a melanoma cell line harboring BRAF V600E, demonstrating decreased cell survival and increased apoptotic activity in xenograft models, and decreased Rb phosphorylation in culture (%%PUBMED:27924459%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"follicular thyroid carcinoma","therapy_id":1066,"normalized_cancer":"Follicular Thyroid Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"The combination of Tafinlar (dabrafenib) and Mekinist (trametinib) is included in guidelines for patients with follicular thyroid carcinoma harboring BRAF V600E who have progressed on therapy and have no further treatment options (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[36198029],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":14530,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Pyrvinium + Vemurafenib","efficacy_evidence":"In a preclinical study, combination treatment with Zelboraf (vemurafenib) and Pyrvinium resulted in decreased viability in colorectal cancer cell lines harboring BRAF V600E in culture, and led to synergistic inhibition of tumor growth in a cell line xenograft model (%%PUBMED:36198029%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[35882450],"response_type":"predicted - sensitive","indication":"pleomorphic xanthoastrocytoma","therapy_id":12793,"normalized_cancer":"Pleomorphic Xanthoastrocytoma","evidence_type":"Actionable","therapy":"Trametinib + Ulixertinib","efficacy_evidence":"In a preclinical study, the combination of Ulixertinib (BVD-523) and Mekinist (trametinib) had a synergistic effect on the induction of apoptosis in a pleomorphic xanthoastrocytoma cell line harboring BRAF V600E in culture (%%PUBMED:35882450%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[39626159],"response_type":"sensitive","indication":"colon cancer","therapy_id":17951,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Erlotinib + Fluorouracil + Vemurafenib","efficacy_evidence":"In a preclinical study, the addition of Adrucil (fluorouracil) to treatment with the combination of Tarceva (erlotinib) and Zelboraf (vemurafenib) resulted in greater inhibition of viability of mouse colon cancer organoids harboring BRAF V600E in culture compared to Adrucil (fluorouracil) or the doublet combination therapy (%%PUBMED:39626159%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - 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and those acquired Sprycel (dasatinib)-resistance in culture (%%PUBMED:27222538%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Binimetinib, Encorafenib","indication":"lung non-small cell carcinoma","therapy_id":1100,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Binimetinib + Encorafenib","efficacy_evidence":"Combination of Braftovi (encorafenib) and Mektovi (binimetinib) is included in guidelines as a first-line or subsequent therapy for advanced or metastatic non-small cell lung cancer patients harboring BRAF V600E mutations (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[37270692],"normalized_drug":"Binimetinib, Encorafenib","indication":"lung non-small cell carcinoma","therapy_id":1100,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Binimetinib + Encorafenib","efficacy_evidence":"In a Phase II trial (PHAROS) that supported FDA approval, Braftovi (encorafenib) and Mektovi (binimetinib) combination therapy resulted in an objective response rate (ORR) of 75% (44/59; 9 complete, 35 partial responses) with a duration of response (DOR) lasting 12 or more months in 59% of treatment-naive patients, and an ORR of 46% (18/39) with a DOR lasting 12 or more months in 33% of previously treated patients with metastatic non-small cell lung cancer harboring BRAF V600E (%%PUBMED:37270692%%; NCT03915951).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"FDA approved - On Companion Diagnostic","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[39615406],"normalized_drug":"Binimetinib, Encorafenib","indication":"lung non-small cell carcinoma","therapy_id":1100,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Binimetinib + Encorafenib","efficacy_evidence":"Combination of Braftovi (encorafenib) and Mektovi (binimetinib) is included in the Pan-Asian Guidelines Adaptation (PAGA) for advanced and metastatic non-small cell lung cancer patients harboring BRAF V600E (%%PUBMED:39615406%%; ESMO.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"predicted - sensitive","pub_med_references":[35046062],"normalized_drug":"Cobimetinib, Vemurafenib","indication":"large cell carcinoma","therapy_id":1657,"normalized_cancer":"Large Cell Lung Carcinoma","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"In a clinical study, a patient with poorly differentiated large cell carcinoma harboring BRAF V600E experienced a complete response lasting at least 2 years on combination treatment with Cotellic (cobimetinib) and Zelboraf (vemurafenib) (%%PUBMED:35046062%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[26438159],"response_type":"sensitive","indication":"melanoma","therapy_id":903,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"RO4987655","efficacy_evidence":"In a preclinical study, RO4987655 inhibited proliferation of melanoma cells harboring BRAF V600E in culture (%%PUBMED:26438159%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[39121480],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":9079,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Tazemetostat + Trametinib","efficacy_evidence":"In a preclinical study, the addition of Tazverik (tazemetostat) sensitized a colorectal cancer cell line harboring BRAF V600E to Mekinist (trametinib) treatment in culture, resulting in decreased cell proliferation (%%PUBMED:39121480%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[36343387],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":14550,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Panobinostat + Vemurafenib","efficacy_evidence":"In a preclinical study, the combination of Zelboraf (vemurafenib) and Farydak (panobinostat) resulted in greater apoptotic activity compared to either agent alone in a colorectal cancer cell line harboring BRAF V600E in culture (%%PUBMED:36343387%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - 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Trametinib","efficacy_evidence":"In a clinical case study, combination treatment with Tafinlar (dabrafenib) and Mekinist (trametinib) led to a partial response after 1 month of treatment in a metastatic pancreatic ductal adenocarcinoma patient harboring BRAF V600E, followed by disease progression, which was detected 12 months later (%%PUBMED:35382161%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[34433654],"response_type":"predicted - sensitive","indication":"high grade glioma","therapy_id":3268,"normalized_cancer":"High-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"LY3009120","efficacy_evidence":"In a preclinical study, LY3009120 treatment led to inhibition of cell viability and growth in a patient-derived glioma cell line harboring BRAF V600E in culture (%%PUBMED:34433654%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Patient cell culture","amp_tier":"II"},{"pub_med_references":[22180495],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":10747,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Irinotecan + Vemurafenib","efficacy_evidence":"In a preclinical study, Zelboraf (vemurafenib) treatment in combination with Camptosar (irinotecan) enhanced tumor growth inhibition and increased survival in a cell line xenograft model of colorectal cancer harboring BRAF V600E (%%PUBMED:22180495%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[36759733],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":15042,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Dasatinib + Gefitinib + Vemurafenib","efficacy_evidence":"In a preclinical study, the combination of Zelboraf (vemurafenib), Iressa (gefitinib), and Sprycel (dasatinib) synergistically inhibited viability in colorectal cancer cell lines harboring BRAF V600E in culture and resulted in greater tumor growth inhibition and tumor regression in patient-derived xenograft (PDX) models to a greater degree than the doublet combinations of Zelboraf (vemurafenib) and Iressa (gefitinib) or Zelboraf (vemurafenib) and Sprycel (dasatinib) (%%PUBMED:36759733%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Pdx & cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[30181415],"normalized_drug":"Dabrafenib","indication":"colon neuroendocrine neoplasm","therapy_id":3,"normalized_cancer":"Gastrointestinal Neuroendocrine Tumors","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a clinical case study, Tafinlar (dabrafenib) treatment of a patient with recurrent neuroendocrine carcinoma of the colon harboring a BRAF V600E mutation resulted in stable disease for 6 months before disease progression (%%PUBMED:30181415%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[20531415,26603897],"response_type":"sensitive","indication":"melanoma","therapy_id":3307,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"SBI-0640726","efficacy_evidence":"In a preclinical study, SBI-0640726 inhibited proliferation and Akt/mTOR signaling in human melanoma cell lines harboring BRAF V600E in culture (%%PUBMED:26603897%%, %%PUBMED:20531415%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[28425764],"normalized_drug":"Dabrafenib, Trametinib","indication":"papillary craniopharyngioma","therapy_id":1066,"normalized_cancer":"Craniopharyngioma, Papillary Type","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, treatment with the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) resulted in decreased tumor size and symptom improvement in a patient with recurrent papillary craniopharyngioma harboring BRAF V600E, with treatment ongoing for at least 7 months (%%PUBMED:28425764%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[35023192],"normalized_drug":"Dabrafenib, Trametinib","indication":"papillary craniopharyngioma","therapy_id":1066,"normalized_cancer":"Craniopharyngioma, Papillary Type","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, treatment with the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) resulted in a 95% decrease in tumor size in a patient with papillary craniopharyngioma harboring BRAF V600E (%%PUBMED:35023192%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[26498373],"normalized_drug":"Dabrafenib, Trametinib","indication":"papillary craniopharyngioma","therapy_id":1066,"normalized_cancer":"Craniopharyngioma, Papillary Type","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, Tafinlar (dabrafenib) treatment resulted in a 70% cyst volume reduction and 52% decreased enhancing volume followed by combination treatment with Mekinist (trametinib) resulting in 81% cyst volume reduction and 85% enhancing volume reduction in a patient with recurrent papillary craniopharyngioma harboring BRAF V600E (%%PUBMED:26498373%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[37683921],"normalized_drug":"Dabrafenib, Trametinib","indication":"papillary craniopharyngioma","therapy_id":1066,"normalized_cancer":"Craniopharyngioma, Papillary Type","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, neoadjuvant treatment with the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) resulted in sustained radiologic response after 3 months of treatment followed by a tumor-free period lasting 2 years from treatment discontinuation in a patient with papillary craniopharyngioma harboring BRAF V600E (%%PUBMED:37683921%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[39234402],"normalized_drug":"Dabrafenib, Trametinib","indication":"renal Wilms' tumor","therapy_id":1066,"normalized_cancer":"Wilms' Tumor","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical study, combination treatment with Tafinlar (dabrafenib) and Mekinist (trametinib) resulted in regression in the metastatic disease of the liver, spleen, and peritoneum along with clinical symptom improvement in an adult patient with metastatic Wilms' tumor harboring BRAF V600E (%%PUBMED:39234402%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[31566309],"normalized_drug":"Cetuximab, Encorafenib","indication":"colorectal cancer","therapy_id":1916,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Encorafenib","efficacy_evidence":"In a Phase III (BEACON CRC) trial that supported FDA approval, Braftovi (encorafenib) and Erbitux (cetuximab) combination treatment (n=113) resulted in improved median overall survival (8.4 vs 5.4 months, HR=0.60, p<0.001), confirmed response rate (20% vs 2%, p<0.001), and median progression-free survival (4.2 vs 1.5 months, HR=0.40, p<0.001) compared to control (n=107) in patients with metastatic colorectal cancer harboring BRAF V600E (%%PUBMED:31566309%%; NCT02928224).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"FDA approved - On Companion Diagnostic","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[39255538],"normalized_drug":"Cetuximab, Encorafenib","indication":"colorectal cancer","therapy_id":1916,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Encorafenib","efficacy_evidence":"In a retrospective analysis, real-world treatment with Erbitux (cetuximab) and Braftovi (encorafenib) with or without Mektovi (binimetinib) led to an objective response rate (ORR) of 32.2% (57/201, 2 complete responses (CR)), disease control rate of 71.2% (126/201), median progression-free survival of 4.5 months, and median overall survival of 9.2 months in metastatic colorectal cancer patients with BRAF V600E, with an ORR of 32% (50/180, 1 CR) in patients treated with doublet therapy (%%PUBMED:39255538%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Clinical Study","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[36307056],"normalized_drug":"Cetuximab, Encorafenib","indication":"colorectal cancer","therapy_id":1916,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Encorafenib","efficacy_evidence":"Braftovi (encorafenib) in combination with Erbitux (cetuximab) is included in guidelines as second-line or subsequent therapy for patients with metastatic colorectal cancer harboring BRAF V600E (%%PUBMED:36307056%%; ESMO.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[37236086],"normalized_drug":"Cetuximab, Encorafenib","indication":"colorectal cancer","therapy_id":1916,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Encorafenib","efficacy_evidence":"Braftovi (encorafenib) in combination with Erbitux (cetuximab) is included in the Pan-Asian Guidelines Adaptation (PAGA) as a second- or subsequent-line therapy for patients with advanced or metastatic colorectal cancer harboring BRAF V600E (%%PUBMED:37236086%%; ESMO.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[27312529],"normalized_drug":"Cetuximab, Encorafenib","indication":"colorectal cancer","therapy_id":1916,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Encorafenib","efficacy_evidence":"In a preclinical study, combination therapy consisting of Erbitux (cetuximab) and Encorafenib (LGX818) inhibited survival of colorectal cancer cell lines harboring BRAF V600E in culture (%%PUBMED:27312529%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[35696748],"normalized_drug":"Cetuximab, Encorafenib","indication":"colorectal cancer","therapy_id":1916,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Encorafenib","efficacy_evidence":"In a retrospective study, combination treatment with Erbitux (cetuximab) and Braftovi (encorafenib) resulted in an objective response rate of 17%, a disease control rate of 65%, a median progression-free survival of 4.6 mo, and a median overall survival of 7.2 mo in patients with metastatic colorectal cancer harboring BRAF V600E (%%PUBMED:35696748%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Clinical Study","amp_tier":"II"},{"pub_med_references":[34667063],"response_type":"predicted - sensitive","indication":"pancreatic ductal adenocarcinoma","therapy_id":12597,"normalized_cancer":"Pancreatic Adenocarcinoma","evidence_type":"Actionable","therapy":"Cobimetinib + Gemcitabine + Nab-paclitaxel","efficacy_evidence":"In a clinical case study, Gemzar (gemcitabine), Abraxane (nab-paclitaxel), and Cotellic (cobimetinib) combination treatment resulted in a complete radiologic response within 6 months of initiation lasting at least 16 months in a patient with microsatellite stable, KRAS wild-type pancreatic ductal adenocarcinoma harboring BRAF V600E (%%PUBMED:34667063%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[38691346],"response_type":"predicted - sensitive","indication":"colorectal cancer","therapy_id":13602,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"PF-07799933","efficacy_evidence":"In a preclinical study, PF-07799933 inhibited Erk phosphorylation in colorectal cancer cells harboring BRAF V600E in culture (%%PUBMED:38691346%%).","cap_asco_evidence_level":"NA","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Biochemical","amp_tier":"NA"},{"pub_med_references":[22389471],"response_type":"sensitive","indication":"melanoma","therapy_id":763,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"GSK2126458","efficacy_evidence":"In a preclinical study, Omipalisib (GSK2126458) inhibited the growth of melanoma cell lines harboring BRAF V600E in culture (%%PUBMED:22389471%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[19276360],"response_type":"sensitive","indication":"colon cancer","therapy_id":1095,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"GDC0879","efficacy_evidence":"In a preclinical study, GDC0879 inhibited survival of colon cancer cell lines harboring BRAF V600E in cell culture and cell line xenograft models (%%PUBMED:19276360%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[38714355],"response_type":"sensitive","indication":"glioblastoma","therapy_id":17539,"normalized_cancer":"Glioblastoma, IDH-Wildtype","evidence_type":"Actionable","therapy":"Mirdametinib + Radiotherapy","efficacy_evidence":"In a preclinical study, the combination of Gomekli (mirdametinib) and radiotherapy synergistically inhibited cell growth of glioblastoma cell lines harboring BRAF V600E in culture (%%PUBMED:38714355%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[35882450],"response_type":"predicted - sensitive","indication":"pleomorphic xanthoastrocytoma","therapy_id":14716,"normalized_cancer":"Pleomorphic Xanthoastrocytoma","evidence_type":"Actionable","therapy":"Selumetinib + Ulixertinib","efficacy_evidence":"In a preclinical study, the combination of Ulixertinib (BVD-523) and Koselugo (selumetinib) inhibited proliferation in a pleomorphic xanthoastrocytoma cell line harboring BRAF V600E in culture (%%PUBMED:35882450%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"no benefit","pub_med_references":[16880785,22394203],"normalized_drug":"Sorafenib","indication":"melanoma","therapy_id":920,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Sorafenib","efficacy_evidence":"In a Phase II study, Nexavar (sorafenib) displayed negligible efficacy in melanoma patients with BRAF V600E mutations (%%PUBMED:16880785%%, %%PUBMED:22394203%%).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"pub_med_references":[18287029],"response_type":"sensitive","indication":"colon cancer","therapy_id":1060,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"PLX4720","efficacy_evidence":"In a preclinical study, PLX4720 inhibited growth of colon cancer cells harboring BRAF V600E in culture and in cell line xenograft models (%%PUBMED:18287029%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[24885690],"normalized_drug":"Sorafenib","indication":"colorectal cancer","therapy_id":920,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Sorafenib","efficacy_evidence":"In a preclinical study, colorectal cancer cell lines harboring a BRAF V600E mutation were sensitive to Nexavar (sorafenib) in culture (%%PUBMED:24885690%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[28939558],"normalized_drug":"Ulixertinib","indication":"colorectal cancer","therapy_id":997,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Ulixertinib","efficacy_evidence":"In a preclinical study, Ulixertinib (BVD-523) inhibited Erk signaling in colorectal cancer cells harboring BRAF V600E, resulted in cell cycle arrest in culture and tumor growth inhibition in cell line xenograft models (%%PUBMED:28939558%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[39190425],"normalized_drug":"Vemurafenib","indication":"histiocytosis","therapy_id":342,"normalized_cancer":"Histiocytosis","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a clinical study, Zelboraf (vemurafenib) treatment resulted in complete remission in 2 pediatric patients with Langerhans cell histiocytosis harboring BRAF V600E (%%PUBMED:39190425%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"Squamous Cell Carcinoma of Unknown Primary","therapy_id":1066,"normalized_cancer":"Squamous Cell Carcinoma, NOS","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"The combination of Tafinlar (dabrafenib) and Mekinist (trametinib) is included in guidelines for patients with squamous cell carcinoma of unknown primary harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[29118233],"response_type":"not applicable","indication":"hairy cell leukemia","therapy_id":1776,"normalized_cancer":"Hairy Cell Leukemia","evidence_type":"Diagnostic","therapy":"N/A","efficacy_evidence":"BRAF V600E is diagnostic and aids in distinguishing classic hairy cell leukemia (cHCL) from variant hairy cell leukemia (HCLv) and other B-cell lymphomas and leukemias (%%PUBMED:29118233%%, NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[18794803],"response_type":"predicted - sensitive","indication":"melanoma","therapy_id":2427,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"U0126","efficacy_evidence":"In a preclinical study, U0126 treatment inhibited Erk phosphorylation and reduced growth of melanoma cells harboring BRAF V600E in culture (%%PUBMED:18794803%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"not predictive","pub_med_references":[29723688],"normalized_drug":"Pembrolizumab","indication":"lung non-small cell carcinoma","therapy_id":1447,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Pembrolizumab","efficacy_evidence":"In a retrospective analysis, non-small cell lung cancer patients harboring BRAF V600E did not demonstrate a significantly different response to treatment with either Keytruda (pembrolizumab), Opdivo (nivolumab), or Tecentriq (atezolizumab), compared to patients with BRAF non-V600E mutations, demonstrating an objective response rate of 25% (3/12) vs 33% (3/9) (p=1.0) and median progression-free survival of 3.7 months vs 4.1 months (p=0.37) (%%PUBMED:29723688%%).","cap_asco_evidence_level":"NA","molecular_profile":"BRAF V600E","approval_status":"Clinical Study - Cohort","amp_tier":"NA"},{"pub_med_references":[39626159],"response_type":"predicted - sensitive","indication":"colon cancer","therapy_id":1992,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Panitumumab + Trametinib","efficacy_evidence":"In a clinical study, treatment with the combination of Vectibix (panitumumab), Tafinlar (dabrafenib), and Mekinist (trametinib) resulted in a clinical response in a pediatric patient with colon cancer harboring BRAF V600E, as well as TP53 G245S, SMAD4 S504R, and PTEN loss, with decreased liver metastases and reduction in CA-19-9 and BRAF V600E VAF levels in the cell free DNA (%%PUBMED:39626159%%; NCT02688517).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[36825105],"normalized_drug":"Dabrafenib, Trametinib","indication":"IDH-wildtype glioblastoma","therapy_id":1066,"normalized_cancer":"Glioblastoma, IDH-Wildtype","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, Tafinlar (dabrafenib) and Mekinist (trametinib) combination therapy resulted in a partial response lasting 9 months in a patient with metastatic MGMT unmethylated, IDH-wildtype glioblastoma harboring BRAF V600E along with amplification of MYC and TERT and loss of CDKN2A/B (%%PUBMED:36825105%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[28645859],"response_type":"sensitive","indication":"melanoma","therapy_id":6241,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"INU-152","efficacy_evidence":"In a preclinical study, INU-152 reduced MEK and ERK phosphorylation and growth of a melanona cell line harboring BRAF V600E in culture, and inhibited tumor growth in xenograft models (%%PUBMED:28645859%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"melanoma","therapy_id":10113,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"JSI-1187","efficacy_evidence":"In a preclinical study, JSI-1187 treatment in a melanoma cell line harboring BRAF V600E led to inhibition of cell proliferation in culture, and tumor growth inhibition in a cell line xenograft model (Cancer Res 2020;80(16 Suppl):Abstract nr 4188).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[32758030],"normalized_drug":"Trametinib","indication":"histiocytic sarcoma","therapy_id":2,"normalized_cancer":"Histiocytic Sarcoma","evidence_type":"Actionable","therapy":"Trametinib","efficacy_evidence":"In a Phase II trial (NCI-MATCH), Mekinist (trametinib) treatment resulted in an objective response rate of 37.9% (11/29) in patients with advanced solid tumors harboring BRAF V600E, 1 patient with histiocytic sarcoma of the brain achieved a partial response with an ongoing progression-free survival at 20.9 months (%%PUBMED:32758030%%; NCT02465060).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[39392364],"normalized_drug":"Binimetinib, Encorafenib","indication":"glomus tumor","therapy_id":1100,"normalized_cancer":"Soft Tissue Cancer","evidence_type":"Actionable","therapy":"Binimetinib + Encorafenib","efficacy_evidence":"In a clinical case study, treatment with the combination of Mektovi (binimetinib) and Braftovi (encorafenib) resulted in a complete response lasting more than 2 years in a patient with metastatic malignant glomus tumor harboring BRAF V600E (%%PUBMED:39392364%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[23629727],"normalized_drug":"Pimasertib","indication":"colorectal cancer","therapy_id":871,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Pimasertib","efficacy_evidence":"In a preclinical study, Pimasertib (MSC1936369B) inhibited proliferation of colorectal cancer cells harboring BRAF V600E in culture (%%PUBMED:23629727%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[37838724],"response_type":"sensitive","indication":"melanoma","therapy_id":16289,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"AZD3514 + Dabrafenib","efficacy_evidence":"In a preclinical study, the addition of AZD3514 to Tafinlar (dabrafenib) treatment inhibited colony formation in melanoma cell lines harboring BRAF V600E in culture (%%PUBMED:37838724%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[36343387],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":14545,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Trametinib + Vorinostat","efficacy_evidence":"In a preclinical study, the combination of Mekinist (trametinib) and Zolinza (vorinostat) resulted in greater apoptotic activity compared to either agent alone in a colorectal cancer cell line harboring BRAF V600E in culture (%%PUBMED:36343387%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[36343387],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":14546,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Romidepsin + Trametinib","efficacy_evidence":"In a preclinical study, the combination of Mekinist (trametinib) and Istodax (romidepsin) resulted in greater apoptotic activity compared to either agent alone in a colorectal cancer cell line harboring BRAF V600E in culture (%%PUBMED:36343387%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[30559419],"normalized_drug":"Plx8394","indication":"melanoma","therapy_id":1041,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"PLX8394","efficacy_evidence":"In a preclinical study, PLX8394 treatment inhibited Erk phosphorylation and reduced proliferation of melanoma cells harboring either monomeric BRAF V600E or dimeric isoform (p61) of V600E in culture (%%PUBMED:30559419%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"no benefit","pub_med_references":[27312529],"normalized_drug":"Vemurafenib","indication":"colorectal cancer","therapy_id":342,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a preclinical study, colorectal cancer cell lines harboring BRAF V600E demonstrated decreased response to Zelboraf (vemurafenib) in culture (%%PUBMED:27312529%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"no benefit","pub_med_references":[26460303],"normalized_drug":"Vemurafenib","indication":"colorectal cancer","therapy_id":342,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase II trial, Zelboraf (vemurafenib) did not demonstrate meaningful clinical activity as a single agent, resulted in partial response in 5% (1/21) and stable disease in 33% (7/21) of patients with metastatic colorectal cancer harboring BRAF V600E (%%PUBMED:26460303%%; NCT00405587).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"response_type":"no benefit","pub_med_references":[22281684],"normalized_drug":"Vemurafenib","indication":"colorectal cancer","therapy_id":342,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a preclinical study, colorectal cancer cell lines harboring BRAF V600E were not sensitive to growth inhibition by Zelboraf (vemurafenib) in culture or xenograft models, due to feedback activation of EGFR signaling (%%PUBMED:22281684%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[34178685],"normalized_drug":"Dabrafenib, Trametinib","indication":"lung papillary adenocarcinoma","therapy_id":1066,"normalized_cancer":"Lung Adenocarcinoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, Tafinlar (dabrafenib) and Mekinist (trametinib) combination treatment resulted in regression of the lesions in the chest, abdomen and brain in a patient with lung papillary carcinoma harboring BRAF V600E but progression was observed 3 months later (%%PUBMED:34178685%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[33537843],"normalized_drug":"Dabrafenib, Trametinib","indication":"intrahepatic cholangiocarcinoma","therapy_id":1066,"normalized_cancer":"Intrahepatic Cholangiocarcinoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, combination treatment with Tafinlar (dabrafenib) and Mekinist (trametinib) in a patient with intrahepatic cholangiocarcinoma harboring BRAF V600E who progressed on chemotherapy led to stable disease at 6 weeks, improvement of lung and liver lesions at 12 weeks after treatment, and response was maintained until disease progression in the liver was observed at 10 months (%%PUBMED:33537843%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[38109210],"normalized_drug":"Dabrafenib, Trametinib","indication":"intrahepatic cholangiocarcinoma","therapy_id":1066,"normalized_cancer":"Intrahepatic Cholangiocarcinoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a Phase II trial (NCI-MATCH), treatment with the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) resulted in an objective response rate of 38% in patients with advanced solid tumors harboring BRAF V600E, with a significantly greater tumor shrinkage observed in patients (n=4) with intrahepatic cholangiocarcinoma compared to the trial average ( -60% vs -35%, P=0.016) (%%PUBMED:38109210%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"intrahepatic cholangiocarcinoma","therapy_id":1066,"normalized_cancer":"Intrahepatic Cholangiocarcinoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Tafinlar (dabrafenib) in combination with Mekinist (trametinib) is included in guidelines as subsequent-line therapy for patients with biliary cancer harboring BRAF V600E, including intrahepatic cholangiocarcinoma (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[24983357],"response_type":"sensitive","indication":"melanoma","therapy_id":2960,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Navitoclax + PLX4720","efficacy_evidence":"In a preclinical study, PLX4720 and navitoclax (ABT-263) worked synergistically to inhibit growth and increase apoptosis of BRAF V600E mutant melanoma cells in culture and in xenografts (%%PUBMED:24983357%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[30323086],"normalized_drug":"Dabrafenib, Trametinib","indication":"salivary gland carcinoma","therapy_id":1066,"normalized_cancer":"Salivary Carcinoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case report, combined Tafinlar (dabrafenib) and Mekinist (trametinib) treatment of a patient with salivary duct carcinoma harboring BRAF V600E resulted in a reduction of metastatic lesions and stable disease lasting 13 months followed by disease progression (%%PUBMED:30323086%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"colorectal cancer","therapy_id":16367,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Encorafenib + IMM-6-415","efficacy_evidence":"In a preclinical study, treatment with the combination of Braftovi (encorafenib) and IMM-6-415 resulted in increased tumor growth inhibition compared to the combination of Mektovi (binimetinib) and Braftovi (encorafenib) in a cell line xenograft model of colorectal cancer harboring BRAF V600E (Mol Cancer Ther (2023) 22 (12_Supplement): A093).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[32758030],"normalized_drug":"Trametinib","indication":"lung adenocarcinoma","therapy_id":2,"normalized_cancer":"Lung Adenocarcinoma","evidence_type":"Actionable","therapy":"Trametinib","efficacy_evidence":"In a Phase II trial (NCI-MATCH), Mekinist (trametinib) treatment resulted in an objective response rate of 37.9% (11/29) in patients with advanced solid tumors harboring BRAF V600E, of 4 patients with lung adenocarcinoma, 1 achieved a partial response with an ongoing progression-free survival (PFS) at 32.5 mo, 3 patients had stable disease for 15.6, 6.6, and 3.6 mo, and an additional unevaluable patient achieved an 81% reduction of measured lesions and a PFS of 12.7 mo (%%PUBMED:32758030%%; NCT02465060).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[37417899],"normalized_drug":"Vemurafenib","indication":"synovial sarcoma","therapy_id":342,"normalized_cancer":"Synovial Sarcoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a clinical case study, Zelboraf (vemurafenib) resulted in a partial response after 4 months of treatment in a patient with intrathoracic synovial sarcoma harboring SS18-SSX1 (e10:e6) and BRAF V600E (%%PUBMED:37417899%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Cetuximab, Encorafenib","indication":"colon cancer","therapy_id":1916,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Encorafenib","efficacy_evidence":"Braftovi (encorafenib) in combination with Erbitux (cetuximab) is included in guidelines as primary or subsequent therapy for patients with colon cancer harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[40373261],"normalized_drug":"Cetuximab, Encorafenib","indication":"colon cancer","therapy_id":1916,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Encorafenib","efficacy_evidence":"In a clinical case study, neoadjuvant treatment with the combination of Braftovi (encorafenib) and Erbitux (cetuximab) resulted in tumor reduction in 2 patients with locally advanced, right-sided colon cancer harboring BRAF V600E (%%PUBMED:40373261%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[38343359],"normalized_drug":"Binimetinib, Encorafenib","indication":"papillary thyroid carcinoma","therapy_id":1100,"normalized_cancer":"Papillary Thyroid Cancer","evidence_type":"Actionable","therapy":"Binimetinib + Encorafenib","efficacy_evidence":"In a Phase II trial, Mektovi (binimetinib) plus Braftovi (encorafenib) demonstrated safety in patients with BRAF V600E-mutant thyroid cancer and resulted in an objective response rate (ORR) of 54.5% (12/22, 12 partial responses (PR)), with an ORR of 47.1% (8/17, 8 PR) and a disease control rate of 100% (17/17) in the differentiated thyroid cancer cohort (all papillary thyroid cancer), and median duration of response, progression-free survival, and overall survival were not reached (%%PUBMED:38343359%%).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"pub_med_references":[33229459],"response_type":"no benefit","indication":"uveal melanoma","therapy_id":11307,"normalized_cancer":"Uveal Melanoma","evidence_type":"Actionable","therapy":"YM-254890","efficacy_evidence":"In a preclinical study, transformed mouse melanocytes expressing BRAF V600E were insensitive to treatment with YM-254890 (%%PUBMED:33229459%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[38565920],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":16826,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + IAG933 + Trametinib","efficacy_evidence":"In a preclinical study, the combination of IAG933, Tafinlar (dabrafenib), and Mekinist (trametinib) inhibited proliferation of colorectal cancer cell lines harboring BRAF V600E in culture (%%PUBMED:38565920%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[38343359],"normalized_drug":"Binimetinib, Encorafenib","indication":"thyroid cancer","therapy_id":1100,"normalized_cancer":"Thyroid Cancer","evidence_type":"Actionable","therapy":"Binimetinib + Encorafenib","efficacy_evidence":"In a Phase II trial, treatment with Mektovi (binimetinib) plus Braftovi (encorafenib) demonstrated safety and activity in patients with BRAF V600E-mutant thyroid cancer, regardless of histological subtype, resulting in an objective response rate of 54.5% (12/22, 12 partial responses), disease control rate of 100% (22/22), and 12-month rate of ongoing response of 90.9%, and median duration of response, median progression-free survival, and median overall survival were not reached (%%PUBMED:38343359%%).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[38096472],"normalized_drug":"Cobimetinib, Vemurafenib","indication":"breast cancer","therapy_id":1657,"normalized_cancer":"Breast Cancer","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"In a Phase II trial (TAPUR), Zelboraf (vemurafenib) and Cotellic (cobimetinib) combination therapy resulted in a complete response that lasted 170 days and 2 partial responses out of 4 patients with advanced breast cancer harboring BRAF V600E (%%PUBMED:38096472%%; NCT02693535).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"melanoma","therapy_id":16367,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Encorafenib + IMM-6-415","efficacy_evidence":"In a preclinical study, treatment with the combination of Braftovi (encorafenib) and IMM-6-415 resulted in increased tumor growth inhibition compared to the combination of Mektovi (binimetinib) and Braftovi (encorafenib) in a cell line xenograft model of melanoma harboring BRAF V600E (Mol Cancer Ther (2023) 22 (12_Supplement): A093).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"resistant","normalized_drug":"Panitumumab","indication":"rectum cancer","therapy_id":845,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Panitumumab","efficacy_evidence":"Vectibix (panitumumab), as a monotherapy, is not indicated for use in rectum cancer patients with BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[22735384],"normalized_drug":"Dabrafenib","indication":"melanoma","therapy_id":3,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a Phase III clinical trial (BREAK-3) that supported FDA approval, Tafinlar (dabrafenib) improved median progression-free survival compared to Deticene (dacarbazine) (5.1 vs 2.7 months, HR=0.3, p<0.0001) in patients with BRAF V600E positive melanoma (%%PUBMED:22735384%%; NCT01227889).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"FDA approved - On Companion Diagnostic","amp_tier":"I"},{"pub_med_references":[25500121],"response_type":"sensitive","indication":"melanoma","therapy_id":3106,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"CCT241161","efficacy_evidence":"In a preclinical study, CCT241161 inhibited growth of a human melanoma cell line harboring BRAF V600E in culture, and induced tumor regression in several BRAF V600E-mutant melanoma patient-derived xenograft models (%%PUBMED:25500121%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"pub_med_references":[33568355],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":11477,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Regorafenib + Trametinib","efficacy_evidence":"In a preclinical study, combination treatment with Stivarga (regorafenib), Tafinlar (dabrafenib), and Mekinist (trametinib) in colorectal cancer cell lines harboring BRAF V600E resulted in suppression of colony formation in culture, and inhibition of tumor growth in a cell line xenograft model (%%PUBMED:33568355%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[27924459],"response_type":"sensitive","indication":"melanoma","therapy_id":5119,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Alpelisib + PLX4720","efficacy_evidence":"In a preclinical study, the combination of Alpelisib (BYL719) and PLX4720 enhanced antitumor activity in a melanoma cell line harboring BRAF V600E, demonstrating decreased cell survival and increased apoptotic activity in xenograft models, and decreased Akt signaling in culture (%%PUBMED:27924459%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[31937621],"response_type":"sensitive","indication":"thyroid cancer","therapy_id":10185,"normalized_cancer":"Thyroid Cancer","evidence_type":"Actionable","therapy":"PLX4720 + Ponatinib","efficacy_evidence":"In a preclinical study, Iclusig (ponatinib) and PLX4720 treatment demonstrated synergy, and inhibited Erk, Mek, and c-jun phosphorylation, reduced cell proliferation, colony formation, and migration, and induced apoptosis in thyroid cancer cells harboring BRAF V600E and in PLX4720-resistant cells harboring BRAF V600E in culture, and inhibited tumor growth, reduced lung and liver metastases, and increased survival in cell line xenograft models (%%PUBMED:31937621%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[33043759],"normalized_drug":"Binimetinib, Encorafenib","indication":"ovarian serous carcinoma","therapy_id":1100,"normalized_cancer":"Serous Ovarian Cancer","evidence_type":"Actionable","therapy":"Binimetinib + Encorafenib","efficacy_evidence":"In a clinical case study, Braftovi (encorafenib) and Mektovi (binimetinib) combination therapy resulted in durable stable disease lasting at least 3.5 years in a patient with low-grade serous ovarian carcinoma harboring BRAF V600E, who was previously treated with the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) (%%PUBMED:33043759%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[32029534],"normalized_drug":"Vemurafenib","indication":"cholangiocarcinoma","therapy_id":342,"normalized_cancer":"Cholangiocarcinoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase II trial (VE-BASKET), responses were seen in patients with cholangiocarcinoma harboring BRAF V600E (n=9) when treated with Zelboraf (vemurafenib), including 2 patients with a partial response (%%PUBMED:32029534%%; NCT01524978).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[37352476],"response_type":"no benefit","indication":"colorectal cancer","therapy_id":2184,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Fluorouracil + Irinotecan + Leucovorin + Oxaliplatin","efficacy_evidence":"In a Phase II trial (FIRE-4.5), the combination of Erbitux (cetuximab) with FOLFOXIRI as first-line therapy did not result in an improved objective response rate (ORR) compared to Avastin (bevacizumab) with FOLFOXIRI, with an ORR of 50.8% (30/59) vs 66.7% (20/30) (P=0.92), a median progression-free survival of 7.6 vs 12.4 months (P=0.003), and a median overall survival of 15.2 vs 22.9 months (P=0.14), respectively, in metastatic colorectal cancer patients harboring BRAF V600E (%%PUBMED:37352476%%).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"response_type":"sensitive","indication":"colorectal cancer","therapy_id":1718,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Panitumumab","efficacy_evidence":"In a Phase Ib/II trial, treatment with the combination of Vectibix (panitumumab) and Tafinlar (dabrafenib) resulted in stable disease in 7/8 colorectal cancer patients harboring a BRAF V600E mutation (J Clin Oncol 32:5s, 2014 (suppl; abstr 3515)).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase Ib/II","amp_tier":"II"},{"pub_med_references":[29431699],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":1718,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Panitumumab","efficacy_evidence":"In a Phase I trial, combination therapy consisting of Tafinlar (dabrafenib) and Vectibix (panitumumab) resulted in an overall response rate of 10% (2/20, 1 complete response, 1 partial response), stable disease in 80% (16/20), and a median progression-free survival of 3.5 months in patients with BRAF V600E colorectal cancer (%%PUBMED:29431699%%; NCT01750918).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase I","amp_tier":"II"},{"response_type":"sensitive","indication":"appendix adenocarcinoma","therapy_id":9562,"normalized_cancer":"Appendiceal Adenocarcinoma","evidence_type":"Actionable","therapy":"Encorafenib + Panitumumab","efficacy_evidence":"Braftovi (encorafenib) in combination with Vectibix (panitumumab) is included in guidelines for patients with advanced or metastatic appendiceal adenocarcinoma harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[36921494],"response_type":"no benefit","indication":"colorectal cancer","therapy_id":15623,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Fluorouracil + Leucovorin + Vemurafenib","efficacy_evidence":"In a Phase II trial (MODUL), patients with metastatic colorectal cancer harboring BRAF V600E did not demonstrate improved progression-free survival when treated with the combination of Zelboraf (vemurafenib), Erbitux (cetuximab), Adrucil (fluorouracil), and Wellcovorin (leucovorin) compared to the control treatment of Avastin (bevacizumab) with a fluoropyrimidine (HR=0.95 and P=0.872) (%%PUBMED:36921494%%; NCT02291289).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"pub_med_references":[25873592],"response_type":"sensitive","indication":"melanoma","therapy_id":1059,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"BI-847325","efficacy_evidence":"In a preclinical study, treatment with BI-847325 resulted in decreased expression of Mcl-1 and Mek, and inhibited growth of melanoma cell lines harboring BRAF V600E in culture, and inhibited tumor growth in xenograft models of BRAF V600E-positive melanoma, including models with BRAF-inhibitor resistance (%%PUBMED:25873592%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[15294323,25500121],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":3105,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"CCT196969","efficacy_evidence":"In a preclinical study, CCT196969 inhibited growth of BRAF-mutant colorectal cancer cell lines in culture (%%PUBMED:25500121%%), which have been reported to harbor BRAF V600E (%%PUBMED:15294323%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[26573800],"response_type":"conflicting","indication":"glioblastoma","therapy_id":849,"normalized_cancer":"Glioblastoma, IDH-Wildtype","evidence_type":"Actionable","therapy":"Mirdametinib","efficacy_evidence":"In a preclinical study, a glioblastoma cell line harboring BRAF V600E demonstrated a decreased response to treatment with Gomekli (mirdametinib), demonstrating increased viability of CD133 positive cells in culture (%%PUBMED:26573800%%).","cap_asco_evidence_level":"NA","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"NA"},{"pub_med_references":[38714355],"response_type":"conflicting","indication":"glioblastoma","therapy_id":849,"normalized_cancer":"Glioblastoma, IDH-Wildtype","evidence_type":"Actionable","therapy":"Mirdametinib","efficacy_evidence":"In a preclinical study, Gomekli (mirdametinib) inhibited growth of glioblastoma cell lines harboring BRAF V600E in culture (%%PUBMED:38714355%%).","cap_asco_evidence_level":"NA","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"NA"},{"pub_med_references":[25665005],"response_type":"sensitive","indication":"lung non-small cell carcinoma","therapy_id":3532,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Trametinib + TW-37","efficacy_evidence":"In a preclinical study, TW-37 enhanced the inhibitory effect of Mekinist (trametinib) on human non-small cell lung cancer cells harboring BRAF V600E in culture (%%PUBMED:25665005%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[30351999],"normalized_drug":"Vemurafenib","indication":"ganglioglioma","therapy_id":342,"normalized_cancer":"Ganglioglioma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase II trial (VE-BASKET), Zelboraf (vemurafenib) treatment resulted in a partial response in a patient with anaplastic ganglioglioma harboring BRAF V600E who stayed on treatment for 13.8 months (%%PUBMED:30351999%%; NCT01524978).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"skin melanoma","therapy_id":1066,"normalized_cancer":"Cutaneous Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Tafinlar (dabrafenib) and Mekinist (trametinib) combination therapy is included in guidelines for cutaneous melanoma patients harboring a BRAF V600 mutation, such as BRAF V600E, as neoadjuvant or adjuvant therapy for stage III disease and as systemic therapy for patients with unresectable or metastatic disease (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"predicted - sensitive","indication":"melanoma","therapy_id":13809,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"CFT1946","efficacy_evidence":"In a Phase I trial, CFT1946 treatment demonstrated safety and preliminary activity in patients with advanced solid tumors (n=25) including melanoma (40%), colorectal cancer (40%), non-small cell lung cancer (8%), and other non-CNS tumors harboring BRAF V600E (n=22), V600K (n=2), or V600R (n=1), with 1 unconfirmed partial response (uPR) and 7 stable diseases in efficacy evaluable patients (n=14) at data cutoff, and 1 additional uPR after data cutoff (Ann Oncol (2024) 35 (Suppl_2): S490-S491; NCT05668585).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase I","amp_tier":"II"},{"pub_med_references":[33568355],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":11479,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + RAF709 + Trametinib","efficacy_evidence":"In a preclinical study, combination treatment with RAF709, Tafinlar (dabrafenib), and Mekinist (trametinib) in colorectal cancer cell lines harboring BRAF V600E resulted in suppression of colony formation in culture (%%PUBMED:33568355%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[26916115],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":3711,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"BI 882370 + Cetuximab","efficacy_evidence":"In a preclinical study, colorectal cancer cells harboring BRAF V600E were sensitive to the combination of BI 882370 and Erbitux (cetuximab) in xenograft models, resulting in tumor growth inhibition and partial tumor regression (%%PUBMED:26916115%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[25500121],"response_type":"sensitive","indication":"melanoma","therapy_id":3105,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"CCT196969","efficacy_evidence":"In a preclinical study, CCT196969 inhibited growth of a human melanoma cell line harboring BRAF V600E in culture, and induced tumor regression in several BRAF V600E-mutant melanoma patient-derived xenograft models (%%PUBMED:25500121%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"pub_med_references":[31618628],"response_type":"sensitive","indication":"melanoma","therapy_id":3105,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"CCT196969","efficacy_evidence":"In a preclinical study, CCT196969 treatment inhibited viability of a melanoma cell line harboring BRAF V600E in culture (%%PUBMED:31618628%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"melanoma","therapy_id":15222,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"PHI-501","efficacy_evidence":"In a preclinical study, PHI-501 inhibited growth and migration and induced apoptosis in a melanoma cell line harboring BRAF V600E and induced dose-dependent tumor growth inhibition in a cell line xenograft model (Cancer Res (2023) 83 (7_Supplement): 1627).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[34969785],"normalized_drug":"Dabrafenib, Trametinib","indication":"lung combined large cell neuroendocrine carcinoma","therapy_id":1066,"normalized_cancer":"Large Cell Neuroendocrine Carcinoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, treatment with the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) resulted in a partial response after 10 weeks in a patient with combined large cell neuroendocrine carcinoma harboring BRAF V600E, who remained recurrence-free for at least a year (%%PUBMED:34969785%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[36759733],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":15049,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Dasatinib + Gefitinib + PLX4720","efficacy_evidence":"In a preclinical study, the combination of PLX4720, Iressa (gefitinib), and Sprycel (dasatinib) inhibited tumor growth in colorectal cancer cell line xenograft models harboring BRAF V600E to a greater degree than the combinations of PLX4720 and Iressa (gefitinib) or PLX4720 and Sprycel (dasatinib) (%%PUBMED:36759733%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[37403699],"response_type":"decreased response","indication":"melanoma","therapy_id":5891,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Toripalimab-tpzi","efficacy_evidence":"In a retrospective analysis, real-world treatment with either Keytruda (pembrolizumab) or Loqtorz (toripalimab-tpzi) resulted in a median disease-free survival of 17 months in melanoma patients harboring BRAF V600E compared to 32 months in patients with wild-type BRAF, NRAS, and KIT (p=0.022) (%%PUBMED:37403699%%).","cap_asco_evidence_level":"NA","molecular_profile":"BRAF V600E","approval_status":"Clinical Study","amp_tier":"NA"},{"pub_med_references":[36759733],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":15046,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Celecoxib + Dabrafenib + Trametinib","efficacy_evidence":"In a preclinical study, the addition of Celecoxib to the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) inhibited tumor growth and induced tumor regression in colorectal cancer patient-derived xenograft (PDX) models harboring BRAF V600E (%%PUBMED:36759733%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"pub_med_references":[29431699],"response_type":"predicted - sensitive","indication":"colorectal cancer","therapy_id":1992,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Panitumumab + Trametinib","efficacy_evidence":"In a Phase I trial, combination therapy consisting of Tafinlar (dabrafenib), Vectibix (panitumumab), and Mekinist (trametinib) resulted in an overall response rate of 21% (19/91, 1 complete response, 18 partial response), stable disease in 65% (59/91), and a median progression-free survival of 4.2 months in patients with BRAF V600E colorectal cancer (%%PUBMED:29431699%%; NCT01750918).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase I","amp_tier":"II"},{"pub_med_references":[37269335],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":15326,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Binimetinib + Encorafenib + PF-07284892","efficacy_evidence":"In a preclinical study, the combination of PF-07284892, Mektovi (binimetinib), and Braftovi (encorafenib) inhibited Erk phosphorylation in colorectal cancer cells harboring BRAF V600E in culture and induced tumor regression in a cell line xenograft model (%%PUBMED:37269335%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib","indication":"follicular thyroid carcinoma","therapy_id":3,"normalized_cancer":"Follicular Thyroid Cancer","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"Tafinlar (dabrafenib) is included in guidelines for patients with recurrent, advanced, or metastatic thyroid follicular carcinoma harboring BRAF V600E for whom clinical trials are not available or appropriate (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[33537843],"response_type":"predicted - sensitive","indication":"endometrial adenocarcinoma","therapy_id":1302,"normalized_cancer":"Endometrial Carcinoma","evidence_type":"Actionable","therapy":"Dabrafenib + Rabeprazole + Rifampin","efficacy_evidence":"In a Phase I trial, combination treatment with Tafinlar (dabrafenib), Rabeprazole, and Rifampin in a patient with metastatic endometrial adenocarcinoma harboring BRAF V600E, that recurred 11 years after original diagnosis and was refractory to treatment with chemotherapy, led to reduction of lung metastases and pelvic tissue mass at three months, but a slight increase in pelvic mass was observed at six months (%%PUBMED:33537843%%; NCT01954043).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","normalized_drug":"Vemurafenib","indication":"larynx cancer","therapy_id":342,"normalized_cancer":"Head and Neck Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase II trial (MyPathway), Zelboraf (vemurafenib) treatment resulted in complete response in a patient with larynx cancer harboring BRAF V600E (%%PUBMED:29320312%%; NCT02091141).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[38691346],"response_type":"predicted - sensitive","indication":"high grade glioma","therapy_id":13603,"normalized_cancer":"High-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"Binimetinib + PF-07799933","efficacy_evidence":"In a Phase I trial, the addition of Mektovi (binimetinib) to treatment with PF-07799933 resulted in a partial response in a patient with high grade glioma harboring BRAF V600E (%%PUBMED:38691346%%; NCT05355701).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[36198029],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":14531,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Axitinib + Vemurafenib","efficacy_evidence":"In a preclinical study, combination treatment with Zelboraf (vemurafenib) and Inlyta (axitinib) resulted in decreased cell viability in colorectal cancer cell lines harboring BRAF V600E in culture, and led to synergistic inhibition of tumor growth in cell line xenograft models (%%PUBMED:36198029%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[23942066],"normalized_drug":"Selumetinib","indication":"colorectal cancer","therapy_id":913,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Selumetinib","efficacy_evidence":"In a preclinical study, Koselugo (selumetinib) decreased tumor growth in a cell line xenograft model of colorectal cancer harboring BRAF V600E (%%PUBMED:23942066%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[30559419],"response_type":"sensitive","indication":"melanoma","therapy_id":3268,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"LY3009120","efficacy_evidence":"In a preclinical study, LY3009120 treatment inhibited Erk phosphorylation and reduced proliferation of a melanoma cells harboring either monomeric BRAF V600E or dimeric isoform (p61) of V600E in culture (%%PUBMED:30559419%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","indication":"melanoma","therapy_id":3268,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"LY3009120","efficacy_evidence":"In a preclinical study, LY3009120 inhibited growth, downstream MAPK signaling and soft agar growth in human melanoma cell lines harboring BRAF V600E in culture (%%PUBMED:26343583%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[39461261],"response_type":"predicted - sensitive","indication":"pancreatic ductal adenocarcinoma","therapy_id":4886,"normalized_cancer":"Pancreatic Adenocarcinoma","evidence_type":"Actionable","therapy":"Binimetinib + Cetuximab + Encorafenib","efficacy_evidence":"In a clinical case study, third-line treatment with the combination of Mektovi (binimetinib), Erbitux (cetuximab), and Braftovi (encorafenib) resulted in a partial response with a 74% decrease in primary tumor size in a patient with metastatic pancreatic ductal adenocarcinoma harboring BRAF V600E (%%PUBMED:39461261%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[38894534],"response_type":"sensitive","indication":"melanoma","therapy_id":17245,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"DSR6434 + unspecified PD-1 antibody + Vemurafenib","efficacy_evidence":"In a preclinical study, treatment with the combination of Zelboraf (vemurafenib), DSR6434, and an anti-PD-1 antibody induced tumor regression and resulted in prolonged progression-free survival compared to either of the doublet combination therapies in a syngeneic mouse model of melanoma harboring BRAF V600E (%%PUBMED:38894534%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"response_type":"sensitive","indication":"rectum cancer","therapy_id":9562,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Encorafenib + Panitumumab","efficacy_evidence":"Braftovi (encorafenib) in combination with Vectibix (panitumumab) is included in guidelines as primary or subsequent therapy for patients with rectal cancer harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","indication":"colon cancer","therapy_id":11094,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Encorafenib + Fluorouracil + Leucovorin + Oxaliplatin","efficacy_evidence":"Braftovi (encorafenib) in combination with Erbitux (cetuximab) and FOLFOX is included in guidelines as initial (category 2A) or subsequent-line (category 2B) therapy for patients with advanced or metastatic colon cancer harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[33229459],"response_type":"no benefit","indication":"skin melanoma","therapy_id":11307,"normalized_cancer":"Cutaneous Melanoma","evidence_type":"Actionable","therapy":"YM-254890","efficacy_evidence":"In a preclinical study, YM-254890 treatment did not inhibit cell viability of a cutaneous melanoma cell line harboring BRAF V600E in culture (%%PUBMED:33229459%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib","indication":"Erdheim-Chester disease","therapy_id":3,"normalized_cancer":"Erdheim-Chester Disease","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"Tafinlar (dabrafenib) is included in guidelines as first-line or subsequent-line therapy for patients with Erdheim-Chester disease harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"predicted - sensitive","pub_med_references":[34232949],"normalized_drug":"Vemurafenib","indication":"IDH-wildtype glioblastoma","therapy_id":342,"normalized_cancer":"Glioblastoma, IDH-Wildtype","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a clinical case study, Zelboraf (vemurafenib) treatment resulted in disease stability over 15 months in a patient with epithelioid glioblastoma harboring BRAF V600E, who previously progressed on conventional treatment options (%%PUBMED:34232949%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"esophagus squamous cell carcinoma","therapy_id":1066,"normalized_cancer":"Esophageal Squamous Cell Carcinoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Tafinlar (dabrafenib) and Mekinist (trametinib) combination therapy is included in guidelines as second-line or subsequent therapy for patients with locally advanced, recurrent, or metastatic esophageal squamous cell carcinoma harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[15294323,25500121],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":3106,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"CCT241161","efficacy_evidence":"In a preclinical study, CCT241161 inhibited growth of colorectal cancer cell lines harboring BRAF V600E in culture (%%PUBMED:25500121%%, %%PUBMED:15294323%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"response_type":"resistant","pub_med_references":[36307056],"normalized_drug":"Cetuximab","indication":"colorectal cancer","therapy_id":694,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab","efficacy_evidence":"Erbitux (cetuximab), as a monotherapy, is not indicated for use in metastatic colorectal cancer patients with BRAF V600E (%%PUBMED:36307056%%; ESMO.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"resistant","pub_med_references":[25673558],"normalized_drug":"Cetuximab","indication":"colorectal cancer","therapy_id":694,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab","efficacy_evidence":"In a meta-analysis, the addition of Erbitux (cetuximab) or Vectibix (panitumumab) to standard of care treatment with chemotherapy did not result in improved progression-free survival (HR=0.88; 95% CI, 0.67-1.14; p=0.33), overall survival (HR=0.91; 95% CI, 0.62-1.34; p=0.63), or objective response rate (relative risk=1.31; 95% CI, 0.83-2.08; p=0.25) in patients with advanced colorectal cancer harboring BRAF V600E (%%PUBMED:25673558%%).","cap_asco_evidence_level":"B","molecular_profile":"BRAF V600E","approval_status":"Clinical Study - Meta-analysis","amp_tier":"I"},{"response_type":"resistant","pub_med_references":[19001320],"normalized_drug":"Cetuximab","indication":"colorectal cancer","therapy_id":694,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab","efficacy_evidence":"In a retrospective analysis, metastatic colorectal cancer patients harboring BRAF V600E demonstrated shorter progression-free survival (p=0.0107) and overall survival (p<0.0001) compared to patients with wild-type BRAF following Vectibix (panitumumab) or Erbitux (cetuximab) therapy with or without chemotherapy, and in a preclinical study, colorectal cancer cell lines harboring BRAF V600E were resistant to Erbitux (cetuximab) in culture (%%PUBMED:19001320%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Clinical Study","amp_tier":"II"},{"pub_med_references":[39391046],"response_type":"predicted - sensitive","indication":"Cancer of Unknown Primary","therapy_id":8515,"normalized_cancer":"Cancer of Unknown Primary","evidence_type":"Actionable","therapy":"Binimetinib + Cetuximab","efficacy_evidence":"In a clinical case study, treatment with the combination of Mektovi (binimetinib) and Erbitux (cetuximab) resulted in a significant but brief response in all lesions in a patient with metastatic cancer of unknown primary harboring BRAF V600E (%%PUBMED:39391046%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[38795180],"response_type":"sensitive","indication":"thyroid cancer","therapy_id":17198,"normalized_cancer":"Thyroid Cancer","evidence_type":"Actionable","therapy":"PLX4720 + Sorafenib","efficacy_evidence":"In a preclinical study, treatment with the combination of PLX4720 and Nexavar (sorafenib) inhibited proliferation of thyroid cancer cell lines harboring BRAF V600E in culture and resulted in greater tumor growth inhibition than PLX4720 alone in a cell line xenograft model (%%PUBMED:38795180%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"no benefit","pub_med_references":[27488531],"normalized_drug":"Palbociclib","indication":"melanoma","therapy_id":850,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Palbociclib","efficacy_evidence":"In a preclinical study, treatment with Ibrance (palbociclib) in a melanoma cell line xenograft model harboring BRAF V600E resulted in no benefit, demonstrating low but continuous growth (%%PUBMED:27488531%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[27312529],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":4544,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + SCH772984","efficacy_evidence":"In a preclinical study, combination therapy consisting of Tafinlar (dabrafenib) and SCH772984 inhibited survival of colorectal cancer cell lines harboring BRAF V600E in culture (%%PUBMED:27312529%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[27222538],"response_type":"sensitive","indication":"thyroid cancer","therapy_id":4601,"normalized_cancer":"Thyroid Cancer","evidence_type":"Actionable","therapy":"Dasatinib + SCH772984","efficacy_evidence":"In a preclinical study, Sprycel (dasatinib) and SCH772984 synergistically inhibited proliferation and induced apoptosis in both parental thyroid cancer cell lines harboring BRAF V600E and those acquired Sprycel (dasatinib)-resistance in culture (%%PUBMED:27222538%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[26208524],"normalized_drug":"Lifirafenib","indication":"colorectal cancer","therapy_id":4025,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Lifirafenib","efficacy_evidence":"In a preclinical study, Lifirafenib (BGB-283) inhibited Braf phosphorylation and cell proliferation in colorectal cancer cell lines harboring BRAF V600E in culture, and resulted in partial tumor regression in both cell line and patient-derived xenograft models (%%PUBMED:26208524%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Pdx & cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"lung non-small cell carcinoma","therapy_id":10701,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Lifirafenib + Mirdametinib","efficacy_evidence":"In a Phase Ib trial, Lifirafenib (BGB-283) and Gomekli (mirdametinib) combination treatment demonstrated safety and activity in patients with advanced solid tumors harboring MAPK pathway alterations, resulting in an objective response rate of 27.8% (15/54, 1 complete and 14 partial responses), including an objective response in a patient with non-small cell lung cancer harboring BRAF V600E (Cancer Res (2023) 83 (8_Supplement): CT033).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase I","amp_tier":"II"},{"pub_med_references":[38728872],"response_type":"sensitive","indication":"anaplastic thyroid carcinoma","therapy_id":2149,"normalized_cancer":"Anaplastic Thyroid Cancer","evidence_type":"Actionable","therapy":"Ravoxertinib","efficacy_evidence":"In a preclinical study, Ravoxertinib (GDC-0994) inhibited viability and colony formation and induced cell cycle arrest in an anaplastic thyroid carcinoma cell line harboring BRAF V600E in culture, and inhibited tumor growth in a cell line xenograft model (%%PUBMED:38728872%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"sensitive","indication":"melanoma","therapy_id":5827,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"ASN003","efficacy_evidence":"In a preclinical study, a melanoma xenograft model harboring BRAF V600E demonstrated tumor regression when treated with ASN003 (Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr B100).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[26267534],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":849,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Mirdametinib","efficacy_evidence":"In a preclinical study, Gomekli (mirdametinib) inhibited growth of colorectal cancer cell lines harboring BRAF V600E in culture (%%PUBMED:26267534%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[39399174],"normalized_drug":"Dabrafenib","indication":"desmoplastic infantile ganglioglioma / desmoplastic infantile astrocytoma","therapy_id":3,"normalized_cancer":"Primary Neuroepithelial Tumor","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a clinical case study, Tafinlar (dabrafenib) treatment resulted in a partial response with resolution of ascites in a pediatric patient with suprasellar metastatic desmoplastic infantile astrocytoma harboring BRAF V600E (%%PUBMED:39399174%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[23792568],"response_type":"predicted - sensitive","indication":"colon cancer","therapy_id":6209,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Sorafenib","efficacy_evidence":"In a clinical case study, a patient with metastatic colon cancer harboring BRAF V600E demonstrated mixed radiographic response with slight progression in some locations and stable disease in other locations for 7 months following treatment with the combination of Nexavar (sorafenib) and Erbitux (cetuximab) (%%PUBMED:23792568%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[32923904],"normalized_drug":"Plx8394","indication":"glioblastoma","therapy_id":1041,"normalized_cancer":"Glioblastoma, IDH-Wildtype","evidence_type":"Actionable","therapy":"PLX8394","efficacy_evidence":"In a clinical case study, PLX8394 treatment resulted in a radiographic partial response and complete resolution of symptoms for 7 months in a patient with glioblastoma harboring BRAF V600E, CDKN2A/B loss and CHEK2 T367fs were also identified in the tumor (%%PUBMED:32923904%%; NCT02428712).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[33537843],"normalized_drug":"Dabrafenib, Trametinib","indication":"cholangiocarcinoma","therapy_id":1066,"normalized_cancer":"Cholangiocarcinoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, combination treatment with Tafinlar (dabrafenib) and Mekinist (trametinib) in a patient with metastatic cholangiocarcinoma harboring BRAF V600E who progressed on chemotherapy led to a sustained metabolic response for six months (%%PUBMED:33537843%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[33568355],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":11478,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + LXH 254 + Trametinib","efficacy_evidence":"In a preclinical study, combination treatment with LXH 254, Tafinlar (dabrafenib), and Mekinist (trametinib) in colorectal cancer cell lines harboring BRAF V600E resulted in suppression of colony formation in culture, and inhibition of tumor growth in a cell line xenograft model (%%PUBMED:33568355%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[26140595],"response_type":"predicted - sensitive","indication":"Advanced Solid Tumor","therapy_id":5443,"normalized_cancer":"All Solid Tumors","evidence_type":"Actionable","therapy":"PF-00477736 + PF3644022","efficacy_evidence":"In a preclinical study, Chk1 inhibitor PF-477736 and MK2 inhibitor PF3644022 synergistically inhibited growth of transformed cells over expressing BRAF V600E in culture, while single agent inhibition had no effect (%%PUBMED:26140595%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[22281684],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":6208,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + PLX4720","efficacy_evidence":"In a preclinical study, the combination of PLX4720 and Erbitux (cetuximab) inhibited tumor growth in colorectal cancer cell line xenograft models harboring BRAF V600E (%%PUBMED:22281684%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[21464044],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":1708,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Lapatinib + Panobinostat","efficacy_evidence":"In a preclinical study, Tykerb (lapatinib) and Faridak (panobinostat) worked synergistically to inhibit growth of BRAF V600E mutant colorectal cancer cells in culture (%%PUBMED:21464044%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"colon cancer","therapy_id":13709,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"ABM-1310 + Binimetinib","efficacy_evidence":"In a preclinical study, combination treatment with ABM-1310 and Mektovi (binimetinib) led to inhibition of tumor growth in a colon cancer cell line xenograft model harboring BRAF V600E (Cancer Res (2020) 80 (16_Supplement): 4038).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[27924459],"response_type":"sensitive","indication":"melanoma","therapy_id":5120,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Erlotinib + PLX4720","efficacy_evidence":"In a preclinical study, the combination of PLX4720 and Tarceva (erlotinib) resulted in antitumor efficacy in a melanoma cell line harboring BRAF V600E, demonstrating decreased cell survival and increased apoptotic activity in xenograft models and culture (%%PUBMED:27924459%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[32182156],"normalized_drug":"Lifirafenib","indication":"ovarian serous carcinoma","therapy_id":4025,"normalized_cancer":"Serous Ovarian Cancer","evidence_type":"Actionable","therapy":"Lifirafenib","efficacy_evidence":"In a Phase I trial, Lifirafenib (BGB-283) treatment demonstrated safety and resulted in partial response (PR) in 15.1% (8/53) of advanced solid tumor patients harboring a BRAF mutation, including 1 patient with BRAF V600E-mutant low-grade serous ovarian cancer (%%PUBMED:32182156%%; NCT02610361).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[37643378],"normalized_drug":"Dabrafenib, Trametinib","indication":"high grade glioma","therapy_id":1066,"normalized_cancer":"High-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a Phase II trial, Tafinlar (dabrafenib) and Mekinist (trametinib) combination treatment resulted in an overall response rate of 56.1% (23/41; 12 complete, 11 partial responses), a clinical benefit rate of 65.9% (27/41), median duration of response of 22.2 months, median progression-free survival of 9.0 months, and median overall survival of 32.8 months in pediatric patients with relapsed or refractory high-grade glioma harboring BRAF V600E (%%PUBMED:37643378%%; NCT02684058).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"high grade glioma","therapy_id":1066,"normalized_cancer":"High-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Tafinlar (dabrafenib) in combination with Mekinist (trametinib) is included in guidelines as adjuvant therapy for pediatric patients with diffuse high-grade gliomas harboring BRAF V600E, or as a preferred regimen for patients with recurrent or progressive disease (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[34838156],"normalized_drug":"Dabrafenib, Trametinib","indication":"high grade glioma","therapy_id":1066,"normalized_cancer":"High-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a Phase II trial (ROAR), Tafinlar (dabrafenib) and Mekinist (trametinib) combination treatment resulted in an objective response rate of 33% (15/45, 3 complete responses, 12 partial responses) in patients with high-grade glioma harboring BRAF V600E, with a median duration of response of 36.9 months, a median progression-free survival of 3.8 months, and an overall survival of 17.6 months (%%PUBMED:34838156%%; NCT02034110).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[39399174],"normalized_drug":"Dabrafenib, Trametinib","indication":"high grade glioma","therapy_id":1066,"normalized_cancer":"High-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, treatment with the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) resulted in a partial response in a pediatric patient with posterior fossa high grade glioma harboring BRAF V600E and deletion of CDKN2A (%%PUBMED:39399174%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[38096472],"normalized_drug":"Cobimetinib, Vemurafenib","indication":"colon neuroendocrine neoplasm","therapy_id":1657,"normalized_cancer":"Gastrointestinal Neuroendocrine Tumors","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"In a Phase II trial (TAPUR), Zelboraf (vemurafenib) and Cotellic (cobimetinib) combination therapy resulted in a partial response in a patient with neuroendocrine carcinoma of the colon harboring BRAF V600E (%%PUBMED:38096472%%; NCT02693535).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[29573941],"normalized_drug":"Binimetinib, Encorafenib","indication":"melanoma","therapy_id":1100,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Binimetinib + Encorafenib","efficacy_evidence":"In a Phase III (COLUMBUS) trial that supported FDA approval, Braftovi (encorafenib) in combination with Mektovi (binimetinib) demonstrated improved tolerability profile and efficacy, resulted in a progression-free survival of 14.9 months in patients with advanced melanoma harboring BRAF V600E/K mutations, comparing to 7.3 months in the Zelboraf (vemurafenib) group (HR=0.54, p<0.0001) (%%PUBMED:29573941%%; NCT01909453), and both BRAF V600E and V600K are on the companion diagnostic.","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"FDA approved - On Companion Diagnostic","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[30219628],"normalized_drug":"Binimetinib, Encorafenib","indication":"melanoma","therapy_id":1100,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Binimetinib + Encorafenib","efficacy_evidence":"In a Phase III (COLUMBUS) trial that supported FDA approval, Braftovi (encorafenib) in combination with Mektovi (binimetinib) resulted in a median overall survival (OS) of 33.6 months, a 1-year OS rate of 77.5%, and a 2-year OS rate of 57.7% in patients with advanced melanoma harboring BRAF V600E/K mutations compared to a median OS of 16.9 months and 1- and 2-year OS rates of 63.1% and 43.2%, respectively, in the Zelboraf (vemurafenib) treated group (%%PUBMED:30219628%%; NCT01909453).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"FDA approved - On Companion Diagnostic","amp_tier":"I"},{"pub_med_references":[29431699],"response_type":"no benefit","indication":"colorectal cancer","therapy_id":1991,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Panitumumab + Trametinib","efficacy_evidence":"In a Phase I trial, combination therapy consisting of Vectibix (panitumumab) and Mekinist (trametinib) resulted in an overall response rate of 0% (0/31), stable disease in 55% (17/31), and a median progression-free survival of 2.6 months in patients with BRAF V600E colorectal cancer (%%PUBMED:29431699%%; NCT01750918).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase I","amp_tier":"II"},{"pub_med_references":[26461489],"response_type":"sensitive","indication":"melanoma","therapy_id":1061,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"PLX4720 + Selumetinib","efficacy_evidence":"In a preclinical study, PLX4720 and Koselugo (selumetinib) worked synergistically to inhibit cell growth in PLX4720-resistant melanoma cell lines harboring BRAF V600E in culture (%%PUBMED:26461489%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[31151904],"normalized_drug":"Selumetinib","indication":"childhood pilocytic astrocytoma","therapy_id":913,"normalized_cancer":"Pilocytic Astrocytoma","evidence_type":"Actionable","therapy":"Selumetinib","efficacy_evidence":"In a Phase I trial, Koselugo (selumetinib) treatment resulted in a sustained partial response (PR) in 36% (9/25) and stable disease in 36% (9/25) of pediatric patients with pilocytic astrocytoma harboring KIAA1549-BRAF (n=18) or BRAF V600E (n=7), with a 2-year progression-free survival of 70%, and 29% (2/7) of the patients harboring BRAF V600E achieved PR (%%PUBMED:31151904%%; NCT01089101).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase I","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[22663011],"normalized_drug":"Trametinib","indication":"melanoma","therapy_id":2,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Trametinib","efficacy_evidence":"In a Phase III trial (METRIC) that supported FDA approval, Mekinist (trametinib) treatment, as compared to Deticine (dacarbazine) or Taxol (paclitaxel) treatment, resulted in improved progression-free survival of 4.8 months versus 1.5 months and an overall six month survival rate of 81% versus 67% in patients with BRAF V600E/K-positive metastatic melanoma (%%PUBMED:22663011%%; NCT01245062).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"FDA approved - On Companion Diagnostic","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[36608320],"normalized_drug":"Binimetinib, Encorafenib","indication":"multiple myeloma","therapy_id":1100,"normalized_cancer":"Plasma Cell Myeloma","evidence_type":"Actionable","therapy":"Binimetinib + Encorafenib","efficacy_evidence":"In a Phase II trial (BIRMA), Mektovi (binimetinib) plus Braftovi (encorafenib) treatment demonstrated safety and efficacy in relapsed/refractory multiple myeloma patients with BRAF V600E, with an overall response rate of 83% (10/12, 1 complete response (CR), 2 near-CR, 6 very good partial responses (PR), and 1 PR), a median duration of response of 4.8 mo, a median progression-free survival of 5.6 mo, and a median overall survival not reached but 66% at 12 mo and 55% at 24 mo (%%PUBMED:36608320%%; NCT02834364).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"pub_med_references":[38728872],"response_type":"sensitive","indication":"papillary thyroid carcinoma","therapy_id":2149,"normalized_cancer":"Papillary Thyroid Cancer","evidence_type":"Actionable","therapy":"Ravoxertinib","efficacy_evidence":"In a preclinical study, Ravoxertinib (GDC-0994) inhibited viability and colony formation in papillary thyroid carcinoma cell lines harboring BRAF V600E in culture (%%PUBMED:38728872%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[26637369],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":4083,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"DT01 + Fluorouracil + Oxaliplatin","efficacy_evidence":"In a preclinical study, DT01 increased sensitivity of human colorectal cancer (CRC) cells harboring BRAF V600E to Eloxatin (oxaliplatin) and Adrucil (5-fluorouracil), and the combination resulted in decreased liver tumor growth in CRC cell line xenograft metastasis models (%%PUBMED:26637369%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[18519791],"response_type":"sensitive","indication":"melanoma","therapy_id":10820,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"C6-ceramide nanoliposome + Sorafenib","efficacy_evidence":"In a preclinical study, Nexavar (sorafenib) treatment in combination with C6-ceramide nanoliposome inhibited Mek and Akt phosphorylation, led to enhanced apoptosis and inhibition of proliferation, and synergistically reduced viability of melanoma cells harboring BRAF V600E in culture, and enhanced inhibition of tumor growth in a cell line xenograft model (%%PUBMED:18519791%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[36759733],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":15048,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Celecoxib + Encorafenib + Panitumumab","efficacy_evidence":"In a preclinical study, the addition of Celecoxib to the combination of Braftovi (encorafenib) and Vectibix (panitumumab) inhibited tumor growth and induced tumor regression in colorectal cancer patient-derived xenograft (PDX) models harboring BRAF V600E to a greater degree than the combination of Braftovi (encorafenib) and Vectibix (panitumumab) (%%PUBMED:36759733%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[38096472],"normalized_drug":"Cobimetinib, Vemurafenib","indication":"ovarian cancer","therapy_id":1657,"normalized_cancer":"Ovarian Cancer","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"In a Phase II trial (TAPUR), Zelboraf (vemurafenib) and Cotellic (cobimetinib) combination therapy resulted in one complete response lasting 5 weeks, 2 partial responses, and 1 with stable disease lasting more than 16 weeks out of 6 patients with advanced ovarian cancer harboring BRAF V600E (%%PUBMED:38096472%%; NCT02693535).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[27222538],"response_type":"sensitive","indication":"thyroid cancer","therapy_id":4599,"normalized_cancer":"Thyroid Cancer","evidence_type":"Actionable","therapy":"Dasatinib + Trametinib","efficacy_evidence":"In a preclinical study, Sprycel (dasatinib) and Mekinist (trametinib) synergistically inhibited proliferation and induced apoptosis in both parental thyroid cancer cell lines harboring BRAF V600E and those acquired Sprycel (dasatinib)-resistance in culture (%%PUBMED:27222538%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Vemurafenib","indication":"follicular thyroid carcinoma","therapy_id":342,"normalized_cancer":"Follicular Thyroid Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"Zelboraf (vemurafenib) is included in guidelines for patients with recurrent, advanced, or metastatic thyroid follicular carcinoma harboring BRAF V600E for whom clinical trials are not available or appropriate (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"decreased response","pub_med_references":[30630828],"normalized_drug":"Nivolumab","indication":"melanoma","therapy_id":1312,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Nivolumab","efficacy_evidence":"In a retrospective analysis, patients with melanoma harboring BRAF V600E (n=84) had decreased response rates (29% vs. 53%, p=0.059), progression-free survival (2.7 vs. 19 months, p=0.049), and overall survival (11.7 vs. 20.4 months, p=0.081) relative to patients with BRAF V600K (n=19) when treated with Keytruda (pembrolizumab) (n=62 and 17 for BRAF V600E and V600K, respectively) or Opdivo (nivolumab) (n=22 and 2 for BRAF V600E and V600K, respectively) (%%PUBMED:30630828%%).","cap_asco_evidence_level":"NA","molecular_profile":"BRAF V600E","approval_status":"Clinical Study - Cohort","amp_tier":"NA"},{"response_type":"sensitive","pub_med_references":[19018267],"normalized_drug":"Ci-1040","indication":"ovarian cancer","therapy_id":699,"normalized_cancer":"Ovarian Cancer","evidence_type":"Actionable","therapy":"CI-1040","efficacy_evidence":"In a preclinical study, CI-1040 inhibited growth of a human ovarian cancer cell line harboring BRAF V600E in culture, and inhibited tumor growth in xenograft models (%%PUBMED:19018267%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[32238401],"normalized_drug":"Dabrafenib, Trametinib","indication":"epithelial predominant Wilms' tumor","therapy_id":1066,"normalized_cancer":"Wilms' Tumor","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, Tafinlar (dabrafenib) and Mekinist (trametinib) combination therapy resulted in a complete radiographic response 4 months after treatment initiation that was maintained for at least 12 months in a pediatric patient with metastatic epithelial-predominant Wilms tumor harboring BRAF V600E (%%PUBMED:32238401%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Cobimetinib, Vemurafenib","indication":"pilocytic astrocytoma","therapy_id":1657,"normalized_cancer":"Pilocytic Astrocytoma","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"Zelboraf (vemurafenib) and Cotellic (cobimetinib) combination therapy is included in guidelines as an adjuvant treatment for patients with pilocytic astrocytoma harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"predicted - sensitive","pub_med_references":[29880583],"normalized_drug":"Dabrafenib","indication":"ganglioglioma","therapy_id":3,"normalized_cancer":"Ganglioglioma","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a clinical case study, Tafinlar (dabrafenib) treatment resulted in partial response 8 weeks after therapy initiation in a pediatric patient with anaplastic ganglioglioma harboring BRAF V600E, but disease progression occurred at 40 weeks due to acquired resistance (%%PUBMED:29880583%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[31502039],"normalized_drug":"Dabrafenib","indication":"ganglioglioma","therapy_id":3,"normalized_cancer":"Ganglioglioma","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a clinical study, Tafinlar (dabrafenib) treatment resulted in symptomatic improvement and clinical efficacy in three pediatric patients with brainstem ganglioglioma harboring BRAF V600E, with decreased tumor volume and treatment continuing for at least 5.5 years in one patient, a significant partial response in another patient, and a partial response in a third patient with tumor regression and ongoing response for at least 2 years (%%PUBMED:31502039%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[39399174],"normalized_drug":"Dabrafenib","indication":"ganglioglioma","therapy_id":3,"normalized_cancer":"Ganglioglioma","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a clinical case study, Tafinlar (dabrafenib) treatment resulted in a partial response in two pediatric patients with ganglioglioma (1 suprasellar ganglioglioma, 1 cervicomedullary ganglioglioma) harboring BRAF V600E (%%PUBMED:39399174%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[34433654],"response_type":"no benefit","indication":"high grade glioma","therapy_id":1728,"normalized_cancer":"High-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"ZM336372","efficacy_evidence":"In a preclinical study, ZM336372 treatment did not lead to inhibition of cell growth in a patient-derived glioma cell line harboring BRAF V600E in culture (%%PUBMED:34433654%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Patient cell culture","amp_tier":"II"},{"response_type":"no benefit","indication":"melanoma","therapy_id":10333,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Cobimetinib + Pembrolizumab + Vemurafenib","efficacy_evidence":"In a Phase I trial, combination of Cotellic (cobimetinib), Zelboraf (vemurafenib), and Keytruda (pembrolizumab) resulted in unreached median progression-free survival and overall survival in patients with advanced melanoma harboring BRAF V600E or V600K mutations, however, the trial was closed due to high incidence of dose-limiting toxicity and decreased health utility at 1 year (J Clin Oncol 39, no. 15_suppl, abstract e21506; NCT02818023).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase I","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[32029534],"normalized_drug":"Vemurafenib","indication":"Advanced Solid Tumor","therapy_id":342,"normalized_cancer":"All Solid Tumors","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase II trial (VE-BASKET), Zelboraf (vemurafenib) treatment resulted in an objective response rate of 33% (56/172) in patients with advanced solid tumors harboring BRAF V600E, including 5 patients with a complete response and 51 patients with a partial response, and led a duration of response of 13.1 months, a progression-free survival of 5.8 months, and an overall survival of 17.6 months (%%PUBMED:32029534%%; NCT01524978).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Vemurafenib","indication":"Advanced Solid Tumor","therapy_id":342,"normalized_cancer":"All Solid Tumors","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase II trial (MyPathway), Zelboraf (vemurafenib) treatment resulted in an objective response of 46% (12/26, 2 complete response, 10 partial response) in patients with advanced solid tumors harboring BRAF V600E, but only 4% (1/23, 1 partial response) in patients harboring non-V600 BRAF mutations (%%PUBMED:29320312%%; NCT02091141).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"pub_med_references":[31618628],"response_type":"sensitive","indication":"melanoma","therapy_id":1034,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Tovorafenib","efficacy_evidence":"In a preclinical study, Ojemda (tovorafenib) treatment inhibited viability of a melanoma cell line harboring BRAF V600E in culture (%%PUBMED:31618628%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[35382161],"normalized_drug":"Cobimetinib, Vemurafenib","indication":"pancreatic ductal adenocarcinoma","therapy_id":1657,"normalized_cancer":"Pancreatic Adenocarcinoma","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"In a clinical case study, combination treatment with Cotellic (cobimetinib) and Zelboraf (vemurafenib) led to a partial response after 1 month of treatment in a microsatellite stable pancreatic ductal adenocarcinoma patient with BRAF V600E and amplification of FGFR1 and NOTCH2, with significant decrease in hepatic metastatic lesions and undetectable lung lesions at 6 months, and a progression-free survival of at least 6 months (%%PUBMED:35382161%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"colorectal cancer","therapy_id":18577,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"RG6344","efficacy_evidence":"In a Phase I trial, RG6344 treatment was well tolerated and demonstrated preliminary activity in patients with advanced solid tumors harboring BRAF V600E (n=64), including melanoma (n=11) and colorectal cancer (n=51), with an objective response rate of 25% (Cancer Res (2025) 85 (8_Supplement_2): CT017).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase I","amp_tier":"II"},{"pub_med_references":[35145907],"response_type":"predicted - sensitive","indication":"pancreatic ductal adenocarcinoma","therapy_id":4234,"normalized_cancer":"Pancreatic Adenocarcinoma","evidence_type":"Actionable","therapy":"Trametinib + Vemurafenib","efficacy_evidence":"In a clinical case study, Zelboraf (vemurafenib) and Mekinist (trametinib) combination treatment resulted in decreased tumor markers in a patient with pancreatic ductal adenocarcinoma harboring BRAF V600E, as well as a germline ATM mutation, and the patient received 13 months of combination therapy and was followed for 24 months (%%PUBMED:35145907%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[28611205],"response_type":"predicted - sensitive","indication":"colorectal cancer","therapy_id":6337,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"LSN3074753","efficacy_evidence":"In a preclinical study, LSN3074753 demonstrated modest efficacy in patient-derived xenograft models of colorectal cancer harboring BRAF V600E, resulted in tumor growth inhibition or regression, but relapse upon discontinuation of treatment (%%PUBMED:28611205%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[32758030],"normalized_drug":"Trametinib","indication":"peritoneal serous papillary adenocarcinoma","therapy_id":2,"normalized_cancer":"Peritoneal Serous Carcinoma","evidence_type":"Actionable","therapy":"Trametinib","efficacy_evidence":"In a Phase II trial (NCI-MATCH), Mekinist (trametinib) treatment resulted in an objective response rate of 37.9% (11/29) in patients with advanced solid tumors harboring BRAF V600E, 1 patient with mucinous-papillary serous adenocarcinoma of the peritoneum achieved a partial response (%%PUBMED:32758030%%; NCT02465060).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[26466569],"response_type":"sensitive","indication":"melanoma","therapy_id":4606,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"PLX7904","efficacy_evidence":"In a preclinical study, PLX7904 inhibited survival of melanoma cell lines harboring monomeric BRAF V600E as well as cells harboring the Zelboraf (vemurafenib)-resistant dimeric BRAF V600E in culture (%%PUBMED:26466569%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Cobimetinib, Vemurafenib","indication":"ganglioglioma","therapy_id":1657,"normalized_cancer":"Ganglioglioma","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"Zelboraf (vemurafenib) and Cotellic (cobimetinib) combination therapy is included in guidelines as an adjuvant treatment for patients with ganglioglioma harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"predicted - sensitive","indication":"melanoma","therapy_id":11379,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"PF-07284890","efficacy_evidence":"In a preclinical study, PF-07284890 treatment led to inhibition of tumor growth, tumor regression, and survival benefit in an intracranial model, and tumor growth inhibition in a subcutaneous cell line xenograft model of melanoma harboring BRAF V600E (Cancer Res 2021;81(13_Suppl):Abstract nr 1473).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[26918217],"normalized_drug":"Vemurafenib","indication":"renal cell carcinoma","therapy_id":342,"normalized_cancer":"Renal Cell Carcinoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a clinical case study, a patient with metastatic renal cell carcinoma harboring BRAF V600E demonstrated a partial response following treatment with Zelboraf (vemurafenib) (%%PUBMED:26918217%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"gastrointestinal stromal tumor","therapy_id":1066,"normalized_cancer":"Gastrointestinal Stromal Tumor","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Tafinlar (dabrafenib) in combination with Mekinist (trametinib) is included in guidelines as neoadjuvant therapy for patients with resectable disease and as first-line systemic therapy for patients with unresectable or metastatic gastrointestinal stromal tumor (GIST) harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[37040395],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":11093,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Encorafenib + Fluorouracil + Irinotecan + Leucovorin","efficacy_evidence":"In a preclinical study, treatment with the combination of Erbitux (cetuximab), Braftovi (encorafenib), and FOLFIRI resulted in increased tumor growth inhibition and tumor regression compared to Erbitux (cetuximab) plus Braftovi (encorafenib) or FOLFIRI alone in patient-derived xenograft (PDX) models of colorectal cancer harboring BRAF V600E and increased survival and tumor growth inhibition in cell line xenograft models (%%PUBMED:37040395%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"pub_med_references":[38691346],"response_type":"predicted - sensitive","indication":"melanoma","therapy_id":13603,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Binimetinib + PF-07799933","efficacy_evidence":"In a Phase I trial, treatment with the combination of PF-07799933 and Mektovi (binimetinib) resulted in a partial response in 2 patients with melanoma harboring BRAF V600E and stable disease in 1 patient (%%PUBMED:38691346%%; NCT05355701).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[31158244],"normalized_drug":"Vemurafenib","indication":"pancreatic endocrine carcinoma","therapy_id":342,"normalized_cancer":"Pancreatic Neuroendocrine Carcinoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a clinical case study, a patient with pancreatic endocrine carcinoma found to harbor BRAF V600E demonstrated stable disease and some tumor shrinkage when treated with Zelboraf (vemurafenib) (%%PUBMED:31158244%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[32234759],"response_type":"sensitive","indication":"melanoma","therapy_id":12556,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"KRT-232 + Navitoclax","efficacy_evidence":"In a preclinical study, the combination of KRT-232 (AMG 232) and Navitoclax (ABT-263) resulted in a greater response than either drug alone in patient-derived xenograft (PDX) models of melanoma harboring BRAF V600E, leading to tumor regression (%%PUBMED:32234759%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[38885476],"normalized_drug":"Binimetinib, Encorafenib","indication":"malignant fibrous histiocytoma","therapy_id":1100,"normalized_cancer":"Undifferentiated Pleomorphic Sarcoma/Malignant Fibrous Histiocytoma/High-Grade Spindle Cell Sarcoma","evidence_type":"Actionable","therapy":"Binimetinib + Encorafenib","efficacy_evidence":"In a clinical case study, treatment with the combination of Mektovi (binimetinib) and Braftovi (encorafenib) resulted in a clinical response after two months in a patient with angiomatoid fibrous histiocytoma harboring BRAF V600E, along with EWSR1-CREB1 (e7:e7), and in a preclinical study, combination treatment with Mektovi (binimetinib) and Braftovi (encorafenib) inhibited viability of cells in culture (%%PUBMED:38885476%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[29701552],"normalized_drug":"Dabrafenib","indication":"papillary craniopharyngioma","therapy_id":3,"normalized_cancer":"Craniopharyngioma, Papillary Type","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a clinical case study, Tafinlar (dabrafenib) treatment resulted in decreased size of the cystic and solid enhancing components of the tumor in a patient with papillary craniopharyngioma harboring BRAF V600E, with stable disease continuing 1 year after discontinuation of treatment (%%PUBMED:29701552%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[31666933],"normalized_drug":"Dabrafenib","indication":"papillary craniopharyngioma","therapy_id":3,"normalized_cancer":"Craniopharyngioma, Papillary Type","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a clinical case study, Tafinlar (dabrafenib) treatment resulted in a complete response of the solid internal nodular enhancement and symptom improvement in a patient with papillary craniopharyngioma harboring BRAF V600E (%%PUBMED:31666933%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[26603897],"response_type":"sensitive","indication":"melanoma","therapy_id":3309,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"SBI-755199","efficacy_evidence":"In a preclinical study, SBI-755199 induced cell death in human melanoma cell lines harboring BRAF V600E in culture (%%PUBMED:26603897%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"response_type":"predicted - 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JSI-1187","efficacy_evidence":"In a preclinical study, combination treatment with Tafinlar (dabrafenib) and JSI-1187 led to synergistic inhibition of tumor growth in a colorectal cancer cell line xenograft model harboring BRAF V600E (Cancer Res 2020;80(16 Suppl):Abstract nr 4188).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[34330842],"response_type":"sensitive","indication":"melanoma","therapy_id":12570,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"ASTX029 + Vemurafenib","efficacy_evidence":"In a preclinical study, combination treatment with ASTX029 and Zelboraf (vemurafenib) resulted in decreased viability of melanoma cells harboring BRAF V600E compared to either agent alone in culture (%%PUBMED:34330842%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[27488531],"response_type":"sensitive","indication":"melanoma","therapy_id":1823,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Mirdametinib + Palbociclib","efficacy_evidence":"In a preclinical study, the combination treatment of Gomekli (mirdametinib) and Ibrance (palbociclib) resulted in significant tumor regression in melanoma cell line xenograft models harboring BRAF V600E and demonstrated a 56% (5/9) complete response rate (%%PUBMED:27488531%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[33229459],"response_type":"no benefit","indication":"skin melanoma","therapy_id":11309,"normalized_cancer":"Cutaneous Melanoma","evidence_type":"Actionable","therapy":"Trametinib + YM-254890","efficacy_evidence":"In a preclinical study, combination treatment with YM-254890 and Mekinist (trametinib) did not result in synergistic inhibition of cell viability of a cutaneous melanoma cell line harboring BRAF V600E in culture (%%PUBMED:33229459%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Cobimetinib, Vemurafenib","indication":"skin melanoma","therapy_id":1657,"normalized_cancer":"Cutaneous Melanoma","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"Zelboraf (vemurafenib) and Cotellic (cobimetinib) combination therapy is included in cutaneous melanoma guidelines for patients with metastatic or unresectable disease harboring a BRAF V600 activating mutation (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"predicted - sensitive","indication":"melanoma","therapy_id":13736,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"IMM-1-104","efficacy_evidence":"In a preclinical study, IMM-1-104 treatment led to tumor growth inhibition in a cell line xenograft model of melanoma harboring BRAF V600E (Mol Cancer Ther 2021;20(12 Suppl):Abstract nr P252).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[39121480],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":17844,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Encorafenib + Tazemetostat","efficacy_evidence":"In a preclinical study, the addition of Tazverik (tazemetostat) sensitized a colorectal cancer cell line harboring BRAF V600E to Braftovi (encorafenib) treatment in culture, resulting in decreased cell proliferation (%%PUBMED:39121480%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Cobimetinib, Vemurafenib","indication":"pleomorphic xanthoastrocytoma","therapy_id":1657,"normalized_cancer":"Pleomorphic Xanthoastrocytoma","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"Zelboraf (vemurafenib) and Cotellic (cobimetinib) combination therapy is included in guidelines as an adjuvant treatment for patients with pleomorphic xanthoastrocytoma harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[22180495],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":10745,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Capecitabine + Vemurafenib","efficacy_evidence":"In a preclinical study, Zelboraf (vemurafenib) treatment in combination with Xeloda (capecitabine) enhanced tumor growth inhibition and increased survival in a cell line xenograft model of colorectal cancer harboring BRAF V600E (%%PUBMED:22180495%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[37164118],"response_type":"sensitive","indication":"melanoma","therapy_id":15389,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"IHMT-RAF-128","efficacy_evidence":"In a preclinical study, IHMT-RAF-128 inhibited proliferation and induced cell cycle arrest and apoptosis in melanoma cell lines harboring BRAF V600E in culture and inhibited tumor growth in a cell line xenograft model (%%PUBMED:37164118%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[21325073,24042735],"normalized_drug":"Gedatolisib","indication":"colon cancer","therapy_id":1040,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Gedatolisib","efficacy_evidence":"In a preclinical study, Gedatolisib (PKI-587) inhibited Braf V600E in vitro and inhibited growth of human colon cancer cells harboring BRAF V600E in culture (%%PUBMED:21325073%%, %%PUBMED:24042735%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[33537843],"normalized_drug":"Dabrafenib, Trametinib","indication":"pancreatic acinar cell adenocarcinoma","therapy_id":1066,"normalized_cancer":"Acinar Cell Carcinoma of the Pancreas","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, combination treatment with Tafinlar (dabrafenib) and Mekinist (trametinib) in a patient with pancreatic acinar cell carcinoma harboring BRAF V600E who had previously progressed on chemotherapy led to a response at 8 weeks, and ongoing clinical and radiological response was still observed at 32 months of treatment (%%PUBMED:33537843%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[32843432],"normalized_drug":"Dabrafenib, Trametinib","indication":"pancreatic acinar cell adenocarcinoma","therapy_id":1066,"normalized_cancer":"Acinar Cell Carcinoma of the Pancreas","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) resulted in near complete remission allowing for debulking surgery and disease control for 12 months in a patient with metastatic pancreatic acinar cell carcinoma harboring BRAF V600E, along with germline PALB2 R414* (%%PUBMED:32843432%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"ganglioglioma","therapy_id":1066,"normalized_cancer":"Ganglioglioma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Combination of Mekinist (trametinib) and Tafinlar (dabrafenib) is included in guidelines as an adjuvant treatment for patients with ganglioglioma harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[38446982],"normalized_drug":"Binimetinib, Encorafenib","indication":"high grade glioma","therapy_id":1100,"normalized_cancer":"High-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"Binimetinib + Encorafenib","efficacy_evidence":"In a Phase II trial, treatment with the combination of Mektovi (binimetinib) and Braftovi (encorafenib) demonstrated safety and activity in patients with high grade glioma harboring BRAF V600E, resulting in a radiographic response rate of 60% (3/5, 1 complete and 2 partial responses), with stable disease in 1 patient, a median duration of response of 10 months, a median progression-free survival of 9.4 months, and a median overall survival of 14.6 months (%%PUBMED:38446982%%; NCT03973918).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"not predictive","pub_med_references":[29723688],"normalized_drug":"Nivolumab","indication":"lung non-small cell carcinoma","therapy_id":1312,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Nivolumab","efficacy_evidence":"In a retrospective analysis, non-small cell lung cancer patients harboring BRAF V600E did not demonstrate a significantly different response to treatment with either Keytruda (pembrolizumab), Opdivo (nivolumab), or Tecentriq (atezolizumab), compared to patients with BRAF non-V600E mutations, demonstrating an objective response rate of 25% (3/12) vs 33% (3/9) (p=1.0) and median progression-free survival of 3.7 months vs 4.1 months (p=0.37) (%%PUBMED:29723688%%).","cap_asco_evidence_level":"NA","molecular_profile":"BRAF V600E","approval_status":"Clinical Study - Cohort","amp_tier":"NA"},{"pub_med_references":[22319199],"response_type":"sensitive","indication":"colon carcinoma","therapy_id":1002,"normalized_cancer":"Bowel Cancer","evidence_type":"Actionable","therapy":"RXDX-105","efficacy_evidence":"In preclinical studies, CEP-32496 (RXDX-105) reduced tumor volume and promoted tumor regression in xenograft models of a BRAF V600E mutant human colon carcinoma cell line (%%PUBMED:22319199%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[36157689],"normalized_drug":"Dabrafenib, Trametinib","indication":"spermatic cord cancer","therapy_id":1066,"normalized_cancer":"Soft Tissue Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, treatment with the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) resulted in a regression of the lung metastasis and progression-free survival of 6.5 months in a patient with undifferentiated sarcoma of the spermatic cord harboring BRAF V600E (%%PUBMED:36157689%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"small intestine adenocarcinoma","therapy_id":1066,"normalized_cancer":"Small Intestinal Carcinoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Tafinlar (dabrafenib) in combination with Mekinist (trametinib) is included in guidelines for patients with advanced or metastatic small bowel adenocarcinoma harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[37733309],"normalized_drug":"Dabrafenib, Trametinib","indication":"low grade glioma","therapy_id":1066,"normalized_cancer":"Low-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a Phase II trial that supported FDA approval, Mekinist (trametinib) plus Tafinlar (dabrafenib) significantly improved overall response rate (47% vs 11%, risk ratio 4.31, p<0.001), clinical benefit rate (86% vs 46%), median progression-free survival (PFS, 20.1 vs 7.4 months, p<0.001, HR 0.31), and 12-month PFS rate (67% vs 26%) compared to standard chemotherapy in pediatric patients of 1 year and older with low-grade glioma harboring BRAF V600E (%%PUBMED:37733309%%; NCT02684058).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"FDA approved","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[34838156],"normalized_drug":"Dabrafenib, Trametinib","indication":"low grade glioma","therapy_id":1066,"normalized_cancer":"Low-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a Phase II trial (ROAR), Tafinlar (dabrafenib) and Mekinist (trametinib) combination treatment resulted in an objective response rate of 69% (9/13, 1 complete response, 6 partial responses, 2 minor responses) in patients with low-grade glioma harboring BRAF V600E, with median duration of response, median progression-free survival, and overall survival time unreached (%%PUBMED:34838156%%; NCT02034110).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"low grade glioma","therapy_id":1066,"normalized_cancer":"Low-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Combination of Mekinist (trametinib) and Tafinlar (dabrafenib) is included in guidelines for patients with recurrent or progressive low grade glioma harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"low grade glioma","therapy_id":1066,"normalized_cancer":"Low-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a Phase I/II trial (Study X2101), Tafinlar (dabrafenib) and Mekinist (trametinib) combination treatment demonstrated manageable toxicity and resulted in an objective response rate of 25% (9/36, 1 complete response, 8 partial responses) and stable disease in 67% (24/36) of pediatric patients with pretreated low-grade glioma harboring BRAF V600E (J Clin Oncol 38, no. 15_suppl (May 20, 2020) 10506; NCT02124772).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase Ib/II","amp_tier":"II"},{"pub_med_references":[25665005],"response_type":"sensitive","indication":"lung non-small cell carcinoma","therapy_id":3530,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Navitoclax + Vemurafenib","efficacy_evidence":"In a preclinical study, Navitoclax (ABT-263) enhanced the inhibitory effect of Zelboraf (vemurafenib) on human non-small cell lung cancer cells harboring BRAF V600E in culture (%%PUBMED:25665005%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"low grade glioma","therapy_id":14102,"normalized_cancer":"Low-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"FCN-159","efficacy_evidence":"In a Phase II trial, FCN-159 treatment was well tolerated and resulted in 6 partial responses, 9 minor responses, and 7 with stable disease in 22 pediatric patients with low-grade glioma harboring BRAF V600E (12/23), KIAA1549-BRAF (8/23), or NF1 mutations (3/23) (Ann Oncol (2023) 34 (suppl_2): S391-S392).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"pub_med_references":[18287029],"response_type":"sensitive","indication":"melanoma","therapy_id":1060,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"PLX4720","efficacy_evidence":"In a preclinical study, PLX4720 inhibited growth of melanoma cells harboring BRAF V600E in culture and in cell line xenograft models (%%PUBMED:18287029%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"pleomorphic xanthoastrocytoma","therapy_id":1066,"normalized_cancer":"Pleomorphic Xanthoastrocytoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Mekinist (trametinib) and Tafinlar (dabrafenib) combination therapy is included in guidelines as an adjuvant treatment for patients with pleomorphic xanthoastrocytoma harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[29632053],"normalized_drug":"Dabrafenib, Trametinib","indication":"pleomorphic xanthoastrocytoma","therapy_id":1066,"normalized_cancer":"Pleomorphic Xanthoastrocytoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, Mekinist (trametinib) and Tafinlar (dabrafenib) combination treatment resulted in clinical benefit that lasted for more than 14 months in a patient with pleomorphic xanthoastrocytoma harboring BRAF V600E (%%PUBMED:29632053%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[37729428],"response_type":"sensitive","indication":"melanoma","therapy_id":16204,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Encorafenib + Talazoparib","efficacy_evidence":"In a preclinical study, treatment with the combination of Talzenna (talazoparib) and Braftovi (encorafenib) synergistically inhibited viability of patient-derived melanoma spheroids harboring BRAF V600E in culture (%%PUBMED:37729428%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Patient cell culture","amp_tier":"II"},{"pub_med_references":[27312529],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":4525,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Dabrafenib","efficacy_evidence":"In a preclinical study, combination therapy consisting of Erbitux (cetuximab) and Tafinlar (dabrafenib) inhibited survival of colorectal cancer cell lines harboring BRAF V600E in culture (%%PUBMED:27312529%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[20538618],"normalized_drug":"Ci-1040","indication":"Advanced Solid Tumor","therapy_id":699,"normalized_cancer":"All Solid Tumors","evidence_type":"Actionable","therapy":"CI-1040","efficacy_evidence":"In a preclinical study, CI-1040 (PD184352) inhibited Erk phosphorylation and growth of transformed cells expressing BRAF V600E in culture (%%PUBMED:20538618%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[23629727],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":4656,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Everolimus + Pimasertib","efficacy_evidence":"In a preclinical study, Pimasertib (MSC1936369B) and Afinitor (everolimus) synergistically inhibited proliferation of colorectal cancer cells harboring BRAF V600E in culture (%%PUBMED:23629727%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[28351928],"response_type":"sensitive","indication":"melanoma","therapy_id":1260,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Encorafenib + Ribociclib","efficacy_evidence":"In a Phase Ib/II trial, Encorafenib (LGX818) and Kisqali (ribociclib) combination treatment resulted in confirmed partial response in 7.1% (2/28), unconfirmed partial response in 10.7% (3/28), and stable disease in 35.7% (10/28) of patients with melanoma harboring BRAF V600E (%%PUBMED:28351928%%).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase Ib/II","amp_tier":"II"},{"pub_med_references":[24398428],"response_type":"sensitive","indication":"melanoma","therapy_id":1684,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Ganetespib + TAK-733","efficacy_evidence":"In a preclinical study, treatment with the Hsp90 inhibitor Ganetespib in combination with the MEK1/2 inhibitor TAK-733 resulted in tumor regression in Zelboraf (vemurafenib)-resistant cell line xenograft models of melanoma harboring BRAF V600E (%%PUBMED:24398428%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[34433654],"response_type":"sensitive","indication":"high grade glioma","therapy_id":12676,"normalized_cancer":"High-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"LY3009120 + Vemurafenib","efficacy_evidence":"In a preclinical study, combination treatment with Zelboraf (vemurafenib) and LY3009120 treatment led to greater inhibition of cell growth compared to either agent alone in a patient-derived glioma cell line harboring BRAF V600E in culture (%%PUBMED:34433654%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Patient cell culture","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[22048237],"normalized_drug":"Selumetinib","indication":"melanoma","therapy_id":913,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Selumetinib","efficacy_evidence":"In a Phase II trial, a favorable response rate to Koselugo (selumetinib) was observed in mutant BRAF but not BRAF wild-type melanoma patients (%%PUBMED:22048237%%).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"pub_med_references":[32816843],"response_type":"predicted - resistant","indication":"melanoma","therapy_id":8871,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"BI-3406","efficacy_evidence":"In a preclinical study, BI-3406 treatment failed to inhibit growth of KRAS wild-type melanoma cells harboring BRAF V600E in culture and in cell line xenograft models (%%PUBMED:32816843%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[36759733],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":15043,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Celecoxib + Vemurafenib","efficacy_evidence":"In a preclinical study, the combination of Zelboraf (vemurafenib) and Celecoxib synergistically inhibited viability in colorectal cancer cell lines harboring BRAF V600E in culture (%%PUBMED:36759733%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Ulixertinib","indication":"glioblastoma","therapy_id":997,"normalized_cancer":"Glioblastoma, IDH-Wildtype","evidence_type":"Actionable","therapy":"Ulixertinib","efficacy_evidence":"In an expanded access program (ULI-EAP-100), Ulixertinib (BVD-523) treatment resulted in clinical benefit in a patient with glioblastoma harboring BRAF V600E who stayed on treatment for 128 days (J Clin Oncol 40, no. 16_suppl (June 01, 2022) e15101; NCT04566393).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[29247021],"normalized_drug":"Ulixertinib","indication":"glioblastoma","therapy_id":997,"normalized_cancer":"Glioblastoma, IDH-Wildtype","evidence_type":"Actionable","therapy":"Ulixertinib","efficacy_evidence":"In a Phase I trial, treatment with Ulixertinib (BVD-523) resulted in a partial response in a patient with glioblastoma harboring BRAF V600E (%%PUBMED:29247021%%; NCT01781429).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[38728872],"response_type":"sensitive","indication":"melanoma","therapy_id":16940,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Ravoxertinib + Vemurafenib","efficacy_evidence":"In a preclinical study, treatment with the combination of Ravoxertinib (GDC-0994) and Zelboraf (vemurafenib) resulted in additive effects, with decreased growth of a melanoma cell line harboring BRAF V600E in culture (%%PUBMED:38728872%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"anaplastic oligodendroglioma","therapy_id":1066,"normalized_cancer":"Oligodendroglioma, IDH-mutant, and 1p/19q-Codeleted","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Combination of Mekinist (trametinib) and Tafinlar (dabrafenib) is included in guidelines for patients with recurrent anaplastic gliomas harboring BRAF V600E, including anaplastic oligodendroglioma (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"oncocytic carcinoma of the thyroid","therapy_id":1066,"normalized_cancer":"Hurthle Cell Thyroid Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"The combination of Tafinlar (dabrafenib) and Mekinist (trametinib) is included in guidelines for patients with thyroid Hurthle cell carcinoma harboring BRAF V600E who have progressed on therapy and have no further treatment options (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[26768652],"response_type":"not applicable","indication":"colon adenocarcinoma","therapy_id":1776,"normalized_cancer":"Colon Adenocarcinoma","evidence_type":"Emerging","therapy":"N/A","efficacy_evidence":"In a post-hoc analysis of a Phase III trial, BRAF V600E mutations in colon adenocarcinoma patients with microsatellite stable tumors were associated with a shorter disease-free survival and overall survival compared to those patients with microsatellite instability tumors, suggesting that BRAF V600E may serve as a future prognostic biomarker in this patient population (%%PUBMED:26768652%%).","cap_asco_evidence_level":"NA","molecular_profile":"BRAF V600E","approval_status":"Phase III","amp_tier":"NA"},{"pub_med_references":[27523909],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":3300,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"TAK-632","efficacy_evidence":"In a preclinical study, TAK-632 inhibited proliferation of colorectal cancer cells harboring BRAF V600E in culture (%%PUBMED:27523909%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[27048951],"response_type":"sensitive","indication":"melanoma","therapy_id":4232,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"DETD-35 + Vemurafenib","efficacy_evidence":"In a preclinical study, DETD-35 and Zelboraf (vemurafenib) synergistically inhibited proliferation and colony formation of melanoma cells harboring BRAF V600E in culture and reduced tumor size in xenograft models (%%PUBMED:27048951%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Atezolizumab, Cobimetinib, Vemurafenib","indication":"skin melanoma","therapy_id":4825,"normalized_cancer":"Cutaneous Melanoma","evidence_type":"Actionable","therapy":"Atezolizumab + Cobimetinib + Vemurafenib","efficacy_evidence":"Zelboraf (vemurafenib) plus Cotellic (cobimetinib) in combination with an immune checkpoint inhibitor, such as Tecentriq (atezolizumab), is included in guidelines as second-line or subsequent therapy (category 2A) for patients with metastatic or unresectable cutaneous melanoma harboring a BRAF V600 mutation, such as BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[36759733],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":15045,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Celecoxib + Trametinib + Vemurafenib","efficacy_evidence":"In a preclinical study, the addition of Celecoxib to the combination of Zelboraf (vemurafenib) and Mekinist (trametinib) synergistically inhibited viability in colorectal cancer cell lines harboring BRAF V600E in culture (%%PUBMED:36759733%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[23242808],"response_type":"sensitive","indication":"melanoma","therapy_id":3131,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Gefitinib + PLX4720","efficacy_evidence":"In a preclinical study, Iressa (gefitinib) in combination with PLX4720 inhibited proliferation and tumorigenicity in human melanoma cell line harboring BRAF V600E and resistant to Braf inhibition in culture and in animal models (%%PUBMED:23242808%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[38565920],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":16824,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + IAG933","efficacy_evidence":"In a preclinical study, the combination of IAG933 and Tafinlar (dabrafenib) inhibited proliferation of colorectal cancer cell lines harboring BRAF V600E in culture (%%PUBMED:38565920%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[39399174],"normalized_drug":"Dabrafenib","indication":"pleomorphic xanthoastrocytoma","therapy_id":3,"normalized_cancer":"Pleomorphic Xanthoastrocytoma","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a clinical case study, Tafinlar (dabrafenib) treatment resulted in 1 partial response and 1 stable disease in 2 patients with tempero-parietal pleomorphic xanthoastrocytoma harboring BRAF V600E and CDKN2A deletion (%%PUBMED:39399174%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[26267534],"response_type":"sensitive","indication":"melanoma","therapy_id":3769,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"DEL-22379","efficacy_evidence":"In a preclinical study, DEL-22379 inhibited growth of melanoma cells harboring BRAF V600E with high levels of ERK dimerization in culture and inhibited tumor progression in melanoma xenograft models harboring BRAF V600E (%%PUBMED:26267534%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[32029534],"normalized_drug":"Vemurafenib","indication":"sarcoma","therapy_id":342,"normalized_cancer":"Sarcoma, NOS","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase II trial (VE-BASKET), responses were seen in sarcoma patients harboring BRAF V600E (n=6) when treated with Zelboraf (vemurafenib), including 1 patient with a complete response and 1 patient with a partial response (%%PUBMED:32029534%%; NCT01524978).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"resistant","normalized_drug":"Panitumumab","indication":"colon cancer","therapy_id":845,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Panitumumab","efficacy_evidence":"Vectibix (panitumumab), as a monotherapy, is not indicated for use in colon cancer patients with BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[37269335],"response_type":"predicted - sensitive","indication":"colorectal cancer","therapy_id":11417,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Encorafenib + PF-07284892","efficacy_evidence":"In a clinical case study, the combination of PF-07284892, Erbitux (cetuximab), and Braftovi (encorafenib) resulted in a 30% tumor reduction in a colorectal cancer patient harboring BRAF V600E, who remained on treatment for 6 months, and the combination inhibited tumor growth in a cell line xenograft model (%%PUBMED:37269335%%; NCT04800822).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"salivary gland cancer","therapy_id":1066,"normalized_cancer":"Salivary Gland Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Tafinlar (dabrafenib) and Mekinist (trametinib) combination therapy is included in guidelines (category 2A) for patients with recurrent, unresectable, or metastatic salivary gland tumors harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[21639808,28961848],"normalized_drug":"Vemurafenib","indication":"melanoma","therapy_id":342,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase III trial (BRIM-3) that supported FDA approval, Zelboraf (vemurafenib), as compared to Deticene (dacarbazine), resulted in an improved overall survival (OS) (13.6 vs 9.7 months, HR=0.81, p=0.03) in patients with BRAF V600E-positive metastatic melanoma, with estimated OS rates of 56%, 30%, 21%, and 17% at 1, 2, 3, and 4 years, respectively (%%PUBMED:28961848%%, %%PUBMED:21639808%%; NCT01006980), and BRAF V600E is included on the companion diagnostic (FDA.gov).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"FDA approved - On Companion Diagnostic","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[20818844],"normalized_drug":"Vemurafenib","indication":"melanoma","therapy_id":342,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase I trial, Zelboraf (vemurafenib) treatment resulted in an overall response rate of 81% (26/32; 2 complete responses, 24 partial responses), and inhibition of tumor Erk and Ccnd1, and reduced cell proliferation in metastatic melanoma patients harboring BRAF V600E (%%PUBMED:20818844%%; NCT00215605).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase I","amp_tier":"II"},{"response_type":"no benefit","pub_med_references":[30181415],"normalized_drug":"Binimetinib","indication":"colon neuroendocrine neoplasm","therapy_id":807,"normalized_cancer":"Gastrointestinal Neuroendocrine Tumors","evidence_type":"Actionable","therapy":"Binimetinib","efficacy_evidence":"In Phase II trial, Mektovi (binimetinib) therapy in a patient with recurrent neuroendocrine carcinoma of the colon harboring a BRAF V600E mutation who had previously progressed on Tafinlar (dabrafenib) resulted in disease progression after two cycles (%%PUBMED:30181415%%; NCT01885195).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"melanoma","therapy_id":16364,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"IMM-6-415","efficacy_evidence":"In a preclinical study, IMM-6-415 treatment inhibited tumor growth in a cell line xenograft model of melanoma harboring BRAF V600E (Mol Cancer Ther (2023) 22 (12_Supplement): A093).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[35882450],"normalized_drug":"Ulixertinib","indication":"pleomorphic xanthoastrocytoma","therapy_id":997,"normalized_cancer":"Pleomorphic Xanthoastrocytoma","evidence_type":"Actionable","therapy":"Ulixertinib","efficacy_evidence":"In a preclinical study, Ulixertinib (BVD-523) reduced metabolic activity and inhibited MAPK pathway activity in a pleomorphic xanthoastrocytoma cell line harboring BRAF V600E in culture, and inhibited tumor growth and improved survival compared to vehicle (48.5 days vs 30 days, respectively) in a xenograft model (%%PUBMED:35882450%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"esophagus adenocarcinoma","therapy_id":1066,"normalized_cancer":"Esophageal Adenocarcinoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Tafinlar (dabrafenib) and Mekinist (trametinib) combination therapy is included in guidelines as second-line or subsequent therapy for patients with locally advanced, recurrent, or metastatic esophageal adenocarcinoma harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[27217440],"response_type":"predicted - sensitive","indication":"high grade glioma","therapy_id":4901,"normalized_cancer":"High-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"Everolimus + Selumetinib","efficacy_evidence":"In a preclinical study, Koselugo (selumetinib) and Afinitor (everolimus) synergistically inhibited growth and induced apoptosis in glioma cell lines in culture, resulted in prolonged survival in cell line xenograft models (%%PUBMED:27217440%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[23365119],"response_type":"sensitive","indication":"thyroid cancer","therapy_id":1707,"normalized_cancer":"Thyroid Cancer","evidence_type":"Actionable","therapy":"Lapatinib + Vemurafenib","efficacy_evidence":"In a preclinical study, the combination of Tykerb (lapatinib) and Zelboraf (vemurafenib) inhibited growth of thyroid cancer cells harboring a BRAF V600E mutation in culture and in BRAF-mutant mouse models of thyroid cancer (%%PUBMED:23365119%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"response_type":"predicted - 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patient with gastrointestinal stromal tumor harboring BRAF V600E (%%PUBMED:38756640%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[23470635],"normalized_drug":"Dabrafenib","indication":"gastrointestinal stromal tumor","therapy_id":3,"normalized_cancer":"Gastrointestinal Stromal Tumor","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a clinical case study, Tafinlar (dabrafenib) treatment resulted in a 20% decrease in tumor size after 24 weeks in a patient with a gastrointestinal stromal tumor harboring BRAF V600E (%%PUBMED:23470635%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[38096472],"normalized_drug":"Cobimetinib, Vemurafenib","indication":"breast malignant phyllodes tumor","therapy_id":1657,"normalized_cancer":"Malignant Phyllodes Tumor of the Breast","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"In a Phase II trial (TAPUR), Zelboraf (vemurafenib) and Cotellic (cobimetinib) combination therapy resulted in a partial response in a patient with a phyllodes tumor of the breast harboring BRAF V600E (%%PUBMED:38096472%%; NCT02693535).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[27048951],"response_type":"sensitive","indication":"melanoma","therapy_id":4230,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"DETD-35","efficacy_evidence":"In a preclinical study, DETD-35 inhibited proliferation and colony formation of melanoma cells harboring BRAF V600E in culture and reduced tumor size in xenograft models (%%PUBMED:27048951%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[16273091],"response_type":"sensitive","indication":"colon cancer","therapy_id":849,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Mirdametinib","efficacy_evidence":"In a preclinical study, Gomekli (mirdametinib) demonstrated antitumor activity against BRAF V600E colon cancer cell line xenografts (%%PUBMED:16273091%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[34337566],"response_type":"sensitive","indication":"diffuse large B-cell lymphoma","therapy_id":8304,"normalized_cancer":"Diffuse Large B-Cell Lymphoma, NOS","evidence_type":"Actionable","therapy":"ERAS-007","efficacy_evidence":"In a preclinical study, ERAS-007 (ASN007) treatment inhibited proliferation of diffuse large B-cell lymphoma cells harboring BRAF V600E in culture (%%PUBMED:34337566%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"cholangiocarcinoma","therapy_id":7465,"normalized_cancer":"Cholangiocarcinoma","evidence_type":"Actionable","therapy":"BGB3245","efficacy_evidence":"In a Phase I trial, BGB3245 treatment demonstrated manageable safety and resulted in a disease control rate of 48% (16/33,1 complete response, 5 confirmed partial responses (PR), 2 unconfirmed PR, and 8 stable disease > 24 weeks) in patients with advanced solid tumors harboring MAPK pathway alterations, including a partial response in a patient with cholangiocarcinoma harboring BRAF V600E (Cancer Res (2023) 83 (8_Supplement): CT031).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[20538618],"response_type":"sensitive","indication":"Advanced Solid Tumor","therapy_id":4281,"normalized_cancer":"All Solid Tumors","evidence_type":"Actionable","therapy":"SB590885","efficacy_evidence":"In a preclinical study, SB590885 inhibited inhibited Erk phosphorylation and cell proliferation of transformed cells expression BRAF V600E in culture (%%PUBMED:20538618%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"response_type":"sensitive","indication":"skin melanoma","therapy_id":1449,"normalized_cancer":"Cutaneous Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + Pembrolizumab + Trametinib","efficacy_evidence":"Tafinlar (dabrafenib) plus Mekinist (trametinib) in combination with an immune checkpoint inhibitor, such as Keytruda (pembrolizumab), is included in guidelines as second-line or subsequent therapy (category 2A) for patients with metastatic or unresectable cutaneous melanoma harboring a BRAF V600 mutation, such as BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[27297867],"response_type":"sensitive","indication":"melanoma","therapy_id":4604,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"PAC-1 + Vemurafenib","efficacy_evidence":"In a preclinical study, the combination of PAC-1 and Zelboraf (vemurafenib) resulted in a synergistic effect when treating melanoma cells harboring BRAF V600E in culture and xenograft models, demonstrating increased apoptosis and decreased tumor volume (%%PUBMED:27297867%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[26267534],"response_type":"sensitive","indication":"colorectal adenocarcinoma","therapy_id":3769,"normalized_cancer":"Colorectal Adenocarcinoma","evidence_type":"Actionable","therapy":"DEL-22379","efficacy_evidence":"In a preclinical study, DEL-22379 inhibited tumor growth in a colorectal adenocarcinoma patient-derived xenograft model harboring BRAF V600E (%%PUBMED:26267534%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"melanoma","therapy_id":18577,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"RG6344","efficacy_evidence":"In a Phase I trial, RG6344 treatment was well tolerated and demonstrated preliminary activity in patients with advanced solid tumors harboring BRAF V600E (n=64), including melanoma (n=11) and colorectal cancer (n=51), with an objective response rate of 25% (Cancer Res (2025) 85 (8_Supplement_2): CT017).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[33273059],"response_type":"sensitive","indication":"melanoma","therapy_id":11152,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"AZD0364","efficacy_evidence":"In a preclinical study, AZD0364 (ATG-017) inhibited cell growth, decreased phosphorylation of Erk target genes, and increased expression of apoptosis markers in melanoma cells harboring BRAF V600E in culture, and resulted in tumor regression in cell line xenograft models (%%PUBMED:33273059%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[37325052],"response_type":"sensitive","indication":"thyroid cancer","therapy_id":10505,"normalized_cancer":"Thyroid Cancer","evidence_type":"Actionable","therapy":"SHP099 + Vemurafenib","efficacy_evidence":"In a preclinical study, the combination of Zelboraf (vemurafenib) and SHP099 inhibited proliferation and induced cell cycle arrest in Zelboraf (vemurafenib)-resistant thyroid cancer cell lines harboring BRAF V600E in culture and inhibited tumor growth in a cell line xenograft model (%%PUBMED:37325052%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[35882450],"response_type":"sensitive","indication":"pleomorphic xanthoastrocytoma","therapy_id":14715,"normalized_cancer":"Pleomorphic Xanthoastrocytoma","evidence_type":"Actionable","therapy":"Binimetinib + Ulixertinib","efficacy_evidence":"In a preclinical study, the combination of Ulixertinib (BVD-523) and Mektovi (binimetinib) inhibited proliferation and had a synergistic effect on induction of apoptosis and inhibition of MAPK pathway activity in a pleomorphic xanthoastrocytoma cell line harboring BRAF V600E in culture, and improved the progressive disease/partial response ratio compared to either drug alone in a zebrafish xenograft model (%%PUBMED:35882450%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[36011019],"normalized_drug":"Dabrafenib","indication":"triple-receptor negative breast cancer","therapy_id":3,"normalized_cancer":"Invasive Breast Carcinoma","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a preclinical study, Tafinlar (dabrafenib) treatment inhibited Mapk signaling and viability in a triple-negative breast cancer cell line harboring BRAF V600E in culture (%%PUBMED:36011019%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[30867592],"normalized_drug":"Cobimetinib","indication":"lymphatic system cancer","therapy_id":1004,"normalized_cancer":"Lymphatic Cancer","evidence_type":"Actionable","therapy":"Cobimetinib","efficacy_evidence":"In a Phase II trial, treatment with Cotellic (cobimetinib) in patients with histiocytic neoplasms resulted in a PET overall response rate of 89% (16/18), with complete response in 72% (13/18) and partial response in 17% (3/18), and resulted in stable disease in 6% (1/18) of patients, including 1 partial response and 3 complete responses in 4 patients with Erdheim-Chester disease harboring BRAF V600E (%%PUBMED:30867592%%; NCT01953926).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"ovary epithelial cancer","therapy_id":1066,"normalized_cancer":"Ovarian Epithelial Tumor","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Tafinlar (dabrafenib) and Mekinist (trametinib) combination therapy is included in guidelines as systemic therapy for patients with recurrent epithelial ovarian, fallopian tube, or primary peritoneal cancer harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","normalized_drug":"Cetuximab, Encorafenib","indication":"rectum cancer","therapy_id":1916,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Encorafenib","efficacy_evidence":"Braftovi (encorafenib) in combination with Erbitux (cetuximab) is included in guidelines as primary or subsequent therapy for patients with rectal cancer harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[32523649],"normalized_drug":"Vemurafenib","indication":"childhood low-grade glioma","therapy_id":342,"normalized_cancer":"Low-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase I trial (PNOC-002), Zelboraf (vemurafenib) treatment was tolerable and resulted in 1 complete response, 5 partial responses, and 13 stable disease in 19 pediatric patients with recurrent low grade gliomas harboring BRAF V600E, including pilocytic astrocytoma (n=10), ganglioglioma (n=5), pleomorphic xanthroastrocytoma (n=2), fibrillary astrocytoma (n=1), and astrocytoma not otherwise specified (n=1) (%%PUBMED:32523649%%; NCT01748149).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase I","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[25309914],"normalized_drug":"Trametinib","indication":"colorectal cancer","therapy_id":2,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Trametinib","efficacy_evidence":"In a preclinical study, colorectal cancer cells harboring a BRAF V600E mutation had increased sensitivity to Mekinist (trametinib) compared to other colorectal cancer lines in culture (%%PUBMED:25309914%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"melanoma","therapy_id":1449,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + Pembrolizumab + Trametinib","efficacy_evidence":"In a Phase II trial (IMPemBra), Keytruda (pembrolizumab) in combination with short-term or intermittent Tafinlar (dabrafenib) plus Mekinist (trametinib) resulted in improved median progression-free survival compared to Keytruda (pembrolizumab) monotherapy (27.0 vs 10.6 mo, p=0.13) in patients with treatment-naive advanced melanoma harboring BRAF V600E (n=26) or V600K (n=6) mutations (J Clin Oncol 38: 2020 (suppl; abstr 10021); NCT02625337).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"response_type":"resistant","pub_med_references":[39626159],"normalized_drug":"Vemurafenib","indication":"colon cancer","therapy_id":342,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a preclinical study, mouse colon cancer organoids harboring BRAF V600E were resistant to Zelboraf (vemurafenib) in culture (%%PUBMED:39626159%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"resistant","normalized_drug":"Cetuximab","indication":"colon cancer","therapy_id":694,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab","efficacy_evidence":"Erbitux (cetuximab), as a monotherapy, is not indicated for use in colon cancer patients with BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[21170960],"normalized_drug":"Regorafenib","indication":"colorectal cancer","therapy_id":890,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Regorafenib","efficacy_evidence":"In a preclinical study, Stivarga (regorafenib) inhibited proliferation of colorectal cancer cells harboring BRAF V600E in culture and suppressed angiogenesis and tumor growth in cell line xenograft models (%%PUBMED:21170960%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[32818466,34838156],"normalized_drug":"Dabrafenib, Trametinib","indication":"Advanced Solid Tumor","therapy_id":1066,"normalized_cancer":"All Solid Tumors","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In 3 Phase II trials (ROAR, NCI-MATCH, X2101) that supported FDA approval, Tafinlar (dabrafenib) and Mekinist (trametinib) combination therapy demonstrated safety and efficacy in adult and pediatric (6 years or older) patients with advanced solid tumors harboring BRAF V600E (%%PUBMED:34838156%%, %%PUBMED:32818466%%, J Clin Oncol 37, no. 15_suppl (May 20, 2019) 3002, J Clin Oncol 38, no. 15_suppl (May 20, 2020) 10506; NCT02034110, NCT02465060, NCT02124772).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"FDA approved","amp_tier":"I"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"Advanced Solid Tumor","therapy_id":1066,"normalized_cancer":"All Solid Tumors","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a Phase II trial (NCI-MATCH), Tafinlar (dabrafenib) and Mekinist (trametinib) combination therapy resulted in an objective response rate of 33.3% (11/33) in patients with advanced solid tumors other than melanoma, thyroid, colorectal, and lung cancer harboring BRAF V600E, with a median duration of response of 12 months, median progression-free survival of 9.4 months, and median overall survival not reached (J Clin Oncol 37, no. 15_suppl (May 20, 2019) 3002; NCT02465060).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[24885690],"normalized_drug":"Dabrafenib","indication":"colorectal cancer","therapy_id":3,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a preclinical study, colorectal cancer cell lines harboring a BRAF V600E mutation had increased sensitivity to Tafinlar (dabrafenib) in culture compared to cell lines with wild-type BRAF (%%PUBMED:24885690%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"colorectal cancer","therapy_id":12741,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Encorafenib + ERAS-007","efficacy_evidence":"In a Phase Ib/II trial (HERKULES), combination treatment with ERAS-007, Erbitux (cetuximab), and Braftovi (encorafenib) demonstrated safety and activity in patients with metastatic colorectal cancer harboring BRAF V600E, resulting in 1 confirmed and 1 unconfirmed partial response of 4 efficacy evaluable patients (J Clin Oncol 41, 2023 (suppl 16; abstr 3557); NCT05039177).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[27297867],"response_type":"sensitive","indication":"melanoma","therapy_id":4603,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"PAC-1 + Trametinib + Vemurafenib","efficacy_evidence":"In a preclinical study, the addition of PAC-1 to Mekinist (trametinib) and Zelboraf (vemurafenib) led to greater levels of caspase-3 activity and apoptosis in melanoma cells harboring BRAF V600E when compared to Zelboraf (vemurafenib) and Mekinist (trametinib) treatment without PAC-1 (%%PUBMED:27297867%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Cetuximab, Encorafenib","indication":"appendix adenocarcinoma","therapy_id":1916,"normalized_cancer":"Appendiceal Adenocarcinoma","evidence_type":"Actionable","therapy":"Cetuximab + Encorafenib","efficacy_evidence":"Braftovi (encorafenib) in combination with Erbitux (cetuximab) is included in guidelines for patients with advanced or metastatic appendiceal adenocarcinoma harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[39018564],"normalized_drug":"Encorafenib","indication":"pseudomyxoma peritonei","therapy_id":796,"normalized_cancer":"Peritoneal Cancer","evidence_type":"Actionable","therapy":"Encorafenib","efficacy_evidence":"In a preclinical study, Braftovi (encorafenib) inhibited viability and induced apoptosis in a patient-derived pseudomyxoma peritonei cell line harboring BRAF V600E in culture and inhibited tumor growth and improved survival of a patient-derived xenograft (PDX) model (%%PUBMED:39018564%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Pdx & cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"colorectal cancer","therapy_id":16364,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"IMM-6-415","efficacy_evidence":"In a preclinical study, IMM-6-415 treatment inhibited tumor growth in a cell line xenograft model of colorectal cancer harboring BRAF V600E (Mol Cancer Ther (2023) 22 (12_Supplement): A093).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"colorectal cancer","therapy_id":17152,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Binimetinib + PLX8394","efficacy_evidence":"In a preclinical study, treatment with the combination of Mektovi (binimetinib) and PLX8394 inhibited viability of colorectal cancer cells harboring BRAF V600E in culture (Cancer Res (2024) 84 (6_Supplement): 4609).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[36108341],"normalized_drug":"Dabrafenib, Trametinib","indication":"hairy cell leukemia","therapy_id":1066,"normalized_cancer":"Hairy Cell Leukemia","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a Phase II trial (ROAR), treatment with the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) demonstrated safety and resulted in an overall response rate of 89.1% (49/55; 36 complete responses, 13 partial responses) in patients with heavily pretreated recurrent/refractory hairy cell leukemia harboring BRAF V600E, with 24-month duration of response, progression-free-survival, and overall survival rates of 97.7%, 94.4% and 94.5%, respectively (%%PUBMED:36108341%%; NCT02034110).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"pub_med_references":[26267534],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":2618,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"SCH772984","efficacy_evidence":"In a preclinical study, SCH772984 inhibited growth of colorectal cancer cell lines harboring BRAF V600E in culture (%%PUBMED:26267534%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[38960393],"response_type":"predicted - sensitive","indication":"skin melanoma","therapy_id":4754,"normalized_cancer":"Cutaneous Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + Nivolumab + Trametinib","efficacy_evidence":"In a clinical case study, treatment with the combination of Mekinist (trametinib), Tafinlar (dabrafenib), and Opdivo (nivolumab) resulted in a partial response in the leptomeningeal disease on the spine and the extracranial melanoma, with the intracranial lesions remaining stable after 6 months, in a patient with cutaneous melanoma harboring BRAF V600E, and a follow-up at least 7 years following diagnosis demonstrated complete remission (%%PUBMED:38960393%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[36713531],"normalized_drug":"Vemurafenib","indication":"hairy cell leukemia","therapy_id":342,"normalized_cancer":"Hairy Cell Leukemia","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a clinical case study, Zelboraf (vemurafenib) treatment resulted in complete resolution of the brain lesions after 3 months of treatment, decreased spleen size, and resolution of leukemic retinopathy in a patient with hairy cell leukemia harboring BRAF V600E (%%PUBMED:36713531%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[26352686],"normalized_drug":"Vemurafenib","indication":"hairy cell leukemia","therapy_id":342,"normalized_cancer":"Hairy Cell Leukemia","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In two Phase II clinical studies, patients with refractory hairy cell leukemia harboring BRAF V600E responded to Zelboraf (vemurafenib) with overall response rates of 96% (25/26) and 100% (24/24) as well as complete response rates of 35% (9/26) and 42% (10/24) with median follow up times of 8 and 12 weeks, respectively (%%PUBMED:26352686%%).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"pub_med_references":[25665005],"response_type":"sensitive","indication":"colon cancer","therapy_id":1386,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Navitoclax + Trametinib","efficacy_evidence":"In a preclinical study, Navitoclax (ABT-263) enhanced the inhibitory effect of Mekinist (trametinib) on human colon cancer cells harboring BRAF V600E in culture (%%PUBMED:25665005%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[22180495],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":10746,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Bevacizumab + Capecitabine + Vemurafenib","efficacy_evidence":"In a preclinical study, Zelboraf (vemurafenib) treatment when combined with Xeloda (capecitabine) and Avastin (bevacizumab) enhanced tumor growth inhibition and increased survival in a cell line xenograft model of colorectal cancer harboring BRAF V600E (%%PUBMED:22180495%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"predicted - sensitive","normalized_drug":"Ulixertinib","indication":"pancreatic ductal adenocarcinoma","therapy_id":997,"normalized_cancer":"Pancreatic Adenocarcinoma","evidence_type":"Actionable","therapy":"Ulixertinib","efficacy_evidence":"In an expanded access program (ULI-EAP-100), Ulixertinib (BVD-523) treatment resulted in clinical benefit in a patient with pancreatic ductal adenocarcinoma harboring BRAF V600E who stayed on treatment for 413 days (J Clin Oncol 40, no. 16_suppl (June 01, 2022) e15101; NCT04566393).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[39399174],"normalized_drug":"Dabrafenib","indication":"anaplastic pleomorphic xanthoastrocytoma","therapy_id":3,"normalized_cancer":"Anaplastic Pleomorphic Xanthoastrocytoma","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a clinical case study, Tafinlar (dabrafenib) treatment resulted in a partial response in a patient with tempero-parietal anaplastic pleomorphic xanthoastrocytoma harboring BRAF V600E (%%PUBMED:39399174%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[36343387],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":14544,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Panobinostat + Trametinib","efficacy_evidence":"In a preclinical study, the combination of Mekinist (trametinib) and Farydak (panobinostat) synergistically inhibited cell viability and induced apoptosis in a colorectal cancer cell line harboring BRAF V600E in culture (%%PUBMED:36343387%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[26438159],"response_type":"sensitive","indication":"melanoma","therapy_id":2011,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"RO5126766","efficacy_evidence":"In a preclinical study, RO5126766 inhibited proliferation of melanoma cells harboring BRAF V600E in culture (%%PUBMED:26438159%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[25422890],"response_type":"sensitive","indication":"melanoma","therapy_id":2011,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"RO5126766","efficacy_evidence":"In a preclinical study, RO5126766 (VS-6766) treatment induced cell cycle arrest, decreased Mek and Erk phosphorylation, and inhibited growth of melanoma cells harboring BRAF V600E in culture (%%PUBMED:25422890%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[34337566],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":8304,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"ERAS-007","efficacy_evidence":"In a preclinical study, ERAS-007 (ASN007) treatment inhibited cell proliferation and Erk signaling in colorectal cancer cell lines harboring BRAF V600E in culture, and induced tumor regression in two patient-derived xenograft (PDX) models (%%PUBMED:34337566%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Pdx & cell culture","amp_tier":"II"},{"response_type":"sensitive","indication":"rectum cancer","therapy_id":18195,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Encorafenib + Fluorouracil + Leucovorin + Oxaliplatin + Panitumumab","efficacy_evidence":"Braftovi (encorafenib) in combination with Vectibix (panitumumab) and FOLFOX is included in guidelines as initial (category 2A) or subsequent-line (category 2B) therapy for patients with advanced or metastatic rectal cancer harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[38976815],"normalized_drug":"Vemurafenib","indication":"childhood pilocytic astrocytoma","therapy_id":342,"normalized_cancer":"Pilocytic Astrocytoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a clinical case study, Zelboraf (vemurafenib) treatment resulted in a partial response in a pediatric patient with pilocytic astrocytoma harboring BRAF V600E (%%PUBMED:38976815%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[32523649],"normalized_drug":"Vemurafenib","indication":"childhood pilocytic astrocytoma","therapy_id":342,"normalized_cancer":"Pilocytic Astrocytoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase I trial (PNOC-002), Zelboraf (vemurafenib) treatment was tolerable and resulted in 1 complete response, 5 partial responses, and 13 stable disease in 19 pediatric patients with recurrent low grade gliomas harboring BRAF V600E, including pilocytic astrocytoma (n=10), ganglioglioma (n=5), pleomorphic xanthroastrocytoma (n=2), fibrillary astrocytoma (n=1), and astrocytoma NOS (n=1) (%%PUBMED:32523649%%; NCT01748149).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase I","amp_tier":"II"},{"pub_med_references":[19276360],"response_type":"sensitive","indication":"melanoma","therapy_id":1095,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"GDC0879","efficacy_evidence":"In a preclinical study, GDC0879 inhibited survival of melanoma cell lines harboring BRAF V600E in cell culture, cell line xenograft and patient-derived xenograft (PDX) models (%%PUBMED:19276360%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Pdx & cell 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with approximately 90% tumor shrinkage and a progression-free survival of 10 months in a patient with metastatic papillary thyroid carcinoma harboring BRAF V600E (%%PUBMED:38489728%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[27460442],"normalized_drug":"Vemurafenib","indication":"papillary thyroid carcinoma","therapy_id":342,"normalized_cancer":"Papillary Thyroid Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase II trial, Zelboraf (vemurafenib) treatment resulted in a partial response in 38.5% (10/26) of patients with metastatic or unresectable, radioactive iodine-refractory papillary thyroid carcinoma harboring BRAF V600E that were multikinase inhibitor-naive, with a disease control rate of 73%, and a median progression-free survival of 18.2 months (%%PUBMED:27460442%%; NCT01286753).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[20818844],"normalized_drug":"Vemurafenib","indication":"papillary thyroid carcinoma","therapy_id":342,"normalized_cancer":"Papillary Thyroid Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase I trial, Zelboraf (vemurafenib) treatment resulted in a complete or partial response in three papillary thyroid carcinoma patients harboring BRAF V600E, with one patient having a response that lasted for 8 months who remained progression-free for 12 months, and another two patients having a stable disease that lasted for 11 and 13 months, respectively (%%PUBMED:20818844%%; NCT00215605).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case 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breast cancer cell line harboring BRAF V600E in culture (%%PUBMED:36011019%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - resistant","pub_med_references":[34433654],"normalized_drug":"Dabrafenib","indication":"high grade glioma","therapy_id":3,"normalized_cancer":"High-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a preclinical study, NF1 knockdown in glioma cell lines harboring BRAF V600E led to decreased inhibition of cell growth and decreased apoptosis on treatment with Tafinlar (dabrafenib) in culture (%%PUBMED:34433654%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NF1 dec exp","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[34433654],"normalized_drug":"Dabrafenib, Trametinib","indication":"high grade 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(%%PUBMED:23288408%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NF1 dec exp","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[23288408],"response_type":"sensitive","indication":"melanoma","therapy_id":4351,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"VX-11e","efficacy_evidence":"In a preclinical study, inhibition of NF1 in a melanoma cell line harboring a BRAF V600E mutation did not affect sensitivity to the ERK inhibitor VX-11e (%%PUBMED:23288408%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NF1 dec exp","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[23288408],"response_type":"resistant","indication":"melanoma","therapy_id":1095,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"GDC0879","efficacy_evidence":"In a preclinical study, shRNA knockdown of NF1 in a BRAF V600E melanoma cell line confered resistance to the RAF inhibitor GDC0879 through sustained MAPK pathway activation (%%PUBMED:23288408%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NF1 dec exp","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[23288408],"response_type":"decreased response","indication":"melanoma","therapy_id":1093,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"AZ628","efficacy_evidence":"In a preclinical study, shRNA knockdown of NF1 in a BRAF V600E melanoma cell line demonstrated partial resistance to the pan-RAF inhibitor AZ628 (%%PUBMED:23288408%%).","cap_asco_evidence_level":"NA","molecular_profile":"BRAF V600E NF1 dec exp","approval_status":"Preclinical","amp_tier":"NA"},{"pub_med_references":[23288408],"response_type":"resistant","indication":"melanoma","therapy_id":1060,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"PLX4720","efficacy_evidence":"In a preclinical study, the shRNA knockdown of NF1 in a BRAF V600E melanoma cell line conferred resistance to RAF inhibitor PLX4720 through sustained MAPK pathway activation (%%PUBMED:23288408%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NF1 dec exp","approval_status":"Preclinical","amp_tier":"II"},{"response_type":"resistant","pub_med_references":[23288408],"normalized_drug":"Vemurafenib","indication":"melanoma","therapy_id":342,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a preclinical study, the shRNA knockdown of NF1 in a BRAF V600E melanoma cell line confers resistance to RAF inhibitor Zelboraf (vemurafenib) through sustained MAPK pathway activation (%%PUBMED:23288408%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NF1 dec exp","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[23288408],"response_type":"decreased response","indication":"melanoma","therapy_id":1061,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"PLX4720 + 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(%%PUBMED:23178117%%).","therapy":"Selumetinib","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Preclinical","normalized_drug":"Selumetinib","pub_med_references":[23178117],"molecular_profile":"BRAF V600E MED12 dec exp","profile_array":[{"type":"M1","gene":"V600E"}],"response_type":"resistant"},{"therapy_id":342,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a preclinical study, knock down of MED12 expression in BRAF V600E melanoma cell lines resulted in resistance to Zelboraf (vemurafenib) or Koselugo (selumetinib) (%%PUBMED:23178117%%).","therapy":"Vemurafenib","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Preclinical - Cell culture","normalized_drug":"Vemurafenib","pub_med_references":[23178117],"molecular_profile":"BRAF V600E MED12 dec 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(talazoparib) and Tafinlar (dabrafenib) synergistically inhibited viability of patient-derived melanoma spheroids harboring BRAF V600E and NRAS Q61K in culture (%%PUBMED:37729428%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NRAS Q61K","approval_status":"Preclinical - Patient cell culture","amp_tier":"II"},{"pub_med_references":[22351686],"response_type":"sensitive","indication":"melanoma","therapy_id":970,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"XL888","efficacy_evidence":"In a preclinical study, treatment with XL888 resulted in increased apoptosis and decreased growth of Zelboraf (vemurafenib)-resistant melanoma cells harboring BRAF V600E along with NRAS Q61K in cell culture (%%PUBMED:22351686%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NRAS Q61K","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[37729428],"response_type":"sensitive","indication":"melanoma","therapy_id":16209,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + Talazoparib + Trametinib","efficacy_evidence":"In a preclinical study, treatment with the combination of Talzenna (talazoparib), Tafinlar (dabrafenib), and Mekinist (trametinib) inhibited tumor growth and improved survival compared to controls in a melanoma patient-derived xenograft (PDX) model harboring BRAF V600E and NRAS Q61K (%%PUBMED:37729428%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NRAS Q61K","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[37729428],"normalized_drug":"Talazoparib","indication":"melanoma","therapy_id":682,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Talazoparib","efficacy_evidence":"In a preclinical study, Talzenna (talazoparib) treatment inhibited tumor growth and led to improved survival compared to controls in a melanoma patient-derived xenograft (PDX) model harboring BRAF V600E and NRAS Q61K (%%PUBMED:37729428%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NRAS Q61K","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"pub_med_references":[38691346],"response_type":"predicted - sensitive","indication":"lung non-small cell carcinoma","therapy_id":13602,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"PF-07799933","efficacy_evidence":"In a preclinical study, PF-07799933 inhibited Erk phosphorylation in melanoma cells harboring BRAF V600E and NRAS Q61K in culture (%%PUBMED:38691346%%).","cap_asco_evidence_level":"NA","molecular_profile":"BRAF V600E NRAS Q61K","approval_status":"Preclinical - Biochemical","amp_tier":"NA"},{"response_type":"predicted - 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culture (%%PUBMED:36622773%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NRAS Q61K","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[28951457],"response_type":"predicted - resistant","indication":"colorectal cancer","therapy_id":1717,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Panitumumab + Vemurafenib","efficacy_evidence":"In a clinical case study, a patient with BRAF V600E colorectal cancer developed progressive disease after a partial response lasting 40 weeks to Vectibix (panitumumab) and Zelboraf (vemurafenib) combination treatment, NRAS Q61K was identified as an acquired mutation at the time of progression (%%PUBMED:28951457%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NRAS Q61K","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[36622773],"response_type":"predicted - 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(%%PUBMED:37729428%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NRAS Q61K","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[22389471],"normalized_drug":"Dabrafenib, Trametinib","indication":"melanoma","therapy_id":1066,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a preclinical study, Talfinlar (dabrafenib) in combination with Mekinist (trametinib) resulted in improved growth inhibition of melanoma cell lines harboring BRAF V600E and NRAS Q61K in culture, compared to either agent alone (%%PUBMED:22389471%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NRAS Q61K","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[34330842],"response_type":"sensitive","indication":"melanoma","therapy_id":6971,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"ASTX029","efficacy_evidence":"In a preclinical study, ASTX029 treatment reduced Erk and Rsk phosphorylation and inhibited growth of a melanoma cell line harboring BRAF V600E and expressing NRAS Q61K in culture (%%PUBMED:34330842%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NRAS Q61K","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[37729428],"response_type":"sensitive","indication":"melanoma","therapy_id":16206,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Encorafenib + Olaparib","efficacy_evidence":"In a preclinical study, treatment with the combination of Lynparza (olaparib) and Braftovi (encorafenib) synergistically inhibited viability of patient-derived melanoma spheroids harboring BRAF V600E and NRAS Q61K in culture (%%PUBMED:37729428%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NRAS Q61K","approval_status":"Preclinical - Patient cell 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V600E demonstrated decreased response to TAK-632-induced inhibition of Erk phosphorylation and colony formation compared to cells expressing BRAF V600E in culture (%%PUBMED:29880583%%).","cap_asco_evidence_level":"NA","molecular_profile":"BRAF L514V BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"NA"},{"pub_med_references":[29880583],"response_type":"predicted - sensitive","indication":"melanoma","therapy_id":7465,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"BGB3245","efficacy_evidence":"In a preclinical study, BGB3245 resulted in similar inhibition of Erk phosphorylation and colony formation in melanoma cells expressing BRAF L514V in cis with V600E and cells expressing BRAF V600E alone in culture (%%PUBMED:29880583%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF L514V BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"decreased 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cells expressing BRAF V600E alone in culture (%%PUBMED:29880583%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF L514V BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"decreased response","pub_med_references":[29880583],"normalized_drug":"Trametinib","indication":"melanoma","therapy_id":2,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Trametinib","efficacy_evidence":"In a preclinical study, melanoma cells expressing BRAF L514V in cis with V600E demonstrated decreased response to Mekinist (trametinib)-induced inhibition of Erk phosphorylation and colony formation compared to cells expressing BRAF V600E in culture (%%PUBMED:29880583%%).","cap_asco_evidence_level":"NA","molecular_profile":"BRAF L514V BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"NA"},{"response_type":"decreased 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inhibited viability of a melanoma cell line harboring BRAF V600E and expressing MAP2K1 K57T in culture (%%PUBMED:36442478%%).","therapy":"Dabrafenib + Trametinib","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Preclinical - Cell culture","normalized_drug":"Dabrafenib, Trametinib","pub_med_references":[36442478],"molecular_profile":"BRAF V600E MAP2K1 K57T","profile_array":[{"type":"M1","gene":"V600E"}],"response_type":"sensitive"},{"therapy_id":342,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a preclinical study, a melanoma cell line harboring BRAF V600E and expressing MAP2K1 K57T was resistant to Zelboraf (vemurafenib) in culture (%%PUBMED:36442478%%).","therapy":"Vemurafenib","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Preclinical - Cell culture","normalized_drug":"Vemurafenib","pub_med_references":[36442478],"molecular_profile":"BRAF V600E MAP2K1 K57T","profile_array":[{"type":"M1","gene":"V600E"}],"response_type":"resistant"},{"therapy_id":796,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a preclinical study, a melanoma cell line harboring BRAF V600E and expressing MAP2K1 K57T was resistant to Braftovi (encorafenib) in culture (%%PUBMED:36442478%%).","therapy":"Encorafenib","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Preclinical - Cell culture","normalized_drug":"Encorafenib","pub_med_references":[36442478],"molecular_profile":"BRAF V600E MAP2K1 K57T","profile_array":[{"type":"M1","gene":"V600E"}],"response_type":"resistant"},{"therapy_id":1100,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a preclinical study, the combination of Braftovi (encorafenib) and Mektovi (binimetinib) synergistically inhibited viability of a melanoma cell line harboring BRAF V600E and expressing MAP2K1 K57T in culture (%%PUBMED:36442478%%).","therapy":"Binimetinib + Encorafenib","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Preclinical - Cell culture","normalized_drug":"Binimetinib, Encorafenib","pub_med_references":[36442478],"molecular_profile":"BRAF V600E MAP2K1 K57T","profile_array":[{"type":"M1","gene":"V600E"}],"response_type":"sensitive"},{"therapy_id":3,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a preclinical study, a melanoma cell line harboring BRAF V600E and expressing MAP2K1 K57T was resistant to Tafinlar (dabrafenib) in culture (%%PUBMED:36442478%%).","therapy":"Dabrafenib","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Preclinical - Cell culture","normalized_drug":"Dabrafenib","pub_med_references":[36442478],"molecular_profile":"BRAF V600E MAP2K1 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MAP2K1 K57T, demonstrated a sustained response greater than 12 months to combined Zelboraf (vemurafenib) and Cotellic (cobimetinib) treatment (%%PUBMED:30341394%%).","therapy":"Cobimetinib + Vemurafenib","evidence_type":"Actionable","normalized_cancer":"Hairy Cell Leukemia","indication":"refractory hairy cell leukemia","approval_status":"Case Reports/Case Series","normalized_drug":"Cobimetinib, Vemurafenib","pub_med_references":[30341394],"molecular_profile":"BRAF V600E MAP2K1 K57T","profile_array":[{"type":"M1","gene":"V600E"}],"response_type":"predicted - sensitive"},{"pub_med_references":[36921494],"response_type":"predicted - resistant","profile_array":[{"type":"M1","gene":"V600E"}],"indication":"colorectal cancer","therapy_id":15623,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Fluorouracil + Leucovorin + Vemurafenib","efficacy_evidence":"In a Phase II trial (MODUL), a patient with metastatic colorectal cancer harboring BRAF V600E was found to have acquired MAP2K1 K57T prior to progression on treatment with the combination of Zelboraf (vemurafenib), Erbitux (cetuximab), Adrucil (fluorouracil), and Wellcovorin (leucovorin) (%%PUBMED:36921494%%; NCT02291289).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E MAP2K1 K57T","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"therapy_id":660,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a retrospective analysis, BRAF V600E was identified at the time of progression on Tagrisso (osimertinib) treatment in a non-small cell lung cancer patient harboring an EGFR exon 19 deletion mutation (%%PUBMED:37806383%%).","therapy":"Osimertinib","evidence_type":"Actionable","normalized_cancer":"Non-Small Cell Lung Cancer","indication":"lung non-small cell carcinoma","approval_status":"Case Reports/Case Series","normalized_drug":"Osimertinib","pub_med_references":[37806383],"molecular_profile":"BRAF V600E EGFR exon 19 del","profile_array":[{"type":"exon del","number":19,"gene":"EGFR"}],"response_type":"predicted - resistant"},{"therapy_id":660,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a clinical study, a patient with non-small cell lung cancer harboring EGFR T790M and an EGFR exon 19 deletion developed progressive disease on treatment with Tagrisso (osimertinib) and was found to have acquired BRAF V600E and lost EGFR T790M in the post-progression liquid and tissue biopsies (%%PUBMED:39317868%%).","therapy":"Osimertinib","evidence_type":"Actionable","normalized_cancer":"Non-Small Cell Lung Cancer","indication":"lung non-small cell carcinoma","approval_status":"Case Reports/Case Series","normalized_drug":"Osimertinib","pub_med_references":[39317868],"molecular_profile":"BRAF V600E EGFR exon 19 del","profile_array":[{"type":"exon del","number":19,"gene":"EGFR"}],"response_type":"predicted - resistant"},{"therapy_id":660,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a clinical case study, a non-small cell lung cancer patient harboring an EGFR exon 19 deletion progressed on treatment with Tagrisso (osimertinib) and was found to have acquired BRAF V600E (%%PUBMED:35952324%%).","therapy":"Osimertinib","evidence_type":"Actionable","normalized_cancer":"Non-Small Cell Lung Cancer","indication":"lung non-small cell carcinoma","approval_status":"Case Reports/Case Series","normalized_drug":"Osimertinib","pub_med_references":[35952324],"molecular_profile":"BRAF V600E EGFR exon 19 del","profile_array":[{"type":"exon del","number":19,"gene":"EGFR"}],"response_type":"predicted - resistant"},{"pub_med_references":[39507030],"response_type":"sensitive","profile_array":[{"type":"exon del","number":19,"gene":"EGFR"}],"indication":"lung non-small cell carcinoma","therapy_id":12100,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Osimertinib + Trametinib","efficacy_evidence":"In a retrospective analysis, treatment with the combination of Tafinlar (dabrafenib), Mekinist (trametinib), and Tagrisso (Osimertinib) resulted in an objective response rate of 61.5% (8/13, all partial responses) and disease control rate of 92.3% (12/13) in non-small cell lung cancer patients harboring EGFR L858R (n=4) or an exon 19 deletion (n=9) and acquired BRAF V600E (%%PUBMED:39507030%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E EGFR exon 19 del","approval_status":"Clinical Study","amp_tier":"II"},{"therapy_id":660,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a clinical case study, Tagrisso (osimertinib) treatment resulted in stable disease with treatment ongoing for at least 12 months in a patient with lung adenocarcinoma harboring BRAF V600E and an EGFR Exon 19 deletion (%%PUBMED:38529368%%).","therapy":"Osimertinib","evidence_type":"Actionable","normalized_cancer":"Lung Adenocarcinoma","indication":"lung adenocarcinoma","approval_status":"Case Reports/Case Series","normalized_drug":"Osimertinib","pub_med_references":[38529368],"molecular_profile":"BRAF V600E EGFR exon 19 del","profile_array":[{"type":"exon del","number":19,"gene":"EGFR"}],"response_type":"predicted - sensitive"},{"therapy_id":1309,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a Phase I trial, a lung adenocarcinoma patient harboring an EGFR exon 19 deletion and EGFR T790M demonstrated a partial response to treatment with Nazartinib (CO-1686), but developed progression in the liver after 11 months, and a post-progression biopsy identified the EGFR exon 19 deletion without EGFR T790M, and emergence of BRAF V600E (%%PUBMED:30123863%%; NCT02108964).","therapy":"Nazartinib","evidence_type":"Actionable","normalized_cancer":"Lung Adenocarcinoma","indication":"lung adenocarcinoma","approval_status":"Case Reports/Case Series","normalized_drug":"Nazartinib","pub_med_references":[30123863],"molecular_profile":"BRAF V600E EGFR exon 19 del","profile_array":[{"type":"exon del","number":19,"gene":"EGFR"}],"response_type":"predicted - resistant"},{"response_type":"predicted - sensitive","pub_med_references":[30181415],"normalized_drug":"Dabrafenib, Trametinib","indication":"colon neuroendocrine neoplasm","therapy_id":1066,"normalized_cancer":"Gastrointestinal Neuroendocrine Tumors","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, combination Tafinlar (dabrafenib) and Mekinist (trametinib) therapy in a patient with Platinol (cisplatin)-resistant metastatic neuroendocrine carcinoma of the colon harboring BRAF V600E and TP53 H214R mutations and amplifications of FLT3 and CDK8 resulted in decreased disease burden with a clinical benefit for 5 months before disease progression (%%PUBMED:30181415%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E CDK8 amp FLT3 amp TP53 H214R","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - resistant","pub_med_references":[30181415],"normalized_drug":"Dabrafenib, Trametinib","indication":"colon neuroendocrine neoplasm","therapy_id":1066,"normalized_cancer":"Gastrointestinal Neuroendocrine Tumors","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, a patient with Platinol (cisplatin)-resistant metastatic neuroendocrine carcinoma of the colon harboring BRAF V600E and TP53 H214R mutations and amplifications of FLT3 and CDK8 who had an initial response to combination Tafinlar (dabrafenib) and Mekinist (trametinib) therapy was found to have acquired an ARID1B Q123* mutation upon disease progression (%%PUBMED:30181415%%).","cap_asco_evidence_level":"D","molecular_profile":"ARID1B Q123* BRAF V600E CDK8 amp FLT3 amp TP53 H214R","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[30867592],"normalized_drug":"Cobimetinib","indication":"lymphatic system cancer","therapy_id":1004,"normalized_cancer":"Lymphatic Cancer","evidence_type":"Actionable","therapy":"Cobimetinib","efficacy_evidence":"In a Phase II trial, treatment with Cotellic (cobimetinib) in patients with histiocytic neoplasms resulted in a PET overall response rate of 89% (16/18), with complete response in 72% (13/18) and partial response in 17% (3/18), and resulted in stable disease in 6% (1/18) of patients, including a complete response in a patient with Langerhans cell histiocytosis harboring BRAF V600E, KRAS G13C, and NRAS G12D (%%PUBMED:30867592%%; NCT01953926).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E KRAS G13C NRAS G12D","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[28951457],"response_type":"predicted - resistant","indication":"colorectal cancer","therapy_id":1917,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Alpelisib + Cetuximab + Encorafenib","efficacy_evidence":"In a clinical case study, a patient with BRAF V600E colorectal cancer developed progressive disease after a partial response lasting 24 weeks to Alpelisib (BYL719), Erbitux (cetuximab), and Braftovi (encorafenib) combination treatment, BRAF V47_D380del (reported as deletion of exons 2-8) was identified as an acquired mutation in peritoneal metastasis at the time of progression (%%PUBMED:28951457%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V47_D380del BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"resistant","pub_med_references":[29605720],"normalized_drug":"Vemurafenib","indication":"melanoma","therapy_id":342,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a preclinical study, expression of BRAF V47_D380del in a melanoma cell line harboring BRAF V600E conferred resistance to Zelboraf (vemurafenib) in culture (%%PUBMED:29605720%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V47_D380del BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - resistant","pub_med_references":[39282524],"normalized_drug":"Binimetinib, Encorafenib","indication":"melanoma","therapy_id":1100,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Binimetinib + Encorafenib","efficacy_evidence":"In a clinical case study, NRAS G13R with progressively increasing variant allele frequency was identified in the circulating tumor DNA of a patient with metastatic melanoma harboring BRAF V600E who progressed on treatment with the combination of Mektovi (binimetinib) and Braftovi (encorafenib) (%%PUBMED:39282524%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NRAS G13R","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[28951457],"response_type":"predicted - sensitive","indication":"colorectal cancer","therapy_id":8106,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"BGB659 + Cetuximab","efficacy_evidence":"In a preclinical study, BGB659 and Erbitux (cetuximab) combination treatment resulted in sustained inhibition of Mek and Erk phosphorylation, lead to tumor regression in patient-derived xenograft models of colorectal cancer harboring BRAF V600E and NRAS G13R (%%PUBMED:28951457%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NRAS G13R","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"pub_med_references":[28951457],"response_type":"predicted - resistant","indication":"colorectal cancer","therapy_id":1917,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Alpelisib + Cetuximab + Encorafenib","efficacy_evidence":"In a clinical case study, a patient with BRAF V600E colorectal cancer developed progressive disease after a partial response lasting 24 weeks to Alpelisib (BYL719), Erbitux (cetuximab), and Braftovi (encorafenib) combination treatment, NRAS G13R was identified as an acquired mutation in liver metastasis at the time of progression (%%PUBMED:28951457%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NRAS G13R","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[28951457],"response_type":"predicted - resistant","indication":"colorectal cancer","therapy_id":1917,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Alpelisib + Cetuximab + Encorafenib","efficacy_evidence":"In a clinical case study, a patient with BRAF V600E colorectal cancer developed progressive disease after a partial response lasting 18 weeks to Alpelisib (BYL719), Erbitux (cetuximab), and Braftovi (encorafenib) combination treatment, KRAS G12A was identified as an acquired mutation at the time of progression (%%PUBMED:28951457%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E KRAS G12A","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[28951457],"response_type":"predicted - resistant","profile_array":[{"type":"M1","gene":"amp"}],"indication":"colorectal cancer","therapy_id":1717,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Panitumumab + Vemurafenib","efficacy_evidence":"In a clinical case study, a patient with BRAF V600E colorectal cancer developed progressive disease after achieving stable disease for 32 weeks with Vectibix (panitumumab) and Zelboraf (vemurafenib) combination treatment, KRAS and MET amplification were identified as acquired alterations at the time of progression (%%PUBMED:28951457%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E KRAS amp MET amp","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[28951457],"response_type":"predicted - resistant","indication":"colorectal cancer","therapy_id":1717,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Panitumumab + Vemurafenib","efficacy_evidence":"In a clinical case study, a patient with BRAF V600E colorectal cancer developed progressive disease after achieving stable disease for 16 weeks with Vectibix (panitumumab) and Zelboraf (vemurafenib) combination treatment, NRAS amplification was identified as an acquired alteration at the time of progression (%%PUBMED:28951457%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NRAS amp","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[28951457],"response_type":"resistant","indication":"colorectal cancer","therapy_id":1711,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Vemurafenib","efficacy_evidence":"In a preclinical study, overexpression of wild-type KRAS in colorectal cancer cell lines harboring BRAF V600E induced Ras activation and Braf/Craf dimerization, conferred resistance to Erbitux (cetuximab) and Zelboraf (vemurafenib) combination treatment in culture and in cell line xenograft models (%%PUBMED:28951457%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E KRAS over exp","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[28951457],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":8106,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"BGB659 + Cetuximab","efficacy_evidence":"In a preclinical study, BGB659 and Erbitux (cetuximab) combination treatment demonstrated enhanced inhibition of Erk phosphorylation and growth in BRAF V600E colorectal cancer cell lines overexpressing Nras in culture (%%PUBMED:28951457%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NRAS over exp","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[28951457],"response_type":"resistant","indication":"colorectal cancer","therapy_id":1711,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Vemurafenib","efficacy_evidence":"In a preclinical study, overexpression of wild-type NRAS in colorectal cancer cell lines harboring BRAF V600E induced Ras activation and Braf/Craf dimerization, conferred resistance to Erbitux (cetuximab) and Zelboraf (vemurafenib) combination treatment in culture and in cell line xenograft models (%%PUBMED:28951457%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NRAS over exp","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[27325282],"response_type":"predicted - resistant","profile_array":[{"type":"M1","gene":"V600E"}],"indication":"rectum mucinous adenocarcinoma","therapy_id":1717,"normalized_cancer":"Mucinous Adenocarcinoma of the Colon and Rectum","evidence_type":"Actionable","therapy":"Panitumumab + Vemurafenib","efficacy_evidence":"In a clinical case study, a patient with microsatellite-stable mucinous rectal cancer harboring BRAF V600E eventually developed resistance to Vectibix (panitumumab) and Zelboraf (vemurafenib) combination therapy, potentially due to acquiring amplification of MET (%%PUBMED:27325282%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E MET amp","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[39313594],"response_type":"predicted - resistant","profile_array":[{"type":"M1","gene":"V600E"}],"indication":"colorectal cancer","therapy_id":4886,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Binimetinib + Cetuximab + Encorafenib","efficacy_evidence":"In a Phase III (BEACON CRC) trial, MET amplification was identified in end-of-treatment ctDNA samples in 19.6% (22/112) of patients with colorectal cancer harboring BRAF V600E following treatment with the combination of Braftovi (encorafenib), Mektovi (binimetinib), and Erbitux (cetuximab) (%%PUBMED:39313594%%; NCT02928224).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E MET amp","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[34994629],"response_type":"predicted - sensitive","profile_array":[{"type":"M1","gene":"V600E"}],"indication":"colon cancer","therapy_id":1338,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Capmatinib + Encorafenib","efficacy_evidence":"In a clinical case study, a patient with left-sided colon cancer harboring BRAF V600E and MET amplification (copy number 31), who had progressed on prior lines of therapy, experienced rapid clinical improvement and a partial metabolic and morphologic response following treatment with the combination of Tabrecta (capmatinib) and Braftovi (encorafenib), until progression after 14 weeks of treatment (%%PUBMED:34994629%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E MET amp","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"therapy_id":1916,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a clinical case study, MET amplification was identified in a patient with rectal adenocarcinoma harboring BRAF V600E after the disease progressed on Braftovi (encorafenib) and Erbitux (cetuximab) treatment (%%PUBMED:35820242%%).","therapy":"Cetuximab + Encorafenib","evidence_type":"Actionable","normalized_cancer":"Rectal Adenocarcinoma","indication":"rectum adenocarcinoma","approval_status":"Case Reports/Case Series","normalized_drug":"Cetuximab, Encorafenib","pub_med_references":[35820242],"molecular_profile":"BRAF V600E MET amp","profile_array":[{"type":"M1","gene":"V600E"}],"response_type":"predicted - resistant"},{"pub_med_references":[27325282],"response_type":"predicted - sensitive","profile_array":[{"type":"M1","gene":"V600E"}],"indication":"rectum mucinous adenocarcinoma","therapy_id":4648,"normalized_cancer":"Mucinous Adenocarcinoma of the Colon and Rectum","evidence_type":"Actionable","therapy":"Crizotinib + Vemurafenib","efficacy_evidence":"In a clinical case study, a patient with microsatellite-stable mucinous rectal cancer harboring BRAF V600E and acquired MET amplification responded to the combination treatment of Xalkori (crizotinib) and Zelboraf (vemurafenib), resulting in a rapid clinical and metabolic response (%%PUBMED:27325282%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E MET amp","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"therapy_id":1916,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a Phase III (BEACON CRC) trial, MET amplification was identified in end-of-treatment ctDNA samples in 17.0% (19/112) of patients with colorectal cancer harboring BRAF V600E following treatment with the combination of Braftovi (encorafenib) and Erbitux (cetuximab) (%%PUBMED:39313594%%; NCT02928224).","therapy":"Cetuximab + Encorafenib","evidence_type":"Actionable","normalized_cancer":"Colorectal Cancer","indication":"colorectal cancer","approval_status":"Case Reports/Case Series","normalized_drug":"Cetuximab, Encorafenib","pub_med_references":[39313594],"molecular_profile":"BRAF V600E MET amp","profile_array":[{"type":"M1","gene":"V600E"}],"response_type":"predicted - resistant"},{"pub_med_references":[35820242],"response_type":"predicted - sensitive","profile_array":[{"type":"M1","gene":"V600E"}],"indication":"rectum adenocarcinoma","therapy_id":4648,"normalized_cancer":"Rectal Adenocarcinoma","evidence_type":"Actionable","therapy":"Crizotinib + Vemurafenib","efficacy_evidence":"In a clinical case study, Zelboraf (vemurafenib) and Xalkori (crizotinib) combination treatment resulted in early radiologic tumor shrinkage in a patient with rectal adenocarcinoma harboring BRAF V600E and MET amplification, however, the tumor progressed after two months (%%PUBMED:35820242%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E MET amp","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[27325282],"response_type":"predicted - resistant","profile_array":[{"type":"M1","gene":"V600E"}],"indication":"colorectal cancer","therapy_id":1917,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Alpelisib + Cetuximab + Encorafenib","efficacy_evidence":"In a preclinical study, emergence of MET amplification was detected in colorectal cancer cells harboring BRAF V600E that acquired resistance to Alpelisib (BYL719), Erbitux (cetuximab), and Braftovi (encorafenib) combination treatment in culture (%%PUBMED:27325282%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E MET amp","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[27325282],"response_type":"predicted - sensitive","profile_array":[{"type":"M1","gene":"V600E"}],"indication":"colorectal cancer","therapy_id":4648,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Crizotinib + Vemurafenib","efficacy_evidence":"In a preclinical study, Xalkori (crizotinib) and Zelboraf (vemurafenib) combination treatment inhibited growth of colorectal cancer cells harboring BRAF V600E and overexpressing Met in culture (%%PUBMED:27325282%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E MET over exp","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[39626159],"response_type":"sensitive","profile_array":[{"type":"M1","gene":"V600E"}],"indication":"colon cancer","therapy_id":17952,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Crizotinib + Erlotinib + Vemurafenib","efficacy_evidence":"In a preclinical study, the addition of Xalkori (crizotinib) to treatment with the combination of Tarceva (erlotinib) and Zelboraf (vemurafenib) inhibited viability in mouse colon cancer organoids harboring BRAF V600E with overexpression of MET in culture (%%PUBMED:39626159%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E MET over exp","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[27325282],"response_type":"resistant","profile_array":[{"type":"M1","gene":"V600E"}],"indication":"colorectal cancer","therapy_id":1717,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Panitumumab + Vemurafenib","efficacy_evidence":"In a preclinical study, overexpressing Met in colorectal cancer cells harboring BRAF V600E conferred resistance to Vectibix (panitumumab) and Zelboraf (vemurafenib) combination treatment in culture (%%PUBMED:27325282%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E MET over exp","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[39626159],"response_type":"resistant","profile_array":[{"type":"M1","gene":"V600E"}],"indication":"colon cancer","therapy_id":1710,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Erlotinib + Vemurafenib","efficacy_evidence":"In a preclinical study, colon cancer organoids harboring BRAF V600E and overexpressing MET were resistant to treatment with the combination of Zelboraf (vemurafenib) and Tarceva (erlotinib) in culture (%%PUBMED:39626159%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E MET over exp","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"lung non-small cell carcinoma","therapy_id":8472,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Osimertinib","efficacy_evidence":"In a clinical case study, a patient with advanced non-small cell lung cancer who lost EGFR T790M, but still harbors EGFR E746_A750del and acquired BRAF V600E demonstrated an improved metabolic response when treated with the combination therapy of Tafinlar (dabrafenib) and Tagrisso (osimertinib) (Journal of Clinical Oncology, 2019, 37, no. 15_suppl).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E EGFR E746_A750del","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - resistant","normalized_drug":"Dabrafenib, Trametinib","indication":"lung non-small cell carcinoma","therapy_id":1066,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, a patient with advanced non-small cell lung cancer who lost EGFR T790M, but still harbors EGFR E746_A750del and acquired BRAF V600E demonstrated continued progression while being treated with the combination therapy of Tafinlar (dabrafenib) and Mekinist (trametinib) (Journal of Clinical Oncology, 2019, 37, no. 15_suppl).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E EGFR E746_A750del","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[39555453],"response_type":"predicted - resistant","indication":"lung adenocarcinoma","therapy_id":6979,"normalized_cancer":"Lung Adenocarcinoma","evidence_type":"Actionable","therapy":"Furmonertinib","efficacy_evidence":"In a clinical case study, a lung adenocarcinoma patient harboring EGFR E746_A750del progressed on treatment with Furmonertinib (alflutinib) and was found to have acquired BRAF V600E (%%PUBMED:39555453%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E EGFR E746_A750del","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[40082212],"response_type":"predicted - sensitive","indication":"lung adenocarcinoma","therapy_id":12100,"normalized_cancer":"Lung Adenocarcinoma","evidence_type":"Actionable","therapy":"Dabrafenib + Osimertinib + Trametinib","efficacy_evidence":"In a clinical case study, treatment with the combination of Tagrisso (osimertinib), Mekinist (trametinib), and Tafinlar (dabrafenib) resulted in a partial response with a total reduction in the target lesion diameters of 30.9% and a progression-free survival ongoing at 13 months in a patient with metastatic lung adenocarcinoma harboring EGFR E746_A750del and BRAF V600E (%%PUBMED:40082212%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E EGFR E746_A750del","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[37533438],"response_type":"predicted - sensitive","indication":"lung adenocarcinoma","therapy_id":12100,"normalized_cancer":"Lung Adenocarcinoma","evidence_type":"Actionable","therapy":"Dabrafenib + Osimertinib + Trametinib","efficacy_evidence":"In a clinical case study, the combination of Tagrisso (osimertinib), Mekinist (trametinib), and Tafinlar (dabrafenib) resulted in disease control lasting 8 months, with complete response in the brain, in a patient with metastatic lung adenocarcinoma and leptomeningeal metastasis harboring BRAF V600E and EGFR E746_A750del (%%PUBMED:37533438%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E EGFR E746_A750del","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[39555453],"normalized_drug":"Dabrafenib, Trametinib","indication":"lung adenocarcinoma","therapy_id":1066,"normalized_cancer":"Lung Adenocarcinoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, treatment with the combination of Mekinist (trametinib) and Tafinlar (dabrafenib) resulted in a partial remission and improvement in the pleural effusion and liver metastasis in a lung adenocarcinoma patient harboring EGFR E746_A750del and BRAF V600E (%%PUBMED:39555453%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E EGFR E746_A750del","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - resistant","pub_med_references":[36849494],"normalized_drug":"Osimertinib","indication":"lung non-small cell carcinoma","therapy_id":660,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Osimertinib","efficacy_evidence":"In a Phase III trial (FLAURA), BRAF V600E was identified at the time of progression on Tagrisso (osimertinib) in a patient with non-small cell lung cancer harboring EGFR E746_A750del (%%PUBMED:36849494%%; NCT02296125).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E EGFR E746_A750del","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[31217909],"response_type":"predicted - sensitive","indication":"glioblastoma","therapy_id":4129,"normalized_cancer":"Glioblastoma, IDH-Wildtype","evidence_type":"Actionable","therapy":"Palbociclib + Vemurafenib","efficacy_evidence":"In a clinical case study, Ibrance (palbociclib) in combination with Zelboraf (vemurafenib) resulted in clinical improvement and stable disease in a patient with epithelioid glioblastoma harboring BRAF V600E and homozygous deletion of CDKN2A and CDKN2B, however, his disease progressed after 10 weeks on treatment (%%PUBMED:31217909%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E CDKN2A del CDKN2B del","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[31085763],"normalized_drug":"Cabozantinib","indication":"papillary thyroid carcinoma","therapy_id":998,"normalized_cancer":"Papillary Thyroid Cancer","evidence_type":"Actionable","therapy":"Cabozantinib","efficacy_evidence":"In a clinical case study, a papillary thyroid carcinoma patient with BRAF V600E who progressed on the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) was found to have an acquired KRAS G12V mutation, and was subsequently treated with Cometriq (Cabometyx, cabozantinib), resulting in a partial response with target lesion reduction of 45% (%%PUBMED:31085763%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E KRAS G12V","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - resistant","pub_med_references":[31085763],"normalized_drug":"Dabrafenib, Trametinib","indication":"papillary thyroid carcinoma","therapy_id":1066,"normalized_cancer":"Papillary Thyroid Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, a papillary thyroid carcinoma patient with BRAF V600E who progressed on the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) was found to have an acquired KRAS G12V mutation (%%PUBMED:31085763%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E KRAS G12V","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - resistant","pub_med_references":[31406350],"normalized_drug":"Dabrafenib, Trametinib","indication":"pancreatic cancer","therapy_id":1066,"normalized_cancer":"Pancreatic Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, a patient with pancreatic cancer harboring CTRC-NTRK1 and BRAF V600E treated with a combination of Tafinlar (dabrafenib) and Mekinist (trametinib) demonstrated tumor regression, but later showed radiographical progression and was found to have acquired KRAS G12D (%%PUBMED:31406350%%).","cap_asco_evidence_level":"D","molecular_profile":"CTRC - NTRK1 BRAF V600E KRAS G12D","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - resistant","pub_med_references":[31406350],"normalized_drug":"Larotrectinib","indication":"pancreatic cancer","therapy_id":2650,"normalized_cancer":"Pancreatic Cancer","evidence_type":"Actionable","therapy":"Larotrectinib","efficacy_evidence":"In a clinical case study, a patient with pancreatic cancer harboring CTRC-NTRK1 progressed on Vitrakvi (larotrectinib) treatment, showing acquisition of BRAF V600E via biopsy testing and BRAF V600E and KRAS G12D via cell-free DNA testing (%%PUBMED:31406350%%).","cap_asco_evidence_level":"D","molecular_profile":"CTRC - NTRK1 BRAF V600E KRAS G12D","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - resistant","pub_med_references":[31406350],"normalized_drug":"Selitrectinib","indication":"pancreatic cancer","therapy_id":5917,"normalized_cancer":"Pancreatic Cancer","evidence_type":"Actionable","therapy":"Selitrectinib","efficacy_evidence":"In a clinical case study, a patient with pancreatic cancer harboring CTRC-NTRK1, BRAF V600E, and KRAS G12D demonstrated resistance to treatment with Selitrectinib (LOXO-195) (%%PUBMED:31406350%%).","cap_asco_evidence_level":"D","molecular_profile":"CTRC - NTRK1 BRAF V600E KRAS G12D","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[31406350],"response_type":"predicted - sensitive","indication":"pancreatic cancer","therapy_id":8908,"normalized_cancer":"Pancreatic Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Larotrectinib + Trametinib","efficacy_evidence":"In a preclinical study, a patient-derived xenograft (PDX) model with pancreatic cancer harboring CTRC-NTRK1, BRAF V600E, and KRAS G12D demonstrated greater tumor growth inhibition when treated with a combination of Tafinlar (dabrafenib), Mekinist (trametinib), and Vitrakvi (larotrectinib) versus a combination of Tafinlar (dabrafenib) and Mekinst (trametinib) only (%%PUBMED:31406350%%).","cap_asco_evidence_level":"D","molecular_profile":"CTRC - NTRK1 BRAF V600E KRAS G12D","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"response_type":"resistant","pub_med_references":[31406350],"normalized_drug":"Selitrectinib","indication":"pancreatic cancer","therapy_id":5917,"normalized_cancer":"Pancreatic Cancer","evidence_type":"Actionable","therapy":"Selitrectinib","efficacy_evidence":"In a preclinical study, a pancreatic cancer cell line harboring TPR-NTRK1 and NTRK1 G595R, and expressing BRAF V600E demonstrated resistance to treatment with Selitrectinib (LOXO-195) in culture (%%PUBMED:31406350%%).","cap_asco_evidence_level":"D","molecular_profile":"TPR - NTRK1 NTRK1 G595R BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[31406350],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":8909,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Selitrectinib + Trametinib","efficacy_evidence":"In a preclinical study, the combination therapy of Tafinlar (dabrafenib), Mekinist (trametinib), and Selitrectinib (LOXO-195) in a colorectal cancer cell line harboring LMNA-NTRK1 and NTRK1 G595R and expressing BRAF V600E demonstrated tumor growth suppression and inhibition of Akt, Erk, and Mek signaling in culture (%%PUBMED:31406350%%).","cap_asco_evidence_level":"D","molecular_profile":"LMNA - NTRK1 NTRK1 G595R BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - resistant","pub_med_references":[31605106],"normalized_drug":"Dabrafenib, Trametinib","indication":"pancreatic ductal adenocarcinoma","therapy_id":1066,"normalized_cancer":"Pancreatic Adenocarcinoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, a pancreatic ductal adenocarcinoma patient harboring CTRC-NTRK1 and BRAF V600E demonstrated progression when treated with the combination therapy of Tafinlar (dabrafenib) and Mekinist (trametinib) (%%PUBMED:31605106%%).","cap_asco_evidence_level":"D","molecular_profile":"CTRC - NTRK1 BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - resistant","pub_med_references":[31605106],"normalized_drug":"Larotrectinib","indication":"pancreatic ductal adenocarcinoma","therapy_id":2650,"normalized_cancer":"Pancreatic Adenocarcinoma","evidence_type":"Actionable","therapy":"Larotrectinib","efficacy_evidence":"In a clinical case study, a pancreatic ductal adenocarcinoma patient harboring CTRC-NTRK1 initially responded to Vitrakvi (larotrectinib), but then progressed after 6 months, and was subsequently found to have acquired BRAF V600E (%%PUBMED:31605106%%).","cap_asco_evidence_level":"D","molecular_profile":"CTRC - NTRK1 BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[31406350],"response_type":"predicted - sensitive","indication":"pancreatic cancer","therapy_id":8918,"normalized_cancer":"Pancreatic Cancer","evidence_type":"Actionable","therapy":"Larotrectinib + Trametinib","efficacy_evidence":"In a preclinical study, the combination therapy of Vitrakvi (larotrectinib) and Mekinist (trametinib) resulted in delayed tumor growth in a Vitrakvi (larotrectinib)-resistant patient-derived xenograft (PDX) model with pancreatic cancer harboring CTRC-NTRK1 and BRAF V600E, but led to controlled tumor growth for 1 month and tumor regression at 3 months in the PDX model with only CTRC-NTRK1, which subsequently revealed a low variant allele frequency for BRAF V600E (%%PUBMED:31406350%%).","cap_asco_evidence_level":"D","molecular_profile":"CTRC - NTRK1 BRAF V600E","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"response_type":"predicted - resistant","pub_med_references":[31605106],"normalized_drug":"Selitrectinib","indication":"pancreatic ductal adenocarcinoma","therapy_id":5917,"normalized_cancer":"Pancreatic Adenocarcinoma","evidence_type":"Actionable","therapy":"Selitrectinib","efficacy_evidence":"In a clinical case study, a pancreatic ductal adenocarcinoma patient harboring CTRC-NTRK1 and BRAF V600E progressed when treated with Selitrectinib (LOXO-195) (%%PUBMED:31605106%%).","cap_asco_evidence_level":"D","molecular_profile":"CTRC - NTRK1 BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"therapy_id":1312,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a clinical case study, a patient with melanoma harboring BRAF V600E developed progressive disease after 12 weeks of Tafinlar (dabrafenib) and Mekinist (trametinib) combination treatment, and progressed again after 106 weeks on anti-PD1 therapy including Opdivo (nivolumab) (90 weeks) followed by Keytruda (pembrolizumab), B2M V5Lfs*30, LRP1B W1344*, MAP2K2 F133L, NF2 Y66*, and TP53 C238F were identified in the post-progression biopsy in addition to BRAF V600E (%%PUBMED:31082388%%).","therapy":"Nivolumab","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Case Reports/Case Series","normalized_drug":"Nivolumab","pub_med_references":[31082388],"molecular_profile":"B2M V5Lfs*30 BRAF V600E LRP1B W1344* MAP2K2 F133L NF2 Y66* TP53 C238F","profile_array":[{"type":"M1","gene":"W1344*"}],"response_type":"predicted - resistant"},{"therapy_id":1066,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a clinical case study, a patient with melanoma harboring BRAF V600E developed progressive disease after 12 weeks of Tafinlar (dabrafenib) and Mekinist (trametinib) combination treatment, and progressed again after 106 weeks on anti-PD1 therapy including Opdivo (nivolumab) (90 weeks) followed by Keytruda (pembrolizumab), B2M V5Lfs*30, LRP1B W1344*, MAP2K2 F133L, NF2 Y66*, and TP53 C238F were identified in the post-progression biopsy in addition to BRAF V600E (%%PUBMED:31082388%%).","therapy":"Dabrafenib + Trametinib","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Case Reports/Case Series","normalized_drug":"Dabrafenib, Trametinib","pub_med_references":[31082388],"molecular_profile":"B2M V5Lfs*30 BRAF V600E LRP1B W1344* MAP2K2 F133L NF2 Y66* TP53 C238F","profile_array":[{"type":"M1","gene":"W1344*"}],"response_type":"predicted - resistant"},{"therapy_id":1447,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a clinical case study, a patient with melanoma harboring BRAF V600E developed progressive disease after 12 weeks of Tafinlar (dabrafenib) and Mekinist (trametinib) combination treatment, and progressed again after 106 weeks on anti-PD1 therapy including Opdivo (nivolumab) (90 weeks) followed by Keytruda (pembrolizumab), B2M V5Lfs*30, LRP1B W1344*, MAP2K2 F133L, NF2 Y66*, and TP53 C238F were identified in the post-progression biopsy in addition to BRAF V600E (%%PUBMED:31082388%%).","therapy":"Pembrolizumab","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Case Reports/Case Series","normalized_drug":"Pembrolizumab","pub_med_references":[31082388],"molecular_profile":"B2M V5Lfs*30 BRAF V600E LRP1B W1344* MAP2K2 F133L NF2 Y66* TP53 C238F","profile_array":[{"type":"M1","gene":"W1344*"}],"response_type":"predicted - resistant"},{"response_type":"predicted - sensitive","pub_med_references":[32007138],"normalized_drug":"Dabrafenib, Trametinib","indication":"melanoma","therapy_id":1066,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a Phase III (COMBI-AD) trial, Tafinlar (dabrafenib) and Mekinist (trametinib) combination therapy compared to placebo resulted in more benefit (HR=0.49, p<0.0001) in TMB low patients with resected melanoma harboring BRAF V600E or V600K, than in TMB high (HR=0.75, p=0.27) patients, however, TMB was not associated with relapse-free survival in the combination treatment group (%%PUBMED:32007138%%; NCT01682083).","cap_asco_evidence_level":"B","molecular_profile":"BRAF V600E TMB low","approval_status":"Phase III","amp_tier":"I"},{"response_type":"resistant","pub_med_references":[30143629],"normalized_drug":"Dabrafenib, Trametinib","indication":"melanoma","therapy_id":1066,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a preclinical study, decreased Sirt6 expression through siRNA knockdown resulted in activation of IGF-1R/AKT pathway, conferred resistance to Tafinlar (dabrafenib) and Mekinist (trametinib) combination treatment in melanoma cell lines and patient-derived melanoma cells harboring BRAF V600E in culture (%%PUBMED:30143629%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E SIRT6 dec exp","approval_status":"Preclinical - Patient cell culture","amp_tier":"II"},{"response_type":"resistant","pub_med_references":[30143629],"normalized_drug":"Vemurafenib","indication":"melanoma","therapy_id":342,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a preclinical study, decreased Sirt6 expression was identified in cells derived from patients with melanoma harboring BRAF V600E at times of disease progression while on Zelboraf (vemurafenib), and melanoma cell lines harboring BRAF V600E and with decreased Sirt6 expression through siRNA knockdown were resistance to Zelboraf (vemurafenib) in cell line xenograft models (%%PUBMED:30143629%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E SIRT6 dec exp","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"resistant","pub_med_references":[30143629],"normalized_drug":"Dabrafenib","indication":"melanoma","therapy_id":3,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a preclinical study, decreased Sirt6 expression through siRNA knockdown resulted in activation of IGF-1R/AKT pathway, conferred resistance to Tafinlar (dabrafenib) in melanoma cell lines and patient-derived melanoma cells harboring BRAF V600E in culture (%%PUBMED:30143629%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E SIRT6 dec exp","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[30143629],"response_type":"sensitive","indication":"melanoma","therapy_id":9382,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + Linsitinib","efficacy_evidence":"In a preclinical study, combination of Tafinlar (dabrafenib) and Linsitinib (OSI-906) enhanced inhibition of Igf1r and Akt phosphorylation, led to apoptosis and reduced proliferation in BRAF V600E melanoma cells with decreased Sirt6 expression via siRNA knockdown in culture, and tumor regression in cell line xenograft models (%%PUBMED:30143629%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E SIRT6 dec exp","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"resistant","pub_med_references":[29605720],"normalized_drug":"Vemurafenib","indication":"melanoma","therapy_id":342,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a preclinical study, a melanoma cell line harboring BRAF V600E was found to have BRAF V47_D380del and BCORL1 Q1076H mutations after acquiring resistance to Zelboraf (vemurafenib), and expression of BRAF V47_D380del and BCORL1 Q1076H in a BRAF V600E-positive melanoma cell line resulted in decreased sensitivity to Zelboraf (vemurafenib) in culture (%%PUBMED:29605720%%).","cap_asco_evidence_level":"D","molecular_profile":"BCORL1 Q1076H BRAF V47_D380del BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"decreased response","pub_med_references":[29605720],"normalized_drug":"Vemurafenib","indication":"melanoma","therapy_id":342,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a preclinical study, expression of BCORL1 Q1076H resulted in decreased sensitivity to Zelboraf (vemurafenib) in a melanoma cell line harboring BRAF V600E in culture (%%PUBMED:29605720%%).","cap_asco_evidence_level":"NA","molecular_profile":"BCORL1 Q1076H BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"NA"},{"response_type":"predicted - 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demonstrated decreased sensitivity to treatment with Cotellic (cobimetinib) and Zelboraf (vemurafenib) compared to cells with wild-type PTEN in culture (%%PUBMED:38854737%%).","cap_asco_evidence_level":"NA","molecular_profile":"BRAF V600E PTEN del","approval_status":"Preclinical - Cell culture","amp_tier":"NA"},{"pub_med_references":[38854737],"response_type":"sensitive","indication":"melanoma","therapy_id":17240,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + Neratinib + Trametinib","efficacy_evidence":"In a preclinical study, the addition of Nerlynx (neratinib) restored sensitivity to Tafinlar (dabrafenib) and Mekinist (trametinib) and led to synergistic inhibition of a melanoma cell line harboring BRAF V600E and engineered via CRISPR-Cas9 to harbor a PTEN knockout in culture (%%PUBMED:38854737%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E PTEN del","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"decreased response","pub_med_references":[38854737],"normalized_drug":"Dabrafenib, Trametinib","indication":"melanoma","therapy_id":1066,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a preclinical study, a melanoma cell line harboring BRAF V600E and engineered via CRISPR-Cas9 to harbor a PTEN knockout demonstrated decreased sensitivity to treatment with Tafinlar (dabrafenib) and Mekinist (trametinib) compared to cells with wild-type PTEN in culture (%%PUBMED:38854737%%).","cap_asco_evidence_level":"NA","molecular_profile":"BRAF V600E PTEN del","approval_status":"Preclinical - Cell culture","amp_tier":"NA"},{"response_type":"decreased response","pub_med_references":[38854737],"normalized_drug":"Binimetinib, Encorafenib","indication":"melanoma","therapy_id":1100,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Binimetinib + Encorafenib","efficacy_evidence":"In a preclinical study, a melanoma cell line harboring BRAF V600E and engineered via CRISPR-Cas9 to harbor a PTEN knockout demonstrated decreased sensitivity to treatment with Mektovi (binimetinib) and Braftovi (encorafenib) compared to cells with wild-type PTEN in culture (%%PUBMED:38854737%%).","cap_asco_evidence_level":"NA","molecular_profile":"BRAF V600E PTEN del","approval_status":"Preclinical - Cell culture","amp_tier":"NA"},{"response_type":"predicted - resistant","pub_med_references":[31980996],"normalized_drug":"Dabrafenib","indication":"melanoma","therapy_id":3,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a clinical case study, Tafinlar (dabrafenib) treatment in a metastatic melanoma patient harboring BRAF V600E and PTEN deletion resulted in disease progression after 2.8 months following an initial partial response (%%PUBMED:31980996%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E PTEN del","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[38854737],"response_type":"sensitive","indication":"melanoma","therapy_id":17242,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Afatinib + Dabrafenib + Trametinib","efficacy_evidence":"In a preclinical study, the addition of Gilotrif (afatinib) restored sensitivity to Tafinlar (dabrafenib) and Mekinist (trametinib) and led to synergistic inhibition of a melanoma cell line harboring BRAF V600E and engineered via CRISPR-Cas9 to harbor a PTEN knockout in culture (%%PUBMED:38854737%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E PTEN del","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"therapy_id":342,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a clinical case study, Zelboraf (vemurafenib) treatment in a metastatic melanoma patient harboring BRAF V600E, CDK4 R24C, and MYC amplification resulted in disease progression after 2.3 months following an initial partial response (%%PUBMED:31980996%%).","therapy":"Vemurafenib","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Case Reports/Case Series","normalized_drug":"Vemurafenib","pub_med_references":[31980996],"molecular_profile":"BRAF V600E CDK4 R24C MYC amp","profile_array":[{"type":"M1","gene":"R24C"}],"response_type":"predicted - resistant"},{"response_type":"predicted - resistant","pub_med_references":[31980996],"normalized_drug":"Vemurafenib","indication":"melanoma","therapy_id":342,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a clinical case study, Zelboraf (vemurafenib) treatment resulted in disease progression within two months in a metastatic melanoma patient harboring BRAF V600E, ATM deletion, and PAX5 deletion (%%PUBMED:31980996%%).","cap_asco_evidence_level":"D","molecular_profile":"ATM del BRAF V600E PAX5 del","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"therapy_id":342,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a clinical case study, Zelboraf (vemurafenib) treatment resulted in disease progression within two months in a metastatic melanoma patient harboring BRAF V600E and MAP2K2 W251* (%%PUBMED:31980996%%).","therapy":"Vemurafenib","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Case Reports/Case Series","normalized_drug":"Vemurafenib","pub_med_references":[31980996],"molecular_profile":"BRAF V600E MAP2K2 W251*","profile_array":[{"type":"M1","gene":"V600E"}],"response_type":"predicted - resistant"},{"therapy_id":3,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a clinical case study, Tafinlar (dabrafenib) treatment resulted in disease progression within 1.2 months in a metastatic melanoma patient harboring BRAF V600E, MITF G6R, and MYC T259I (%%PUBMED:31980996%%).","therapy":"Dabrafenib","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Case Reports/Case Series","normalized_drug":"Dabrafenib","pub_med_references":[31980996],"molecular_profile":"BRAF V600E MITF G6R MYC T259I","profile_array":[{"type":"M1","gene":"V600E"}],"response_type":"predicted - resistant"},{"response_type":"predicted - resistant","pub_med_references":[31980996],"normalized_drug":"Vemurafenib","indication":"melanoma","therapy_id":342,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a clinical case study, Zelboraf (vemurafenib) treatment resulted in disease progression within 2 months following an initial partial response in a metastatic melanoma patient harboring BRAF V600E, BRAF S602T, NF1 P1951S, and PAX5 deletion (%%PUBMED:31980996%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E BRAF S602T NF1 P1951S PAX5 del","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[31925410],"response_type":"resistant","profile_array":[{"type":"M1","gene":"V600E"}],"indication":"melanoma","therapy_id":4351,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"VX-11e","efficacy_evidence":"In a preclinical study, expression of MAPK1 L107E in melanoma cells harboring BRAF V600E conferred resistance to VX-11e treatment in culture (%%PUBMED:31925410%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E MAPK1 L107E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"therapy_id":699,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a preclinical study, expression of MAP2K1 I99T in melanoma cells harboring BRAF V600E conferred resistance to CI-1040 (PD184352) treatment in culture (%%PUBMED:19915144%%).","therapy":"CI-1040","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Preclinical - Cell culture","normalized_drug":"Ci-1040","pub_med_references":[19915144],"molecular_profile":"BRAF V600E MAP2K1 I99T","profile_array":[{"type":"M1","gene":"V600E"}],"response_type":"resistant"},{"therapy_id":2,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a preclinical study, melanoma cells harboring BRAF V600E and expressing MAP2K1 I99T demonstrated resistance to Mekinist (trametinib) treatment in culture (%%PUBMED:31925410%%).","therapy":"Trametinib","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Preclinical - Cell culture","normalized_drug":"Trametinib","pub_med_references":[31925410],"molecular_profile":"BRAF V600E MAP2K1 I99T","profile_array":[{"type":"M1","gene":"V600E"}],"response_type":"resistant"},{"therapy_id":913,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a preclinical study, expression of MAP2K1 I99T in melanoma cells harboring BRAF V600E conferred resistance to Koselugo (selumetinib) treatment in culture (%%PUBMED:19915144%%).","therapy":"Selumetinib","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Preclinical - Cell culture","normalized_drug":"Selumetinib","pub_med_references":[19915144],"molecular_profile":"BRAF V600E MAP2K1 I99T","profile_array":[{"type":"M1","gene":"V600E"}],"response_type":"resistant"},{"therapy_id":3,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a preclinical study, melanoma cells harboring BRAF V600E and expressing MAP2K1 I99T demonstrated resistance to Tafinlar (dabrafenib) treatment in culture (%%PUBMED:31925410%%).","therapy":"Dabrafenib","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Preclinical - Cell culture","normalized_drug":"Dabrafenib","pub_med_references":[31925410],"molecular_profile":"BRAF V600E MAP2K1 I99T","profile_array":[{"type":"M1","gene":"V600E"}],"response_type":"resistant"},{"therapy_id":3,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a preclinical study, melanoma cells harboring BRAF V600E and expressing MAP2K1 I99G demonstrated resistance to Tafinlar (dabrafenib) treatment in culture (%%PUBMED:31925410%%).","therapy":"Dabrafenib","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Preclinical - Cell culture","normalized_drug":"Dabrafenib","pub_med_references":[31925410],"molecular_profile":"BRAF V600E MAP2K1 I99G","profile_array":[{"type":"M1","gene":"V600E"}],"response_type":"resistant"},{"therapy_id":2,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a preclinical study, melanoma cells harboring BRAF V600E and expressing MAP2K1 I99G demonstrated resistance to Mekinist (trametinib) treatment in culture (%%PUBMED:31925410%%).","therapy":"Trametinib","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Preclinical - Cell culture","normalized_drug":"Trametinib","pub_med_references":[31925410],"molecular_profile":"BRAF V600E MAP2K1 I99G","profile_array":[{"type":"M1","gene":"V600E"}],"response_type":"resistant"},{"therapy_id":3,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a preclinical study, melanoma cells harboring BRAF V600E and expressing MAP2K1 I99M demonstrated sensitivity to Tafinlar (dabrafenib) treatment similar to cells expressing wild-type MAP2K1 in culture (%%PUBMED:31925410%%).","therapy":"Dabrafenib","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Preclinical - Cell culture","normalized_drug":"Dabrafenib","pub_med_references":[31925410],"molecular_profile":"BRAF V600E MAP2K1 I99M","profile_array":[{"type":"M1","gene":"V600E"}],"response_type":"sensitive"},{"therapy_id":2,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a preclinical study, melanoma cells harboring BRAF V600E and expressing MAP2K1 I99M demonstrated sensitivity to Mekinist (trametinib) treatment similar to cells expressing wild-type MAP2K1 in culture (%%PUBMED:31925410%%).","therapy":"Trametinib","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Preclinical - Cell culture","normalized_drug":"Trametinib","pub_med_references":[31925410],"molecular_profile":"BRAF V600E MAP2K1 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inhibit colony formation and reduce Erk activation in a melanoma cell line harboring BRAF V600E that was found to have acquired a STAG2 D193N mutation in culture (%%PUBMED:27500726%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E STAG2 D193N","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[23031422],"normalized_drug":"Dabrafenib","indication":"melanoma","therapy_id":3,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a clinical case study, a patient with rapidly growing malignant melanoma harboring BRAF V600E and V600M achieved a 60% reduction in tumor size 1 week following treatment with Tafinlar (dabrafenib), and the tumor completely disappeared 1 month after beginning treatment (%%PUBMED:23031422%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E BRAF V600M","approval_status":"Case Reports/Case 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study, a patient with metastatic giant sarcomatoid melanoma harboring BRAF V600E and CDKN2A R80* achieved a partial response following four months of treatment with the combination of Tafinlar (dabrafenib) and Mekinist (trametinib), and reached a complete response with regression of lung and bone metastases after one year of treatment (%%PUBMED:32922664%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E CDKN2A R80*","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"resistant","pub_med_references":[36622773],"normalized_drug":"Dabrafenib, Trametinib","indication":"melanoma","therapy_id":1066,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a preclinical study, a melanoma cell line overexpressing BRAF V600E was resistant to the combination of Mekinist (trametinib) and Tafinlar (dabrafenib) in culture (%%PUBMED:36622773%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E BRAF over exp","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"resistant","pub_med_references":[30559419],"normalized_drug":"Vemurafenib","indication":"melanoma","therapy_id":342,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a preclinical study, a cell line xenograft model of melanoma overexpressing BRAF V600E demonstrated resistance to Zelboraf (vemurafenib) treatment (%%PUBMED:30559419%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E BRAF over exp","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[36622773],"response_type":"sensitive","indication":"melanoma","therapy_id":14824,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + DS03090629","efficacy_evidence":"In a preclinical study, the combination of DS03090629 and Tafinlar (dabrafenib) inhibited Erk phosphorylation and proliferation in a melanoma cell line overexpressing BRAF V600E in culture and induced tumor regression in a cell line xenograft model (%%PUBMED:36622773%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E BRAF over exp","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"resistant","pub_med_references":[36622773],"normalized_drug":"Dabrafenib","indication":"melanoma","therapy_id":3,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a preclinical study, a melanoma cell line overexpressing BRAF V600E was resistant to Tafinlar (dabrafenib) in culture (%%PUBMED:36622773%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E BRAF over exp","approval_status":"Preclinical - Cell 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(%%PUBMED:36622773%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E BRAF over exp","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[30559419],"normalized_drug":"Plx8394","indication":"melanoma","therapy_id":1041,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"PLX8394","efficacy_evidence":"In a preclinical study, PLX8394 treatment inhibited Erk signaling and reduced tumor growth in a Zelboraf (vemurafenib)-resistant cell line xenograft model of melanoma overexpressing BRAF V600E (%%PUBMED:30559419%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E BRAF over exp","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[32816843],"response_type":"predicted - resistant","indication":"colorectal cancer","therapy_id":8871,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"BI-3406","efficacy_evidence":"In a preclinical study, BI-3406 treatment failed to inhibit growth of colorectal cancer cells harboring BRAF V600E and BRAF T119S in culture (%%PUBMED:32816843%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF T119S BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[31744895],"response_type":"predicted - sensitive","indication":"colorectal cancer","therapy_id":4588,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"LY3214996","efficacy_evidence":"In a preclinical study, a colorectal cancer cell line harboring BRAF V600E and BRAF T119S was sensitive to treatment with LY3214996 in culture, demonstrating decreased cell proliferation (%%PUBMED:31744895%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF T119S BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - 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Series","amp_tier":"II"},{"pub_med_references":[33273059],"response_type":"sensitive","profile_array":[{"type":"M1","gene":"V600E"}],"indication":"melanoma","therapy_id":11152,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"AZD0364","efficacy_evidence":"In a preclinical study, AZD0364 (ATG-017) decreased phosphorylation of Erk target genes and increased expression of apoptosis markers in melanoma cells harboring BRAF V600E, MAP2K1 Q56P, and NRAS Q61R in culture, and inhibited tumor growth in cell line xenograft models (%%PUBMED:33273059%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E MAP2K1 Q56P NRAS Q61R","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[29142786],"normalized_drug":"Pembrolizumab","indication":"lung adenocarcinoma","therapy_id":1447,"normalized_cancer":"Lung Adenocarcinoma","evidence_type":"Actionable","therapy":"Pembrolizumab","efficacy_evidence":"In a clinical case study, a patient with CD274 (PD-L1)-positive (IHC = 90% of tumor cells) metastatic lung adenocarcinoma who progressed after an 18-month response to Tafinlar (dabrafenib) treatment based on the presence of BRAF V600E, was then treated with Keytruda (pembrolizumab) for two cycles, and achieved an early response and remained progression-free 7 months after initiating immunotherapy (%%PUBMED:29142786%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E CD274 pos","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[29142786],"normalized_drug":"Dabrafenib","indication":"lung adenocarcinoma","therapy_id":3,"normalized_cancer":"Lung Adenocarcinoma","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a clinical case study, a patient with CD274 (PD-L1)-positive (IHC = 90% of tumor cells) metastatic lung adenocarcinoma harboring BRAF V600E achieved a partial response to treatment with Tafinlar (dabrafenib) and remained stable with improved performance status for 18 months until disease progression, and subsequently achieved a response to Keytruda (pembrolizumab) treatment (%%PUBMED:29142786%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E CD274 pos","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[39036436],"response_type":"predicted - sensitive","indication":"glioblastoma","therapy_id":17805,"normalized_cancer":"Glioblastoma, IDH-Wildtype","evidence_type":"Actionable","therapy":"Binimetinib + Encorafenib + Nivolumab + Temozolomide","efficacy_evidence":"In a clinical case study, the addition of Mektovi (binimetinib) and Braftovi (encorafenib) to treatment with the combination of Opdivo (nivolumab) and Temodar (temozolomide) resulted in a complete response after 6 months in a patient with CD274 (PD-L1), PDCD1 (PD-1)-positive glioblastoma harboring BRAF V600E, and the patient remained progression-free for at least 20 months while on treatment (%%PUBMED:39036436%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E CD274 pos","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[32859654],"normalized_drug":"Dabrafenib, Trametinib","indication":"lung non-small cell carcinoma","therapy_id":1066,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical study, combination treatment with Tafinlar (dabrafenib) and Mekinist (trametinib) resulted in stable disease as best response in a non-small cell lung cancer patient harboring BRAF V600E, tested in tissue and plasma, and AKT1 E17K, tested in plasma only (%%PUBMED:32859654%%).","cap_asco_evidence_level":"D","molecular_profile":"AKT1 E17K BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[32859654],"normalized_drug":"Vemurafenib","indication":"lung non-small cell carcinoma","therapy_id":342,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a clinical study, Zelboraf (vemurafenib) resulted in a partial response for 3.7 months in a non-small cell lung cancer patient harboring BRAF V600E, tested in tissue and plasma, and ERBB2 (HER2) amplification, tested in plasma only (%%PUBMED:32859654%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E ERBB2 amp","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[32859654],"normalized_drug":"Vemurafenib","indication":"lung non-small cell carcinoma","therapy_id":342,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a clinical study, Zelboraf (vemurafenib) treatment resulted in stable disease for 3.3 months in a non-small cell lung cancer patient harboring BRAF V600E, tested in tissue and plasma, and FGFR2 A553D, tested in plasma only (%%PUBMED:32859654%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E FGFR2 A553D","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[32859654],"normalized_drug":"Dabrafenib, Trametinib","indication":"lung non-small cell carcinoma","therapy_id":1066,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical study, combination treatment with Tafinlar (dabrafenib) and Mekinist (trametinib) resulted in stable disease as best response in a non-small cell lung cancer patient harboring BRAF V600E, tested in plasma and tissue, and NTRK3 P612T, tested in plasma only (%%PUBMED:32859654%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NTRK3 P612T","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[32859654],"normalized_drug":"Vemurafenib","indication":"lung non-small cell carcinoma","therapy_id":342,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a clinical study, Zelboraf (vemurafenib) treatment resulted in stable disease for 6.4 months in a non-small cell lung cancer patient harboring BRAF V600E, tested in tissue and plasma, and PIK3CA E545K, tested in plasma only (%%PUBMED:32859654%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E PIK3CA E545K","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - 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Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical study, a non-small cell lung cancer patient harboring BRAF V600E, tested in tissue, and IDH1 R132C, tested in plasma, demonstrated disease progression when treated with the combination of Tafinlar (dabrafenib) and Mekinist (trametinib), and was found, via circulating tumor DNA testing, to have acquired KRAS G12V, KRAS Q61R, U2AF1 R156H (%%PUBMED:32859654%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E IDH1 R132C KRAS G12V KRAS Q61R U2AF1 R156H","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - resistant","pub_med_references":[32859654],"normalized_drug":"Dabrafenib, Trametinib","indication":"lung non-small cell carcinoma","therapy_id":1066,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical study, a non-small cell lung cancer patient harboring BRAF V600E demonstrated disease progression when treated with the combination of Tafinlar (dabrafenib) and Mekinist (trametinib), and was found, via circulating tumor DNA testing, to have acquired U2AF1 Q157P (%%PUBMED:32859654%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E U2AF1 Q157P","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[33824136],"response_type":"resistant","indication":"pancreatic ductal adenocarcinoma","therapy_id":7769,"normalized_cancer":"Pancreatic Adenocarcinoma","evidence_type":"Actionable","therapy":"Adagrasib","efficacy_evidence":"In a preclinical study, Krazati (adagrasib) failed to inhibit phosphorylation of Erk and Rsk in pancreatic ductal adenocarcinoma cells expressing BRAF V600E and KRAS G12C in culture (%%PUBMED:33824136%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E KRAS G12C","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[37611121],"response_type":"predicted - resistant","indication":"large cell neuroendocrine carcinoma","therapy_id":10876,"normalized_cancer":"Large Cell Neuroendocrine Carcinoma","evidence_type":"Actionable","therapy":"Divarasib","efficacy_evidence":"In a Phase I trial, BRAF V600E was identified in the post-progression circulating tumor DNA of a patient with lung large cell neuroendocrine carcinoma harboring KRAS G12C who previously responded to treatment with Divarasib (GDC-6036) (%%PUBMED:37611121%%; NCT04449874).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E KRAS G12C","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - resistant","pub_med_references":[36967525],"normalized_drug":"Cobimetinib, Vemurafenib","indication":"ovarian serous cystadenocarcinoma","therapy_id":1657,"normalized_cancer":"Serous Ovarian Cancer","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"In a clinical case study, a patient with low-grade serous cystadenocarcinoma of the ovary harboring BRAF V600E demonstrated progressive disease on treatment with the combination of Zelboraf (vemurafenib) and Cotellic (cobimetinib) and was found to have acquired KRAS G12C (%%PUBMED:36967525%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E KRAS G12C","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[34161704],"response_type":"predicted - resistant","profile_array":[{"type":"M1","gene":"H95R"}],"indication":"colorectal cancer","therapy_id":7769,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Adagrasib","efficacy_evidence":"In a Phase Ib/II trial, a colorectal cancer patient harboring KRAS G12C who initially responded to treatment with Krazati (adagrasib) progressed and through circulating tumor DNA testing was found to have acquired several mutations including KRAS H95Q, KRAS H95R, KRAS G12R/D/V, KRAS G13D, KRAS Q61H, MAP2K1 K57N/T, CCDC6-RET, and BRAF V600E (%%PUBMED:34161704%%; NCT03785249).","cap_asco_evidence_level":"D","molecular_profile":"CCDC6 - RET BRAF V600E KRAS G12C KRAS G12R KRAS G12V KRAS G13D KRAS Q61H KRAS H95Q KRAS H95R MAP2K1 K57N MAP2K1 K57T","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[34161704],"response_type":"predicted - resistant","indication":"lung adenocarcinoma","therapy_id":7769,"normalized_cancer":"Lung Adenocarcinoma","evidence_type":"Actionable","therapy":"Adagrasib","efficacy_evidence":"In a Phase Ib/II trial, a lung adenocarcinoma patient harboring KRAS G12C who initially responded to treatment with Krazati (adagrasib) progressed and through circulating tumor DNA testing was found to have acquired several mutations including KRAS G12V/W, KRAS R68S, KRAS H95D, and BRAF V600E (%%PUBMED:34161704%%; NCT03785249).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E KRAS G12C KRAS G12V KRAS G12W KRAS R68S KRAS H95D","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[33953400],"response_type":"predicted - resistant","indication":"melanoma","therapy_id":7209,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Belvarafenib","efficacy_evidence":"In a Phase I trial, a melanoma patient harboring BRAF V600E initially demonstrated stable disease on treatment with Belvarafenib (HM95573), however, later developed disease progression likely due to the acquisition of a secondary resistance mutation ARAF P462L (%%PUBMED:33953400%%; NCT03118817).","cap_asco_evidence_level":"D","molecular_profile":"ARAF P462L BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[33953400],"response_type":"predicted - resistant","indication":"melanoma","therapy_id":7209,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Belvarafenib","efficacy_evidence":"In a Phase I trial, a melanoma patient harboring BRAF V600E initially demonstrated stable disease on treatement with Belvarafenib (HM95573), however, later developed disease progression likely due to the acquisition of a secondary resistance mutation ARAF G377R, and expression of ARAF G377R in a melanoma cell line harboring BRAF V600E conferred resistance to Belvarafenib (HM95573) in culture (%%PUBMED:33953400%%; NCT03118817).","cap_asco_evidence_level":"D","molecular_profile":"ARAF G377R BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[33953400],"response_type":"predicted - resistant","indication":"nephroblastoma","therapy_id":7209,"normalized_cancer":"Wilms' Tumor","evidence_type":"Actionable","therapy":"Belvarafenib","efficacy_evidence":"In a Phase I trial, a nephroblastoma patient harboring BRAF V600E initially demonstrated stable disease on treatment with Belvarafenib (HM95573), however, later developed disease progression likely due to the acquisition of a secondary resistance mutation, ARAF G387N (%%PUBMED:33953400%%; NCT03118817).","cap_asco_evidence_level":"D","molecular_profile":"ARAF G387N BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[33953400],"response_type":"predicted - resistant","indication":"melanoma","therapy_id":7209,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Belvarafenib","efficacy_evidence":"In a preclinical study, a melanoma cell line harboring BRAF V600E and expressing ARAF G387N was resistant to treatment with Belvarafenib (HM95573) in culture (%%PUBMED:33953400%%).","cap_asco_evidence_level":"D","molecular_profile":"ARAF G387N BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[31744895],"response_type":"predicted - sensitive","indication":"melanoma","therapy_id":4588,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"LY3214996","efficacy_evidence":"In a preclinical study, a melanoma cell 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(%%PUBMED:37729428%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NRAS Q61R","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"pub_med_references":[37729428],"response_type":"sensitive","indication":"melanoma","therapy_id":16204,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Encorafenib + Talazoparib","efficacy_evidence":"In a preclinical study, treatment with the combination of Talzenna (talazoparib) and Braftovi (encorafenib) synergistically inhibited viability of patient-derived melanoma spheroids harboring BRAF V600E and NRAS Q61R in culture (%%PUBMED:37729428%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NRAS Q61R","approval_status":"Preclinical - Patient cell 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controls in a melanoma patient-derived xenograft (PDX) model harboring BRAF V600E and NRAS Q61R (%%PUBMED:37729428%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NRAS Q61R","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"pub_med_references":[37729428],"response_type":"sensitive","indication":"melanoma","therapy_id":16205,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Binimetinib + Encorafenib + Talazoparib","efficacy_evidence":"In a preclinical study, treatment with the combination of Talzenna (talazoparib), Braftovi (encorafenib), and Mektovi (binimetinib) synergistically inhibited viability of patient-derived melanoma spheroids harboring BRAF V600E and NRAS Q61H in culture (%%PUBMED:37729428%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NRAS Q61H","approval_status":"Preclinical - Patient cell culture","amp_tier":"II"},{"pub_med_references":[37729428],"response_type":"sensitive","indication":"melanoma","therapy_id":16204,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Encorafenib + Talazoparib","efficacy_evidence":"In a preclinical study, treatment with the combination of Talzenna (talazoparib) and Braftovi (encorafenib) synergistically inhibited viability of patient-derived melanoma spheroids harboring BRAF V600E and NRAS Q61H in culture (%%PUBMED:37729428%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NRAS Q61H","approval_status":"Preclinical - Patient cell culture","amp_tier":"II"},{"pub_med_references":[37713162],"response_type":"resistant","indication":"anaplastic thyroid carcinoma","therapy_id":16264,"normalized_cancer":"Anaplastic Thyroid Cancer","evidence_type":"Actionable","therapy":"Dasatinib + MK2206 + Trametinib","efficacy_evidence":"In a preclinical study, the addition of MK2206 did not sensitize an anaplastic thyroid cancer cell line harboring BRAF V600E and PIK3CA E542k to Sprycel (dasatinib) and Mekinist (trametinib) combination treatment in culture (%%PUBMED:37713162%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E PIK3CA E542K","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[37713162],"response_type":"resistant","indication":"anaplastic thyroid carcinoma","therapy_id":4599,"normalized_cancer":"Anaplastic Thyroid Cancer","evidence_type":"Actionable","therapy":"Dasatinib + Trametinib","efficacy_evidence":"In a preclinical study, an anaplastic thyroid cancer cell line harboring BRAF V600E and PIK3CA E542K was resistant to the combination of Sprycel (dasatinib) and Mekinist (trametinib) in culture (%%PUBMED:37713162%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E PIK3CA E542K","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[37713162],"response_type":"sensitive","indication":"anaplastic thyroid carcinoma","therapy_id":16262,"normalized_cancer":"Anaplastic Thyroid Cancer","evidence_type":"Actionable","therapy":"GSK2334470 + Trametinib","efficacy_evidence":"In a preclinical study, the addition of GSK2334470 sensitized an anaplastic thyroid cancer cell line harboring BRAF V600E and PIK3CA E542K to Mekinist (trametinib) treatment as demonstrated by a reduction in viability in culture (%%PUBMED:37713162%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E PIK3CA E542K","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[37713162],"response_type":"resistant","indication":"anaplastic thyroid carcinoma","therapy_id":4599,"normalized_cancer":"Anaplastic Thyroid Cancer","evidence_type":"Actionable","therapy":"Dasatinib + Trametinib","efficacy_evidence":"In a preclinical study, an anaplastic thyroid cancer cell line harboring BRAF V600E and PIK3CA N1044S was resistant to the combination of Sprycel (dasatinib) and Mekinist (trametinib) in culture (%%PUBMED:37713162%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E PIK3CA N1044S","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[37713162],"response_type":"sensitive","indication":"anaplastic thyroid carcinoma","therapy_id":16262,"normalized_cancer":"Anaplastic Thyroid Cancer","evidence_type":"Actionable","therapy":"GSK2334470 + Trametinib","efficacy_evidence":"In a preclinical study, the addition of GSK2334470 sensitized an anaplastic thyroid cancer cell line harboring BRAF V600E and PIK3CA N1044S to Mekinist (trametinib) treatment as demonstrated by a reduction in viability in culture (%%PUBMED:37713162%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E PIK3CA N1044S","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[37713162],"response_type":"resistant","indication":"anaplastic thyroid carcinoma","therapy_id":16264,"normalized_cancer":"Anaplastic Thyroid Cancer","evidence_type":"Actionable","therapy":"Dasatinib + MK2206 + Trametinib","efficacy_evidence":"In a preclinical study, the addition of MK2206 did not sensitize an anaplastic thyroid cancer cell line harboring BRAF V600E and PIK3CA N1044S to Sprycel (dasatinib) and Mekinist (trametinib) combination treatment in culture (%%PUBMED:37713162%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E PIK3CA N1044S","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[37713162],"response_type":"sensitive","profile_array":[{"type":"M1","gene":"PIK3CA"}],"indication":"anaplastic thyroid carcinoma","therapy_id":4599,"normalized_cancer":"Anaplastic Thyroid Cancer","evidence_type":"Actionable","therapy":"Dasatinib + Trametinib","efficacy_evidence":"In a preclinical study, the combination of Sprycel (dasatinib) and Mekinist (trametinib) inhibited viability of an anaplastic thyroid cancer cell line harboring BRAF V600E and PIK3CA M1043I in culture (%%PUBMED:37713162%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E PIK3CA M1043I","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[37713162],"response_type":"sensitive","indication":"papillary thyroid carcinoma","therapy_id":4599,"normalized_cancer":"Papillary Thyroid Cancer","evidence_type":"Actionable","therapy":"Dasatinib + Trametinib","efficacy_evidence":"In a preclinical study, the combination of Sprycel (dasatinib) and Mekinist (trametinib) inhibited viability of a papillary thyroid cancer cell line harboring BRAF V600E and PIK3CA E542K and W11C in culture (%%PUBMED:37713162%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E PIK3CA W11C PIK3CA E542K","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"resistant","pub_med_references":[37838724],"normalized_drug":"Dabrafenib, Trametinib","indication":"melanoma","therapy_id":1066,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a preclinical study, melanoma cell lines harboring BRAF V600E with AR overexpression were resistant to the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) in culture (%%PUBMED:37838724%%).","cap_asco_evidence_level":"D","molecular_profile":"AR over exp BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[37838724],"normalized_drug":"Azd3514","indication":"melanoma","therapy_id":2826,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"AZD3514","efficacy_evidence":"In a preclinical study, AZD3514 inhibited proliferation and induced cell death in BRAF inhibitor-resistant melanoma cell lines with AR overexpression and harboring BRAF V600E in culture and decreased tumor growth in a cell line xenograft model and syngeneic mouse model (%%PUBMED:37838724%%).","cap_asco_evidence_level":"D","molecular_profile":"AR over exp BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"response_type":"resistant","pub_med_references":[37838724],"normalized_drug":"Dabrafenib","indication":"melanoma","therapy_id":3,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a preclinical study, melanoma cell lines harboring BRAF V600E demonstrated resistance to Tafinlar (dabrafenib), and were found to have increased AR expression (%%PUBMED:37838724%%).","cap_asco_evidence_level":"D","molecular_profile":"AR over exp BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[37838724],"response_type":"sensitive","indication":"melanoma","therapy_id":15932,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"ARCC4","efficacy_evidence":"In a preclinical study, ARCC4 inhibited proliferation and induced cell death in BRAF inhibitor-resistant melanoma cell lines with AR overexpression and harboring BRAF V600E in culture (%%PUBMED:37838724%%).","cap_asco_evidence_level":"D","molecular_profile":"AR over exp BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - resistant","pub_med_references":[38229767],"normalized_drug":"Lorlatinib","indication":"lung adenocarcinoma","therapy_id":869,"normalized_cancer":"Lung Adenocarcinoma","evidence_type":"Actionable","therapy":"Lorlatinib","efficacy_evidence":"In a clinical case study, BRAF V600E and ALK V1180L were identified in a post-progression biopsy in a lung adenocarcinoma patient harboring HIP1-ALK who progressed on third-line treatment with Lorbrena (lorlatinib) (%%PUBMED:38229767%%).","cap_asco_evidence_level":"D","molecular_profile":"HIP1 - ALK ALK V1180L BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - resistant","pub_med_references":[37748191],"normalized_drug":"Dabrafenib, Trametinib","indication":"lung non-small cell carcinoma","therapy_id":1066,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, ERRFI1 D297Tfs*3 and S265Hfs*14 were identified upon progression on the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) in a patient with non-small cell lung cancer harboring BRAF V600E (%%PUBMED:37748191%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E ERRFI1 S265Hfs*14 ERRFI1 D297Tfs*3","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - resistant","pub_med_references":[30036146],"normalized_drug":"Vemurafenib","indication":"colon adenocarcinoma","therapy_id":342,"normalized_cancer":"Colon Adenocarcinoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a clinical case study, KRAS G12R was identified in post-progression biopsy in a patient with metastatic colon adenocarcinoma harboring BRAF V600E who previously responded to Zelboraf (vemurafenib) treatment (%%PUBMED:30036146%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E KRAS G12R","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[37611121],"response_type":"predicted - resistant","indication":"colorectal cancer","therapy_id":10876,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Divarasib","efficacy_evidence":"In a Phase I trial, KRAS G12V, KRAS G12A, KRAS G12D, KRAS Y96D, KRAS A146T, BRAF V600E, and KRAS amplification were identified in the post-progression circulating tumor DNA of a patient with colorectal cancer harboring KRAS G12C who previously responded to treatment with Divarasib (GDC-6036) (%%PUBMED:37611121%%; NCT04449874).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E KRAS G12A KRAS G12C KRAS G12D KRAS G12V KRAS Y96D KRAS A146T KRAS amp","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[38429896],"normalized_drug":"Dabrafenib, Trametinib","indication":"lung adenocarcinoma","therapy_id":1066,"normalized_cancer":"Lung Adenocarcinoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, second-line treatment with the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) resulted in a clinical response lasting at least 5 years in a patient with lung adenocarcinoma harboring BRAF V600E and high CD274 (PD-L1) expression (TPS=100%) who did not respond to first-line Keytruda (pembrolizumab) (%%PUBMED:38429896%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E CD274 over exp","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[39507030],"response_type":"sensitive","indication":"lung non-small cell carcinoma","therapy_id":12100,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Osimertinib + Trametinib","efficacy_evidence":"In a retrospective analysis, Tafinlar (dabrafenib), Mekinist (trametinib), and Tagrisso (Osimertinib) combined therapy led to an objective response rate of 61.5% (8/13, all partial responses) and disease control rate of 92.3% (12/13) in non-small cell lung cancer patients harboring EGFR L858R (n=4) or an exon 19 deletion (n=9) and acquired BRAF V600E, and in a preclinical study, inhibited proliferation in a patient-derived organoid model harboring EGFR L858R and BRAF V600E in culture (%%PUBMED:39507030%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E EGFR L858R","approval_status":"Clinical Study","amp_tier":"II"},{"pub_med_references":[35952324],"response_type":"sensitive","indication":"lung non-small cell carcinoma","therapy_id":12100,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Osimertinib + Trametinib","efficacy_evidence":"In a clinical case study, treatment with the combination of Tafinlar (dabrafenib), Mekinist (trametinib), and Tagrisso (Osimertinib) resulted in a partial response that was ongoing after 9 months in a patient with non-small cell lung cancer harboring EGFR L858R and BRAF V600E (%%PUBMED:35952324%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E EGFR L858R","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - resistant","pub_med_references":[35952324],"normalized_drug":"Osimertinib","indication":"lung non-small cell carcinoma","therapy_id":660,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Osimertinib","efficacy_evidence":"In a clinical case study, a non-small cell lung cancer patient harboring EGFR L858R progressed on treatment with Tagrisso (osimertinib) and was found to have acquired BRAF V600E (%%PUBMED:35952324%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E EGFR L858R","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[34707694],"normalized_drug":"Dabrafenib, Trametinib","indication":"lung adenocarcinoma","therapy_id":1066,"normalized_cancer":"Lung Adenocarcinoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, treatment with the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) resulted in a partial response after 24 days in a patient with metastatic lung adenocarcinoma harboring EGFR L858R and BRAF V600E (%%PUBMED:34707694%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E EGFR L858R","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - resistant","pub_med_references":[34707694],"normalized_drug":"Afatinib","indication":"lung adenocarcinoma","therapy_id":623,"normalized_cancer":"Lung Adenocarcinoma","evidence_type":"Actionable","therapy":"Afatinib","efficacy_evidence":"In a clinical case study, BRAF V600E was identified in the bone metastasis of a patient with metastatic lung adenocarcinoma harboring EGFR L858R who progressed on treatment with Gilotrif (afatinib) (%%PUBMED:34707694%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E EGFR L858R","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[38449561],"response_type":"predicted - resistant","indication":"lung adenocarcinoma","therapy_id":2224,"normalized_cancer":"Lung Adenocarcinoma","evidence_type":"Actionable","therapy":"Osimertinib + Savolitinib","efficacy_evidence":"In a retrospective analysis, a patient with lung adenocarcinoma harboring EGFR L858R developed progressive disease on treatment with the combination of Tagrisso (osimertinib) and Savolitinib (AZD6094), and was found to have acquired BRAF V600E (%%PUBMED:38449561%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E EGFR L858R","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[38711893],"response_type":"predicted - sensitive","profile_array":[{"type":"M1","gene":"V600E"}],"indication":"colon adenocarcinoma","therapy_id":16933,"normalized_cancer":"Colon Adenocarcinoma","evidence_type":"Actionable","therapy":"Crizotinib + Regorafenib + Tislelizumab","efficacy_evidence":"In a clinical case study, treatment with the combination of Tevimbra (tislelizumab), Stivarga (regorafenib), and Xalkori (crizotinib) resulted in a partial response in the primary tumor and liver metastases in a patient with metastatic colon adenocarcinoma harboring BRAF V600E, MET amplification, and TPM4-ALK (%%PUBMED:38711893%%).","cap_asco_evidence_level":"D","molecular_profile":"TPM4 - ALK BRAF V600E MET amp","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[34660287],"response_type":"predicted - resistant","profile_array":[{"type":"M1","gene":"L858R"}],"indication":"lung adenocarcinoma","therapy_id":7668,"normalized_cancer":"Lung Adenocarcinoma","evidence_type":"Actionable","therapy":"Crizotinib + Gefitinib","efficacy_evidence":"In a retrospective analysis, a patient with lung adenocarcinoma harboring EGFR L858R and MET amplification (CN=6.6) developed progressive disease on treatment with the combination of Iressa (gefitinib) and Xalkori (crizotinib), and was found to have acquired BRAF V600E, MET D1228H, and MYC amplification (%%PUBMED:34660287%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E EGFR L858R MET D1228H MET amp","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"therapy_id":342,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a clinical case study, a deletion of BRAF exons 4-8 was identified in the post-progression biopsy of a melanoma patient harboring BRAF V600E who was treated with Zelboraf (vemurafenib) (%%PUBMED:22113612%%).","therapy":"Vemurafenib","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Case Reports/Case Series","normalized_drug":"Vemurafenib","pub_med_references":[22113612],"molecular_profile":"BRAF del exon4-8 BRAF V600E","profile_array":[{"type":"del exon","number":4,"gene":"BRAF"}],"response_type":"predicted - resistant"},{"pub_med_references":[38691346],"response_type":"sensitive","profile_array":[{"type":"del exon","number":4,"gene":"BRAF"}],"indication":"melanoma","therapy_id":13603,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Binimetinib + PF-07799933","efficacy_evidence":"In a preclinical study, treatment with the combination of PF-07799933 and Mektovi (binimetinib) resulted in tumor regression in a patient-derived xenograft (PDX) model of melanoma harboring BRAF V600E and a BRAF exon 4-8 deletion variant (reported as p61 splice variant) (%%PUBMED:38691346%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF del exon4-8 BRAF V600E","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"therapy_id":1066,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a clinical case study, a BRAF exon 4-8 deletion variant (reported as p61) was identified in the post-progression plasma ctDNA of two patients with metastatic melanoma harboring BRAF V600E who previously responded to treatment with the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) (%%PUBMED:33216826%%).","therapy":"Dabrafenib + Trametinib","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Case Reports/Case Series","normalized_drug":"Dabrafenib, Trametinib","pub_med_references":[33216826],"molecular_profile":"BRAF del exon4-8 BRAF V600E","profile_array":[{"type":"del exon","number":4,"gene":"BRAF"}],"response_type":"predicted - resistant"},{"pub_med_references":[38691346],"response_type":"predicted - sensitive","profile_array":[{"type":"del exon","number":2,"gene":"BRAF"}],"indication":"papillary thyroid carcinoma","therapy_id":13603,"normalized_cancer":"Papillary Thyroid Cancer","evidence_type":"Actionable","therapy":"Binimetinib + PF-07799933","efficacy_evidence":"In a Phase I trial, treatment with the combination of PF-07799933 and Mektovi (binimetinib) resulted in a partial response with a tumor reduction of 80% in a patient with papillary thyroid carcinoma harboring BRAF V600E and a deletion of BRAF exons 2-8 (reported as p48 splice variant) (%%PUBMED:38691346%%; NCT05355701).","cap_asco_evidence_level":"D","molecular_profile":"BRAF del exon2-8 BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"therapy_id":342,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a clinical case study, a deletion of BRAF exons 2-8 was identified in the post-progression biopsy of a melanoma patient harboring BRAF V600E who was treated with Zelboraf (vemurafenib) (%%PUBMED:22113612%%).","therapy":"Vemurafenib","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Case Reports/Case Series","normalized_drug":"Vemurafenib","pub_med_references":[22113612],"molecular_profile":"BRAF del exon2-8 BRAF V600E","profile_array":[{"type":"del exon","number":2,"gene":"BRAF"}],"response_type":"predicted - resistant"},{"therapy_id":342,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a clinical case study, a deletion of BRAF exons 4-10 was identified in the post-progression biopsy of a melanoma patient harboring BRAF V600E who was treated with Zelboraf (vemurafenib) (%%PUBMED:22113612%%).","therapy":"Vemurafenib","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Case Reports/Case 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proliferation and synergistically decreased viability in a patient-derived colorectal cancer cell line harboring BRAF V600E and PTEN R173C (%%PUBMED:39145064%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E PTEN R173C","approval_status":"Preclinical - Patient cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[39500140],"normalized_drug":"Dabrafenib, Trametinib","indication":"melanoma","therapy_id":1066,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a retrospective analysis, treatment with the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) resulted in a partial response with an overall survival of 51.1 months and a duration of treatment of 4.1 months in a melanoma patient harboring BRAF V600E and IDH1 R132C (%%PUBMED:39500140%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E IDH1 R132C","approval_status":"Case Reports/Case 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cancer","therapy_id":4525,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Dabrafenib","efficacy_evidence":"In a preclinical study, a colorectal cancer cell line harboring BRAF V600E and expressing EGFR S464L was resistant to treatment with the combination of Tafinlar (dabrafenib) and Erbitux (cetuximab) in culture (%%PUBMED:39424923%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E EGFR S464L","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[39424923],"response_type":"resistant","profile_array":[{"type":"M1","gene":"V600E"}],"indication":"colorectal cancer","therapy_id":4525,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Dabrafenib","efficacy_evidence":"In a preclinical study, Tafinlar (dabrafenib) and Erbitux (cetuximab) combination treatment inhibited senescence in a colorectal cancer cell line harboring BRAF V600E and expressing MAP2K1 Y130C in culture (%%PUBMED:39424923%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E MAP2K1 Y130C","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[39424923],"response_type":"resistant","profile_array":[{"type":"M1","gene":"V600E"}],"indication":"colorectal cancer","therapy_id":4525,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Dabrafenib","efficacy_evidence":"In a preclinical study, Tafinlar (dabrafenib) and Erbitux (cetuximab) combination treatment increased growth of a colorectal cancer cell line harboring BRAF V600E and expressing MAP2K2 Y134H in culture (%%PUBMED:39424923%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E MAP2K2 Y134H","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"therapy_id":2,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a preclinical study, Mekinist (trametinib) treatment increased growth of a colorectal cancer cell line harboring BRAF V600E and expressing MAP2K2 Y134H in culture (%%PUBMED:39424923%%).","therapy":"Trametinib","evidence_type":"Actionable","normalized_cancer":"Colorectal Cancer","indication":"colorectal cancer","approval_status":"Preclinical - Cell culture","normalized_drug":"Trametinib","pub_med_references":[39424923],"molecular_profile":"BRAF V600E MAP2K2 Y134H","profile_array":[{"type":"M1","gene":"V600E"}],"response_type":"resistant"},{"pub_med_references":[39424923],"response_type":"resistant","profile_array":[{"type":"M1","gene":"V600E"}],"indication":"colorectal cancer","therapy_id":4525,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Dabrafenib","efficacy_evidence":"In a preclinical study, Tafinlar (dabrafenib) and Erbitux (cetuximab) combination treatment inhibited senescence in a colorectal cancer cell line harboring BRAF V600E and expressing MAP2K1 S194P in culture (%%PUBMED:39424923%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E MAP2K1 S194P","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"resistant","pub_med_references":[39574163],"normalized_drug":"Vemurafenib","indication":"melanoma","therapy_id":342,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a preclinical study, melanoma cells harboring BRAF V600E and overexpressing PDE4D were resistant to Zelboraf (vemurafenib) in culture (%%PUBMED:39574163%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E PDE4D over exp","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[39574163],"response_type":"resistant","indication":"melanoma","therapy_id":17922,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Roflumilast + Vemurafenib","efficacy_evidence":"In a preclinical study, melanoma cells harboring BRAF V600E and overexpressing PDE4D were resistant to the combination of Roflumilast and Zelboraf (vemurafenib) in culture (%%PUBMED:39574163%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E PDE4D over exp","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"resistant","pub_med_references":[39574163],"normalized_drug":"Cobimetinib","indication":"melanoma","therapy_id":1004,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Cobimetinib","efficacy_evidence":"In a preclinical study, melanoma cells harboring BRAF V600E and overexpressing PDE4D were resistant to Cotellic (cobimetinib) in culture (%%PUBMED:39574163%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E PDE4D over exp","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - resistant","pub_med_references":[39611930],"normalized_drug":"Trastuzumab","indication":"Her2-receptor positive breast cancer","therapy_id":947,"normalized_cancer":"Breast Neoplasm, NOS","evidence_type":"Actionable","therapy":"Trastuzumab","efficacy_evidence":"In a retrospective analysis, PIK3CA H1047Y, PTEN Q17Rfs*26, and BRAF V600E were identified in the post-progression biopsy of an ERBB2 (HER2)-positive breast cancer patient who demonstrated resistance to treatment with Herceptin (trastuzumab) plus chemotherapy (%%PUBMED:39611930%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E ERBB2 pos PIK3CA H1047Y PTEN Q17Rfs*26","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"therapy_id":660,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a clinical case study, a non-small cell lung cancer patient harboring an EGFR exon 19 deletion progressed on treatment with Tagrisso (osimertinib) and was found to have acquired BRAF V600E and N581S (%%PUBMED:35952324%%).","therapy":"Osimertinib","evidence_type":"Actionable","normalized_cancer":"Non-Small Cell Lung Cancer","indication":"lung non-small cell carcinoma","approval_status":"Case Reports/Case Series","normalized_drug":"Osimertinib","pub_med_references":[35952324],"molecular_profile":"BRAF N581S BRAF V600E EGFR exon 19 del","profile_array":[{"type":"exon del","number":19,"gene":"EGFR"}],"response_type":"predicted - resistant"},{"pub_med_references":[39626159],"response_type":"predicted - resistant","profile_array":[{"type":"M1","gene":"amp"}],"indication":"colon cancer","therapy_id":1992,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Panitumumab + Trametinib","efficacy_evidence":"In a clinical study, BRAF amplification and MET amplification were identified in the liver biopsy of a pediatric patient with colon cancer harboring BRAF V600E, as well as TP53 G245S, SMAD4 S504R, and PTEN loss, who progressed on treatment with the combination of Vectibix (panitumumab), Tafinlar (dabrafenib), and Mekinist (trametinib) (%%PUBMED:39626159%%; NCT02688517).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E BRAF amp MET amp","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - resistant","pub_med_references":[37806383],"normalized_drug":"Osimertinib","indication":"lung non-small cell carcinoma","therapy_id":660,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Osimertinib","efficacy_evidence":"In a retrospective analysis, BRAF V600E and FGFR3 K650E were identified at the time of progression on Tagrisso (osimertinib) treatment in a non-small cell lung cancer patient harboring EGFR L858R (%%PUBMED:37806383%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E EGFR L858R FGFR3 K650E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[34376578],"response_type":"predicted - sensitive","indication":"melanoma","therapy_id":6754,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Palbociclib + Ulixertinib","efficacy_evidence":"In a preclinical study, combination treatment with Ibrance (palbociclib) and Ulixertinib (BVD-523) led to inhibition of tumor growth in a patient-derived xenograft (PDX) model of melanoma harboring BRAF V600E, NRAS G12V, and CDKN2A copy number loss (%%PUBMED:34376578%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E CDKN2A del NRAS G12V","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"pub_med_references":[34376578],"response_type":"predicted - sensitive","indication":"melanoma","therapy_id":1368,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Palbociclib + Trametinib","efficacy_evidence":"In a preclinical study, combination treatment with Ibrance (palbociclib) and Mekinist (trametinib) led to inhibition of tumor growth in a patient-derived xenograft (PDX) model of melanoma harboring BRAF V600E, NRAS G12V, and CDKN2A copy number loss (%%PUBMED:34376578%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E CDKN2A del NRAS G12V","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"therapy_id":698,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a retrospective analysis of a Phase III trial (J-ALEX), BRAF V600E was identified in the post-progression cell-free DNA of a patient with non-small lung cancer with ALK rearrangement who progressed on treatment with Alecensa (alectinib) (%%PUBMED:40912045%%).","therapy":"Alectinib","evidence_type":"Actionable","normalized_cancer":"Non-Small Cell Lung Cancer","indication":"lung non-small cell carcinoma","approval_status":"Case Reports/Case Series","normalized_drug":"Alectinib","pub_med_references":[40912045],"molecular_profile":"ALK rearrange BRAF V600E","profile_array":[{"type":"rearrange","gene":"ALK"}],"response_type":"predicted - resistant"},{"pub_med_references":[24112705],"response_type":"resistant","indication":"melanoma","therapy_id":1060,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"PLX4720","efficacy_evidence":"In a preclinical study, a melanoma cell line harboring BRAF V600E and expressing F516G was resistant to PLX4720 in culture (%%PUBMED:24112705%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF F516G BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[24112705],"response_type":"sensitive","indication":"melanoma","therapy_id":2427,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"U0126","efficacy_evidence":"In a preclinical study, U0126 inhibited Erk phosphorylation and downstream signaling and viability in a melanoma cell line harboring BRAF V600E and expressing BRAF F516G in culture (%%PUBMED:24112705%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF F516G BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"resistant","pub_med_references":[40481178],"normalized_drug":"Vemurafenib","indication":"colorectal cancer","therapy_id":342,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a preclinical study, Src-overexpressing colorectal cancer cell lines harboring BRAF V600E were resistant to Zelboraf (vemurafenib) in culture (%%PUBMED:40481178%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E SRC over exp","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"resistant","pub_med_references":[40481178],"normalized_drug":"Encorafenib","indication":"colorectal cancer","therapy_id":796,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Encorafenib","efficacy_evidence":"In a preclinical study, Src-overexpressing colorectal cancer cell lines harboring BRAF V600E were resistant to Braftovi (encorafenib) in culture (%%PUBMED:40481178%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E SRC over exp","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - resistant","pub_med_references":[36849494],"normalized_drug":"Osimertinib","indication":"lung non-small cell carcinoma","therapy_id":660,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Osimertinib","efficacy_evidence":"In a Phase III trial (FLAURA), EGFR C797S, BRAF V600E, and PIK3CA H1047R were identified at the time of progression on Tagrisso (osimertinib) in a patient with non-small cell lung cancer harboring EGFR E746_A750del (%%PUBMED:36849494%%; NCT02296125).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E EGFR E746_A750del EGFR C797S PIK3CA H1047R","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - resistant","pub_med_references":[36849494],"normalized_drug":"Osimertinib","indication":"lung non-small cell carcinoma","therapy_id":660,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Osimertinib","efficacy_evidence":"In a Phase III trial (FLAURA), EGFR C797S, BRAF V600E, and SPTBN1-ALK were identified at the time of progression on Tagrisso (osimertinib) in a patient with non-small cell lung cancer harboring EGFR E746_A750del (%%PUBMED:36849494%%; NCT02296125).","cap_asco_evidence_level":"D","molecular_profile":"SPTBN1 - ALK BRAF V600E EGFR E746_A750del EGFR C797S","approval_status":"Case Reports/Case Series","amp_tier":"II"}],"extended_evidence":[{"pub_med_references":[29674508],"response_type":"predicted - sensitive","indication":"melanoma","therapy_id":1217,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Vemurafenib + XL888","efficacy_evidence":"In a Phase I trial, combined Zelboraf (vemurafenib) and XL888 treatment in patients with unresectable, BRAF inhibitor naive, metastatic melanoma harboring BRAF V600E (n=20) or V600K (n=1) resulted in complete and partial responses in 15% (3/20) and 60% (12/20) of evaluable patients, respectively, a 9.2-month median progression free survival, and a 34.6-month overall survival (%%PUBMED:29674508%%).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E/K","approval_status":"Phase I","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Vemurafenib","indication":"skin melanoma","therapy_id":342,"normalized_cancer":"Cutaneous Melanoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"Zelboraf (vemurafenib) therapy is included in cutaneous melanoma guidelines for patients with metastatic or unresectable disease harboring a BRAF V600 activating mutation (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E/K","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[22663011],"normalized_drug":"Trametinib","indication":"melanoma","therapy_id":2,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Trametinib","efficacy_evidence":"In a Phase III trial (METRIC) that supported FDA approval, Mekinist (trametinib) treatment, as compared to Deticine (dacarbazine) or Taxol (paclitaxel) treatment, resulted in improved progression-free survival of 4.8 months versus 1.5 months and an overall six month survival rate of 81% versus 67% in patients with BRAF V600E/K positive metastatic melanoma (%%PUBMED:22663011%%; NCT01245062).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E/K","approval_status":"FDA approved - On Companion Diagnostic","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[22805292],"normalized_drug":"Trametinib","indication":"melanoma","therapy_id":2,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Trametinib","efficacy_evidence":"In a Phase I trial, Mekinist (trametinib) resulted in complete response in 7% (2/30), partial response in 33% (10/30), and stable disease in 37% (11/30) of BRAF-mutant melanoma patients (%%PUBMED:22805292%%; NCT00687622).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E/K","approval_status":"Phase I","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[27480103],"normalized_drug":"Cobimetinib, Vemurafenib","indication":"melanoma","therapy_id":1657,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"In a Phase III trial (coBRIM) that supported FDA approval, treatment with the combination of Zelboraf (vemurafenib) and Cotellic (cobimetinib) resulted in an improved progression-free survival of 12.3 months, compared to 7.2 months with Zelboraf (vemurafenib) plus placebo, among patients with BRAF V600-mutated metastatic melanoma, and BRAF V600E and BRAF V600K are on the companion diagnostic (%%PUBMED:27480103%%; NCT01689519).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E/K","approval_status":"FDA approved - On Companion Diagnostic","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[33020646],"normalized_drug":"Dabrafenib, Trametinib","indication":"melanoma","therapy_id":1066,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a Phase II trial (S1320), intermittent dosing (3-week-off, 5-week-on) of Tafinlar (dabrafenib) and Mekinist (trametinib) did not improve median progression-free survival (5.5 v 9.0 months; HR=1.36, p=0.064, two-sided alpha=0.2) compared to continuous dosing in melanoma patients harboring BRAF V600E or V600K, and there were no significant differences in median overall survival, treatment response, or toxicity between the two treatment groups (%%PUBMED:33020646%%; NCT02196181).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E/K","approval_status":"Phase II","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[25399551],"normalized_drug":"Dabrafenib, Trametinib","indication":"melanoma","therapy_id":1066,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a Phase III trial (COMBI-v) that supported FDA approval, the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) resulted in an improved overall survival rate at 12 months (72% vs 65%, HR=0.69, p=0.005), median progression-free survival (11.4 vs 7.3 months, HR=0.56, p<0.001), and objective response rate (64% vs 51%, p<0.001) compared to Zelboraf (vemurafenib) in melanoma patients harboring BRAF V600E or V600K (%%PUBMED:25399551%%; NCT01597908).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E/K","approval_status":"FDA approved - On Companion Diagnostic","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[28891408],"normalized_drug":"Dabrafenib, Trametinib","indication":"melanoma","therapy_id":1066,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a Phase III trial (COMBI-AD) that supported FDA approval, adjuvant treatment with the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) resulted in an improved estimated 3-year relapse-free survival rate (58% vs 39%, HR=0.47, P<0.001) and 3-year overall survival rate (86% vs 77%, HR=0.57; 95% CI, 0.42 to 0.79, P=0.0006) compared to placebo in stage III melanoma patients harboring BRAF V600E or V600K mutations (%%PUBMED:28891408%%; NCT01682083).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E/K","approval_status":"FDA approved - On Companion Diagnostic","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[30959471],"normalized_drug":"Binimetinib, Encorafenib","indication":"skin melanoma","therapy_id":1100,"normalized_cancer":"Cutaneous Melanoma","evidence_type":"Actionable","therapy":"Binimetinib + Encorafenib","efficacy_evidence":"Braftovi (encorafenib) in combination with Mektovi (binimetinib) is included in guidelines as first-line and second-line therapy for patients with metastatic or unresectable cutaneous melanoma harboring BRAF V600E or V600K mutations (%%PUBMED:30959471%%; NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E/K","approval_status":"Guideline","amp_tier":"I"},{"response_type":"predicted - sensitive","pub_med_references":[32182156],"normalized_drug":"Lifirafenib","indication":"melanoma","therapy_id":4025,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Lifirafenib","efficacy_evidence":"In a Phase I trial, Lifirafenib (BGB-283) treatment resulted in partial response in 15.1% (8/53) of solid tumor patients with BRAF mutations, including 5 of 23 patients with melanoma harboring BRAF V600E or V600K overall, and in the dose expansion phase 57.1% (4/7) patient with BRAF V600-mutant melanoma had a partial response (%%PUBMED:32182156%%; NCT02610361).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E/K","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[29573941],"normalized_drug":"Binimetinib, Encorafenib","indication":"melanoma","therapy_id":1100,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Binimetinib + Encorafenib","efficacy_evidence":"In a Phase III (COLUMBUS) trial that supported FDA approval, Braftovi (encorafenib) in combination with Mektovi (binimetinib) demonstrated improved tolerability profile and efficacy, resulted in a progression-free survival of 14.9 months in patients with advanced melanoma harboring BRAF V600E/K mutations, comparing to 7.3 months in the Zelboraf (vemurafenib) group (HR=0.54, p<0.0001) (%%PUBMED:29573941%%; NCT01909453) and both BRAF V600E and V600K are on the companion diagnostic.","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E/K","approval_status":"FDA approved - On Companion Diagnostic","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[30219628],"normalized_drug":"Binimetinib, Encorafenib","indication":"melanoma","therapy_id":1100,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Binimetinib + Encorafenib","efficacy_evidence":"In a Phase III (COLUMBUS) trial that supported FDA approval, Braftovi (encorafenib) in combination with Mektovi (binimetinib) resulted in a median overall survival (OS) of 33.6 months, a 1-year OS rate of 77.5%, and a 2-year OS rate of 57.7% in patients with advanced melanoma harboring BRAF V600E/K mutations compared to a median OS of 16.9 months and 1- and 2-year OS rates of 63.1% and 43.2%, respectively, in the Zelboraf (vemurafenib) treated group (%%PUBMED:30219628%%; NCT01909453).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E/K","approval_status":"FDA approved - On Companion Diagnostic","amp_tier":"I"},{"pub_med_references":[27974663],"response_type":"predicted - sensitive","profile_array":[{"type":"act mut","gene":"BRAF"}],"indication":"colorectal cancer","therapy_id":12380,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"VX-11e + WEHI-539","efficacy_evidence":"In a preclinical study, inhibition of Erk signaling by VX-11e sensitized colorectal cancer cell lines harboring KRAS or BRAF activating mutations to WEHI-539 in culture (%%PUBMED:27974663%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF act mut","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"therapy_id":1041,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a preclinical study, PLX8394 had been shown to block survival and growth of vemurafenib/PLX4720-resistant cells harboring distinct BRAF activating mutations (%%PUBMED:24422853%%).","therapy":"PLX8394","evidence_type":"Actionable","normalized_cancer":"All Solid Tumors","indication":"Advanced Solid Tumor","approval_status":"Preclinical","normalized_drug":"Plx8394","pub_med_references":[24422853],"molecular_profile":"BRAF act mut","profile_array":[{"type":"act mut","gene":"BRAF"}],"response_type":"sensitive"},{"response_type":"sensitive","profile_array":[{"type":"act mut","gene":"BRAF"}],"normalized_drug":"Binimetinib, Encorafenib","indication":"Advanced Solid Tumor","therapy_id":1100,"normalized_cancer":"All Solid Tumors","evidence_type":"Actionable","therapy":"Binimetinib + Encorafenib","efficacy_evidence":"In a Phase Ib/II trial, Mektovi (binimetinib), in combination with Encorafenib (LGX818), demonstrated safety and efficacy in patients with BRAF mutant advanced solid tumors (J Clin Oncol 31, 2013 (suppl; abstr 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(%%PUBMED:27307593%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF mutant","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"therapy_id":2,"amp_tier":"II","cap_asco_evidence_level":"C","efficacy_evidence":"In a Phase II trial (NCI-MATCH), Mekinist (trametinib) treatment did not demonstrate clinical activity in patients with advanced solid tumors or lymphoma harboring BRAF fusion (n=1) or non-V600 mutations (n=31), resulted in a partial response in 3% (1/32) and stable disease in 31% (10/32) of the patients, with a median progression-free survival of 1.8 months, and a median overall survival of 5.7 months (%%PUBMED:31924734%%; NCT02465060).","therapy":"Trametinib","evidence_type":"Actionable","normalized_cancer":"All Solid Tumors","indication":"Advanced Solid Tumor","approval_status":"Phase II","normalized_drug":"Trametinib","pub_med_references":[31924734],"molecular_profile":"BRAF mutant","profile_array":[{"type":"mutant","gene":"BRAF"}],"response_type":"no 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regression in patient-derived xenograft models of BRAF-mutant cervical carcinoma (Cancer Res 2017;77(13 Suppl):Abstract nr 5168).","cap_asco_evidence_level":"D","molecular_profile":"BRAF mutant","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"therapy_id":2,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a preclinical study, Mekinist (trametinib) inhibited growth of human pancreatic adenocarcinoma cells harboring mutant BRAF in culture (%%PUBMED:26343583%%).","therapy":"Trametinib","evidence_type":"Actionable","normalized_cancer":"Pancreatic Adenocarcinoma","indication":"pancreatic adenocarcinoma","approval_status":"Preclinical","normalized_drug":"Trametinib","molecular_profile":"BRAF mutant","profile_array":[{"type":"mutant","gene":"BRAF"}],"response_type":"sensitive"},{"response_type":"sensitive","profile_array":[{"type":"mutant","gene":"BRAF"}],"indication":"colorectal cancer","therapy_id":1034,"normalized_cancer":"Colorectal 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those who never received immunotherapy (%%PUBMED:31367539%%).","cap_asco_evidence_level":"NA","molecular_profile":"BRAF mutant","approval_status":"Clinical Study","amp_tier":"NA"},{"response_type":"unknown","profile_array":[{"type":"mutant","gene":"BRAF"}],"indication":"lung non-small cell carcinoma","therapy_id":10383,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"unspecified immune checkpoint inhibitor","efficacy_evidence":"In a retrospective clinical study, patients with non-small cell lung cancer harboring rare targetable drivers (RTD) (BRAF, ERBB2/3, RET, MET, ROS1, NTRK) who received immune checkpoint inhibitors (ICI) achieved longer median overall survival (mOS) (32 vs 13 mo, p=0.01) compared to those who did not receive ICI, mOS was not reached in patients harboring BRAF non-V600E (n=5) mutations, although RTD type was not associated with OS in a univariate analysis (%%PUBMED:30268448%%).","cap_asco_evidence_level":"NA","molecular_profile":"BRAF mutant","approval_status":"Clinical Study - Cohort","amp_tier":"NA"},{"pub_med_references":[26351322],"response_type":"sensitive","profile_array":[{"type":"mutant","gene":"BRAF"}],"indication":"colorectal cancer","therapy_id":4791,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"AZ628 + Selumetinib","efficacy_evidence":"In a preclinical study, Koselugo (selumetinib) and AZ628 synergistically inhibited Mapk signaling and cell proliferation in BRAF mutant colorectal cancer cell lines in culture (%%PUBMED:26351322%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF mutant","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","profile_array":[{"type":"mutant","gene":"BRAF"}],"indication":"Advanced Solid Tumor","therapy_id":1034,"normalized_cancer":"All Solid 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mutant","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[30482852],"response_type":"predicted - sensitive","profile_array":[{"type":"mutant","gene":"BRAF"}],"indication":"melanoma","therapy_id":9743,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"UNC2025 + Vemurafenib","efficacy_evidence":"In a preclinical study, the combination therapy of UNC2025 and Zelboraf (vemurafenib) resulted in greater inhibition of colony formation and apoptotic induction in melanoma cells harboring a BRAF mutation in culture and led to a higher degree of tumor growth inhibition in a patient derived xenograft (PDX) model of melanoma with a BRAF mutation when compared to either therapy alone (%%PUBMED:30482852%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF mutant","approval_status":"Preclinical - Pdx & cell culture","amp_tier":"II"},{"pub_med_references":[25873592],"response_type":"predicted - 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(%%PUBMED:27307593%%).","therapy":"Buparlisib","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Preclinical - Cell line xenograft","normalized_drug":"Buparlisib","pub_med_references":[27307593],"molecular_profile":"BRAF mutant","profile_array":[{"type":"mutant","gene":"BRAF"}],"response_type":"sensitive"},{"response_type":"predicted - sensitive","profile_array":[{"type":"mutant","gene":"BRAF"}],"indication":"pancreatic cancer","therapy_id":5747,"normalized_cancer":"Pancreatic Cancer","evidence_type":"Actionable","therapy":"KO-947","efficacy_evidence":"In a preclinical study, KO-947 inhibited Erk signaling and induced tumor regression in patient-derived xenograft models of BRAF-mutant pancreatic cancer (Cancer Res 2017;77(13 Suppl):Abstract nr 5168).","cap_asco_evidence_level":"D","molecular_profile":"BRAF mutant","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"response_type":"not applicable","profile_array":[{"type":"mutant","gene":"BRAF"}],"indication":"splenic marginal zone lymphoma","therapy_id":1776,"normalized_cancer":"Splenic Marginal Zone Lymphoma","evidence_type":"Diagnostic","therapy":"N/A","efficacy_evidence":"BRAF mutations aid in the diagnosis of splenic marginal zone lymphoma (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF mutant","approval_status":"Guideline","amp_tier":"I"},{"response_type":"no benefit","profile_array":[{"type":"mutant","gene":"BRAF"}],"indication":"Advanced Solid Tumor","therapy_id":2874,"normalized_cancer":"All Solid Tumors","evidence_type":"Actionable","therapy":"CC-90003","efficacy_evidence":"In a Phase Ia trial, CC-90003 treatment did not result in any objective responses and demonstrated toxicity in advanced solid tumor patients harboring KRAS, NRAS, or BRAF mutations (AJ Clin Oncol 35, 2017 (suppl; abstr 2577)).","cap_asco_evidence_level":"C","molecular_profile":"BRAF mutant","approval_status":"Phase 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months in BRAF inhibitor-pretreated patients (%%PUBMED:28611198%%; NCT01436656).","therapy":"Encorafenib","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Phase I","normalized_drug":"Encorafenib","pub_med_references":[28611198],"molecular_profile":"BRAF mutant","profile_array":[{"type":"mutant","gene":"BRAF"}],"response_type":"sensitive"},{"response_type":"predicted - sensitive","profile_array":[{"type":"mutant","gene":"BRAF"}],"normalized_drug":"Binimetinib, Encorafenib","indication":"Advanced Solid Tumor","therapy_id":1100,"normalized_cancer":"All Solid Tumors","evidence_type":"Actionable","therapy":"Binimetinib + Encorafenib","efficacy_evidence":"In a Phase II trial (BEAVER), Mektovi (binimetinib) and Braftovi (encorafenib) combination therapy demonstrated safety and preliminary efficacy in advanced solid tumor patients harboring BRAF non-V600E mutations including class 1 (n=1), class 2 (n=4), and class 3 (n=5), with an objective response rate of 22% (2/9) and a partial response in a patient with ampullary cancer harboring BRAF D594G and an unconfirmed PR in a melanoma patient harboring BRAF G469S (Annals of Oncology 32 (2021): S596; NCT03839342).","cap_asco_evidence_level":"C","molecular_profile":"BRAF mutant","approval_status":"Phase II","amp_tier":"II"},{"response_type":"predicted - sensitive","profile_array":[{"type":"mutant","gene":"BRAF"}],"indication":"stomach carcinoma","therapy_id":5747,"normalized_cancer":"Stomach Adenocarcinoma","evidence_type":"Actionable","therapy":"KO-947","efficacy_evidence":"In a preclinical study, KO-947 inhibited Erk signaling and induced tumor regression in patient-derived xenograft models of BRAF-mutant gastric carcinoma (Cancer Res 2017;77(13 Suppl):Abstract nr 5168).","cap_asco_evidence_level":"D","molecular_profile":"BRAF mutant","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"response_type":"predicted - 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complete response in 33% (1/3) and partial response in 67% (2/3) of BRAFi-nau00efve melanoma patients harboring BRAF mutations (J Clin Oncol 33, 2015 (suppl; abstr 9076)).","cap_asco_evidence_level":"C","molecular_profile":"BRAF mutant","approval_status":"Phase I","amp_tier":"II"},{"pub_med_references":[27307593],"response_type":"sensitive","profile_array":[{"type":"mutant","gene":"BRAF"}],"indication":"melanoma","therapy_id":1337,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Buparlisib + Encorafenib","efficacy_evidence":"In a preclinical study, the combination of Buparlisib (BKM120) and Encorafenib (LGX818) resulted in improved cell growth inhibition compared to either agent alone in a metastatic melanoma cell line harboring a BRAF mutation in culture (%%PUBMED:27307593%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF mutant","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - 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regression in 50% (5/10) of patient-derived xenograft (PDX) models of colorectal cancer harboring BRAF mutations (J Clin Oncol 38: 2020 (suppl; abstr 3585)).","cap_asco_evidence_level":"D","molecular_profile":"BRAF mutant","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"therapy_id":913,"amp_tier":"II","cap_asco_evidence_level":"C","efficacy_evidence":"In a Phase I study, Koselugo (selumetinib) demonstrated an increase in iodine uptake and retention in a subgroup of patients with thyroid cancer that was refractory to radioiodine, including patients with BRAF and NRAS mutations (%%PUBMED:23406027%%).","therapy":"Selumetinib","evidence_type":"Actionable","normalized_cancer":"Thyroid Cancer","indication":"thyroid cancer","approval_status":"Phase I","normalized_drug":"Selumetinib","pub_med_references":[23406027],"molecular_profile":"BRAF mutant","profile_array":[{"type":"mutant","gene":"BRAF"}],"response_type":"predicted - 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however, the trial was terminated early due to poor accrual (%%PUBMED:30120161%%; NCT02175654).","therapy":"Regorafenib","evidence_type":"Actionable","normalized_cancer":"Colorectal Cancer","indication":"colorectal cancer","approval_status":"Phase II","normalized_drug":"Regorafenib","pub_med_references":[30120161],"molecular_profile":"BRAF mutant","profile_array":[{"type":"mutant","gene":"BRAF"}],"response_type":"no benefit"},{"pub_med_references":[37219686],"response_type":"sensitive","profile_array":[{"type":"mutant","gene":"BRAF"}],"indication":"melanoma","therapy_id":1034,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Tovorafenib","efficacy_evidence":"In a Phase I trial, Ojemda (tovorafenib) treatment resulted in stable disease in 23% (5/22) of patients with advanced solid tumors in the dose escalation phase, an objective response rate of 15% (10/68) in the dose expansion phase with responses in 50% (8/16) of patients with RAF and MEK inhibitor-naive BRAF-mutant melanoma, an overall median duration of response of 6.0 months, and a median progression-free survival of 1.9 months (%%PUBMED:37219686%%; NCT01425008).","cap_asco_evidence_level":"C","molecular_profile":"BRAF mutant","approval_status":"Phase I","amp_tier":"II"},{"response_type":"sensitive","profile_array":[{"type":"mutant","gene":"BRAF"}],"indication":"melanoma","therapy_id":1034,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Tovorafenib","efficacy_evidence":"In a preclinical study, Ojemda (tovorafenib) demonstrated efficacy in BRAF mutant xenograft models of melanoma and colorectal cancer (J Clin Oncol 31, 2013 (suppl; abstr e13529)).","cap_asco_evidence_level":"D","molecular_profile":"BRAF mutant","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[28611205],"response_type":"sensitive","profile_array":[{"type":"mutant","gene":"BRAF"}],"indication":"colorectal 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of 94% (34/36), and median progression-free survival of 23 months in patients with BRAF V600-mutant metastatic melanoma, including 29 patients (81%) harboring BRAF V600E and 4 patients (11%) harboring BRAF V600K (%%PUBMED:33020648%%; NCT02967692).","cap_asco_evidence_level":"B","molecular_profile":"BRAF V600X","approval_status":"Phase III","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[30285222],"normalized_drug":"Dabrafenib, Trametinib","indication":"lung non-small cell carcinoma","therapy_id":1066,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"The combination of Tafinlar (dabrafenib) and Mekinist (trametinib) is included in guidelines as first-line therapy for patients with metastatic non-small cell lung cancer harboring a BRAF V600 mutation, or as subsequent therapy in patients harboring BRAF V600 mutations that have not received prior BRAF/MEK inhibitor therapy (%%PUBMED:30285222%%; ESMO.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600X","approval_status":"Guideline","amp_tier":"I"},{"response_type":"predicted - sensitive","pub_med_references":[31506385],"normalized_drug":"Dabrafenib","indication":"Advanced Solid Tumor","therapy_id":3,"normalized_cancer":"All Solid Tumors","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a Phase I trial (BRF116013), Tafinlar (dabrafenib) treatment was well tolerated and demonstrated preliminary efficacy, resulted in a median duration of treatment of 75.6 week in pediatric patients with BRAF V600-mutant advanced solid tumors, including low-grade (n=15) and high-grade (n=8) gliomas, Langerhans cell histiocytosis (n=2), neuroblastoma (n=1), and papillary thyroid cancer (n=1) (%%PUBMED:31506385%%; NCT01677741).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600X","approval_status":"Phase I","amp_tier":"II"},{"response_type":"predicted - 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a BRAF V600 mutation resulted in a best objective response rate of 76.5% (13/17), with a complete response in 17.6% (3/17), a median progression-free survival of 10.9 months, a median overall survival of 46.2 months, and median duration of confirmed response of 10.6 months (%%PUBMED:31171876%%; NCT01656642).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600X","approval_status":"Phase Ib/II","amp_tier":"II"},{"response_type":"sensitive","indication":"subependymal giant cell astrocytoma","therapy_id":1034,"normalized_cancer":"Low-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"Tovorafenib","efficacy_evidence":"Ojemda (tovorafenib) is included in guidelines (category 2A) for patients with recurrent or progressive circumscribed glioma, including subependymal giant cell astrocytoma, harboring BRAF fusions, rearrangements, or BRAF V600 mutations (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600X","approval_status":"Guideline","amp_tier":"I"},{"response_type":"predicted - sensitive","pub_med_references":[32182156],"normalized_drug":"Lifirafenib","indication":"Advanced Solid Tumor","therapy_id":4025,"normalized_cancer":"All Solid Tumors","evidence_type":"Actionable","therapy":"Lifirafenib","efficacy_evidence":"In a Phase I trial, Lifirafenib (BGB-283) treatment demonstrated safety and resulted in partial response (PR) in 15.1% (8/53) of advanced solid tumor patients harboring a BRAF mutation, including 5 patients with BRAF V600E/K-mutant melanoma, 2 patients with BRAF V600E-mutant thyroid cancer, and 1 patient with BRAF V600E-mutant low-grade serous ovarian carcinoma, complete response in 1.9% (1/53), in a patient with melanoma, and stable disease in 50.9% (27/53) (%%PUBMED:32182156%%; NCT02610361).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600X","approval_status":"Phase I","amp_tier":"II"},{"pub_med_references":[37978284],"response_type":"sensitive","indication":"childhood low-grade glioma","therapy_id":1034,"normalized_cancer":"Low-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"Tovorafenib","efficacy_evidence":"In a Phase II trial (FIREFLY-1) that supported FDA approval, Ojemda (tovorafenib) was well tolerated and resulted in an overall response rate (ORR) per RAPNO criteria of 51% (39/76, 28 partial and 11 minor responses), clinical benefit rate (CBR) of 82% (62/76), and median duration of response of 13.8 mo in pediatric patients with low-grade glioma harboring BRAF fusions, rearrangements, or BRAF V600 mutations, with an ORR of 50% (6/12) in patients harboring BRAF V600E (%%PUBMED:37978284%%; NCT04775485).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600X","approval_status":"FDA approved","amp_tier":"I"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"skin melanoma","therapy_id":1066,"normalized_cancer":"Cutaneous Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Tafinlar (dabrafenib) and Mekinist (trametinib) combination therapy is included in guidelines as neoadjuvant or adjuvant therapy for stage III disease and as second-line or subsequent therapy for patients with metastatic or unresectable cutaneous melanoma harboring a BRAF V600 mutation (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600X","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[39550033],"normalized_drug":"Dabrafenib, Trametinib","indication":"skin melanoma","therapy_id":1066,"normalized_cancer":"Cutaneous Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"BRAF inhibitor plus MEK inhibitor combination therapy, such as Tafinlar (dabrafenib) plus Mekinist (trametinib), is included in guidelines for cutaneous melanoma patients with unresectable or metastatic disease harboring a BRAF V600 mutation (%%PUBMED:39550033%%; ESMO.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600X","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[24265152],"response_type":"sensitive","indication":"melanoma","therapy_id":4653,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"MK2206 + Trametinib","efficacy_evidence":"In a preclinical study, the combination of MK2206 and Mekinist (trametinib) inhibited growth of BRAF V600-mutant melanoma cell lines in culture, with increased efficacy over either agent alone (%%PUBMED:24265152%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600X","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[24265152],"response_type":"sensitive","indication":"melanoma","therapy_id":3773,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Selumetinib + Vemurafenib","efficacy_evidence":"In a preclinical study, the combination of Koselugo (selumetinib) and Zelboraf (vemurafenib) inhibited growth of BRAF V600-mutant melanoma cell lines in culture, with increased efficacy over either agent alone (%%PUBMED:24265152%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600X","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[31959346],"normalized_drug":"Vemurafenib","indication":"lung non-small cell carcinoma","therapy_id":342,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase II trial, Zelboraf (vemurafenib) treatment resulted in a objective response rate of 44.8% (43/96), median duration of response of 6.4 months, median progression-free survival of 5.2 months, and median overall survival of 10 months in non-small cell lung cancer patients with BRAF V600 mutations (%%PUBMED:31959346%%; NCT02304809).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600X","approval_status":"Phase II","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[26287849],"normalized_drug":"Vemurafenib","indication":"lung non-small cell carcinoma","therapy_id":342,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase II trial, treatment with Zelboraf (vemurafenib) resulted in an overall response rate of 42% (8/19, 8 partial responses) in patients with non-small cell lung cancer harboring BRAF V600 mutations, with a median progression-free survival of 7.3 months (%%PUBMED:26287849%%; NCT01524978}.","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600X","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Vemurafenib","indication":"skin melanoma","therapy_id":342,"normalized_cancer":"Cutaneous Melanoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"Zelboraf (vemurafenib) therapy is included in guidelines for patients with unresectable or metastatic cutaneous melanoma harboring BRAF V600 activating mutations, in cases where BRAF/MEK inhibitor combination therapy is contraindicated (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600X","approval_status":"Guideline","amp_tier":"I"},{"response_type":"predicted - sensitive","indication":"melanoma","therapy_id":11201,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Binimetinib + Encorafenib + Pembrolizumab","efficacy_evidence":"In a Phase I trial (IMMU-Target), Mektovi (binimetinib), Braftovi (encorafenib), and Keytruda (pembrolizumab) demonstrated safety and preliminary efficacy in treatment naive patients with advanced melanoma harboring BRAF V600 mutations, resulting in an overall response rate of 64% (9/14), with a 12-month progression-free survival rate of 37.5% (n=8) and 60% (n=6) at the two tested dose levels, respectively (J Clin Oncol 39, no. 15_suppl (May 20, 2021) 9532; NCT02902042).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600X","approval_status":"Phase I","amp_tier":"II"},{"response_type":"predicted - sensitive","normalized_drug":"Cobimetinib, Vemurafenib","indication":"lung non-small cell carcinoma","therapy_id":1657,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"In a Phase II trial, treatment with the combination of Zelboraf (vemurafenib) and Cotellic (cobimetinib) resulted in an objective response rate (ORR) of 50% (18/36), median progression-free survival of 7.9 months, and overall survival of 15.9 months in patients with advanced solid tumors harboring a BRAF V600 mutation and an ORR of 42% (10/24) in treatment-naive patients with non-small cell lung cancer harboring a BRAF V600 mutation (Ann Oncol (2024) 35 (Suppl_2): S498).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600X","approval_status":"Phase II","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Cobimetinib, Vemurafenib","indication":"skin melanoma","therapy_id":1657,"normalized_cancer":"Cutaneous Melanoma","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"Zelboraf (vemurafenib) and Cotellic (cobimetinib) combination therapy is included in guidelines as a second-line or subsequent therapy for patients with metastatic or unresectable cutaneous melanoma harboring a BRAF V600 activating mutation (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600X","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[39550033],"normalized_drug":"Cobimetinib, Vemurafenib","indication":"skin melanoma","therapy_id":1657,"normalized_cancer":"Cutaneous Melanoma","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"BRAF inhibitor plus MEK inhibitor combination therapy, such as Cotellic (cobimetinib) plus Zelboraf (vemurafenib), is included in guidelines for cutaneous melanoma patients with unresectable or metastatic disease harboring a BRAF V600 mutation (%%PUBMED:39550033%%; ESMO.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600X","approval_status":"Guideline","amp_tier":"I"},{"response_type":"predicted - sensitive","pub_med_references":[40411977],"normalized_drug":"Binimetinib, Encorafenib","indication":"melanoma","therapy_id":1100,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Binimetinib + Encorafenib","efficacy_evidence":"In a retrospective analysis, real-world treatment with the combination of Mektovi (binimetinib) and Braftovi (encorafenib) demonstrated activity in melanoma patients with brain metastases harboring a BRAF V600 mutation, with an objective response rate of 69.4% (125/180, 4 complete and 121 partial responses), median progression-free survival of 5.5 months, and median overall survival of 11.9 months (%%PUBMED:40411977%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600X","approval_status":"Clinical Study","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[31811016],"normalized_drug":"Dabrafenib","indication":"ganglioglioma","therapy_id":3,"normalized_cancer":"Ganglioglioma","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a Phase I/II trial, Tafinlar (dabrafenib) treatment resulted in a partial response in a pediatric patient with BRAF V600-mutant ganglioglioma (%%PUBMED:31811016%%; NCT01677741).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600X","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[24265152],"response_type":"sensitive","indication":"melanoma","therapy_id":1974,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Buparlisib + Trametinib","efficacy_evidence":"In a preclinical study, the combination of Buparlisib (BKM120) and Mekinist (trametinib) inhibited growth of BRAF V600-mutant melanoma cell lines in culture, with increased efficacy over either agent alone (%%PUBMED:24265152%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600X","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"melanoma","therapy_id":4754,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + Nivolumab + Trametinib","efficacy_evidence":"In a Phase II trial, combination of Tafinlar (dabrafenib), Mekinist (trametinib), and Opdivo (nivolumab) resulted in an objective response rate (ORR) of 92% (24/27, 3 CR, 21 PR) in patients with MEK inhibitor-naive, BRAF V600-mutated melanoma, with a median progression-free survival of 8.5 mos, ORR was 88% (14/16) and 100% (10/10) in PD1 refractory or naive patients, 57% (4/7) of patients with brain metastasis achieved intracranial response (J Clin Oncol 39, no. 15_suppl (May 20, 2021) 9520; NCT02910700).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600X","approval_status":"Phase II","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"lung non-small cell carcinoma","therapy_id":15985,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Tunlametinib + Vemurafenib","efficacy_evidence":"In a Phase I trial, the combination of Tunlametinib (HL-085) and Zelboraf (vemurafenib) demonstrated safety and resulted in an objective response rate of 60.6% (20/33), a median duration of response of 11.3 months, and a median progression free survival of 11.7 months in patients with advanced non-small cell lung cancer harboring a BRAF V600 mutation (Ann Oncol (2023) 34 (suppl_2): S790; NCT03781219).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600X","approval_status":"Phase I","amp_tier":"II"},{"pub_med_references":[26287849],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":1711,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Vemurafenib","efficacy_evidence":"In a Phase II trial, treatment with the combination of Zelboraf (vemurafenib) and Erbitux (cetuximab) resulted in an overall response rate of 4% (1/26), stable disease in 69% (18/26), and a median progression-free survival of 3.7 months in patients with BRAF V600-mutant colorectal cancer (%%PUBMED:26287849%%; NCT01524978).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600X","approval_status":"Phase II","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[36130145],"normalized_drug":"Ipilimumab, Nivolumab","indication":"melanoma","therapy_id":1627,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Ipilimumab + Nivolumab","efficacy_evidence":"In a retrospective analysis, melanoma patients harboring BRAF V600 mutations (V600E/K/R/D or V600_K601delinsE) treated with the combination of Yervoy (ipilimumab) and Opdivo (nivolumab) demonstrated significantly improved median progression-free survival (10.1 vs 5.2 months; P=0.0057) and median overall survival (not reached vs 16.9 months; P<0.0001) compared to patients without BRAF V600 mutations (%%PUBMED:36130145%%).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600X","approval_status":"Clinical Study - Cohort","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib","indication":"skin melanoma","therapy_id":3,"normalized_cancer":"Cutaneous Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"Tafinlar (dabrafenib) therapy is included in guidelines for patients with unresectable or metastatic cutaneous melanoma harboring BRAF V600 activating mutations, in cases where BRAF/MEK inhibitor combination therapy is contraindicated (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600X","approval_status":"Guideline","amp_tier":"I"},{"response_type":"predicted - sensitive","pub_med_references":[26287849],"normalized_drug":"Vemurafenib","indication":"cholangiocarcinoma","therapy_id":342,"normalized_cancer":"Cholangiocarcinoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase II trial, treatment with Zelboraf (vemurafenib) resulted in partial response in 12% (1/8) and stable disease in 50% (4/8) of cholangiocarcinoma patients with BRAF V600 mutations (%%PUBMED:26287849%%; NCT01524978).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600X","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[24265152],"response_type":"sensitive","indication":"melanoma","therapy_id":4234,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Trametinib + Vemurafenib","efficacy_evidence":"In a preclinical study, the combination of Mekinist (trametinib) and Zelboraf (vemurafenib) inhibited growth of BRAF V600-mutant melanoma cell lines in culture, with increased efficacy over either agent alone (%%PUBMED:24265152%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600X","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[31811016],"normalized_drug":"Dabrafenib","indication":"low grade glioma","therapy_id":3,"normalized_cancer":"Low-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a Phase I/II trial, Tafinlar (dabrafenib) treatment was well tolerated and demonstrated preliminary efficacy, resulted in an objective response rate of 44% (14/32, 1 complete response, 13 partial response) and a disease control rate of 78% (25/32), with a median duration of response of 26 months in pediatric patients with BRAF V600-mutant low-grade gliomas (%%PUBMED:31811016%%; NCT01677741).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600X","approval_status":"Phase Ib/II","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[29188284],"normalized_drug":"Vemurafenib","indication":"Erdheim-Chester disease","therapy_id":342,"normalized_cancer":"Erdheim-Chester Disease","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase II trial (VE-BASKET) that supported FDA approval, Zelboraf (vemurafenib) treatment resulted in an objective response rate of 54.5% (12/22, 1 complete and 11 partial responses) in patients with Erdheim-Chester disease harboring BRAF V600 mutations, with a 2-year progression-free survival rate of 83% and 2-year overall survival rate of 95% (%%PUBMED:29188284%%; NCT01524978).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600X","approval_status":"FDA approved","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[23414587],"normalized_drug":"Binimetinib","indication":"melanoma","therapy_id":807,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Binimetinib","efficacy_evidence":"In a Phase II trial, Mektovi (binimetinib) treatment resulted in a partial response in 20% (8/41) of melanoma patients harboring BRAF V600 mutations, including V600E (33/41), V600K (5/41), and V600R (1/41) (%%PUBMED:23414587%%; NCT01320085).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600X","approval_status":"Phase II","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[36375115],"normalized_drug":"Trametinib","indication":"low grade glioma","therapy_id":2,"normalized_cancer":"Low-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"Trametinib","efficacy_evidence":"In a Phase I/II trial, Mekinist (trametinib) treatment demonstrated a manageable safety profile in pediatric patients with BRAF V600-mutant low grade glioma, and resulted in an objective response rate of 15.4% (2/13, all partial responses), a clinical benefit rate of 61.5% (8/13), a median progression-free survival of 16.4 months, and median duration of response not reached (%%PUBMED:36375115%%; NCT02124772).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600X","approval_status":"Phase Ib/II","amp_tier":"II"},{"response_type":"predicted - sensitive","normalized_drug":"Plx8394","indication":"Advanced Solid Tumor","therapy_id":1041,"normalized_cancer":"All Solid Tumors","evidence_type":"Actionable","therapy":"PLX8394","efficacy_evidence":"In a Phase I/II trial, PLX8394 treatment resulted in a partial response in 39% (9/23) of patients with MAPK inhibitor-naive advanced solid tumors (excluding colorectal cancer) harboring BRAF V600X with a median duration of response of 32 months, and resulted in a partial response in 18% (3/17) and stable disease in 29% of patients previously treated with a MAPK inhibitor (J Clin Oncol 41, 2023 (suppl 16; abstr 3006); NCT02428712).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600X","approval_status":"Phase Ib/II","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[39550033],"normalized_drug":"Binimetinib, Encorafenib","indication":"skin melanoma","therapy_id":1100,"normalized_cancer":"Cutaneous Melanoma","evidence_type":"Actionable","therapy":"Binimetinib + Encorafenib","efficacy_evidence":"BRAF inhibitor plus MEK inhibitor combination therapy, such as Mektovi (binimetinib) plus Braftovi (encorafenib), is included in guidelines for cutaneous melanoma patients with unresectable or metastatic disease harboring a BRAF V600 mutation (%%PUBMED:39550033%%; ESMO.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600X","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","normalized_drug":"Binimetinib, Encorafenib","indication":"skin melanoma","therapy_id":1100,"normalized_cancer":"Cutaneous Melanoma","evidence_type":"Actionable","therapy":"Binimetinib + Encorafenib","efficacy_evidence":"Mektovi (binimetinib) and Braftovi (encorafenib) combination therapy is included in guidelines as a second-line or subsequent therapy for patients with metastatic or unresectable cutaneous melanoma harboring a BRAF V600 activating mutation (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600X","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[35022320],"response_type":"predicted - sensitive","indication":"melanoma","therapy_id":9169,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + Hydroxychloroquine + Trametinib","efficacy_evidence":"In a Phase I/II trial (BAMM), the combination of Tafinlar (dabrafenib), Mekinist (trametinib), and Plaquenil (hydroxychloroquine sulfate) resulted in a 1-year progression-free survival (PFS) rate of 48.2%, a median PFS of 11.2 mo, a response rate (RR) of 85% (29/34, 14 complete, 15 partial responses), and median overall survival (OS) of 26.5 mo in patients with advanced BRAF V600-mutant melanoma, RR, mPFS, and OS were 88%, 7.3, and 22 mo in patients with elevated LDH (n=16) (%%PUBMED:35022320%%; NCT02257424).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600X","approval_status":"Phase Ib/II","amp_tier":"II"},{"response_type":"sensitive","indication":"pilocytic astrocytoma","therapy_id":1034,"normalized_cancer":"Pilocytic Astrocytoma","evidence_type":"Actionable","therapy":"Tovorafenib","efficacy_evidence":"Ojemda (tovorafenib) is included in guidelines (category 2A) for patients with recurrent or progressive circumscribed glioma, including pilocytic astrocytoma, harboring BRAF fusions, rearrangements, or BRAF V600 mutations (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600X","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[24265152],"response_type":"sensitive","indication":"melanoma","therapy_id":1322,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Buparlisib + Vemurafenib","efficacy_evidence":"In a preclinical study, the combination of Buparlisib (BKM120) and Zelboraf (vemurafenib) inhibited growth of BRAF V600-mutant melanoma cell lines in culture, with increased efficacy over either agent alone (%%PUBMED:24265152%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600X","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","indication":"skin melanoma","therapy_id":1449,"normalized_cancer":"Cutaneous Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + Pembrolizumab + Trametinib","efficacy_evidence":"Tafinlar (dabrafenib) plus Mekinist (trametinib) in combination with an immune checkpoint inhibitor, such as Keytruda (pembrolizumab), is included in guidelines as second-line or subsequent therapy (category 2A) for patients with metastatic or unresectable cutaneous melanoma harboring a BRAF V600 mutation (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600X","approval_status":"Guideline","amp_tier":"I"},{"response_type":"predicted - sensitive","pub_med_references":[36375115],"normalized_drug":"Dabrafenib, Trametinib","indication":"low grade glioma","therapy_id":1066,"normalized_cancer":"Low-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a Phase I/II trial, Mekinist (trametinib) and Tafinlar (dabrafenib) combination treatment demonstrated a manageable safety profile in pediatric patients with BRAF V600-mutant low-grade glioma, and resulted in an objective response rate of 25% (9/36, all partial responses), a clinical benefit rate of 88.9% (32/36), a median duration of response of 33.6 months, and a median progression-free survival of 36.9 months (%%PUBMED:36375115%%; NCT02124772).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600X","approval_status":"Phase Ib/II","amp_tier":"II"},{"response_type":"no benefit","pub_med_references":[26287849],"normalized_drug":"Vemurafenib","indication":"colorectal cancer","therapy_id":342,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase II trial, treatment with Zelboraf (vemurafenib) in colorectal cancer patients with BRAF V600 mutations did not result in clinical benefit, with no patients achieving response, and 50% (5/10) demonstrating progressive disease (%%PUBMED:26287849%%; NCT01524978).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600X","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[26811525],"normalized_drug":"Dabrafenib, Trametinib","indication":"melanoma","therapy_id":1066,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a Phase I/II clinical trial, patients with BRAF V600 mutant melanoma (n=78) treated with the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) had a median overall survival of greater than 2 years (%%PUBMED:26811525%%).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600X","approval_status":"Phase Ib/II","amp_tier":"II"},{"response_type":"sensitive","indication":"melanoma","therapy_id":5827,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"ASN003","efficacy_evidence":"In a preclinical study, melanoma patient derived xenograft (PDX) model harboring a BRAF V600 mutation demonstrated antitumor activity when treated with ASN003 (J Clin Oncol 35, 2017 (suppl; abstr e14102)).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600X","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"brain cancer","therapy_id":9125,"normalized_cancer":"Primary Brain Tumor","evidence_type":"Actionable","therapy":"ABM-1310","efficacy_evidence":"In a Phase I trial, ABM-1310 treatment was well tolerated and resulted in preliminary antitumor activity with 3 partial responses and 8 stable disease among 13 patients with brain tumors harboring BRAF V600 mutations, including a partial response in a patient with glioblastoma and 2 partial responses in patients with pleomorphic xanthoastrocytoma (Ann Oncol (2024) 35 (suppl_2): S411; NCT05892653).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600X","approval_status":"Phase I","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"colorectal cancer","therapy_id":15985,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Tunlametinib + Vemurafenib","efficacy_evidence":"In a Phase I trial, the combination of Tunlametinib (HL-085) and Zelboraf (vemurafenib) demonstrated safety and resulted in an objective response rate of 25.0% (6/24), a median duration of response of 5.5 months, and a median progression free survival of 6.2 months in patients with advanced colorectal cancer harboring a BRAF V600 mutation (Ann Oncol (2023) 34 (suppl_2): S790; NCT03781219).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600X","approval_status":"Phase I","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[27480103],"normalized_drug":"Cobimetinib, Vemurafenib","indication":"melanoma","therapy_id":1657,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"In a Phase III trial, combination treatment with Zelboraf (vemurafenib) and Cotellic (cobimetinib) resulted in an improved progression-free survival of 12.3 months compared to 7.2 months with Zelboraf (vemurafenib) alone among patients with BRAF V600-mutated metastatic melanoma (%%PUBMED:27480103%%; NCT01689519).","cap_asco_evidence_level":"B","molecular_profile":"BRAF V600X","approval_status":"Phase III","amp_tier":"I"},{"pub_med_references":[24265152],"response_type":"sensitive","indication":"melanoma","therapy_id":4635,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"MK2206 + Vemurafenib","efficacy_evidence":"In a preclinical study, the combination of MK2206 and Zelboraf (vemurafenib) inhibited growth of BRAF V600-mutant melanoma cell lines in culture, with increased efficacy over either agent alone (%%PUBMED:24265152%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600X","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Atezolizumab, Cobimetinib, Vemurafenib","indication":"skin melanoma","therapy_id":4825,"normalized_cancer":"Cutaneous Melanoma","evidence_type":"Actionable","therapy":"Atezolizumab + Cobimetinib + Vemurafenib","efficacy_evidence":"Zelboraf (vemurafenib) plus Cotellic (cobimetinib) in combination with an immune checkpoint inhibitor, such as Tecentriq (atezolizumab), is included in guidelines as second-line or subsequent therapy (category 2A) for patients with metastatic or unresectable cutaneous melanoma harboring a BRAF V600 mutation (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600X","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[24265152],"response_type":"sensitive","indication":"melanoma","therapy_id":4652,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Buparlisib + Selumetinib","efficacy_evidence":"In a preclinical study, the combination of Buparlisib (BKM120) and Koselugo (selumetinib) inhibited growth of BRAF V600-mutant melanoma cell lines in culture, with increased efficacy over either agent alone (%%PUBMED:24265152%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600X","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"Advanced Solid Tumor","therapy_id":9125,"normalized_cancer":"All Solid Tumors","evidence_type":"Actionable","therapy":"ABM-1310","efficacy_evidence":"In a Phase I trial, ABM-1310 treatment was tolerated and demonstrated preliminary efficacy in patients with advanced solid tumors harboring BRAF V600X, resulting in 2 partial responses (1 pleomorphic xanthroastrocytoma, 1 glioblastoma) and 8 stable diseases among 16 evaluable patients (J Clin Oncol 41, 2023 (suppl 16; abstr 3098); NCT04190628).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600X","approval_status":"Phase I","amp_tier":"II"},{"response_type":"predicted - sensitive","normalized_drug":"Cobimetinib, Vemurafenib","indication":"Advanced Solid Tumor","therapy_id":1657,"normalized_cancer":"All Solid Tumors","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"In a Phase II trial, treatment with the combination of Zelboraf (vemurafenib) and Cotellic (cobimetinib) resulted in an objective response rate (ORR) of 50% (18/36), median progression-free survival of 7.9 months, and overall survival of 15.9 months in patients with advanced solid tumors harboring a BRAF V600 mutation and an ORR of 42% (10/24) in treatment-naive patients with non-small cell lung cancer harboring a BRAF V600 mutation (Ann Oncol (2024) 35 (Suppl_2): S498).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600X","approval_status":"Phase II","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"Advanced Solid Tumor","therapy_id":11782,"normalized_cancer":"All Solid Tumors","evidence_type":"Actionable","therapy":"Belvarafenib + Cobimetinib","efficacy_evidence":"In a Phase Ib trial, combination treatment with Belvarafenib (HM95573) and Cotellic (cobimetinib) was well-tolerated and demonstrated safety, and led to a confirmed partial response in 33.3% (3/9) solid tumor patients harboring BRAF V600 mutations (Annals of Oncology 32 (2021): S595; NCT03284502).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600X","approval_status":"Phase I","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"melanoma","therapy_id":15373,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"ABM-1310 + Cobimetinib","efficacy_evidence":"In a Phase I trial, the combination of ABM-1310 and Cotellic (cobimetinib) was tolerated and demonstrated preliminary efficacy in patients with advanced solid tumors harboring BRAF V600X, resulting in 1 partial response in a patient with melanoma and 1 stable disease among 3 evaluable patients (J Clin Oncol 41, 2023 (suppl 16; abstr 3098); NCT04190628).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600X","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","indication":"pleomorphic xanthoastrocytoma","therapy_id":1034,"normalized_cancer":"Pleomorphic Xanthoastrocytoma","evidence_type":"Actionable","therapy":"Tovorafenib","efficacy_evidence":"Ojemda (tovorafenib) is included in guidelines (category 2A) for patients with recurrent or progressive circumscribed glioma, including pleomorphic xanthoastrocytoma, harboring BRAF fusions, rearrangements, or BRAF V600 mutations (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600X","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","indication":"melanoma","therapy_id":1453,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + KRT-232 + Trametinib","efficacy_evidence":"In a Phase I trial, the combination therapy of KRT-232 (AMG 232), Mekinist (trametinib), and Tafinlar (dabrafenib) in 6 patients with metastatic cutaneous melanoma harboring a BRAF V600 mutation resulted in 4 patients with a partial response and 2 patients with stable disease, and of the 6 patients, all experienced tumor reduction (J Clin Oncol 35, 2017 (suppl; abstr 2575)).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600X","approval_status":"Phase I","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[32534646],"normalized_drug":"Atezolizumab, Cobimetinib, Vemurafenib","indication":"melanoma","therapy_id":4825,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Atezolizumab + Cobimetinib + Vemurafenib","efficacy_evidence":"In a Phase III trial (IMspire150) that supported FDA approval, addition of Tecentriq (atezolizumab) to Zelboraf (vemurafenib) and Cotellic (cobimetinib) combination therapy significantly improved progression-free survival (15.1 vs 10.6 months, HR=0.78, p=0.025) compared to control in patients with advanced or metastatic melanoma harboring BRAF V600 mutations (%%PUBMED:32534646%%; NCT02908672).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600X","approval_status":"FDA approved","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[31171876],"normalized_drug":"Atezolizumab, Cobimetinib, Vemurafenib","indication":"melanoma","therapy_id":4825,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Atezolizumab + Cobimetinib + Vemurafenib","efficacy_evidence":"In a Phase Ib trial, the combination therapy of Tecentriq (atezolizumab), Zelboraf (vemurafenib), and Cotellic (cobimetinib) in patients with metastatic melanoma harboring a BRAF V600 mutation resulted in a best objective response rate of 71.8% (28/39), with a complete response in 20.5% (8/39), a median progression-free survival of 12.9 months, a median overall survival not yet reached, and median duration of confirmed response of 17.4 months (%%PUBMED:31171876%%; NCT01656642).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600X","approval_status":"Phase Ib/II","amp_tier":"II"}],"gene_variant_descriptions":[{"pub_med_references":[15035987,18697864],"description":"BRAF V600E (previously reported as V599E) lies within the activation segment of the kinase domain of the Braf protein (PMID: 15035987). V600E confers a gain of function to the Braf protein as demonstrated by increased Braf kinase activity, downstream signaling, and the ability to transform cells in culture (PMID: 15035987, PMID: 29533785, PMID: 18697864)."}],"protein_effect":"gain of function","cap_asco_evidence_level":null,"polymorphism":null,"transforming_activity":true,"associated_with_drug_resistance":null}],"phastcons100way":[{"version":"14-Apr-2021","conservation_score":["1.000"]}],"phylop100way":[{"version":"13-Apr-2021","conservation_score":["9.201"]}],"maxentscan":null,"variant_pubmed_automap":[{"version":"22-Jul-2025","pub_med_references":[15009715,15277467,15294323,15342696,15356020,15694309,15735849,15781663,15782118,15811117,15902486,15947100,15947103,15948115,15948220,15998781,16001072,16007166,16021577,16024606,16079850,16123397,16143123,16219636,16219715,16266992,16268813,16299399,16361694,16403224,16410717,16452550,16487015,16540682,16551863,16557238,16567964,16601293,16606457,16647954,16691193,16702958,16757326,16757355,16772349,16801397,16818621,16818623,16873291,16880785,16890795,16896265,16918957,16932068,16964246,16964379,16983703,17001349,17006850,17044028,17054470,17065421,17082247,17087942,17096326,17101316,17119056,17148775,17159251,17159915,17186541,17199440,17199737,17260021,17273161,17293392,17295241,17298986,17299132,17312306,17317846,17355635,17363500,17374713,17381488,17387744,17409425,17415708,17427169,17429154,17440063,17453004,17453358,17464312,17465858,17478764,17488796,17510423,17518771,17520704,17542667,17545526,17566669,17641411,17685465,17693984,17696195,17696956,17714762,17717450,17721188,17724477,17727338,17785355,17824790,17854396,17868408,17878251,17914558,17942460,17950780,17956956,17962436,17962726,17972530,17974567,17989125,18006922,18032947,18056475,18058267,18061181,18070147,18089783,18096441,18098337,18186519,18227705,18235983,18280030,18283163,18287029,18310286,18310287,18310288,18360353,18383861,18393366,18403637,18408659,18426810,18428050,18451216,18451217,18462259,18470905,18473997,18491251,18519771,18524847,18556776,18559533,18591935,18615679,18615680,18621636,18628431,18631381,18636014,18644254,18669866,18676742,18676837,18676857,18679422,18682506,18697864,18710471,18715233,18718023,18753363,18757433,18778891,18782444,18790768,18794153,18794803,18798261,18806830,18829479,18840924,18945298,18985043,19001320,19010912,19014278,19016743,19033861,19034577,19040996,19055826,19066305,19076977,19079609,19087308,19088048,19126563,19147753,19152441,19156774,19158841,19159571,19169486,19190079,19190105,19190129,19200582,19207009,19208736,19213871,19269016,19274086,19276360,19289622,19338646,19342899,19351826,19355825,19358278,19363522,19370505,19371126,19383316,19383812,19389934,19393416,19398955,19404918,19414674,19415957,19424571,19430299,19440799,19441164,19474002,19475551,19498322,19500021,19534623,19547661,19561230,19561646,19572146,19574281,19582761,19603018,19626635,19627734,19637313,19652585,19659611,19663727,19669908,19672964,19693938,19710001,19724275,19738388,19745699,19752400,19765726,19850689,19855373,19861538,19878585,19880792,19881948,19883729,19893009,19903742,19913280,19913317,19919630,19931546,19936769,19949877,19959686,20001715,20012784,20023270,20025539,20027224,20068183,20102720,20130576,20149136,20156809,20162668,20171085,20177422,20179705,20186005,20187782,20197478,20200438,20230995,20233436,20299678,20300843,20367313,20369307,20381446,20393746,20406109,20410389,20412787,20413299,20417091,20417200,20425073,20447069,20459574,20470206,20472680,20473281,20473912,20485284,20489114,20494973,20496269,20501503,20518413,20519626,20531415,20543822,20551059,20551065,20564403,20570909,20576522,20605766,20607744,20607849,20616366,20630094,20631031,20635392,20640859,20645028,20647301,20652698,20668238,20670148,20674547,20679909,20682701,20716222,20730472,20735442,20806365,20818844,20837233,20854070,20857202,20924129,20925915,20926530,20942773,20944096,20945104,20952593,20953721,20959475,20962618,20972475,21048359,21049459,21051014,21081656,21098728,21102416,21107323,21113787,21131838,21131919,21134548,21134562,21136722,21167555,21169256,21179278,21185263,21190184,21190444,21199003,21206909,21220306,21221869,21224857,21227391,21239517,21249150,21251608,21263251,21274720,21279555,21289333,21295327,21307665,21315413,21326296,21343559,21349766,21351275,21352266,21354060,21355020,21358618,21385081,21412762,21430505,21430779,21430780,21431280,21436632,21441079,21447722,21447745,21449767,21455633,21457162,21458265,21479234,21483012,21496703,21498916,21505227,21511245,21512141,21516079,21519026,21521301,21526955,21527556,21527587,21554046,21558395,21568726,21570823,21587258,21594703,21609347,21610151,21615873,21615881,21635872,21636552,21638088,21639808,21653734,21659424,21660283,21663470,21666714,21671463,21681432,21693616,21694724,21707687,21708284,21716161,21717063,21726664,21730105,21733000,21733555,21738740,21743435,21750866,21770473,21774961,21788131,21791485,21793228,21795305,21796448,21802280,21803329,21818706,21825258,21826256,21826673,21827678,21844014,21859834,21862261,21875464,21879273,21882184,21884820,21889780,21897114,21900390,21903858,21905615,21906875,21910720,21937738,21940036,21943394,21945875,21948220,21979329,21995398,2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report","therapeutic_context":"dabrafenib","pub_med_references":[22608338,23470635]},{"effect":"gain-of-function","evidence":"consensus","pathway":"activation","source":"FDA","status":"FDA-approved","therapeutic_context":"vemurafenib, dabrafenib, trametinib, dabrafenib + trametinib"},{"effect":"gain-of-function","evidence":"emerging","pathway":"activation","source":"J Clin Oncol 2013;31 (suppl; abstr 9028)","status":"early trials","therapeutic_context":"BRAF inhibitors"},{"effect":"gain-of-function","evidence":"emerging","pathway":"activation","source":"22389471, 21156289","status":"preclinical","therapeutic_context":"BRAF inhibitors + PI3K pathway inhibitors","pub_med_references":[21156289,22389471]},{"effect":"gain-of-function","evidence":"emerging","pathway":"activation","source":"22351686","status":"preclinical","therapeutic_context":"BRAF inhibitors + HSP90 inhibitors","pub_med_references":[22351686]},{"effect":"gain-of-function","evidence":"emerging","pathway":"activation","source":"22997239.0","status":"preclinical","therapeutic_context":"BRAF inhibitors + CDK2/4 inhibitors"},{"effect":"gain-of-function","evidence":"emerging","pathway":"activation","source":"23614898, 22997239","status":"preclinical","therapeutic_context":"preclinical","pub_med_references":[22997239,23614898]},{"effect":"gain-of-function","evidence":"emerging","pathway":"activation","source":"22608338, 20818844, 23489023","status":"early trials","therapeutic_context":"vemurafenib, dabrafenib","pub_med_references":[20818844,22608338,23489023]},{"effect":"gain-of-function","evidence":"emerging","pathway":"activation","source":"22241789","status":"early trials","therapeutic_context":"MEK inhibitors","pub_med_references":[22241789]},{"effect":"gain-of-function","evidence":"emerging","pathway":"activation","source":"23406027","status":"early trials","therapeutic_context":"MEK-enhanced radioiodine uptake","pub_med_references":[23406027]},{"effect":"gain-of-function","evidence":"emerging","pathway":"activation","source":"J Clin Oncol 2013;31(suppl; abstr 9029)","status":"early trials","therapeutic_context":"BRAF inhibitors + MEK inhibitors"},{"effect":"gain-of-function","evidence":"emerging","pathway":"activation","source":"22773810","status":"case report","therapeutic_context":"EGFR TKIs","pub_med_references":[22773810]},{"effect":"gain-of-function","evidence":"emerging","pathway":"activation","source":"23524406, 22608338, J Clin Oncol 2013;31: (suppl; abstr 8009)","status":"early trials","therapeutic_context":"dabrafenib","pub_med_references":[22608338,23524406]},{"effect":"gain-of-function","evidence":"emerging","pathway":"activation","source":"22743296","status":"case 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report","therapeutic_context":"vemurafenib","pub_med_references":[23612012]}],"pub_med_references":[12068308,12460918,12460919,14679157,15035987,18541894,19001320,19010912,19018267,19238210,19255327,19404918,19537845,19561230,19773371,20350999,20368568,20413299,20619739,20630094,20818844,20857202,21129611,21156289,21163703,21426297,21483012,21594703,21639808,21663470,21683865,21975775,22038996,22048237,22180495,22241789,22281684,22351686,22356324,22389471,22448344,22536370,22586120,22608338,22649091,22663011,22735384,22743296,22773810,22805292,22972589,22997239,23020132,23031422,23251002,23325582,23406027,23470635,23489023,23524406,23549875,23612012,23614898,23812671,23833300,23845441,23918947,23934108,24107445,24163374,24354346,24388723,24396464,24508103,24570209,24576830,24583796,24586605,24594804,25024077,25157968,25370471,25989278,26678033],"hgvs":"ENST00000288602:c.1799T>A"}],"lumc_lovd":[{"version":"19-Jan-2026","genes":[{"gene_id":2273,"hgnc_id":1097,"gene_symbol":"BRAF"}],"individuals":[{"gender":"unknown","variants":[{"is_current":true,"is_lifted_over":false,"lovd_link":"https://databases.lovd.nl/shared/variants/0000062043","pathogenicity":{"clinical_classification_submitter":"Pathogenic","effect_submitter":"functionAffected","effect_symbol":"+/."},"variant_info":[{"variant_id":"10190071404531360004","variant_notation":"chr7:140453136 A⇒T"}]}]}],"is_lifted_over":false,"pathogenicities":[{"clinical_classification_submitter":"Pathogenic","effect_submitter":"functionAffected","effect_symbol":"+/.","lovd_link":"https://databases.lovd.nl/shared/variants/0001029395"},{"clinical_classification_submitter":"Pathogenic","effect_submitter":"functionAffected","effect_symbol":"+/.","lovd_link":"https://databases.lovd.nl/shared/variants/0001052863"}]}],"oncokb":[{"version":"v5.4","allele_exist":true,"diagnostic_implications":[{"abstracts":[],"alterations":["V600E"],"description":"","level_of_evidence":"LEVEL_Dx2","pmids":["20519626","30157397","24938183","26637772"],"tumor_type":{"children":{},"code":"LCH","color":"LightSalmon","id":792,"level":4,"main_type":{"id":null,"name":"Histiocytosis","tumor_form":"LIQUID"},"name":"Langerhans Cell Histiocytosis","parent":"HDCN","tissue":"Myeloid","tumor_form":"LIQUID"}},{"abstracts":[],"alterations":["V600E"],"description":"","level_of_evidence":"LEVEL_Dx3","pmids":["25422482","26637772"],"tumor_type":{"children":{},"code":"ECD","color":"LightSalmon","id":854,"level":4,"main_type":{"id":null,"name":"Histiocytosis","tumor_form":"LIQUID"},"name":"Erdheim-Chester Disease","parent":"HDCN","tissue":"Myeloid","tumor_form":"LIQUID"}},{"abstracts":[],"alterations":["V600E"],"description":"","level_of_evidence":"LEVEL_Dx2","pmids":["23347903","25480661","22072557","21910720","22210875","25120816","22028477","21663470","26071465","22531170"],"tumor_type":{"children":{},"code":"HCL","color":"LimeGreen","id":962,"level":5,"main_type":{"id":null,"name":"Mature B-Cell Neoplasms","tumor_form":"LIQUID"},"name":"Hairy Cell Leukemia","parent":"MBN","tissue":"Lymphoid","tumor_form":"LIQUID"}},{"abstracts":[],"alterations":["Oncogenic Mutations"],"description":"","level_of_evidence":"LEVEL_Dx3","pmids":["22237106"],"tumor_type":{"children":{},"code":"ETPLL","color":"LimeGreen","id":757,"level":4,"main_type":{"id":null,"name":"T-Lymphoblastic Leukemia/Lymphoma","tumor_form":"LIQUID"},"name":"Early T-Cell Precursor Lymphoblastic Leukemia","parent":"TLL","tissue":"Lymphoid","tumor_form":"LIQUID"}}],"diagnostic_summary":"","gene_exist":true,"gene_summary":"BRAF, an intracellular kinase, is frequently mutated in melanoma, thyroid and lung cancers among others.","highest_diagnostic_implication_level":"LEVEL_Dx2","highest_fda_level":"LEVEL_Fda2","highest_prognostic_implication_level":null,"highest_resistance_level":null,"highest_sensitive_level":"LEVEL_1","hotspot":true,"last_update":"02/05/2025","mutation_effect":{"citations":{"abstracts":[],"pmids":["25417114","20179705","23833300","26091043","26343582","12068308","30351999","25079552","28783719","19251651","15035987"]},"description":"The class I activating exon 15 BRAF V600E mutation is located in the kinase domain of the BRAF protein and is highly recurrent in melanoma, lung and thyroid cancer, among others (PMID: 28783719, 26091043, 25079552, 23833300, 25417114, 28783719, 12068308). This mutation has been comprehensively biologically characterized and has been shown to activate the downstream MAPK pathway independent of RAS (PMID: 15035987, 12068308, 19251651, 26343582), to render BRAF constitutively activated in monomeric form (PMID: 20179705), and to retain sensitivity to RAF monomer inhibitors such as vemurafenib and dabrafenib (PMID:26343582, 28783719, 20179705, 30351999).","knowneffect":"Gain-of-function"},"oncogenic":"Oncogenic","other_significant_resistance_levels":null,"other_significant_sensitive_levels":null,"prognostic_implications":null,"prognostic_summary":"","query":{"canonicaltranscript":null,"referencegenome":"GRCh37","hugosymbol":"BRAF","entrezgeneid":673,"alterationtype":null,"alteration":"V600E","id":null,"tumortype":null,"hgvs":null,"svtype":null,"proteinstart":null,"hgvsinfo":null,"consequence":null,"proteinend":null},"treatments":[{"abstracts":[],"alterations":["V600E"],"description":"Dabrafenib is an orally bioavailable RAF inhibitor that is FDA-approved for use in patients with BRAF V600E- and V600K-mutant metastatic melanoma. FDA approval is based on the randomized Phase III trial in which dabrafenib (150 mg orally twice daily) was compared with dacarbazine (1000 mg/m2 intravenously every three weeks) in 250 patients with BRAF V600E-mutated metastatic melanoma. Dabrafenib was associated with improved progression-free survival (median 5.1 months vs. 2.7 months with dacarbazine; hazard ratio = 0.30, p<0.0001) (PMID: 22735384). Dabrafenib may also be effective against brain metastases, as demonstrated by a Phase II trial in which approximately 40% of previously untreated and 30% of previously treated patients experienced an overall intracranial response and a separate trial in which nine out of ten patients had a reduction in the size of their brain metastases (PMID: 23051966, 22608338).","approved_indications":[],"drugs":[{"drug_name":"Dabrafenib","ncit_code":"C82386"}],"fda_level":"LEVEL_Fda2","level":"LEVEL_1","level_associated_cancer_type":{"children":{},"code":"MEL","color":"Black","id":257,"level":2,"main_type":{"id":null,"name":"Melanoma","tumor_form":"SOLID"},"name":"Melanoma","parent":"SKIN","tissue":"Skin","tumor_form":"SOLID"},"pmids":["22608338","23051966","22735384"]},{"abstracts":[{"abstract":"Bouffet et al. Abstract# LGG-49, Neuro-Oncology 2020.","link":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7715318"},{"abstract":"Bouffet et al. Abstract# LBA2002, ASCO 2022.","link":"https://ascopubs.org/doi/abs/10.1200/JCO.2022.40.17_suppl.LBA2002"}],"alterations":["V600E"],"description":"Dabrafenib, an orally bioavailable RAF inhibitor, and trametinib, an orally bioavailable MEK1/2 inhibitor, are FDA-approved in combination for the treatment of patients with solid tumors other than colorectal harboring BRAF V600E mutation. FDA approval was based on data from 131 adult patients with solid tumors treated with dabrafenib and trametinib in the BRF117019 and NCI-MATCH trials and 36 pediatric patients treated with dabrafenib and trametinib in the CTMT212X2101 study. Of the 131 adult patients treated with dabrafenib and trametinib, the overall response rate was 41% (54/131; 95% CI = 33-50) and of the 36 pediatric patients treated with dabrafenib and trametinib (low-grade glioma, n=34; high-grade glioma, n=2), the overall response rate was 25% (95% CI = 12-24) (PMID: 32818466, 34838156, 32758030)(Abstract: Bouffet et al. Abstract# LGG-49, Neuro-Oncology 2020. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7715318/). In the randomized, Phase II study of dabrafenib and trametinib in 110 patients with BRAF V600–mutant pediatric low-grade glioma (dabrafenib + trametinib treatment, n=37; carboplatin + vincristine treatment, n=37), the overall response rate was 47% (95% CI= 35%-59%) with dabrafenib and trametinib and 11% (95% CI= 3%-25%) with carboplatin and vincristine, and the progression-free survival was 20.1 months (95% CI= 12.8 mo-not estimable) with dabrafenib and trametinib and 7.4 months (95% CI= 3.6-11.8 mo) with carboplatin and vincristine (Abstract: Bouffet et al. Abstract# LBA2002, ASCO 2022. https://ascopubs.org/doi/abs/10.1200/JCO.2022.40.17_suppl.LBA2002). FDA approval was supported by results in COMBI-d, COMBI-v and BRF113928 studies in melanoma and lung cancer (PMID: 23020132, 25399551, 27283860).","approved_indications":[],"drugs":[{"drug_name":"Dabrafenib","ncit_code":"C82386"},{"drug_name":"Trametinib","ncit_code":"C77908"}],"fda_level":"LEVEL_Fda2","level":"LEVEL_1","level_associated_cancer_type":{"children":{},"code":"","color":"","id":5,"level":-1,"main_type":{"id":null,"name":"All Solid Tumors","tumor_form":"SOLID"},"name":"","parent":null,"tissue":"","tumor_form":"SOLID"},"pmids":["32758030","27283860","23020132","32818466","25399551","34838156"]},{"abstracts":[],"alterations":["V600E"],"description":"Dabrafenib, an orally bioavailable RAF inhibitor, and trametinib, an orally bioavailable MEK1/2 inhibitor, are FDA-approved alone or in combination for the treatment of patients with locally advanced or metastatic anaplastic thyroid cancer (ATC) with BRAF V600E mutation and with no satisfactory locoregional treatment options. FDA approval was based on results of the Phase II study of dabrafenib combined with trametinib in patients with BRAF V600E-positive ATC in which the overall response rate in sixteen evaluable patients was 69% (11/16; 95% CI= 41%-89%)(PMID: 29072975).","approved_indications":[],"drugs":[{"drug_name":"Dabrafenib","ncit_code":"C82386"},{"drug_name":"Trametinib","ncit_code":"C77908"}],"fda_level":"LEVEL_Fda2","level":"LEVEL_1","level_associated_cancer_type":{"children":{},"code":"THAP","color":"Teal","id":297,"level":2,"main_type":{"id":null,"name":"Thyroid Cancer","tumor_form":"SOLID"},"name":"Anaplastic Thyroid Cancer","parent":"THYROID","tissue":"Thyroid","tumor_form":"SOLID"},"pmids":["29072975"]},{"abstracts":[{"abstract":"Bouffet et al. Abstract# LGG-49, Neuro-Oncology 2020.","link":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7715318"}],"alterations":["V600E"],"description":"Dabrafenib, an orally bioavailable RAF inhibitor, and trametinib, an orally bioavailable MEK1/2 inhibitor, are FDA-approved in combination for the treatment of patients with solid tumors other than colorectal harboring BRAF V600E mutation. FDA approval was based on data from 131 adult patients with solid tumors treated with dabrafenib and trametinib in the BRF117019 and NCI-MATCH trials and 36 pediatric patients treated with dabrafenib and trametinib in the CTMT212X2101 study. Of the 131 adult patients treated with dabrafenib and trametinib, the overall response rate was 41% (54/131; 95% CI = 33-50) and of the 36 pediatric patients treated with dabrafenib and trametinib (low-grade glioma, n=34; high-grade glioma, n=2), the overall response rate was 25% (95% CI = 12-24) (PMID: 32818466, 34838156, 32758030)(Abstract: Bouffet et al. Abstract# LGG-49, Neuro-Oncology 2020. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7715318/). Approval was supported by results in COMBI-d, COMBI-v and BRF113928 studies in melanoma and lung cancer (PMID: 23020132, 25399551, 27283860). In the Phase II ROAR basket trial of dabrafenib + trametinib in patients with BRAF V600E-mutated rare cancers (biliary tract cancer, n=43), the overall response rate was 53%, the median progression-free survival was nine months (95% CI = 5.5, 9.4) and the median overall survival was 13.5 months (95% CI = 10.4, 17.6) (PMID: 37059834). Of the 43 patients with biliary tract cancer, 53% of patients (23/43) had a partial response and 37% (16/43) had stable disease (PMID: 37059834). Additionally, in subprotocol H of the NCI-MATCH basket trial of dabrafenib + trametinib in patients with BRAF V600E-mutant solid tumors (n=4 patients with intrahepatic cholangiocarcinoma), the overall response rate was 100%, with 4/4 patients achieving a partial response (PMID: 32758030).","approved_indications":[],"drugs":[{"drug_name":"Dabrafenib","ncit_code":"C82386"},{"drug_name":"Trametinib","ncit_code":"C77908"}],"fda_level":"LEVEL_Fda2","level":"LEVEL_1","level_associated_cancer_type":{"children":{},"code":"BILIARY_TRACT","color":"Green","id":153,"level":1,"main_type":{"id":null,"name":"Biliary Tract Cancer","tumor_form":"SOLID"},"name":"Biliary Tract","parent":"TISSUE","tissue":"Biliary Tract","tumor_form":"SOLID"},"pmids":["32758030","37059834","27283860","23020132","32818466","25399551","34838156"]},{"abstracts":[{"abstract":"Bouffet et al. Abstract# LGG-49, Neuro-Oncology 2020.","link":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7715318"}],"alterations":["V600E"],"description":"Dabrafenib, an orally bioavailable RAF inhibitor, and trametinib, an orally bioavailable MEK1/2 inhibitor, are FDA-approved in combination for the treatment of patients with solid tumors other than colorectal harboring BRAF V600E mutation. FDA approval was based on data from 131 adult patients with solid tumors treated with dabrafenib and trametinib in the BRF117019 and NCI-MATCH trials and 36 pediatric patients treated with dabrafenib and trametinib in the CTMT212X2101 study. Of the 131 adult patients treated with dabrafenib and trametinib, the overall response rate was 41% (54/131; 95% CI = 33-50) and of the 36 pediatric patients treated with dabrafenib and trametinib (low-grade glioma, n=34; high-grade glioma, n=2), the overall response rate was 25% (95% CI = 12-24) (PMID: 32818466, 34838156, 32758030)(Abstract: Bouffet et al. Abstract# LGG-49, Neuro-Oncology 2020. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7715318/). Approval was supported by results in COMBI-d, COMBI-v and BRF113928 studies in melanoma and lung cancer (PMID: 23020132, 25399551, 27283860). In the Phase II ROAR basket trial of dabrafenib + trametinib in patients with BRAF V600E-mutated rare cancers (biliary tract cancer, n=43), the overall response rate was 53%, the median progression-free survival was nine months (95% CI = 5.5, 9.4) and the median overall survival was 13.5 months (95% CI = 10.4, 17.6) (PMID: 37059834). Of the 43 patients with biliary tract cancer, 53% of patients (23/43) had a partial response and 37% (16/43) had stable disease (PMID: 37059834). Additionally, in subprotocol H of the NCI-MATCH basket trial of dabrafenib + trametinib in patients with BRAF V600E-mutant solid tumors (n=4 patients with intrahepatic cholangiocarcinoma), the overall response rate was 100%, with 4/4 patients achieving a partial response (PMID: 32758030).","approved_indications":[],"drugs":[{"drug_name":"Dabrafenib","ncit_code":"C82386"},{"drug_name":"Trametinib","ncit_code":"C77908"}],"fda_level":"LEVEL_Fda2","level":"LEVEL_1","level_associated_cancer_type":{"children":{},"code":"","color":"MIXED","id":63,"level":0,"main_type":{"id":null,"name":"Hepatobiliary Cancer","tumor_form":"SOLID"},"name":"","parent":null,"tissue":"MIXED","tumor_form":"SOLID"},"pmids":["32758030","37059834","27283860","23020132","32818466","25399551","34838156"]},{"abstracts":[],"alterations":["V600E"],"description":"Dabrafenib, a small molecule RAF inhibitor, and trametinib, a small molecule MEK1/2 inhibitor, are FDA-approved in combination for the treatment of pediatric patients 1 year of age and older with low-grade glioma (LGG) with a BRAF V600E mutation who require systemic therapy. FDA approval is based on the results of the Phase II Study CDRB436G2201 (NCT02684058) of dabrafenib plus trametinib versus carboplatin plus vincristine in 110 patients with BRAF V600-mutant LGG, as assessed by local or central laboratory tests. In the Phase II Study CDRB436G2201 (NCT02684058), the dabrafenib plus trametinib cohort (n=73 [n=70, V600E; n=3, other]) demonstrated an overall response rate (ORR) of 47% (95% CI=35-59), with a 3% (n=2) complete response (CR) rate, a 44% (n=32) partial response (PR) rate and a 41% (n=30) stable disease (SD) rate, and a median duration of response (DOR) of 20.3 months (95% CI=12.0-NE) while the chemotherapy cohort (n=37 [n=35, V600E; n=1, other; n=1, nonmutant]) demonstrated an ORR of 11% (95% CI=3-25) (OR=7.19 [95% CI=2.30-22.40]; RR=4.31 [95% CI=1.70-11.20]; p<0.001), with a 3% (n=1) CR rate, an 8% (n=3) PR rate and a 41% (n=15) SD rate, and a median DOR that was not estimable (95% CI=6.6-NE) (PMID: 37733309).","approved_indications":[],"drugs":[{"drug_name":"Dabrafenib","ncit_code":"C82386"},{"drug_name":"Trametinib","ncit_code":"C77908"}],"fda_level":"LEVEL_Fda2","level":"LEVEL_1","level_associated_cancer_type":{"children":{},"code":"LGGNOS","color":"Gray","id":646,"level":3,"main_type":{"id":null,"name":"Glioma","tumor_form":"SOLID"},"name":"Low-Grade Glioma, NOS","parent":"ENCG","tissue":"CNS/Brain","tumor_form":"SOLID"},"pmids":["37733309"]},{"abstracts":[],"alterations":["V600E","V600K"],"description":"Dabrafenib, an orally bioavailable RAF inhibitor, and trametinib, an orally bioavailable MEK1/2 inhibitor, are FDA-approved alone or in combination for the treatment of patients with metastatic melanoma harboring a V600E or V600K BRAF mutation. FDA approval of dabrafenib in combination with trametinib was based on results from an open-label Phase III study of combination therapy versus dabrafenib monotherapy in 247 patients with metastatic melanoma who were naive to treatment with BRAF inhibitors. Combined dabrafenib and trametinib, administered in full monotherapy doses, improved the response rate in patients with BRAF V600-mutant metastatic melanoma versus dabrafenib monotherapy (67% vs.51%; p<0.002). However, median progression-free survival improved by only 2 weeks (9.3 months vs 8.8 months; HR = 0.75) compared with dabrafenib monotherapy (PMID: 23020132). Combination therapy is associated with less cutaneous toxicity than monotherapy, but systemic toxicity may be increased (PMID: 25287827, 25399551). Follow-up trials have demonstrated that all clinical measures inclusive of overall and median progression-free survival as well as objective response rates, median duration of response and number of patients with complete response favored patients treated with combination dabrafenib and trametinib, administered in full monotherapy doses, compared to either dabrafenib or vemurafenib monotherapy, including patients who previously progressed on BRAF inhibitor monotherapy (PMID: 25287827, 25399551, 25265492). Additionally, patients with melanoma treated with dabrafenib and trametinib in both the neoadjuvant and adjuvant settings have improved survival over patients given standard of care (PMID: 29361468, 28991513, 28891408). Promising clinical data has also suggested that addition of an immunotherapy agent to combination RAF and MEK inhibitor treatment may improve rate of overall response and duration of response in melanoma patients (PMID: 31171876, 31171879, 31171878).","approved_indications":[],"drugs":[{"drug_name":"Dabrafenib","ncit_code":"C82386"},{"drug_name":"Trametinib","ncit_code":"C77908"}],"fda_level":"LEVEL_Fda2","level":"LEVEL_1","level_associated_cancer_type":{"children":{},"code":"MEL","color":"Black","id":257,"level":2,"main_type":{"id":null,"name":"Melanoma","tumor_form":"SOLID"},"name":"Melanoma","parent":"SKIN","tissue":"Skin","tumor_form":"SOLID"},"pmids":["31171876","28891408","31171878","31171879","25265492","25287827","29361468","28991513","23020132","25399551"]},{"abstracts":[],"alterations":["V600E"],"description":"Dabrafenib, an orally bioavailable RAF inhibitor, and trametinib, an orally bioavailable MEK1/2 inhibitor, are FDA-approved alone or in combination for the treatment of patients with metastatic non-small cell lung cancer (NSCLC) with BRAF V600E mutation. FDA approval was based on a Phase II, multicenter, non-randomized, open-label study of dabrafenib in combination with trametinib in patients with chemotherapy-pretreated, metastatic, stage IV BRAF(V600E)-mutant non-small cell lung cancer, in which 36 of 57 patients (63%) achieved overall tumor response, with two patients experiencing durable complete responses and 34 patients having durable partial responses (PMID: 27283860). In the third arm of that study, which included patients with untreated, metastatic, stage IV BRAF(V600E)-mutant non-small cell lung cancer, 23 of 26 patients (64%, 95% CI 46-79) had an overall response, with two patients (6%) having durable complete response and 21 (58%) having partial response (PMID: 28919011).","approved_indications":[],"drugs":[{"drug_name":"Dabrafenib","ncit_code":"C82386"},{"drug_name":"Trametinib","ncit_code":"C77908"}],"fda_level":"LEVEL_Fda2","level":"LEVEL_1","level_associated_cancer_type":{"children":{},"code":"","color":"Gainsboro","id":102,"level":0,"main_type":{"id":null,"name":"Non-Small Cell Lung Cancer","tumor_form":"SOLID"},"name":"","parent":null,"tissue":"Lung","tumor_form":"SOLID"},"pmids":["28919011","27283860"]},{"abstracts":[],"alterations":["V600E","V600K"],"description":"The combination of encorafenib, an inhibitor of V600E- or V600K-mutant BRAF, and binimetinib, an inhibitor of MEK1/2, is FDA-approved in combination for patients with unresectable or metastatic melanoma with a BRAF V600E or V600K mutation. FDA approval was based on the results of the Phase III COLUMBUS trial of combined encorafenib plus binimetinib versus single-agent vemurafenib in 577 patients with BRAF V600E- or V600K-mutant metastatic melanoma in which the median progression-free survival was 14.9 months (95% CI = 11.0-18.5) in the encorafenib plus binimetinib group versus 7.3 months (95% CI = 5.6-8.2) in the single agent vemurafenib group (HR= 0.54, 95% CI = 0.41-0.71; p<0·0001) (PMID: 29573941). In the five-year update of the Phase III COLUMBUS trial, the progression-free survival and overall survival were 23% and 35% respectively in the encorafenib plus binimetinib group (n=192) versus 10% and 21% respectively in the single agent vemurafenib group (n=191), and the median duration of response and disease control rate were 18.6 months and 92.2% in the encorafenib plus binimetinib group versus 12.3 months and 81.2% in the single-agent vemurafenib group (PMID: 35862871).","approved_indications":[],"drugs":[{"drug_name":"Encorafenib","ncit_code":"C98283"},{"drug_name":"Binimetinib","ncit_code":"C84865"}],"fda_level":"LEVEL_Fda2","level":"LEVEL_1","level_associated_cancer_type":{"children":{},"code":"MEL","color":"Black","id":257,"level":2,"main_type":{"id":null,"name":"Melanoma","tumor_form":"SOLID"},"name":"Melanoma","parent":"SKIN","tissue":"Skin","tumor_form":"SOLID"},"pmids":["29573941","35862871"]},{"abstracts":[],"alterations":["V600E"],"description":"Encorafenib, a small molecule inhibitor of RAF kinases, and binimetinib, a small molecule inhibitor of MEK1/2 kinases, are FDA-approved in combination for the treatment of patients with BRAF V600E mutant non-small cell lung cancer (NSCLC). FDA approval was based on the Phase II, open-label, multicenter, single-arm PHAROS study of encorafenib in combination with binimetinib in treatment-naïve (n=59) and previously treated (n=39) patients with BRAF V600E-mutant metastatic NSCLC (PMID: 37270692). In the Phase II PHAROS study, the objective response rate and duration of response for treatment-naïve patients were 72% (95% CI=62, 85) and 44 months (95% CI=23.1, NE), with 15% experiencing a complete response and 59% experiencing a partial response, compared to 46% (95% CI=30, 63) and 18 months (95% CI=7.4, NE) in previously treated patients, with 10% experiencing a complete response and 36% experiencing a partial response (PMID: 37270692).","approved_indications":[],"drugs":[{"drug_name":"Encorafenib","ncit_code":"C98283"},{"drug_name":"Binimetinib","ncit_code":"C84865"}],"fda_level":"LEVEL_Fda2","level":"LEVEL_1","level_associated_cancer_type":{"children":{},"code":"","color":"Gainsboro","id":102,"level":0,"main_type":{"id":null,"name":"Non-Small Cell Lung Cancer","tumor_form":"SOLID"},"name":"","parent":null,"tissue":"Lung","tumor_form":"SOLID"},"pmids":["37270692"]},{"abstracts":[],"alterations":["V600E"],"description":"Encorafenib, a small molecule RAF-targeted inhibitor, and cetuximab, an anti-EGFR antibody, are FDA-approved in combination for the treatment of adult patients with metastatic CRC with a BRAF V600E mutation, as detected by an FDA-approved test, after prior therapy. BRAF V600E mutations for treatment with encorafenib plus cetuximab were detected by the FoundationOne Liquid CDx, the MI Cancer Seek assay or the therascreen BRAF V600E RGQ PCR Kit. FDA approval was based on results of the Phase III BEACON (NCT02928224) study of encorafenib plus cetuximab (n=220) versus triplet treatment (including a MEK1/2 inhibitor) versus chemotherapy (n=221) in 665 patients with BRAF V600E-mutant colorectal cancer. \n\nIn the Phase III BEACON (NCT02928224) trial, the overall response rate (complete or partial response) was 20% (95% CI=13-29) in the doublet arm versus 2% (95% CI=<1%-7%) in the chemotherapy arm (n=221), with median overall survival of 8.4 months in the doublet arm (95% CI= 7.5-11.0) and 5.4 months in the chemotherapy arm (95% CI= 4.8-6.6) (PMID: 31566309).","approved_indications":[],"drugs":[{"drug_name":"Encorafenib","ncit_code":"C98283"},{"drug_name":"Cetuximab","ncit_code":"C1723"}],"fda_level":"LEVEL_Fda2","level":"LEVEL_1","level_associated_cancer_type":{"children":{},"code":"","color":"SaddleBrown","id":40,"level":0,"main_type":{"id":null,"name":"Colorectal Cancer","tumor_form":"SOLID"},"name":"","parent":null,"tissue":"Bowel","tumor_form":"SOLID"},"pmids":["31566309"]},{"abstracts":[],"alterations":["V600E"],"description":"Encorafenib, a small molecule RAF-targeted inhibitor, and cetuximab, an anti-EGFR antibody, are FDA-approved in combination with FOLFOX6 for the treatment of patients with metastatic colorectal cancer (mCRC) with a BRAF V600E mutation, as detected by an FDA-approved test. BRAF V600E mutations were detected by the therascreen BRAF V600E RGQ PCR Kit. FDA approval was based on the results of the Phase III BREAKWATER (NCT04607421) trial of encorafenib plus cetuximab versus encorafenib plus cetuximab with FOLFOX6 versus standard-of-care in 479 patients with BRAF V600E-mutant mCRC.\n\nIn the Phase III BREAKWATER (NCT04607421) trial, the encorafenib plus cetuximab with FOLFOX6 cohort (n=110) demonstrated an overall response rate (ORR) of 60.9% (95% CI=51.6-69.5), with a 2.7% (n=3) complete response (CR) rate, 58.2% (n=64) partial response (PR) rate and 28.2% (n=31) stable disease (SD) rate, and a median duration of response (DOR) of 13.9 months (95% CI=8.5-NE) (PMID: 39863775). The standard-of-care cohort (n=110) demonstrated an ORR of 40.0% (95% CI=31.3-49.3) (odds ratio=2.443 [95% CI=1.403-4.253; 99.8% CI=1.019-5.855]; p=0.0008), with a 1.8% (n=2) CR rate, 38.2% (n=42) PR rate and 30.9% (n=34) SD rate, and a median DOR of 11.1 months (95% CI=6.7-12.7) (PMID: 39863775).","approved_indications":[],"drugs":[{"drug_name":"Encorafenib","ncit_code":"C98283"},{"drug_name":"Cetuximab","ncit_code":"C1723"},{"drug_name":"FOLFOX Regimen","ncit_code":"C11197"}],"fda_level":"LEVEL_Fda2","level":"LEVEL_1","level_associated_cancer_type":{"children":{},"code":"","color":"SaddleBrown","id":40,"level":0,"main_type":{"id":null,"name":"Colorectal Cancer","tumor_form":"SOLID"},"name":"","parent":null,"tissue":"Bowel","tumor_form":"SOLID"},"pmids":["39863775"]},{"abstracts":[],"alterations":["V600"],"description":"Tovorafenib is an orally available, pan-RAF small molecule inhibitor that is FDA-approved for the treatment of pediatric patients six months of age and older with relapsed or refractory pediatric low-grade glioma (LGG) harboring a BRAF fusion or rearrangement, or BRAF V600 mutation. FDA approval was based on the results of the Phase II FIREFLY-1 (NCT04775485) trial of tovorafenib in 76 patients (median age=8 years old [range=2-21]) with relapsed or refractory pediatric LGG harboring an activating BRAF alteration based on local laboratory testing. In the Phase II FIREFLY-1 (NCT04775485) trial, the overall RAPNO-LGG cohort demonstrated an objective response rate (ORR) of 51% (95% CI=40-63), with a 37% (n=28) partial response rate and 14% (n=11) minor response rate, a median duration of response (DOR) of 13.8 months (95% CI=11.3-NE) in 39 patients and a median progression-free survival of 13.8 months (95% CI=8.3-16.9) (PMID: 37978284). The BRAF V600E mutation subcohort (n=12) demonstrated an ORR of 50% (95% CI=21-79) and a median DOR that was not evaluable (95% CI=8.4-NE) (PMID: 37978284).","approved_indications":[],"drugs":[{"drug_name":"Tovorafenib","ncit_code":"C106254"}],"fda_level":"LEVEL_Fda2","level":"LEVEL_1","level_associated_cancer_type":{"children":{},"code":"LGGNOS","color":"Gray","id":646,"level":3,"main_type":{"id":null,"name":"Glioma","tumor_form":"SOLID"},"name":"Low-Grade Glioma, NOS","parent":"ENCG","tissue":"CNS/Brain","tumor_form":"SOLID"},"pmids":["37978284"]},{"abstracts":[],"alterations":["V600E","V600K"],"description":"Trametinib is an oral small molecule inhibitor of MEK1/2 that is FDA-approved alone or with dabrafenib for the treatment of patients with metastatic melanoma harboring a V600E or V600K BRAF mutation. In an open-label, randomized Phase III trial, patients with BRAF V600E/K-mutated unresectable, metastatic melanoma received oral trametinib (2 mg once daily) or an intravenous regimen of either dacarbazine (1000 mg/m2) or paclitaxel (175 mg/m2) every three weeks. Trametinib demonstrated improved progression-free survival (HR for disease progression or death = 0.45) and six-month overall survival (81% vs. 67%; death HR = 0.54; p=0.01) (PMID: 22663011). However, like other MEK inhibitors, the benefit of trametinib is limited by adverse reactions, most notably grade three or four rash and diarrhea (PMID: 22663011). Trametinib is not typically used as monotherapy for patients with BRAF V600K melanoma given its lower response rate compared to BRAF inhibitors and combined BRAF and MEK inhibitors. Patients previously treated with a RAF inhibitor appear to be less likely than untreated patients to respond to trametinib treatment (PMID: 22663011), and FDA guidelines state that trametinib as a monotherapy is not indicated for these patients. Dabrafenib and trametinib are FDA-approved as a combination therapy, which has superior clinical outcomes compared to dabrafenib or trametinib monotherapy (PMID: 25399551, 25265492). Additionally, patients with melanoma treated with dabrafenib and trametinib in both the neoadjuvant and adjuvant settings had improved survival over patients given standard of care (PMID: 29361468).","approved_indications":[],"drugs":[{"drug_name":"Trametinib","ncit_code":"C77908"}],"fda_level":"LEVEL_Fda2","level":"LEVEL_1","level_associated_cancer_type":{"children":{},"code":"MEL","color":"Black","id":257,"level":2,"main_type":{"id":null,"name":"Melanoma","tumor_form":"SOLID"},"name":"Melanoma","parent":"SKIN","tissue":"Skin","tumor_form":"SOLID"},"pmids":["29361468","25399551","22663011","25265492"]},{"abstracts":[],"alterations":["V600"],"description":"Vemurafenib is an orally available, small molecule RAF-targeted inhibitor that is FDA-approved for the treatment of patients with Erdheim-Chester disease (ECD) with BRAF V600 mutation. FDA approval was based on the results of the Phase II VE-BASKET (NCT01524978) trial of vemurafenib in 26 patients with BRAF V600-mutant non-melanoma cancers (n=22, ECD; n=4, Langerhans cell histiocytosis [LCH]).\nIn the Phase II VE-BASKET (NCT01524978) trial, the ECD cohort demonstrated an overall response rate of 54.5% (12/22) (95% CI=32.2-75.6), with one patient (4.5%) achieving complete response and eleven patients (50%) achieving partial response, and the median progression-free survival and overall survival were not reached (PMID: 29188284, 26287849).","approved_indications":[],"drugs":[{"drug_name":"Vemurafenib","ncit_code":"C64768"}],"fda_level":"LEVEL_Fda2","level":"LEVEL_1","level_associated_cancer_type":{"children":{},"code":"ECD","color":"LightSalmon","id":854,"level":4,"main_type":{"id":null,"name":"Histiocytosis","tumor_form":"LIQUID"},"name":"Erdheim-Chester Disease","parent":"HDCN","tissue":"Myeloid","tumor_form":"LIQUID"},"pmids":["26287849","29188284"]},{"abstracts":[],"alterations":["V600E"],"description":"Vemurafenib is an orally available kinse inhibitor of V600-mutant BRAF that is FDA-approved for treatment of patients with unresectable or metastatic melanoma with the BRAF V600E mutation. Vemurafenib has been shown to have nearly equivalent activity against melanomas with BRAF V600E and V600K mutations (PMID: 24508103). In a randomized Phase III trial comparing vemurafenib (960 mg orally twice daily) with dacarbazine (1000 mg/m2 i.v. every 3 weeks) for treatment-naive, metastatic, BRAF V600E-mutant melanoma, vemurafenib was associated with better overall survival (median survival 13.6 months vs. 9.7 months; hazard ratio 0.70, p=.0008) and longer median progression-free survival (6.9 months vs. 1.6 months) (PMID: 24508103). Final overall survival data from the BRIM-3 study showed that the survival advantage of vemurafenib over dacarbazine persisted through the 4-year landmark, with survival rates for vemurafenib and dacarbazine at the 4-year landmark being 17.0% and 15.6%, respectively (PMID: 28961848). However, a trial evaluating clinical outcomes in patients with melanoma treated with either combination therapy of dabrafenib and trametinib compared to those treated with vemurafenib monotherapy demonstrated improved survival outcomes in the combination-therapy group compared to the vemurafenib group (PMID: 25399551).","approved_indications":[],"drugs":[{"drug_name":"Vemurafenib","ncit_code":"C64768"}],"fda_level":"LEVEL_Fda2","level":"LEVEL_1","level_associated_cancer_type":{"children":{},"code":"MEL","color":"Black","id":257,"level":2,"main_type":{"id":null,"name":"Melanoma","tumor_form":"SOLID"},"name":"Melanoma","parent":"SKIN","tissue":"Skin","tumor_form":"SOLID"},"pmids":["28961848","24508103","25399551"]},{"abstracts":[],"alterations":["V600"],"description":"The combination of vemurafenib, an inhibitor of V600-mutant BRAF, and cobimetinib, an inhibitor of MEK1/2, with atezolizumab, an immunotherapeutic PD-L1 antibody, is FDA-approved for patients with BRAF V600 mutation-positive unresectable or metastatic melanoma. FDA approval was based on the results of the Phase III double-blind, randomized, placebo-controlled IMspire150 trial of Atezolizumab + Cobimetinib + Vemurafenib versus Placebo + Cobimetinib + Vemurafenib in 514 patients with BRAF V600-mutant melanoma in which the median progression-free survival was 15.1 mos (95% CI=11.4,18.4) in the triplet arm versus 10.6 mos (95% CI=9.3,12.7) in the doublet + placebo arm (HR=0.78; 95% CI= 0.63, 0.97; p=0.0249) (PMID: 32534646).","approved_indications":[],"drugs":[{"drug_name":"Vemurafenib","ncit_code":"C64768"},{"drug_name":"Atezolizumab","ncit_code":"C106250"},{"drug_name":"Cobimetinib","ncit_code":"C68923"}],"fda_level":"LEVEL_Fda2","level":"LEVEL_1","level_associated_cancer_type":{"children":{},"code":"MEL","color":"Black","id":257,"level":2,"main_type":{"id":null,"name":"Melanoma","tumor_form":"SOLID"},"name":"Melanoma","parent":"SKIN","tissue":"Skin","tumor_form":"SOLID"},"pmids":["32534646"]},{"abstracts":[],"alterations":["V600E","V600K"],"description":"The RAF inhibitor vemurafenib in combination with the MEK inhibitor cobimetinib is FDA-approved for the treatment of patients with BRAF V600-mutant metastatic or unresectable locally advanced melanoma. FDA approval was based on results from the randomized Phase III coBRIM trial of combined vemurafenib and cobimetinib versus vemurafenib and placebo in 495 patients with metastatic BRAF V600-mutant melanoma that demonstrated superior clinical benefit measures in the combination versus the control arm. Specifically, median progression-free survival was 9.9 months in the combination arm versus 6.2 months in the control arm (HR = 0.51), with a complete response rate of 10% versus 4%, respectively, and interim nine-month overall survival of 81% versus 73%, respectively (PMID: 25265494). Follow-up analysis of the coBRIM trial showed two-year overall survival was 48.3% in the combination group versus 38.0% in the monotherapy group (PMID: 27480103), and five-year followup of the BRIM7 study showed a median overall survival of 31.8 months and a five-year survival rate of 39.2% (PMID: 31732523).","approved_indications":[],"drugs":[{"drug_name":"Vemurafenib","ncit_code":"C64768"},{"drug_name":"Cobimetinib","ncit_code":"C68923"}],"fda_level":"LEVEL_Fda2","level":"LEVEL_1","level_associated_cancer_type":{"children":{},"code":"MEL","color":"Black","id":257,"level":2,"main_type":{"id":null,"name":"Melanoma","tumor_form":"SOLID"},"name":"Melanoma","parent":"SKIN","tissue":"Skin","tumor_form":"SOLID"},"pmids":["27480103","31732523","25265494"]},{"abstracts":[],"alterations":["V600E"],"description":"Encorafenib, a small molecule inhibitor of RAF kinase, and panitumumab, an antibody that targets EGFR, are NCCN-compendium listed in combination as level 2A therapy for patients with BRAF V600E-positive colorectal cancer. In the Phase III BEACON study of encorafenib + cetuximab, another EGFR antibody, versus triplet treatment (including a MEK1/2 inhibitor) versus chemotherapy in 665 patients with BRAF V600E-mutant colorectal cancer, the overall response rate (complete or partial response) was 20% (95% CI= 13-29) in the doublet arm (n=220) versus 2% (95% CI= <1%-7%) in the chemotherapy arm (n=221), with median overall survival of 8.4 months in the doublet arm (95% CI= 7.5-11.0) and 5.4 months in the control arm (95% CI= 4.8-6.6) (PMID: 31566309). Panitumumab has also been used in doublet and triplet combination therapy, with a response rate in one study of 26% (PMID: 29431699).","approved_indications":[],"drugs":[{"drug_name":"Encorafenib","ncit_code":"C98283"},{"drug_name":"Panitumumab","ncit_code":"C1857"}],"fda_level":"LEVEL_Fda2","level":"LEVEL_2","level_associated_cancer_type":{"children":{},"code":"","color":"SaddleBrown","id":40,"level":0,"main_type":{"id":null,"name":"Colorectal Cancer","tumor_form":"SOLID"},"name":"","parent":null,"tissue":"Bowel","tumor_form":"SOLID"},"pmids":["29431699","31566309"]},{"abstracts":[],"alterations":["V600E"],"description":"Selumetinib is a small molecule tyrosine kinase inhibitor of MEK1/2. In stratum one of the phase II PBTC study of selumetinib in 25 patients with pilocytic astrocytoma harboring a KIAA1549–BRAF fusion or BRAF V600E mutation, seven of eighteen patients with a KIAA1549–BRAF fusion had a partial response to treatment (PMID: 31151904). Additionally, the two year progression-free survival rate for the BRAF study population (n=25) was 70% (95% CI = 47–85) (PMID: 31151904).","approved_indications":[],"drugs":[{"drug_name":"Selumetinib","ncit_code":"C66939"}],"fda_level":"LEVEL_Fda2","level":"LEVEL_2","level_associated_cancer_type":{"children":{},"code":"PAST","color":"Gray","id":452,"level":3,"main_type":{"id":null,"name":"Glioma","tumor_form":"SOLID"},"name":"Pilocytic Astrocytoma","parent":"ENCG","tissue":"CNS/Brain","tumor_form":"SOLID"},"pmids":["31151904"]},{"abstracts":[],"alterations":["V600E"],"description":"Vemurafenib is an orally available kinse inhibitor of V600-mutant BRAF that is FDA-approved for treatment of patients with various BRAF V600-harboring tumors, including melanoma and Edheim-Chester Disease (ECD). Vemurafenib is listed as a 2A therapeutic in the NCCN guidelines for Hairy Cell Leukemia (HCL) based on data from two Phase II trials. In one study of vemurafenib in patients with BRAF V600E-mutant HCL (n=24), the overall response rate was 100%, with 42% of patients (10 of 24) having complete responses, with a response duration of 11.7 months and one year progression free and overall survival rates of 73% and 91%, repectively (PMID: 26352686). In another study of vemurafenib in patients with BRAF V600E-mutant HCL (n=26), the overall response rate was 96%, with 35% of patients (9 of 26) having complete responses (PMID: 26352686).","approved_indications":[],"drugs":[{"drug_name":"Vemurafenib","ncit_code":"C64768"}],"fda_level":"LEVEL_Fda2","level":"LEVEL_2","level_associated_cancer_type":{"children":{},"code":"HCL","color":"LimeGreen","id":962,"level":5,"main_type":{"id":null,"name":"Mature B-Cell Neoplasms","tumor_form":"LIQUID"},"name":"Hairy Cell Leukemia","parent":"MBN","tissue":"Lymphoid","tumor_form":"LIQUID"},"pmids":["26352686"]},{"abstracts":[],"alterations":["V600"],"description":"Vemurafenib is an orally available, small molecule RAF-targeted inhibitor that is FDA-approved for the treatment of patients with Erdheim-Chester disease (ECD) with BRAF V600 mutation. Vemurafenib and dabrafenib are listed as monotherapies in the NCCN Histiocytic Neoplasms Guidelines (V3.2024) under the section \"Principles of Systemic Therapy\" as recommended treatment regimens for patients with Langerhans cell histiocytosis (LCH) harboring BRAF V600E mutations. NCCN recommendation was based on the results of the Phase II VE-BASKET (NCT01524978) and case reports.\nIn the Phase II VE-BASKET (NCT01524978) trial, all four patients of the LCH cohort achieved partial response (PMID: 29188284). In the case series evaluating the use of BRAF inhibitors in six adult patients with BRAF V600E‐mutant LCH, patients treated with vemurafenib monotherapy (n=3) achieved one complete response (CR), one partial response (PR) and one stable disease (SD) response while patients treated with dabrafenib monotherapy (n=3) achieved one CR and two PRs (PMID: 32985015). In a separate case report, a patient with BRAF V600E-mutant LCH was treated with dabrafenib plus trametinib and demonstrated a sustained metabolic response (PMID: 30154124).","approved_indications":[],"drugs":[{"drug_name":"Vemurafenib","ncit_code":"C64768"}],"fda_level":"LEVEL_Fda3","level":"LEVEL_2","level_associated_cancer_type":{"children":{},"code":"LCH","color":"LightSalmon","id":792,"level":4,"main_type":{"id":null,"name":"Histiocytosis","tumor_form":"LIQUID"},"name":"Langerhans Cell Histiocytosis","parent":"HDCN","tissue":"Myeloid","tumor_form":"LIQUID"},"pmids":["32985015","29188284","30154124"]},{"abstracts":[],"alterations":["V600E"],"description":"The RAF inhibitor vemurafenib in combination with the MEK inhibitor cobimetinib is FDA-approved for patients with BRAF V600E-positive melanoma, non-small cell lung cancer, and anaplastic thyroid cancer, and is NCCN-listed for patients with low-grade glioma, anaplastic glioma, and glioblastoma. Patients with various glioma subtypes harboring BRAF V600E mutations have shown responses to RAF and MEK inhibition. Three out of five patients with anaplastic astrocytoma had a response (one partial response, two stable disease) to vemurafenib monotherapy (PMID: 30351999). One patient with high-grade glioma (NOS) had stable disease in response to vemurafenib monotherapy (PMID:30351999). Four out of eight patients with glioma (NOS) had a response (one partial response, three stable disease, two progressive disease, two not evaluable) to vemurafenib monotherapy (PMID: 26287849). One patient with anaplastic oligoastrocytoma had stable disease in response to vemurafenib monotherapy (PMID: 30462564). Four of seven patients with glioblastoma multiforme had a response (one complete response, three stable disease, one progressive disease, two not evaluable) to vemurafenib monotherapy (PMID: 30351999, 24725538). Four patients with glioblastoma (including epithelioid glioblastoma) had a response (one “near-complete” response, three stable disease) to either dabrafenib monotherapy (n=2) or vemurafenib monotherapy (n=2) (PMID: 29621181, 29039591, 33117675, 34232949).","approved_indications":[],"drugs":[{"drug_name":"Vemurafenib","ncit_code":"C64768"},{"drug_name":"Cobimetinib","ncit_code":"C68923"}],"fda_level":"LEVEL_Fda3","level":"LEVEL_2","level_associated_cancer_type":{"children":{},"code":"DIFG","color":"Gray","id":284,"level":2,"main_type":{"id":null,"name":"Glioma","tumor_form":"SOLID"},"name":"Diffuse Glioma","parent":"BRAIN","tissue":"CNS/Brain","tumor_form":"SOLID"},"pmids":["24725538","29039591","30462564","34232949","29621181","30351999","26287849","33117675"]},{"abstracts":[],"alterations":["V600E"],"description":"The RAF inhibitor vemurafenib in combination with the MEK inhibitor cobimetinib is FDA-approved for patients with melanoma, non-small cell lung cancer, and anaplastic thyroid cancer, and is NCCN-listed for patients with low-grade glioma, anaplastic glioma, and glioblastoma. Patients with various glioma subtypes harboring BRAF V600E mutations have shown responses to RAF and MEK inhibition. Six patients with ganglioglioma had a partial response to either vemurafenib monotherapy (n=2), vemurafenib + cobimetinib (n=1), or dabrafenib monotherapy (n=​​3)(PMID: 25524464, 31985841, 26579623, 31502039). Twelve out of thirteen patients with pleomorphic xanthoastrocytoma had a response (one complete response, one “near-complete” response, six partial response, four stable disease) to either dabrafenib + trametinib (n=2) or vemurafenib monotherapy (n=11) (PMID: 28984141, 26287849, 30351999). Three patients with anaplastic pleomorphic xanthoastrocytoma had a response (one complete response, one “near-complete” response, one partial response) to either vemurafenib monotherapy (n=1) or dabrafenib monotherapy (n=2)(PMID: 25092772, 29039591). One patient with low-grade glioma, NOS had a partial response to dabrafenib monotherapy (PMID: 27398937). Two patients with pilocytic astrocytoma had a response (one partial response, one stable disease) to vemurafenib monotherapy (PMID: 30351999). Three of four patients with anaplastic ganglioglioma had a response (one partial response, one \"significant response\", one stable disease, one not evaluable) to either dabrafenib + trametinib (n=1) or vemurafenib monotherapy (n=3)(PMID: 29380516, 30351999). One patient with pilomyxoid astrocytoma had a partial response to vemurafenib monotherapy (PMID: 24821190).","approved_indications":[],"drugs":[{"drug_name":"Vemurafenib","ncit_code":"C64768"},{"drug_name":"Cobimetinib","ncit_code":"C68923"}],"fda_level":"LEVEL_Fda3","level":"LEVEL_2","level_associated_cancer_type":{"children":{},"code":"ENCG","color":"Gray","id":277,"level":2,"main_type":{"id":null,"name":"Glioma","tumor_form":"SOLID"},"name":"Encapsulated Glioma","parent":"BRAIN","tissue":"CNS/Brain","tumor_form":"SOLID"},"pmids":["25524464","29039591","31985841","25092772","31502039","27398937","29380516","28984141","24821190","30351999","26579623","26287849"]},{"abstracts":[],"alterations":["V600E"],"description":"The RAF inhibitor vemurafenib in combination with the MEK inhibitor cobimetinib is FDA-approved for patients with melanoma, non-small cell lung cancer, and anaplastic thyroid cancer, and is NCCN-compendium listed as recommended treatment of central nervous system cancers such as pilocytic astrocytoma, pleomorphic xanthoastrocytoma (PXA) and ganglioglioma. In a case series of two patients with BRAF V600E-mutant PXA, combination treatment of dabrafenib with trametinib led to partial responses by RANO criteria in both patients (PMID: 28984141). In a case report of a sixteen-year-old female with BRAF V600E-mutant anaplastic ganglioglioma, dabrafenib and trametinib in combination led to a significant response that was maintained at least six months after treatment initiation (PMID: 29380516). In a separate case report of a 28-year-old man with BRAF V600E-mutant anaplastic ganglioglioma, combination treatment of vemurafenib and cobimetinib led to a complete response after three months, with no evidence of recurrence after sixteen months of treatment (PMID: 30120137).","approved_indications":[],"drugs":[{"drug_name":"Vemurafenib","ncit_code":"C64768"},{"drug_name":"Cobimetinib","ncit_code":"C68923"}],"fda_level":"LEVEL_Fda3","level":"LEVEL_2","level_associated_cancer_type":{"children":{},"code":"PXA","color":"Gray","id":416,"level":3,"main_type":{"id":null,"name":"Glioma","tumor_form":"SOLID"},"name":"Pleomorphic Xanthoastrocytoma","parent":"ENCG","tissue":"CNS/Brain","tumor_form":"SOLID"},"pmids":["30120137","29380516","28984141"]},{"abstracts":[],"alterations":["V600E"],"description":"The RAF inhibitor vemurafenib in combination with the MEK inhibitor cobimetinib is FDA-approved for patients with melanoma, non-small cell lung cancer, and anaplastic thyroid cancer, and is NCCN-compendium listed as recommended treatment of central nervous system cancers such as pilocytic astrocytoma, pleomorphic xanthoastrocytoma (PXA) and ganglioglioma. In a case series of two patients with BRAF V600E-mutant PXA, combination treatment of dabrafenib with trametinib led to partial responses by RANO criteria in both patients (PMID: 28984141). In a case report of a sixteen-year-old female with BRAF V600E-mutant anaplastic ganglioglioma, dabrafenib and trametinib in combination led to a significant response that was maintained at least six months after treatment initiation (PMID: 29380516). In a separate case report of a 28-year-old man with BRAF V600E-mutant anaplastic ganglioglioma, combination treatment of vemurafenib and cobimetinib led to a complete response after three months, with no evidence of recurrence after sixteen months of treatment (PMID: 30120137).","approved_indications":[],"drugs":[{"drug_name":"Vemurafenib","ncit_code":"C64768"},{"drug_name":"Cobimetinib","ncit_code":"C68923"}],"fda_level":"LEVEL_Fda3","level":"LEVEL_2","level_associated_cancer_type":{"children":{},"code":"GNG","color":"Gray","id":609,"level":3,"main_type":{"id":null,"name":"Glioma","tumor_form":"SOLID"},"name":"Ganglioglioma","parent":"ENCG","tissue":"CNS/Brain","tumor_form":"SOLID"},"pmids":["30120137","29380516","28984141"]},{"abstracts":[],"alterations":["V600E"],"description":"The RAF inhibitor vemurafenib in combination with the MEK inhibitor cobimetinib is FDA-approved for patients with melanoma, non-small cell lung cancer, and anaplastic thyroid cancer, and is NCCN-compendium listed as recommended treatment of central nervous system cancers such as pilocytic astrocytoma, pleomorphic xanthoastrocytoma (PXA) and ganglioglioma. In a case series of two patients with BRAF V600E-mutant PXA, combination treatment of dabrafenib with trametinib led to partial responses by RANO criteria in both patients (PMID: 28984141). In a case report of a sixteen-year-old female with BRAF V600E-mutant anaplastic ganglioglioma, dabrafenib and trametinib in combination led to a significant response that was maintained at least six months after treatment initiation (PMID: 29380516). In a separate case report of a 28-year-old man with BRAF V600E-mutant anaplastic ganglioglioma, combination treatment of vemurafenib and cobimetinib led to a complete response after three months, with no evidence of recurrence after sixteen months of treatment (PMID: 30120137).","approved_indications":[],"drugs":[{"drug_name":"Vemurafenib","ncit_code":"C64768"},{"drug_name":"Cobimetinib","ncit_code":"C68923"}],"fda_level":"LEVEL_Fda3","level":"LEVEL_2","level_associated_cancer_type":{"children":{},"code":"PAST","color":"Gray","id":452,"level":3,"main_type":{"id":null,"name":"Glioma","tumor_form":"SOLID"},"name":"Pilocytic Astrocytoma","parent":"ENCG","tissue":"CNS/Brain","tumor_form":"SOLID"},"pmids":["30120137","29380516","28984141"]},{"abstracts":[],"alterations":["V600"],"description":"Vemurafenib is an orally available, small molecule RAF-targeted inhibitor that is FDA-approved for the treatment of patients with Erdheim-Chester disease (ECD) with BRAF V600 mutation. Vemurafenib and dabrafenib are listed as monotherapies in the NCCN Histiocytic Neoplasms Guidelines (V3.2024) under the section \"Principles of Systemic Therapy\" as recommended treatment regimens for patients with Langerhans cell histiocytosis (LCH) harboring BRAF V600E mutations. NCCN recommendation was based on the results of the Phase II VE-BASKET (NCT01524978) and case reports.\nIn the Phase II VE-BASKET (NCT01524978) trial, all four patients of the LCH cohort achieved partial response (PMID: 29188284). In the case series evaluating the use of BRAF inhibitors in six adult patients with BRAF V600E‐mutant LCH, patients treated with vemurafenib monotherapy (n=3) achieved one complete response (CR), one partial response (PR) and one stable disease (SD) response while patients treated with dabrafenib monotherapy (n=3) achieved one CR and two PRs (PMID: 32985015). In a separate case report, a patient with BRAF V600E-mutant LCH was treated with dabrafenib plus trametinib and demonstrated a sustained metabolic response (PMID: 30154124).","approved_indications":[],"drugs":[{"drug_name":"Dabrafenib","ncit_code":"C82386"}],"fda_level":"LEVEL_Fda3","level":"LEVEL_2","level_associated_cancer_type":{"children":{},"code":"LCH","color":"LightSalmon","id":792,"level":4,"main_type":{"id":null,"name":"Histiocytosis","tumor_form":"LIQUID"},"name":"Langerhans Cell Histiocytosis","parent":"HDCN","tissue":"Myeloid","tumor_form":"LIQUID"},"pmids":["32985015","29188284","30154124"]},{"abstracts":[],"alterations":["V600"],"description":"Vemurafenib is an orally available, small molecule RAF-targeted inhibitor that is FDA-approved for the treatment of patients with Erdheim-Chester disease (ECD) with BRAF V600 mutation. Vemurafenib and dabrafenib are listed as monotherapies in the NCCN Histiocytic Neoplasms Guidelines (V3.2024) under the section \"Principles of Systemic Therapy\" as recommended treatment regimens for patients with ECD and Langerhans cell histiocytosis (LCH) harboring BRAF V600E mutations. There is promising clinical data to support the use of vemurafenib and dabrafenib as monotherapies in patients with non-ECD and non-LCH BRAF V600-mutant histiocytic neoplasms.\nIn a case study, a patient with heterozygous BRAF V600E-mutant histiocytic sarcoma was treated with vemurafenib and maintained both clinical and radiologic tumor responses for three months until disease progression (PMID: 25209580). In a second case study, a patient with BRAF V600E-mutant histiocytic sarcoma was treated with vemurafenib plus chemotherapy, antibiotics and steroids and remained in complete remission eighteen months after treatment initiation (PMID: 31376203). In a third case study, a pediatric patient with BRAF V600E-mutant mixed systemic Rosai-Dorfman-Destombes disease and LCH reported sustained clinical and radiographic responses after treatment with dabrafenib prior to disease relapse at thirteen months (PMID: 31213430).","approved_indications":[],"drugs":[{"drug_name":"Vemurafenib","ncit_code":"C64768"}],"fda_level":"LEVEL_Fda3","level":"LEVEL_3A","level_associated_cancer_type":{"children":{},"code":"","color":"LightSalmon","id":29,"level":0,"main_type":{"id":null,"name":"Histiocytosis","tumor_form":"LIQUID"},"name":"","parent":null,"tissue":"Myeloid","tumor_form":"LIQUID"},"pmids":["31376203","31213430","25209580"]},{"abstracts":[],"alterations":["V600"],"description":"Vemurafenib is an orally available, small molecule RAF-targeted inhibitor that is FDA-approved for the treatment of patients with Erdheim-Chester disease (ECD) with BRAF V600 mutation. Vemurafenib and dabrafenib are listed as monotherapies in the NCCN Histiocytic Neoplasms Guidelines (V3.2024) under the section \"Principles of Systemic Therapy\" as recommended treatment regimens for patients with ECD and Langerhans cell histiocytosis (LCH) harboring BRAF V600E mutations. There is promising clinical data to support the use of vemurafenib and dabrafenib as monotherapies in patients with non-ECD and non-LCH BRAF V600-mutant histiocytic neoplasms.\nIn a case study, a patient with heterozygous BRAF V600E-mutant histiocytic sarcoma was treated with vemurafenib and maintained both clinical and radiologic tumor responses for three months until disease progression (PMID: 25209580). In a second case study, a patient with BRAF V600E-mutant histiocytic sarcoma was treated with vemurafenib plus chemotherapy, antibiotics and steroids and remained in complete remission eighteen months after treatment initiation (PMID: 31376203). In a third case study, a pediatric patient with BRAF V600E-mutant mixed systemic Rosai-Dorfman-Destombes disease and LCH reported sustained clinical and radiographic responses after treatment with dabrafenib prior to disease relapse at thirteen months (PMID: 31213430).","approved_indications":[],"drugs":[{"drug_name":"Dabrafenib","ncit_code":"C82386"}],"fda_level":"LEVEL_Fda3","level":"LEVEL_3A","level_associated_cancer_type":{"children":{},"code":"","color":"LightSalmon","id":29,"level":0,"main_type":{"id":null,"name":"Histiocytosis","tumor_form":"LIQUID"},"name":"","parent":null,"tissue":"Myeloid","tumor_form":"LIQUID"},"pmids":["31376203","31213430","25209580"]}],"tumor_type_summary":"","variant_exist":true,"variant_summary":"The BRAF V600E mutation is known to be 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b/tests/fixtures/example_response_germline.json new file mode 100644 index 0000000..b71a8a0 --- /dev/null +++ b/tests/fixtures/example_response_germline.json @@ -0,0 +1 @@ +{"chromosome":"chr7","alt":"T","ref":"A","pos":140453136,"variant_id":"10190071404531360004","regions":{"uniprot_regions":{"version":"07-Feb-2026","items":[{"absolute_positon":2611797646,"amino_acid":"M1-E46,V47-E80,A81-V168,V169-G203,G203-F237,V238-D287,D287-G327,G327-D380,D381-G393,G393-M438,K439-G478,G478-R506,R506-D565,D565-N581,N581-M620,A621-Q664,I665-Q709,I710-H766","chromo":"chr7","colour":"255,0,0","description":null,"length":194265,"position":140430465,"protein":"BRAF_HUMAN","type":"homo_sapiens proteome sequences","pub_med_references":null},{"absolute_positon":2611801728,"amino_acid":"I457-L717","chromo":"chr7","colour":"153,153,255","description":"Protein 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Case Rep Genet. 2015;2015:131852. PMID: 26064708. Evangelidou et al., Biomed Res Int. 2013;2013:346762. PMID: 23555083. Friedman et al., Mol Psychiatry. 2008 Mar;13(3):261-6. PMID: 17646849. Kale et al., Case Rep Genet. 2016;2016:6046351. PMID: 28053794. Lopes et al., Neurogenetics. 2018 Jan;19(1):27-40. PMID: 29260337. Rush et al., Am J Med Genet A. 2013 Jul;161A(7):1726-32. PMID: 23696251. Rossi et al., Eur J Med Genet. Nov-Dec 2008;51(6):631-8. 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Tumour",1],"tissue_freq":["Stomach",1]},{"drug_name":"Cetuximab","somatic_status":null,"zygosity":null,"gene":"BRAF","transcript":"ENST00000288602.6","census_gene":"Yes","pub_med_references":[24553385],"histology_freq":["Carcinoma",1],"tissue_freq":["Large Intestine",1]}]}]}],"ncbi_clinvar2":[{"version":"07-Feb-2026","review_status":"criteria provided, conflicting classifications","review_stars":1,"variation_id":13961,"num_submitters":21,"pub_med_references":[12068308,12198537,12447372,12619120,12644542,12670889,12794760,12960123,14513361,14602780,15001635,15126572,15181070,15342696,15356022,15386408,15687339,15998781,16015629,16174717,16187918,16772349,17374713,17488796,17785355,18398503,19571295,20818844,20823850,21107320,21107323,22039425,22113612,22281684,23302800,23685455,24512911,24670642,24717435,25079330,25950823,28854169,29925953,31891627,34476331],"clinical_significance":["Conflicting Classifications Of Pathogenicity"],"last_evaluation":"20260201","origin":null,"accessions":[{"submissions":[{"submission_description":["This sequence change replaces valine, which is neutral and non-polar, with glutamic acid, which is acidic and polar, at codon 600 of the BRAF protein (p.Val600Glu). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has been reported as a known somatic variant in various cancers but has not been reported in the literature in individuals affected with germline BRAF-related conditions. ClinVar contains an entry for this variant (Variation ID: 13961). Invitae Evidence Modeling incorporating data from in vitro experimental studies (internal data) indicates that this missense variant is expected to disrupt BRAF function with a positive predictive value of 95%. This variant disrupts the p.Val600 amino acid residue in BRAF. Other variant(s) that disrupt this residue have been determined to be pathogenic (internal data). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance."],"submitter_name":"Labcorp Genetics (formerly Invitae), Labcorp","review_date":20250123,"origin":"germline","method":"clinical testing","submitter_date":20250207,"diseases":[{"symbols":{"medgen":"CN166718"}}],"review_description":"Uncertain significance","date_updated":20250225,"clinical_significance":["Uncertain significance"],"review_status":"criteria provided, single submitter","accession_id":"SCV005812663"}],"variation_id":13961,"submission_description":[],"title":"NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) AND RASopathy","review_date":20250123,"diseases":[{"symbols":{"medgen":"C5555857","mondo":"MONDO:0021060"},"normalized_disease":["Rasopathy"],"names":["Rasopathy","Rasopathies","Noonan Spectrum Disorder"]}],"date_created":20250225,"variant_id":10190071404531360004,"review_description":"Uncertain significance","clinical_significance":["Uncertain significance"],"allele_id":29000,"accession_id":"RCV005089260"},{"submissions":[{"submission_description":["The BRAF c.1799T>A (p.Val600Glu) variant was identified at an allelic fraction consistent with somatic origin. This variant is absent from the general population (gnomAD v.3.1.2), indicating it is not a common variant. This variant occurs in a highly conserved residue within the CR3 activation segment, amino acids 594-627, of BRAF that is defined as a critical functional domain (Wellbrock C, et al., PMID: 15520807; Gelb BD, et al., PMID: 29493581). The BRAF c.1799T>A (p.Val600Glu) variant in a somatic state has been reported in multiple individuals affected with sporadic vascular malformations, brain arteriovenous malformation (BAVM) and spinal arteriovenous malformation (SAVM) (Hong T, et al., PMID: 30544177; Al-Olabi L, et al., PMID: 29461977; Goss JA, et al., PMID: 31891627; Li H, et al., PMID: 34530633). The BRAF c.1799T>A (p.Val600Glu) variant has been reported in the ClinVar database as pathogenic by numerous submitters (ClinVar ID: 13961). Computational predictors indicate that the variant is damaging, evidence that correlates with impact to BRAF function. In support of this prediction, functional studies show constitutively active kinase activity (Rodriguez-Viciana P, et al., PMID: 16439621; Sarkozy A, et al., PMID:19206169; Al-Olabi L, et al., PMID: 29461977). Based on an internally developed protocol informed by the ACMG/AMP guidelines (Richards S et al., PMID: 25741868) and gene-specific practices from the ClinGen Criteria Specification Registry, this variant is classified as pathogenic."],"submitter_name":"Clinical Genomics Laboratory, Washington University in St. Louis","review_date":20231022,"origin":"somatic","method":"clinical testing","submitter_date":20231212,"diseases":[{"normalized_disease":["Vascular Malformation"],"names":["Vascular Malformation"]}],"review_description":"Pathogenic","date_updated":20231224,"clinical_significance":["Pathogenic"],"review_status":"criteria provided, single submitter","accession_id":"SCV004176942"}],"variation_id":13961,"submission_description":[],"title":"NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) AND Vascular malformation","review_date":20231022,"diseases":[{"symbols":{"medgen":"C0158570","mondo":"MONDO:0024291"},"normalized_disease":["Vascular Malformation"],"names":["Vascular Malformation","Vascular Malformations"]}],"date_created":20231224,"variant_id":10190071404531360004,"review_description":"Pathogenic","clinical_significance":["Pathogenic"],"allele_id":29000,"accession_id":"RCV003458334"},{"submissions":[{"submitter_date":20240424,"submission_description":["ASSESSED FOR SOMATIC SAMPLE ONLY. FOR ANY GERMLINE INDICATION, PLEASE REASSESS."],"submitter_name":"Ambry Genetics","review_date":20220523,"origin":"germline","method":"clinical testing","finding":[{"symbols":{"medgen":"CN230736"}}],"review_description":"Likely pathogenic","date_updated":20240501,"clinical_significance":["Likely pathogenic"],"review_status":"criteria provided, single submitter","accession_id":"SCV005022010"}],"variation_id":13961,"submission_description":[],"title":"NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) AND Cardiovascular phenotype","review_date":20220523,"diseases":[{"symbols":{"medgen":"CN230736"},"names":["Cardiovascular Phenotype"]}],"date_created":20240501,"variant_id":10190071404531360004,"review_description":"Likely pathogenic","clinical_significance":["Likely pathogenic"],"allele_id":29000,"accession_id":"RCV004018627"},{"submissions":[{"submission_description":["The Val600Glu variant in BRAF was observed at very low levels (VAF 0.3-2%) in lymphatic malformation tissue from three unrelated individuals using high depth NGS (VANseq), confirmatory digital droplet PCR, and BRAF V600E immunohistochemistry."],"submitter_name":"James Bennett Lab, Seattle Childrens Research Institute","review_date":20220209,"origin":"somatic","method":"research","finding":[{"symbols":{"hp":"HP:0100766"},"normalized_phenotype":["Abnormal Lymphatic Vessel Morphology"]}],"submitter_date":20220325,"diseases":[{"symbols":{"hp":"HP:0100764"}}],"review_description":"Pathogenic","date_updated":20250803,"clinical_significance":["Pathogenic"],"review_status":"no assertion criteria provided","accession_id":"SCV002318371"}],"variation_id":13961,"submission_description":[],"title":"NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) AND Lymphangioma","review_date":20220209,"diseases":[{"symbols":{"medgen":"C0024221","mondo":"MONDO:0002013","human_phenotype_ontology":"HP:0100764"},"normalized_disease":["Lymphangioma"],"names":["Lymphangioma"]}],"date_created":20220328,"variant_id":10190071404531360004,"review_description":"Pathogenic","clinical_significance":["Pathogenic"],"allele_id":29000,"accession_id":"RCV002051586"},{"submissions":[{"submission_description":[],"submitter_name":"Xiao lab, Department of Pathology, Memorial Sloan Kettering Cancer Center","review_date":20190831,"origin":"somatic","method":"clinical testing","submitter_date":20190912,"diseases":[{"normalized_cancer":["Plasma Cell Myeloma"],"symbols":{"orphanet":"ORPHA29073"},"normalized_disease":["Plasma Cell Myeloma"],"names":["Plasma Cell Myeloma"]}],"review_description":"Likely pathogenic","date_updated":20191223,"clinical_significance":["Likely pathogenic"],"review_status":"no assertion criteria provided","accession_id":"SCV001132084"}],"variation_id":13961,"submission_description":[],"title":"NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) AND Multiple myeloma","review_date":20190831,"diseases":[{"symbols":{"omim":"254500","medgen":"C0026764","orphanet":"85443","mesh":"D009101","mondo":"MONDO:0009693","human_phenotype_ontology":"HP:0006775"},"normalized_disease":["Plasma Cell Myeloma"],"names":["Plasma Cell Myeloma","Plasma Cell Myeloma","Multiple Myeloma, Somatic"],"normalized_cancer":["Plasma Cell Myeloma"],"keyword":"Hereditary cancer syndrome"}],"date_created":20170308,"variant_id":10190071404531360004,"review_description":"Likely pathogenic","clinical_significance":["Likely pathogenic"],"allele_id":29000,"accession_id":"RCV000430562"},{"submissions":[{"submission_description":[],"submitter_name":"Pediatric Oncology, Johns Hopkins University","review_date":20190215,"origin":"somatic","method":"clinical testing","submitter_date":20200116,"diseases":[{"normalized_cancer":["Wilms' Tumor"],"normalized_disease":["Kidney Wilms Tumor"],"names":["Kidney Wilms Tumor"]}],"review_description":"Pathogenic","date_updated":20250413,"clinical_significance":["Pathogenic"],"review_status":"no assertion criteria provided","accession_id":"SCV001147031"}],"variation_id":13961,"submission_description":[],"title":"NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) AND Nephroblastoma","review_date":20190215,"diseases":[{"normalized_cancer":["Wilms' Tumor"],"symbols":{"medgen":"C0027708","mesh":"D009396","mondo":"MONDO:0006058","human_phenotype_ontology":"HP:0000115"},"normalized_disease":["Kidney Wilms Tumor"],"names":["Kidney Wilms Tumor","Kidney Wilms Tumor","Kidney Wilms Tumor"]}],"date_created":20200719,"variant_id":10190071404531360004,"review_description":"Pathogenic","clinical_significance":["Pathogenic"],"allele_id":29000,"accession_id":"RCV001248834"},{"submissions":[{"submission_description":[],"submitter_name":"Yale Center for Mendelian Genomics, Yale University","review_date":20150507,"origin":"somatic","method":"literature only","submitter_date":20171127,"diseases":[{"names":["Cystic Epithelial Invagination Containing Papillae Lined By Columnar Epithelium"]}],"review_description":"Pathogenic","date_updated":20180714,"clinical_significance":["Pathogenic"],"review_status":"no assertion criteria provided","accession_id":"SCV000784606"},{"submission_description":[],"submitter_name":"Yale Center for Mendelian Genomics, Yale University","review_date":20150507,"origin":"somatic","method":"literature only","submitter_date":20220321,"diseases":[{"names":["Cystic Epithelial Invagination Containing Papillae Lined By Columnar Epithelium"]}],"review_description":"Pathogenic","date_updated":20220328,"clinical_significance":["Pathogenic"],"review_status":"no assertion criteria provided","accession_id":"SCV002106413"}],"variation_id":13961,"submission_description":[],"title":"NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) AND Cystic epithelial invagination containing papillae lined by columnar epithelium","review_date":20150507,"diseases":[{"names":["Cystic Epithelial Invagination Containing Papillae Lined By Columnar Epithelium"]}],"date_created":20180714,"variant_id":10190071404531360004,"review_description":"Pathogenic","clinical_significance":["Pathogenic"],"allele_id":29000,"accession_id":"RCV000662278"},{"submissions":[{"submission_description":["Variant has Tier I (strong) clinical significance as a diagnostic inclusion criterion in thyroid gland papillary carcinoma, based on the following evidence: 1) Documented in one or more cancer databases (e.g., St. Jude Pecan, COSMIC, CIViC, OncoKB). 2) Appears in one or more well-established professional guidelines (e.g., World Health Organization [WHO]; National Comprehensive Cancer Network [NCCN]) as providing diagnostic, prognostic, or therapeutic information. 3) Information in the literature supports potential biologic effect of variant. 4) Diagnostic for a specific tumor type/classification based on well-powered studies with expert-level consensus (Evidence Level B; PMIDs: 25417114, 12970315, 14508525, 21878896)."],"submitter_name":"Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital","review_date":20241218,"origin":"somatic","method":"clinical testing","submitter_date":20251120,"diseases":[{"symbols":{"mondo":"MONDO:0005075"}}],"date_updated":20251122,"clinical_significance":[],"review_status":"criteria provided, single submitter","accession_id":"SCV007105546"},{"pub_med_references":[12068308,12198537,12447372,12619120,12644542,12670889,12794760,12960123,14513361,14602780,15001635,15126572,15181070,15342696,15356022,15386408,15687339,15998781,16015629,16174717,16187918,16772349,17374713,17488796,17785355,18398503,19571295,20818844,20823850,21107320,21107323,22113612,22281684,23302800,23685455,24512911,24670642,24717435,25079330,28854169,29925953],"submission_description":["The val600-to-glu (V600E) mutation caused by a 1799T-A transversion in the BRAF gene was previously designated VAL599GLU (1796T-A). Kumar et al. (2003) noted that an earlier version of the BRAF sequence showed a discrepancy of 3 nucleotides in exon 1; based on the corrected sequence, they proposed a change in nucleotide numbering after nucleotide 94 (the ATG codon) by +3 and a corresponding codon change of +1.","Malignant Melanoma","Davies et al. (2002) identified a 1799T-A transversion in exon 15 of the BRAF gene that leads to a val600-to-glu (V600E) substitution. This mutation accounted for 92% of BRAF mutations in malignant melanoma (see 155600). The V600E mutation is an activating mutation resulting in constitutive activation of BRAF and downstream signal transduction in the MAP kinase pathway.","To evaluate the timing of mutations in BRAF during melanocyte neoplasia, Pollock et al. (2003) carried out mutation analysis on microdissected melanoma and nevi samples. They observed mutations resulting in the V600E amino acid substitution in 41 (68%) of 60 melanoma metastases, 4 (80%) of 5 primary melanomas, and, unexpectedly, in 63 (82%) of 77 nevi. The data suggested that mutational activation of the RAS/RAF/MAPK pathway in nevi is a critical step in the initiation of melanocytic neoplasia but alone is insufficient for melanoma tumorigenesis.","Lang et al. (2003) failed to find the V600E mutation as a germline mutation in 42 cases of familial melanoma studied. Their collection of families included 15 with and 24 without detected mutations in CDKN2A (600160). They did, however, find the V600E mutation in 6 (27%) of 22 samples of secondary (metastatic) melanomas studied. Meyer et al. (2003) found no V600E mutation in 172 melanoma patients comprising 46 familial cases, 21 multiple melanoma patients, and 106 cases with at least 1 first-degree relative suffering from other cancers. They concluded, therefore, that the common somatic BRAF mutation V600E does not contribute to polygenic or familial melanoma predisposition.","Kim et al. (2003) stated that V600E, the most common of BRAF mutations, had not been identified in tumors with mutations of the KRAS gene (190070). This mutually exclusive relationship supports the hypothesis that BRAF (V600E) and KRAS mutations exert equivalent effects in tumorigenesis (Rajagopalan et al., 2002; Singer et al., 2003).","Flaherty et al. (2010) reported complete or partial regression of V600E-associated metastatic melanoma in 81% of patients treated with an inhibitor (PLX4032) specific to the V600E mutation. Among 16 patients in a dose-escalation cohort, 10 had a partial response, and 1 had a complete response. Among 32 patients in an extension cohort, 24 had a partial response, and 2 had a complete response. The estimated median progression-free survival among all patients was more than 7 months. Responses were observed at all sites of disease, including bone, liver, and small bowel. Tumor biopsy specimens from 7 patients showed markedly reduced levels of phosphorylated ERK (600997), cyclin D1 (168461), and Ki67 (MKI67; 176741) at day 15 compared to baseline, indicating inhibition of the MAP kinase pathway. Three additional patients with V600E-associated papillary thyroid also showed a partial or complete response.","Bollag et al. (2010) described the structure-guided discovery of PLX4032 (RG7204), a potent inhibitor of oncogenic BRAF kinase activity. PLX4032 was cocrystallized with a protein construct that contained the kinase domain of BRAF(V600E). In a clinical trial, patients exposed to higher plasma levels of PLX4032 experienced tumor regression; in patients with tumor regressions, pathway analysis typically showed greater than 80% inhibition of cytoplasmic ERK phosphorylation. Bollag et al. (2010) concluded that their data demonstrated that BRAF-mutant melanomas are highly dependent on BRAF kinase activity.","Patients with BRAF(V600E)-positive melanomas exhibit an initial antitumor response to the RAF kinase inhibitor PLX4032, but acquired drug resistance almost invariably develops. Johannessen et al. (2010) identified MAP3K8 (191195), encoding COT (cancer Osaka thyroid oncogene) as a MAPK pathway agonist that drives resistance to RAF inhibition in BRAF(V600E) cell lines. COT activates ERK primarily through MARK/ERK (MEK)-dependent mechanisms that do not require RAF signaling. Moreover, COT expression is associated with de novo resistance in BRAF(V600E) cultured cell lines and acquired resistance in melanoma cells and tissue obtained from relapsing patients following treatment with MEK or RAF inhibitors. Johannessen et al. (2010) further identified combinatorial MAPK pathway inhibition or targeting of COT kinase activity as possible therapeutic strategies for reducing MAPK pathway activation in this setting.","Nazarian et al. (2010) showed that acquired resistance to PLX4032, a novel class I RAF-selective inhibitor, develops by mutually exclusive PDGFRB (173410) upregulation or NRAS (164790) mutations but not through secondary mutations in BRAF(V600E). Nazarian et al. (2010) used PLX4032-resistant sublines artificially derived from BRAF (V600E)-positive melanoma cell lines and validated key findings in PLX4032-resistant tumors and tumor-matched, short-term cultures from clinical trial patients. Induction of PDGFRB RNA, protein and tyrosine phosphorylation emerged as a dominant feature of acquired PLX4032 resistance in a subset of melanoma sublines, patient-derived biopsies, and short-term cultures. PDGFRB upregulated tumor cells have low activated RAS levels and, when treated with PLX4032, do not reactivate the MAPK pathway significantly. In another subset, high levels of activated N-RAS resulting from mutations lead to significant MAPK pathway reactivation upon PLX4032 treatment. Knockdown of PDGFRB or NRAS reduced growth of the respective PLX4032-resistant subsets. Overexpression of PDGFRB or NRAS(Q61K) conferred PLX4032 resistance to PLX4032-sensitive parental cell lines. Importantly, Nazarian et al. (2010) showed that MAPK reactivation predicts MEK inhibitor sensitivity. Thus, Nazarian et al. (2010) concluded that melanomas escape BRAF(V600E) targeting not through secondary BRAF(V600E) mutations but via receptor tyrosine kinase (RTK)-mediated activation of alternative survival pathway(s) or activated RAS-mediated reactivation of the MAPK pathway, suggesting additional therapeutic strategies.","Poulikakos et al. (2011) identified a novel resistance mechanism for melanomas with BRAF(V600E) treated with RAF inhibitors. The authors found that a subset of cells resistant to vemurafenib (PLX4032, RG7204) express a 61-kD variant form of BRAF(V600E), p61BRAF(V600E), that lacks exons 4 through 8, a region that encompasses the RAS-binding domain. p61BRAF(V600E) showed enhanced dimerization in cells with low levels of RAS activation, as compared to full-length BRAF(V600E). In cells in which p61BRAF(V600E) was expressed endogenously or ectopically, ERK signaling was resistant to the RAF inhibitor. Moreover, a mutation that abolished the dimerization of p61BRAF(V600E) restored its sensitivity to vemurafenib. Finally, Poulikakos et al. (2011) identified BRAF(V600E) splicing variants lacking the RAS-binding domain in the tumors of 6 of 19 patients with acquired resistance to vemurafenib. Poulikakos et al. (2011) concluded that their data supported the model that inhibition of ERK signaling by RAF inhibitors is dependent on levels of RAS-GTP too low to support RAF dimerization and identified a novel mechanism of acquired resistance in patients: expression of splicing isoforms of BRAF(V600E) that dimerize in a RAS-independent manner.","Thakur et al. (2013) investigated the cause and consequences of vemurafenib resistance using 2 independently-derived primary human melanoma xenograft models in which drug resistance is selected by continuous vemurafenib administration. In one of these models, resistant tumors showed continued dependency on BRAF(V600E)-MEK-ERK signaling owing to elevated BRAF(V600E) expression. Thakur et al. (2013) showed that vemurafenib-resistant melanomas become drug-dependent for their continued proliferation, such that cessation of drug administration leads to regression of established drug-resistant tumors. Thakur et al. (2013) further demonstrated that a discontinuous dosing strategy, which exploits the fitness disadvantage displayed by drug-resistant cells in the absence of the drug, forestalls the onset of lethal drug-resistant disease. Thakur et al. (2013) concluded that their data highlighted the concept that drug-resistant cells may also display drug dependency, such that altered dosing may prevent the emergence of lethal drug resistance. These observations may contribute to sustaining the durability of vemurafenib response with the ultimate goal of curative therapy for the subset of melanoma patients with BRAF mutations.","Using metabolic profiling and functional perturbations, Kaplon et al. (2013) showed that the mitochondrial gatekeeper pyruvate dehydrogenase (PDH; 300502) is a crucial mediator of senescence induced by BRAF(V600E), an oncogene commonly mutated in melanoma and other cancers. BRAF(V600E)-induced senescence is accompanied by simultaneous suppression of the PDH-inhibitory enzyme pyruvate dehydrogenase kinase-1 (PDK1; 602524) and induction of the PDH-activating enzyme pyruvate dehydrogenase phosphatase-2 (PDP2; 615499). The resulting combined activation of PDH enhanced the use of pyruvate in the tricarboxylic acid cycle, causing increased respiration and redox stress. Abrogation of oncogene-induced senescence (OIS), a rate-limiting step towards oncogenic transformation, coincided with reversion of these processes. Further supporting a crucial role of PDH in OIS, enforced normalization of either PDK1 or PDP2 expression levels inhibited PDH and abrogated OIS, thereby licensing BRAF(V600E)-driven melanoma development. Finally, depletion of PDK1 eradicated melanoma subpopulations resistant to targeted BRAF inhibition, and caused regression of established melanomas.","Sun et al. (2014) showed that 6 out of 16 BRAF(V600E)-positive melanoma tumors analyzed acquired EGFR (131550) expression after the development of resistance to inhibitors of BRAF or MEK (176872). Using a chromatin regulator-focused short hairpin RNA (shRNA) library, Sun et al. (2014) found that suppression of SRY-box 10 (SOX10; 602229) in melanoma causes activation of TGF-beta (190180) signaling, thus leading to upregulation of EGFR and platelet-derived growth factor receptor-beta (PDGFRB; 173410), which confer resistance to BRAF and MEK inhibitors. Expression of EGFR in melanoma or treatment with TGF-beta results in a slow-growth phenotype with cells displaying hallmarks of oncogene-induced senescence. However, EGFR expression or exposure to TGF-beta becomes beneficial for proliferation in the presence of BRAF or MEK inhibitors. In a heterogeneous population of melanoma cells that have varying levels of SOX10 suppression, cells with low SOX10 and consequently high EGFR expression are rapidly enriched in the presence of drug treatment, but this is reversed when the treatment is discontinued. Sun et al. (2014) found evidence for SOX10 loss and/or activation of TGF-beta signaling in 4 of the 6 EGFR-positive drug-resistant melanoma patient samples. Sun et al. (2014) concluded that their findings provided a rationale for why some BRAF or MEK inhibitor-resistant melanoma patients may regain sensitivity to these drugs after a 'drug holiday' and identified patients with EGFR-positive melanoma as a group that may benefit from retreatment after a drug holiday.","Boussemart et al. (2014) demonstrated that the persistent formation of the eIF4F complex, comprising the eIF4E (133440) cap-binding protein, the eIF4G (600495) scaffolding protein, and the eIF4A (602641) RNA helicase, is associated with resistance to anti-BRAF (164757), anti-MEK, and anti-BRAF plus anti-MEK drug combinations in BRAF(V600)-mutant melanoma, colon, and thyroid cancer cell lines. Resistance to treatment and maintenance of eIF4F complex formation is associated with 1 of 3 mechanisms: reactivation of MAPK (see 176948) signaling; persistent ERK-independent phosphorylation of the inhibitory eIF4E-binding protein 4EBP1 (602223); or increased proapoptotic BMF (606266)-dependent degradation of eIF4G. The development of an in situ method to detect the eIF4E-eIF4G interactions showed that eIF4F complex formation is decreased in tumors that respond to anti-BRAF therapy and increased in resistant metastases compared to tumors before treatment. Strikingly, inhibiting the eIF4F complex, either by blocking the eIF4E-eIF4G interaction or by targeting eIF4A, synergized with inhibiting BRAF(V600) to kill the cancer cells. eIF4F appeared not only to be an indicator of both innate and acquired resistance, but also a therapeutic target. Boussemart et al. (2014) concluded that combinations of drugs targeting BRAF (and/or MEK) and eIF4F may overcome most of the resistance mechanisms in BRAF(V600)-mutant cancers.","Colorectal Carcinoma","Rajagopalan et al. (2002) identified the V600E mutation in 28 of 330 colorectal tumors (see 114500) screened for BRAF mutations. In all cases the mutation was heterozygous and occurred somatically.","Domingo et al. (2004) pointed out that the V600E hotspot mutation had been found in colorectal tumors that showed inherited mutation in a DNA mismatch repair (MMR) gene, such as MLH1 (120436) or MSH2 (609309). These mutations had been shown to occur almost exclusively in tumors located in the proximal colon and with hypermethylation of MLH1, the gene involved in the initial steps of development of these tumors; however, BRAF mutations were not detected in those cases with or presumed to have germline mutation in either MLH1 or MSH2. Domingo et al. (2004) studied mutation analysis of the BRAF hotspot as a possible low-cost effective strategy for genetic testing for hereditary nonpolyposis colorectal cancer (HNPCC; 120435). The V600E mutation was found in 82 (40%) of 206 sporadic tumors with high microsatellite instability (MSI-H) but in none of 111 tested HNPCC tumors or in 45 cases showing abnormal MSH2 immunostaining. Domingo et al. (2004) concluded that detection of the V600E mutation in a colorectal MSI-H tumor argues against the presence of germline mutation in either MLH1 or MSH2, and that screening of these MMR genes can be avoided in cases positive for V600E.","Lubomierski et al. (2005) analyzed 45 colorectal carcinomas with MSI and 37 colorectal tumors without MSI but with similar clinical characteristics and found that BRAF was mutated more often in tumors with MSI than without (27% vs 5%, p = 0.016). The most prevalent BRAF alteration, V600E, occurred only in tumors with MSI and was associated with more frequent MLH1 promoter methylation and loss of MLH1. The median age of patients with BRAF V600E was older than that of those without V600E (78 vs 49 years, p = 0.001). There were no BRAF alterations in patients with germline mutations of mismatch repair genes. Lubomierski et al. (2005) concluded that tumors with MSI caused by epigenetic MLH1 silencing have a mutational background distinct from that of tumors with genetic loss of mismatch repair, and suggested that there are 2 genetically distinct entities of microsatellite unstable tumors.","Tol et al. (2009) detected a somatic V600E mutation in 45 (8.7%) of 519 metastatic colorectal tumors. Patients with BRAF-mutated tumors had significantly shorter median progression-free and median overall survival compared to patients with wildtype BRAF tumors, regardless of the use of cetuximab. Tol et al. (2009) suggested that the BRAF mutation may be a negative prognostic factor in these patients.","Inhibition of the BRAF(V600E) oncoprotein by the small-molecule drug PLX4032 (vemurafenib) is highly effective in the treatment of melanoma. However, colon cancer patients harboring the same BRAF(V600E) oncogenic lesion have poor prognosis and show only a very limited response to this drug. To investigate the cause of this limited therapeutic effect in BRAF(V600E) mutant colon cancer, Prahallad et al. (2012) performed an RNA interference-based genetic screen in human cells to search for kinases whose knockdown synergizes with BRAF(V600E) inhibition. They reported that blockade of the epidermal growth factor receptor (EGFR; 131550) shows strong synergy with BRAF(V600E) inhibition. Prahallad et al. (2012) found in multiple BRAF(V600E) mutant colon cancers that inhibition of EGFR by the antibody drug cetuximab or the small-molecule drugs gefitinib or erlotinib is strongly synergistic with BRAF(V600E) inhibition, both in vitro and in vivo. Mechanistically, Prahallad et al. (2012) found that BRAF(V600E) inhibition causes a rapid feedback activation of EGFR, which supports continued proliferation in the presence of BRAF(V600E) inhibition. Melanoma cells express low levels of EGFR and are therefore not subject to this feedback activation. Consistent with this, Prahallad et al. (2012) found that ectopic expression of EGFR in melanoma cells is sufficient to cause resistance to PLX4032. Prahallad et al. (2012) concluded that BRAF(V600E) mutant colon cancers (approximately 8 to 10% of all colon cancers) might benefit from combination therapy consisting of BRAF and EGFR inhibitors.","Gala et al. (2014) identified the BRAF V600E mutation in 18 of 19 sessile serrated adenomas from 19 unrelated patients with sessile serrated polyposis cancer syndrome (SSPCS; 617108).","Papillary Thyroid Carcinoma","Kimura et al. (2003) identified the V600E mutation in 28 (35.8%) of 78 papillary thyroid cancers (PTC; see 188550); it was not found in any of the other types of differentiated follicular neoplasms arising from the same cell type (0 of 46). RET (see 164761)/PTC mutations and RAS (see 190020) mutations were each identified in 16.4% of PTCs, but there was no overlap in the 3 mutations. Kimura et al. (2003) concluded that thyroid cell transformation to papillary cancer takes place through constitutive activation of effectors along the RET/PTC-RAS-BRAF signaling pathway.","Xing et al. (2004) studied various thyroid tumor types for the most common BRAF mutation, 1799T-A, by DNA sequencing. They found a high and similar frequency (45%) of the 1799T-A mutation in 2 geographically distinct papillary thyroid cancer patient populations, 1 composed of sporadic cases from North America, and the other from Kiev, Ukraine, that included individuals who were exposed to the Chernobyl nuclear accident. In contrast, Xing et al. (2004) found BRAF mutations in only 20% of anaplastic thyroid cancers and in no medullary thyroid cancers or benign thyroid hyperplasia. They also confirmed previous reports that the BRAF 1799T-A mutation did not occur in benign thyroid adenomas or follicular thyroid cancers. They concluded that frequent occurrence of BRAF mutation is associated with PTC, irrespective of geographic origin, and is apparently not a radiation-susceptible mutation.","Nikiforova et al. (2003) analyzed 320 thyroid tumors and 6 anaplastic carcinoma cell lines and detected BRAF mutations in 45 papillary carcinomas (38%), 2 poorly differentiated carcinomas (13%), 3 (10%) anaplastic carcinomas (10%), and 5 thyroid anaplastic carcinoma cell lines (83%) but not in follicular, Hurthle cell, and medullary carcinomas, follicular and Hurthle cell adenomas, or benign hyperplastic nodules. All mutations involved a T-to-A transversion at nucleotide 1799. All BRAF-positive poorly differentiated and anaplastic carcinomas contained areas of preexisting papillary carcinoma, and mutation was present in both the well differentiated and dedifferentiated components. The authors concluded that BRAF mutations are restricted to papillary carcinomas and poorly differentiated and anaplastic carcinomas arising from papillary carcinomas, and that they are associated with distinct phenotypic and biologic properties of papillary carcinomas and may participate in progression to poorly differentiated and anaplastic carcinomas.","Hypothesizing that childhood thyroid carcinomas may be associated with a different prevalence of the BRAF 1799T-A mutation compared with adult cases, Kumagai et al. (2004) examined 31 cases of Japanese childhood thyroid carcinoma and an additional 48 cases of PTC from Ukraine, all of whom were less than 17 years of age at the time of the Chernobyl accident. The BRAF 1799T-A mutation was found in only 1 of 31 Japanese cases (3.4%) and in none of the 15 Ukrainian cases operated on before the age of 15 years, although it was found in 8 of 33 Ukrainian young adult cases (24.2%). Kumagai et al. (2004) concluded that the BRAF 1799T-A mutation is uncommon in childhood thyroid carcinomas.","Puxeddu et al. (2004) found the V600E substitution in 24 of 60 PTCs (40%) but in none of 6 follicular adenomas, 5 follicular carcinomas, or 1 anaplastic carcinoma. Nine of the 60 PTCs (15%) presented expression of a RET/PTC rearrangement. A genetico-clinical association analysis showed a statistically significant correlation between BRAF mutation and development of PTCs of the classic papillary histotype (P = 0.038). No link could be detected between expression of BRAF V600E and age at diagnosis, gender, dimension, local invasiveness of the primary cancer, presence of lymph node metastases, tumor stage, or multifocality of the disease. The authors concluded that these data clearly confirmed that BRAF V600E was the most common genetic alteration found to that time in adult sporadic PTCs, that it is unique for this thyroid cancer histotype, and that it might drive the development of PTCs of the classic papillary subtype.","Xing et al. (2004) demonstrated detection of the 1799T-A mutation on thyroid cytologic specimens from fine needle aspiration biopsy (FNAB). Prospective analysis showed that 50% of the nodules that proved to be PTCs on surgical histopathology were correctly diagnosed by BRAF mutation analysis on FNAB specimens; there were no false positive findings.","Xing et al. (2005) studied the relationships between the BRAF V600E mutation and clinicopathologic outcomes, including recurrence, in 219 PTC patients. The authors concluded that in patients with PTC, BRAF mutation is associated with poorer clinicopathologic outcomes and independently predicts recurrence. Therefore, BRAF mutation may be a useful molecular marker to assist in risk stratification for patients with PTC.","In a series of 52 classic PTCs, Porra et al. (2005) found that low SLC5A8 (608044) expression was highly significantly associated with the presence of the BRAF 1799T-A mutation. SLC5A8 expression was selectively downregulated (40-fold) in PTCs of classical form; methylation-specific PCR analyses showed that SLC5A8 was methylated in 90% of classic PTCs and in about 20% of other PTCs. Porra et al. (2005) concluded that their data identified a relationship between the methylation-associated silencing of the tumor-suppressor gene SLC5A8 and the 1799T-A point mutation of the BRAF gene in the classic PTC subtype of thyroid carcinomas.","Vasko et al. (2005) studied the relationship between the BRAF 1799T-A mutation and lymph node metastasis of PTC by examining the mutation in both the primary tumors and their paired lymph node metastases. Their findings indicated that the high prevalence of BRAF mutation in lymph node-metastasized PTC tissues from BRAF mutation-positive primary tumors and the possible de novo formation of BRAF mutation in lymph node-metastasized PTC were consistent with a role of BRAF mutation in facilitating the metastasis and progression of PTC in lymph nodes.","In a patient with congenital hypothyroidism and long-standing goiter due to mutation in the thyroglobulin gene (see TG, 188540; and TDH3, 274700), who was also found to have multifocal follicular carcinoma of the thyroid, Hishinuma et al. (2005) identified somatic heterozygosity for the V600E mutation in the BRAF gene in the cancerous thyroid tissue.","Liu et al. (2007) used BRAF siRNA to transfect stably several BRAF mutation-harboring PTC cell lines, isolated clones with stable suppression of BRAF, and assessed their ability to proliferate, transform, and grow xenograft tumors in nude mice. They found that the V600E mutation not only initiates PTC but also maintains the proliferation, transformation, and tumorigenicity of PTC cells harboring the BRAF mutation, and that the growth of tumors derived from such cells continues to depend on the V600E mutation.","Jo et al. (2006) found that of 161 PTC patients, 102 (63.4%) had the BRAF V600E mutation and that these patients had significantly larger tumor sizes and significantly higher expression of vascular endothelial growth factor (VEGF; 192240) compared to patients without this mutation. The level of VEGF expression was closely correlated with tumor size, extrathyroidal invasion, and stage. Jo et al. (2006) concluded that the relatively high levels of VEGF expression may be related to poorer clinical outcomes and recurrences in BRAF V600E(+) PTC.","Durante et al. (2007) found that the BRAF V600E mutation in PTCs is associated with reduced expression of key genes involved in iodine metabolism. They noted that this effect may alter the effectiveness of diagnostic and/or therapeutic use of radioiodine in BRAF-mutation PTCs.","Lupi et al. (2007) found a BRAF mutation in 219 of 500 cases (43.8%) of PTC. The most common BRAF mutation, V600E, was found in 214 cases (42.8%). BRAF V600E was associated with extrathyroidal invasion (p less than 0.0001), multicentricity (p = 0.0026), presence of nodal metastases (p = 0.0009), class III versus classes I and II (p less than 0.00000006), and absence of tumor capsule (p less than 0.0001), in particular, in follicular- and micro-PTC variants. By multivariate analysis, the absence of tumor capsule remained the only parameter associated (p = 0.0005) with the BRAF V600E mutation. The authors concluded that the BRAF V600E mutation is associated with high-risk PTC and, in particular, in follicular variant with invasive tumor growth.","Flaherty et al. (2010) reported complete or partial regression of V600E-associated papillary thyroid cancer in 3 patients treated with an inhibitor (PLX4032) specific to the V600E mutation.","Nonseminomatous Germ Cell Tumors","In 3 (9%) of 32 nonseminomatous germ cell tumors (see 273300) with a mixture of embryonal carcinoma, yolk sac tumor, choriocarcinoma, and mature teratoma, Sommerer et al. (2005) identified the activating 1796T-A mutation in the BRAF gene; the mutation was present within the embryonic carcinoma component.","Astrocytoma","Pfister et al. (2008) identified a somatic V600E mutation in 4 (6%) of 66 pediatric low-grade astrocytomas (see 137800). Thirty (45%) of the 66 tumors had a copy number gain spanning the BRAF locus, indicating a novel mechanism of MAPK (176948) pathway activation in these tumors.","Role in Neurodegeneration","Mass et al. (2017) hypothesized that a somatic BRAF(V600E) mutation in the erythromyeloid lineage may cause neurodegeneration. Mass et al. (2017) showed that mosaic expression of BRAF(V600E) in mouse erythromyeloid progenitors results in clonal expansion of tissue-resident macrophages and a severe late-onset neurodegenerative disorder. This is associated with accumulation of ERK-activated amoeboid microglia in mice, and is also observed in human patients with histiocytoses. In the mouse model, neurobehavioral signs, astrogliosis, deposition of amyloid precursor protein, synaptic loss, and neuronal death were driven by ERK-activated microglia and were preventable by BRAF inhibition. Mass et al. (2017) suggested that the results identified the fetal precursors of tissue-resident macrophages as a potential cell of origin for histiocytoses and demonstrated that a somatic mutation in the erythromyeloid progenitor lineage in mice can drive late-onset neurodegeneration.","Variant Function","Brady et al. (2014) showed that decreasing the levels of CTR1 (603085), or mutations in MEK1 (176872) that disrupt copper binding, decreased BRAF(V600E)-driven signaling and tumorigenesis in mice and human cell settings. Conversely, a MEK1-MEK5 (602520) chimera that phosphorylated ERK1/2 independently of copper or an active ERK2 restored the tumor growth of murine cells lacking Ctr1. Copper chelators used in the treatment of Wilson disease (277900) decreased tumor growth of human or murine cells that were either transformed by BRAF(V600E) or engineered to be resistant to BRAF inhibition. Brady et al. (2014) concluded that copper chelation therapy could be repurposed to treat cancers containing the BRAF(V600E) mutation.","Rapino et al. (2018) showed in humans that the enzymes that catalyze modifications of wobble uridine-34 (U34) tRNA are key players of the protein synthesis rewiring that is induced by the transformation driven by the BRAF V600E oncogene and by resistance to targeted therapy in melanoma. Rapino et al. (2018) showed that BRAF V600E-expressing melanoma cells are dependent on U34 enzymes for survival, and that concurrent inhibition of MAPK signaling and ELP3 (612722) or CTU1 (612694) and/or CTU2 (617057) synergizes to kill melanoma cells. Activation of the PI3K signaling pathway, one of the most common mechanisms of acquired resistance to MAPK therapeutic agents, markedly increases the expression of U34 enzymes. Mechanistically, U34 enzymes promote glycolysis in melanoma cells through the direct, codon-dependent, regulation of the translation of HIF1A (603348) mRNA and the maintenance of high levels of HIF1-alpha protein. Therefore, the acquired resistance to anti-BRAF therapy is associated with high levels of U34 enzymes and HIF1-alpha. Rapino et al. (2018) concluded that U34 enzymes promote the survival and resistance to therapy of melanoma cells by regulating specific mRNA translation."],"submitter_name":"OMIM","review_date":20140904,"origin":"somatic","method":"literature only","submitter_date":20220317,"diseases":[{"normalized_cancer":["Papillary Thyroid Cancer"],"names":["Thyroid Carcinoma, Papillary, Somatic"]}],"review_description":"Pathogenic","date_updated":20220328,"clinical_significance":["Pathogenic"],"review_status":"no assertion criteria provided","accession_id":"SCV000035249"}],"variation_id":13961,"submission_description":[],"title":"NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) AND Papillary thyroid carcinoma","review_date":20140904,"diseases":[{"pub_med":[26389271,26389258],"normalized_cancer":["Papillary Thyroid Cancer"],"symbols":{"medgen":"C0238463","orphanet":"146","mesh":"D000077273","mondo":"MONDO:0005075","human_phenotype_ontology":"HP:0002895"},"normalized_disease":["Thyroid Gland Papillary Carcinoma"],"names":["Thyroid Gland Papillary Carcinoma","Nonmedullary Thyroid Carcinoma, Papillary","Thyroid Carcinoma, Papillary, Somatic","Thyroid Gland Papillary Carcinoma"]}],"pub_med_references":[12068308,12198537,12447372,12619120,12644542,12670889,12794760,12960123,14513361,14602780,15001635,15126572,15181070,15342696,15356022,15386408,15687339,15998781,16015629,16174717,16187918,16772349,17374713,17488796,17785355,18398503,19571295,20818844,20823850,21107320,21107323,22113612,22281684,23302800,23685455,24512911,24670642,24717435,25079330,28854169,29925953],"date_created":20130404,"variant_id":10190071404531360004,"review_description":"Pathogenic","clinical_significance":["Pathogenic"],"allele_id":29000,"accession_id":"RCV000014993"},{"submissions":[{"submission_description":["Vemurafenib and cobimetinib combination is an FDA approved first line treatment for BRAF V600E mutant metastatic melanoma based on clinical data including the Phase III coBRIM trial. The cobas 4800 BRAF V600 Mutation Test is approved as an FDA companion test for Cotellic (cobimetinib) in combination with Zelboraf (vemurafenib)."],"submitter_name":"Wagner Lab, Nationwide Children's Hospital","review_date":20181101,"origin":"somatic","method":"curation","submitter_date":20250226,"diseases":[{"normalized_cancer":["Melanoma"],"normalized_disease":["Melanoma"],"names":["Melanoma"]}],"date_updated":20250304,"clinical_significance":[],"review_status":"criteria provided, single submitter","accession_id":"SCV005870910"},{"submission_description":["Combination treatment of BRAF inhibitor dabrafenib and MEK inhibitor trametinib is recommended for adjuvant treatment of stage III or recurrent melanoma with BRAF V600E mutation detected by the approved THxID kit, as well as first line treatment for metastatic melanoma. The treatments are FDA approved based on studies including the Phase III COMBI-V, COMBI-D and COMBI-AD Trials. Combination therapy is now recommended above BRAF inhibitor monotherapy. Cutaneous squamous-cell carcinoma and keratoacanthoma occur at lower rates with combination therapy than with BRAF inhibitor alone."],"submitter_name":"CIViC knowledgebase, Washington University School of Medicine","review_date":20180515,"origin":"somatic","method":"curation","submitter_date":20240216,"diseases":[{"normalized_cancer":["Melanoma"],"normalized_disease":["Melanoma"],"names":["Melanoma"]}],"date_updated":20240220,"clinical_significance":[],"review_status":"criteria provided, single submitter","accession_id":"SCV004565360"},{"pub_med_references":[12068308,12198537,12447372,12619120,12644542,12670889,12794760,12960123,14513361,14602780,15001635,15126572,15181070,15342696,15356022,15386408,15687339,15998781,16015629,16174717,16187918,16772349,17374713,17488796,17785355,18398503,19571295,20818844,20823850,21107320,21107323,22113612,22281684,23302800,23685455,24512911,24670642,24717435,25079330,28854169,29925953],"submission_description":["The val600-to-glu (V600E) mutation caused by a 1799T-A transversion in the BRAF gene was previously designated VAL599GLU (1796T-A). Kumar et al. (2003) noted that an earlier version of the BRAF sequence showed a discrepancy of 3 nucleotides in exon 1; based on the corrected sequence, they proposed a change in nucleotide numbering after nucleotide 94 (the ATG codon) by +3 and a corresponding codon change of +1.","Malignant Melanoma","Davies et al. (2002) identified a 1799T-A transversion in exon 15 of the BRAF gene that leads to a val600-to-glu (V600E) substitution. This mutation accounted for 92% of BRAF mutations in malignant melanoma (see 155600). The V600E mutation is an activating mutation resulting in constitutive activation of BRAF and downstream signal transduction in the MAP kinase pathway.","To evaluate the timing of mutations in BRAF during melanocyte neoplasia, Pollock et al. (2003) carried out mutation analysis on microdissected melanoma and nevi samples. They observed mutations resulting in the V600E amino acid substitution in 41 (68%) of 60 melanoma metastases, 4 (80%) of 5 primary melanomas, and, unexpectedly, in 63 (82%) of 77 nevi. The data suggested that mutational activation of the RAS/RAF/MAPK pathway in nevi is a critical step in the initiation of melanocytic neoplasia but alone is insufficient for melanoma tumorigenesis.","Lang et al. (2003) failed to find the V600E mutation as a germline mutation in 42 cases of familial melanoma studied. Their collection of families included 15 with and 24 without detected mutations in CDKN2A (600160). They did, however, find the V600E mutation in 6 (27%) of 22 samples of secondary (metastatic) melanomas studied. Meyer et al. (2003) found no V600E mutation in 172 melanoma patients comprising 46 familial cases, 21 multiple melanoma patients, and 106 cases with at least 1 first-degree relative suffering from other cancers. They concluded, therefore, that the common somatic BRAF mutation V600E does not contribute to polygenic or familial melanoma predisposition.","Kim et al. (2003) stated that V600E, the most common of BRAF mutations, had not been identified in tumors with mutations of the KRAS gene (190070). This mutually exclusive relationship supports the hypothesis that BRAF (V600E) and KRAS mutations exert equivalent effects in tumorigenesis (Rajagopalan et al., 2002; Singer et al., 2003).","Flaherty et al. (2010) reported complete or partial regression of V600E-associated metastatic melanoma in 81% of patients treated with an inhibitor (PLX4032) specific to the V600E mutation. Among 16 patients in a dose-escalation cohort, 10 had a partial response, and 1 had a complete response. Among 32 patients in an extension cohort, 24 had a partial response, and 2 had a complete response. The estimated median progression-free survival among all patients was more than 7 months. Responses were observed at all sites of disease, including bone, liver, and small bowel. Tumor biopsy specimens from 7 patients showed markedly reduced levels of phosphorylated ERK (600997), cyclin D1 (168461), and Ki67 (MKI67; 176741) at day 15 compared to baseline, indicating inhibition of the MAP kinase pathway. Three additional patients with V600E-associated papillary thyroid also showed a partial or complete response.","Bollag et al. (2010) described the structure-guided discovery of PLX4032 (RG7204), a potent inhibitor of oncogenic BRAF kinase activity. PLX4032 was cocrystallized with a protein construct that contained the kinase domain of BRAF(V600E). In a clinical trial, patients exposed to higher plasma levels of PLX4032 experienced tumor regression; in patients with tumor regressions, pathway analysis typically showed greater than 80% inhibition of cytoplasmic ERK phosphorylation. Bollag et al. (2010) concluded that their data demonstrated that BRAF-mutant melanomas are highly dependent on BRAF kinase activity.","Patients with BRAF(V600E)-positive melanomas exhibit an initial antitumor response to the RAF kinase inhibitor PLX4032, but acquired drug resistance almost invariably develops. Johannessen et al. (2010) identified MAP3K8 (191195), encoding COT (cancer Osaka thyroid oncogene) as a MAPK pathway agonist that drives resistance to RAF inhibition in BRAF(V600E) cell lines. COT activates ERK primarily through MARK/ERK (MEK)-dependent mechanisms that do not require RAF signaling. Moreover, COT expression is associated with de novo resistance in BRAF(V600E) cultured cell lines and acquired resistance in melanoma cells and tissue obtained from relapsing patients following treatment with MEK or RAF inhibitors. Johannessen et al. (2010) further identified combinatorial MAPK pathway inhibition or targeting of COT kinase activity as possible therapeutic strategies for reducing MAPK pathway activation in this setting.","Nazarian et al. (2010) showed that acquired resistance to PLX4032, a novel class I RAF-selective inhibitor, develops by mutually exclusive PDGFRB (173410) upregulation or NRAS (164790) mutations but not through secondary mutations in BRAF(V600E). Nazarian et al. (2010) used PLX4032-resistant sublines artificially derived from BRAF (V600E)-positive melanoma cell lines and validated key findings in PLX4032-resistant tumors and tumor-matched, short-term cultures from clinical trial patients. Induction of PDGFRB RNA, protein and tyrosine phosphorylation emerged as a dominant feature of acquired PLX4032 resistance in a subset of melanoma sublines, patient-derived biopsies, and short-term cultures. PDGFRB upregulated tumor cells have low activated RAS levels and, when treated with PLX4032, do not reactivate the MAPK pathway significantly. In another subset, high levels of activated N-RAS resulting from mutations lead to significant MAPK pathway reactivation upon PLX4032 treatment. Knockdown of PDGFRB or NRAS reduced growth of the respective PLX4032-resistant subsets. Overexpression of PDGFRB or NRAS(Q61K) conferred PLX4032 resistance to PLX4032-sensitive parental cell lines. Importantly, Nazarian et al. (2010) showed that MAPK reactivation predicts MEK inhibitor sensitivity. Thus, Nazarian et al. (2010) concluded that melanomas escape BRAF(V600E) targeting not through secondary BRAF(V600E) mutations but via receptor tyrosine kinase (RTK)-mediated activation of alternative survival pathway(s) or activated RAS-mediated reactivation of the MAPK pathway, suggesting additional therapeutic strategies.","Poulikakos et al. (2011) identified a novel resistance mechanism for melanomas with BRAF(V600E) treated with RAF inhibitors. The authors found that a subset of cells resistant to vemurafenib (PLX4032, RG7204) express a 61-kD variant form of BRAF(V600E), p61BRAF(V600E), that lacks exons 4 through 8, a region that encompasses the RAS-binding domain. p61BRAF(V600E) showed enhanced dimerization in cells with low levels of RAS activation, as compared to full-length BRAF(V600E). In cells in which p61BRAF(V600E) was expressed endogenously or ectopically, ERK signaling was resistant to the RAF inhibitor. Moreover, a mutation that abolished the dimerization of p61BRAF(V600E) restored its sensitivity to vemurafenib. Finally, Poulikakos et al. (2011) identified BRAF(V600E) splicing variants lacking the RAS-binding domain in the tumors of 6 of 19 patients with acquired resistance to vemurafenib. Poulikakos et al. (2011) concluded that their data supported the model that inhibition of ERK signaling by RAF inhibitors is dependent on levels of RAS-GTP too low to support RAF dimerization and identified a novel mechanism of acquired resistance in patients: expression of splicing isoforms of BRAF(V600E) that dimerize in a RAS-independent manner.","Thakur et al. (2013) investigated the cause and consequences of vemurafenib resistance using 2 independently-derived primary human melanoma xenograft models in which drug resistance is selected by continuous vemurafenib administration. In one of these models, resistant tumors showed continued dependency on BRAF(V600E)-MEK-ERK signaling owing to elevated BRAF(V600E) expression. Thakur et al. (2013) showed that vemurafenib-resistant melanomas become drug-dependent for their continued proliferation, such that cessation of drug administration leads to regression of established drug-resistant tumors. Thakur et al. (2013) further demonstrated that a discontinuous dosing strategy, which exploits the fitness disadvantage displayed by drug-resistant cells in the absence of the drug, forestalls the onset of lethal drug-resistant disease. Thakur et al. (2013) concluded that their data highlighted the concept that drug-resistant cells may also display drug dependency, such that altered dosing may prevent the emergence of lethal drug resistance. These observations may contribute to sustaining the durability of vemurafenib response with the ultimate goal of curative therapy for the subset of melanoma patients with BRAF mutations.","Using metabolic profiling and functional perturbations, Kaplon et al. (2013) showed that the mitochondrial gatekeeper pyruvate dehydrogenase (PDH; 300502) is a crucial mediator of senescence induced by BRAF(V600E), an oncogene commonly mutated in melanoma and other cancers. BRAF(V600E)-induced senescence is accompanied by simultaneous suppression of the PDH-inhibitory enzyme pyruvate dehydrogenase kinase-1 (PDK1; 602524) and induction of the PDH-activating enzyme pyruvate dehydrogenase phosphatase-2 (PDP2; 615499). The resulting combined activation of PDH enhanced the use of pyruvate in the tricarboxylic acid cycle, causing increased respiration and redox stress. Abrogation of oncogene-induced senescence (OIS), a rate-limiting step towards oncogenic transformation, coincided with reversion of these processes. Further supporting a crucial role of PDH in OIS, enforced normalization of either PDK1 or PDP2 expression levels inhibited PDH and abrogated OIS, thereby licensing BRAF(V600E)-driven melanoma development. Finally, depletion of PDK1 eradicated melanoma subpopulations resistant to targeted BRAF inhibition, and caused regression of established melanomas.","Sun et al. (2014) showed that 6 out of 16 BRAF(V600E)-positive melanoma tumors analyzed acquired EGFR (131550) expression after the development of resistance to inhibitors of BRAF or MEK (176872). Using a chromatin regulator-focused short hairpin RNA (shRNA) library, Sun et al. (2014) found that suppression of SRY-box 10 (SOX10; 602229) in melanoma causes activation of TGF-beta (190180) signaling, thus leading to upregulation of EGFR and platelet-derived growth factor receptor-beta (PDGFRB; 173410), which confer resistance to BRAF and MEK inhibitors. Expression of EGFR in melanoma or treatment with TGF-beta results in a slow-growth phenotype with cells displaying hallmarks of oncogene-induced senescence. However, EGFR expression or exposure to TGF-beta becomes beneficial for proliferation in the presence of BRAF or MEK inhibitors. In a heterogeneous population of melanoma cells that have varying levels of SOX10 suppression, cells with low SOX10 and consequently high EGFR expression are rapidly enriched in the presence of drug treatment, but this is reversed when the treatment is discontinued. Sun et al. (2014) found evidence for SOX10 loss and/or activation of TGF-beta signaling in 4 of the 6 EGFR-positive drug-resistant melanoma patient samples. Sun et al. (2014) concluded that their findings provided a rationale for why some BRAF or MEK inhibitor-resistant melanoma patients may regain sensitivity to these drugs after a 'drug holiday' and identified patients with EGFR-positive melanoma as a group that may benefit from retreatment after a drug holiday.","Boussemart et al. (2014) demonstrated that the persistent formation of the eIF4F complex, comprising the eIF4E (133440) cap-binding protein, the eIF4G (600495) scaffolding protein, and the eIF4A (602641) RNA helicase, is associated with resistance to anti-BRAF (164757), anti-MEK, and anti-BRAF plus anti-MEK drug combinations in BRAF(V600)-mutant melanoma, colon, and thyroid cancer cell lines. Resistance to treatment and maintenance of eIF4F complex formation is associated with 1 of 3 mechanisms: reactivation of MAPK (see 176948) signaling; persistent ERK-independent phosphorylation of the inhibitory eIF4E-binding protein 4EBP1 (602223); or increased proapoptotic BMF (606266)-dependent degradation of eIF4G. The development of an in situ method to detect the eIF4E-eIF4G interactions showed that eIF4F complex formation is decreased in tumors that respond to anti-BRAF therapy and increased in resistant metastases compared to tumors before treatment. Strikingly, inhibiting the eIF4F complex, either by blocking the eIF4E-eIF4G interaction or by targeting eIF4A, synergized with inhibiting BRAF(V600) to kill the cancer cells. eIF4F appeared not only to be an indicator of both innate and acquired resistance, but also a therapeutic target. Boussemart et al. (2014) concluded that combinations of drugs targeting BRAF (and/or MEK) and eIF4F may overcome most of the resistance mechanisms in BRAF(V600)-mutant cancers.","Colorectal Carcinoma","Rajagopalan et al. (2002) identified the V600E mutation in 28 of 330 colorectal tumors (see 114500) screened for BRAF mutations. In all cases the mutation was heterozygous and occurred somatically.","Domingo et al. (2004) pointed out that the V600E hotspot mutation had been found in colorectal tumors that showed inherited mutation in a DNA mismatch repair (MMR) gene, such as MLH1 (120436) or MSH2 (609309). These mutations had been shown to occur almost exclusively in tumors located in the proximal colon and with hypermethylation of MLH1, the gene involved in the initial steps of development of these tumors; however, BRAF mutations were not detected in those cases with or presumed to have germline mutation in either MLH1 or MSH2. Domingo et al. (2004) studied mutation analysis of the BRAF hotspot as a possible low-cost effective strategy for genetic testing for hereditary nonpolyposis colorectal cancer (HNPCC; 120435). The V600E mutation was found in 82 (40%) of 206 sporadic tumors with high microsatellite instability (MSI-H) but in none of 111 tested HNPCC tumors or in 45 cases showing abnormal MSH2 immunostaining. Domingo et al. (2004) concluded that detection of the V600E mutation in a colorectal MSI-H tumor argues against the presence of germline mutation in either MLH1 or MSH2, and that screening of these MMR genes can be avoided in cases positive for V600E.","Lubomierski et al. (2005) analyzed 45 colorectal carcinomas with MSI and 37 colorectal tumors without MSI but with similar clinical characteristics and found that BRAF was mutated more often in tumors with MSI than without (27% vs 5%, p = 0.016). The most prevalent BRAF alteration, V600E, occurred only in tumors with MSI and was associated with more frequent MLH1 promoter methylation and loss of MLH1. The median age of patients with BRAF V600E was older than that of those without V600E (78 vs 49 years, p = 0.001). There were no BRAF alterations in patients with germline mutations of mismatch repair genes. Lubomierski et al. (2005) concluded that tumors with MSI caused by epigenetic MLH1 silencing have a mutational background distinct from that of tumors with genetic loss of mismatch repair, and suggested that there are 2 genetically distinct entities of microsatellite unstable tumors.","Tol et al. (2009) detected a somatic V600E mutation in 45 (8.7%) of 519 metastatic colorectal tumors. Patients with BRAF-mutated tumors had significantly shorter median progression-free and median overall survival compared to patients with wildtype BRAF tumors, regardless of the use of cetuximab. Tol et al. (2009) suggested that the BRAF mutation may be a negative prognostic factor in these patients.","Inhibition of the BRAF(V600E) oncoprotein by the small-molecule drug PLX4032 (vemurafenib) is highly effective in the treatment of melanoma. However, colon cancer patients harboring the same BRAF(V600E) oncogenic lesion have poor prognosis and show only a very limited response to this drug. To investigate the cause of this limited therapeutic effect in BRAF(V600E) mutant colon cancer, Prahallad et al. (2012) performed an RNA interference-based genetic screen in human cells to search for kinases whose knockdown synergizes with BRAF(V600E) inhibition. They reported that blockade of the epidermal growth factor receptor (EGFR; 131550) shows strong synergy with BRAF(V600E) inhibition. Prahallad et al. (2012) found in multiple BRAF(V600E) mutant colon cancers that inhibition of EGFR by the antibody drug cetuximab or the small-molecule drugs gefitinib or erlotinib is strongly synergistic with BRAF(V600E) inhibition, both in vitro and in vivo. Mechanistically, Prahallad et al. (2012) found that BRAF(V600E) inhibition causes a rapid feedback activation of EGFR, which supports continued proliferation in the presence of BRAF(V600E) inhibition. Melanoma cells express low levels of EGFR and are therefore not subject to this feedback activation. Consistent with this, Prahallad et al. (2012) found that ectopic expression of EGFR in melanoma cells is sufficient to cause resistance to PLX4032. Prahallad et al. (2012) concluded that BRAF(V600E) mutant colon cancers (approximately 8 to 10% of all colon cancers) might benefit from combination therapy consisting of BRAF and EGFR inhibitors.","Gala et al. (2014) identified the BRAF V600E mutation in 18 of 19 sessile serrated adenomas from 19 unrelated patients with sessile serrated polyposis cancer syndrome (SSPCS; 617108).","Papillary Thyroid Carcinoma","Kimura et al. (2003) identified the V600E mutation in 28 (35.8%) of 78 papillary thyroid cancers (PTC; see 188550); it was not found in any of the other types of differentiated follicular neoplasms arising from the same cell type (0 of 46). RET (see 164761)/PTC mutations and RAS (see 190020) mutations were each identified in 16.4% of PTCs, but there was no overlap in the 3 mutations. Kimura et al. (2003) concluded that thyroid cell transformation to papillary cancer takes place through constitutive activation of effectors along the RET/PTC-RAS-BRAF signaling pathway.","Xing et al. (2004) studied various thyroid tumor types for the most common BRAF mutation, 1799T-A, by DNA sequencing. They found a high and similar frequency (45%) of the 1799T-A mutation in 2 geographically distinct papillary thyroid cancer patient populations, 1 composed of sporadic cases from North America, and the other from Kiev, Ukraine, that included individuals who were exposed to the Chernobyl nuclear accident. In contrast, Xing et al. (2004) found BRAF mutations in only 20% of anaplastic thyroid cancers and in no medullary thyroid cancers or benign thyroid hyperplasia. They also confirmed previous reports that the BRAF 1799T-A mutation did not occur in benign thyroid adenomas or follicular thyroid cancers. They concluded that frequent occurrence of BRAF mutation is associated with PTC, irrespective of geographic origin, and is apparently not a radiation-susceptible mutation.","Nikiforova et al. (2003) analyzed 320 thyroid tumors and 6 anaplastic carcinoma cell lines and detected BRAF mutations in 45 papillary carcinomas (38%), 2 poorly differentiated carcinomas (13%), 3 (10%) anaplastic carcinomas (10%), and 5 thyroid anaplastic carcinoma cell lines (83%) but not in follicular, Hurthle cell, and medullary carcinomas, follicular and Hurthle cell adenomas, or benign hyperplastic nodules. All mutations involved a T-to-A transversion at nucleotide 1799. All BRAF-positive poorly differentiated and anaplastic carcinomas contained areas of preexisting papillary carcinoma, and mutation was present in both the well differentiated and dedifferentiated components. The authors concluded that BRAF mutations are restricted to papillary carcinomas and poorly differentiated and anaplastic carcinomas arising from papillary carcinomas, and that they are associated with distinct phenotypic and biologic properties of papillary carcinomas and may participate in progression to poorly differentiated and anaplastic carcinomas.","Hypothesizing that childhood thyroid carcinomas may be associated with a different prevalence of the BRAF 1799T-A mutation compared with adult cases, Kumagai et al. (2004) examined 31 cases of Japanese childhood thyroid carcinoma and an additional 48 cases of PTC from Ukraine, all of whom were less than 17 years of age at the time of the Chernobyl accident. The BRAF 1799T-A mutation was found in only 1 of 31 Japanese cases (3.4%) and in none of the 15 Ukrainian cases operated on before the age of 15 years, although it was found in 8 of 33 Ukrainian young adult cases (24.2%). Kumagai et al. (2004) concluded that the BRAF 1799T-A mutation is uncommon in childhood thyroid carcinomas.","Puxeddu et al. (2004) found the V600E substitution in 24 of 60 PTCs (40%) but in none of 6 follicular adenomas, 5 follicular carcinomas, or 1 anaplastic carcinoma. Nine of the 60 PTCs (15%) presented expression of a RET/PTC rearrangement. A genetico-clinical association analysis showed a statistically significant correlation between BRAF mutation and development of PTCs of the classic papillary histotype (P = 0.038). No link could be detected between expression of BRAF V600E and age at diagnosis, gender, dimension, local invasiveness of the primary cancer, presence of lymph node metastases, tumor stage, or multifocality of the disease. The authors concluded that these data clearly confirmed that BRAF V600E was the most common genetic alteration found to that time in adult sporadic PTCs, that it is unique for this thyroid cancer histotype, and that it might drive the development of PTCs of the classic papillary subtype.","Xing et al. (2004) demonstrated detection of the 1799T-A mutation on thyroid cytologic specimens from fine needle aspiration biopsy (FNAB). Prospective analysis showed that 50% of the nodules that proved to be PTCs on surgical histopathology were correctly diagnosed by BRAF mutation analysis on FNAB specimens; there were no false positive findings.","Xing et al. (2005) studied the relationships between the BRAF V600E mutation and clinicopathologic outcomes, including recurrence, in 219 PTC patients. The authors concluded that in patients with PTC, BRAF mutation is associated with poorer clinicopathologic outcomes and independently predicts recurrence. Therefore, BRAF mutation may be a useful molecular marker to assist in risk stratification for patients with PTC.","In a series of 52 classic PTCs, Porra et al. (2005) found that low SLC5A8 (608044) expression was highly significantly associated with the presence of the BRAF 1799T-A mutation. SLC5A8 expression was selectively downregulated (40-fold) in PTCs of classical form; methylation-specific PCR analyses showed that SLC5A8 was methylated in 90% of classic PTCs and in about 20% of other PTCs. Porra et al. (2005) concluded that their data identified a relationship between the methylation-associated silencing of the tumor-suppressor gene SLC5A8 and the 1799T-A point mutation of the BRAF gene in the classic PTC subtype of thyroid carcinomas.","Vasko et al. (2005) studied the relationship between the BRAF 1799T-A mutation and lymph node metastasis of PTC by examining the mutation in both the primary tumors and their paired lymph node metastases. Their findings indicated that the high prevalence of BRAF mutation in lymph node-metastasized PTC tissues from BRAF mutation-positive primary tumors and the possible de novo formation of BRAF mutation in lymph node-metastasized PTC were consistent with a role of BRAF mutation in facilitating the metastasis and progression of PTC in lymph nodes.","In a patient with congenital hypothyroidism and long-standing goiter due to mutation in the thyroglobulin gene (see TG, 188540; and TDH3, 274700), who was also found to have multifocal follicular carcinoma of the thyroid, Hishinuma et al. (2005) identified somatic heterozygosity for the V600E mutation in the BRAF gene in the cancerous thyroid tissue.","Liu et al. (2007) used BRAF siRNA to transfect stably several BRAF mutation-harboring PTC cell lines, isolated clones with stable suppression of BRAF, and assessed their ability to proliferate, transform, and grow xenograft tumors in nude mice. They found that the V600E mutation not only initiates PTC but also maintains the proliferation, transformation, and tumorigenicity of PTC cells harboring the BRAF mutation, and that the growth of tumors derived from such cells continues to depend on the V600E mutation.","Jo et al. (2006) found that of 161 PTC patients, 102 (63.4%) had the BRAF V600E mutation and that these patients had significantly larger tumor sizes and significantly higher expression of vascular endothelial growth factor (VEGF; 192240) compared to patients without this mutation. The level of VEGF expression was closely correlated with tumor size, extrathyroidal invasion, and stage. Jo et al. (2006) concluded that the relatively high levels of VEGF expression may be related to poorer clinical outcomes and recurrences in BRAF V600E(+) PTC.","Durante et al. (2007) found that the BRAF V600E mutation in PTCs is associated with reduced expression of key genes involved in iodine metabolism. They noted that this effect may alter the effectiveness of diagnostic and/or therapeutic use of radioiodine in BRAF-mutation PTCs.","Lupi et al. (2007) found a BRAF mutation in 219 of 500 cases (43.8%) of PTC. The most common BRAF mutation, V600E, was found in 214 cases (42.8%). BRAF V600E was associated with extrathyroidal invasion (p less than 0.0001), multicentricity (p = 0.0026), presence of nodal metastases (p = 0.0009), class III versus classes I and II (p less than 0.00000006), and absence of tumor capsule (p less than 0.0001), in particular, in follicular- and micro-PTC variants. By multivariate analysis, the absence of tumor capsule remained the only parameter associated (p = 0.0005) with the BRAF V600E mutation. The authors concluded that the BRAF V600E mutation is associated with high-risk PTC and, in particular, in follicular variant with invasive tumor growth.","Flaherty et al. (2010) reported complete or partial regression of V600E-associated papillary thyroid cancer in 3 patients treated with an inhibitor (PLX4032) specific to the V600E mutation.","Nonseminomatous Germ Cell Tumors","In 3 (9%) of 32 nonseminomatous germ cell tumors (see 273300) with a mixture of embryonal carcinoma, yolk sac tumor, choriocarcinoma, and mature teratoma, Sommerer et al. (2005) identified the activating 1796T-A mutation in the BRAF gene; the mutation was present within the embryonic carcinoma component.","Astrocytoma","Pfister et al. (2008) identified a somatic V600E mutation in 4 (6%) of 66 pediatric low-grade astrocytomas (see 137800). Thirty (45%) of the 66 tumors had a copy number gain spanning the BRAF locus, indicating a novel mechanism of MAPK (176948) pathway activation in these tumors.","Role in Neurodegeneration","Mass et al. (2017) hypothesized that a somatic BRAF(V600E) mutation in the erythromyeloid lineage may cause neurodegeneration. Mass et al. (2017) showed that mosaic expression of BRAF(V600E) in mouse erythromyeloid progenitors results in clonal expansion of tissue-resident macrophages and a severe late-onset neurodegenerative disorder. This is associated with accumulation of ERK-activated amoeboid microglia in mice, and is also observed in human patients with histiocytoses. In the mouse model, neurobehavioral signs, astrogliosis, deposition of amyloid precursor protein, synaptic loss, and neuronal death were driven by ERK-activated microglia and were preventable by BRAF inhibition. Mass et al. (2017) suggested that the results identified the fetal precursors of tissue-resident macrophages as a potential cell of origin for histiocytoses and demonstrated that a somatic mutation in the erythromyeloid progenitor lineage in mice can drive late-onset neurodegeneration.","Variant Function","Brady et al. (2014) showed that decreasing the levels of CTR1 (603085), or mutations in MEK1 (176872) that disrupt copper binding, decreased BRAF(V600E)-driven signaling and tumorigenesis in mice and human cell settings. Conversely, a MEK1-MEK5 (602520) chimera that phosphorylated ERK1/2 independently of copper or an active ERK2 restored the tumor growth of murine cells lacking Ctr1. Copper chelators used in the treatment of Wilson disease (277900) decreased tumor growth of human or murine cells that were either transformed by BRAF(V600E) or engineered to be resistant to BRAF inhibition. Brady et al. (2014) concluded that copper chelation therapy could be repurposed to treat cancers containing the BRAF(V600E) mutation.","Rapino et al. (2018) showed in humans that the enzymes that catalyze modifications of wobble uridine-34 (U34) tRNA are key players of the protein synthesis rewiring that is induced by the transformation driven by the BRAF V600E oncogene and by resistance to targeted therapy in melanoma. Rapino et al. (2018) showed that BRAF V600E-expressing melanoma cells are dependent on U34 enzymes for survival, and that concurrent inhibition of MAPK signaling and ELP3 (612722) or CTU1 (612694) and/or CTU2 (617057) synergizes to kill melanoma cells. Activation of the PI3K signaling pathway, one of the most common mechanisms of acquired resistance to MAPK therapeutic agents, markedly increases the expression of U34 enzymes. Mechanistically, U34 enzymes promote glycolysis in melanoma cells through the direct, codon-dependent, regulation of the translation of HIF1A (603348) mRNA and the maintenance of high levels of HIF1-alpha protein. Therefore, the acquired resistance to anti-BRAF therapy is associated with high levels of U34 enzymes and HIF1-alpha. Rapino et al. (2018) concluded that U34 enzymes promote the survival and resistance to therapy of melanoma cells by regulating specific mRNA translation."],"submitter_name":"OMIM","review_date":20140904,"origin":"somatic","method":"literature only","submitter_date":20220317,"diseases":[{"normalized_cancer":["MELANOMA, MALIGNANT, SOMATIC"],"normalized_disease":["Melanoma, Cutaneous Malignant, Susceptibility to, 1"],"names":["Melanoma, Cutaneous Malignant, Susceptibility to, 1"]}],"review_description":"Pathogenic","date_updated":20220328,"clinical_significance":["Pathogenic"],"review_status":"no assertion criteria provided","accession_id":"SCV000035247"}],"variation_id":13961,"submission_description":[],"title":"NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) AND Melanoma","review_date":20140904,"diseases":[{"pub_med":[26389333,26389258],"symbols":{"medgen":"C0025202","mesh":"D008545","mondo":"MONDO:0005105","human_phenotype_ontology":"HP:0007474"},"normalized_disease":["Melanoma"],"names":["Melanoma"],"normalized_cancer":["Melanoma"],"keyword":"Neoplasm"}],"pub_med_references":[12068308,12198537,12447372,12619120,12644542,12670889,12794760,12960123,14513361,14602780,15001635,15126572,15181070,15342696,15356022,15386408,15687339,15998781,16015629,16174717,16187918,16772349,17374713,17488796,17785355,18398503,19571295,20818844,20823850,21107320,21107323,22113612,22281684,23302800,23685455,24512911,24670642,24717435,25079330,28854169,29925953],"date_created":20131031,"variant_id":10190071404531360004,"review_description":"Pathogenic","clinical_significance":["Pathogenic"],"allele_id":29000,"accession_id":"RCV000067669"},{"submissions":[{"pub_med_references":[12068308,12198537,12447372,12619120,12644542,12670889,12794760,12960123,14513361,14602780,15001635,15126572,15181070,15342696,15356022,15386408,15687339,15998781,16015629,16174717,16187918,16772349,17374713,17488796,17785355,18398503,19571295,20818844,20823850,21107320,21107323,22113612,22281684,23302800,23685455,24512911,24670642,24717435,25079330,28854169,29925953],"submission_description":["The val600-to-glu (V600E) mutation caused by a 1799T-A transversion in the BRAF gene was previously designated VAL599GLU (1796T-A). Kumar et al. (2003) noted that an earlier version of the BRAF sequence showed a discrepancy of 3 nucleotides in exon 1; based on the corrected sequence, they proposed a change in nucleotide numbering after nucleotide 94 (the ATG codon) by +3 and a corresponding codon change of +1.","Malignant Melanoma","Davies et al. (2002) identified a 1799T-A transversion in exon 15 of the BRAF gene that leads to a val600-to-glu (V600E) substitution. This mutation accounted for 92% of BRAF mutations in malignant melanoma (see 155600). The V600E mutation is an activating mutation resulting in constitutive activation of BRAF and downstream signal transduction in the MAP kinase pathway.","To evaluate the timing of mutations in BRAF during melanocyte neoplasia, Pollock et al. (2003) carried out mutation analysis on microdissected melanoma and nevi samples. They observed mutations resulting in the V600E amino acid substitution in 41 (68%) of 60 melanoma metastases, 4 (80%) of 5 primary melanomas, and, unexpectedly, in 63 (82%) of 77 nevi. The data suggested that mutational activation of the RAS/RAF/MAPK pathway in nevi is a critical step in the initiation of melanocytic neoplasia but alone is insufficient for melanoma tumorigenesis.","Lang et al. (2003) failed to find the V600E mutation as a germline mutation in 42 cases of familial melanoma studied. Their collection of families included 15 with and 24 without detected mutations in CDKN2A (600160). They did, however, find the V600E mutation in 6 (27%) of 22 samples of secondary (metastatic) melanomas studied. Meyer et al. (2003) found no V600E mutation in 172 melanoma patients comprising 46 familial cases, 21 multiple melanoma patients, and 106 cases with at least 1 first-degree relative suffering from other cancers. They concluded, therefore, that the common somatic BRAF mutation V600E does not contribute to polygenic or familial melanoma predisposition.","Kim et al. (2003) stated that V600E, the most common of BRAF mutations, had not been identified in tumors with mutations of the KRAS gene (190070). This mutually exclusive relationship supports the hypothesis that BRAF (V600E) and KRAS mutations exert equivalent effects in tumorigenesis (Rajagopalan et al., 2002; Singer et al., 2003).","Flaherty et al. (2010) reported complete or partial regression of V600E-associated metastatic melanoma in 81% of patients treated with an inhibitor (PLX4032) specific to the V600E mutation. Among 16 patients in a dose-escalation cohort, 10 had a partial response, and 1 had a complete response. Among 32 patients in an extension cohort, 24 had a partial response, and 2 had a complete response. The estimated median progression-free survival among all patients was more than 7 months. Responses were observed at all sites of disease, including bone, liver, and small bowel. Tumor biopsy specimens from 7 patients showed markedly reduced levels of phosphorylated ERK (600997), cyclin D1 (168461), and Ki67 (MKI67; 176741) at day 15 compared to baseline, indicating inhibition of the MAP kinase pathway. Three additional patients with V600E-associated papillary thyroid also showed a partial or complete response.","Bollag et al. (2010) described the structure-guided discovery of PLX4032 (RG7204), a potent inhibitor of oncogenic BRAF kinase activity. PLX4032 was cocrystallized with a protein construct that contained the kinase domain of BRAF(V600E). In a clinical trial, patients exposed to higher plasma levels of PLX4032 experienced tumor regression; in patients with tumor regressions, pathway analysis typically showed greater than 80% inhibition of cytoplasmic ERK phosphorylation. Bollag et al. (2010) concluded that their data demonstrated that BRAF-mutant melanomas are highly dependent on BRAF kinase activity.","Patients with BRAF(V600E)-positive melanomas exhibit an initial antitumor response to the RAF kinase inhibitor PLX4032, but acquired drug resistance almost invariably develops. Johannessen et al. (2010) identified MAP3K8 (191195), encoding COT (cancer Osaka thyroid oncogene) as a MAPK pathway agonist that drives resistance to RAF inhibition in BRAF(V600E) cell lines. COT activates ERK primarily through MARK/ERK (MEK)-dependent mechanisms that do not require RAF signaling. Moreover, COT expression is associated with de novo resistance in BRAF(V600E) cultured cell lines and acquired resistance in melanoma cells and tissue obtained from relapsing patients following treatment with MEK or RAF inhibitors. Johannessen et al. (2010) further identified combinatorial MAPK pathway inhibition or targeting of COT kinase activity as possible therapeutic strategies for reducing MAPK pathway activation in this setting.","Nazarian et al. (2010) showed that acquired resistance to PLX4032, a novel class I RAF-selective inhibitor, develops by mutually exclusive PDGFRB (173410) upregulation or NRAS (164790) mutations but not through secondary mutations in BRAF(V600E). Nazarian et al. (2010) used PLX4032-resistant sublines artificially derived from BRAF (V600E)-positive melanoma cell lines and validated key findings in PLX4032-resistant tumors and tumor-matched, short-term cultures from clinical trial patients. Induction of PDGFRB RNA, protein and tyrosine phosphorylation emerged as a dominant feature of acquired PLX4032 resistance in a subset of melanoma sublines, patient-derived biopsies, and short-term cultures. PDGFRB upregulated tumor cells have low activated RAS levels and, when treated with PLX4032, do not reactivate the MAPK pathway significantly. In another subset, high levels of activated N-RAS resulting from mutations lead to significant MAPK pathway reactivation upon PLX4032 treatment. Knockdown of PDGFRB or NRAS reduced growth of the respective PLX4032-resistant subsets. Overexpression of PDGFRB or NRAS(Q61K) conferred PLX4032 resistance to PLX4032-sensitive parental cell lines. Importantly, Nazarian et al. (2010) showed that MAPK reactivation predicts MEK inhibitor sensitivity. Thus, Nazarian et al. (2010) concluded that melanomas escape BRAF(V600E) targeting not through secondary BRAF(V600E) mutations but via receptor tyrosine kinase (RTK)-mediated activation of alternative survival pathway(s) or activated RAS-mediated reactivation of the MAPK pathway, suggesting additional therapeutic strategies.","Poulikakos et al. (2011) identified a novel resistance mechanism for melanomas with BRAF(V600E) treated with RAF inhibitors. The authors found that a subset of cells resistant to vemurafenib (PLX4032, RG7204) express a 61-kD variant form of BRAF(V600E), p61BRAF(V600E), that lacks exons 4 through 8, a region that encompasses the RAS-binding domain. p61BRAF(V600E) showed enhanced dimerization in cells with low levels of RAS activation, as compared to full-length BRAF(V600E). In cells in which p61BRAF(V600E) was expressed endogenously or ectopically, ERK signaling was resistant to the RAF inhibitor. Moreover, a mutation that abolished the dimerization of p61BRAF(V600E) restored its sensitivity to vemurafenib. Finally, Poulikakos et al. (2011) identified BRAF(V600E) splicing variants lacking the RAS-binding domain in the tumors of 6 of 19 patients with acquired resistance to vemurafenib. Poulikakos et al. (2011) concluded that their data supported the model that inhibition of ERK signaling by RAF inhibitors is dependent on levels of RAS-GTP too low to support RAF dimerization and identified a novel mechanism of acquired resistance in patients: expression of splicing isoforms of BRAF(V600E) that dimerize in a RAS-independent manner.","Thakur et al. (2013) investigated the cause and consequences of vemurafenib resistance using 2 independently-derived primary human melanoma xenograft models in which drug resistance is selected by continuous vemurafenib administration. In one of these models, resistant tumors showed continued dependency on BRAF(V600E)-MEK-ERK signaling owing to elevated BRAF(V600E) expression. Thakur et al. (2013) showed that vemurafenib-resistant melanomas become drug-dependent for their continued proliferation, such that cessation of drug administration leads to regression of established drug-resistant tumors. Thakur et al. (2013) further demonstrated that a discontinuous dosing strategy, which exploits the fitness disadvantage displayed by drug-resistant cells in the absence of the drug, forestalls the onset of lethal drug-resistant disease. Thakur et al. (2013) concluded that their data highlighted the concept that drug-resistant cells may also display drug dependency, such that altered dosing may prevent the emergence of lethal drug resistance. These observations may contribute to sustaining the durability of vemurafenib response with the ultimate goal of curative therapy for the subset of melanoma patients with BRAF mutations.","Using metabolic profiling and functional perturbations, Kaplon et al. (2013) showed that the mitochondrial gatekeeper pyruvate dehydrogenase (PDH; 300502) is a crucial mediator of senescence induced by BRAF(V600E), an oncogene commonly mutated in melanoma and other cancers. BRAF(V600E)-induced senescence is accompanied by simultaneous suppression of the PDH-inhibitory enzyme pyruvate dehydrogenase kinase-1 (PDK1; 602524) and induction of the PDH-activating enzyme pyruvate dehydrogenase phosphatase-2 (PDP2; 615499). The resulting combined activation of PDH enhanced the use of pyruvate in the tricarboxylic acid cycle, causing increased respiration and redox stress. Abrogation of oncogene-induced senescence (OIS), a rate-limiting step towards oncogenic transformation, coincided with reversion of these processes. Further supporting a crucial role of PDH in OIS, enforced normalization of either PDK1 or PDP2 expression levels inhibited PDH and abrogated OIS, thereby licensing BRAF(V600E)-driven melanoma development. Finally, depletion of PDK1 eradicated melanoma subpopulations resistant to targeted BRAF inhibition, and caused regression of established melanomas.","Sun et al. (2014) showed that 6 out of 16 BRAF(V600E)-positive melanoma tumors analyzed acquired EGFR (131550) expression after the development of resistance to inhibitors of BRAF or MEK (176872). Using a chromatin regulator-focused short hairpin RNA (shRNA) library, Sun et al. (2014) found that suppression of SRY-box 10 (SOX10; 602229) in melanoma causes activation of TGF-beta (190180) signaling, thus leading to upregulation of EGFR and platelet-derived growth factor receptor-beta (PDGFRB; 173410), which confer resistance to BRAF and MEK inhibitors. Expression of EGFR in melanoma or treatment with TGF-beta results in a slow-growth phenotype with cells displaying hallmarks of oncogene-induced senescence. However, EGFR expression or exposure to TGF-beta becomes beneficial for proliferation in the presence of BRAF or MEK inhibitors. In a heterogeneous population of melanoma cells that have varying levels of SOX10 suppression, cells with low SOX10 and consequently high EGFR expression are rapidly enriched in the presence of drug treatment, but this is reversed when the treatment is discontinued. Sun et al. (2014) found evidence for SOX10 loss and/or activation of TGF-beta signaling in 4 of the 6 EGFR-positive drug-resistant melanoma patient samples. Sun et al. (2014) concluded that their findings provided a rationale for why some BRAF or MEK inhibitor-resistant melanoma patients may regain sensitivity to these drugs after a 'drug holiday' and identified patients with EGFR-positive melanoma as a group that may benefit from retreatment after a drug holiday.","Boussemart et al. (2014) demonstrated that the persistent formation of the eIF4F complex, comprising the eIF4E (133440) cap-binding protein, the eIF4G (600495) scaffolding protein, and the eIF4A (602641) RNA helicase, is associated with resistance to anti-BRAF (164757), anti-MEK, and anti-BRAF plus anti-MEK drug combinations in BRAF(V600)-mutant melanoma, colon, and thyroid cancer cell lines. Resistance to treatment and maintenance of eIF4F complex formation is associated with 1 of 3 mechanisms: reactivation of MAPK (see 176948) signaling; persistent ERK-independent phosphorylation of the inhibitory eIF4E-binding protein 4EBP1 (602223); or increased proapoptotic BMF (606266)-dependent degradation of eIF4G. The development of an in situ method to detect the eIF4E-eIF4G interactions showed that eIF4F complex formation is decreased in tumors that respond to anti-BRAF therapy and increased in resistant metastases compared to tumors before treatment. Strikingly, inhibiting the eIF4F complex, either by blocking the eIF4E-eIF4G interaction or by targeting eIF4A, synergized with inhibiting BRAF(V600) to kill the cancer cells. eIF4F appeared not only to be an indicator of both innate and acquired resistance, but also a therapeutic target. Boussemart et al. (2014) concluded that combinations of drugs targeting BRAF (and/or MEK) and eIF4F may overcome most of the resistance mechanisms in BRAF(V600)-mutant cancers.","Colorectal Carcinoma","Rajagopalan et al. (2002) identified the V600E mutation in 28 of 330 colorectal tumors (see 114500) screened for BRAF mutations. In all cases the mutation was heterozygous and occurred somatically.","Domingo et al. (2004) pointed out that the V600E hotspot mutation had been found in colorectal tumors that showed inherited mutation in a DNA mismatch repair (MMR) gene, such as MLH1 (120436) or MSH2 (609309). These mutations had been shown to occur almost exclusively in tumors located in the proximal colon and with hypermethylation of MLH1, the gene involved in the initial steps of development of these tumors; however, BRAF mutations were not detected in those cases with or presumed to have germline mutation in either MLH1 or MSH2. Domingo et al. (2004) studied mutation analysis of the BRAF hotspot as a possible low-cost effective strategy for genetic testing for hereditary nonpolyposis colorectal cancer (HNPCC; 120435). The V600E mutation was found in 82 (40%) of 206 sporadic tumors with high microsatellite instability (MSI-H) but in none of 111 tested HNPCC tumors or in 45 cases showing abnormal MSH2 immunostaining. Domingo et al. (2004) concluded that detection of the V600E mutation in a colorectal MSI-H tumor argues against the presence of germline mutation in either MLH1 or MSH2, and that screening of these MMR genes can be avoided in cases positive for V600E.","Lubomierski et al. (2005) analyzed 45 colorectal carcinomas with MSI and 37 colorectal tumors without MSI but with similar clinical characteristics and found that BRAF was mutated more often in tumors with MSI than without (27% vs 5%, p = 0.016). The most prevalent BRAF alteration, V600E, occurred only in tumors with MSI and was associated with more frequent MLH1 promoter methylation and loss of MLH1. The median age of patients with BRAF V600E was older than that of those without V600E (78 vs 49 years, p = 0.001). There were no BRAF alterations in patients with germline mutations of mismatch repair genes. Lubomierski et al. (2005) concluded that tumors with MSI caused by epigenetic MLH1 silencing have a mutational background distinct from that of tumors with genetic loss of mismatch repair, and suggested that there are 2 genetically distinct entities of microsatellite unstable tumors.","Tol et al. (2009) detected a somatic V600E mutation in 45 (8.7%) of 519 metastatic colorectal tumors. Patients with BRAF-mutated tumors had significantly shorter median progression-free and median overall survival compared to patients with wildtype BRAF tumors, regardless of the use of cetuximab. Tol et al. (2009) suggested that the BRAF mutation may be a negative prognostic factor in these patients.","Inhibition of the BRAF(V600E) oncoprotein by the small-molecule drug PLX4032 (vemurafenib) is highly effective in the treatment of melanoma. However, colon cancer patients harboring the same BRAF(V600E) oncogenic lesion have poor prognosis and show only a very limited response to this drug. To investigate the cause of this limited therapeutic effect in BRAF(V600E) mutant colon cancer, Prahallad et al. (2012) performed an RNA interference-based genetic screen in human cells to search for kinases whose knockdown synergizes with BRAF(V600E) inhibition. They reported that blockade of the epidermal growth factor receptor (EGFR; 131550) shows strong synergy with BRAF(V600E) inhibition. Prahallad et al. (2012) found in multiple BRAF(V600E) mutant colon cancers that inhibition of EGFR by the antibody drug cetuximab or the small-molecule drugs gefitinib or erlotinib is strongly synergistic with BRAF(V600E) inhibition, both in vitro and in vivo. Mechanistically, Prahallad et al. (2012) found that BRAF(V600E) inhibition causes a rapid feedback activation of EGFR, which supports continued proliferation in the presence of BRAF(V600E) inhibition. Melanoma cells express low levels of EGFR and are therefore not subject to this feedback activation. Consistent with this, Prahallad et al. (2012) found that ectopic expression of EGFR in melanoma cells is sufficient to cause resistance to PLX4032. Prahallad et al. (2012) concluded that BRAF(V600E) mutant colon cancers (approximately 8 to 10% of all colon cancers) might benefit from combination therapy consisting of BRAF and EGFR inhibitors.","Gala et al. (2014) identified the BRAF V600E mutation in 18 of 19 sessile serrated adenomas from 19 unrelated patients with sessile serrated polyposis cancer syndrome (SSPCS; 617108).","Papillary Thyroid Carcinoma","Kimura et al. (2003) identified the V600E mutation in 28 (35.8%) of 78 papillary thyroid cancers (PTC; see 188550); it was not found in any of the other types of differentiated follicular neoplasms arising from the same cell type (0 of 46). RET (see 164761)/PTC mutations and RAS (see 190020) mutations were each identified in 16.4% of PTCs, but there was no overlap in the 3 mutations. Kimura et al. (2003) concluded that thyroid cell transformation to papillary cancer takes place through constitutive activation of effectors along the RET/PTC-RAS-BRAF signaling pathway.","Xing et al. (2004) studied various thyroid tumor types for the most common BRAF mutation, 1799T-A, by DNA sequencing. They found a high and similar frequency (45%) of the 1799T-A mutation in 2 geographically distinct papillary thyroid cancer patient populations, 1 composed of sporadic cases from North America, and the other from Kiev, Ukraine, that included individuals who were exposed to the Chernobyl nuclear accident. In contrast, Xing et al. (2004) found BRAF mutations in only 20% of anaplastic thyroid cancers and in no medullary thyroid cancers or benign thyroid hyperplasia. They also confirmed previous reports that the BRAF 1799T-A mutation did not occur in benign thyroid adenomas or follicular thyroid cancers. They concluded that frequent occurrence of BRAF mutation is associated with PTC, irrespective of geographic origin, and is apparently not a radiation-susceptible mutation.","Nikiforova et al. (2003) analyzed 320 thyroid tumors and 6 anaplastic carcinoma cell lines and detected BRAF mutations in 45 papillary carcinomas (38%), 2 poorly differentiated carcinomas (13%), 3 (10%) anaplastic carcinomas (10%), and 5 thyroid anaplastic carcinoma cell lines (83%) but not in follicular, Hurthle cell, and medullary carcinomas, follicular and Hurthle cell adenomas, or benign hyperplastic nodules. All mutations involved a T-to-A transversion at nucleotide 1799. All BRAF-positive poorly differentiated and anaplastic carcinomas contained areas of preexisting papillary carcinoma, and mutation was present in both the well differentiated and dedifferentiated components. The authors concluded that BRAF mutations are restricted to papillary carcinomas and poorly differentiated and anaplastic carcinomas arising from papillary carcinomas, and that they are associated with distinct phenotypic and biologic properties of papillary carcinomas and may participate in progression to poorly differentiated and anaplastic carcinomas.","Hypothesizing that childhood thyroid carcinomas may be associated with a different prevalence of the BRAF 1799T-A mutation compared with adult cases, Kumagai et al. (2004) examined 31 cases of Japanese childhood thyroid carcinoma and an additional 48 cases of PTC from Ukraine, all of whom were less than 17 years of age at the time of the Chernobyl accident. The BRAF 1799T-A mutation was found in only 1 of 31 Japanese cases (3.4%) and in none of the 15 Ukrainian cases operated on before the age of 15 years, although it was found in 8 of 33 Ukrainian young adult cases (24.2%). Kumagai et al. (2004) concluded that the BRAF 1799T-A mutation is uncommon in childhood thyroid carcinomas.","Puxeddu et al. (2004) found the V600E substitution in 24 of 60 PTCs (40%) but in none of 6 follicular adenomas, 5 follicular carcinomas, or 1 anaplastic carcinoma. Nine of the 60 PTCs (15%) presented expression of a RET/PTC rearrangement. A genetico-clinical association analysis showed a statistically significant correlation between BRAF mutation and development of PTCs of the classic papillary histotype (P = 0.038). No link could be detected between expression of BRAF V600E and age at diagnosis, gender, dimension, local invasiveness of the primary cancer, presence of lymph node metastases, tumor stage, or multifocality of the disease. The authors concluded that these data clearly confirmed that BRAF V600E was the most common genetic alteration found to that time in adult sporadic PTCs, that it is unique for this thyroid cancer histotype, and that it might drive the development of PTCs of the classic papillary subtype.","Xing et al. (2004) demonstrated detection of the 1799T-A mutation on thyroid cytologic specimens from fine needle aspiration biopsy (FNAB). Prospective analysis showed that 50% of the nodules that proved to be PTCs on surgical histopathology were correctly diagnosed by BRAF mutation analysis on FNAB specimens; there were no false positive findings.","Xing et al. (2005) studied the relationships between the BRAF V600E mutation and clinicopathologic outcomes, including recurrence, in 219 PTC patients. The authors concluded that in patients with PTC, BRAF mutation is associated with poorer clinicopathologic outcomes and independently predicts recurrence. Therefore, BRAF mutation may be a useful molecular marker to assist in risk stratification for patients with PTC.","In a series of 52 classic PTCs, Porra et al. (2005) found that low SLC5A8 (608044) expression was highly significantly associated with the presence of the BRAF 1799T-A mutation. SLC5A8 expression was selectively downregulated (40-fold) in PTCs of classical form; methylation-specific PCR analyses showed that SLC5A8 was methylated in 90% of classic PTCs and in about 20% of other PTCs. Porra et al. (2005) concluded that their data identified a relationship between the methylation-associated silencing of the tumor-suppressor gene SLC5A8 and the 1799T-A point mutation of the BRAF gene in the classic PTC subtype of thyroid carcinomas.","Vasko et al. (2005) studied the relationship between the BRAF 1799T-A mutation and lymph node metastasis of PTC by examining the mutation in both the primary tumors and their paired lymph node metastases. Their findings indicated that the high prevalence of BRAF mutation in lymph node-metastasized PTC tissues from BRAF mutation-positive primary tumors and the possible de novo formation of BRAF mutation in lymph node-metastasized PTC were consistent with a role of BRAF mutation in facilitating the metastasis and progression of PTC in lymph nodes.","In a patient with congenital hypothyroidism and long-standing goiter due to mutation in the thyroglobulin gene (see TG, 188540; and TDH3, 274700), who was also found to have multifocal follicular carcinoma of the thyroid, Hishinuma et al. (2005) identified somatic heterozygosity for the V600E mutation in the BRAF gene in the cancerous thyroid tissue.","Liu et al. (2007) used BRAF siRNA to transfect stably several BRAF mutation-harboring PTC cell lines, isolated clones with stable suppression of BRAF, and assessed their ability to proliferate, transform, and grow xenograft tumors in nude mice. They found that the V600E mutation not only initiates PTC but also maintains the proliferation, transformation, and tumorigenicity of PTC cells harboring the BRAF mutation, and that the growth of tumors derived from such cells continues to depend on the V600E mutation.","Jo et al. (2006) found that of 161 PTC patients, 102 (63.4%) had the BRAF V600E mutation and that these patients had significantly larger tumor sizes and significantly higher expression of vascular endothelial growth factor (VEGF; 192240) compared to patients without this mutation. The level of VEGF expression was closely correlated with tumor size, extrathyroidal invasion, and stage. Jo et al. (2006) concluded that the relatively high levels of VEGF expression may be related to poorer clinical outcomes and recurrences in BRAF V600E(+) PTC.","Durante et al. (2007) found that the BRAF V600E mutation in PTCs is associated with reduced expression of key genes involved in iodine metabolism. They noted that this effect may alter the effectiveness of diagnostic and/or therapeutic use of radioiodine in BRAF-mutation PTCs.","Lupi et al. (2007) found a BRAF mutation in 219 of 500 cases (43.8%) of PTC. The most common BRAF mutation, V600E, was found in 214 cases (42.8%). BRAF V600E was associated with extrathyroidal invasion (p less than 0.0001), multicentricity (p = 0.0026), presence of nodal metastases (p = 0.0009), class III versus classes I and II (p less than 0.00000006), and absence of tumor capsule (p less than 0.0001), in particular, in follicular- and micro-PTC variants. By multivariate analysis, the absence of tumor capsule remained the only parameter associated (p = 0.0005) with the BRAF V600E mutation. The authors concluded that the BRAF V600E mutation is associated with high-risk PTC and, in particular, in follicular variant with invasive tumor growth.","Flaherty et al. (2010) reported complete or partial regression of V600E-associated papillary thyroid cancer in 3 patients treated with an inhibitor (PLX4032) specific to the V600E mutation.","Nonseminomatous Germ Cell Tumors","In 3 (9%) of 32 nonseminomatous germ cell tumors (see 273300) with a mixture of embryonal carcinoma, yolk sac tumor, choriocarcinoma, and mature teratoma, Sommerer et al. (2005) identified the activating 1796T-A mutation in the BRAF gene; the mutation was present within the embryonic carcinoma component.","Astrocytoma","Pfister et al. (2008) identified a somatic V600E mutation in 4 (6%) of 66 pediatric low-grade astrocytomas (see 137800). Thirty (45%) of the 66 tumors had a copy number gain spanning the BRAF locus, indicating a novel mechanism of MAPK (176948) pathway activation in these tumors.","Role in Neurodegeneration","Mass et al. (2017) hypothesized that a somatic BRAF(V600E) mutation in the erythromyeloid lineage may cause neurodegeneration. Mass et al. (2017) showed that mosaic expression of BRAF(V600E) in mouse erythromyeloid progenitors results in clonal expansion of tissue-resident macrophages and a severe late-onset neurodegenerative disorder. This is associated with accumulation of ERK-activated amoeboid microglia in mice, and is also observed in human patients with histiocytoses. In the mouse model, neurobehavioral signs, astrogliosis, deposition of amyloid precursor protein, synaptic loss, and neuronal death were driven by ERK-activated microglia and were preventable by BRAF inhibition. Mass et al. (2017) suggested that the results identified the fetal precursors of tissue-resident macrophages as a potential cell of origin for histiocytoses and demonstrated that a somatic mutation in the erythromyeloid progenitor lineage in mice can drive late-onset neurodegeneration.","Variant Function","Brady et al. (2014) showed that decreasing the levels of CTR1 (603085), or mutations in MEK1 (176872) that disrupt copper binding, decreased BRAF(V600E)-driven signaling and tumorigenesis in mice and human cell settings. Conversely, a MEK1-MEK5 (602520) chimera that phosphorylated ERK1/2 independently of copper or an active ERK2 restored the tumor growth of murine cells lacking Ctr1. Copper chelators used in the treatment of Wilson disease (277900) decreased tumor growth of human or murine cells that were either transformed by BRAF(V600E) or engineered to be resistant to BRAF inhibition. Brady et al. (2014) concluded that copper chelation therapy could be repurposed to treat cancers containing the BRAF(V600E) mutation.","Rapino et al. (2018) showed in humans that the enzymes that catalyze modifications of wobble uridine-34 (U34) tRNA are key players of the protein synthesis rewiring that is induced by the transformation driven by the BRAF V600E oncogene and by resistance to targeted therapy in melanoma. Rapino et al. (2018) showed that BRAF V600E-expressing melanoma cells are dependent on U34 enzymes for survival, and that concurrent inhibition of MAPK signaling and ELP3 (612722) or CTU1 (612694) and/or CTU2 (617057) synergizes to kill melanoma cells. Activation of the PI3K signaling pathway, one of the most common mechanisms of acquired resistance to MAPK therapeutic agents, markedly increases the expression of U34 enzymes. Mechanistically, U34 enzymes promote glycolysis in melanoma cells through the direct, codon-dependent, regulation of the translation of HIF1A (603348) mRNA and the maintenance of high levels of HIF1-alpha protein. Therefore, the acquired resistance to anti-BRAF therapy is associated with high levels of U34 enzymes and HIF1-alpha. Rapino et al. (2018) concluded that U34 enzymes promote the survival and resistance to therapy of melanoma cells by regulating specific mRNA translation."],"submitter_name":"OMIM","review_date":20140904,"origin":"somatic","method":"literature only","submitter_date":20220317,"diseases":[{"normalized_cancer":["NONSEMINOMATOUS GERM CELL TUMORS, SOMATIC"],"names":["Nonseminomatous Germ Cell Tumors, Somatic"]}],"review_description":"Pathogenic","date_updated":20220328,"clinical_significance":["Pathogenic"],"review_status":"no assertion criteria provided","accession_id":"SCV000043966"}],"variation_id":13961,"submission_description":["The val600-to-glu (V600E) mutation caused by a 1799T-A transversion in the BRAF gene was previously designated VAL599GLU (1796T-A). Kumar et al. (2003) noted that an earlier version of the BRAF sequence showed a discrepancy of 3 nucleotides in exon 1; based on the corrected sequence, they proposed a change in nucleotide numbering after nucleotide 94 (the ATG codon) by +3 and a corresponding codon change of +1.","Malignant Melanoma","Davies et al. (2002) identified a 1799T-A transversion in exon 15 of the BRAF gene that leads to a val600-to-glu (V600E) substitution. This mutation accounted for 92% of BRAF mutations in malignant melanoma (see 155600). The V600E mutation is an activating mutation resulting in constitutive activation of BRAF and downstream signal transduction in the MAP kinase pathway.","To evaluate the timing of mutations in BRAF during melanocyte neoplasia, Pollock et al. (2003) carried out mutation analysis on microdissected melanoma and nevi samples. They observed mutations resulting in the V600E amino acid substitution in 41 (68%) of 60 melanoma metastases, 4 (80%) of 5 primary melanomas, and, unexpectedly, in 63 (82%) of 77 nevi. The data suggested that mutational activation of the RAS/RAF/MAPK pathway in nevi is a critical step in the initiation of melanocytic neoplasia but alone is insufficient for melanoma tumorigenesis.","Lang et al. (2003) failed to find the V600E mutation as a germline mutation in 42 cases of familial melanoma studied. Their collection of families included 15 with and 24 without detected mutations in CDKN2A (600160). They did, however, find the V600E mutation in 6 (27%) of 22 samples of secondary (metastatic) melanomas studied. Meyer et al. (2003) found no V600E mutation in 172 melanoma patients comprising 46 familial cases, 21 multiple melanoma patients, and 106 cases with at least 1 first-degree relative suffering from other cancers. They concluded, therefore, that the common somatic BRAF mutation V600E does not contribute to polygenic or familial melanoma predisposition.","Kim et al. (2003) stated that V600E, the most common of BRAF mutations, had not been identified in tumors with mutations of the KRAS gene (190070). This mutually exclusive relationship supports the hypothesis that BRAF (V600E) and KRAS mutations exert equivalent effects in tumorigenesis (Rajagopalan et al., 2002; Singer et al., 2003).","Flaherty et al. (2010) reported complete or partial regression of V600E-associated metastatic melanoma in 81% of patients treated with an inhibitor (PLX4032) specific to the V600E mutation. Among 16 patients in a dose-escalation cohort, 10 had a partial response, and 1 had a complete response. Among 32 patients in an extension cohort, 24 had a partial response, and 2 had a complete response. The estimated median progression-free survival among all patients was more than 7 months. Responses were observed at all sites of disease, including bone, liver, and small bowel. Tumor biopsy specimens from 7 patients showed markedly reduced levels of phosphorylated ERK (600997), cyclin D1 (168461), and Ki67 (MKI67; 176741) at day 15 compared to baseline, indicating inhibition of the MAP kinase pathway. Three additional patients with V600E-associated papillary thyroid also showed a partial or complete response.","Bollag et al. (2010) described the structure-guided discovery of PLX4032 (RG7204), a potent inhibitor of oncogenic BRAF kinase activity. PLX4032 was cocrystallized with a protein construct that contained the kinase domain of BRAF(V600E). In a clinical trial, patients exposed to higher plasma levels of PLX4032 experienced tumor regression; in patients with tumor regressions, pathway analysis typically showed greater than 80% inhibition of cytoplasmic ERK phosphorylation. Bollag et al. (2010) concluded that their data demonstrated that BRAF-mutant melanomas are highly dependent on BRAF kinase activity.","Patients with BRAF(V600E)-positive melanomas exhibit an initial antitumor response to the RAF kinase inhibitor PLX4032, but acquired drug resistance almost invariably develops. Johannessen et al. (2010) identified MAP3K8 (191195), encoding COT (cancer Osaka thyroid oncogene) as a MAPK pathway agonist that drives resistance to RAF inhibition in BRAF(V600E) cell lines. COT activates ERK primarily through MARK/ERK (MEK)-dependent mechanisms that do not require RAF signaling. Moreover, COT expression is associated with de novo resistance in BRAF(V600E) cultured cell lines and acquired resistance in melanoma cells and tissue obtained from relapsing patients following treatment with MEK or RAF inhibitors. Johannessen et al. (2010) further identified combinatorial MAPK pathway inhibition or targeting of COT kinase activity as possible therapeutic strategies for reducing MAPK pathway activation in this setting.","Nazarian et al. (2010) showed that acquired resistance to PLX4032, a novel class I RAF-selective inhibitor, develops by mutually exclusive PDGFRB (173410) upregulation or NRAS (164790) mutations but not through secondary mutations in BRAF(V600E). Nazarian et al. (2010) used PLX4032-resistant sublines artificially derived from BRAF (V600E)-positive melanoma cell lines and validated key findings in PLX4032-resistant tumors and tumor-matched, short-term cultures from clinical trial patients. Induction of PDGFRB RNA, protein and tyrosine phosphorylation emerged as a dominant feature of acquired PLX4032 resistance in a subset of melanoma sublines, patient-derived biopsies, and short-term cultures. PDGFRB upregulated tumor cells have low activated RAS levels and, when treated with PLX4032, do not reactivate the MAPK pathway significantly. In another subset, high levels of activated N-RAS resulting from mutations lead to significant MAPK pathway reactivation upon PLX4032 treatment. Knockdown of PDGFRB or NRAS reduced growth of the respective PLX4032-resistant subsets. Overexpression of PDGFRB or NRAS(Q61K) conferred PLX4032 resistance to PLX4032-sensitive parental cell lines. Importantly, Nazarian et al. (2010) showed that MAPK reactivation predicts MEK inhibitor sensitivity. Thus, Nazarian et al. (2010) concluded that melanomas escape BRAF(V600E) targeting not through secondary BRAF(V600E) mutations but via receptor tyrosine kinase (RTK)-mediated activation of alternative survival pathway(s) or activated RAS-mediated reactivation of the MAPK pathway, suggesting additional therapeutic strategies.","Poulikakos et al. (2011) identified a novel resistance mechanism for melanomas with BRAF(V600E) treated with RAF inhibitors. The authors found that a subset of cells resistant to vemurafenib (PLX4032, RG7204) express a 61-kD variant form of BRAF(V600E), p61BRAF(V600E), that lacks exons 4 through 8, a region that encompasses the RAS-binding domain. p61BRAF(V600E) showed enhanced dimerization in cells with low levels of RAS activation, as compared to full-length BRAF(V600E). In cells in which p61BRAF(V600E) was expressed endogenously or ectopically, ERK signaling was resistant to the RAF inhibitor. Moreover, a mutation that abolished the dimerization of p61BRAF(V600E) restored its sensitivity to vemurafenib. Finally, Poulikakos et al. (2011) identified BRAF(V600E) splicing variants lacking the RAS-binding domain in the tumors of 6 of 19 patients with acquired resistance to vemurafenib. Poulikakos et al. (2011) concluded that their data supported the model that inhibition of ERK signaling by RAF inhibitors is dependent on levels of RAS-GTP too low to support RAF dimerization and identified a novel mechanism of acquired resistance in patients: expression of splicing isoforms of BRAF(V600E) that dimerize in a RAS-independent manner.","Thakur et al. (2013) investigated the cause and consequences of vemurafenib resistance using 2 independently-derived primary human melanoma xenograft models in which drug resistance is selected by continuous vemurafenib administration. In one of these models, resistant tumors showed continued dependency on BRAF(V600E)-MEK-ERK signaling owing to elevated BRAF(V600E) expression. Thakur et al. (2013) showed that vemurafenib-resistant melanomas become drug-dependent for their continued proliferation, such that cessation of drug administration leads to regression of established drug-resistant tumors. Thakur et al. (2013) further demonstrated that a discontinuous dosing strategy, which exploits the fitness disadvantage displayed by drug-resistant cells in the absence of the drug, forestalls the onset of lethal drug-resistant disease. Thakur et al. (2013) concluded that their data highlighted the concept that drug-resistant cells may also display drug dependency, such that altered dosing may prevent the emergence of lethal drug resistance. These observations may contribute to sustaining the durability of vemurafenib response with the ultimate goal of curative therapy for the subset of melanoma patients with BRAF mutations.","Using metabolic profiling and functional perturbations, Kaplon et al. (2013) showed that the mitochondrial gatekeeper pyruvate dehydrogenase (PDH; 300502) is a crucial mediator of senescence induced by BRAF(V600E), an oncogene commonly mutated in melanoma and other cancers. BRAF(V600E)-induced senescence is accompanied by simultaneous suppression of the PDH-inhibitory enzyme pyruvate dehydrogenase kinase-1 (PDK1; 602524) and induction of the PDH-activating enzyme pyruvate dehydrogenase phosphatase-2 (PDP2; 615499). The resulting combined activation of PDH enhanced the use of pyruvate in the tricarboxylic acid cycle, causing increased respiration and redox stress. Abrogation of oncogene-induced senescence (OIS), a rate-limiting step towards oncogenic transformation, coincided with reversion of these processes. Further supporting a crucial role of PDH in OIS, enforced normalization of either PDK1 or PDP2 expression levels inhibited PDH and abrogated OIS, thereby licensing BRAF(V600E)-driven melanoma development. Finally, depletion of PDK1 eradicated melanoma subpopulations resistant to targeted BRAF inhibition, and caused regression of established melanomas.","Sun et al. (2014) showed that 6 out of 16 BRAF(V600E)-positive melanoma tumors analyzed acquired EGFR (131550) expression after the development of resistance to inhibitors of BRAF or MEK (176872). Using a chromatin regulator-focused short hairpin RNA (shRNA) library, Sun et al. (2014) found that suppression of SRY-box 10 (SOX10; 602229) in melanoma causes activation of TGF-beta (190180) signaling, thus leading to upregulation of EGFR and platelet-derived growth factor receptor-beta (PDGFRB; 173410), which confer resistance to BRAF and MEK inhibitors. Expression of EGFR in melanoma or treatment with TGF-beta results in a slow-growth phenotype with cells displaying hallmarks of oncogene-induced senescence. However, EGFR expression or exposure to TGF-beta becomes beneficial for proliferation in the presence of BRAF or MEK inhibitors. In a heterogeneous population of melanoma cells that have varying levels of SOX10 suppression, cells with low SOX10 and consequently high EGFR expression are rapidly enriched in the presence of drug treatment, but this is reversed when the treatment is discontinued. Sun et al. (2014) found evidence for SOX10 loss and/or activation of TGF-beta signaling in 4 of the 6 EGFR-positive drug-resistant melanoma patient samples. Sun et al. (2014) concluded that their findings provided a rationale for why some BRAF or MEK inhibitor-resistant melanoma patients may regain sensitivity to these drugs after a 'drug holiday' and identified patients with EGFR-positive melanoma as a group that may benefit from retreatment after a drug holiday.","Boussemart et al. (2014) demonstrated that the persistent formation of the eIF4F complex, comprising the eIF4E (133440) cap-binding protein, the eIF4G (600495) scaffolding protein, and the eIF4A (602641) RNA helicase, is associated with resistance to anti-BRAF (164757), anti-MEK, and anti-BRAF plus anti-MEK drug combinations in BRAF(V600)-mutant melanoma, colon, and thyroid cancer cell lines. Resistance to treatment and maintenance of eIF4F complex formation is associated with 1 of 3 mechanisms: reactivation of MAPK (see 176948) signaling; persistent ERK-independent phosphorylation of the inhibitory eIF4E-binding protein 4EBP1 (602223); or increased proapoptotic BMF (606266)-dependent degradation of eIF4G. The development of an in situ method to detect the eIF4E-eIF4G interactions showed that eIF4F complex formation is decreased in tumors that respond to anti-BRAF therapy and increased in resistant metastases compared to tumors before treatment. Strikingly, inhibiting the eIF4F complex, either by blocking the eIF4E-eIF4G interaction or by targeting eIF4A, synergized with inhibiting BRAF(V600) to kill the cancer cells. eIF4F appeared not only to be an indicator of both innate and acquired resistance, but also a therapeutic target. Boussemart et al. (2014) concluded that combinations of drugs targeting BRAF (and/or MEK) and eIF4F may overcome most of the resistance mechanisms in BRAF(V600)-mutant cancers.","Colorectal Carcinoma","Rajagopalan et al. (2002) identified the V600E mutation in 28 of 330 colorectal tumors (see 114500) screened for BRAF mutations. In all cases the mutation was heterozygous and occurred somatically.","Domingo et al. (2004) pointed out that the V600E hotspot mutation had been found in colorectal tumors that showed inherited mutation in a DNA mismatch repair (MMR) gene, such as MLH1 (120436) or MSH2 (609309). These mutations had been shown to occur almost exclusively in tumors located in the proximal colon and with hypermethylation of MLH1, the gene involved in the initial steps of development of these tumors; however, BRAF mutations were not detected in those cases with or presumed to have germline mutation in either MLH1 or MSH2. Domingo et al. (2004) studied mutation analysis of the BRAF hotspot as a possible low-cost effective strategy for genetic testing for hereditary nonpolyposis colorectal cancer (HNPCC; 120435). The V600E mutation was found in 82 (40%) of 206 sporadic tumors with high microsatellite instability (MSI-H) but in none of 111 tested HNPCC tumors or in 45 cases showing abnormal MSH2 immunostaining. Domingo et al. (2004) concluded that detection of the V600E mutation in a colorectal MSI-H tumor argues against the presence of germline mutation in either MLH1 or MSH2, and that screening of these MMR genes can be avoided in cases positive for V600E.","Lubomierski et al. (2005) analyzed 45 colorectal carcinomas with MSI and 37 colorectal tumors without MSI but with similar clinical characteristics and found that BRAF was mutated more often in tumors with MSI than without (27% vs 5%, p = 0.016). The most prevalent BRAF alteration, V600E, occurred only in tumors with MSI and was associated with more frequent MLH1 promoter methylation and loss of MLH1. The median age of patients with BRAF V600E was older than that of those without V600E (78 vs 49 years, p = 0.001). There were no BRAF alterations in patients with germline mutations of mismatch repair genes. Lubomierski et al. (2005) concluded that tumors with MSI caused by epigenetic MLH1 silencing have a mutational background distinct from that of tumors with genetic loss of mismatch repair, and suggested that there are 2 genetically distinct entities of microsatellite unstable tumors.","Tol et al. (2009) detected a somatic V600E mutation in 45 (8.7%) of 519 metastatic colorectal tumors. Patients with BRAF-mutated tumors had significantly shorter median progression-free and median overall survival compared to patients with wildtype BRAF tumors, regardless of the use of cetuximab. Tol et al. (2009) suggested that the BRAF mutation may be a negative prognostic factor in these patients.","Inhibition of the BRAF(V600E) oncoprotein by the small-molecule drug PLX4032 (vemurafenib) is highly effective in the treatment of melanoma. However, colon cancer patients harboring the same BRAF(V600E) oncogenic lesion have poor prognosis and show only a very limited response to this drug. To investigate the cause of this limited therapeutic effect in BRAF(V600E) mutant colon cancer, Prahallad et al. (2012) performed an RNA interference-based genetic screen in human cells to search for kinases whose knockdown synergizes with BRAF(V600E) inhibition. They reported that blockade of the epidermal growth factor receptor (EGFR; 131550) shows strong synergy with BRAF(V600E) inhibition. Prahallad et al. (2012) found in multiple BRAF(V600E) mutant colon cancers that inhibition of EGFR by the antibody drug cetuximab or the small-molecule drugs gefitinib or erlotinib is strongly synergistic with BRAF(V600E) inhibition, both in vitro and in vivo. Mechanistically, Prahallad et al. (2012) found that BRAF(V600E) inhibition causes a rapid feedback activation of EGFR, which supports continued proliferation in the presence of BRAF(V600E) inhibition. Melanoma cells express low levels of EGFR and are therefore not subject to this feedback activation. Consistent with this, Prahallad et al. (2012) found that ectopic expression of EGFR in melanoma cells is sufficient to cause resistance to PLX4032. Prahallad et al. (2012) concluded that BRAF(V600E) mutant colon cancers (approximately 8 to 10% of all colon cancers) might benefit from combination therapy consisting of BRAF and EGFR inhibitors.","Gala et al. (2014) identified the BRAF V600E mutation in 18 of 19 sessile serrated adenomas from 19 unrelated patients with sessile serrated polyposis cancer syndrome (SSPCS; 617108).","Papillary Thyroid Carcinoma","Kimura et al. (2003) identified the V600E mutation in 28 (35.8%) of 78 papillary thyroid cancers (PTC; see 188550); it was not found in any of the other types of differentiated follicular neoplasms arising from the same cell type (0 of 46). RET (see 164761)/PTC mutations and RAS (see 190020) mutations were each identified in 16.4% of PTCs, but there was no overlap in the 3 mutations. Kimura et al. (2003) concluded that thyroid cell transformation to papillary cancer takes place through constitutive activation of effectors along the RET/PTC-RAS-BRAF signaling pathway.","Xing et al. (2004) studied various thyroid tumor types for the most common BRAF mutation, 1799T-A, by DNA sequencing. They found a high and similar frequency (45%) of the 1799T-A mutation in 2 geographically distinct papillary thyroid cancer patient populations, 1 composed of sporadic cases from North America, and the other from Kiev, Ukraine, that included individuals who were exposed to the Chernobyl nuclear accident. In contrast, Xing et al. (2004) found BRAF mutations in only 20% of anaplastic thyroid cancers and in no medullary thyroid cancers or benign thyroid hyperplasia. They also confirmed previous reports that the BRAF 1799T-A mutation did not occur in benign thyroid adenomas or follicular thyroid cancers. They concluded that frequent occurrence of BRAF mutation is associated with PTC, irrespective of geographic origin, and is apparently not a radiation-susceptible mutation.","Nikiforova et al. (2003) analyzed 320 thyroid tumors and 6 anaplastic carcinoma cell lines and detected BRAF mutations in 45 papillary carcinomas (38%), 2 poorly differentiated carcinomas (13%), 3 (10%) anaplastic carcinomas (10%), and 5 thyroid anaplastic carcinoma cell lines (83%) but not in follicular, Hurthle cell, and medullary carcinomas, follicular and Hurthle cell adenomas, or benign hyperplastic nodules. All mutations involved a T-to-A transversion at nucleotide 1799. All BRAF-positive poorly differentiated and anaplastic carcinomas contained areas of preexisting papillary carcinoma, and mutation was present in both the well differentiated and dedifferentiated components. The authors concluded that BRAF mutations are restricted to papillary carcinomas and poorly differentiated and anaplastic carcinomas arising from papillary carcinomas, and that they are associated with distinct phenotypic and biologic properties of papillary carcinomas and may participate in progression to poorly differentiated and anaplastic carcinomas.","Hypothesizing that childhood thyroid carcinomas may be associated with a different prevalence of the BRAF 1799T-A mutation compared with adult cases, Kumagai et al. (2004) examined 31 cases of Japanese childhood thyroid carcinoma and an additional 48 cases of PTC from Ukraine, all of whom were less than 17 years of age at the time of the Chernobyl accident. The BRAF 1799T-A mutation was found in only 1 of 31 Japanese cases (3.4%) and in none of the 15 Ukrainian cases operated on before the age of 15 years, although it was found in 8 of 33 Ukrainian young adult cases (24.2%). Kumagai et al. (2004) concluded that the BRAF 1799T-A mutation is uncommon in childhood thyroid carcinomas.","Puxeddu et al. (2004) found the V600E substitution in 24 of 60 PTCs (40%) but in none of 6 follicular adenomas, 5 follicular carcinomas, or 1 anaplastic carcinoma. Nine of the 60 PTCs (15%) presented expression of a RET/PTC rearrangement. A genetico-clinical association analysis showed a statistically significant correlation between BRAF mutation and development of PTCs of the classic papillary histotype (P = 0.038). No link could be detected between expression of BRAF V600E and age at diagnosis, gender, dimension, local invasiveness of the primary cancer, presence of lymph node metastases, tumor stage, or multifocality of the disease. The authors concluded that these data clearly confirmed that BRAF V600E was the most common genetic alteration found to that time in adult sporadic PTCs, that it is unique for this thyroid cancer histotype, and that it might drive the development of PTCs of the classic papillary subtype.","Xing et al. (2004) demonstrated detection of the 1799T-A mutation on thyroid cytologic specimens from fine needle aspiration biopsy (FNAB). Prospective analysis showed that 50% of the nodules that proved to be PTCs on surgical histopathology were correctly diagnosed by BRAF mutation analysis on FNAB specimens; there were no false positive findings.","Xing et al. (2005) studied the relationships between the BRAF V600E mutation and clinicopathologic outcomes, including recurrence, in 219 PTC patients. The authors concluded that in patients with PTC, BRAF mutation is associated with poorer clinicopathologic outcomes and independently predicts recurrence. Therefore, BRAF mutation may be a useful molecular marker to assist in risk stratification for patients with PTC.","In a series of 52 classic PTCs, Porra et al. (2005) found that low SLC5A8 (608044) expression was highly significantly associated with the presence of the BRAF 1799T-A mutation. SLC5A8 expression was selectively downregulated (40-fold) in PTCs of classical form; methylation-specific PCR analyses showed that SLC5A8 was methylated in 90% of classic PTCs and in about 20% of other PTCs. Porra et al. (2005) concluded that their data identified a relationship between the methylation-associated silencing of the tumor-suppressor gene SLC5A8 and the 1799T-A point mutation of the BRAF gene in the classic PTC subtype of thyroid carcinomas.","Vasko et al. (2005) studied the relationship between the BRAF 1799T-A mutation and lymph node metastasis of PTC by examining the mutation in both the primary tumors and their paired lymph node metastases. Their findings indicated that the high prevalence of BRAF mutation in lymph node-metastasized PTC tissues from BRAF mutation-positive primary tumors and the possible de novo formation of BRAF mutation in lymph node-metastasized PTC were consistent with a role of BRAF mutation in facilitating the metastasis and progression of PTC in lymph nodes.","In a patient with congenital hypothyroidism and long-standing goiter due to mutation in the thyroglobulin gene (see TG, 188540; and TDH3, 274700), who was also found to have multifocal follicular carcinoma of the thyroid, Hishinuma et al. (2005) identified somatic heterozygosity for the V600E mutation in the BRAF gene in the cancerous thyroid tissue.","Liu et al. (2007) used BRAF siRNA to transfect stably several BRAF mutation-harboring PTC cell lines, isolated clones with stable suppression of BRAF, and assessed their ability to proliferate, transform, and grow xenograft tumors in nude mice. They found that the V600E mutation not only initiates PTC but also maintains the proliferation, transformation, and tumorigenicity of PTC cells harboring the BRAF mutation, and that the growth of tumors derived from such cells continues to depend on the V600E mutation.","Jo et al. (2006) found that of 161 PTC patients, 102 (63.4%) had the BRAF V600E mutation and that these patients had significantly larger tumor sizes and significantly higher expression of vascular endothelial growth factor (VEGF; 192240) compared to patients without this mutation. The level of VEGF expression was closely correlated with tumor size, extrathyroidal invasion, and stage. Jo et al. (2006) concluded that the relatively high levels of VEGF expression may be related to poorer clinical outcomes and recurrences in BRAF V600E(+) PTC.","Durante et al. (2007) found that the BRAF V600E mutation in PTCs is associated with reduced expression of key genes involved in iodine metabolism. They noted that this effect may alter the effectiveness of diagnostic and/or therapeutic use of radioiodine in BRAF-mutation PTCs.","Lupi et al. (2007) found a BRAF mutation in 219 of 500 cases (43.8%) of PTC. The most common BRAF mutation, V600E, was found in 214 cases (42.8%). BRAF V600E was associated with extrathyroidal invasion (p less than 0.0001), multicentricity (p = 0.0026), presence of nodal metastases (p = 0.0009), class III versus classes I and II (p less than 0.00000006), and absence of tumor capsule (p less than 0.0001), in particular, in follicular- and micro-PTC variants. By multivariate analysis, the absence of tumor capsule remained the only parameter associated (p = 0.0005) with the BRAF V600E mutation. The authors concluded that the BRAF V600E mutation is associated with high-risk PTC and, in particular, in follicular variant with invasive tumor growth.","Flaherty et al. (2010) reported complete or partial regression of V600E-associated papillary thyroid cancer in 3 patients treated with an inhibitor (PLX4032) specific to the V600E mutation.","Nonseminomatous Germ Cell Tumors","In 3 (9%) of 32 nonseminomatous germ cell tumors (see 273300) with a mixture of embryonal carcinoma, yolk sac tumor, choriocarcinoma, and mature teratoma, Sommerer et al. (2005) identified the activating 1796T-A mutation in the BRAF gene; the mutation was present within the embryonic carcinoma component.","Astrocytoma","Pfister et al. (2008) identified a somatic V600E mutation in 4 (6%) of 66 pediatric low-grade astrocytomas (see 137800). Thirty (45%) of the 66 tumors had a copy number gain spanning the BRAF locus, indicating a novel mechanism of MAPK (176948) pathway activation in these tumors.","Role in Neurodegeneration","Mass et al. (2017) hypothesized that a somatic BRAF(V600E) mutation in the erythromyeloid lineage may cause neurodegeneration. Mass et al. (2017) showed that mosaic expression of BRAF(V600E) in mouse erythromyeloid progenitors results in clonal expansion of tissue-resident macrophages and a severe late-onset neurodegenerative disorder. This is associated with accumulation of ERK-activated amoeboid microglia in mice, and is also observed in human patients with histiocytoses. In the mouse model, neurobehavioral signs, astrogliosis, deposition of amyloid precursor protein, synaptic loss, and neuronal death were driven by ERK-activated microglia and were preventable by BRAF inhibition. Mass et al. (2017) suggested that the results identified the fetal precursors of tissue-resident macrophages as a potential cell of origin for histiocytoses and demonstrated that a somatic mutation in the erythromyeloid progenitor lineage in mice can drive late-onset neurodegeneration.","Variant Function","Brady et al. (2014) showed that decreasing the levels of CTR1 (603085), or mutations in MEK1 (176872) that disrupt copper binding, decreased BRAF(V600E)-driven signaling and tumorigenesis in mice and human cell settings. Conversely, a MEK1-MEK5 (602520) chimera that phosphorylated ERK1/2 independently of copper or an active ERK2 restored the tumor growth of murine cells lacking Ctr1. Copper chelators used in the treatment of Wilson disease (277900) decreased tumor growth of human or murine cells that were either transformed by BRAF(V600E) or engineered to be resistant to BRAF inhibition. Brady et al. (2014) concluded that copper chelation therapy could be repurposed to treat cancers containing the BRAF(V600E) mutation.","Rapino et al. (2018) showed in humans that the enzymes that catalyze modifications of wobble uridine-34 (U34) tRNA are key players of the protein synthesis rewiring that is induced by the transformation driven by the BRAF V600E oncogene and by resistance to targeted therapy in melanoma. Rapino et al. (2018) showed that BRAF V600E-expressing melanoma cells are dependent on U34 enzymes for survival, and that concurrent inhibition of MAPK signaling and ELP3 (612722) or CTU1 (612694) and/or CTU2 (617057) synergizes to kill melanoma cells. Activation of the PI3K signaling pathway, one of the most common mechanisms of acquired resistance to MAPK therapeutic agents, markedly increases the expression of U34 enzymes. Mechanistically, U34 enzymes promote glycolysis in melanoma cells through the direct, codon-dependent, regulation of the translation of HIF1A (603348) mRNA and the maintenance of high levels of HIF1-alpha protein. Therefore, the acquired resistance to anti-BRAF therapy is associated with high levels of U34 enzymes and HIF1-alpha. Rapino et al. (2018) concluded that U34 enzymes promote the survival and resistance to therapy of melanoma cells by regulating specific mRNA translation."],"title":"NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) AND Nongerminomatous germ cell tumor","review_date":20140904,"diseases":[{"symbols":{"medgen":"C1266158","mondo":"MONDO:0021656"},"normalized_disease":["Nongerminomatous Germ Cell Tumor"],"names":["Nongerminomatous Germ Cell Tumor","Nonseminomatous Germ Cell Tumors, Somatic","Nongerminomatous Germ Cell Tumor","Non-Seminomatous Germ-Cell Tumors"],"normalized_cancer":["Nongerminomatous germ cell tumor","NONSEMINOMATOUS GERM CELL TUMORS, SOMATIC","Germ cell tumor, nonseminomatous","Non-seminomatous germ-cell tumors"],"keyword":"Neoplasm"}],"pub_med_references":[12068308,12198537,12447372,12619120,12644542,12670889,12794760,12960123,14513361,14602780,15001635,15126572,15181070,15342696,15356022,15386408,15687339,15998781,16015629,16174717,16187918,16772349,17374713,17488796,17785355,18398503,19571295,20818844,20823850,21107320,21107323,22113612,22281684,23302800,23685455,24512911,24670642,24717435,25079330,28854169,29925953],"date_created":20130404,"variant_id":10190071404531360004,"review_description":"Pathogenic","clinical_significance":["Pathogenic"],"allele_id":29000,"accession_id":"RCV000022677"},{"submissions":[{"pub_med_references":[12068308,12198537,12447372,12619120,12644542,12670889,12794760,12960123,14513361,14602780,15001635,15126572,15181070,15342696,15356022,15386408,15687339,15998781,16015629,16174717,16187918,16772349,17374713,17488796,17785355,18398503,19571295,20818844,20823850,21107320,21107323,22113612,22281684,23302800,23685455,24512911,24670642,24717435,25079330,28854169,29925953],"submission_description":["The val600-to-glu (V600E) mutation caused by a 1799T-A transversion in the BRAF gene was previously designated VAL599GLU (1796T-A). Kumar et al. (2003) noted that an earlier version of the BRAF sequence showed a discrepancy of 3 nucleotides in exon 1; based on the corrected sequence, they proposed a change in nucleotide numbering after nucleotide 94 (the ATG codon) by +3 and a corresponding codon change of +1.","Malignant Melanoma","Davies et al. (2002) identified a 1799T-A transversion in exon 15 of the BRAF gene that leads to a val600-to-glu (V600E) substitution. This mutation accounted for 92% of BRAF mutations in malignant melanoma (see 155600). The V600E mutation is an activating mutation resulting in constitutive activation of BRAF and downstream signal transduction in the MAP kinase pathway.","To evaluate the timing of mutations in BRAF during melanocyte neoplasia, Pollock et al. (2003) carried out mutation analysis on microdissected melanoma and nevi samples. They observed mutations resulting in the V600E amino acid substitution in 41 (68%) of 60 melanoma metastases, 4 (80%) of 5 primary melanomas, and, unexpectedly, in 63 (82%) of 77 nevi. The data suggested that mutational activation of the RAS/RAF/MAPK pathway in nevi is a critical step in the initiation of melanocytic neoplasia but alone is insufficient for melanoma tumorigenesis.","Lang et al. (2003) failed to find the V600E mutation as a germline mutation in 42 cases of familial melanoma studied. Their collection of families included 15 with and 24 without detected mutations in CDKN2A (600160). They did, however, find the V600E mutation in 6 (27%) of 22 samples of secondary (metastatic) melanomas studied. Meyer et al. (2003) found no V600E mutation in 172 melanoma patients comprising 46 familial cases, 21 multiple melanoma patients, and 106 cases with at least 1 first-degree relative suffering from other cancers. They concluded, therefore, that the common somatic BRAF mutation V600E does not contribute to polygenic or familial melanoma predisposition.","Kim et al. (2003) stated that V600E, the most common of BRAF mutations, had not been identified in tumors with mutations of the KRAS gene (190070). This mutually exclusive relationship supports the hypothesis that BRAF (V600E) and KRAS mutations exert equivalent effects in tumorigenesis (Rajagopalan et al., 2002; Singer et al., 2003).","Flaherty et al. (2010) reported complete or partial regression of V600E-associated metastatic melanoma in 81% of patients treated with an inhibitor (PLX4032) specific to the V600E mutation. Among 16 patients in a dose-escalation cohort, 10 had a partial response, and 1 had a complete response. Among 32 patients in an extension cohort, 24 had a partial response, and 2 had a complete response. The estimated median progression-free survival among all patients was more than 7 months. Responses were observed at all sites of disease, including bone, liver, and small bowel. Tumor biopsy specimens from 7 patients showed markedly reduced levels of phosphorylated ERK (600997), cyclin D1 (168461), and Ki67 (MKI67; 176741) at day 15 compared to baseline, indicating inhibition of the MAP kinase pathway. Three additional patients with V600E-associated papillary thyroid also showed a partial or complete response.","Bollag et al. (2010) described the structure-guided discovery of PLX4032 (RG7204), a potent inhibitor of oncogenic BRAF kinase activity. PLX4032 was cocrystallized with a protein construct that contained the kinase domain of BRAF(V600E). In a clinical trial, patients exposed to higher plasma levels of PLX4032 experienced tumor regression; in patients with tumor regressions, pathway analysis typically showed greater than 80% inhibition of cytoplasmic ERK phosphorylation. Bollag et al. (2010) concluded that their data demonstrated that BRAF-mutant melanomas are highly dependent on BRAF kinase activity.","Patients with BRAF(V600E)-positive melanomas exhibit an initial antitumor response to the RAF kinase inhibitor PLX4032, but acquired drug resistance almost invariably develops. Johannessen et al. (2010) identified MAP3K8 (191195), encoding COT (cancer Osaka thyroid oncogene) as a MAPK pathway agonist that drives resistance to RAF inhibition in BRAF(V600E) cell lines. COT activates ERK primarily through MARK/ERK (MEK)-dependent mechanisms that do not require RAF signaling. Moreover, COT expression is associated with de novo resistance in BRAF(V600E) cultured cell lines and acquired resistance in melanoma cells and tissue obtained from relapsing patients following treatment with MEK or RAF inhibitors. Johannessen et al. (2010) further identified combinatorial MAPK pathway inhibition or targeting of COT kinase activity as possible therapeutic strategies for reducing MAPK pathway activation in this setting.","Nazarian et al. (2010) showed that acquired resistance to PLX4032, a novel class I RAF-selective inhibitor, develops by mutually exclusive PDGFRB (173410) upregulation or NRAS (164790) mutations but not through secondary mutations in BRAF(V600E). Nazarian et al. (2010) used PLX4032-resistant sublines artificially derived from BRAF (V600E)-positive melanoma cell lines and validated key findings in PLX4032-resistant tumors and tumor-matched, short-term cultures from clinical trial patients. Induction of PDGFRB RNA, protein and tyrosine phosphorylation emerged as a dominant feature of acquired PLX4032 resistance in a subset of melanoma sublines, patient-derived biopsies, and short-term cultures. PDGFRB upregulated tumor cells have low activated RAS levels and, when treated with PLX4032, do not reactivate the MAPK pathway significantly. In another subset, high levels of activated N-RAS resulting from mutations lead to significant MAPK pathway reactivation upon PLX4032 treatment. Knockdown of PDGFRB or NRAS reduced growth of the respective PLX4032-resistant subsets. Overexpression of PDGFRB or NRAS(Q61K) conferred PLX4032 resistance to PLX4032-sensitive parental cell lines. Importantly, Nazarian et al. (2010) showed that MAPK reactivation predicts MEK inhibitor sensitivity. Thus, Nazarian et al. (2010) concluded that melanomas escape BRAF(V600E) targeting not through secondary BRAF(V600E) mutations but via receptor tyrosine kinase (RTK)-mediated activation of alternative survival pathway(s) or activated RAS-mediated reactivation of the MAPK pathway, suggesting additional therapeutic strategies.","Poulikakos et al. (2011) identified a novel resistance mechanism for melanomas with BRAF(V600E) treated with RAF inhibitors. The authors found that a subset of cells resistant to vemurafenib (PLX4032, RG7204) express a 61-kD variant form of BRAF(V600E), p61BRAF(V600E), that lacks exons 4 through 8, a region that encompasses the RAS-binding domain. p61BRAF(V600E) showed enhanced dimerization in cells with low levels of RAS activation, as compared to full-length BRAF(V600E). In cells in which p61BRAF(V600E) was expressed endogenously or ectopically, ERK signaling was resistant to the RAF inhibitor. Moreover, a mutation that abolished the dimerization of p61BRAF(V600E) restored its sensitivity to vemurafenib. Finally, Poulikakos et al. (2011) identified BRAF(V600E) splicing variants lacking the RAS-binding domain in the tumors of 6 of 19 patients with acquired resistance to vemurafenib. Poulikakos et al. (2011) concluded that their data supported the model that inhibition of ERK signaling by RAF inhibitors is dependent on levels of RAS-GTP too low to support RAF dimerization and identified a novel mechanism of acquired resistance in patients: expression of splicing isoforms of BRAF(V600E) that dimerize in a RAS-independent manner.","Thakur et al. (2013) investigated the cause and consequences of vemurafenib resistance using 2 independently-derived primary human melanoma xenograft models in which drug resistance is selected by continuous vemurafenib administration. In one of these models, resistant tumors showed continued dependency on BRAF(V600E)-MEK-ERK signaling owing to elevated BRAF(V600E) expression. Thakur et al. (2013) showed that vemurafenib-resistant melanomas become drug-dependent for their continued proliferation, such that cessation of drug administration leads to regression of established drug-resistant tumors. Thakur et al. (2013) further demonstrated that a discontinuous dosing strategy, which exploits the fitness disadvantage displayed by drug-resistant cells in the absence of the drug, forestalls the onset of lethal drug-resistant disease. Thakur et al. (2013) concluded that their data highlighted the concept that drug-resistant cells may also display drug dependency, such that altered dosing may prevent the emergence of lethal drug resistance. These observations may contribute to sustaining the durability of vemurafenib response with the ultimate goal of curative therapy for the subset of melanoma patients with BRAF mutations.","Using metabolic profiling and functional perturbations, Kaplon et al. (2013) showed that the mitochondrial gatekeeper pyruvate dehydrogenase (PDH; 300502) is a crucial mediator of senescence induced by BRAF(V600E), an oncogene commonly mutated in melanoma and other cancers. BRAF(V600E)-induced senescence is accompanied by simultaneous suppression of the PDH-inhibitory enzyme pyruvate dehydrogenase kinase-1 (PDK1; 602524) and induction of the PDH-activating enzyme pyruvate dehydrogenase phosphatase-2 (PDP2; 615499). The resulting combined activation of PDH enhanced the use of pyruvate in the tricarboxylic acid cycle, causing increased respiration and redox stress. Abrogation of oncogene-induced senescence (OIS), a rate-limiting step towards oncogenic transformation, coincided with reversion of these processes. Further supporting a crucial role of PDH in OIS, enforced normalization of either PDK1 or PDP2 expression levels inhibited PDH and abrogated OIS, thereby licensing BRAF(V600E)-driven melanoma development. Finally, depletion of PDK1 eradicated melanoma subpopulations resistant to targeted BRAF inhibition, and caused regression of established melanomas.","Sun et al. (2014) showed that 6 out of 16 BRAF(V600E)-positive melanoma tumors analyzed acquired EGFR (131550) expression after the development of resistance to inhibitors of BRAF or MEK (176872). Using a chromatin regulator-focused short hairpin RNA (shRNA) library, Sun et al. (2014) found that suppression of SRY-box 10 (SOX10; 602229) in melanoma causes activation of TGF-beta (190180) signaling, thus leading to upregulation of EGFR and platelet-derived growth factor receptor-beta (PDGFRB; 173410), which confer resistance to BRAF and MEK inhibitors. Expression of EGFR in melanoma or treatment with TGF-beta results in a slow-growth phenotype with cells displaying hallmarks of oncogene-induced senescence. However, EGFR expression or exposure to TGF-beta becomes beneficial for proliferation in the presence of BRAF or MEK inhibitors. In a heterogeneous population of melanoma cells that have varying levels of SOX10 suppression, cells with low SOX10 and consequently high EGFR expression are rapidly enriched in the presence of drug treatment, but this is reversed when the treatment is discontinued. Sun et al. (2014) found evidence for SOX10 loss and/or activation of TGF-beta signaling in 4 of the 6 EGFR-positive drug-resistant melanoma patient samples. Sun et al. (2014) concluded that their findings provided a rationale for why some BRAF or MEK inhibitor-resistant melanoma patients may regain sensitivity to these drugs after a 'drug holiday' and identified patients with EGFR-positive melanoma as a group that may benefit from retreatment after a drug holiday.","Boussemart et al. (2014) demonstrated that the persistent formation of the eIF4F complex, comprising the eIF4E (133440) cap-binding protein, the eIF4G (600495) scaffolding protein, and the eIF4A (602641) RNA helicase, is associated with resistance to anti-BRAF (164757), anti-MEK, and anti-BRAF plus anti-MEK drug combinations in BRAF(V600)-mutant melanoma, colon, and thyroid cancer cell lines. Resistance to treatment and maintenance of eIF4F complex formation is associated with 1 of 3 mechanisms: reactivation of MAPK (see 176948) signaling; persistent ERK-independent phosphorylation of the inhibitory eIF4E-binding protein 4EBP1 (602223); or increased proapoptotic BMF (606266)-dependent degradation of eIF4G. The development of an in situ method to detect the eIF4E-eIF4G interactions showed that eIF4F complex formation is decreased in tumors that respond to anti-BRAF therapy and increased in resistant metastases compared to tumors before treatment. Strikingly, inhibiting the eIF4F complex, either by blocking the eIF4E-eIF4G interaction or by targeting eIF4A, synergized with inhibiting BRAF(V600) to kill the cancer cells. eIF4F appeared not only to be an indicator of both innate and acquired resistance, but also a therapeutic target. Boussemart et al. (2014) concluded that combinations of drugs targeting BRAF (and/or MEK) and eIF4F may overcome most of the resistance mechanisms in BRAF(V600)-mutant cancers.","Colorectal Carcinoma","Rajagopalan et al. (2002) identified the V600E mutation in 28 of 330 colorectal tumors (see 114500) screened for BRAF mutations. In all cases the mutation was heterozygous and occurred somatically.","Domingo et al. (2004) pointed out that the V600E hotspot mutation had been found in colorectal tumors that showed inherited mutation in a DNA mismatch repair (MMR) gene, such as MLH1 (120436) or MSH2 (609309). These mutations had been shown to occur almost exclusively in tumors located in the proximal colon and with hypermethylation of MLH1, the gene involved in the initial steps of development of these tumors; however, BRAF mutations were not detected in those cases with or presumed to have germline mutation in either MLH1 or MSH2. Domingo et al. (2004) studied mutation analysis of the BRAF hotspot as a possible low-cost effective strategy for genetic testing for hereditary nonpolyposis colorectal cancer (HNPCC; 120435). The V600E mutation was found in 82 (40%) of 206 sporadic tumors with high microsatellite instability (MSI-H) but in none of 111 tested HNPCC tumors or in 45 cases showing abnormal MSH2 immunostaining. Domingo et al. (2004) concluded that detection of the V600E mutation in a colorectal MSI-H tumor argues against the presence of germline mutation in either MLH1 or MSH2, and that screening of these MMR genes can be avoided in cases positive for V600E.","Lubomierski et al. (2005) analyzed 45 colorectal carcinomas with MSI and 37 colorectal tumors without MSI but with similar clinical characteristics and found that BRAF was mutated more often in tumors with MSI than without (27% vs 5%, p = 0.016). The most prevalent BRAF alteration, V600E, occurred only in tumors with MSI and was associated with more frequent MLH1 promoter methylation and loss of MLH1. The median age of patients with BRAF V600E was older than that of those without V600E (78 vs 49 years, p = 0.001). There were no BRAF alterations in patients with germline mutations of mismatch repair genes. Lubomierski et al. (2005) concluded that tumors with MSI caused by epigenetic MLH1 silencing have a mutational background distinct from that of tumors with genetic loss of mismatch repair, and suggested that there are 2 genetically distinct entities of microsatellite unstable tumors.","Tol et al. (2009) detected a somatic V600E mutation in 45 (8.7%) of 519 metastatic colorectal tumors. Patients with BRAF-mutated tumors had significantly shorter median progression-free and median overall survival compared to patients with wildtype BRAF tumors, regardless of the use of cetuximab. Tol et al. (2009) suggested that the BRAF mutation may be a negative prognostic factor in these patients.","Inhibition of the BRAF(V600E) oncoprotein by the small-molecule drug PLX4032 (vemurafenib) is highly effective in the treatment of melanoma. However, colon cancer patients harboring the same BRAF(V600E) oncogenic lesion have poor prognosis and show only a very limited response to this drug. To investigate the cause of this limited therapeutic effect in BRAF(V600E) mutant colon cancer, Prahallad et al. (2012) performed an RNA interference-based genetic screen in human cells to search for kinases whose knockdown synergizes with BRAF(V600E) inhibition. They reported that blockade of the epidermal growth factor receptor (EGFR; 131550) shows strong synergy with BRAF(V600E) inhibition. Prahallad et al. (2012) found in multiple BRAF(V600E) mutant colon cancers that inhibition of EGFR by the antibody drug cetuximab or the small-molecule drugs gefitinib or erlotinib is strongly synergistic with BRAF(V600E) inhibition, both in vitro and in vivo. Mechanistically, Prahallad et al. (2012) found that BRAF(V600E) inhibition causes a rapid feedback activation of EGFR, which supports continued proliferation in the presence of BRAF(V600E) inhibition. Melanoma cells express low levels of EGFR and are therefore not subject to this feedback activation. Consistent with this, Prahallad et al. (2012) found that ectopic expression of EGFR in melanoma cells is sufficient to cause resistance to PLX4032. Prahallad et al. (2012) concluded that BRAF(V600E) mutant colon cancers (approximately 8 to 10% of all colon cancers) might benefit from combination therapy consisting of BRAF and EGFR inhibitors.","Gala et al. (2014) identified the BRAF V600E mutation in 18 of 19 sessile serrated adenomas from 19 unrelated patients with sessile serrated polyposis cancer syndrome (SSPCS; 617108).","Papillary Thyroid Carcinoma","Kimura et al. (2003) identified the V600E mutation in 28 (35.8%) of 78 papillary thyroid cancers (PTC; see 188550); it was not found in any of the other types of differentiated follicular neoplasms arising from the same cell type (0 of 46). RET (see 164761)/PTC mutations and RAS (see 190020) mutations were each identified in 16.4% of PTCs, but there was no overlap in the 3 mutations. Kimura et al. (2003) concluded that thyroid cell transformation to papillary cancer takes place through constitutive activation of effectors along the RET/PTC-RAS-BRAF signaling pathway.","Xing et al. (2004) studied various thyroid tumor types for the most common BRAF mutation, 1799T-A, by DNA sequencing. They found a high and similar frequency (45%) of the 1799T-A mutation in 2 geographically distinct papillary thyroid cancer patient populations, 1 composed of sporadic cases from North America, and the other from Kiev, Ukraine, that included individuals who were exposed to the Chernobyl nuclear accident. In contrast, Xing et al. (2004) found BRAF mutations in only 20% of anaplastic thyroid cancers and in no medullary thyroid cancers or benign thyroid hyperplasia. They also confirmed previous reports that the BRAF 1799T-A mutation did not occur in benign thyroid adenomas or follicular thyroid cancers. They concluded that frequent occurrence of BRAF mutation is associated with PTC, irrespective of geographic origin, and is apparently not a radiation-susceptible mutation.","Nikiforova et al. (2003) analyzed 320 thyroid tumors and 6 anaplastic carcinoma cell lines and detected BRAF mutations in 45 papillary carcinomas (38%), 2 poorly differentiated carcinomas (13%), 3 (10%) anaplastic carcinomas (10%), and 5 thyroid anaplastic carcinoma cell lines (83%) but not in follicular, Hurthle cell, and medullary carcinomas, follicular and Hurthle cell adenomas, or benign hyperplastic nodules. All mutations involved a T-to-A transversion at nucleotide 1799. All BRAF-positive poorly differentiated and anaplastic carcinomas contained areas of preexisting papillary carcinoma, and mutation was present in both the well differentiated and dedifferentiated components. The authors concluded that BRAF mutations are restricted to papillary carcinomas and poorly differentiated and anaplastic carcinomas arising from papillary carcinomas, and that they are associated with distinct phenotypic and biologic properties of papillary carcinomas and may participate in progression to poorly differentiated and anaplastic carcinomas.","Hypothesizing that childhood thyroid carcinomas may be associated with a different prevalence of the BRAF 1799T-A mutation compared with adult cases, Kumagai et al. (2004) examined 31 cases of Japanese childhood thyroid carcinoma and an additional 48 cases of PTC from Ukraine, all of whom were less than 17 years of age at the time of the Chernobyl accident. The BRAF 1799T-A mutation was found in only 1 of 31 Japanese cases (3.4%) and in none of the 15 Ukrainian cases operated on before the age of 15 years, although it was found in 8 of 33 Ukrainian young adult cases (24.2%). Kumagai et al. (2004) concluded that the BRAF 1799T-A mutation is uncommon in childhood thyroid carcinomas.","Puxeddu et al. (2004) found the V600E substitution in 24 of 60 PTCs (40%) but in none of 6 follicular adenomas, 5 follicular carcinomas, or 1 anaplastic carcinoma. Nine of the 60 PTCs (15%) presented expression of a RET/PTC rearrangement. A genetico-clinical association analysis showed a statistically significant correlation between BRAF mutation and development of PTCs of the classic papillary histotype (P = 0.038). No link could be detected between expression of BRAF V600E and age at diagnosis, gender, dimension, local invasiveness of the primary cancer, presence of lymph node metastases, tumor stage, or multifocality of the disease. The authors concluded that these data clearly confirmed that BRAF V600E was the most common genetic alteration found to that time in adult sporadic PTCs, that it is unique for this thyroid cancer histotype, and that it might drive the development of PTCs of the classic papillary subtype.","Xing et al. (2004) demonstrated detection of the 1799T-A mutation on thyroid cytologic specimens from fine needle aspiration biopsy (FNAB). Prospective analysis showed that 50% of the nodules that proved to be PTCs on surgical histopathology were correctly diagnosed by BRAF mutation analysis on FNAB specimens; there were no false positive findings.","Xing et al. (2005) studied the relationships between the BRAF V600E mutation and clinicopathologic outcomes, including recurrence, in 219 PTC patients. The authors concluded that in patients with PTC, BRAF mutation is associated with poorer clinicopathologic outcomes and independently predicts recurrence. Therefore, BRAF mutation may be a useful molecular marker to assist in risk stratification for patients with PTC.","In a series of 52 classic PTCs, Porra et al. (2005) found that low SLC5A8 (608044) expression was highly significantly associated with the presence of the BRAF 1799T-A mutation. SLC5A8 expression was selectively downregulated (40-fold) in PTCs of classical form; methylation-specific PCR analyses showed that SLC5A8 was methylated in 90% of classic PTCs and in about 20% of other PTCs. Porra et al. (2005) concluded that their data identified a relationship between the methylation-associated silencing of the tumor-suppressor gene SLC5A8 and the 1799T-A point mutation of the BRAF gene in the classic PTC subtype of thyroid carcinomas.","Vasko et al. (2005) studied the relationship between the BRAF 1799T-A mutation and lymph node metastasis of PTC by examining the mutation in both the primary tumors and their paired lymph node metastases. Their findings indicated that the high prevalence of BRAF mutation in lymph node-metastasized PTC tissues from BRAF mutation-positive primary tumors and the possible de novo formation of BRAF mutation in lymph node-metastasized PTC were consistent with a role of BRAF mutation in facilitating the metastasis and progression of PTC in lymph nodes.","In a patient with congenital hypothyroidism and long-standing goiter due to mutation in the thyroglobulin gene (see TG, 188540; and TDH3, 274700), who was also found to have multifocal follicular carcinoma of the thyroid, Hishinuma et al. (2005) identified somatic heterozygosity for the V600E mutation in the BRAF gene in the cancerous thyroid tissue.","Liu et al. (2007) used BRAF siRNA to transfect stably several BRAF mutation-harboring PTC cell lines, isolated clones with stable suppression of BRAF, and assessed their ability to proliferate, transform, and grow xenograft tumors in nude mice. They found that the V600E mutation not only initiates PTC but also maintains the proliferation, transformation, and tumorigenicity of PTC cells harboring the BRAF mutation, and that the growth of tumors derived from such cells continues to depend on the V600E mutation.","Jo et al. (2006) found that of 161 PTC patients, 102 (63.4%) had the BRAF V600E mutation and that these patients had significantly larger tumor sizes and significantly higher expression of vascular endothelial growth factor (VEGF; 192240) compared to patients without this mutation. The level of VEGF expression was closely correlated with tumor size, extrathyroidal invasion, and stage. Jo et al. (2006) concluded that the relatively high levels of VEGF expression may be related to poorer clinical outcomes and recurrences in BRAF V600E(+) PTC.","Durante et al. (2007) found that the BRAF V600E mutation in PTCs is associated with reduced expression of key genes involved in iodine metabolism. They noted that this effect may alter the effectiveness of diagnostic and/or therapeutic use of radioiodine in BRAF-mutation PTCs.","Lupi et al. (2007) found a BRAF mutation in 219 of 500 cases (43.8%) of PTC. The most common BRAF mutation, V600E, was found in 214 cases (42.8%). BRAF V600E was associated with extrathyroidal invasion (p less than 0.0001), multicentricity (p = 0.0026), presence of nodal metastases (p = 0.0009), class III versus classes I and II (p less than 0.00000006), and absence of tumor capsule (p less than 0.0001), in particular, in follicular- and micro-PTC variants. By multivariate analysis, the absence of tumor capsule remained the only parameter associated (p = 0.0005) with the BRAF V600E mutation. The authors concluded that the BRAF V600E mutation is associated with high-risk PTC and, in particular, in follicular variant with invasive tumor growth.","Flaherty et al. (2010) reported complete or partial regression of V600E-associated papillary thyroid cancer in 3 patients treated with an inhibitor (PLX4032) specific to the V600E mutation.","Nonseminomatous Germ Cell Tumors","In 3 (9%) of 32 nonseminomatous germ cell tumors (see 273300) with a mixture of embryonal carcinoma, yolk sac tumor, choriocarcinoma, and mature teratoma, Sommerer et al. (2005) identified the activating 1796T-A mutation in the BRAF gene; the mutation was present within the embryonic carcinoma component.","Astrocytoma","Pfister et al. (2008) identified a somatic V600E mutation in 4 (6%) of 66 pediatric low-grade astrocytomas (see 137800). Thirty (45%) of the 66 tumors had a copy number gain spanning the BRAF locus, indicating a novel mechanism of MAPK (176948) pathway activation in these tumors.","Role in Neurodegeneration","Mass et al. (2017) hypothesized that a somatic BRAF(V600E) mutation in the erythromyeloid lineage may cause neurodegeneration. Mass et al. (2017) showed that mosaic expression of BRAF(V600E) in mouse erythromyeloid progenitors results in clonal expansion of tissue-resident macrophages and a severe late-onset neurodegenerative disorder. This is associated with accumulation of ERK-activated amoeboid microglia in mice, and is also observed in human patients with histiocytoses. In the mouse model, neurobehavioral signs, astrogliosis, deposition of amyloid precursor protein, synaptic loss, and neuronal death were driven by ERK-activated microglia and were preventable by BRAF inhibition. Mass et al. (2017) suggested that the results identified the fetal precursors of tissue-resident macrophages as a potential cell of origin for histiocytoses and demonstrated that a somatic mutation in the erythromyeloid progenitor lineage in mice can drive late-onset neurodegeneration.","Variant Function","Brady et al. (2014) showed that decreasing the levels of CTR1 (603085), or mutations in MEK1 (176872) that disrupt copper binding, decreased BRAF(V600E)-driven signaling and tumorigenesis in mice and human cell settings. Conversely, a MEK1-MEK5 (602520) chimera that phosphorylated ERK1/2 independently of copper or an active ERK2 restored the tumor growth of murine cells lacking Ctr1. Copper chelators used in the treatment of Wilson disease (277900) decreased tumor growth of human or murine cells that were either transformed by BRAF(V600E) or engineered to be resistant to BRAF inhibition. Brady et al. (2014) concluded that copper chelation therapy could be repurposed to treat cancers containing the BRAF(V600E) mutation.","Rapino et al. (2018) showed in humans that the enzymes that catalyze modifications of wobble uridine-34 (U34) tRNA are key players of the protein synthesis rewiring that is induced by the transformation driven by the BRAF V600E oncogene and by resistance to targeted therapy in melanoma. Rapino et al. (2018) showed that BRAF V600E-expressing melanoma cells are dependent on U34 enzymes for survival, and that concurrent inhibition of MAPK signaling and ELP3 (612722) or CTU1 (612694) and/or CTU2 (617057) synergizes to kill melanoma cells. Activation of the PI3K signaling pathway, one of the most common mechanisms of acquired resistance to MAPK therapeutic agents, markedly increases the expression of U34 enzymes. Mechanistically, U34 enzymes promote glycolysis in melanoma cells through the direct, codon-dependent, regulation of the translation of HIF1A (603348) mRNA and the maintenance of high levels of HIF1-alpha protein. Therefore, the acquired resistance to anti-BRAF therapy is associated with high levels of U34 enzymes and HIF1-alpha. Rapino et al. (2018) concluded that U34 enzymes promote the survival and resistance to therapy of melanoma cells by regulating specific mRNA translation."],"submitter_name":"OMIM","review_date":20140904,"origin":"somatic","method":"literature only","submitter_date":20220317,"diseases":[{"normalized_cancer":["ASTROCYTOMA, LOW-GRADE, SOMATIC"],"names":["Astrocytoma, Low-Grade, Somatic"]}],"review_description":"Pathogenic","date_updated":20220328,"clinical_significance":["Pathogenic"],"review_status":"no assertion criteria provided","accession_id":"SCV000035250"}],"variation_id":13961,"submission_description":["The val600-to-glu (V600E) mutation caused by a 1799T-A transversion in the BRAF gene was previously designated VAL599GLU (1796T-A). Kumar et al. (2003) noted that an earlier version of the BRAF sequence showed a discrepancy of 3 nucleotides in exon 1; based on the corrected sequence, they proposed a change in nucleotide numbering after nucleotide 94 (the ATG codon) by +3 and a corresponding codon change of +1.","Malignant Melanoma","Davies et al. (2002) identified a 1799T-A transversion in exon 15 of the BRAF gene that leads to a val600-to-glu (V600E) substitution. This mutation accounted for 92% of BRAF mutations in malignant melanoma (see 155600). The V600E mutation is an activating mutation resulting in constitutive activation of BRAF and downstream signal transduction in the MAP kinase pathway.","To evaluate the timing of mutations in BRAF during melanocyte neoplasia, Pollock et al. (2003) carried out mutation analysis on microdissected melanoma and nevi samples. They observed mutations resulting in the V600E amino acid substitution in 41 (68%) of 60 melanoma metastases, 4 (80%) of 5 primary melanomas, and, unexpectedly, in 63 (82%) of 77 nevi. The data suggested that mutational activation of the RAS/RAF/MAPK pathway in nevi is a critical step in the initiation of melanocytic neoplasia but alone is insufficient for melanoma tumorigenesis.","Lang et al. (2003) failed to find the V600E mutation as a germline mutation in 42 cases of familial melanoma studied. Their collection of families included 15 with and 24 without detected mutations in CDKN2A (600160). They did, however, find the V600E mutation in 6 (27%) of 22 samples of secondary (metastatic) melanomas studied. Meyer et al. (2003) found no V600E mutation in 172 melanoma patients comprising 46 familial cases, 21 multiple melanoma patients, and 106 cases with at least 1 first-degree relative suffering from other cancers. They concluded, therefore, that the common somatic BRAF mutation V600E does not contribute to polygenic or familial melanoma predisposition.","Kim et al. (2003) stated that V600E, the most common of BRAF mutations, had not been identified in tumors with mutations of the KRAS gene (190070). This mutually exclusive relationship supports the hypothesis that BRAF (V600E) and KRAS mutations exert equivalent effects in tumorigenesis (Rajagopalan et al., 2002; Singer et al., 2003).","Flaherty et al. (2010) reported complete or partial regression of V600E-associated metastatic melanoma in 81% of patients treated with an inhibitor (PLX4032) specific to the V600E mutation. Among 16 patients in a dose-escalation cohort, 10 had a partial response, and 1 had a complete response. Among 32 patients in an extension cohort, 24 had a partial response, and 2 had a complete response. The estimated median progression-free survival among all patients was more than 7 months. Responses were observed at all sites of disease, including bone, liver, and small bowel. Tumor biopsy specimens from 7 patients showed markedly reduced levels of phosphorylated ERK (600997), cyclin D1 (168461), and Ki67 (MKI67; 176741) at day 15 compared to baseline, indicating inhibition of the MAP kinase pathway. Three additional patients with V600E-associated papillary thyroid also showed a partial or complete response.","Bollag et al. (2010) described the structure-guided discovery of PLX4032 (RG7204), a potent inhibitor of oncogenic BRAF kinase activity. PLX4032 was cocrystallized with a protein construct that contained the kinase domain of BRAF(V600E). In a clinical trial, patients exposed to higher plasma levels of PLX4032 experienced tumor regression; in patients with tumor regressions, pathway analysis typically showed greater than 80% inhibition of cytoplasmic ERK phosphorylation. Bollag et al. (2010) concluded that their data demonstrated that BRAF-mutant melanomas are highly dependent on BRAF kinase activity.","Patients with BRAF(V600E)-positive melanomas exhibit an initial antitumor response to the RAF kinase inhibitor PLX4032, but acquired drug resistance almost invariably develops. Johannessen et al. (2010) identified MAP3K8 (191195), encoding COT (cancer Osaka thyroid oncogene) as a MAPK pathway agonist that drives resistance to RAF inhibition in BRAF(V600E) cell lines. COT activates ERK primarily through MARK/ERK (MEK)-dependent mechanisms that do not require RAF signaling. Moreover, COT expression is associated with de novo resistance in BRAF(V600E) cultured cell lines and acquired resistance in melanoma cells and tissue obtained from relapsing patients following treatment with MEK or RAF inhibitors. Johannessen et al. (2010) further identified combinatorial MAPK pathway inhibition or targeting of COT kinase activity as possible therapeutic strategies for reducing MAPK pathway activation in this setting.","Nazarian et al. (2010) showed that acquired resistance to PLX4032, a novel class I RAF-selective inhibitor, develops by mutually exclusive PDGFRB (173410) upregulation or NRAS (164790) mutations but not through secondary mutations in BRAF(V600E). Nazarian et al. (2010) used PLX4032-resistant sublines artificially derived from BRAF (V600E)-positive melanoma cell lines and validated key findings in PLX4032-resistant tumors and tumor-matched, short-term cultures from clinical trial patients. Induction of PDGFRB RNA, protein and tyrosine phosphorylation emerged as a dominant feature of acquired PLX4032 resistance in a subset of melanoma sublines, patient-derived biopsies, and short-term cultures. PDGFRB upregulated tumor cells have low activated RAS levels and, when treated with PLX4032, do not reactivate the MAPK pathway significantly. In another subset, high levels of activated N-RAS resulting from mutations lead to significant MAPK pathway reactivation upon PLX4032 treatment. Knockdown of PDGFRB or NRAS reduced growth of the respective PLX4032-resistant subsets. Overexpression of PDGFRB or NRAS(Q61K) conferred PLX4032 resistance to PLX4032-sensitive parental cell lines. Importantly, Nazarian et al. (2010) showed that MAPK reactivation predicts MEK inhibitor sensitivity. Thus, Nazarian et al. (2010) concluded that melanomas escape BRAF(V600E) targeting not through secondary BRAF(V600E) mutations but via receptor tyrosine kinase (RTK)-mediated activation of alternative survival pathway(s) or activated RAS-mediated reactivation of the MAPK pathway, suggesting additional therapeutic strategies.","Poulikakos et al. (2011) identified a novel resistance mechanism for melanomas with BRAF(V600E) treated with RAF inhibitors. The authors found that a subset of cells resistant to vemurafenib (PLX4032, RG7204) express a 61-kD variant form of BRAF(V600E), p61BRAF(V600E), that lacks exons 4 through 8, a region that encompasses the RAS-binding domain. p61BRAF(V600E) showed enhanced dimerization in cells with low levels of RAS activation, as compared to full-length BRAF(V600E). In cells in which p61BRAF(V600E) was expressed endogenously or ectopically, ERK signaling was resistant to the RAF inhibitor. Moreover, a mutation that abolished the dimerization of p61BRAF(V600E) restored its sensitivity to vemurafenib. Finally, Poulikakos et al. (2011) identified BRAF(V600E) splicing variants lacking the RAS-binding domain in the tumors of 6 of 19 patients with acquired resistance to vemurafenib. Poulikakos et al. (2011) concluded that their data supported the model that inhibition of ERK signaling by RAF inhibitors is dependent on levels of RAS-GTP too low to support RAF dimerization and identified a novel mechanism of acquired resistance in patients: expression of splicing isoforms of BRAF(V600E) that dimerize in a RAS-independent manner.","Thakur et al. (2013) investigated the cause and consequences of vemurafenib resistance using 2 independently-derived primary human melanoma xenograft models in which drug resistance is selected by continuous vemurafenib administration. In one of these models, resistant tumors showed continued dependency on BRAF(V600E)-MEK-ERK signaling owing to elevated BRAF(V600E) expression. Thakur et al. (2013) showed that vemurafenib-resistant melanomas become drug-dependent for their continued proliferation, such that cessation of drug administration leads to regression of established drug-resistant tumors. Thakur et al. (2013) further demonstrated that a discontinuous dosing strategy, which exploits the fitness disadvantage displayed by drug-resistant cells in the absence of the drug, forestalls the onset of lethal drug-resistant disease. Thakur et al. (2013) concluded that their data highlighted the concept that drug-resistant cells may also display drug dependency, such that altered dosing may prevent the emergence of lethal drug resistance. These observations may contribute to sustaining the durability of vemurafenib response with the ultimate goal of curative therapy for the subset of melanoma patients with BRAF mutations.","Using metabolic profiling and functional perturbations, Kaplon et al. (2013) showed that the mitochondrial gatekeeper pyruvate dehydrogenase (PDH; 300502) is a crucial mediator of senescence induced by BRAF(V600E), an oncogene commonly mutated in melanoma and other cancers. BRAF(V600E)-induced senescence is accompanied by simultaneous suppression of the PDH-inhibitory enzyme pyruvate dehydrogenase kinase-1 (PDK1; 602524) and induction of the PDH-activating enzyme pyruvate dehydrogenase phosphatase-2 (PDP2; 615499). The resulting combined activation of PDH enhanced the use of pyruvate in the tricarboxylic acid cycle, causing increased respiration and redox stress. Abrogation of oncogene-induced senescence (OIS), a rate-limiting step towards oncogenic transformation, coincided with reversion of these processes. Further supporting a crucial role of PDH in OIS, enforced normalization of either PDK1 or PDP2 expression levels inhibited PDH and abrogated OIS, thereby licensing BRAF(V600E)-driven melanoma development. Finally, depletion of PDK1 eradicated melanoma subpopulations resistant to targeted BRAF inhibition, and caused regression of established melanomas.","Sun et al. (2014) showed that 6 out of 16 BRAF(V600E)-positive melanoma tumors analyzed acquired EGFR (131550) expression after the development of resistance to inhibitors of BRAF or MEK (176872). Using a chromatin regulator-focused short hairpin RNA (shRNA) library, Sun et al. (2014) found that suppression of SRY-box 10 (SOX10; 602229) in melanoma causes activation of TGF-beta (190180) signaling, thus leading to upregulation of EGFR and platelet-derived growth factor receptor-beta (PDGFRB; 173410), which confer resistance to BRAF and MEK inhibitors. Expression of EGFR in melanoma or treatment with TGF-beta results in a slow-growth phenotype with cells displaying hallmarks of oncogene-induced senescence. However, EGFR expression or exposure to TGF-beta becomes beneficial for proliferation in the presence of BRAF or MEK inhibitors. In a heterogeneous population of melanoma cells that have varying levels of SOX10 suppression, cells with low SOX10 and consequently high EGFR expression are rapidly enriched in the presence of drug treatment, but this is reversed when the treatment is discontinued. Sun et al. (2014) found evidence for SOX10 loss and/or activation of TGF-beta signaling in 4 of the 6 EGFR-positive drug-resistant melanoma patient samples. Sun et al. (2014) concluded that their findings provided a rationale for why some BRAF or MEK inhibitor-resistant melanoma patients may regain sensitivity to these drugs after a 'drug holiday' and identified patients with EGFR-positive melanoma as a group that may benefit from retreatment after a drug holiday.","Boussemart et al. (2014) demonstrated that the persistent formation of the eIF4F complex, comprising the eIF4E (133440) cap-binding protein, the eIF4G (600495) scaffolding protein, and the eIF4A (602641) RNA helicase, is associated with resistance to anti-BRAF (164757), anti-MEK, and anti-BRAF plus anti-MEK drug combinations in BRAF(V600)-mutant melanoma, colon, and thyroid cancer cell lines. Resistance to treatment and maintenance of eIF4F complex formation is associated with 1 of 3 mechanisms: reactivation of MAPK (see 176948) signaling; persistent ERK-independent phosphorylation of the inhibitory eIF4E-binding protein 4EBP1 (602223); or increased proapoptotic BMF (606266)-dependent degradation of eIF4G. The development of an in situ method to detect the eIF4E-eIF4G interactions showed that eIF4F complex formation is decreased in tumors that respond to anti-BRAF therapy and increased in resistant metastases compared to tumors before treatment. Strikingly, inhibiting the eIF4F complex, either by blocking the eIF4E-eIF4G interaction or by targeting eIF4A, synergized with inhibiting BRAF(V600) to kill the cancer cells. eIF4F appeared not only to be an indicator of both innate and acquired resistance, but also a therapeutic target. Boussemart et al. (2014) concluded that combinations of drugs targeting BRAF (and/or MEK) and eIF4F may overcome most of the resistance mechanisms in BRAF(V600)-mutant cancers.","Colorectal Carcinoma","Rajagopalan et al. (2002) identified the V600E mutation in 28 of 330 colorectal tumors (see 114500) screened for BRAF mutations. In all cases the mutation was heterozygous and occurred somatically.","Domingo et al. (2004) pointed out that the V600E hotspot mutation had been found in colorectal tumors that showed inherited mutation in a DNA mismatch repair (MMR) gene, such as MLH1 (120436) or MSH2 (609309). These mutations had been shown to occur almost exclusively in tumors located in the proximal colon and with hypermethylation of MLH1, the gene involved in the initial steps of development of these tumors; however, BRAF mutations were not detected in those cases with or presumed to have germline mutation in either MLH1 or MSH2. Domingo et al. (2004) studied mutation analysis of the BRAF hotspot as a possible low-cost effective strategy for genetic testing for hereditary nonpolyposis colorectal cancer (HNPCC; 120435). The V600E mutation was found in 82 (40%) of 206 sporadic tumors with high microsatellite instability (MSI-H) but in none of 111 tested HNPCC tumors or in 45 cases showing abnormal MSH2 immunostaining. Domingo et al. (2004) concluded that detection of the V600E mutation in a colorectal MSI-H tumor argues against the presence of germline mutation in either MLH1 or MSH2, and that screening of these MMR genes can be avoided in cases positive for V600E.","Lubomierski et al. (2005) analyzed 45 colorectal carcinomas with MSI and 37 colorectal tumors without MSI but with similar clinical characteristics and found that BRAF was mutated more often in tumors with MSI than without (27% vs 5%, p = 0.016). The most prevalent BRAF alteration, V600E, occurred only in tumors with MSI and was associated with more frequent MLH1 promoter methylation and loss of MLH1. The median age of patients with BRAF V600E was older than that of those without V600E (78 vs 49 years, p = 0.001). There were no BRAF alterations in patients with germline mutations of mismatch repair genes. Lubomierski et al. (2005) concluded that tumors with MSI caused by epigenetic MLH1 silencing have a mutational background distinct from that of tumors with genetic loss of mismatch repair, and suggested that there are 2 genetically distinct entities of microsatellite unstable tumors.","Tol et al. (2009) detected a somatic V600E mutation in 45 (8.7%) of 519 metastatic colorectal tumors. Patients with BRAF-mutated tumors had significantly shorter median progression-free and median overall survival compared to patients with wildtype BRAF tumors, regardless of the use of cetuximab. Tol et al. (2009) suggested that the BRAF mutation may be a negative prognostic factor in these patients.","Inhibition of the BRAF(V600E) oncoprotein by the small-molecule drug PLX4032 (vemurafenib) is highly effective in the treatment of melanoma. However, colon cancer patients harboring the same BRAF(V600E) oncogenic lesion have poor prognosis and show only a very limited response to this drug. To investigate the cause of this limited therapeutic effect in BRAF(V600E) mutant colon cancer, Prahallad et al. (2012) performed an RNA interference-based genetic screen in human cells to search for kinases whose knockdown synergizes with BRAF(V600E) inhibition. They reported that blockade of the epidermal growth factor receptor (EGFR; 131550) shows strong synergy with BRAF(V600E) inhibition. Prahallad et al. (2012) found in multiple BRAF(V600E) mutant colon cancers that inhibition of EGFR by the antibody drug cetuximab or the small-molecule drugs gefitinib or erlotinib is strongly synergistic with BRAF(V600E) inhibition, both in vitro and in vivo. Mechanistically, Prahallad et al. (2012) found that BRAF(V600E) inhibition causes a rapid feedback activation of EGFR, which supports continued proliferation in the presence of BRAF(V600E) inhibition. Melanoma cells express low levels of EGFR and are therefore not subject to this feedback activation. Consistent with this, Prahallad et al. (2012) found that ectopic expression of EGFR in melanoma cells is sufficient to cause resistance to PLX4032. Prahallad et al. (2012) concluded that BRAF(V600E) mutant colon cancers (approximately 8 to 10% of all colon cancers) might benefit from combination therapy consisting of BRAF and EGFR inhibitors.","Gala et al. (2014) identified the BRAF V600E mutation in 18 of 19 sessile serrated adenomas from 19 unrelated patients with sessile serrated polyposis cancer syndrome (SSPCS; 617108).","Papillary Thyroid Carcinoma","Kimura et al. (2003) identified the V600E mutation in 28 (35.8%) of 78 papillary thyroid cancers (PTC; see 188550); it was not found in any of the other types of differentiated follicular neoplasms arising from the same cell type (0 of 46). RET (see 164761)/PTC mutations and RAS (see 190020) mutations were each identified in 16.4% of PTCs, but there was no overlap in the 3 mutations. Kimura et al. (2003) concluded that thyroid cell transformation to papillary cancer takes place through constitutive activation of effectors along the RET/PTC-RAS-BRAF signaling pathway.","Xing et al. (2004) studied various thyroid tumor types for the most common BRAF mutation, 1799T-A, by DNA sequencing. They found a high and similar frequency (45%) of the 1799T-A mutation in 2 geographically distinct papillary thyroid cancer patient populations, 1 composed of sporadic cases from North America, and the other from Kiev, Ukraine, that included individuals who were exposed to the Chernobyl nuclear accident. In contrast, Xing et al. (2004) found BRAF mutations in only 20% of anaplastic thyroid cancers and in no medullary thyroid cancers or benign thyroid hyperplasia. They also confirmed previous reports that the BRAF 1799T-A mutation did not occur in benign thyroid adenomas or follicular thyroid cancers. They concluded that frequent occurrence of BRAF mutation is associated with PTC, irrespective of geographic origin, and is apparently not a radiation-susceptible mutation.","Nikiforova et al. (2003) analyzed 320 thyroid tumors and 6 anaplastic carcinoma cell lines and detected BRAF mutations in 45 papillary carcinomas (38%), 2 poorly differentiated carcinomas (13%), 3 (10%) anaplastic carcinomas (10%), and 5 thyroid anaplastic carcinoma cell lines (83%) but not in follicular, Hurthle cell, and medullary carcinomas, follicular and Hurthle cell adenomas, or benign hyperplastic nodules. All mutations involved a T-to-A transversion at nucleotide 1799. All BRAF-positive poorly differentiated and anaplastic carcinomas contained areas of preexisting papillary carcinoma, and mutation was present in both the well differentiated and dedifferentiated components. The authors concluded that BRAF mutations are restricted to papillary carcinomas and poorly differentiated and anaplastic carcinomas arising from papillary carcinomas, and that they are associated with distinct phenotypic and biologic properties of papillary carcinomas and may participate in progression to poorly differentiated and anaplastic carcinomas.","Hypothesizing that childhood thyroid carcinomas may be associated with a different prevalence of the BRAF 1799T-A mutation compared with adult cases, Kumagai et al. (2004) examined 31 cases of Japanese childhood thyroid carcinoma and an additional 48 cases of PTC from Ukraine, all of whom were less than 17 years of age at the time of the Chernobyl accident. The BRAF 1799T-A mutation was found in only 1 of 31 Japanese cases (3.4%) and in none of the 15 Ukrainian cases operated on before the age of 15 years, although it was found in 8 of 33 Ukrainian young adult cases (24.2%). Kumagai et al. (2004) concluded that the BRAF 1799T-A mutation is uncommon in childhood thyroid carcinomas.","Puxeddu et al. (2004) found the V600E substitution in 24 of 60 PTCs (40%) but in none of 6 follicular adenomas, 5 follicular carcinomas, or 1 anaplastic carcinoma. Nine of the 60 PTCs (15%) presented expression of a RET/PTC rearrangement. A genetico-clinical association analysis showed a statistically significant correlation between BRAF mutation and development of PTCs of the classic papillary histotype (P = 0.038). No link could be detected between expression of BRAF V600E and age at diagnosis, gender, dimension, local invasiveness of the primary cancer, presence of lymph node metastases, tumor stage, or multifocality of the disease. The authors concluded that these data clearly confirmed that BRAF V600E was the most common genetic alteration found to that time in adult sporadic PTCs, that it is unique for this thyroid cancer histotype, and that it might drive the development of PTCs of the classic papillary subtype.","Xing et al. (2004) demonstrated detection of the 1799T-A mutation on thyroid cytologic specimens from fine needle aspiration biopsy (FNAB). Prospective analysis showed that 50% of the nodules that proved to be PTCs on surgical histopathology were correctly diagnosed by BRAF mutation analysis on FNAB specimens; there were no false positive findings.","Xing et al. (2005) studied the relationships between the BRAF V600E mutation and clinicopathologic outcomes, including recurrence, in 219 PTC patients. The authors concluded that in patients with PTC, BRAF mutation is associated with poorer clinicopathologic outcomes and independently predicts recurrence. Therefore, BRAF mutation may be a useful molecular marker to assist in risk stratification for patients with PTC.","In a series of 52 classic PTCs, Porra et al. (2005) found that low SLC5A8 (608044) expression was highly significantly associated with the presence of the BRAF 1799T-A mutation. SLC5A8 expression was selectively downregulated (40-fold) in PTCs of classical form; methylation-specific PCR analyses showed that SLC5A8 was methylated in 90% of classic PTCs and in about 20% of other PTCs. Porra et al. (2005) concluded that their data identified a relationship between the methylation-associated silencing of the tumor-suppressor gene SLC5A8 and the 1799T-A point mutation of the BRAF gene in the classic PTC subtype of thyroid carcinomas.","Vasko et al. (2005) studied the relationship between the BRAF 1799T-A mutation and lymph node metastasis of PTC by examining the mutation in both the primary tumors and their paired lymph node metastases. Their findings indicated that the high prevalence of BRAF mutation in lymph node-metastasized PTC tissues from BRAF mutation-positive primary tumors and the possible de novo formation of BRAF mutation in lymph node-metastasized PTC were consistent with a role of BRAF mutation in facilitating the metastasis and progression of PTC in lymph nodes.","In a patient with congenital hypothyroidism and long-standing goiter due to mutation in the thyroglobulin gene (see TG, 188540; and TDH3, 274700), who was also found to have multifocal follicular carcinoma of the thyroid, Hishinuma et al. (2005) identified somatic heterozygosity for the V600E mutation in the BRAF gene in the cancerous thyroid tissue.","Liu et al. (2007) used BRAF siRNA to transfect stably several BRAF mutation-harboring PTC cell lines, isolated clones with stable suppression of BRAF, and assessed their ability to proliferate, transform, and grow xenograft tumors in nude mice. They found that the V600E mutation not only initiates PTC but also maintains the proliferation, transformation, and tumorigenicity of PTC cells harboring the BRAF mutation, and that the growth of tumors derived from such cells continues to depend on the V600E mutation.","Jo et al. (2006) found that of 161 PTC patients, 102 (63.4%) had the BRAF V600E mutation and that these patients had significantly larger tumor sizes and significantly higher expression of vascular endothelial growth factor (VEGF; 192240) compared to patients without this mutation. The level of VEGF expression was closely correlated with tumor size, extrathyroidal invasion, and stage. Jo et al. (2006) concluded that the relatively high levels of VEGF expression may be related to poorer clinical outcomes and recurrences in BRAF V600E(+) PTC.","Durante et al. (2007) found that the BRAF V600E mutation in PTCs is associated with reduced expression of key genes involved in iodine metabolism. They noted that this effect may alter the effectiveness of diagnostic and/or therapeutic use of radioiodine in BRAF-mutation PTCs.","Lupi et al. (2007) found a BRAF mutation in 219 of 500 cases (43.8%) of PTC. The most common BRAF mutation, V600E, was found in 214 cases (42.8%). BRAF V600E was associated with extrathyroidal invasion (p less than 0.0001), multicentricity (p = 0.0026), presence of nodal metastases (p = 0.0009), class III versus classes I and II (p less than 0.00000006), and absence of tumor capsule (p less than 0.0001), in particular, in follicular- and micro-PTC variants. By multivariate analysis, the absence of tumor capsule remained the only parameter associated (p = 0.0005) with the BRAF V600E mutation. The authors concluded that the BRAF V600E mutation is associated with high-risk PTC and, in particular, in follicular variant with invasive tumor growth.","Flaherty et al. (2010) reported complete or partial regression of V600E-associated papillary thyroid cancer in 3 patients treated with an inhibitor (PLX4032) specific to the V600E mutation.","Nonseminomatous Germ Cell Tumors","In 3 (9%) of 32 nonseminomatous germ cell tumors (see 273300) with a mixture of embryonal carcinoma, yolk sac tumor, choriocarcinoma, and mature teratoma, Sommerer et al. (2005) identified the activating 1796T-A mutation in the BRAF gene; the mutation was present within the embryonic carcinoma component.","Astrocytoma","Pfister et al. (2008) identified a somatic V600E mutation in 4 (6%) of 66 pediatric low-grade astrocytomas (see 137800). Thirty (45%) of the 66 tumors had a copy number gain spanning the BRAF locus, indicating a novel mechanism of MAPK (176948) pathway activation in these tumors.","Role in Neurodegeneration","Mass et al. (2017) hypothesized that a somatic BRAF(V600E) mutation in the erythromyeloid lineage may cause neurodegeneration. Mass et al. (2017) showed that mosaic expression of BRAF(V600E) in mouse erythromyeloid progenitors results in clonal expansion of tissue-resident macrophages and a severe late-onset neurodegenerative disorder. This is associated with accumulation of ERK-activated amoeboid microglia in mice, and is also observed in human patients with histiocytoses. In the mouse model, neurobehavioral signs, astrogliosis, deposition of amyloid precursor protein, synaptic loss, and neuronal death were driven by ERK-activated microglia and were preventable by BRAF inhibition. Mass et al. (2017) suggested that the results identified the fetal precursors of tissue-resident macrophages as a potential cell of origin for histiocytoses and demonstrated that a somatic mutation in the erythromyeloid progenitor lineage in mice can drive late-onset neurodegeneration.","Variant Function","Brady et al. (2014) showed that decreasing the levels of CTR1 (603085), or mutations in MEK1 (176872) that disrupt copper binding, decreased BRAF(V600E)-driven signaling and tumorigenesis in mice and human cell settings. Conversely, a MEK1-MEK5 (602520) chimera that phosphorylated ERK1/2 independently of copper or an active ERK2 restored the tumor growth of murine cells lacking Ctr1. Copper chelators used in the treatment of Wilson disease (277900) decreased tumor growth of human or murine cells that were either transformed by BRAF(V600E) or engineered to be resistant to BRAF inhibition. Brady et al. (2014) concluded that copper chelation therapy could be repurposed to treat cancers containing the BRAF(V600E) mutation.","Rapino et al. (2018) showed in humans that the enzymes that catalyze modifications of wobble uridine-34 (U34) tRNA are key players of the protein synthesis rewiring that is induced by the transformation driven by the BRAF V600E oncogene and by resistance to targeted therapy in melanoma. Rapino et al. (2018) showed that BRAF V600E-expressing melanoma cells are dependent on U34 enzymes for survival, and that concurrent inhibition of MAPK signaling and ELP3 (612722) or CTU1 (612694) and/or CTU2 (617057) synergizes to kill melanoma cells. Activation of the PI3K signaling pathway, one of the most common mechanisms of acquired resistance to MAPK therapeutic agents, markedly increases the expression of U34 enzymes. Mechanistically, U34 enzymes promote glycolysis in melanoma cells through the direct, codon-dependent, regulation of the translation of HIF1A (603348) mRNA and the maintenance of high levels of HIF1-alpha protein. Therefore, the acquired resistance to anti-BRAF therapy is associated with high levels of U34 enzymes and HIF1-alpha. Rapino et al. (2018) concluded that U34 enzymes promote the survival and resistance to therapy of melanoma cells by regulating specific mRNA translation."],"title":"NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) AND Astrocytoma, low-grade, somatic","review_date":20140904,"diseases":[{"normalized_cancer":["Astrocytoma, low-grade, somatic"],"symbols":{"medgen":"C2674727"},"names":["Astrocytoma, Low-Grade, Somatic"]}],"pub_med_references":[12068308,12198537,12447372,12619120,12644542,12670889,12794760,12960123,14513361,14602780,15001635,15126572,15181070,15342696,15356022,15386408,15687339,15998781,16015629,16174717,16187918,16772349,17374713,17488796,17785355,18398503,19571295,20818844,20823850,21107320,21107323,22113612,22281684,23302800,23685455,24512911,24670642,24717435,25079330,28854169,29925953],"date_created":20130404,"variant_id":10190071404531360004,"review_description":"Pathogenic","clinical_significance":["Pathogenic"],"allele_id":29000,"accession_id":"RCV000014994"},{"submissions":[{"pub_med_references":[12068308,12198537,12447372,12619120,12644542,12670889,12794760,12960123,14513361,14602780,15001635,15126572,15181070,15342696,15356022,15386408,15687339,15998781,16015629,16174717,16187918,16772349,17374713,17488796,17785355,18398503,19571295,20818844,20823850,21107320,21107323,22113612,22281684,23302800,23685455,24512911,24670642,24717435,25079330,28854169,29925953],"submission_description":["The val600-to-glu (V600E) mutation caused by a 1799T-A transversion in the BRAF gene was previously designated VAL599GLU (1796T-A). Kumar et al. (2003) noted that an earlier version of the BRAF sequence showed a discrepancy of 3 nucleotides in exon 1; based on the corrected sequence, they proposed a change in nucleotide numbering after nucleotide 94 (the ATG codon) by +3 and a corresponding codon change of +1.","Malignant Melanoma","Davies et al. (2002) identified a 1799T-A transversion in exon 15 of the BRAF gene that leads to a val600-to-glu (V600E) substitution. This mutation accounted for 92% of BRAF mutations in malignant melanoma (see 155600). The V600E mutation is an activating mutation resulting in constitutive activation of BRAF and downstream signal transduction in the MAP kinase pathway.","To evaluate the timing of mutations in BRAF during melanocyte neoplasia, Pollock et al. (2003) carried out mutation analysis on microdissected melanoma and nevi samples. They observed mutations resulting in the V600E amino acid substitution in 41 (68%) of 60 melanoma metastases, 4 (80%) of 5 primary melanomas, and, unexpectedly, in 63 (82%) of 77 nevi. The data suggested that mutational activation of the RAS/RAF/MAPK pathway in nevi is a critical step in the initiation of melanocytic neoplasia but alone is insufficient for melanoma tumorigenesis.","Lang et al. (2003) failed to find the V600E mutation as a germline mutation in 42 cases of familial melanoma studied. Their collection of families included 15 with and 24 without detected mutations in CDKN2A (600160). They did, however, find the V600E mutation in 6 (27%) of 22 samples of secondary (metastatic) melanomas studied. Meyer et al. (2003) found no V600E mutation in 172 melanoma patients comprising 46 familial cases, 21 multiple melanoma patients, and 106 cases with at least 1 first-degree relative suffering from other cancers. They concluded, therefore, that the common somatic BRAF mutation V600E does not contribute to polygenic or familial melanoma predisposition.","Kim et al. (2003) stated that V600E, the most common of BRAF mutations, had not been identified in tumors with mutations of the KRAS gene (190070). This mutually exclusive relationship supports the hypothesis that BRAF (V600E) and KRAS mutations exert equivalent effects in tumorigenesis (Rajagopalan et al., 2002; Singer et al., 2003).","Flaherty et al. (2010) reported complete or partial regression of V600E-associated metastatic melanoma in 81% of patients treated with an inhibitor (PLX4032) specific to the V600E mutation. Among 16 patients in a dose-escalation cohort, 10 had a partial response, and 1 had a complete response. Among 32 patients in an extension cohort, 24 had a partial response, and 2 had a complete response. The estimated median progression-free survival among all patients was more than 7 months. Responses were observed at all sites of disease, including bone, liver, and small bowel. Tumor biopsy specimens from 7 patients showed markedly reduced levels of phosphorylated ERK (600997), cyclin D1 (168461), and Ki67 (MKI67; 176741) at day 15 compared to baseline, indicating inhibition of the MAP kinase pathway. Three additional patients with V600E-associated papillary thyroid also showed a partial or complete response.","Bollag et al. (2010) described the structure-guided discovery of PLX4032 (RG7204), a potent inhibitor of oncogenic BRAF kinase activity. PLX4032 was cocrystallized with a protein construct that contained the kinase domain of BRAF(V600E). In a clinical trial, patients exposed to higher plasma levels of PLX4032 experienced tumor regression; in patients with tumor regressions, pathway analysis typically showed greater than 80% inhibition of cytoplasmic ERK phosphorylation. Bollag et al. (2010) concluded that their data demonstrated that BRAF-mutant melanomas are highly dependent on BRAF kinase activity.","Patients with BRAF(V600E)-positive melanomas exhibit an initial antitumor response to the RAF kinase inhibitor PLX4032, but acquired drug resistance almost invariably develops. Johannessen et al. (2010) identified MAP3K8 (191195), encoding COT (cancer Osaka thyroid oncogene) as a MAPK pathway agonist that drives resistance to RAF inhibition in BRAF(V600E) cell lines. COT activates ERK primarily through MARK/ERK (MEK)-dependent mechanisms that do not require RAF signaling. Moreover, COT expression is associated with de novo resistance in BRAF(V600E) cultured cell lines and acquired resistance in melanoma cells and tissue obtained from relapsing patients following treatment with MEK or RAF inhibitors. Johannessen et al. (2010) further identified combinatorial MAPK pathway inhibition or targeting of COT kinase activity as possible therapeutic strategies for reducing MAPK pathway activation in this setting.","Nazarian et al. (2010) showed that acquired resistance to PLX4032, a novel class I RAF-selective inhibitor, develops by mutually exclusive PDGFRB (173410) upregulation or NRAS (164790) mutations but not through secondary mutations in BRAF(V600E). Nazarian et al. (2010) used PLX4032-resistant sublines artificially derived from BRAF (V600E)-positive melanoma cell lines and validated key findings in PLX4032-resistant tumors and tumor-matched, short-term cultures from clinical trial patients. Induction of PDGFRB RNA, protein and tyrosine phosphorylation emerged as a dominant feature of acquired PLX4032 resistance in a subset of melanoma sublines, patient-derived biopsies, and short-term cultures. PDGFRB upregulated tumor cells have low activated RAS levels and, when treated with PLX4032, do not reactivate the MAPK pathway significantly. In another subset, high levels of activated N-RAS resulting from mutations lead to significant MAPK pathway reactivation upon PLX4032 treatment. Knockdown of PDGFRB or NRAS reduced growth of the respective PLX4032-resistant subsets. Overexpression of PDGFRB or NRAS(Q61K) conferred PLX4032 resistance to PLX4032-sensitive parental cell lines. Importantly, Nazarian et al. (2010) showed that MAPK reactivation predicts MEK inhibitor sensitivity. Thus, Nazarian et al. (2010) concluded that melanomas escape BRAF(V600E) targeting not through secondary BRAF(V600E) mutations but via receptor tyrosine kinase (RTK)-mediated activation of alternative survival pathway(s) or activated RAS-mediated reactivation of the MAPK pathway, suggesting additional therapeutic strategies.","Poulikakos et al. (2011) identified a novel resistance mechanism for melanomas with BRAF(V600E) treated with RAF inhibitors. The authors found that a subset of cells resistant to vemurafenib (PLX4032, RG7204) express a 61-kD variant form of BRAF(V600E), p61BRAF(V600E), that lacks exons 4 through 8, a region that encompasses the RAS-binding domain. p61BRAF(V600E) showed enhanced dimerization in cells with low levels of RAS activation, as compared to full-length BRAF(V600E). In cells in which p61BRAF(V600E) was expressed endogenously or ectopically, ERK signaling was resistant to the RAF inhibitor. Moreover, a mutation that abolished the dimerization of p61BRAF(V600E) restored its sensitivity to vemurafenib. Finally, Poulikakos et al. (2011) identified BRAF(V600E) splicing variants lacking the RAS-binding domain in the tumors of 6 of 19 patients with acquired resistance to vemurafenib. Poulikakos et al. (2011) concluded that their data supported the model that inhibition of ERK signaling by RAF inhibitors is dependent on levels of RAS-GTP too low to support RAF dimerization and identified a novel mechanism of acquired resistance in patients: expression of splicing isoforms of BRAF(V600E) that dimerize in a RAS-independent manner.","Thakur et al. (2013) investigated the cause and consequences of vemurafenib resistance using 2 independently-derived primary human melanoma xenograft models in which drug resistance is selected by continuous vemurafenib administration. In one of these models, resistant tumors showed continued dependency on BRAF(V600E)-MEK-ERK signaling owing to elevated BRAF(V600E) expression. Thakur et al. (2013) showed that vemurafenib-resistant melanomas become drug-dependent for their continued proliferation, such that cessation of drug administration leads to regression of established drug-resistant tumors. Thakur et al. (2013) further demonstrated that a discontinuous dosing strategy, which exploits the fitness disadvantage displayed by drug-resistant cells in the absence of the drug, forestalls the onset of lethal drug-resistant disease. Thakur et al. (2013) concluded that their data highlighted the concept that drug-resistant cells may also display drug dependency, such that altered dosing may prevent the emergence of lethal drug resistance. These observations may contribute to sustaining the durability of vemurafenib response with the ultimate goal of curative therapy for the subset of melanoma patients with BRAF mutations.","Using metabolic profiling and functional perturbations, Kaplon et al. (2013) showed that the mitochondrial gatekeeper pyruvate dehydrogenase (PDH; 300502) is a crucial mediator of senescence induced by BRAF(V600E), an oncogene commonly mutated in melanoma and other cancers. BRAF(V600E)-induced senescence is accompanied by simultaneous suppression of the PDH-inhibitory enzyme pyruvate dehydrogenase kinase-1 (PDK1; 602524) and induction of the PDH-activating enzyme pyruvate dehydrogenase phosphatase-2 (PDP2; 615499). The resulting combined activation of PDH enhanced the use of pyruvate in the tricarboxylic acid cycle, causing increased respiration and redox stress. Abrogation of oncogene-induced senescence (OIS), a rate-limiting step towards oncogenic transformation, coincided with reversion of these processes. Further supporting a crucial role of PDH in OIS, enforced normalization of either PDK1 or PDP2 expression levels inhibited PDH and abrogated OIS, thereby licensing BRAF(V600E)-driven melanoma development. Finally, depletion of PDK1 eradicated melanoma subpopulations resistant to targeted BRAF inhibition, and caused regression of established melanomas.","Sun et al. (2014) showed that 6 out of 16 BRAF(V600E)-positive melanoma tumors analyzed acquired EGFR (131550) expression after the development of resistance to inhibitors of BRAF or MEK (176872). Using a chromatin regulator-focused short hairpin RNA (shRNA) library, Sun et al. (2014) found that suppression of SRY-box 10 (SOX10; 602229) in melanoma causes activation of TGF-beta (190180) signaling, thus leading to upregulation of EGFR and platelet-derived growth factor receptor-beta (PDGFRB; 173410), which confer resistance to BRAF and MEK inhibitors. Expression of EGFR in melanoma or treatment with TGF-beta results in a slow-growth phenotype with cells displaying hallmarks of oncogene-induced senescence. However, EGFR expression or exposure to TGF-beta becomes beneficial for proliferation in the presence of BRAF or MEK inhibitors. In a heterogeneous population of melanoma cells that have varying levels of SOX10 suppression, cells with low SOX10 and consequently high EGFR expression are rapidly enriched in the presence of drug treatment, but this is reversed when the treatment is discontinued. Sun et al. (2014) found evidence for SOX10 loss and/or activation of TGF-beta signaling in 4 of the 6 EGFR-positive drug-resistant melanoma patient samples. Sun et al. (2014) concluded that their findings provided a rationale for why some BRAF or MEK inhibitor-resistant melanoma patients may regain sensitivity to these drugs after a 'drug holiday' and identified patients with EGFR-positive melanoma as a group that may benefit from retreatment after a drug holiday.","Boussemart et al. (2014) demonstrated that the persistent formation of the eIF4F complex, comprising the eIF4E (133440) cap-binding protein, the eIF4G (600495) scaffolding protein, and the eIF4A (602641) RNA helicase, is associated with resistance to anti-BRAF (164757), anti-MEK, and anti-BRAF plus anti-MEK drug combinations in BRAF(V600)-mutant melanoma, colon, and thyroid cancer cell lines. Resistance to treatment and maintenance of eIF4F complex formation is associated with 1 of 3 mechanisms: reactivation of MAPK (see 176948) signaling; persistent ERK-independent phosphorylation of the inhibitory eIF4E-binding protein 4EBP1 (602223); or increased proapoptotic BMF (606266)-dependent degradation of eIF4G. The development of an in situ method to detect the eIF4E-eIF4G interactions showed that eIF4F complex formation is decreased in tumors that respond to anti-BRAF therapy and increased in resistant metastases compared to tumors before treatment. Strikingly, inhibiting the eIF4F complex, either by blocking the eIF4E-eIF4G interaction or by targeting eIF4A, synergized with inhibiting BRAF(V600) to kill the cancer cells. eIF4F appeared not only to be an indicator of both innate and acquired resistance, but also a therapeutic target. Boussemart et al. (2014) concluded that combinations of drugs targeting BRAF (and/or MEK) and eIF4F may overcome most of the resistance mechanisms in BRAF(V600)-mutant cancers.","Colorectal Carcinoma","Rajagopalan et al. (2002) identified the V600E mutation in 28 of 330 colorectal tumors (see 114500) screened for BRAF mutations. In all cases the mutation was heterozygous and occurred somatically.","Domingo et al. (2004) pointed out that the V600E hotspot mutation had been found in colorectal tumors that showed inherited mutation in a DNA mismatch repair (MMR) gene, such as MLH1 (120436) or MSH2 (609309). These mutations had been shown to occur almost exclusively in tumors located in the proximal colon and with hypermethylation of MLH1, the gene involved in the initial steps of development of these tumors; however, BRAF mutations were not detected in those cases with or presumed to have germline mutation in either MLH1 or MSH2. Domingo et al. (2004) studied mutation analysis of the BRAF hotspot as a possible low-cost effective strategy for genetic testing for hereditary nonpolyposis colorectal cancer (HNPCC; 120435). The V600E mutation was found in 82 (40%) of 206 sporadic tumors with high microsatellite instability (MSI-H) but in none of 111 tested HNPCC tumors or in 45 cases showing abnormal MSH2 immunostaining. Domingo et al. (2004) concluded that detection of the V600E mutation in a colorectal MSI-H tumor argues against the presence of germline mutation in either MLH1 or MSH2, and that screening of these MMR genes can be avoided in cases positive for V600E.","Lubomierski et al. (2005) analyzed 45 colorectal carcinomas with MSI and 37 colorectal tumors without MSI but with similar clinical characteristics and found that BRAF was mutated more often in tumors with MSI than without (27% vs 5%, p = 0.016). The most prevalent BRAF alteration, V600E, occurred only in tumors with MSI and was associated with more frequent MLH1 promoter methylation and loss of MLH1. The median age of patients with BRAF V600E was older than that of those without V600E (78 vs 49 years, p = 0.001). There were no BRAF alterations in patients with germline mutations of mismatch repair genes. Lubomierski et al. (2005) concluded that tumors with MSI caused by epigenetic MLH1 silencing have a mutational background distinct from that of tumors with genetic loss of mismatch repair, and suggested that there are 2 genetically distinct entities of microsatellite unstable tumors.","Tol et al. (2009) detected a somatic V600E mutation in 45 (8.7%) of 519 metastatic colorectal tumors. Patients with BRAF-mutated tumors had significantly shorter median progression-free and median overall survival compared to patients with wildtype BRAF tumors, regardless of the use of cetuximab. Tol et al. (2009) suggested that the BRAF mutation may be a negative prognostic factor in these patients.","Inhibition of the BRAF(V600E) oncoprotein by the small-molecule drug PLX4032 (vemurafenib) is highly effective in the treatment of melanoma. However, colon cancer patients harboring the same BRAF(V600E) oncogenic lesion have poor prognosis and show only a very limited response to this drug. To investigate the cause of this limited therapeutic effect in BRAF(V600E) mutant colon cancer, Prahallad et al. (2012) performed an RNA interference-based genetic screen in human cells to search for kinases whose knockdown synergizes with BRAF(V600E) inhibition. They reported that blockade of the epidermal growth factor receptor (EGFR; 131550) shows strong synergy with BRAF(V600E) inhibition. Prahallad et al. (2012) found in multiple BRAF(V600E) mutant colon cancers that inhibition of EGFR by the antibody drug cetuximab or the small-molecule drugs gefitinib or erlotinib is strongly synergistic with BRAF(V600E) inhibition, both in vitro and in vivo. Mechanistically, Prahallad et al. (2012) found that BRAF(V600E) inhibition causes a rapid feedback activation of EGFR, which supports continued proliferation in the presence of BRAF(V600E) inhibition. Melanoma cells express low levels of EGFR and are therefore not subject to this feedback activation. Consistent with this, Prahallad et al. (2012) found that ectopic expression of EGFR in melanoma cells is sufficient to cause resistance to PLX4032. Prahallad et al. (2012) concluded that BRAF(V600E) mutant colon cancers (approximately 8 to 10% of all colon cancers) might benefit from combination therapy consisting of BRAF and EGFR inhibitors.","Gala et al. (2014) identified the BRAF V600E mutation in 18 of 19 sessile serrated adenomas from 19 unrelated patients with sessile serrated polyposis cancer syndrome (SSPCS; 617108).","Papillary Thyroid Carcinoma","Kimura et al. (2003) identified the V600E mutation in 28 (35.8%) of 78 papillary thyroid cancers (PTC; see 188550); it was not found in any of the other types of differentiated follicular neoplasms arising from the same cell type (0 of 46). RET (see 164761)/PTC mutations and RAS (see 190020) mutations were each identified in 16.4% of PTCs, but there was no overlap in the 3 mutations. Kimura et al. (2003) concluded that thyroid cell transformation to papillary cancer takes place through constitutive activation of effectors along the RET/PTC-RAS-BRAF signaling pathway.","Xing et al. (2004) studied various thyroid tumor types for the most common BRAF mutation, 1799T-A, by DNA sequencing. They found a high and similar frequency (45%) of the 1799T-A mutation in 2 geographically distinct papillary thyroid cancer patient populations, 1 composed of sporadic cases from North America, and the other from Kiev, Ukraine, that included individuals who were exposed to the Chernobyl nuclear accident. In contrast, Xing et al. (2004) found BRAF mutations in only 20% of anaplastic thyroid cancers and in no medullary thyroid cancers or benign thyroid hyperplasia. They also confirmed previous reports that the BRAF 1799T-A mutation did not occur in benign thyroid adenomas or follicular thyroid cancers. They concluded that frequent occurrence of BRAF mutation is associated with PTC, irrespective of geographic origin, and is apparently not a radiation-susceptible mutation.","Nikiforova et al. (2003) analyzed 320 thyroid tumors and 6 anaplastic carcinoma cell lines and detected BRAF mutations in 45 papillary carcinomas (38%), 2 poorly differentiated carcinomas (13%), 3 (10%) anaplastic carcinomas (10%), and 5 thyroid anaplastic carcinoma cell lines (83%) but not in follicular, Hurthle cell, and medullary carcinomas, follicular and Hurthle cell adenomas, or benign hyperplastic nodules. All mutations involved a T-to-A transversion at nucleotide 1799. All BRAF-positive poorly differentiated and anaplastic carcinomas contained areas of preexisting papillary carcinoma, and mutation was present in both the well differentiated and dedifferentiated components. The authors concluded that BRAF mutations are restricted to papillary carcinomas and poorly differentiated and anaplastic carcinomas arising from papillary carcinomas, and that they are associated with distinct phenotypic and biologic properties of papillary carcinomas and may participate in progression to poorly differentiated and anaplastic carcinomas.","Hypothesizing that childhood thyroid carcinomas may be associated with a different prevalence of the BRAF 1799T-A mutation compared with adult cases, Kumagai et al. (2004) examined 31 cases of Japanese childhood thyroid carcinoma and an additional 48 cases of PTC from Ukraine, all of whom were less than 17 years of age at the time of the Chernobyl accident. The BRAF 1799T-A mutation was found in only 1 of 31 Japanese cases (3.4%) and in none of the 15 Ukrainian cases operated on before the age of 15 years, although it was found in 8 of 33 Ukrainian young adult cases (24.2%). Kumagai et al. (2004) concluded that the BRAF 1799T-A mutation is uncommon in childhood thyroid carcinomas.","Puxeddu et al. (2004) found the V600E substitution in 24 of 60 PTCs (40%) but in none of 6 follicular adenomas, 5 follicular carcinomas, or 1 anaplastic carcinoma. Nine of the 60 PTCs (15%) presented expression of a RET/PTC rearrangement. A genetico-clinical association analysis showed a statistically significant correlation between BRAF mutation and development of PTCs of the classic papillary histotype (P = 0.038). No link could be detected between expression of BRAF V600E and age at diagnosis, gender, dimension, local invasiveness of the primary cancer, presence of lymph node metastases, tumor stage, or multifocality of the disease. The authors concluded that these data clearly confirmed that BRAF V600E was the most common genetic alteration found to that time in adult sporadic PTCs, that it is unique for this thyroid cancer histotype, and that it might drive the development of PTCs of the classic papillary subtype.","Xing et al. (2004) demonstrated detection of the 1799T-A mutation on thyroid cytologic specimens from fine needle aspiration biopsy (FNAB). Prospective analysis showed that 50% of the nodules that proved to be PTCs on surgical histopathology were correctly diagnosed by BRAF mutation analysis on FNAB specimens; there were no false positive findings.","Xing et al. (2005) studied the relationships between the BRAF V600E mutation and clinicopathologic outcomes, including recurrence, in 219 PTC patients. The authors concluded that in patients with PTC, BRAF mutation is associated with poorer clinicopathologic outcomes and independently predicts recurrence. Therefore, BRAF mutation may be a useful molecular marker to assist in risk stratification for patients with PTC.","In a series of 52 classic PTCs, Porra et al. (2005) found that low SLC5A8 (608044) expression was highly significantly associated with the presence of the BRAF 1799T-A mutation. SLC5A8 expression was selectively downregulated (40-fold) in PTCs of classical form; methylation-specific PCR analyses showed that SLC5A8 was methylated in 90% of classic PTCs and in about 20% of other PTCs. Porra et al. (2005) concluded that their data identified a relationship between the methylation-associated silencing of the tumor-suppressor gene SLC5A8 and the 1799T-A point mutation of the BRAF gene in the classic PTC subtype of thyroid carcinomas.","Vasko et al. (2005) studied the relationship between the BRAF 1799T-A mutation and lymph node metastasis of PTC by examining the mutation in both the primary tumors and their paired lymph node metastases. Their findings indicated that the high prevalence of BRAF mutation in lymph node-metastasized PTC tissues from BRAF mutation-positive primary tumors and the possible de novo formation of BRAF mutation in lymph node-metastasized PTC were consistent with a role of BRAF mutation in facilitating the metastasis and progression of PTC in lymph nodes.","In a patient with congenital hypothyroidism and long-standing goiter due to mutation in the thyroglobulin gene (see TG, 188540; and TDH3, 274700), who was also found to have multifocal follicular carcinoma of the thyroid, Hishinuma et al. (2005) identified somatic heterozygosity for the V600E mutation in the BRAF gene in the cancerous thyroid tissue.","Liu et al. (2007) used BRAF siRNA to transfect stably several BRAF mutation-harboring PTC cell lines, isolated clones with stable suppression of BRAF, and assessed their ability to proliferate, transform, and grow xenograft tumors in nude mice. They found that the V600E mutation not only initiates PTC but also maintains the proliferation, transformation, and tumorigenicity of PTC cells harboring the BRAF mutation, and that the growth of tumors derived from such cells continues to depend on the V600E mutation.","Jo et al. (2006) found that of 161 PTC patients, 102 (63.4%) had the BRAF V600E mutation and that these patients had significantly larger tumor sizes and significantly higher expression of vascular endothelial growth factor (VEGF; 192240) compared to patients without this mutation. The level of VEGF expression was closely correlated with tumor size, extrathyroidal invasion, and stage. Jo et al. (2006) concluded that the relatively high levels of VEGF expression may be related to poorer clinical outcomes and recurrences in BRAF V600E(+) PTC.","Durante et al. (2007) found that the BRAF V600E mutation in PTCs is associated with reduced expression of key genes involved in iodine metabolism. They noted that this effect may alter the effectiveness of diagnostic and/or therapeutic use of radioiodine in BRAF-mutation PTCs.","Lupi et al. (2007) found a BRAF mutation in 219 of 500 cases (43.8%) of PTC. The most common BRAF mutation, V600E, was found in 214 cases (42.8%). BRAF V600E was associated with extrathyroidal invasion (p less than 0.0001), multicentricity (p = 0.0026), presence of nodal metastases (p = 0.0009), class III versus classes I and II (p less than 0.00000006), and absence of tumor capsule (p less than 0.0001), in particular, in follicular- and micro-PTC variants. By multivariate analysis, the absence of tumor capsule remained the only parameter associated (p = 0.0005) with the BRAF V600E mutation. The authors concluded that the BRAF V600E mutation is associated with high-risk PTC and, in particular, in follicular variant with invasive tumor growth.","Flaherty et al. (2010) reported complete or partial regression of V600E-associated papillary thyroid cancer in 3 patients treated with an inhibitor (PLX4032) specific to the V600E mutation.","Nonseminomatous Germ Cell Tumors","In 3 (9%) of 32 nonseminomatous germ cell tumors (see 273300) with a mixture of embryonal carcinoma, yolk sac tumor, choriocarcinoma, and mature teratoma, Sommerer et al. (2005) identified the activating 1796T-A mutation in the BRAF gene; the mutation was present within the embryonic carcinoma component.","Astrocytoma","Pfister et al. (2008) identified a somatic V600E mutation in 4 (6%) of 66 pediatric low-grade astrocytomas (see 137800). Thirty (45%) of the 66 tumors had a copy number gain spanning the BRAF locus, indicating a novel mechanism of MAPK (176948) pathway activation in these tumors.","Role in Neurodegeneration","Mass et al. (2017) hypothesized that a somatic BRAF(V600E) mutation in the erythromyeloid lineage may cause neurodegeneration. Mass et al. (2017) showed that mosaic expression of BRAF(V600E) in mouse erythromyeloid progenitors results in clonal expansion of tissue-resident macrophages and a severe late-onset neurodegenerative disorder. This is associated with accumulation of ERK-activated amoeboid microglia in mice, and is also observed in human patients with histiocytoses. In the mouse model, neurobehavioral signs, astrogliosis, deposition of amyloid precursor protein, synaptic loss, and neuronal death were driven by ERK-activated microglia and were preventable by BRAF inhibition. Mass et al. (2017) suggested that the results identified the fetal precursors of tissue-resident macrophages as a potential cell of origin for histiocytoses and demonstrated that a somatic mutation in the erythromyeloid progenitor lineage in mice can drive late-onset neurodegeneration.","Variant Function","Brady et al. (2014) showed that decreasing the levels of CTR1 (603085), or mutations in MEK1 (176872) that disrupt copper binding, decreased BRAF(V600E)-driven signaling and tumorigenesis in mice and human cell settings. Conversely, a MEK1-MEK5 (602520) chimera that phosphorylated ERK1/2 independently of copper or an active ERK2 restored the tumor growth of murine cells lacking Ctr1. Copper chelators used in the treatment of Wilson disease (277900) decreased tumor growth of human or murine cells that were either transformed by BRAF(V600E) or engineered to be resistant to BRAF inhibition. Brady et al. (2014) concluded that copper chelation therapy could be repurposed to treat cancers containing the BRAF(V600E) mutation.","Rapino et al. (2018) showed in humans that the enzymes that catalyze modifications of wobble uridine-34 (U34) tRNA are key players of the protein synthesis rewiring that is induced by the transformation driven by the BRAF V600E oncogene and by resistance to targeted therapy in melanoma. Rapino et al. (2018) showed that BRAF V600E-expressing melanoma cells are dependent on U34 enzymes for survival, and that concurrent inhibition of MAPK signaling and ELP3 (612722) or CTU1 (612694) and/or CTU2 (617057) synergizes to kill melanoma cells. Activation of the PI3K signaling pathway, one of the most common mechanisms of acquired resistance to MAPK therapeutic agents, markedly increases the expression of U34 enzymes. Mechanistically, U34 enzymes promote glycolysis in melanoma cells through the direct, codon-dependent, regulation of the translation of HIF1A (603348) mRNA and the maintenance of high levels of HIF1-alpha protein. Therefore, the acquired resistance to anti-BRAF therapy is associated with high levels of U34 enzymes and HIF1-alpha. Rapino et al. (2018) concluded that U34 enzymes promote the survival and resistance to therapy of melanoma cells by regulating specific mRNA translation."],"submitter_name":"OMIM","review_date":20140904,"origin":"somatic","method":"literature only","submitter_date":20220317,"diseases":[{"normalized_cancer":["COLORECTAL CANCER, SOMATIC"],"normalized_disease":["Colorectal Cancer"],"names":["Colorectal Cancer"]}],"review_description":"Pathogenic","date_updated":20220328,"clinical_significance":["Pathogenic"],"review_status":"no assertion criteria provided","accession_id":"SCV000035248"}],"variation_id":13961,"submission_description":["The val600-to-glu (V600E) mutation caused by a 1799T-A transversion in the BRAF gene was previously designated VAL599GLU (1796T-A). Kumar et al. (2003) noted that an earlier version of the BRAF sequence showed a discrepancy of 3 nucleotides in exon 1; based on the corrected sequence, they proposed a change in nucleotide numbering after nucleotide 94 (the ATG codon) by +3 and a corresponding codon change of +1.","Malignant Melanoma","Davies et al. (2002) identified a 1799T-A transversion in exon 15 of the BRAF gene that leads to a val600-to-glu (V600E) substitution. This mutation accounted for 92% of BRAF mutations in malignant melanoma (see 155600). The V600E mutation is an activating mutation resulting in constitutive activation of BRAF and downstream signal transduction in the MAP kinase pathway.","To evaluate the timing of mutations in BRAF during melanocyte neoplasia, Pollock et al. (2003) carried out mutation analysis on microdissected melanoma and nevi samples. They observed mutations resulting in the V600E amino acid substitution in 41 (68%) of 60 melanoma metastases, 4 (80%) of 5 primary melanomas, and, unexpectedly, in 63 (82%) of 77 nevi. The data suggested that mutational activation of the RAS/RAF/MAPK pathway in nevi is a critical step in the initiation of melanocytic neoplasia but alone is insufficient for melanoma tumorigenesis.","Lang et al. (2003) failed to find the V600E mutation as a germline mutation in 42 cases of familial melanoma studied. Their collection of families included 15 with and 24 without detected mutations in CDKN2A (600160). They did, however, find the V600E mutation in 6 (27%) of 22 samples of secondary (metastatic) melanomas studied. Meyer et al. (2003) found no V600E mutation in 172 melanoma patients comprising 46 familial cases, 21 multiple melanoma patients, and 106 cases with at least 1 first-degree relative suffering from other cancers. They concluded, therefore, that the common somatic BRAF mutation V600E does not contribute to polygenic or familial melanoma predisposition.","Kim et al. (2003) stated that V600E, the most common of BRAF mutations, had not been identified in tumors with mutations of the KRAS gene (190070). This mutually exclusive relationship supports the hypothesis that BRAF (V600E) and KRAS mutations exert equivalent effects in tumorigenesis (Rajagopalan et al., 2002; Singer et al., 2003).","Flaherty et al. (2010) reported complete or partial regression of V600E-associated metastatic melanoma in 81% of patients treated with an inhibitor (PLX4032) specific to the V600E mutation. Among 16 patients in a dose-escalation cohort, 10 had a partial response, and 1 had a complete response. Among 32 patients in an extension cohort, 24 had a partial response, and 2 had a complete response. The estimated median progression-free survival among all patients was more than 7 months. Responses were observed at all sites of disease, including bone, liver, and small bowel. Tumor biopsy specimens from 7 patients showed markedly reduced levels of phosphorylated ERK (600997), cyclin D1 (168461), and Ki67 (MKI67; 176741) at day 15 compared to baseline, indicating inhibition of the MAP kinase pathway. Three additional patients with V600E-associated papillary thyroid also showed a partial or complete response.","Bollag et al. (2010) described the structure-guided discovery of PLX4032 (RG7204), a potent inhibitor of oncogenic BRAF kinase activity. PLX4032 was cocrystallized with a protein construct that contained the kinase domain of BRAF(V600E). In a clinical trial, patients exposed to higher plasma levels of PLX4032 experienced tumor regression; in patients with tumor regressions, pathway analysis typically showed greater than 80% inhibition of cytoplasmic ERK phosphorylation. Bollag et al. (2010) concluded that their data demonstrated that BRAF-mutant melanomas are highly dependent on BRAF kinase activity.","Patients with BRAF(V600E)-positive melanomas exhibit an initial antitumor response to the RAF kinase inhibitor PLX4032, but acquired drug resistance almost invariably develops. Johannessen et al. (2010) identified MAP3K8 (191195), encoding COT (cancer Osaka thyroid oncogene) as a MAPK pathway agonist that drives resistance to RAF inhibition in BRAF(V600E) cell lines. COT activates ERK primarily through MARK/ERK (MEK)-dependent mechanisms that do not require RAF signaling. Moreover, COT expression is associated with de novo resistance in BRAF(V600E) cultured cell lines and acquired resistance in melanoma cells and tissue obtained from relapsing patients following treatment with MEK or RAF inhibitors. Johannessen et al. (2010) further identified combinatorial MAPK pathway inhibition or targeting of COT kinase activity as possible therapeutic strategies for reducing MAPK pathway activation in this setting.","Nazarian et al. (2010) showed that acquired resistance to PLX4032, a novel class I RAF-selective inhibitor, develops by mutually exclusive PDGFRB (173410) upregulation or NRAS (164790) mutations but not through secondary mutations in BRAF(V600E). Nazarian et al. (2010) used PLX4032-resistant sublines artificially derived from BRAF (V600E)-positive melanoma cell lines and validated key findings in PLX4032-resistant tumors and tumor-matched, short-term cultures from clinical trial patients. Induction of PDGFRB RNA, protein and tyrosine phosphorylation emerged as a dominant feature of acquired PLX4032 resistance in a subset of melanoma sublines, patient-derived biopsies, and short-term cultures. PDGFRB upregulated tumor cells have low activated RAS levels and, when treated with PLX4032, do not reactivate the MAPK pathway significantly. In another subset, high levels of activated N-RAS resulting from mutations lead to significant MAPK pathway reactivation upon PLX4032 treatment. Knockdown of PDGFRB or NRAS reduced growth of the respective PLX4032-resistant subsets. Overexpression of PDGFRB or NRAS(Q61K) conferred PLX4032 resistance to PLX4032-sensitive parental cell lines. Importantly, Nazarian et al. (2010) showed that MAPK reactivation predicts MEK inhibitor sensitivity. Thus, Nazarian et al. (2010) concluded that melanomas escape BRAF(V600E) targeting not through secondary BRAF(V600E) mutations but via receptor tyrosine kinase (RTK)-mediated activation of alternative survival pathway(s) or activated RAS-mediated reactivation of the MAPK pathway, suggesting additional therapeutic strategies.","Poulikakos et al. (2011) identified a novel resistance mechanism for melanomas with BRAF(V600E) treated with RAF inhibitors. The authors found that a subset of cells resistant to vemurafenib (PLX4032, RG7204) express a 61-kD variant form of BRAF(V600E), p61BRAF(V600E), that lacks exons 4 through 8, a region that encompasses the RAS-binding domain. p61BRAF(V600E) showed enhanced dimerization in cells with low levels of RAS activation, as compared to full-length BRAF(V600E). In cells in which p61BRAF(V600E) was expressed endogenously or ectopically, ERK signaling was resistant to the RAF inhibitor. Moreover, a mutation that abolished the dimerization of p61BRAF(V600E) restored its sensitivity to vemurafenib. Finally, Poulikakos et al. (2011) identified BRAF(V600E) splicing variants lacking the RAS-binding domain in the tumors of 6 of 19 patients with acquired resistance to vemurafenib. Poulikakos et al. (2011) concluded that their data supported the model that inhibition of ERK signaling by RAF inhibitors is dependent on levels of RAS-GTP too low to support RAF dimerization and identified a novel mechanism of acquired resistance in patients: expression of splicing isoforms of BRAF(V600E) that dimerize in a RAS-independent manner.","Thakur et al. (2013) investigated the cause and consequences of vemurafenib resistance using 2 independently-derived primary human melanoma xenograft models in which drug resistance is selected by continuous vemurafenib administration. In one of these models, resistant tumors showed continued dependency on BRAF(V600E)-MEK-ERK signaling owing to elevated BRAF(V600E) expression. Thakur et al. (2013) showed that vemurafenib-resistant melanomas become drug-dependent for their continued proliferation, such that cessation of drug administration leads to regression of established drug-resistant tumors. Thakur et al. (2013) further demonstrated that a discontinuous dosing strategy, which exploits the fitness disadvantage displayed by drug-resistant cells in the absence of the drug, forestalls the onset of lethal drug-resistant disease. Thakur et al. (2013) concluded that their data highlighted the concept that drug-resistant cells may also display drug dependency, such that altered dosing may prevent the emergence of lethal drug resistance. These observations may contribute to sustaining the durability of vemurafenib response with the ultimate goal of curative therapy for the subset of melanoma patients with BRAF mutations.","Using metabolic profiling and functional perturbations, Kaplon et al. (2013) showed that the mitochondrial gatekeeper pyruvate dehydrogenase (PDH; 300502) is a crucial mediator of senescence induced by BRAF(V600E), an oncogene commonly mutated in melanoma and other cancers. BRAF(V600E)-induced senescence is accompanied by simultaneous suppression of the PDH-inhibitory enzyme pyruvate dehydrogenase kinase-1 (PDK1; 602524) and induction of the PDH-activating enzyme pyruvate dehydrogenase phosphatase-2 (PDP2; 615499). The resulting combined activation of PDH enhanced the use of pyruvate in the tricarboxylic acid cycle, causing increased respiration and redox stress. Abrogation of oncogene-induced senescence (OIS), a rate-limiting step towards oncogenic transformation, coincided with reversion of these processes. Further supporting a crucial role of PDH in OIS, enforced normalization of either PDK1 or PDP2 expression levels inhibited PDH and abrogated OIS, thereby licensing BRAF(V600E)-driven melanoma development. Finally, depletion of PDK1 eradicated melanoma subpopulations resistant to targeted BRAF inhibition, and caused regression of established melanomas.","Sun et al. (2014) showed that 6 out of 16 BRAF(V600E)-positive melanoma tumors analyzed acquired EGFR (131550) expression after the development of resistance to inhibitors of BRAF or MEK (176872). Using a chromatin regulator-focused short hairpin RNA (shRNA) library, Sun et al. (2014) found that suppression of SRY-box 10 (SOX10; 602229) in melanoma causes activation of TGF-beta (190180) signaling, thus leading to upregulation of EGFR and platelet-derived growth factor receptor-beta (PDGFRB; 173410), which confer resistance to BRAF and MEK inhibitors. Expression of EGFR in melanoma or treatment with TGF-beta results in a slow-growth phenotype with cells displaying hallmarks of oncogene-induced senescence. However, EGFR expression or exposure to TGF-beta becomes beneficial for proliferation in the presence of BRAF or MEK inhibitors. In a heterogeneous population of melanoma cells that have varying levels of SOX10 suppression, cells with low SOX10 and consequently high EGFR expression are rapidly enriched in the presence of drug treatment, but this is reversed when the treatment is discontinued. Sun et al. (2014) found evidence for SOX10 loss and/or activation of TGF-beta signaling in 4 of the 6 EGFR-positive drug-resistant melanoma patient samples. Sun et al. (2014) concluded that their findings provided a rationale for why some BRAF or MEK inhibitor-resistant melanoma patients may regain sensitivity to these drugs after a 'drug holiday' and identified patients with EGFR-positive melanoma as a group that may benefit from retreatment after a drug holiday.","Boussemart et al. (2014) demonstrated that the persistent formation of the eIF4F complex, comprising the eIF4E (133440) cap-binding protein, the eIF4G (600495) scaffolding protein, and the eIF4A (602641) RNA helicase, is associated with resistance to anti-BRAF (164757), anti-MEK, and anti-BRAF plus anti-MEK drug combinations in BRAF(V600)-mutant melanoma, colon, and thyroid cancer cell lines. Resistance to treatment and maintenance of eIF4F complex formation is associated with 1 of 3 mechanisms: reactivation of MAPK (see 176948) signaling; persistent ERK-independent phosphorylation of the inhibitory eIF4E-binding protein 4EBP1 (602223); or increased proapoptotic BMF (606266)-dependent degradation of eIF4G. The development of an in situ method to detect the eIF4E-eIF4G interactions showed that eIF4F complex formation is decreased in tumors that respond to anti-BRAF therapy and increased in resistant metastases compared to tumors before treatment. Strikingly, inhibiting the eIF4F complex, either by blocking the eIF4E-eIF4G interaction or by targeting eIF4A, synergized with inhibiting BRAF(V600) to kill the cancer cells. eIF4F appeared not only to be an indicator of both innate and acquired resistance, but also a therapeutic target. Boussemart et al. (2014) concluded that combinations of drugs targeting BRAF (and/or MEK) and eIF4F may overcome most of the resistance mechanisms in BRAF(V600)-mutant cancers.","Colorectal Carcinoma","Rajagopalan et al. (2002) identified the V600E mutation in 28 of 330 colorectal tumors (see 114500) screened for BRAF mutations. In all cases the mutation was heterozygous and occurred somatically.","Domingo et al. (2004) pointed out that the V600E hotspot mutation had been found in colorectal tumors that showed inherited mutation in a DNA mismatch repair (MMR) gene, such as MLH1 (120436) or MSH2 (609309). These mutations had been shown to occur almost exclusively in tumors located in the proximal colon and with hypermethylation of MLH1, the gene involved in the initial steps of development of these tumors; however, BRAF mutations were not detected in those cases with or presumed to have germline mutation in either MLH1 or MSH2. Domingo et al. (2004) studied mutation analysis of the BRAF hotspot as a possible low-cost effective strategy for genetic testing for hereditary nonpolyposis colorectal cancer (HNPCC; 120435). The V600E mutation was found in 82 (40%) of 206 sporadic tumors with high microsatellite instability (MSI-H) but in none of 111 tested HNPCC tumors or in 45 cases showing abnormal MSH2 immunostaining. Domingo et al. (2004) concluded that detection of the V600E mutation in a colorectal MSI-H tumor argues against the presence of germline mutation in either MLH1 or MSH2, and that screening of these MMR genes can be avoided in cases positive for V600E.","Lubomierski et al. (2005) analyzed 45 colorectal carcinomas with MSI and 37 colorectal tumors without MSI but with similar clinical characteristics and found that BRAF was mutated more often in tumors with MSI than without (27% vs 5%, p = 0.016). The most prevalent BRAF alteration, V600E, occurred only in tumors with MSI and was associated with more frequent MLH1 promoter methylation and loss of MLH1. The median age of patients with BRAF V600E was older than that of those without V600E (78 vs 49 years, p = 0.001). There were no BRAF alterations in patients with germline mutations of mismatch repair genes. Lubomierski et al. (2005) concluded that tumors with MSI caused by epigenetic MLH1 silencing have a mutational background distinct from that of tumors with genetic loss of mismatch repair, and suggested that there are 2 genetically distinct entities of microsatellite unstable tumors.","Tol et al. (2009) detected a somatic V600E mutation in 45 (8.7%) of 519 metastatic colorectal tumors. Patients with BRAF-mutated tumors had significantly shorter median progression-free and median overall survival compared to patients with wildtype BRAF tumors, regardless of the use of cetuximab. Tol et al. (2009) suggested that the BRAF mutation may be a negative prognostic factor in these patients.","Inhibition of the BRAF(V600E) oncoprotein by the small-molecule drug PLX4032 (vemurafenib) is highly effective in the treatment of melanoma. However, colon cancer patients harboring the same BRAF(V600E) oncogenic lesion have poor prognosis and show only a very limited response to this drug. To investigate the cause of this limited therapeutic effect in BRAF(V600E) mutant colon cancer, Prahallad et al. (2012) performed an RNA interference-based genetic screen in human cells to search for kinases whose knockdown synergizes with BRAF(V600E) inhibition. They reported that blockade of the epidermal growth factor receptor (EGFR; 131550) shows strong synergy with BRAF(V600E) inhibition. Prahallad et al. (2012) found in multiple BRAF(V600E) mutant colon cancers that inhibition of EGFR by the antibody drug cetuximab or the small-molecule drugs gefitinib or erlotinib is strongly synergistic with BRAF(V600E) inhibition, both in vitro and in vivo. Mechanistically, Prahallad et al. (2012) found that BRAF(V600E) inhibition causes a rapid feedback activation of EGFR, which supports continued proliferation in the presence of BRAF(V600E) inhibition. Melanoma cells express low levels of EGFR and are therefore not subject to this feedback activation. Consistent with this, Prahallad et al. (2012) found that ectopic expression of EGFR in melanoma cells is sufficient to cause resistance to PLX4032. Prahallad et al. (2012) concluded that BRAF(V600E) mutant colon cancers (approximately 8 to 10% of all colon cancers) might benefit from combination therapy consisting of BRAF and EGFR inhibitors.","Gala et al. (2014) identified the BRAF V600E mutation in 18 of 19 sessile serrated adenomas from 19 unrelated patients with sessile serrated polyposis cancer syndrome (SSPCS; 617108).","Papillary Thyroid Carcinoma","Kimura et al. (2003) identified the V600E mutation in 28 (35.8%) of 78 papillary thyroid cancers (PTC; see 188550); it was not found in any of the other types of differentiated follicular neoplasms arising from the same cell type (0 of 46). RET (see 164761)/PTC mutations and RAS (see 190020) mutations were each identified in 16.4% of PTCs, but there was no overlap in the 3 mutations. Kimura et al. (2003) concluded that thyroid cell transformation to papillary cancer takes place through constitutive activation of effectors along the RET/PTC-RAS-BRAF signaling pathway.","Xing et al. (2004) studied various thyroid tumor types for the most common BRAF mutation, 1799T-A, by DNA sequencing. They found a high and similar frequency (45%) of the 1799T-A mutation in 2 geographically distinct papillary thyroid cancer patient populations, 1 composed of sporadic cases from North America, and the other from Kiev, Ukraine, that included individuals who were exposed to the Chernobyl nuclear accident. In contrast, Xing et al. (2004) found BRAF mutations in only 20% of anaplastic thyroid cancers and in no medullary thyroid cancers or benign thyroid hyperplasia. They also confirmed previous reports that the BRAF 1799T-A mutation did not occur in benign thyroid adenomas or follicular thyroid cancers. They concluded that frequent occurrence of BRAF mutation is associated with PTC, irrespective of geographic origin, and is apparently not a radiation-susceptible mutation.","Nikiforova et al. (2003) analyzed 320 thyroid tumors and 6 anaplastic carcinoma cell lines and detected BRAF mutations in 45 papillary carcinomas (38%), 2 poorly differentiated carcinomas (13%), 3 (10%) anaplastic carcinomas (10%), and 5 thyroid anaplastic carcinoma cell lines (83%) but not in follicular, Hurthle cell, and medullary carcinomas, follicular and Hurthle cell adenomas, or benign hyperplastic nodules. All mutations involved a T-to-A transversion at nucleotide 1799. All BRAF-positive poorly differentiated and anaplastic carcinomas contained areas of preexisting papillary carcinoma, and mutation was present in both the well differentiated and dedifferentiated components. The authors concluded that BRAF mutations are restricted to papillary carcinomas and poorly differentiated and anaplastic carcinomas arising from papillary carcinomas, and that they are associated with distinct phenotypic and biologic properties of papillary carcinomas and may participate in progression to poorly differentiated and anaplastic carcinomas.","Hypothesizing that childhood thyroid carcinomas may be associated with a different prevalence of the BRAF 1799T-A mutation compared with adult cases, Kumagai et al. (2004) examined 31 cases of Japanese childhood thyroid carcinoma and an additional 48 cases of PTC from Ukraine, all of whom were less than 17 years of age at the time of the Chernobyl accident. The BRAF 1799T-A mutation was found in only 1 of 31 Japanese cases (3.4%) and in none of the 15 Ukrainian cases operated on before the age of 15 years, although it was found in 8 of 33 Ukrainian young adult cases (24.2%). Kumagai et al. (2004) concluded that the BRAF 1799T-A mutation is uncommon in childhood thyroid carcinomas.","Puxeddu et al. (2004) found the V600E substitution in 24 of 60 PTCs (40%) but in none of 6 follicular adenomas, 5 follicular carcinomas, or 1 anaplastic carcinoma. Nine of the 60 PTCs (15%) presented expression of a RET/PTC rearrangement. A genetico-clinical association analysis showed a statistically significant correlation between BRAF mutation and development of PTCs of the classic papillary histotype (P = 0.038). No link could be detected between expression of BRAF V600E and age at diagnosis, gender, dimension, local invasiveness of the primary cancer, presence of lymph node metastases, tumor stage, or multifocality of the disease. The authors concluded that these data clearly confirmed that BRAF V600E was the most common genetic alteration found to that time in adult sporadic PTCs, that it is unique for this thyroid cancer histotype, and that it might drive the development of PTCs of the classic papillary subtype.","Xing et al. (2004) demonstrated detection of the 1799T-A mutation on thyroid cytologic specimens from fine needle aspiration biopsy (FNAB). Prospective analysis showed that 50% of the nodules that proved to be PTCs on surgical histopathology were correctly diagnosed by BRAF mutation analysis on FNAB specimens; there were no false positive findings.","Xing et al. (2005) studied the relationships between the BRAF V600E mutation and clinicopathologic outcomes, including recurrence, in 219 PTC patients. The authors concluded that in patients with PTC, BRAF mutation is associated with poorer clinicopathologic outcomes and independently predicts recurrence. Therefore, BRAF mutation may be a useful molecular marker to assist in risk stratification for patients with PTC.","In a series of 52 classic PTCs, Porra et al. (2005) found that low SLC5A8 (608044) expression was highly significantly associated with the presence of the BRAF 1799T-A mutation. SLC5A8 expression was selectively downregulated (40-fold) in PTCs of classical form; methylation-specific PCR analyses showed that SLC5A8 was methylated in 90% of classic PTCs and in about 20% of other PTCs. Porra et al. (2005) concluded that their data identified a relationship between the methylation-associated silencing of the tumor-suppressor gene SLC5A8 and the 1799T-A point mutation of the BRAF gene in the classic PTC subtype of thyroid carcinomas.","Vasko et al. (2005) studied the relationship between the BRAF 1799T-A mutation and lymph node metastasis of PTC by examining the mutation in both the primary tumors and their paired lymph node metastases. Their findings indicated that the high prevalence of BRAF mutation in lymph node-metastasized PTC tissues from BRAF mutation-positive primary tumors and the possible de novo formation of BRAF mutation in lymph node-metastasized PTC were consistent with a role of BRAF mutation in facilitating the metastasis and progression of PTC in lymph nodes.","In a patient with congenital hypothyroidism and long-standing goiter due to mutation in the thyroglobulin gene (see TG, 188540; and TDH3, 274700), who was also found to have multifocal follicular carcinoma of the thyroid, Hishinuma et al. (2005) identified somatic heterozygosity for the V600E mutation in the BRAF gene in the cancerous thyroid tissue.","Liu et al. (2007) used BRAF siRNA to transfect stably several BRAF mutation-harboring PTC cell lines, isolated clones with stable suppression of BRAF, and assessed their ability to proliferate, transform, and grow xenograft tumors in nude mice. They found that the V600E mutation not only initiates PTC but also maintains the proliferation, transformation, and tumorigenicity of PTC cells harboring the BRAF mutation, and that the growth of tumors derived from such cells continues to depend on the V600E mutation.","Jo et al. (2006) found that of 161 PTC patients, 102 (63.4%) had the BRAF V600E mutation and that these patients had significantly larger tumor sizes and significantly higher expression of vascular endothelial growth factor (VEGF; 192240) compared to patients without this mutation. The level of VEGF expression was closely correlated with tumor size, extrathyroidal invasion, and stage. Jo et al. (2006) concluded that the relatively high levels of VEGF expression may be related to poorer clinical outcomes and recurrences in BRAF V600E(+) PTC.","Durante et al. (2007) found that the BRAF V600E mutation in PTCs is associated with reduced expression of key genes involved in iodine metabolism. They noted that this effect may alter the effectiveness of diagnostic and/or therapeutic use of radioiodine in BRAF-mutation PTCs.","Lupi et al. (2007) found a BRAF mutation in 219 of 500 cases (43.8%) of PTC. The most common BRAF mutation, V600E, was found in 214 cases (42.8%). BRAF V600E was associated with extrathyroidal invasion (p less than 0.0001), multicentricity (p = 0.0026), presence of nodal metastases (p = 0.0009), class III versus classes I and II (p less than 0.00000006), and absence of tumor capsule (p less than 0.0001), in particular, in follicular- and micro-PTC variants. By multivariate analysis, the absence of tumor capsule remained the only parameter associated (p = 0.0005) with the BRAF V600E mutation. The authors concluded that the BRAF V600E mutation is associated with high-risk PTC and, in particular, in follicular variant with invasive tumor growth.","Flaherty et al. (2010) reported complete or partial regression of V600E-associated papillary thyroid cancer in 3 patients treated with an inhibitor (PLX4032) specific to the V600E mutation.","Nonseminomatous Germ Cell Tumors","In 3 (9%) of 32 nonseminomatous germ cell tumors (see 273300) with a mixture of embryonal carcinoma, yolk sac tumor, choriocarcinoma, and mature teratoma, Sommerer et al. (2005) identified the activating 1796T-A mutation in the BRAF gene; the mutation was present within the embryonic carcinoma component.","Astrocytoma","Pfister et al. (2008) identified a somatic V600E mutation in 4 (6%) of 66 pediatric low-grade astrocytomas (see 137800). Thirty (45%) of the 66 tumors had a copy number gain spanning the BRAF locus, indicating a novel mechanism of MAPK (176948) pathway activation in these tumors.","Role in Neurodegeneration","Mass et al. (2017) hypothesized that a somatic BRAF(V600E) mutation in the erythromyeloid lineage may cause neurodegeneration. Mass et al. (2017) showed that mosaic expression of BRAF(V600E) in mouse erythromyeloid progenitors results in clonal expansion of tissue-resident macrophages and a severe late-onset neurodegenerative disorder. This is associated with accumulation of ERK-activated amoeboid microglia in mice, and is also observed in human patients with histiocytoses. In the mouse model, neurobehavioral signs, astrogliosis, deposition of amyloid precursor protein, synaptic loss, and neuronal death were driven by ERK-activated microglia and were preventable by BRAF inhibition. Mass et al. (2017) suggested that the results identified the fetal precursors of tissue-resident macrophages as a potential cell of origin for histiocytoses and demonstrated that a somatic mutation in the erythromyeloid progenitor lineage in mice can drive late-onset neurodegeneration.","Variant Function","Brady et al. (2014) showed that decreasing the levels of CTR1 (603085), or mutations in MEK1 (176872) that disrupt copper binding, decreased BRAF(V600E)-driven signaling and tumorigenesis in mice and human cell settings. Conversely, a MEK1-MEK5 (602520) chimera that phosphorylated ERK1/2 independently of copper or an active ERK2 restored the tumor growth of murine cells lacking Ctr1. Copper chelators used in the treatment of Wilson disease (277900) decreased tumor growth of human or murine cells that were either transformed by BRAF(V600E) or engineered to be resistant to BRAF inhibition. Brady et al. (2014) concluded that copper chelation therapy could be repurposed to treat cancers containing the BRAF(V600E) mutation.","Rapino et al. (2018) showed in humans that the enzymes that catalyze modifications of wobble uridine-34 (U34) tRNA are key players of the protein synthesis rewiring that is induced by the transformation driven by the BRAF V600E oncogene and by resistance to targeted therapy in melanoma. Rapino et al. (2018) showed that BRAF V600E-expressing melanoma cells are dependent on U34 enzymes for survival, and that concurrent inhibition of MAPK signaling and ELP3 (612722) or CTU1 (612694) and/or CTU2 (617057) synergizes to kill melanoma cells. Activation of the PI3K signaling pathway, one of the most common mechanisms of acquired resistance to MAPK therapeutic agents, markedly increases the expression of U34 enzymes. Mechanistically, U34 enzymes promote glycolysis in melanoma cells through the direct, codon-dependent, regulation of the translation of HIF1A (603348) mRNA and the maintenance of high levels of HIF1-alpha protein. Therefore, the acquired resistance to anti-BRAF therapy is associated with high levels of U34 enzymes and HIF1-alpha. Rapino et al. (2018) concluded that U34 enzymes promote the survival and resistance to therapy of melanoma cells by regulating specific mRNA translation."],"title":"NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) AND Carcinoma of colon","review_date":20140904,"diseases":[{"pub_med":[19042984,25006736,17060676,22138009,24996433,22855150,23012255,25373533,23852704,23429431,34043773],"symbols":{"medgen":"C0699790","mondo":"MONDO:0002032"},"normalized_disease":["Malignant Colon Neoplasm"],"names":["Malignant Colon Neoplasm","Malignant Colon Neoplasm","Malignant Colon Neoplasm"],"normalized_cancer":["Bowel"],"keyword":"Hereditary cancer syndrome"}],"pub_med_references":[12068308,12198537,12447372,12619120,12644542,12670889,12794760,12960123,14513361,14602780,15001635,15126572,15181070,15342696,15356022,15386408,15687339,15998781,16015629,16174717,16187918,16772349,17374713,17488796,17785355,18398503,19571295,20818844,20823850,21107320,21107323,22113612,22281684,23302800,23685455,24512911,24670642,24717435,25079330,28854169,29925953],"date_created":20130404,"variant_id":10190071404531360004,"review_description":"Pathogenic","clinical_significance":["Pathogenic"],"allele_id":29000,"accession_id":"RCV000014992"},{"submissions":[{"submission_description":[],"submitter_name":"Clinical Genetics and Genomics, Karolinska University Hospital","review_date":20140711,"origin":"germline","method":"clinical testing","submitter_date":20201126,"diseases":[{"names":["Not Provided"]}],"review_description":"Pathogenic","date_updated":20201212,"clinical_significance":["Pathogenic"],"review_status":"criteria provided, single submitter","accession_id":"SCV001450230"},{"submission_description":[],"submitter_name":"Eurofins Ntd Llc (ga)","review_date":20131008,"origin":"germline","method":"clinical testing","submitter_date":20180919,"diseases":[{"names":["Not Provided"]}],"review_description":"Pathogenic","date_updated":20250413,"clinical_significance":["Pathogenic"],"review_status":"criteria provided, single submitter","accession_id":"SCV000112810"},{"submitter_name":"Department of Pathology and Laboratory Medicine, Sinai Health System","submission_description":[],"origin":"unknown","method":"clinical testing","submitter_date":20210331,"diseases":[{"names":["Not Provided"]}],"review_description":"Uncertain significance","date_updated":20210413,"clinical_significance":["Uncertain significance"],"review_status":"no assertion criteria provided","accession_id":"SCV001550994"},{"submitter_name":"Sylvester Comprehensive Cancer Center, University of Miami","submission_description":["BRAF V600E variant is involved in encoding cytoplasmic serine/threonine kinases within the MAPK pathway. The NCCN Guidelines state that BRAF mutations are an indicative prognostic marker with poor clinical outcome. It it recommended to do baseline genomic genotyping of the patient's primary or metastatic tumor tissue at diagnosis if the patient is stage IV. BRAF V600E is mutated in about 15% of all cancers (El-Osta et. al, 2011). Frequency of all RAF mutations is 2.2% within pancreatic cancer, where BRAF V600E is one of the more common variants, and is actionable (Hendifar et al., 2021)"],"origin":"somatic","method":"clinical testing","submitter_date":20211006,"diseases":[{"symbols":{"medgen":"CN517202"}}],"review_description":"Pathogenic","date_updated":20250803,"clinical_significance":["Pathogenic"],"review_status":"no assertion criteria provided","accession_id":"SCV001962698"}],"variation_id":13961,"submission_description":[],"title":"NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) AND not provided","review_date":20140711,"diseases":[{"symbols":{"medgen":"C3661900"},"names":["Not Provided","None Provided"]}],"date_created":20140117,"variant_id":10190071404531360004,"review_description":"Pathogenic","clinical_significance":["Pathogenic"],"allele_id":29000,"accession_id":"RCV000080903"},{"submissions":[{"submission_description":[],"submitter_name":"Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine","review_date":20090529,"origin":"somatic","method":"clinical testing","submitter_date":20190321,"diseases":[{"symbols":{"mesh":"D002289"}}],"review_description":"Pathogenic","date_updated":20150131,"clinical_significance":["Pathogenic"],"review_status":"no assertion criteria provided","accession_id":"SCV000061601"}],"variation_id":13961,"submission_description":[],"title":"NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) AND Non-small cell lung carcinoma","review_date":20090529,"diseases":[{"pub_med":[24868098,24673736,24627688,23667368,30813707],"normalized_cancer":["Non-Small Cell Lung Cancer"],"symbols":{"medgen":"C0007131","mesh":"D002289","mondo":"MONDO:0005233","human_phenotype_ontology":"HP:0030358"},"normalized_disease":["Non-Small Cell Lung Carcinoma"],"names":["Non-Small Cell Lung Carcinoma","Non-Small Cell Lung Carcinoma"],"disease_mechanism":"Other"}],"date_created":20130503,"variant_id":10190071404531360004,"review_description":"Pathogenic","clinical_significance":["Pathogenic"],"allele_id":29000,"accession_id":"RCV000037936"},{"title":"NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) AND Ganglioglioma","submissions":[{"submission_description":["Variant has Tier I (strong) clinical significance as a diagnostic inclusion criterion in ganglioglioma, based on the following evidence: 1) Documented in one or more cancer databases (e.g., St. Jude Pecan, COSMIC, CIViC, OncoKB). 2) Appears in one or more well-established professional guidelines (e.g., World Health Organization [WHO]; National Comprehensive Cancer Network [NCCN]) as providing diagnostic, prognostic, or therapeutic information. 3) Information in the literature supports potential biologic effect of variant (PMID: 17496922). 4) Diagnostic for a specific tumor type/classification according to professional guidelines (Evidence Level A; PMIDs: 34185076, 20156809, 21274720, 29880043, 32289278, 24238153)."],"submitter_name":"Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital","review_date":20241226,"origin":"somatic","method":"clinical testing","submitter_date":20251120,"diseases":[{"symbols":{"mondo":"MONDO:0016733"}}],"date_updated":20251122,"clinical_significance":[],"review_status":"criteria provided, single submitter","accession_id":"SCV007105544"}],"variation_id":13961,"submission_description":[],"diseases":[{"normalized_cancer":["Mixed cell tumors containing both neural ganglionic cells and neural glial cell components"],"symbols":{"medgen":"C0206716","mondo":"MONDO:0016733","human_phenotype_ontology":"HP:0033664"},"normalized_disease":["Ganglioglioma"],"names":["Ganglioglioma","Mixed Cell Tumors Containing Both Neural Ganglionic Cells Neural Glial Cell Components"]}],"date_created":20251122,"variant_id":10190071404531360004,"clinical_significance":[],"allele_id":29000,"accession_id":"RCV006253603"},{"title":"NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) AND Pilocytic astrocytoma","submissions":[{"submission_description":["Variant has Tier I (strong) clinical significance as a diagnostic inclusion criterion in pilocytic astrocytoma, based on the following evidence: 1) Documented in one or more cancer databases (e.g., St. Jude Pecan, COSMIC, CIViC, OncoKB). 2) Appears in one or more well-established professional guidelines (e.g., World Health Organization [WHO]; National Comprehensive Cancer Network [NCCN]) as providing diagnostic, prognostic, or therapeutic information. 3) Information in the literature supports potential biologic effect of variant (PMID: 17496922). 4) Diagnostic for a specific tumor type/classification based on well-powered studies with expert-level consensus (Evidence Level B; PMIDs: 23583981, 23817572, 32289278, 34718782)."],"submitter_name":"Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital","review_date":20241030,"origin":"somatic","method":"clinical testing","submitter_date":20251120,"diseases":[{"symbols":{"mondo":"MONDO:0016691"}}],"date_updated":20251122,"clinical_significance":[],"review_status":"criteria provided, single submitter","accession_id":"SCV007105549"}],"variation_id":13961,"submission_description":[],"diseases":[{"normalized_cancer":["Pilocytic Astrocytoma"],"symbols":{"medgen":"C0334583","mondo":"MONDO:0016691","human_phenotype_ontology":"HP:0033680"},"normalized_disease":["Pilocytic Astrocytoma"],"names":["Pilocytic Astrocytoma","Pilocytic Astrocytoma, Somatic"]}],"date_created":20251122,"variant_id":10190071404531360004,"clinical_significance":[],"allele_id":29000,"accession_id":"RCV006253599"},{"title":"NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) AND Malignant glioma","submissions":[{"submission_description":["Variant has Tier I (strong) clinical significance as a diagnostic inclusion criterion in malignant glioma, based on the following evidence: 1) Documented in one or more cancer databases (e.g., St. Jude Pecan, COSMIC, CIViC, OncoKB). 2) Appears in one or more well-established professional guidelines (e.g., World Health Organization [WHO]; National Comprehensive Cancer Network [NCCN]) as providing diagnostic, prognostic, or therapeutic information. 3) Information in the literature supports potential biologic effect of variant (PMID: 17496922). 4) Diagnostic for a specific tumor type/classification based on well-powered studies with expert-level consensus (Evidence Level B; PMIDs: 23583981, 28912153, 28966033, 25752754, 23552385, 29763623)."],"submitter_name":"Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital","review_date":20250603,"origin":"somatic","method":"clinical testing","submitter_date":20251120,"diseases":[{"symbols":{"mondo":"MONDO:0100342"}}],"date_updated":20251122,"clinical_significance":[],"review_status":"criteria provided, single submitter","accession_id":"SCV007105131"}],"variation_id":13961,"submission_description":[],"diseases":[{"normalized_cancer":["Malignant glioma"],"symbols":{"medgen":"C0555198","mondo":"MONDO:0100342"},"normalized_disease":["Malignant Glioma"],"names":["Malignant Glioma"]}],"date_created":20251122,"variant_id":10190071404531360004,"clinical_significance":[],"allele_id":29000,"accession_id":"RCV006253604"},{"title":"NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) AND Diffuse midline glioma, H3 K27M-mutant","submissions":[{"submission_description":["Variant has Tier I (strong) clinical significance as a diagnostic inclusion criterion in diffuse midline glioma, H3 K27M-mutant, based on the following evidence: 1) Documented in one or more cancer databases (e.g., St. Jude Pecan, COSMIC, CIViC, OncoKB). 2) Appears in one or more well-established professional guidelines (e.g., World Health Organization [WHO]; National Comprehensive Cancer Network [NCCN]) as providing diagnostic, prognostic, or therapeutic information. 3) Information in the literature supports potential biologic effect of variant. 4) Diagnostic for a specific tumor type/classification based on well-powered studies with expert-level consensus (Evidence Level B)."],"submitter_name":"Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital","review_date":20221226,"origin":"somatic","method":"clinical testing","submitter_date":20251120,"diseases":[{"symbols":{"mondo":"MONDO:0957196"}}],"date_updated":20251122,"clinical_significance":[],"review_status":"criteria provided, single submitter","accession_id":"SCV007105098"}],"variation_id":13961,"submission_description":[],"diseases":[{"normalized_cancer":["Diffuse Glioma"],"symbols":{"medgen":"C4289688","mondo":"MONDO:0957196"},"normalized_disease":["Diffuse Midline Glioma, H3 K27M-Mutant"],"names":["Diffuse Midline Glioma, H3 K27M-Mutant"]}],"date_created":20251122,"variant_id":10190071404531360004,"clinical_significance":[],"allele_id":29000,"accession_id":"RCV006253605"},{"title":"NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) AND Malignant peripheral nerve sheath tumor","submissions":[{"submission_description":["Variant has Tier I (strong) clinical significance as a diagnostic inclusion criterion in malignant peripheral nerve sheath tumor, based on the following evidence: 1) Documented in one or more cancer databases (e.g., St. Jude Pecan, COSMIC, CIViC, OncoKB). 2) Information in the literature supports potential biologic effect of variant. 3) Diagnostic for a specific tumor type/classification based on well-powered studies with expert-level consensus (Evidence Level B; PMIDs: 36067829, 24366910, 30099373)."],"submitter_name":"Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital","review_date":20250606,"origin":"somatic","method":"clinical testing","submitter_date":20251120,"diseases":[{"symbols":{"mondo":"MONDO:0017827"}}],"date_updated":20251122,"clinical_significance":[],"review_status":"criteria provided, single submitter","accession_id":"SCV007105134"}],"variation_id":13961,"submission_description":[],"diseases":[{"normalized_cancer":["Malignant Peripheral Nerve Sheath Tumor"],"symbols":{"medgen":"C0751690","mondo":"MONDO:0017827"},"normalized_disease":["Malignant Peripheral Nerve Sheath Tumor"],"names":["Malignant Peripheral Nerve Sheath Tumor"]}],"date_created":20251122,"variant_id":10190071404531360004,"clinical_significance":[],"allele_id":29000,"accession_id":"RCV006253606"},{"title":"NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) AND IDH-wildtype glioblastoma","submissions":[{"submission_description":["Variant has Tier I (strong) clinical significance as a diagnostic inclusion criterion in IDH-wildtype glioblastoma, based on the following evidence: 1) Documented in one or more cancer databases (e.g., St. Jude Pecan, COSMIC, CIViC, OncoKB). 2) Appears in one or more well-established professional guidelines (e.g., World Health Organization [WHO]; National Comprehensive Cancer Network [NCCN]) as providing diagnostic, prognostic, or therapeutic information. 3) Information in the literature supports potential biologic effect of variant (PMID: 17496922). 4) Diagnostic for a specific tumor type/classification based on well-powered studies with expert-level consensus (Evidence Level B; PMIDs: 28990704, 23552385, 29105198, 29532523, 24127995)."],"submitter_name":"Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital","review_date":20241119,"origin":"somatic","method":"clinical testing","submitter_date":20251120,"diseases":[{"symbols":{"mondo":"MONDO:0850335"}}],"date_updated":20251122,"clinical_significance":[],"review_status":"criteria provided, single submitter","accession_id":"SCV007105125"}],"variation_id":13961,"submission_description":[],"diseases":[{"symbols":{"medgen":"CN372125","mondo":"MONDO:0850335"},"normalized_disease":["Idh-Wildtype Glioblastoma"],"names":["Idh-Wildtype Glioblastoma"]}],"date_created":20251122,"variant_id":10190071404531360004,"clinical_significance":[],"allele_id":29000,"accession_id":"RCV006253607"},{"title":"NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) AND Diffuse leptomeningeal glioneuronal tumor","submissions":[{"submission_description":["Variant has Tier I (strong) clinical significance as a diagnostic inclusion criterion in diffuse leptomeningeal glioneuronal tumor, based on the following evidence: 1) Documented in one or more cancer databases (e.g., St. Jude Pecan, COSMIC, CIViC, OncoKB). 2) Appears in one or more well-established professional guidelines (e.g., World Health Organization [WHO]; National Comprehensive Cancer Network [NCCN]) as providing diagnostic, prognostic, or therapeutic information. 3) Information in the literature supports potential biologic effect of variant (PMID: 17496922). 4) Diagnostic for a specific tumor type/classification according to professional guidelines (Evidence Level A; PMIDs: 26994902, 32605662, 36382112)."],"submitter_name":"Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital","review_date":20231207,"origin":"somatic","method":"clinical testing","submitter_date":20251120,"diseases":[{"symbols":{"mondo":"MONDO:0858956"}}],"date_updated":20251122,"clinical_significance":[],"review_status":"criteria provided, single submitter","accession_id":"SCV007105110"}],"variation_id":13961,"submission_description":[],"diseases":[{"normalized_cancer":["Diffuse leptomeningeal glioneuronal tumor"],"symbols":{"medgen":"C4329735","mondo":"MONDO:0858956"},"normalized_disease":["Diffuse Leptomeningeal Glioneuronal Tumor"],"names":["Diffuse Leptomeningeal Glioneuronal Tumor"]}],"date_created":20251122,"variant_id":10190071404531360004,"clinical_significance":[],"allele_id":29000,"accession_id":"RCV006253608"},{"title":"NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) AND Nodular ganglioneuroblastoma","submissions":[{"submission_description":["Variant has Tier II (potential) clinical significance as a diagnostic inclusion criterion in nodular ganglioneuroblastoma, based on the following evidence: 1) Documented in one or more cancer databases (e.g., St. Jude Pecan, COSMIC, CIViC, OncoKB). 2) Information in the literature supports potential biologic effect of variant (PMID: 17496922). 3) Diagnostic significance based on multiple small studies (Evidence Level C; PMIDs: 22142829, 26121087, 34331515)."],"submitter_name":"Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital","review_date":20240320,"origin":"somatic","method":"clinical testing","submitter_date":20251120,"diseases":[{"symbols":{"mondo":"MONDO:0003325"}}],"date_updated":20251122,"clinical_significance":[],"review_status":"criteria provided, single submitter","accession_id":"SCV007105113"}],"variation_id":13961,"submission_description":[],"diseases":[{"symbols":{"medgen":"C1517445","mondo":"MONDO:0003325"},"normalized_disease":["Nodular Ganglioneuroblastoma"],"names":["Nodular Ganglioneuroblastoma"]}],"date_created":20251122,"variant_id":10190071404531360004,"clinical_significance":[],"allele_id":29000,"accession_id":"RCV006253609"},{"title":"NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) AND Polymorphous low grade neuroepithelial tumor of the young","submissions":[{"submission_description":["Variant has Tier I (strong) clinical significance as a diagnostic inclusion criterion in polymorphous low grade neuroepithelial tumor of the young, based on the following evidence: 1) Documented in one or more cancer databases (e.g., St. Jude Pecan, COSMIC, CIViC, OncoKB). 2) Appears in one or more well-established professional guidelines (e.g., World Health Organization [WHO]; National Comprehensive Cancer Network [NCCN]) as providing diagnostic, prognostic, or therapeutic information. 3) Information in the literature supports potential biologic effect of variant (PMID: 17496922). 4) Diagnostic for a specific tumor type/classification according to professional guidelines (Evidence Level A; PMIDs: 27812792, 29701169, 30926558, 31520766, 31617914)."],"submitter_name":"Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital","review_date":20240531,"origin":"somatic","method":"clinical testing","submitter_date":20251120,"diseases":[{"symbols":{"mondo":"MONDO:0858959"}}],"date_updated":20251122,"clinical_significance":[],"review_status":"criteria provided, single submitter","accession_id":"SCV007105118"}],"variation_id":13961,"submission_description":[],"diseases":[{"normalized_cancer":["Low-Grade Neuroepithelial Tumor"],"symbols":{"medgen":"C5556330","mondo":"MONDO:0858959"},"normalized_disease":["Polymorphous Low Grade Neuroepithelial Tumor The Young"],"names":["Polymorphous Low Grade Neuroepithelial Tumor The Young","Polymorphous Low Grade Neuroepithelial Tumour The Young"]}],"date_created":20251122,"variant_id":10190071404531360004,"clinical_significance":[],"allele_id":29000,"accession_id":"RCV006253610"},{"title":"NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) AND Diffuse low-grade glioma, MAPK pathway–altered","submissions":[{"submission_description":["Variant has Tier I (strong) clinical significance as a diagnostic inclusion criterion in diffuse low-grade glioma, MAPK pathway–altered, based on the following evidence: 1) Documented in one or more cancer databases (e.g., St. Jude Pecan, COSMIC, CIViC, OncoKB). 2) Appears in one or more well-established professional guidelines (e.g., World Health Organization [WHO]; National Comprehensive Cancer Network [NCCN]) as providing diagnostic, prognostic, or therapeutic information. 3) Diagnostic for a specific tumor type/classification according to professional guidelines (Evidence Level A)."],"submitter_name":"Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital","review_date":20240904,"origin":"somatic","method":"clinical testing","submitter_date":20251120,"diseases":[{"symbols":{"mondo":"MONDO:0859614"}}],"date_updated":20251122,"clinical_significance":[],"review_status":"criteria provided, single submitter","accession_id":"SCV007105121"}],"variation_id":13961,"submission_description":[],"diseases":[{"normalized_cancer":["Low-Grade Glioma, NOS"],"symbols":{"medgen":"CN372173","mondo":"MONDO:0859614"},"normalized_disease":["Diffuse Low-Grade Glioma, Mapk Pathway???Altered"],"names":["Diffuse Low-Grade Glioma, Mapk Pathway???Altered"]}],"date_created":20251122,"variant_id":10190071404531360004,"clinical_significance":[],"allele_id":29000,"accession_id":"RCV006253611"},{"title":"NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) AND Benign metanephric tumor","submissions":[{"submission_description":["Variant has Tier I (strong) clinical significance as a diagnostic inclusion criterion in benign metanephric tumor, based on the following evidence: 1) Documented in one or more cancer databases (e.g., St. Jude Pecan, COSMIC, CIViC, OncoKB). 2) Appears in one or more well-established professional guidelines (e.g., World Health Organization [WHO]; National Comprehensive Cancer Network [NCCN]) as providing diagnostic, prognostic, or therapeutic information. 3) Information in the literature supports potential biologic effect of variant (PMID: 17496922). 4) Diagnostic for a specific tumor type/classification according to professional guidelines (Evidence Level A; PMIDs: 26796506, 26014474, 27769870, 32371339)."],"submitter_name":"Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital","review_date":20250130,"origin":"somatic","method":"clinical testing","submitter_date":20251120,"diseases":[{"symbols":{"mondo":"MONDO:0018738"}}],"date_updated":20251122,"clinical_significance":[],"review_status":"criteria provided, single submitter","accession_id":"SCV007105133"}],"variation_id":13961,"submission_description":[],"diseases":[{"normalized_cancer":["Benign metanephric tumor","Benign metanephric tumour"],"symbols":{"medgen":"C5681098","mondo":"MONDO:0018738"},"normalized_disease":["Benign Metanephric Tumor"],"names":["Benign Metanephric Tumor","Benign Metanephric Tumour"]}],"date_created":20251122,"variant_id":10190071404531360004,"clinical_significance":[],"allele_id":29000,"accession_id":"RCV006253612"},{"title":"NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) AND Dysembryoplastic neuroepithelial tumor","submissions":[{"submission_description":["Variant has Tier I (strong) clinical significance as a diagnostic inclusion criterion in dysembryoplastic neuroepithelial tumor, based on the following evidence: 1) Documented in one or more cancer databases (e.g., St. Jude Pecan, COSMIC, CIViC, OncoKB). 2) Appears in one or more well-established professional guidelines (e.g., World Health Organization [WHO]; National Comprehensive Cancer Network [NCCN]) as providing diagnostic, prognostic, or therapeutic information. 3) Information in the literature supports potential biologic effect of variant (PMID: 17496922). 4) Diagnostic for a specific tumor type/classification based on well-powered studies with expert-level consensus (Evidence Level B; PMIDs: 25346165, 26810070, 23442159, 31617914, 32164789)."],"submitter_name":"Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital","review_date":20251105,"origin":"somatic","method":"clinical testing","submitter_date":20251120,"diseases":[{"symbols":{"mondo":"MONDO:0005505"}}],"date_updated":20251122,"clinical_significance":[],"review_status":"criteria provided, single submitter","accession_id":"SCV007105140"}],"variation_id":13961,"submission_description":[],"diseases":[{"normalized_cancer":["Dysembryoplastic Neuroepithelial Tumor"],"symbols":{"medgen":"C1266177","mondo":"MONDO:0005505","human_phenotype_ontology":"HP:0033703"},"normalized_disease":["Dysembryoplastic Neuroepithelial Tumor"],"names":["Dysembryoplastic Neuroepithelial Tumor"]}],"date_created":20251122,"variant_id":10190071404531360004,"clinical_significance":[],"allele_id":29000,"accession_id":"RCV006253613"},{"title":"NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) AND Pleomorphic xanthoastrocytoma","submissions":[{"submission_description":["Variant has Tier I (strong) clinical significance as a diagnostic inclusion criterion in pleomorphic xanthoastrocytoma, based on the following evidence: 1) Documented in one or more cancer databases (e.g., St. Jude Pecan, COSMIC, CIViC, OncoKB). 2) Appears in one or more well-established professional guidelines (e.g., World Health Organization [WHO]; National Comprehensive Cancer Network [NCCN]) as providing diagnostic, prognostic, or therapeutic information. 3) Information in the literature supports potential biologic effect of variant (PMIDs: 15035987, 12068308, 19251651, 26343582). 4) Diagnostic for a specific tumor type/classification according to professional guidelines (Evidence Level A; PMIDs: 21274720, 21479234, 30051528, 32619305, 32289278)."],"submitter_name":"Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital","review_date":20250512,"origin":"somatic","method":"clinical testing","submitter_date":20251120,"diseases":[{"symbols":{"mondo":"MONDO:0016690"}}],"date_updated":20251122,"clinical_significance":[],"review_status":"criteria provided, single submitter","accession_id":"SCV007105547"}],"variation_id":13961,"submission_description":[],"diseases":[{"normalized_cancer":["Pleomorphic Xanthoastrocytoma"],"symbols":{"medgen":"C0334586","mondo":"MONDO:0016690","human_phenotype_ontology":"HP:0033682"},"normalized_disease":["Pleomorphic Xanthoastrocytoma"],"names":["Pleomorphic Xanthoastrocytoma"]}],"date_created":20251122,"variant_id":10190071404531360004,"clinical_significance":[],"allele_id":29000,"accession_id":"RCV006253602"},{"title":"NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) AND Alveolar rhabdomyosarcoma","submissions":[{"submission_description":["Variant has Tier II (potential) clinical significance as a diagnostic inclusion criterion in alveolar rhabdomyosarcoma, based on the following evidence: 1) Documented in one or more cancer databases (e.g., St. Jude Pecan, COSMIC, CIViC, OncoKB). 2) Information in the literature supports potential biologic effect of variant (PMID: 17496922). 3) Diagnostic significance based on multiple small studies (Evidence Level C; 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malformation","disease_description":null,"disease_symbol":null,"disease_alt_symbol":null,"evidences":{}}],"siftscore":null,"siftprediction":null,"polyphenscore":null,"polyphenprediction":null,"evidences":{"pub_med_references":[12068308,12198537,12447372,12619120,12644542,12670889,12794760,12960123,14500344,14513361,14602780,15001635,15126572,15181070,15342696,15356022,15386408,15687339,15998781,16015629,16174717,16187918,16772349,17374713,17488796,17785355,18398503,19571295,20818844,20823850,21107320,21107323,21917714,22113612,22281684,23263490,23302800,23685455,24455489,24512911,24670642,24717435,25079330,28854169,29925953],"cosmic_study":[]},"xrefs":{"cosmicmutationid":["COSV56056643","COSV56059110"],"clinvaraccession":[]},"variant_type":"Disease","disease":"Adenomas and Adenocarcinomas","disease_symbol":null,"disease_alt_symbol":null,"bed_comments":null,"pub_med_references":[12068308,12198537,12447372,12619120,12644542,12670889,12794760,12960123,14500344,14513361,14602780,15001635,15126572,15181070,15342696,15356022,15386408,15687339,15998781,16015629,16174717,16187918,16772349,17374713,17488796,17785355,18398503,19571295,20818844,20823850,21107320,21107323,21917714,22113612,22281684,23263490,23302800,23685455,24455489,24512911,24670642,24717435,25079330,28854169,29925953]}]}],"weill_cornell_medicine_pmkb":[{"version":"08-Nov-2024","items":[{"tier":1,"definition":["BRAF V600E","BRAF codon(s) 600 any"],"interpretations":"Eighty percent of all thyroid cancers are papillary thyroid carcinomas (PTCs). BRAF is part of the mitogen-activated protein kinase (MAPK) signaling pathway and V600E is an activating mutation of BRAF. The BRAF V600E mutation has been reported in 45% of patients with papillary thyroid carcinoma. The BRAF V600E-like PTC's (BVL) and the RAS-like PTC (RL-PTC) are fundamentally different in their genomic, epigenomic, and proteomic profiles. Presence of a BRAF p.Val600Glu (V600E) mutation is highly specific for papillary thyroid carcinoma and is only rarely associated with the follicular variant PTC , other well-differentiated thyroid neoplasms or nodular goiters. The possible prognostic impact of BRAF V600E mutations in papillary carcinoma of the thyroid continues to be studied. \nFDA approved dabrafenib and trametinib administered together for the treatment of BRAF V600E mutation-positive anaplastic thyroid cancer. ","tissues":["Thyroid"],"tumour_types":["Papillary Carcinoma"],"disease_or_trait":null,"pub_med_references":[12068308,25417114,25422487],"variants":[{"definition":"BRAF V600E","type":"variantId","coding_impact":"any","variants":["10190071404531360004","10380071407533360004"],"gene_id":2273},{"aa_positions":[600],"definition":"BRAF codon(s) 600 any","type":"codon","coding_impact":"any","gene_id":2273}]},{"tier":1,"definition":["BRAF V600E","BRAF codon(s) 600 any","BRAF V600D","BRAF V600K","BRAF V600R","BRAF V600M","BRAF V600G"],"interpretations":"Presence of a BRAF c.1799T>A, p.Val600Glu (V600E) mutation in a microsatellite unstable colorectal carcinoma indicates that the tumor is probably sporadic and not associated with Lynch syndrome (HNPCC). However, if a BRAF mutation is not detected, the tumor may either be sporadic or Lynch syndrome associated. Detection of BRAF mutations may also be useful in determining patient eligibility for anti-EGFR treatment. Approximately 8--15% of colorectal cancer (CRC) tumors harbor BRAF mutations. The presence of BRAF mutation is significantly associated with right-sided colon cancers and is associated with decreased overall survival. Some studies have reported that patients with metastatic CRC (mCRC) that harbor BRAF mutations do not respond to anti-EGFR antibody agents cetuximab or panitumumab in the chemotherapy-refractory setting. BRAF V600-mutated CRCs may not be sensitive to V600E targeted TKIs.\n\nDrug: Vemurafenib + Panitumumab,\nEncorafenib + Binimetinib + Cetuximab,\nRadiation + Trametinib + Fluorouracil","tissues":["Colon","Rectum"],"tumour_types":["Adenocarcinoma"],"disease_or_trait":null,"pub_med_references":[12068308,17195912,19001320,19571295,19616446,19884556,22281684,23438367],"variants":[{"definition":"BRAF V600E","type":"variantId","coding_impact":"any","variants":["10190071404531360004","10380071407533360004"],"gene_id":2273},{"aa_positions":[600],"definition":"BRAF codon(s) 600 any","type":"codon","coding_impact":"any","gene_id":2273}]},{"tier":1,"definition":["BRAF V600E","BRAF codon(s) 600 any","BRAF V600D","BRAF V600K","BRAF V600R","BRAF V600M","BRAF V600G"],"interpretations":"B-RAF is a member of the RAF-family of kinases which plays an important role in the RAS-RAF-MEK-ERK mitotic signaling pathway. BRAF mutations are present in approximately 50% to 60% of cutaneous melanomas and are also present at lower frequencies in other melanoma subtypes. The hotspot for mutations in BRAF is at codon Val600 and the most common one is p.Val600Glu (V600E). Various B-Raf inhibitors(Vemurafenib, Dabrafenib) have been FDA approved for melanoma therapy in certain settings.\nDrug: \nVemurafenib\nDabrafenib\nDabrafenib + Trametinib\nVemurafenib + Cobimetinib\nTrametinib","tissues":["Skin"],"tumour_types":["Melanoma"],"disease_or_trait":null,"pub_med_references":[12068308,22157295,23415641,23770823,24331719],"variants":[{"definition":"BRAF V600E","type":"variantId","coding_impact":"any","variants":["10190071404531360004","10380071407533360004"],"gene_id":2273},{"aa_positions":[600],"definition":"BRAF codon(s) 600 any","type":"codon","coding_impact":"any","gene_id":2273}]},{"tier":1,"definition":["BRAF V600E","BRAF codon(s) 600 any"],"interpretations":"BRAF alterations have been described in a wide spectrum of brain tumors, including in gliomas and glioneuronal tumors. BRAFV600E mutations have been found in approximately 10--15% of pilocytic astrocytoma and in approximately 5--10% of pediatric diffusely infiltrating gliomas, including diffuse astrocytomas (WHO grade II), anaplastic astrocytomas (WHO grade III) and glioblastomas (WHO grade IV), but in less than 2% of comparable adult gliomas. This mutation is potentially targetable.","tissues":["Spinal Cord","Brain","Supratentorial","Infratentorial"],"tumour_types":["Glioblastoma","Pleomorphic Xanthoastrocytoma","Ganglioglioma","Neuroepithelial Neoplasm","NOS","Neuroepithelial neoplasm","high grade","Astrocytoma","Pilocytic"],"disease_or_trait":null,"pub_med_references":[21274720,23547069,24725538],"variants":[{"definition":"BRAF V600E","type":"variantId","coding_impact":"any","variants":["10190071404531360004","10380071407533360004"],"gene_id":2273},{"aa_positions":[600],"definition":"BRAF codon(s) 600 any","type":"codon","coding_impact":"any","gene_id":2273}]},{"tier":1,"definition":["BRAF V600E","BRAF codon(s) 600 any"],"interpretations":"B-RAF is a member of the RAF-family of kinases which plays an important role in the RAS-RAF-MEK-ERK mitotic signaling pathway. Mutations of B-RAF have been described in up to 40-70% of Langerhans cell histiocytosis and approximately 50% of Erdheim-Chester disease. The hotspot for mutations in BRAF is at codon Val600 and these are activating mutations. The most common activating mutation is p.Val600Glu(V600E). Various B-Raf inhibitors(Vemurafenib, Dabrafenib) have been FDA approved for therapy for some tumor types in certain settings, and clinical trials for advanced BRAF V600 mutation-positive tumors using targeted therapy (often in combination with other therapy) may be available (clinical trials.gov).\n","tissues":["Bone","Lung","Bone Marrow","Lymph Node","Skin"],"tumour_types":["Langerhans Cell Histiocytosis","Histiocytic and Dendritic Cell Neoplasms"],"disease_or_trait":null,"pub_med_references":null,"variants":[{"definition":"BRAF V600E","type":"variantId","coding_impact":"any","variants":["10190071404531360004","10380071407533360004"],"gene_id":2273},{"aa_positions":[600],"definition":"BRAF codon(s) 600 any","type":"codon","coding_impact":"any","gene_id":2273}]},{"tier":1,"definition":["BRAF V600E"],"interpretations":"Mutations in beta catenin (CTNNB1) are seen in about 90% of adamantinomatous craniopharyngiomas and mutations in BRAF (V600E) in papillary craniopharyngiomas. Adamantinomatous and papillary craniopharyngiomas have been shown to carry clonal mutations that are typically mutually exclusive but may occasionally coexist. These findings indicate that the adamantinomatous and papillary subtypes have distinct molecular underpinnings, each principally driven by mutations in a single well-established oncogene - CTNNB1 in the adamantinomatous form and BRAF in the papillary form, independent of age. This may have implications for the diagnosis and treatment of these tumors. Treatment with the BRAF inhibitor vemurafenib has been reported to result in disease stabilization in a patient with a papillary craniopharyngioma with a BRAF V600E mutation.","tissues":["Brain"],"tumour_types":["Craniopharyngioma"],"disease_or_trait":null,"pub_med_references":[24715106],"variants":[{"definition":"BRAF V600E","type":"variantId","coding_impact":"any","variants":["10190071404531360004","10380071407533360004"],"gene_id":2273}]},{"tier":1,"definition":["BRAF V600E"],"interpretations":"BRAF is part of the mitogen-activated protein kinase (MAPK) signaling pathway and V600E is an activating mutation of BRAF. The BRAF V600E mutation has been reported in 45% of patients with papillary thyroid carcinoma, which comprise 80 % of all thyroid cancers. Presence of a BRAF p.Val600Glu (V600E) mutation is highly specific for papillary thyroid carcinoma and is only rarely associated with the follicular variant PTC, other thyroid neoplasms, or nodular goiters. Anaplastic thyroid carcinomas are rare, highly aggressive, undifferentiated tumors that comprise 1% to 2% of all thyroid cancers in the United States. Well-differentiated papillary thyroid cancer, in which BRAF V600 mutations are an early and common driver mutation, precedes or coexists with approximately 50% of anaplastic thyroid carcinomas. Between 20% and 50% of anaplastic thyroid carcinomas harbor activating BRAF V600 mutations, with unknown prognostic significance. The possible prognostic impact of BRAF V600E mutations in carcinoma of the thyroid continues to be studied. ","tissues":["Thyroid"],"tumour_types":["Carcinoma"],"disease_or_trait":null,"pub_med_references":null,"variants":[{"definition":"BRAF V600E","type":"variantId","coding_impact":"any","variants":["10190071404531360004","10380071407533360004"],"gene_id":2273}]},{"tier":1,"definition":["BRAF V600D","BRAF codon(s) 600 any"],"interpretations":"Drug\nVemurafenib\nDabrafenib\nDabrafenib + Trametinib\nVemurafenib + Cobimetinib","tissues":null,"tumour_types":["Melanoma"],"disease_or_trait":null,"pub_med_references":null,"variants":[{"aa_positions":[600],"definition":"BRAF codon(s) 600 any","type":"codon","coding_impact":"any","gene_id":2273}]},{"tier":1,"definition":["BRAF codon(s) 600 any","BRAF V600G"],"interpretations":"Vemurafenib","tissues":null,"tumour_types":["Langerhans Cell Histiocytosis"],"disease_or_trait":null,"pub_med_references":null,"variants":[{"aa_positions":[600],"definition":"BRAF codon(s) 600 any","type":"codon","coding_impact":"any","gene_id":2273}]},{"tier":1,"definition":["BRAF codon(s) 600 any","BRAF V600M"],"interpretations":"Vemurafenib\nDabrafenib\nDabrafenib + Trametinib\nVemurafenib + Cobimetinib\nVemurafenib + Panitumumab\nEncorafenib + Binimetinib + Cetuximab\nRadiation + Trametinib + Fluorouracil","tissues":["Colon","Lung"],"tumour_types":["Melanoma","Langerhans Cell Histiocytosis","Non-Small Cell Lung Carcinoma"],"disease_or_trait":null,"pub_med_references":[19884556,23438367,27080216],"variants":[{"aa_positions":[600],"definition":"BRAF codon(s) 600 any","type":"codon","coding_impact":"any","gene_id":2273}]},{"tier":1,"definition":["BRAF V600D","BRAF V600E","BRAF V600K","BRAF V600R","BRAF codon(s) 600 any"],"interpretations":"B-RAF is a member of the RAF-family of kinases which plays an important role in the RAS-RAF-MEK-ERK mitotic signaling pathway. Mutations of B-RAF have been described in up to 100% of Hairy cell leukemia, 40-70% of Langerhans cell histiocytosis, approximately 50% of Erdheim-Chester disease, approximately 5% of diffuse large B cell lymphoma and plasma cell neoplasms and less than 5% of chronic lymphocytic leukemia. Some types of Hairy Cell Leukemia (eg, Hairy Cell Leukemia-Variant, Hairy Cell Leukemia with IgHV4-34 rearrangement) are negative for BRAF V600E mutation and may have MAP2K1 mutations. While some reports have found that 10-20% of cases of acute leukemias (ALL or AML) may have BRAF mutations, other reports have described no BRAF in those diseases or in myeloid diseases such as MDS or CML. The hotspot for mutations in BRAF is at codon Val600 and these are activating mutations. The most common activating mutation is p.Val600Glu(V600E). B-Raf inhibitors(eg, Vemurafenib) have been FDA approved for therapy for various tumor types and have been used in Hairy Cell Leukemia in some clinical settings, including in combination with other therapy.","tissues":["Blood","Bone Marrow"],"tumour_types":["Hairy Cell Leukemia"],"disease_or_trait":null,"pub_med_references":[22230299,22639828,23009221,23088640,24428489,24495477],"variants":[{"definition":"BRAF V600E","type":"variantId","coding_impact":"any","variants":["10190071404531360004","10380071407533360004"],"gene_id":2273},{"aa_positions":[600],"definition":"BRAF codon(s) 600 any","type":"codon","coding_impact":"any","gene_id":2273}]},{"tier":2,"definition":["BRAF V600E"],"interpretations":"B-RAF is a member of the RAF-family of kinases which plays an important role in the RAS-RAF-MEK-ERK mitotic signaling pathway. Mutations of B-RAF have been described in <2% of head and neck squamous cell carcinomas. The hotspot for mutations in BRAF is at codon Val600 and the most common one is p.Val600Glu (V600E). Various B-RAF inhibitors have been FDA approved for cancer therapy in certain settings. ","tissues":["Larynx","Oral Cavity"],"tumour_types":["Squamous Cell Carcinoma"],"disease_or_trait":null,"pub_med_references":[12068308],"variants":[{"definition":"BRAF V600E","type":"variantId","coding_impact":"any","variants":["10190071404531360004","10380071407533360004"],"gene_id":2273}]},{"tier":2,"definition":["BRAF V600D","BRAF V600E","BRAF V600K","BRAF V600R","BRAF codon(s) 600 any","BRAF any mutation"],"interpretations":"B-RAF is a member of the RAF-family of kinases which plays an important role in the RAS-RAF-MEK-ERK mitotic signaling pathway. Mutations of B-RAF have been described in up to 100% of Hairy cell leukemia, 40-70% of Langerhans cell histiocytosis, approximately 50% of Erdheim-Chester disease, approximately 5% of diffuse large B cell lymphoma and plasma cell neoplasms and less than 5% of chronic lymphocytic leukemia. While some reports have found that 10-20% of cases of acute leukemias (ALL or AML) may have BRAF mutations, other reports have described no BRAF in those diseases or in myeloid diseases such as MDS or CML. The hotspot for mutations in BRAF is at codon Val600 and these are activating mutations. The most common activating mutation is p.Val600Glu(V600E). Various B-Raf inhibitors(Vemurafenib, Dabrafenib) have been FDA approved for therapy for some tumor types in certain clinical settings. ","tissues":["Blood","Bone Marrow"],"tumour_types":["Acute Leukemia of Unspecified Cell Type","Acute Myeloid Leukemia","Anemia","Unspecified","Atypical Chronic Myeloid Leukemia","B Lymphoblastic Leukemia/Lymphoma","Chronic Myeloid Leukemia","Chronic Myelomonocytic Leukemia","Chronic Neutrophilic Leukemia","Cytopenia","Eosinophilia","Essential Thrombocythemia","Leukocytosis","Leukopenia","Mast Cell Neoplasm","MDS with Ring Sideroblasts","Monocytosis","Myelodysplastic Syndrome","Myelodysplastic/Myeloproliferative Neoplasm","Myeloproliferative Neoplasm","Myeloid Neoplasm","Other Acute Leukemia","Polycythemia Vera","Polycythemia","Primary Myelofibrosis","T Lymphoblastic Leukemia/Lymphoma","Thrombocytopenia","Thrombocytosis","Chronic Lymphocytic Leukemia","Diffuse Large B Cell Lymphoma"],"disease_or_trait":null,"pub_med_references":[22230299,22639828,23009221,23088640,24428489,24495477],"variants":[{"definition":"BRAF V600E","type":"variantId","coding_impact":"any","variants":["10190071404531360004","10380071407533360004"],"gene_id":2273},{"aa_positions":[600],"definition":"BRAF codon(s) 600 any","type":"codon","coding_impact":"any","gene_id":2273}]},{"tier":2,"definition":["BRAF V600E"],"interpretations":"BRAF is a member of the RAF-family of kinases which plays an important role in the RAS-RAF-MEK-ERK mitotic signaling pathway. The hotspot for mutations in BRAF is at codon Val600 and these are activating mutations. The most common activating mutation is p.Val600Glu(V600E). Activating BRAF(V600E) (Val600Glu) mutations have been identified in approximately 1-2% of lung adenocarcinomas. Various BRAF inhibitors (Vemurafenib, Dabrafenib, and Trametinib) have been FDA approved for therapy for some tumor types in certain clinical settings. Of note, Dabrafenib and Trametinib are approved for metastatic non-small cell lung cancer (NSCLC) harboring BRAF V600E mutations.","tissues":["Lung"],"tumour_types":["Adenocarcinoma"],"disease_or_trait":null,"pub_med_references":[22663011,27080216],"variants":[{"definition":"BRAF V600E","type":"variantId","coding_impact":"any","variants":["10190071404531360004","10380071407533360004"],"gene_id":2273}]},{"tier":2,"definition":["BRAF V600E"],"interpretations":"B-RAF is a member of the RAF-family of kinases which plays an important role in the RAS-RAF-MEK-ERK mitotic signaling pathway. The hotspot for mutations in BRAF is at codon Val600 and these are activating mutations. The most common activating mutation is p.Val600Glu(V600E). Various B-Raf inhibitors(Vemurafenib, Dabrafenib) have been FDA approved for therapy for some tumor types in certain settings, and clinical trials for advanced BRAF V600 mutation-positive tumors using targeted therapy (often in combination with other therapy) may be available (clinical trials.gov). It has been found that BRAF V600E has a mutation frequency of 2% in pancreatic cancer. A small study showed that no BRAF mutations were present in cases without KRAS mutations and in the few cases with BRAF mutations, a KRAS mutation was also present. ","tissues":["Pancreas"],"tumour_types":["Adenocarcinoma"],"disease_or_trait":null,"pub_med_references":null,"variants":[{"definition":"BRAF V600E","type":"variantId","coding_impact":"any","variants":["10190071404531360004","10380071407533360004"],"gene_id":2273}]},{"tier":2,"definition":["BRAF V600E"],"interpretations":"BRAF is a member of the RAF-family of kinases which plays an important role in the RAS-RAF-MEK-ERK mitotic signaling pathway. The hotspot for mutations in BRAF is at codon Val600 and these are activating mutations. The most common activating mutation is p.Val600Glu(V600E). BRAF mutation frequencies are highly controversial in biliary tract cancers ranging from 0 to 33% for BRAF V600E. As most studies with high BRAF mutation rates were performed on European cohorts, this has raised the question of whether these discordant results represent a regional difference in the genetics of biliary tract cancer. In large cohort of biliary tract cancers including intrahepatic cholangiocarcinomas, extrahepatic cholangiocarcinomas, and adenocarcinomas of the gallbladder, BRAF V600E mutations were only rarely found in intrahepatic cholangiocarcinomas and were not identified in any cases of gallbladder adenocarcinoma. The clinicopathologic significance of BRAF V600E remains to be further elucidated in adenocarcinoma of the gallbladder. Various BRAF inhibitors (Vemurafenib, Dabrafenib) have been FDA approved for therapy for some tumor types in certain settings. These results should be interpreted in the clinical and radiographic context. ","tissues":["Gall Bladder"],"tumour_types":["Adenocarcinoma"],"disease_or_trait":null,"pub_med_references":null,"variants":[{"definition":"BRAF V600E","type":"variantId","coding_impact":"any","variants":["10190071404531360004","10380071407533360004"],"gene_id":2273}]},{"tier":2,"definition":["BRAF V600E"],"interpretations":"BRAF is a member of the RAF-family of kinases which plays an important role in the RAS-RAF-MEK-ERK mitotic signaling pathway. BRAF V600E lies within the activation segment of the kinase domain of the BRAF protein and confers a gain of function. BRAF mutations are infrequent in urothelial carcinoma and are identified in 3-5% of cases. Various BRAF inhibitors (Vemurafenib, Dabrafenib) have been FDA approved for therapy for some tumor types in certain settings. The use of BRAF inhibitors in a number of other cancer types harboring BRAF V600E mutations are under investigation (clinicaltrials.gov). The clinicopathologic effects of BRAF in urothelial carcinoma remains to be fully elucidated.","tissues":["Kidney","Bladder","Ureter"],"tumour_types":["Urothelial Carcinoma"],"disease_or_trait":null,"pub_med_references":null,"variants":[{"definition":"BRAF V600E","type":"variantId","coding_impact":"any","variants":["10190071404531360004","10380071407533360004"],"gene_id":2273}]}]}],"wustl_civic":[{"version":"19-Jan-2026","items":[{"asco_entry":null,"clinical_significance":"Positive","disease":"Thyroid Cancer","doid":"1781","drug_interaction_type":null,"drugs":null,"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/79","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"BRAF V600E is shown to be associated with the tall-cell variant of papillary thyroid cancer.","evidence_status":"accepted","evidence_type":"Diagnostic","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:24 UTC","nct_ids":null,"normalized_drug":null,"phenotypes":null,"pub_med_references":[21594703],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":[{"amp_category":"Tier I - Level A","assertion_civic_url":"https://civicdb.org/links/assertions/7","assertion_description":"Combination treatment of BRAF inhibitor dabrafenib and MEK inhibitor trametinib is recommended for adjuvant treatment of stage III or recurrent melanoma with BRAF V600E mutation detected by the approved THxID kit, as well as first line treatment for metastatic melanoma. The treatments are FDA approved based on studies including the Phase III COMBI-V, COMBI-D and COMBI-AD Trials. Combination therapy is now recommended above BRAF inhibitor monotherapy. Cutaneous squamous-cell carcinoma and keratoacanthoma occur at lower rates with combination therapy than with BRAF inhibitor alone.","assertion_direction":"Supports","assertion_id":"7","assertion_summary":"BRAF V600E mutant melanoma is sensitive to dabrafenib and trametinib combination therapy","assertion_type":"Predictive","clinical_significance":"Sensitivity/Response","disease":"Melanoma","doid":"1909","drugs":["Trametinib","Dabrafenib"],"evidence_item_ids":["6940","6178","3758","6938"],"fda_companion_test":true,"gene":"BRAF","nccn_guideline":"Melanoma","nccn_guideline_version":"2.2018","normalized_drug":["Dabrafenib, Trametinib"],"regulatory_approval":true},{"amp_category":"Tier I - Level A","assertion_civic_url":"https://civicdb.org/links/assertions/10","assertion_description":"Vemurafenib and cobimetinib combination is an FDA approved first line treatment for BRAF V600E mutant metastatic melanoma based on clinical data including the Phase III coBRIM trial. The cobas 4800 BRAF V600 Mutation Test is approved as an FDA companion test for Cotellic (cobimetinib) in combination with Zelboraf (vemurafenib).","assertion_direction":"Supports","assertion_id":"10","assertion_summary":"BRAF V600E mutant melanoma is sensitive to vemurafenib and cobimetinib combination therapy","assertion_type":"Predictive","clinical_significance":"Sensitivity/Response","disease":"Melanoma","doid":"1909","drugs":["Vemurafenib","Cobimetinib"],"evidence_item_ids":["6044","6966","1421"],"fda_companion_test":true,"gene":"BRAF","nccn_guideline":"Melanoma","nccn_guideline_version":"2.2018","normalized_drug":["Cobimetinib, Vemurafenib"],"regulatory_approval":true},{"amp_category":"Tier I - Level A","assertion_civic_url":"https://civicdb.org/links/assertions/20","assertion_description":"BRAF V600E was associated with worse prognosis in Phase II and III colorectal cancer, with a stronger effect in MSI-Low or MSI-Stable tumors. In metastatic CRC, V600E was associated with worse prognosis, and meta-analysis showed BRAF mutation in CRC associated with multiple negative prognostic markers.","assertion_direction":"Supports","assertion_id":"20","assertion_summary":"BRAF V600E indicates poor prognosis in advanced colorectal cancer","assertion_type":"Prognostic","clinical_significance":"Poor Outcome","disease":"Colorectal Cancer","doid":"9256","drugs":null,"evidence_item_ids":["1552","7156","7157","7158","7159","103"],"fda_companion_test":false,"gene":"BRAF","nccn_guideline":"Colon Cancer","nccn_guideline_version":"2.2017","normalized_drug":null,"regulatory_approval":null}],"civic_variant_evidence_score":"CA123643","variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":[{"molecular_profile":{"evidence_item_ids":[73],"name":"BRAF V600E AND BRAF 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Triplet therapy resulted in better TGI and ILS compared to any agent in isolation or capecitabine + vemurafenib doublet therapy (p <0.05, p <0.0001, for all comparisons).","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":["Bevacizumab","Capecitabine","Vemurafenib"],"phenotypes":null,"pub_med_references":[22180495],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":null,"drugs":["Vemurafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/99","evidence_direction":"Supports","evidence_level":"D","evidence_statement":"This preclinical study examined vemurafenib efficacy on various colorectal cancer cell lines and in mouse xenograft experiments. Of the cell lines tested, six harbored BRAF V600E (and WT KRAS) and three harbored BRAF WT (but mutant KRAS). Of the six BRAF V600E expressing cell lines, four were sensitive to vemurafenib (IC50 ranging between 0.025 and 0.35 uM; HT29, Colo205, Colo741, LS411N). Cell lines expressing the BRAF V600E mutation responded better to vemurafenib treatment than cells wildtype for BRAF as measured by reduced cellular proliferation and inhibition of MET and ERK phosphorylation (none of the three BRAF wt cell lines had IC50s less than 10uM). Authors note that one of the vemurafenib-resistant cell lines harboring BRAF V600E (RKO) harbored a concurrent activating PIK3CA H1047R mutation. Nude, athymic mice with HT29 xenografts treated with vemurafenib experienced substantial tumor inhibition and increased lifespan at every dose tested, though authors found 75 mg/kg twice daily to be optimal (95% tumor growth inhibition, 90% increased lifespan compared to vehicle treated controls).","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":["Vemurafenib"],"phenotypes":null,"pub_med_references":[22180495],"rating":"2","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Poor Outcome","disease":"Papillary Thyroid Carcinoma","doid":"3969","drug_interaction_type":null,"drugs":null,"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/102","evidence_direction":"Does Not Support","evidence_level":"B","evidence_statement":"Unlike other studies that suggest a poorer outcome, BRAF mutation in this study was not correlated with poorer prognosis in papillary thyroid cancer.","evidence_status":"accepted","evidence_type":"Prognostic","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":null,"phenotypes":null,"pub_med_references":[24354346],"rating":"5","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Poor Outcome","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":null,"drugs":null,"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/103","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"V600E is associated with adverse pathological features of colorectal cancer. 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study of 691 cetuximab treated patients with metastatic, chemotherapy refractory colorectal cancer. Of those, 30 patients harbored BRAF V600E, were KRAS, NRAS and PIK3CA wt, and had individual response data. One patient (who harbored BRAF V600E in low copy number) responded, 11 had stable disease, and 18 progressed. Treatments included cetuximab + irinotecan (n=20), cetuximab monotherapy (n=5), cetuximab + FOLFIRI (n=4), and cetuximab + oxaliplatin + 5FU (n=1). Median PFS was 8 weeks (2-32 weeks), median OS was 25 weeks (4-237 weeks), and median number of previous chemotherapy lines was 2 (0-4). Median age was 61 years old (42-78) and there were 16 males and 14 females. Authors concluded that BRAF mutation (23/24 of mutants were BRAF V600E) was strongly associated with poor response to cetuximab and suggested that mutation status of BRAF is more informative than those of NRAS and PIK3CA exon 20 for predicting cetuximab response (second only to KRAS).","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":["Cetuximab"],"phenotypes":null,"pub_med_references":[20619739],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Poor Outcome","disease":"Multiple Myeloma","doid":"9538","drug_interaction_type":null,"drugs":null,"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/463","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"In patients with multiple myeloma, those with BRAF V600E had shorter overall survival than wild-type.","evidence_status":"accepted","evidence_type":"Prognostic","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:24 UTC","nct_ids":null,"normalized_drug":null,"phenotypes":null,"pub_med_references":[23612012],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Poor Outcome","disease":"Papillary Thyroid Carcinoma","doid":"3969","drug_interaction_type":null,"drugs":null,"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/656","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"In patients with papillary thyroid cancer harboring both BRAF V600E and the TERT promotor mutation C228T (N=35), recurrence-free survival is worse than in patients harboring one of these mutations (N=159 BRAF, N=26 TERT promoter mutated) or no mutations in either gene (N=287)(P<0.001).","evidence_status":"accepted","evidence_type":"Prognostic","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":null,"phenotypes":null,"pub_med_references":[25024077],"rating":"5","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Melanoma","doid":"1909","drug_interaction_type":null,"drugs":["Pictilisib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/757","evidence_direction":"Supports","evidence_level":"C","evidence_statement":"One patient with BRAF V600E mutated melanoma (with no detected PI3K pathway deregulation) had a partial response on treatment with pictilisib, a PI3K inhibitor, for 9.5 months. Study was a phase-1 with 60 patients enrolled.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:24 UTC","nct_ids":null,"normalized_drug":["Pictilisib"],"phenotypes":null,"pub_med_references":[25370471],"rating":"2","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Resistance","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":"Substitutes","drugs":["Cetuximab","Panitumumab"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/816","evidence_direction":"Does Not Support","evidence_level":"B","evidence_statement":"This meta-analysis of 7 randomized control trials evaluating overall survival (OS) (8 for progression free survival) could not definitely state that survival benefit of anti-EGFR monoclonal antibodies is limited to patients with wild type BRAF. In other words, the authors believe that there is insufficient data to justify the exclusion of anti-EGFR monoclonal antibody therapy for patients with mutant BRAF. In these studies, mutant BRAF specifically meant the V600E mutation.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:24 UTC","nct_ids":null,"normalized_drug":["Cetuximab, Panitumumab"],"phenotypes":null,"pub_med_references":[25989278],"rating":"4","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Resistance","disease":"Melanoma","doid":"1909","drug_interaction_type":null,"drugs":["MEK Inhibitor RO4987655"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/994","evidence_direction":"Does Not Support","evidence_level":"B","evidence_statement":"This was a phase I expansion and pharmacodynamic study of oral MEK inhibitor RO4987655 on advanced cancer. Of 17 patients with BRAF V600E melanoma, 4 achieved partial response, 5 experienced stable disease lasting longer than 16 weeks, and 8 experienced disease progression (including 2 with prior vemurafenib treatment). One of the partial responders had a concomitant EGFR mutation, and two of the stable disease patients had other concomitant mutations (in RET or MET). The median days on treatment was 113 (18-366) for BRAF V600E melanoma patients and 107 (17-323) for BRAF V600 wildtype patients (n=23). Patients with BRAF V600E mutant melanoma experienced similar response rates (24% vs 20%) and rates of metabolic response measured by decrease in FDG uptake assessed by FDG-PET (86% vs 75%) compared to non-BRAF mutant patients. Patients with melanoma, either BRAF wt or V600E, experienced significant decreases in Ki67 expression by day 15 of MEK inhibitor treatment (P<0.02). The authors conclude that RO4987655 has clinical activity in BRAF V600E and BRAF wt melanoma.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":null,"phenotypes":null,"pub_med_references":[24947927],"rating":"2","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Melanoma","doid":"1909","drug_interaction_type":"Combination","drugs":["Dactolisib","Selumetinib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/1005","evidence_direction":"Supports","evidence_level":"D","evidence_statement":"49 BRAF-mutant melanoma cell lines from patients not previously treated with BRAF inhibition were analyzed. 21 exhibited primary resistance to BRAF inhibition using PLX4720. Inhibition of MEK1/2 (AZD6244 [selumetinib]) and PI3K/mTOR (BEZ235 [dactolisib]) was the most effective approach to counteract resistance in comparison to inhibition with the PLX4720 (progenitor of vemurafenib)-BEZ235 (where response was assessed by apoptosis, viability, p-ERK, p-Akt inhibition).","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":["Dactolisib","Selumetinib"],"phenotypes":null,"pub_med_references":[26678033],"rating":"2","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Positive","disease":"Hairy Cell Leukemia","doid":"285","drug_interaction_type":null,"drugs":null,"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/1127","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"In 47 patients with Hairy Cell Leukemia, sequencing discovered a V600E mutation in all 47 of the sequenced patients.","evidence_status":"accepted","evidence_type":"Diagnostic","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:24 UTC","nct_ids":null,"normalized_drug":null,"phenotypes":null,"pub_med_references":[21663470],"rating":"4","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Cancer","doid":"162","drug_interaction_type":null,"drugs":["Cobimetinib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/1141","evidence_direction":"Supports","evidence_level":"D","evidence_statement":"Preclinical study analyzing the differential response to MEK inhibitors in KRAS and BRAF mutant cancer cell lines and mouse xenografts. Inhibition of active, phosphorylated MEK by GDC-0973 (cobimetinib) is required for strong inhibition of the MAPK pathway in BRAF-mutant tumours. This study provides mechanistic rationale for improved efficacy of cobimetinib in BRAF-mutant models compared to MEK inhibitors acting through an alternative mechanism (GDC-0623 and G-573).","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:24 UTC","nct_ids":null,"normalized_drug":["Cobimetinib"],"phenotypes":null,"pub_med_references":[23934108],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Melanoma","doid":"1909","drug_interaction_type":null,"drugs":["Vemurafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/1398","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"The BRIM-3 Phase III trial NCT01006980 assessed BRAF inhibitor vemurafenib versus dacarbazine in 598 patients with treatment naive metastatic melanoma and confirmed V600E mutation. Significant differences were seen in overall survival (13.3 months with vemurafenib vs. 10.0 months with dacarbazine) and median progression free survival (6.9 months with vemurafenib vs. 1.6 months with dacarbazine)","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:24 UTC","nct_ids":["NCT01006980"],"normalized_drug":["Vemurafenib"],"phenotypes":null,"pub_med_references":[24508103],"rating":"5","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":null,"drugs":["Vemurafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/1405","evidence_direction":"Does Not Support","evidence_level":"B","evidence_statement":"In this Phase II pilot study (NCT00405587) of BRAF V600 inhibitor vemurafenib in 21 metastatic colorectal cancer (CRC) patients with BRAF V600E, one patient had a durable 21 week partial response, and seven patients had 8 week stable disease as best response. Median progression free survival was 2.1 months and median overall survival was 7.7 months. The authors conclude that single agent vemurafenib did not show meaningful activity in V600E CRC, in contrast to the significant vemurafenib activity against V600 in melanoma.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:24 UTC","nct_ids":["NCT00405587"],"normalized_drug":["Vemurafenib"],"phenotypes":null,"pub_med_references":[26460303],"rating":"4","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Reduced Sensitivity","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":null,"drugs":["Dabrafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/1406","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"In trial NCT00880321, dabrafenib was tested in various solid tumor types harboring mutant BRAF after establishing dosage of 150 mg twice daily. In nine colorectal cancer patients with established V600E mutation, 1 confirmed response, 7 instances of stable disease, and 1 case of progressive disease was seen, which contrasted strongly with a 56% confirmed response rate seen in metastatic V600E melanoma patients similarly treated in the same study.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2025-12-17 19:06:25 UTC","nct_ids":["NCT00880321"],"normalized_drug":["Dabrafenib"],"phenotypes":null,"pub_med_references":[22608338],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":"Combination","drugs":["Vemurafenib","Cetuximab","Gefitinib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/1408","evidence_direction":"Supports","evidence_level":"D","evidence_statement":"5 of 7 colorectal cancer (CRC) cell lines with BRAF V600E mutation were resistant to treatment with the BRAF inhibitor vemurafenib. An RNAi screen in the WiDr cell line (a V600E CRC line) identified EGFR as an enhancer for survival when exposed to vemurafenib. Treatment with vemurafenib and EGFR inhibitor (cetuximab or gefitinib) in V600E CRC cells (WiDr, VACO432 and KM20) showed inhibited growth as well as induction of the cleaved PARP apoptotic marker. WiDr and VACO432 cells were injected into immunodeficient mice. Modest response was seen with vemurafenib treatment, while combination treatment showed considerable tumor growth inhibition as compared to control.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:24 UTC","nct_ids":null,"normalized_drug":["Cetuximab","Gefitinib","Vemurafenib"],"phenotypes":null,"pub_med_references":[22281684],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Skin Melanoma","doid":"8923","drug_interaction_type":null,"drugs":["Vemurafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/1409","evidence_direction":"Supports","evidence_level":"A","evidence_statement":"Phase 3 randomized clinical trial comparing vemurafenib with dacarbazine in 675 patients with previously untreated, metastatic melanoma with the BRAF V600E mutation. At 6 months, overall survival was 84% (95% confidence interval [CI], 78 to 89) in the vemurafenib group and 64% (95% CI, 56 to 73) in the dacarbazine group. A relative reduction of 63% in the risk of death and of 74% in the risk of either death or disease progression was observed with vemurafenib as compared with dacarbazine (P<0.001 for both comparisons).","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:24 UTC","nct_ids":["NCT01006980"],"normalized_drug":["Vemurafenib"],"phenotypes":null,"pub_med_references":[21639808],"rating":"5","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Skin Melanoma","doid":"8923","drug_interaction_type":null,"drugs":["Vemurafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/1410","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"Phase 2 trial in 132 patients with previously treated metastatic melanoma with BRAF V600E mutation. Confirmed overall response rate was 53% (95% confidence interval [CI], 44 to 62; 6% with a complete response and 47% with a partial response), median duration of response was 6.7 months (95% CI, 5.6 to 8.6), and median progression-free survival was 6.8 months (95% CI, 5.6 to 8.1). Median overall survival was 15.9 months (95% CI, 11.6 to 18.3).","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:24 UTC","nct_ids":["NCT00949702"],"normalized_drug":["Vemurafenib"],"phenotypes":null,"pub_med_references":[22356324],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":"Combination","drugs":["Panitumumab","Vemurafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/1413","evidence_direction":"Does Not Support","evidence_level":"B","evidence_statement":"Treatment response to mutant BRAF inhibitor vemurafenib and EGFR inhibitor panitumumab was assayed in 12 patients with metastatic colorectal cancer (CRC) who had progressed on chemotherapy. Two patients had confirmed partial responses, and 2 showed stable disease over 6 months. The authors conclude that although some efficacy is seen, only a small subset of patients respond to this treatment and the responses are not durable.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:24 UTC","nct_ids":null,"normalized_drug":["Panitumumab","Vemurafenib"],"phenotypes":null,"pub_med_references":[25589621],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Papillary Thyroid Carcinoma","doid":"3969","drug_interaction_type":null,"drugs":["Vemurafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/1414","evidence_direction":"Supports","evidence_level":"C","evidence_statement":"A 73 year old patient with prior history of breast cancer presented with metastatic papillary thyroid carcinoma. After two treatments of I-131 a comprehensive tumor profile revealed BRAF V600E as the only genetic alteration on a near diploid genome with trisomy 1q. Vemurafenib treatment resulted in improvement of symptoms and considerable reductions in tumor mass, and after 23 months the patient remained on therapy with well controlled disease.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:24 UTC","nct_ids":null,"normalized_drug":["Vemurafenib"],"phenotypes":null,"pub_med_references":[24987354],"rating":"4","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Melanoma","doid":"1909","drug_interaction_type":"Combination","drugs":["Vemurafenib","Cobimetinib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/1421","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"In this Phase III trial (coBRIM, NCT01689519) of 495 V600 mutant melanoma patients, 344 had V600E mutation. 174 patients were treated with vemurafenib and placebo, and 170 were treated with vemurafenib and cobimetinib and tested for progression free survival. 88 of 174 monotherapy group patients had an event with median progression free survival of 6.5 months. In the combination group 58 of 174 patients had an event with median progression-free survival not met, however, when in combination with other V600 mutations median progression-free survival was 9.9 months with combination treatment. Median time to followup for the whole cohort was 7.3 months. Hazard Ratio for progression or death was 0.57 (0.41-0.80).","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":["NCT01689519"],"normalized_drug":["Cobimetinib, Vemurafenib"],"phenotypes":null,"pub_med_references":[25265494],"rating":"4","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":"Combination","drugs":["GDC-0879","Dactolisib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/1428","evidence_direction":"Supports","evidence_level":"D","evidence_statement":"In a mouse model of BRAF V600E colorectal cancer, western blots from tumors in mice treated with BRAF inhibitor GDC-0879 and PI3K/mTOR inhibitor BEZ235 showed stronger reduction in phospho-Akt and phospho-S6 than PI3K/mTOR inhibitor alone, and combination inhibition also resulted in stronger phospho-ERK inhibition in tumors than did BRAF inhibition alone. Increased apoptosis in tumors was seen in dual treatment conditions with increased TUNEL-positive cells. In vehicle treated mice, area of colon covered by tumor increased, while treatment with single agent inhibitors caused growth inhibition resulting in no change in colon area covered by tumors. Administration of dual inhibitors induced tumor regression apparent in a decrease of colonic area covered by tumors over the course of treatment.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:24 UTC","nct_ids":null,"normalized_drug":["Dactolisib"],"phenotypes":null,"pub_med_references":[23549875],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Gastrointestinal Neuroendocrine Tumor","doid":"0050626","drug_interaction_type":"Combination","drugs":["Trametinib","Vemurafenib","Dabrafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/1430","evidence_direction":"Supports","evidence_level":"C","evidence_statement":"BRAF mutations were identified in 9% of 108 cases of high-grade colorectal neuroendocrine tumors (80% V600E). Two patients were treated with a combination of BRAF and MEK inhibition and exhibited durable response (beyond 7 and 9 months, respectively). Urinary BRAF V600E tumor DNA correlated with disease response in one of the patients. BRAF and MEK inhibition was either dabrafenib+trametinib (case 1) or vemurafenib+trametinib (case 2).","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:24 UTC","nct_ids":null,"normalized_drug":["Dabrafenib","Trametinib","Vemurafenib"],"phenotypes":null,"pub_med_references":[27048246],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Poor Outcome","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":null,"drugs":null,"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/1552","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"In a study of 908 patients with colorectal cancer, 45 patients had BRAF V600E mutations and 589 patients were BRAF wild type. BRAF V600E mutations were more likely to be proximal tumors (68.9%, 20.7%; p<0.0001), they were more likely to be poorly differentiated (17.7%, 1.9%; p<0.0001), they were more likely to be mucinous carcinoma type (20.0%, 4.2%; p=0.0003), they were more likely to have lymphatic invasion (77.6%, 49.9%; p=0.0003), and they had a shorter survival time (31.1 mo, 41.6 mo; p=0.001). The 3-year survival rate was significantly poorer in the V600E group when compared to the wild type group (63.8%, 87.9%; p<0.0001).","evidence_status":"accepted","evidence_type":"Prognostic","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:24 UTC","nct_ids":null,"normalized_drug":null,"phenotypes":null,"pub_med_references":[27404270],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Hairy Cell Leukemia","doid":"285","drug_interaction_type":null,"drugs":["Vemurafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/1579","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"Two clinical trials evaluated the effects of vemurafenib in 54 patients with BRAF (V600E) positive hairy-cell leukemia. The overall response rate was 98% with 19/54 having a complete response and 34/54 having a partial response. In the Italian study (n=25), the median relapse-free survival was 9 months and in the U.S. study (n=24), rate of progression-free survival was 73% with overall survival rate of 91%.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:24 UTC","nct_ids":["NCT01711632"],"normalized_drug":["Vemurafenib"],"phenotypes":null,"pub_med_references":[26352686],"rating":"2","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":"Combination","drugs":["Vemurafenib","Panitumumab"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/1589","evidence_direction":"Supports","evidence_level":"C","evidence_statement":"Case report of a patient with BRAF V600E mutant metastatic colorectal cancer. Combined EGFR and BRAF inhibition (panitumumab and vemurafenib) showed an initial partial response for 4 months with subsequent disease progression.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:24 UTC","nct_ids":null,"normalized_drug":["Panitumumab","Vemurafenib"],"phenotypes":null,"pub_med_references":[27325282],"rating":"2","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Papillary Thyroid Carcinoma","doid":"3969","drug_interaction_type":null,"drugs":["Vemurafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/1591","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"Open-label non-randomised phase 2 trial in patients with recurrent or metastatic BRAF V600E mutant papillary thyroid cancer refractory to radioactive iodine. Patients had (cohort 2) or had not (cohort 1) previously been treated with VEGFR inhibitors. 51 patients were enrolled (26 cohort 1, 25 cohort 2). In cohort 1, partial response was achieved in ten (38.5%) patients. Nine patients achieved stable disease for at least 6 months (35%). Median PFS was 18.2 months and median OS not reached after a median follow-up pf 18.8 months. In cohort 2, six patients (27.3%) achieved a partial response and another six patients achieved stable disease for at least six months. Median PFS was 8.9 months and median OS was 14.4. months.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:24 UTC","nct_ids":["NCT01286753"],"normalized_drug":["Vemurafenib"],"phenotypes":null,"pub_med_references":[27460442],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Multiple Myeloma","doid":"9538","drug_interaction_type":null,"drugs":["Vemurafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/1698","evidence_direction":"Supports","evidence_level":"C","evidence_statement":"A 65-year-old man presented with stage II myeloma. He was initially treated with chemotherapy and he received an autologous stem cell transplant. Sequencing of the recurrent tumor harbored BRAF V600E mutation and he was treated with vemurafenib. After 7 weeks of treatment, the patient relapsed and died.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:24 UTC","nct_ids":null,"normalized_drug":["Vemurafenib"],"phenotypes":null,"pub_med_references":[24997557],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Multiple Myeloma","doid":"9538","drug_interaction_type":null,"drugs":["Vemurafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/1699","evidence_direction":"Supports","evidence_level":"C","evidence_statement":"A 54-year-old man presented with stage II myeloma. He was initially treated with chemotherapy and received an autologous stem cell transplant. Genomic profiling of the bone biopsy revealed BRAF V600E activating mutation and the patient was treated with vemurafenib. At 4-months post treatment (time of case study report) the patient maintains near-resolution of hypermetabolic lesions.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:24 UTC","nct_ids":null,"normalized_drug":["Vemurafenib"],"phenotypes":null,"pub_med_references":[24997557],"rating":"2","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Melanoma","doid":"1909","drug_interaction_type":null,"drugs":["Vemurafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/1749","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"Multicenter, phase 1, dose-escalation trial of PLX4032 (Vemurafenib). Treatment of metastatic melanoma with PLX4032 in patients with tumors that carry the V600E BRAF mutation resulted in complete or partial tumor regression in the majority of patients (N=37/48). Patients without the V600E mutation had evidence of tumor regression.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":["Vemurafenib"],"phenotypes":null,"pub_med_references":[20818844],"rating":"4","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":"Combination","drugs":["Vemurafenib","Irinotecan","Cetuximab"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/1902","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"Phase 1b study of vemurafenib, cetuximab and irinotecan in 19 patients with colorectal cancer (1 with appendiceal cancer). Six of 17 evaluable patients achieved an objective response, 15 patients total had either stable disease or radiographic response (the patient with appendiceal cancer had disease progression). Estimated median PFS was 7.7 months. Effect of the combined treatment was also observed in xenograft and cell line studies.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:24 UTC","nct_ids":["NCT01787500"],"normalized_drug":["Cetuximab","Irinotecan","Vemurafenib"],"phenotypes":null,"pub_med_references":[27729313],"rating":"4","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Poor Outcome","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":null,"drugs":null,"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/1940","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"In a study of 468 colorectal cancer samples, 61 patients had micro-satellite instability and there was a statistically significantly better prognosis for BRAF WT patients relative to BRAF (V600E)-mutated patients (Log-rank P=0.0903).","evidence_status":"accepted","evidence_type":"Prognostic","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":null,"phenotypes":null,"pub_med_references":null,"rating":"4","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Resistance","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":"Substitutes","drugs":["Panitumumab","Cetuximab"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/2115","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"In metastatic colorectal cancer patients with wildtype KRAS status, those with a BRAF V600E mutation were less likely to respond to treatment with cetuximab or panitumumab than those with wildtype BRAF (0% vs. 32% , P=0.029). Regardless of KRAS status, patients with BRAF mutations had reduced progression-free and overall survival (P=0.0107 and P <0.0001, respectively). Transfection of the colorectal cancer cell line DiFi with a BRAF V600E expression vector conferred decreased sensitivity to cetuximab and panitumumab in comparison to cells transfected with empty vector.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:24 UTC","nct_ids":null,"normalized_drug":["Cetuximab, Panitumumab"],"phenotypes":null,"pub_med_references":[19001320],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Poor Outcome","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":null,"drugs":null,"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/2116","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"In a study of metastatic colorectal cancer patients who received 5-FU-based first-line chemotherapy, those with BRAF V600E mutations had reduced progression-free survival (4.3mo vs. 12.5mo, HR:4.9, 95%CI:2.7-9.0, P<0.0001, univariate analysis; HR:4.0, 95%CI:2.2-7.4, P<0.0001, multivariate analysis) and reduced overall survival (10.9mo vs. 40.5mo, HR:4.5, 95%CI:2.4-8.4, P<0.0001, univariate analysis; HR:4.1, 95%CI:2.1-8.0, P<0.0001, multivariate analysis) compared to those with wildtype BRAF.","evidence_status":"accepted","evidence_type":"Prognostic","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-12-03 08:11:19 UTC","nct_ids":null,"normalized_drug":null,"phenotypes":null,"pub_med_references":[19603024],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Resistance","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":null,"drugs":["Oxaliplatin"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/2117","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"Of 100 metastatic colorectal cancer patients treated with oxaliplatin-based first-line therapy, the 6 patients with either BRAF V600E or D594K had reduced progression-free survival compared to 94 patients with wildtype BRAF (5.0mo vs. 11.7mo, HR:6.4, 95%CI:2.6-15.6, P<0.0001).","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:24 UTC","nct_ids":null,"normalized_drug":["Oxaliplatin"],"phenotypes":null,"pub_med_references":[19603024],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Resistance","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":null,"drugs":["Irinotecan"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/2118","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"The presence of BRAF V600E or D594K was associated with reduced progression-free survival in 5 patients with metastatic colorectal cancer treated with irinotecan-based first line therapy (3.5mo vs. 12.8mo, HR:4.1, 95%CI:1.5-11.3, P=0.006) when compared to 39 patients with wildtype BRAF.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":["Irinotecan"],"phenotypes":null,"pub_med_references":[19603024],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Resistance","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":"Combination","drugs":["Oxaliplatin","Bevacizumab","Capecitabine"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/2121","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"In a study of metastatic colorectal cancer patients treated with capecitabine, oxaliplatin, and bevacizumab, those with BRAF V600E mutations had reduced progression-free survival (5.9mo vs. 12.2mo, P=0.003) and reduced overall survival (15.0mo vs. 24.6mo, P=0.002) compared to those with wildtype BRAF.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":["Bevacizumab, Capecitabine, Oxaliplatin"],"phenotypes":null,"pub_med_references":[19571295],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Melanoma","doid":"1909","drug_interaction_type":null,"drugs":["Trametinib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/2135","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"In a study of 322 advanced melanoma patients with BRAF-V600E (N=281), BRAF-V600K (N=40), or both mutations (N=1), treatment with trametinib was associated with improved progression-free survival (4.8mo vs. 1.5mo; HR: 0.45, 95% CI: 0.33-0.63, P<0.001) compared to chemotherapy control group. Additionally, treatment with trametinib was associated with increased 6-month overall survival (HR: 0.54, 95% CI: 0.32-0.92, P=0.01). The authors note similar outcomes for the primary efficacy population (V600E only) and the intention-to-treat population.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":["NCT01245062"],"normalized_drug":["Trametinib"],"phenotypes":null,"pub_med_references":[22663011],"rating":"4","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Poor Outcome","disease":"Papillary Thyroid Carcinoma","doid":"3969","drug_interaction_type":null,"drugs":null,"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/2137","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"In a study of 102 papillary thyroid cancer patients with a 15 year median follow-up time, those with BRAF V600E mutations had reduced overall survival compared to those with wildtype BRAF (P=0.015, log-rank test). The presence of BRAF V600E was associated with poorer outcome as defined by persistent disease or death (Odds ratio:14.63, 95%CI:1.28-167.29, P=0.03, multivariate analysis.","evidence_status":"accepted","evidence_type":"Prognostic","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:24 UTC","nct_ids":null,"normalized_drug":null,"phenotypes":null,"pub_med_references":[18682506],"rating":"4","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Poor Outcome","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":null,"drugs":null,"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/2362","evidence_direction":"Does Not Support","evidence_level":"C","evidence_statement":"This study examined outcomes of 240 rectum cancer patients treated with total mesorectal excision therapy. Tumor samples were obtained at the time of surgery and genotyped for BRAF exon 15 mutations. BRAF V600E was identified in 5 cases. The authors reported that no differences were found in overall survival between patients with and without BRAF mutations (P > 0.1).","evidence_status":"accepted","evidence_type":"Prognostic","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":null,"phenotypes":null,"pub_med_references":[19903786],"rating":"2","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Poor Outcome","disease":"Papillary Thyroid Carcinoma","doid":"3969","drug_interaction_type":null,"drugs":null,"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/2503","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"In a meta-analysis of 8 studies, papillary thyroid cancer patients with BRAF V600E mutation had a higher frequency of recurrence and persistent disease compared to those with wildtype BRAF (28.5% vs. 12.8% , Risk ratio:2.14, 95%CI:1.67-2.74, P<0.00001).","evidence_status":"accepted","evidence_type":"Prognostic","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":null,"phenotypes":null,"pub_med_references":[21882184],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Lung Non-small Cell Carcinoma","doid":"3908","drug_interaction_type":"Combination","drugs":["Trametinib","Dabrafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/3017","evidence_direction":"Supports","evidence_level":"A","evidence_statement":"Patients with BRAF V600E-mutant NSCLC (n=57) were enrolled into a phase 2, multicentre, non-randomised, open-label study, administering dabrafenib plus trametinib. The overall response rate was 36/57 (63.2%, [95% CI 49.3-75.6]) and the median progression-free survival was 9.7 months (95% CI 6.9-19.6). At data cutoff (11.6 months of follow-up), 18/36 (50%) confirmed responses were ongoing and 23/57 (40%) of patients had died.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":["NCT01336634"],"normalized_drug":["Dabrafenib, Trametinib"],"phenotypes":null,"pub_med_references":[27283860],"rating":"4","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Resistance","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":"Combination","drugs":["FOLFOX-4 Regimen","Cetuximab"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/3739","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"In a retrospective study of 148 treatment naive metastatic colorectal cancer patients, patients with BRAF V600E and wildtype NRAS/KRAS (n=14) mutation treated with FOLFOX4 plus cetuximab were associated with a decreased progression free survival (7.2mo vs. 9.7mo, HR:0.39, 95% CI:0.21-0.72, P=0.0017), and decreased overall survival (11.7mo vs. 28.5mo, HR:0.23, 95% CI:0.12-0.41, P<0.0001), as compared to patients with wildtype BRAF, NRAS and KRAS.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:24 UTC","nct_ids":null,"normalized_drug":["Cetuximab","Folfox"],"phenotypes":null,"pub_med_references":[25666295],"rating":"4","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Melanoma","doid":"1909","drug_interaction_type":null,"drugs":["Vemurafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/3750","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"In a phase 2 clinical trial (NCT00949702) of 132 BRAF mutation positive metastatic melanoma patients treated with vemurafenib monotherapy, patients harboring BRAF V600E (n=123) or V600K (n=9) mutations were associated with a favorable objective response rate (53% per RECIST v1.1 criteria, 70/132), with 6% (8/132) and 47% (62/132) of patients achieving complete response and partial response, respectively.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":["Vemurafenib"],"phenotypes":null,"pub_med_references":[23569304],"rating":"4","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Melanoma","doid":"1909","drug_interaction_type":null,"drugs":["Vemurafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/3755","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"In a clinical study (NCT01307397) of Polish, stage IIIC/IV, melanoma patients with metastases (n=75) harboring BRAF V600 mutation (as detected by cobas 4800 BRAF V600 Mutation Test), median overall survival was 61.9% (95% CI: 50.1-73.6) and median progression free survival was 7.4 months (95% CI: 5.5-9.2). Median duration of response was 7.4 months (95% CI: 5.7-9.2), with 3% (2/75) and 43% (29/75) of patients achieving a complete and partial response, respectively.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":["Vemurafenib"],"phenotypes":null,"pub_med_references":[26557775],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Melanoma","doid":"1909","drug_interaction_type":null,"drugs":["Vemurafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/3757","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"In a retrospective study of 300 stage IV melanoma patients, patients with BRAF V600E mutation (n=175) were associated with a 4.8% (8/167) complete response, a 58.1% (97/167) partial response and stable disease in 22.2% (37/167) of cases, while 15% (25/167) of patients harboring BRAF V600E experienced progressive disease.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":["Vemurafenib"],"phenotypes":null,"pub_med_references":[25524477],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Skin Melanoma","doid":"8923","drug_interaction_type":"Combination","drugs":["Trametinib","Dabrafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/3758","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"In a clinical trial (NCT01597908) of 704 metastatic melanoma patients, patients harboring a BRAF V600E mutation and treated with vemurafenib (n=317) were associated with a 51% response rate, as compared to a 64% response rate (p<0.001) in V600E mutation positive patients treated with dabrafenib and trametinib combination therapy (n=312). Median progression-free survival was 11.4 months in the combination-therapy group and 7.3 months in the vemurafenib group (hazard ratio, 0.56; 95% CI, 0.46 to 0.69; P<0.001).","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":["NCT01597908"],"normalized_drug":["Dabrafenib, Trametinib"],"phenotypes":null,"pub_med_references":[25399551],"rating":"4","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Childhood Pilocytic Astrocytoma","doid":"6812","drug_interaction_type":null,"drugs":["Vemurafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/3777","evidence_direction":"Supports","evidence_level":"C","evidence_statement":"In a case report, a 28 month old patient with a cervicomedullary low grade glioma compatible with pilocytic astrocytoma which was resected had a second lesion consistent with a ganglioglioma 3 years later. This mass progressed under treatment at which point PCR amplification of BRAF exon 15 and subsequent Sanger sequencing the initial biopsy revealed the tumor harbored a BRAF V600E mutation. Based on these results, vemurafenib monotherapy was started and radiological and clinical response was noted after 3 months of treatment, which was sustained after 6 months of therapy. Prior to vemurafenib treatment, the patient had undergone tracheotomy, was treated with standard chemotherapy and underwent another surgery, but had developed progressive disease.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":["Vemurafenib"],"phenotypes":null,"pub_med_references":[25524464],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Ovarian Serous Carcinoma","doid":"0050933","drug_interaction_type":null,"drugs":["Vemurafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/3787","evidence_direction":"Supports","evidence_level":"C","evidence_statement":"A stage 4B, low-grade papillary serous ovarian adenocarcinoma patient, harboring a BRAF V600E mutation was associated with response to vemurafenib monotherapy. The patient was treated with standard chemotherapy, hormone therapy and bevacizumab prior to the identification of the BRAF V600E mutation; next, the patient was treated with paclitaxel and an anti-HER3 antibody and finally with vemurafenib, obtaining a partial response of greater than 1 year.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":["Vemurafenib"],"phenotypes":null,"pub_med_references":[26490654],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Resistance","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":null,"drugs":["Panitumumab"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/3827","evidence_direction":"Supports","evidence_level":"C","evidence_statement":"One patient participating in a large retrospective study of EGFR monoclonal antibodies in metastatic colorectal cancer had a tumor which harbored BRAF V600E, was wildtype for NRAS, KRAS and PIK3CA, and had individual response data. This patient was was a male treated with panitumumab monotherapy as 1st line therapy who experienced progressive disease (PFS: 7 weeks; OS: 10 weeks).","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":["Panitumumab"],"phenotypes":null,"pub_med_references":[20619739],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Cholangiocarcinoma","doid":"4947","drug_interaction_type":"Combination","drugs":["Dabrafenib","Trametinib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/5902","evidence_direction":"Supports","evidence_level":"C","evidence_statement":"Chemotherapy-refractory, metastatic cholangiocarcinoma with CNS involvement and a BRAF V600E mutation had a partial response at 8 weeks to dabrafenib and trametinib combination with complete radiologic regression at 12 weeks. At 6 months the patient was still on treatment.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":["Dabrafenib, Trametinib"],"phenotypes":null,"pub_med_references":[28480077],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Intrahepatic Cholangiocarcinoma","doid":"4928","drug_interaction_type":"Combination","drugs":["Trametinib","Dabrafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/5903","evidence_direction":"Supports","evidence_level":"C","evidence_statement":"Two cases of patients with BRAF V600E positive, refractory intrahepatic cholangiocarcinoma showed excellent clinical and radiographic response to combination dabrafenib and trametinib treatment. One patient achieved complete remission at 6 months with progression at 9 months and the other partial remission at 2 months and no progression as of 5 months.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":["Dabrafenib, Trametinib"],"phenotypes":null,"pub_med_references":[28078132],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Intrahepatic Cholangiocarcinoma","doid":"4928","drug_interaction_type":"Combination","drugs":["Dabrafenib","Trametinib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/5904","evidence_direction":"Supports","evidence_level":"C","evidence_statement":"Dabrafenib and trametinib combination showed durable response for a patient with standard chemotherapy and radiation refractory, poorly differentiated, intrahepatic cholangiocarcinoma harboring BRAF V600E. At time of publication, 8.5 months, the patient was still on treatment.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":["Dabrafenib, Trametinib"],"phenotypes":null,"pub_med_references":[25435907],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Cholangiocarcinoma","doid":"4947","drug_interaction_type":"Combination","drugs":["Vemurafenib","Irinotecan","Panitumumab"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/5906","evidence_direction":"Supports","evidence_level":"C","evidence_statement":"A 31 year old patient with metastatic cholangiocarcinoma with BRAF V600E was treated with vemurafenib, panitumumab and irinotecan triplet therapy. By 2 months, 50% reduction of tumor volume was noted, including multiple lung metastases, complete clinical response was noted by CT 6 months post therapy and this treatment was continued.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":["Irinotecan","Panitumumab","Vemurafenib"],"phenotypes":null,"pub_med_references":[26687137],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Lung Non-small Cell Carcinoma","doid":"3908","drug_interaction_type":null,"drugs":["Vemurafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/5958","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"The phase 2a MyPathway study assigned patients with HER2, EGFR, BRAF or SHH alterations to treatment with pertuzumab plus trastuzumab, erlotinib, vemurafenib, or vismodegib, respectively. Within the BRAF mutant group, fourteen patients had refractory BRAF V600E-mutated NSCLC (adenocarcinoma, n = 13; sarcomatoid, n = 1). Six patients (43%; 95% CI, 18% to 71%) had objective responses (one CR, five PR), and two additional patients had SD > 120 days. The median DOR was 5 months (range, 4 to 14 months).","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":["NCT02091141"],"normalized_drug":["Vemurafenib"],"phenotypes":null,"pub_med_references":null,"rating":"4","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Ovarian Cancer","doid":"2394","drug_interaction_type":null,"drugs":["Vemurafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/5959","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"The phase 2a MyPathway study assigned patients with HER2, EGFR, BRAF or SHH alterations to treatment with pertuzumab plus trastuzumab, erlotinib, vemurafenib, or vismodegib, respectively. Among 4 patients with BRAF V600E mutant ovarian cancer, 2 had a partial response and one had stable disease > 120days.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":["NCT02091141"],"normalized_drug":["Vemurafenib"],"phenotypes":null,"pub_med_references":null,"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":null,"drugs":["Vemurafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/5960","evidence_direction":"Supports","evidence_level":"C","evidence_statement":"The phase 2a MyPathway study assigned patients with HER2, EGFR, BRAF or SHH alterations to treatment with pertuzumab plus trastuzumab, erlotinib, vemurafenib, or vismodegib, respectively. Among 2 patients with BRAF V600E mutant colorectal cancer, 1 had a partial response.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":["NCT02091141"],"normalized_drug":["Vemurafenib"],"phenotypes":null,"pub_med_references":null,"rating":"2","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Anaplastic Thyroid Carcinoma","doid":"0080522","drug_interaction_type":"Combination","drugs":["Vemurafenib","Pertuzumab"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/5961","evidence_direction":"Supports","evidence_level":"C","evidence_statement":"The phase 2a MyPathway study assigned patients with HER2, EGFR, BRAF or SHH alterations to treatment with pertuzumab plus trastuzumab, erlotinib, vemurafenib, or vismodegib, respectively. One patient with BRAF V600E mutant anaplastic thyroid cancer had a complete response.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":["NCT02091141"],"normalized_drug":["Pertuzumab","Vemurafenib"],"phenotypes":null,"pub_med_references":null,"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Laryngeal Squamous Cell Carcinoma","doid":"2876","drug_interaction_type":null,"drugs":["Vemurafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/5962","evidence_direction":"Supports","evidence_level":"C","evidence_statement":"The phase 2a MyPathway study assigned patients with HER2, EGFR, BRAF or SHH alterations to treatment with pertuzumab plus trastuzumab, erlotinib, vemurafenib, or vismodegib, respectively. One patient with BRAF V600E mutant laryngeal cancer had a partial response with vemurafenib.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":["NCT02091141"],"normalized_drug":["Vemurafenib"],"phenotypes":null,"pub_med_references":null,"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Anaplastic Thyroid Carcinoma","doid":"0080522","drug_interaction_type":null,"drugs":["Vemurafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/6045","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"In a phase 2 “basket” study of vemurafenib in BRAF V600-positive non-melanoma cancers, seven patients with anaplastic thyroid cancer were enrolled. All 7 patients had V600E mutations. One complete response and one partial response was observed, for a response rate of 29%.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":["NCT01524978"],"normalized_drug":["Vemurafenib"],"phenotypes":null,"pub_med_references":[26287849],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":"Combination","drugs":["Panitumumab","Trametinib","Dabrafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/6123","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"In this trial, 142 patients with metastatic, BRAF V600E mutant colorectal cancer were randomized to receive either BRAF inhibitor dabrafenib (D) + EGFR inhibitor panitumumab (P); or a triple therapy of D + P and MEK inhibition with trametinib (T) or T + P. Confirmed response rates for D+P (n=20), D+T+P (n=91), and T+P (n=31) were 10%, 21%, and 0%, respectively.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":["Dabrafenib","Panitumumab","Trametinib"],"phenotypes":null,"pub_med_references":[29431699],"rating":"4","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Colorectal Adenocarcinoma","doid":"0050861","drug_interaction_type":"Combination","drugs":["Panitumumab","Trametinib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/6124","evidence_direction":"Does Not Support","evidence_level":"B","evidence_statement":"In this trial, 142 patients with metastatic, BRAF V600E mutant colorectal cancer were randomized to receive either BRAF inhibitor dabrafenib (D) + EGFR inhibitor panitumumab (P); or a triple therapy of D + P and MEK inhibition with trametinib (T) or T + P. Confirmed response rates for D+P (n=20), D+T+P (n=91), and T+P (n=31) were 10%, 21%, and 0%, respectively.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":["Panitumumab","Trametinib"],"phenotypes":null,"pub_med_references":[29431699],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Melanoma","doid":"1909","drug_interaction_type":"Combination","drugs":["Dabrafenib","Trametinib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/6178","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"Adjuvant dual treatment with BRAF inhibitor dabrafenib and MEK inhibitor trametinib was administered to patients with stage III resected melenoma with V600E or V600K mutation in this stage III trial (COMBO-AD, NCT01682083). 792 (91%) patients had V600E, and were administered dabrafenib and trametinib or placebo for 12 months. In subsequent analysis, relapse or death occurred in 150/397 patients (38%) in the treatment group and 229/395 patients (58%) in the placebo group for a 95% CI Hazard Ratio of 0.48 (0.39-0.58).","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":["NCT01682083"],"normalized_drug":["Dabrafenib, Trametinib"],"phenotypes":null,"pub_med_references":[28891408],"rating":"5","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Melanoma","doid":"1909","drug_interaction_type":"Combination","drugs":["Dabrafenib","Trametinib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/6938","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"In this Phase III trial (NCT01584648 COMBI-d), previously untreated patients with unresectable stage IIIC or IV melanoma with BRAF V600E (359 patients) or V600K (61 patients) received dabrafenib and trametinib or dabrafenib alone with primary endpoint of progression free survival and secondary endpoints including disease response. The hazard ratio for progression or death in the V600E group was 0.81 for dabrafenib-trametinib vs dabrafenib-alone. Of 179 V600E patients in the dabrafenib-trametinib group, 68% of patients had a response, which was 15 percentage points higher than in the dabrafenib-alone group (95% CI, 4 to 24; P=0.006).","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":["NCT01584648"],"normalized_drug":["Dabrafenib, Trametinib"],"phenotypes":null,"pub_med_references":[25265492],"rating":"5","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Melanoma","doid":"1909","drug_interaction_type":"Combination","drugs":["Trametinib","Dabrafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/6940","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"In this Phase I and II study (NCT01072175) patients with metastatic melanoma were given dabrafenib and trametinib combination therapy vs. dabrafenib monotherapy. From V600E patients, 45 received monotherapy and 92 received combination therapy. Hazard ratio for progression or death was 0.43 (95% CI, 0.27-0.71). Both patients with the BRAF V600E and V600K mutation showed significant improvement in progression-free survival.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":["NCT01072175"],"normalized_drug":["Dabrafenib, Trametinib"],"phenotypes":null,"pub_med_references":[23020132],"rating":"4","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Anaplastic Thyroid Carcinoma","doid":"0080522","drug_interaction_type":"Combination","drugs":["Trametinib","Dabrafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/6975","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"Interim analysis of a basket trial evaluating the combination of dabrafenib (BRAF inhibitor) and trametinib (MEK inhibitor) in previously treated V600E-mutated patients showed 11/16 patients with anaplastic thyroid carcinoma responded to treatment (overall response rate 69%; 95% CI, 41% to 89%). Seven patients had ongoing responses. Median duration of response, progression-free survival, and overall survival were not reached after 120 weeks.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":["NCT02034110"],"normalized_drug":["Dabrafenib, Trametinib"],"phenotypes":null,"pub_med_references":[29072975],"rating":"4","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Poor Outcome","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":null,"drugs":null,"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/7156","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"Patients with completely resected colorectal adenocarcinoma (Stage II-III) were treated with fluorouracil and leucovorin +/- ironotecan. Of the 1,307 FFPE samples tested, V600E was observed in 31 Stage II samples (7.6%) and 72 Stage III samples (7.9%). V600E was prognostic for overall survival, but not for relapse-free survival, in patients with stages II and III combined, and in stage III alone. For all MSI low and stable tumors, BRAF V600E positive samples had a hazard ratio (HR) of 2.19 (95% CI, 1.43 to 3.37, P=0.00034). For all samples in the cohort (MSI-H and MSI-L) BRAF V600E positive samples had a 1.66 HR (95% CI, 1.15 to 2.40, P=0.0069). The authors note prognostic value for BRAF V600E, especially in non-MSI high tumors.","evidence_status":"accepted","evidence_type":"Prognostic","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":null,"phenotypes":null,"pub_med_references":[20008640],"rating":"4","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Poor Outcome","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":null,"drugs":null,"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/7157","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"The CRYSTAL Phase III Trial evaluated efficacy of irinotecan, fluorouracil, and leucovorin (FOLFIRI) with or without Cetuximab for colorectal cancer patients who presented with unresectable metastatic disease. BRAF mutation status (V600E) was analyzed via LightMix BRAF V600E Kit. V600E mutations were detected in 60/999 tumor samples (6%), 59 of which were wild-type for KRAS. When comparing patients with wildtype KRAS (n=625), BRAF V600E tumors had worse outcomes relative to BRAF wildtype. For patients with BRAF V600E tumors (n=566), median overall survival (OS) was 25.1 months with cetuximab and 21.6 months without cetuximab. For patients with wildtype BRAF (n=59), median OS was 14.1 months with cetuximab and 10.3 months without cetuximab.","evidence_status":"accepted","evidence_type":"Prognostic","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":null,"phenotypes":null,"pub_med_references":[21502544],"rating":"4","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Poor Outcome","disease":"Childhood Low-grade Glioma","doid":"0080830","drug_interaction_type":null,"drugs":null,"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/7191","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"Using Sanger sequencing, BRAFV600E mutations were identified in 21 of 285 patients with PLGGs (7.4%). This mutation was enriched in hemispheric tumors (p<0.007) and was associated with shorter progression-free survival (p=0.011) and overall survival (p=0.032) [mt (n=18) vs wt (n=166)].","evidence_status":"accepted","evidence_type":"Prognostic","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":null,"phenotypes":["Pediatric onset","Early young adult onset"],"pub_med_references":[29948154],"rating":"4","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":{"asco_citation_id":"168986","asco_abstract_id":"688"},"clinical_significance":"Sensitivity/Response","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":"Combination","drugs":["Cetuximab","Encorafenib","Binimetinib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/7260","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"In a phase III trial, patients with BRAF V600E mutated metastatic colorectal cancer received triplet combination with encorafenib + binimetinib + cetuximab in a second or third-line setting. In the safety-lead in part of this trial, 30 patients were given triplet therapy, of which 29 with V600E mutation were included in the efficacy analysis. The objective response rate was 48% [95%CI: 29.4 - 67.5], median PFS was 8.0 mo [95%CI: 5.6 - 9.3], and median OS was 15.3 mo [95%CI: 9.6 - not reached]. The author concluded that triplet therapy was well tolerated and PFS and OS were substantially improved over historical standard of care.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":["NCT02928224"],"normalized_drug":["Binimetinib","Cetuximab","Encorafenib"],"phenotypes":null,"pub_med_references":null,"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":{"asco_citation_id":"169315","asco_abstract_id":"187"},"clinical_significance":"Sensitivity/Response","disease":"Biliary Tract Cancer","doid":"4607","drug_interaction_type":"Combination","drugs":["Trametinib","Dabrafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/7264","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"In a phase II trial, 33 patients with advanced or metastatic biliary tract cancer (BTC) received dabrafenib (D) and trametinib (T) in a second or higher line therapeutic context. Of the 33 patients, 30 had BRAF V600E mutated tumors, and 32 were evaluable. Objective response rate was 41% (13/32; 95% CI, 24 - 59%). Median PFS was 7.2 months (95% CI, 4.6 - 10.1 months), and median OS was 11.3 months (95% CI, 7.3 - 17.6 months). The author concluded that D+T therapy should be considered for patients with BRAF V600E mutated BTC.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":["NCT02034110"],"normalized_drug":["Dabrafenib, Trametinib"],"phenotypes":null,"pub_med_references":null,"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Langerhans Cell Sarcoma","doid":"7146","drug_interaction_type":null,"drugs":["Vemurafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/7583","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"Off-label use of vemurafenib to treat BRAF V600E mutation-positive, refractory, childhood Langerhans cell histiocytosis (LCH) was evaluated. Fifty-four patients from 12 countries were treated with vemurafenib 20 mg/kg/day. Because LCH is a heterogeneous systemic disease, the quantitative Disease Activity Score (DAS), which reflects overall LCH extension, was used as an evaluation criterion. At 8 weeks, 38 patients had CRs (non-active disease) and 16 had PRs (active disease better). DAS decreased from a median value of 7 to 0 between VMF initiation and day 60 (P < 0.001).","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":["Vemurafenib"],"phenotypes":null,"pub_med_references":[31513482],"rating":"4","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":"Combination","drugs":["Encorafenib","Binimetinib","Cetuximab"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/7612","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"665 patients with BRAF V600E-mutated metastatic CRC were enrolled In this open-label, phase 3 trial. Patients were randomly assigned in a 1:1:1 ratio to receive encorafenib, binimetinib, and cetuximab (triplet-therapy group); encorafenib and cetuximab (doublet-therapy group); or the investigators’ choice of either cetuximab and irinotecan or cetuximab and FOLFIRI. The median overall survival was 9.0 months in the triplet-therapy group and 5.4 months in the control group (hazard ratio for death, 0.52; 95% confidence interval [CI], 0.39 to 0.70; P<0.001). The confirmed response rate was 26% (95% CI, 18 to 35) in the triplet-therapy group and 2% (95% CI, 0 to 7) in the control group (triplet group vs. control P<0.001). The median progression-free survival in the triplet-therapy group was 4.3 months (95% CI, 4.1 to 5.2) and 1.5 months (95% CI, 1.5 to 1.7) in the control group (hazard ratio for disease progression or death, 0.38; 95% CI, 0.29 to 0.49; P<0.001).","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":["NCT02928224"],"normalized_drug":["Binimetinib","Cetuximab","Encorafenib"],"phenotypes":null,"pub_med_references":[31566309],"rating":"5","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":"Combination","drugs":["Vemurafenib","Irinotecan","Cetuximab"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/8506","evidence_direction":"Supports","evidence_level":"D","evidence_statement":"This in vivo study examined the efficacy of various treatments on athymic nude mice xenografted with colorectal cancer HT29 cells, which harbor BRAF V600E. The authors sought to understand whether the addition of vemurafenib (a BRAF V600E inhibitor) to agents approved for the treatment of metastatic colorectal cancer increased therapeutic efficacy, and which combinations worked best. Irinotecan, cetuximab and vemurafenib combination therapy resulted in >100% tumor growth inhibition (TGI) and 250% increased lifespan (ILS) compared to vehicle treated controls. Of the ten treated mice, nine experienced partial response and one experienced a complete response. Compared to all doublet and single agent combinations of vemurafenib, irinotecan, and cetuximab, triplet therapy produced the best TGI and ILS (p<0.05, p <0.0001 for all comparisons).","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":["Cetuximab","Irinotecan","Vemurafenib"],"phenotypes":null,"pub_med_references":[22180495],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":"Combination","drugs":["Vemurafenib","Erlotinib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/8507","evidence_direction":"Supports","evidence_level":"D","evidence_statement":"This in vivo study examined the efficacy of various treatments on athymic nude mice xenografted with colorectal cancer HT29 cells, which harbor BRAF V600E. The authors sought to understand whether the addition of vemurafenib (a BRAF V600E inhibitor) to agents approved for the treatment of metastatic colorectal cancer increased therapeutic efficacy, and which combinations worked best. Erlotinib and vemurafenib combination therapy resulted in >100% tumor growth inhibition (TGI) and 142% increased lifespan (ILS) compared to vehicle treated controls. Of ten treated mice, 9 experienced partial response. Doublet therapy produced a greater increase in TGI and ILS than either agent in isolation.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":["Erlotinib","Vemurafenib"],"phenotypes":null,"pub_med_references":[22180495],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Papillary Thyroid Carcinoma","doid":"3969","drug_interaction_type":null,"drugs":["Vemurafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/9018","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"Open label phase 2 (Clinical Level B) trial including patients from across the globe (USA, Italy, and the Netherlands) investigating sensitivity to Vemurafenib in patients that have BRAF V600E-positive papillary thyroid cancer that have become resistant to radioactive iodine (the standard treatment). There were 116 patients identified for this trial, 51 of which met the conditions to be included. These 51 patients were split into two cohorts: 1) patients that had never been treated with a multikinase inhibitor targeting VEGFR and 2) patients that have previously been treated with a VEGFR multikinase inhibitor. In cohort 1, ten of 26 patients had best overall response. Best overall response was defined as the proportion of patients with a complete or partial response, however these ten patients were all partial response. In the same cohort 1, nine had achieved stable disease control for at least six months; therefore, 19 patients achieved disease control (73% of total cohort 1, 95% CI 52-88). In cohort 2, of 23 eligible patients, six had a partial response as best overall response and six had stable disease control for at least six months; therefore, 12 patients achieved disease control. (55% of total cohort 2, 95% CI 32-76). The authors conclude that vemurafenib is a potential treatment option for late-stage BRAF V600E-positive papillary thyroid cancer for treatment in patients naïve to a multikinase inhibitor (Cohort 1) and to patients that have been previously treated with a multikinase inhibitor (Cohort 2).","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":["NCT01286753"],"normalized_drug":["Vemurafenib"],"phenotypes":null,"pub_med_references":[27460442],"rating":"4","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Poor Outcome","disease":"Papillary Thyroid Carcinoma","doid":"3969","drug_interaction_type":null,"drugs":null,"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/9170","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"Clinical study including 219 patients with papillary thyroid cancer (PTC) to determine a correlation between the BRAF V600E mutation and poor oncological outcome. This study found that 107 of the 219 (49%) patients had this mutation signifying that the BRAF V600E mutation is one of the most commonly occurring among PTC patients. This cohort was split into two groups—BRAF+ and BRAF-. Of the 107 patients that were BRAF+, 25% had tumor reoccurrence compared with 9% in the BRAF- group (P=0.004). Multivariate analysis was performed to assess BRAF correlation independent of known contributing factors to cancer such as age, gender, and multifocality. The results showed that the BRAF mutation is indicative/contributes to lymph node metastasis, associated with tumor reoccurrence, stage, and that recurrent disease was more extensive and required more aggressive treatments in BRAF+ patients compared with BRAF- patients. The authors conclude that PTC patients with the BRAF V600E mutation have worse clinicopathological outcomes, and that the BRAF mutation can be used to assess risk stratification in patients with PTC.","evidence_status":"accepted","evidence_type":"Prognostic","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":null,"normalized_drug":null,"phenotypes":null,"pub_med_references":[16174717],"rating":"4","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Colorectal Cancer","doid":"9256","drug_interaction_type":"Combination","drugs":["Cetuximab","Encorafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/9851","evidence_direction":"Supports","evidence_level":"A","evidence_statement":"The open-label phase 3 BEACON CRC trial included 665 patients with BRAF V600E-mutated metastatic CRC. Patients were randomly assigned in a 1:1:1 ratio to receive encorafenib, binimetinib, and cetuximab (triplet-therapy group); encorafenib and cetuximab (doublet-therapy group); or the investigators’ choice of either cetuximab and irinotecan or cetuximab and FOLFIRI. The median overall survival was 8.4 months (95% CI, 7.5 to 11.0) in the doublet-therapy group and 5.4 months (95% CI, 4.8 to 6.6) in the control group, with a significantly lower risk of death compared to the control group (hazard ratio for death doublet-group vs. control, 0.60; 95% CI, 0.45 to 0.79; P<0.001). The confirmed response rate was 26% (95% CI, 18 to 35) in the triplet-therapy group, 20% in the doublet-therapy group (95% CI 13 to 29) and 2% (95% CI, 0 to 7) in the control group (doublet group vs. control P<0.001). Median PFS was 4.2 months (95% CI, 3.7 to 5.4) in the doublet-therapy group, and 1.5 months (95% CI, 1.5 to 1.7) in the control group (hazard ratio for disease progression doublet-group vs control, 0.40; 95% CI, 0.31 to 0.52, P<0.001).","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2023-01-09 21:46:25 UTC","nct_ids":["NCT02928224"],"normalized_drug":["Cetuximab, Encorafenib"],"phenotypes":null,"pub_med_references":[31566309],"rating":"5","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Cancer","doid":"162","drug_interaction_type":"Combination","drugs":["Dabrafenib","Trametinib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/11672","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"This NCI-MATCH trial was conducted in 35 patients of which 29 were included in the primary efficacy analysis with tumors with BRAF V600E mutations, and treated with a combination of dabrafenib and trametinib. The ORR was 37.9% (90% CI, 22.9-54.9). The median PFS and median OS were 11.4 months (90% CI, 8.4-16.3) and 28.6 months respectively. Meaningful results were achieved with this treatment with an overall DCR of 75.9%.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2024-01-22 16:58:55 UTC","nct_ids":null,"normalized_drug":["Dabrafenib, Trametinib"],"phenotypes":null,"pub_med_references":[32758030],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Low Grade Glioma","doid":"0080829","drug_interaction_type":null,"drugs":["Vemurafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/11770","evidence_direction":"Supports","evidence_level":"B","evidence_statement":"In this trial, 19 patients with pediatric brain tumours (1 patient with Astrocytoma, 1 with Fibrillary Astrocytoma, 10 with Pilocytic Astrocytoma, 5 with Ganglioglioma and 2 with Pleomorphic Xanthoastrocytoma) harbouring BRAF V600E were treated with vemurafenib. The study reported a positive response to the treatment, with 1 complete response, 5 partial responses, and 13 patients with stable disease.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2024-03-25 21:25:38 UTC","nct_ids":["NCT01748149"],"normalized_drug":["Vemurafenib"],"phenotypes":null,"pub_med_references":[32523649],"rating":"3","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Solid Tumor","doid":null,"drug_interaction_type":"Combination","drugs":["Dabrafenib","Trametinib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/12161","evidence_direction":"Supports","evidence_level":"A","evidence_statement":"In this trial, patients with advanced rare tumours harbouring BRAF V600E mutations were treated with a combination of dabrafenib and trametinib. The study included eight distinct cohorts: anaplastic thyroid carcinoma (ATC) (n=36), biliary tract cancer (BTC)(n=43), gastrointestinal stromal tumour (GIST) (n=1), adenocarcinoma of the small intestine (ASI) (n=3), low-grade glioma (LGG) (n=13), high-grade glioma (HGG)(n=45), hairy cell leukemia(HCL) (n=55), and multiple myeloma (MM)(n=19). The overall response rates for these cohorts were 56%, 53%, 0%, 67%, 54%, 33%, 89%, and 50% respectively. The median duration of response varied, with 14.4 months for anaplastic thyroid carcinoma, 8.9 months for biliary tract cancer, 7.7 months for adenocarcinoma of the small intestine, 31.2 months for high-grade glioma, and 11.1 months in multiple myeloma. In the remaining cohorts, the duration of response was not reached. Progression-free survival was measured at 6.7 months for ATC, 9.0 months for BTC, 9.5 months for ASI, 5.5 months for HGG, and 6.3 months for MM. PFS could not be evaluated in the LGG and HCL groups due to small patient numbers. The overall survival was 14.5 months for ATC, 13.5 months for BTC, 17.6 months for HGG, 21.8 months for ASI, and 33.9 months for MM cohorts. OS could not be evaluated for the LGG and HCL groups due to a low number of deaths. Adverse events were reported in 97.6% of the patients (n=201), with 87.9% (n=181) of these being related to the study treatment. Serious adverse events occurred in 45.1% (n=93) of patients across all cohorts.","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2025-01-24 17:19:02 UTC","nct_ids":["NCT02034110"],"normalized_drug":["Dabrafenib, Trametinib"],"phenotypes":null,"pub_med_references":[37059834],"rating":"4","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null},{"asco_entry":null,"clinical_significance":"Sensitivity/Response","disease":"Low Grade Glioma","doid":"0080829","drug_interaction_type":"Combination","drugs":["Trametinib","Dabrafenib"],"entrez_id":null,"evidence_civic_url":"https://civicdb.org/links/evidence_items/12162","evidence_direction":"Supports","evidence_level":"A","evidence_statement":"In this trial, patients with pediatric (age <18 years) low-grade gliomas harbouring BRAF V600E (n=49), were treated with either trametinib monotherapy (n=13) or dabrafenib + trametinib (n=36). In patients treated with trametinib monotherapy, 15% (95% CI, 1.9-45.4; n=2) had objective PRs, and 46% (n=6) had stable disease for 12 or more weeks after the first dose of therapy. The estimated 24-month duration of response (DOR) was 100%. The median PFS was 16.4 months (95% CI, 3.2 to NR). In patients treated with a combination of trametinib and dabrafenib 25% (95% CI, 12.1-42.2; n=9) had objective PRs and 64% (n=23) experienced stable disease. The median DOR was 33.6 months (95% CI, 11.2 - NR), while the 24-month DOR was 80% (95% CI, 30-100). The median PFS was 36.9 months (95% CI, 36.0 - NR).","evidence_status":"accepted","evidence_type":"Predictive","gene":"BRAF","gene_civic_url":null,"last_review_date":"2025-01-13 16:55:37 UTC","nct_ids":["NCT02124772"],"normalized_drug":["Dabrafenib, Trametinib"],"phenotypes":null,"pub_med_references":[36375115],"rating":"4","representative_transcript":"ENST00000288602.6","transcripts":null,"variant":"V600E","variant_civic_url":"https://civicdb.org/links/variants/12","variant_origin":"Somatic","variant_summary":null,"assertion_details":null,"civic_variant_evidence_score":null,"variant_groups":null,"molecular_profile_civic_url":"https://civicdb.org/links/molecular_profiles/12","molecular_profiles":null}]}],"saphetor_known_pathogenicity":[{"version":"19-Mar-2026","items":[{"annotations":{"NCBI ClinVar2":[{"functions":["coding"],"coding_impact":"missense","acmg_confirmed":false,"acmg_class":"Uncertain Significance","acmg_reannotated":"Pathogenic","source":"NCBI 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07:13:43","id":1624,"saphetorClass":"pathogenic","user_id":261,"variant_id":10190071404531360004},{"functions":["coding"],"coding_impact":"missense","acmg_confirmed":true,"acmg_class":"Pathogenic","acmg_reannotated":"Pathogenic","source":"Saphetor VarSome Comment","codon":600,"gene_symbol":"BRAF","hgvs":"V600E","transcript":"NM_004333.6","comment":"","flagged_at_timestamp":"2018-02-06 10:26:11","id":1737,"saphetorClass":"pathogenic","user_id":2582,"variant_id":10190071404531360004},{"functions":["coding"],"coding_impact":"missense","acmg_confirmed":true,"acmg_class":"Pathogenic","acmg_reannotated":"Pathogenic","source":"Saphetor VarSome Comment","codon":600,"gene_symbol":"BRAF","hgvs":"V600E","transcript":"NM_004333.6","comment":"","flagged_at_timestamp":"2019-03-30 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(%%PUBMED:23263490%%, %%PUBMED:22281684%%, and %%PUBMED:17374713%%), and also citing 9 articles (%%PUBMED:29925953%%, %%PUBMED:28854169%%, %%PUBMED:25079330%%, %%PUBMED:24717435%%, %%PUBMED:24670642%%, and 4 more).","Supporting: a VarSome user has classified this variant as Pathogenic, confirmed by a functional study, mentioned in %%PUBMED:18287029%%."]},{"name":"PM1","met_criteria":true,"user_explain":["Hot-spot of length 17 amino-acids has 46 missense/in-frame variants (37 pathogenic variants, 9 uncertain variants, and no benign), which qualifies as strong pathogenic.","UniProt protein BRAF_HUMAN domain 'Protein kinase' has 293 missense/in-frame variants (132 pathogenic variants, 160 uncertain variants, and 1 benign variant), which qualifies as moderate pathogenic.","Limiting strength to Moderate due to co-occurrence with other predictive evidence."]},{"name":"PM5","met_criteria":true,"user_explain":["Alternative variant ##chr7:140453137 C⇒T## (Val600Met) is classified Likely Pathogenic, 1 star, by ClinVar (confirmed using the germline classifier).","Alternative variant ##chr7:140453137 C⇒G## (Val600Leu) is classified Pathogenic, 2 stars, by ClinVar (confirmed using the germline classifier).","Alternative variant ##chr7:140453137 C⇒A## (Val600Leu) is classified Likely Pathogenic, 1 star, by ClinVar (confirmed using the germline classifier).","Alternative variant ##chr7:140453136 A⇒C## (Val600Gly) is classified Pathogenic, 3 stars, by ClinVar (confirmed using the germline classifier).","4 pathogenic alternative variants identified.","Limiting strength to Moderate due to co-occurrence with other predictive evidence."]},{"name":"PP3","met_criteria":true,"user_explain":["MetaRNN = 0.883 is between 0.841 and 0.939 ⇒ moderate pathogenic."],"strength":"Moderate"},{"name":"PM2","met_criteria":true,"user_explain":["Variant not found in gnomAD genomes, good gnomAD genomes coverage = 30.6.","GnomAD exomes allele count = 1 is less than 5 for AD gene BRAF, good gnomAD 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treatment with the combination of Braftovi (encorafenib) and Sprycel (dasatinib) induced apoptosis and cell cycle arrest, inhibited colony formation and migration, and synergistically inhibited viability in colorectal cancer cell lines harboring BRAF V600E in culture and increased tumor growth inhibition in cell line and patient-derived xenograft (PDX) models compared to either drug alone (%%PUBMED:40481178%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Pdx & cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[38096472],"normalized_drug":"Cobimetinib, Vemurafenib","indication":"pancreatic cancer","therapy_id":1657,"normalized_cancer":"Pancreatic Cancer","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"In a Phase II trial (TAPUR), Zelboraf (vemurafenib) and Cotellic (cobimetinib) combination therapy resulted in a partial response in 2 patients with pancreatic cancer harboring BRAF V600E (%%PUBMED:38096472%%; NCT02693535).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[31618628],"normalized_drug":"Lifirafenib","indication":"melanoma","therapy_id":4025,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Lifirafenib","efficacy_evidence":"In a preclinical study, Lifirafenib (BGB-283) treatment inhibited viability of a melanoma cell line harboring BRAF V600E in culture (%%PUBMED:31618628%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[26208524],"normalized_drug":"Lifirafenib","indication":"melanoma","therapy_id":4025,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Lifirafenib","efficacy_evidence":"In a preclinical study, Lifirafenib (BGB-283) inhibited Braf phosphorylation and cell proliferation in melanoma cell lines harboring BRAF V600E in culture (%%PUBMED:26208524%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Vemurafenib","indication":"oncocytic carcinoma of the thyroid","therapy_id":342,"normalized_cancer":"Hurthle Cell Thyroid Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"Zelboraf (vemurafenib) is included in guidelines for patients with recurrent, advanced, or metastatic thyroid Hurthle cell carcinoma harboring BRAF V600E for whom clinical trials are not available or appropriate (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[38691346],"response_type":"predicted - sensitive","indication":"pleomorphic xanthoastrocytoma","therapy_id":13602,"normalized_cancer":"Pleomorphic Xanthoastrocytoma","evidence_type":"Actionable","therapy":"PF-07799933","efficacy_evidence":"In a Phase I trial, PF-07799933 treatment resulted in a complete response in a patient with pleomorphic xanthoastrocytoma harboring BRAF V600E (%%PUBMED:38691346%%; NCT05355701).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"decreased response","pub_med_references":[30630828],"normalized_drug":"Pembrolizumab","indication":"melanoma","therapy_id":1447,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Pembrolizumab","efficacy_evidence":"In a retrospective analysis, patients with melanoma harboring BRAF V600E (n=84) had decreased response rates (29% vs. 53%, p=0.059), progression-free survival (2.7 vs. 19 months, p=0.049), and overall survival (11.7 vs. 20.4 months, p=0.081) relative to patients with BRAF V600K (n=19) when treated with Keytruda (pembrolizumab) (n=62 and 17 for BRAF V600E and V600K, respectively) or Opdivo (nivolumab) (n=22 and 2 for BRAF V600E and V600K, respectively) (%%PUBMED:30630828%%).","cap_asco_evidence_level":"NA","molecular_profile":"BRAF V600E","approval_status":"Clinical Study","amp_tier":"NA"},{"response_type":"decreased response","pub_med_references":[37403699],"normalized_drug":"Pembrolizumab","indication":"melanoma","therapy_id":1447,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Pembrolizumab","efficacy_evidence":"In a retrospective analysis, real-world treatment with either Keytruda (pembrolizumab) or Toripalimab (JS001) resulted in a median disease-free survival of 17 months in melanoma patients harboring BRAF V600E compared to 32 months in patients with wild-type BRAF, NRAS, and KIT (p=0.022) (%%PUBMED:37403699%%).","cap_asco_evidence_level":"NA","molecular_profile":"BRAF V600E","approval_status":"Clinical Study","amp_tier":"NA"},{"response_type":"sensitive","pub_med_references":[39018564],"normalized_drug":"Cetuximab, Encorafenib","indication":"pseudomyxoma peritonei","therapy_id":1916,"normalized_cancer":"Peritoneal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Encorafenib","efficacy_evidence":"In a preclinical study, treatment with the combination of Braftovi (encorafenib) and Erbitux (cetuximab) inhibited viability and induced apoptosis in a patient-derived pseudomyxoma peritonei cell line harboring BRAF V600E in culture and inhibited tumor growth and improved survival of a patient-derived xenograft (PDX) model (%%PUBMED:39018564%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Pdx & cell culture","amp_tier":"II"},{"pub_med_references":[26461489],"response_type":"sensitive","indication":"melanoma","therapy_id":3699,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Cediranib + PLX4720 + Selumetinib","efficacy_evidence":"In a preclinical study, PLX4720, Cediranib (AZD-2171) and Koselugo (selumetinib) worked synergistically to inhibit cell growth in PLX4720-resistant melanoma cell lines harboring BRAF V600E in culture (%%PUBMED:26461489%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","indication":"colon cancer","therapy_id":18195,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Encorafenib + Fluorouracil + Leucovorin + Oxaliplatin + Panitumumab","efficacy_evidence":"Braftovi (encorafenib) in combination with Vectibix (panitumumab) and FOLFOX is included in guidelines as initial (category 2A) or subsequent-line (category 2B) therapy for patients with advanced or metastatic colon cancer harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"predicted - sensitive","pub_med_references":[36847048],"normalized_drug":"Dabrafenib, Trametinib","indication":"large cell neuroendocrine carcinoma","therapy_id":1066,"normalized_cancer":"Large Cell Neuroendocrine Carcinoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, treatment with the combination of Mekinist (trametinib) and Tafinlar (dabrafenib) resulted in a partial response in one of the lesions and a complete response in other lesions after 1 month in a patient with large cell neuroendocrine carcinoma of unknown primary harboring BRAF V600E (%%PUBMED:36847048%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[28551618],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":15620,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Binimetinib + Trifluridine-tipiracil hydrochloride","efficacy_evidence":"In a preclinical study, the addition of Mektovi (binimetinib) enhanced the efficacy of Lonsurf (trifluridine/tipiracil hydrochloride) treatment and synergistically inhibited proliferation in colorectal cancer cells harboring BRAF V600E in culture (%%PUBMED:28551618%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[31085763],"normalized_drug":"Dabrafenib, Trametinib","indication":"papillary thyroid carcinoma","therapy_id":1066,"normalized_cancer":"Papillary Thyroid Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, a papillary thyroid carcinoma patient who progressed on Lenvima (lenvatinib) was found to harbor BRAF V600E and was treated with the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) on a clinical trial, resulting in partial response in the thyroid bed, cervical and intrathoracic lymph nodes, and pulmonary lesions, with a decrease in target lesion size of 67%, and the patient remained on treatment for 18 months before stopping due to progression (%%PUBMED:31085763%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"papillary thyroid carcinoma","therapy_id":1066,"normalized_cancer":"Papillary Thyroid Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"The combination of Tafinlar (dabrafenib) and Mekinist (trametinib) is included in guidelines for patients with papillary thyroid carcinoma harboring BRAF V600E who have progressed on therapy and have no further treatment options (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[26392102],"normalized_drug":"Dabrafenib, Trametinib","indication":"colorectal cancer","therapy_id":1066,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a Phase Ib/II trial, treatment with the combination of Mekinist (trametinib) and Tafinlar (dabrafenib) resulted in partial response or better in 12% (5/43), including 1 complete response, and stable disease in 51% (22/43) of patients with colorectal cancer harboring BRAF V600E (%%PUBMED:26392102%%).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase Ib/II","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[27312529],"normalized_drug":"Dabrafenib, Trametinib","indication":"colorectal cancer","therapy_id":1066,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a preclinical study, combination therapy consisting of Tafinlar (dabrafenib) and Mekinist (trametinib) inhibited survival of colorectal cancer cell lines harboring BRAF V600E in culture (%%PUBMED:27312529%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[26208524],"normalized_drug":"Lifirafenib","indication":"Advanced Solid Tumor","therapy_id":4025,"normalized_cancer":"All Solid Tumors","evidence_type":"Actionable","therapy":"Lifirafenib","efficacy_evidence":"In a preclinical study, Lifirafenib (BGB-283) inhibited viability of a variety of cancer cell lines harboring BRAF V600E in culture (%%PUBMED:26208524%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[27312529],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":4542,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Dabrafenib + SCH772984","efficacy_evidence":"In a preclinical study, combination therapy consisting of Erbitux (cetuximab), Tafinlar (dabrafenib), and SCH772984 inhibited survival of colorectal cancer cell lines harboring BRAF V600E in culture (%%PUBMED:27312529%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[27312529],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":4543,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + SCH772984","efficacy_evidence":"In a preclinical study, combination therapy consisting of Erbitux (cetuximab) and SCH772984 inhibited survival of colorectal cancer cell lines harboring BRAF V600E in culture (%%PUBMED:27312529%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[38992135],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":17518,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"MTX-531 + Trametinib","efficacy_evidence":"In a preclinical study, treatment with the combination of Mekinist (trametinib) and MTX-531 inhibited tumor growth with a 40% partial response rate and increased survival in a patient-derived xenograft (PDX) model of colorectal cancer harboring BRAF V600E (%%PUBMED:38992135%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"pub_med_references":[39574163],"response_type":"sensitive","indication":"melanoma","therapy_id":17922,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Roflumilast + Vemurafenib","efficacy_evidence":"In a preclinical study, treatment with the combination of Roflumilast and Zelboraf (vemurafenib) inhibited colony formation and resulted in decreased spheroid size of melanoma cells harboring BRAF V600E in culture, and led to greater inhibition of tumor growth in a cell line xenograft model compared to Zelboraf (vemurafenib) alone (%%PUBMED:39574163%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[38795180],"response_type":"sensitive","indication":"thyroid cancer","therapy_id":17199,"normalized_cancer":"Thyroid Cancer","evidence_type":"Actionable","therapy":"Lenvatinib + PLX4720","efficacy_evidence":"In a preclinical study, treatment with the combination of PLX4720 and Lenvima (lenvatinib) inhibited proliferation of thyroid cancer cell lines harboring BRAF V600E in culture and resulted in greater tumor growth inhibition than PLX4720 alone in a cell line xenograft model (%%PUBMED:38795180%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"predicted - sensitive","normalized_drug":"Binimetinib, Encorafenib","indication":"Advanced Solid Tumor","therapy_id":1100,"normalized_cancer":"All Solid Tumors","evidence_type":"Actionable","therapy":"Binimetinib + Encorafenib","efficacy_evidence":"In a Phase II trial (BELIEVE), treatment with the combination of Braftovi (encorafenib) and Mektovi (binimetinib) resulted in an objective response rate of 32.7%, median progression-free survival (PFS) of 4.8 months, and 6-month PFS rate of 37.5% in patients with advanced solid tumors harboring BRAF V600E (n=43), other BRAF mutation (n=5), or a BRAF fusion (n=1) (Ann Oncol (2024) 35 (Suppl_2): S497).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[32067683],"normalized_drug":"Vemurafenib","indication":"salivary gland carcinoma","therapy_id":342,"normalized_cancer":"Salivary Carcinoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase II (MyPathway) trial, Zelboraf (vemurafenib) treatment resulted in a partial response in a patient with advanced salivary gland carcinoma harboring BRAF V600E, with a progression-free survival of 18.5 months (%%PUBMED:32067683%%; NCT02091141).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[37808191],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":15985,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Tunlametinib + Vemurafenib","efficacy_evidence":"In a preclinical study, treatment with the combination of Tunlametinib (HL-085) and Zelboraf (vemurafenib) synergistically inhibited proliferation of a colorectal cancer cell line harboring BRAF V600E in culture (%%PUBMED:37808191%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[31217909],"normalized_drug":"Vemurafenib","indication":"glioblastoma","therapy_id":342,"normalized_cancer":"Glioblastoma, IDH-Wildtype","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a clinical case study, Zelboraf (vemurafenib) treatment resulted in tumor regression as confirmed by MRI after 3-weeks of treatment in a patient with epithelioid glioblastoma harboring BRAF V600E (%%PUBMED:31217909%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[31386052],"normalized_drug":"Vemurafenib","indication":"glioblastoma","therapy_id":342,"normalized_cancer":"Glioblastoma, IDH-Wildtype","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a clinical case study, Zelboraf (vemurafenib) treatment resulted in a partial response 1 week after treatment in a patient with epithelioid type glioblastoma harboring BRAF V600E, although the patient soon passed due to complications (%%PUBMED:31386052%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[30351999],"normalized_drug":"Vemurafenib","indication":"glioblastoma","therapy_id":342,"normalized_cancer":"Glioblastoma, IDH-Wildtype","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase II trial (VE-BASKET), Zelboraf (vemurafenib) treatment resulted in stable disease as best response in 3 of 6 patients with glioblastoma harboring BRAF V600E, with stable disease lasting 3.6, 3.7, and 12.9 months, respectively (%%PUBMED:30351999%%; NCT01524978).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[36759733],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":15039,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Saracatinib + Vemurafenib","efficacy_evidence":"In a preclinical study, the combination of Zelboraf (vemurafenib) and Saracatinib (AZD0530) synergistically inhibited viability in colorectal cancer cell lines harboring BRAF V600E in culture (%%PUBMED:36759733%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[38343359],"normalized_drug":"Binimetinib, Encorafenib","indication":"anaplastic thyroid carcinoma","therapy_id":1100,"normalized_cancer":"Anaplastic Thyroid Cancer","evidence_type":"Actionable","therapy":"Binimetinib + Encorafenib","efficacy_evidence":"In a Phase II trial, Mektovi (binimetinib) and Braftovi (encorafenib) combination therapy demonstrated safety and activity in patients with thyroid cancer harboring BRAF V600E, resulting in an objective response rate (ORR) of 54.5% (12/22, 12 partial responses (PR)), with an ORR of 80% (4/5, 4 PR) and a disease control rate of 100% (5/5) in patients with anaplastic thyroid cancer, and median duration of response, progression-free survival, and overall survival were not reached (%%PUBMED:38343359%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[33043759],"normalized_drug":"Dabrafenib, Trametinib","indication":"ovarian serous carcinoma","therapy_id":1066,"normalized_cancer":"Serous Ovarian Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, Tafinlar (dabrafenib) and Mekinist (trametinib) combination therapy resulted in a complete response after 8 months of treatment in a patient with low-grade serous ovarian carcinoma harboring BRAF V600E (%%PUBMED:33043759%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[35242981],"normalized_drug":"Dabrafenib, Trametinib","indication":"ovarian serous carcinoma","therapy_id":1066,"normalized_cancer":"Serous Ovarian Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, Tafinlar (dabrafenib) and Mekinist (trametinib) combination treatment resulted in a partial response lasting at least 2.5 years in one patient with low grade serous ovarian carcinoma harboring BRAF V600E, and resulted in a complete metabolic response after 4 months of treatment in a second patient (%%PUBMED:35242981%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[26916115],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":3712,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Afatinib + BI 882370","efficacy_evidence":"In a preclinical study, colorectal cancer cells harboring BRAF V600E were sensitive to the combination of BI 882370 and Gilotrif (afatinib) in xenograft models, resulting in tumor growth inhibition and partial tumor regression (%%PUBMED:26916115%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"Adenocarcinoma of Unknown Primary","therapy_id":1066,"normalized_cancer":"Adenocarcinoma, NOS","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"The combination of Tafinlar (dabrafenib) and Mekinist (trametinib) is included in guidelines for patients with adenocarcinoma of unknown primary harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[30104724],"response_type":"resistant","indication":"melanoma","therapy_id":7839,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"RMC-4550","efficacy_evidence":"In a preclinical study, RMC-4550 did not inhibit Erk phosphorylation or proliferation of melanoma cells harboring BRAF V600E in culture (%%PUBMED:30104724%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"conflicting","pub_med_references":[27523909],"normalized_drug":"Vemurafenib","indication":"thyroid cancer","therapy_id":342,"normalized_cancer":"Thyroid Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a preclinical study, thyroid cancer cells harboring BRAF V600E demonstrated decreased sensitivity to Zelboraf (vemurafenib) in culture (%%PUBMED:27523909%%).","cap_asco_evidence_level":"NA","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"NA"},{"response_type":"conflicting","normalized_drug":"Vemurafenib","indication":"thyroid cancer","therapy_id":342,"normalized_cancer":"Thyroid Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase II trial (MyPathway), Zelboraf (vemurafenib) treatment resulted in complete response in a patient with anaplastic thyroid cancer harboring BRAF V600E (%%PUBMED:29320312%%; NCT02091141).","cap_asco_evidence_level":"NA","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"NA"},{"response_type":"sensitive","normalized_drug":"Encorafenib","indication":"melanoma","therapy_id":796,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Encorafenib","efficacy_evidence":"In preclinical studies, Encorafenib (LGX818) treatment of human melanoma xenograft models with BRAF V600E significantly decreased Mek activation and resulted in tumor regression (Cancer Res: 72(8) Suppl 1, Abstract #3790).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[30559419],"normalized_drug":"Encorafenib","indication":"melanoma","therapy_id":796,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Encorafenib","efficacy_evidence":"In a preclinical study, Braftovi (encorafenib) treatment inhibited Erk phosphorylation and reduced proliferation of melanoma cells harboring monomeric BRAF V600E in culture (%%PUBMED:30559419%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[25285888],"normalized_drug":"Dabrafenib","indication":"thyroid gland carcinoma","therapy_id":3,"normalized_cancer":"Thyroid Cancer","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a Phase I trial, Tafinlar (dabrafenib) treatment resulted in a partial response in 29% (4/14) and stable disease in 43% (6/14) of patients with thyroid carcinoma harboring BRAF V600E, with 64% (9/14) of patients achieved at least a 10% decrease by RECIST, and a median progression-free survival of 11.3 months among responders (%%PUBMED:25285888%%; NCT00880321).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[33568355],"response_type":"sensitive","indication":"melanoma","therapy_id":11478,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + LXH 254 + Trametinib","efficacy_evidence":"In a preclinical study, combination treatment with LXH 254, Tafinlar (dabrafenib), and Mekinist (trametinib) in a melanoma cell line harboring BRAF V600E resulted in suppression of colony formation in culture (%%PUBMED:33568355%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"gastroesophageal junction adenocarcinoma","therapy_id":1066,"normalized_cancer":"Adenocarcinoma of the Gastroesophageal Junction","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Tafinlar (dabrafenib) and Mekinist (trametinib) combination therapy is included in guidelines as second-line or subsequent therapy for patients with locally advanced, recurrent, or metastatic gastroesophageal junction adenocarcinoma harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"resistant","pub_med_references":[22649091],"normalized_drug":"Dasatinib","indication":"lung carcinoma","therapy_id":717,"normalized_cancer":"Lung Cancer","evidence_type":"Actionable","therapy":"Dasatinib","efficacy_evidence":"In a preclinical study, Sprycel (dasatinib) failed to induce apoptosis in lung carcinoma cells expressing BRAF V600E (%%PUBMED:22649091%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"ovarian serous carcinoma","therapy_id":7465,"normalized_cancer":"Serous Ovarian Cancer","evidence_type":"Actionable","therapy":"BGB3245","efficacy_evidence":"In a Phase I trial, BGB3245 treatment demonstrated manageable safety and resulted in a disease control rate of 48% (16/33,1 complete response, 5 confirmed partial responses (PR), 2 unconfirmed PR, and 8 stable disease > 24 weeks) in patients with advanced solid tumors harboring MAPK pathway alterations, including a partial response in a patient with low grade serous ovarian carcinoma harboring BRAF V600E (Cancer Res (2023) 83 (8_Supplement): CT031).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[27523909],"response_type":"sensitive","indication":"thyroid cancer","therapy_id":3300,"normalized_cancer":"Thyroid Cancer","evidence_type":"Actionable","therapy":"TAK-632","efficacy_evidence":"In a preclinical study, TAK-632 inhibited proliferation of thyroid cancer cells harboring BRAF V600E in culture (%%PUBMED:27523909%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[26810733],"response_type":"sensitive","indication":"melanoma","therapy_id":6368,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"EBI-907","efficacy_evidence":"In a preclinical study, EBI-907 inhibited BRAF and ERK signaling, resulted in growth inhibition of melanoma cells harboring BRAF V600E in culture and in cell line xenograft models (%%PUBMED:26810733%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[27362227],"response_type":"resistant","indication":"colorectal cancer","therapy_id":4504,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"SHP099","efficacy_evidence":"In a preclincial study, colorectal cancer cell lines harboring BRAF V600E demonstrated resistance to SHP099 in culture (%%PUBMED:27362227%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[34956922],"normalized_drug":"Dabrafenib, Trametinib","indication":"thyroid gland carcinoma","therapy_id":1066,"normalized_cancer":"Thyroid Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, Mekinist (trametinib) and Tafinlar (dabrafenib) combination treatment resulted in a partial response after 3 months in a patient with metastatic squamous cell carcinoma of the thyroid harboring BRAF V600E (%%PUBMED:34956922%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[33568355],"response_type":"sensitive","indication":"melanoma","therapy_id":11479,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + RAF709 + Trametinib","efficacy_evidence":"In a preclinical study, combination treatment with RAF709, Tafinlar (dabrafenib), and Mekinist (trametinib) in melanoma cell line harboring BRAF V600E resulted in suppression of colony formation in culture (%%PUBMED:33568355%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[28784858],"normalized_drug":"Dabrafenib","indication":"pilocytic astrocytoma","therapy_id":3,"normalized_cancer":"Pilocytic Astrocytoma","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a clinical case study, Tafinlar (dabrafenib) treatment resulted in a near complete response and resolution of leptomeningeal dissemination in a patient with pilocytic astrocytoma harboring BRAF V600E (%%PUBMED:28784858%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[22180495],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":1331,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Irinotecan + Vemurafenib","efficacy_evidence":"In a preclinical study, Zelboraf (vemurafenib) treatment in combination with Erbitux (cetuximab) and Camptosar (irinotecan) enhanced tumor growth inhibition and increased survival in a cell line xenograft model of colorectal cancer harboring BRAF V600E (%%PUBMED:22180495%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[33356422],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":1331,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Irinotecan + Vemurafenib","efficacy_evidence":"In a Phase II trial (SWOG1406), addition of Zelboraf (vemurafenib) to Camptosar (irinotecan) plus Erbitux (cetuximab) improved progression-free survival (4.4 vs. 2.0 mo, HR 0.50, p=0.001), response rate (17% vs 4%, p=0.05), and disease control rate (67% vs. 22%, p<0.001) in patients with metastatic colorectal cancer harboring BRAF V600E (%%PUBMED:33356422%%; NCT02164916).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[32182156],"normalized_drug":"Lifirafenib","indication":"thyroid cancer","therapy_id":4025,"normalized_cancer":"Thyroid Cancer","evidence_type":"Actionable","therapy":"Lifirafenib","efficacy_evidence":"In a Phase I trial, Lifirafenib (BGB-283) treatment resulted in partial response in 15.1% (8/53) of solid tumor patients with BRAF mutations, including 2 thyroid cancer patients harboring BRAF V600E (1 in dose-escalation phase, 1 in the dose-expansion), and in the dose-expansion phase 1 of 3 thyroid cancer patients harboring a BRAF V600 mutation demonstrated a partial response and 2 demonstrated stable disease, resulting in a disease control rate of 100% (3/3) (%%PUBMED:32182156%%; NCT02610361).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[27424159],"normalized_drug":"Cobimetinib","indication":"melanoma","therapy_id":1004,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Cobimetinib","efficacy_evidence":"In a Phase I trial, Cotellic (cobimetinib) treatment resulted in a confirmed partial response in six melanoma patients harboring BRAF V600E (%%PUBMED:27424159%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[25665005],"response_type":"sensitive","indication":"melanoma","therapy_id":1386,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Navitoclax + Trametinib","efficacy_evidence":"In a preclinical study, Navitoclax (ABT-263) enhanced the inhibitory effect of Mekinist (trametinib) on human melanoma cells harboring BRAF V600E in culture (%%PUBMED:25665005%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[31848189],"response_type":"predicted - sensitive","indication":"colorectal cancer","therapy_id":2149,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Ravoxertinib","efficacy_evidence":"In a Phase I trial, two colorectal cancer patients harboring BRAF V600E achieved partial responses lasting 21 and 73 weeks following treatment with Ravoxertinib (GDC-0994) (%%PUBMED:31848189%%; NCT01875705).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[31566309],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":4886,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Binimetinib + Cetuximab + Encorafenib","efficacy_evidence":"In a Phase III (BEACON CRC) trial, Braftovi (encorafenib), Mektovi (binimetinib), and Erbitux (cetuximab) combination treatment (n=111) resulted in improved median overall survival (9.0 vs 5.4 months, HR=0.52, p<0.001), confirmed response rate (26% vs 2%, p<0.001), and median progression-free survival (4.3 vs 1.5 months, HR=0.38, p<0.001) compared to control (n=107) in patients with metastatic colorectal cancer harboring BRAF V600E (%%PUBMED:31566309%%; NCT02928224).","cap_asco_evidence_level":"B","molecular_profile":"BRAF V600E","approval_status":"Phase III","amp_tier":"I"},{"pub_med_references":[39255538],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":4886,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Binimetinib + Cetuximab + Encorafenib","efficacy_evidence":"In a retrospective analysis, real-world treatment with Erbitux (cetuximab) and Braftovi (encorafenib) with or without Mektovi (binimetinib) led to an objective response rate (ORR) of 32.2% (57/201, 2 complete responses (CR)), disease control rate of 71.2% (126/201), median progression-free survival of 4.5 months, and median overall survival of 9.2 months in metastatic colorectal cancer patients with BRAF V600E, with an ORR of 33.3% (7/21, 1 CR) in patients treated with triplet therapy (%%PUBMED:39255538%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Clinical Study","amp_tier":"II"},{"pub_med_references":[35696748],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":4886,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Binimetinib + Cetuximab + Encorafenib","efficacy_evidence":"In a retrospective study, combination treatment with Mektovi (binimetinib), Erbitux (cetuximab), and Braftovi (encorafenib) resulted in an objective response rate of 31%, a disease control rate of 78%, a median progression-free survival of 4.2 mo, and a median overall survival of 7.1 mo in patients with metastatic colorectal cancer harboring BRAF V600E (%%PUBMED:35696748%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Clinical Study","amp_tier":"II"},{"pub_med_references":[36763936],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":4886,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Binimetinib + Cetuximab + Encorafenib","efficacy_evidence":"In a Phase II (ANCHOR CRC) trial, Braftovi (encorafenib), Mektovi (binimetinib), and Erbitux (cetuximab) combination treatment (n=95) demonstrated an acceptable safety profile and resulted in a confirmed objective response rate of 47.8% (44/92), a disease control rate of 88% (81/92), a median progression-free survival of 5.8 months, and a median overall survival of 18.3 months in patients with metastatic colorectal cancer harboring BRAF V600E (%%PUBMED:36763936%%; NCT03693170).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Selumetinib","indication":"pilocytic astrocytoma","therapy_id":913,"normalized_cancer":"Pilocytic Astrocytoma","evidence_type":"Actionable","therapy":"Selumetinib","efficacy_evidence":"Koselugo (selumetinib) is included in guidelines for patients with recurrent or progressive pilocytic astrocytoma harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[36409971],"normalized_drug":"Cobimetinib, Vemurafenib","indication":"colorectal cancer","therapy_id":1657,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"In a Phase II trial (TAPUR), the combination of Cotellic (cobimetinib) and Zelboraf (vemurafenib) resulted in an objective response rate of 30% (8/27; all partial responses), a disease control rate of 52% (14/27), a median progression-free survival of 15.7 weeks, and a median overall survival of 38.9 weeks in patients with colorectal cancer harboring BRAF V600E (n=26) or K601E (n=1) (%%PUBMED:36409971%%; NCT02693535).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[28649441],"normalized_drug":"Cobimetinib, Vemurafenib","indication":"colorectal cancer","therapy_id":1657,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"In a preclinical study, the combination of Cotellic (cobimetinib) and Zelboraf (vemurafenib) inhibited tumor growth in a cell line xenograft model of colorectal cancer harboring BRAF V600E (%%PUBMED:28649441%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[33595872],"response_type":"sensitive","indication":"thyroid cancer","therapy_id":4544,"normalized_cancer":"Thyroid Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + SCH772984","efficacy_evidence":"In a preclinical study, combination treatment with Tafinlar (dabrafenib) and SCH772984 synergistically inhibited cell growth of thyroid cancer cell lines harboring BRAF V600E in culture, and inhibited tumor growth in a cell line xenograft model (%%PUBMED:33595872%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[26603897],"response_type":"sensitive","indication":"melanoma","therapy_id":3310,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"SBI-0640756 + Vemurafenib","efficacy_evidence":"In a preclinical study, Zelboraf (vemurafenib) in combination with SBI-0640756 inhibited the association of eIF4G1 and eIF4E in Zelboraf (vemurafenib) resistant human melanoma cell lines harboring BRAF V600E in culture and reduced tumor growth in xenograft models (%%PUBMED:26603897%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[33953400],"response_type":"predicted - sensitive","indication":"melanoma","therapy_id":7209,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Belvarafenib","efficacy_evidence":"In a preclinical study, Belvarafenib (HM95573) treatment led to inhibition of tumor growth in a melanoma cell line xenograft model harboring BRAF V600E (%%PUBMED:33953400%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[27312529],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":1711,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Vemurafenib","efficacy_evidence":"In a preclinical study, Zelboraf (vemurafenib) and Erbitux (cetuximab) combination treatment inhibited survival of colorectal cancer cell lines harboring BRAF V600E in culture (%%PUBMED:27312529%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[22180495],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":1711,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Vemurafenib","efficacy_evidence":"In a preclinical study, Zelboraf (vemurafenib) treatment in combination with Erbitux (cetuximab) enhanced tumor growth inhibition and increased survival in a cell line xenograft model of colorectal cancer harboring BRAF V600E (%%PUBMED:22180495%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[24523613],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":1711,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Vemurafenib","efficacy_evidence":"In a clinical case study, the combination of Zelboraf (vemurafenib) and Erbitux (cetuximab) was tolerated and showed clinical benefit in a patient with BRAF V600E mutant colorectal cancer (%%PUBMED:24523613%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[41066726],"normalized_drug":"Plx8394","indication":"histiocytosis","therapy_id":1041,"normalized_cancer":"Histiocytosis","evidence_type":"Actionable","therapy":"PLX8394","efficacy_evidence":"In a Phase I/II trial (PLX120-03), PLX8394 treatment resulted in clinical symptom improvement and stable disease ongoing for at least 6.5 years in a young adult patient with recurrent neurodegenerative Langerhans cell histiocytosis harboring BRAF V600E (%%PUBMED:41066726%%; NCT02428712).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[38096472],"normalized_drug":"Cobimetinib, Vemurafenib","indication":"clear cell sarcoma","therapy_id":1657,"normalized_cancer":"Clear Cell Sarcoma","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"In a Phase II trial (TAPUR), Zelboraf (vemurafenib) and Cotellic (cobimetinib) combination therapy resulted in a partial response in a patient with clear cell sarcoma harboring BRAF V600E (%%PUBMED:38096472%%; NCT02693535).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[37729428],"response_type":"sensitive","indication":"melanoma","therapy_id":16205,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Binimetinib + Encorafenib + Talazoparib","efficacy_evidence":"In a preclinical study, treatment with the combination of Talzenna (talazoparib), Braftovi (encorafenib), and Mektovi (binimetinib) synergistically inhibited viability of patient-derived melanoma spheroids harboring BRAF V600E in culture (%%PUBMED:37729428%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Patient cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[30556047],"normalized_drug":"Dabrafenib, Trametinib","indication":"glomus tumor","therapy_id":1066,"normalized_cancer":"Soft Tissue Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, treatment with the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) resulted in decreased tumor size lasting at least 9 months in an adolescent (18 years old) patient with malignant glomus tumor harboring BRAF V600E (%%PUBMED:30556047%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[35882450],"response_type":"sensitive","indication":"pleomorphic xanthoastrocytoma","therapy_id":14717,"normalized_cancer":"Pleomorphic Xanthoastrocytoma","evidence_type":"Actionable","therapy":"Ulixertinib + Vinblastine","efficacy_evidence":"In a preclinical study, the combination of Ulixertinib (BVD-523) and Velban (vinblastine) inhibited proliferation and had a synergistic effect on induction of apoptosis in a pleomorphic xanthoastrocytoma cell line harboring BRAF V600E in culture (%%PUBMED:35882450%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[39232586],"normalized_drug":"Dabrafenib, Trametinib","indication":"biliary tract cancer","therapy_id":1066,"normalized_cancer":"Biliary Tract Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Tafinlar (dabrafenib) in combination with Mekinist (trametinib) is included in the Pan-Asian Guidelines Adaptation (PAGA) for biliary tract cancer patients harboring BRAF V600E who have progressed on one or more lines of systemic therapy (%%PUBMED:39232586%%; ESMO.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"biliary tract cancer","therapy_id":1066,"normalized_cancer":"Biliary Tract Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Tafinlar (dabrafenib) in combination with Mekinist (trametinib) is included in guidelines as subsequent-line therapy for patients with biliary tract cancer harboring BRAF V600E, including intrahepatic cholangiocarcinoma, extrahepatic cholangiocarcinoma, and gallbladder cancer (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[39864891],"normalized_drug":"Dabrafenib, Trametinib","indication":"biliary tract cancer","therapy_id":1066,"normalized_cancer":"Biliary Tract Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Tafinlar (dabrafenib) in combination with Mekinist (trametinib) is included in guidelines as second or later-line therapy for patients with biliary tract cancer harboring BRAF V600E (%%PUBMED:39864891%%; ESMO.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[32818466],"normalized_drug":"Dabrafenib, Trametinib","indication":"biliary tract cancer","therapy_id":1066,"normalized_cancer":"Biliary Tract Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a Phase II trial (ROAR), Tafinlar (dabrafenib) in combination with Mekinist (trametinib) demonstrated a manageable safety profile and resulted in an overall response rate of 51% (22/43, all partial responses) in patients with biliary tract cancer harboring BRAF V600E, with a median duration of response of 9 months, a median progression-free survival of 9 months, and a median overall survival of 14 months (%%PUBMED:32818466%%; NCT02034110).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"pub_med_references":[22389471],"response_type":"sensitive","indication":"melanoma","therapy_id":4004,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + GSK2126458","efficacy_evidence":"In a preclinical study, Tafinlar (dabrafenib) in combination with Omipalisib (GSK2126458) resulted in improved growth inhibition of human melanoma cell lines harboring BRAF V600E in culture (%%PUBMED:22389471%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[32234759],"response_type":"predicted - resistant","indication":"melanoma","therapy_id":1452,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"KRT-232","efficacy_evidence":"In a preclinical study, patient-derived xenograft (PDX) models of melanoma harboring BRAF V600E demonstrated resistance to treatment with KRT-232 (AMG 232) (%%PUBMED:32234759%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"pub_med_references":[26461489],"response_type":"sensitive","indication":"melanoma","therapy_id":3700,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"PLX4720 + Tivozanib","efficacy_evidence":"In a preclinical study, PLX4720 and Tivozanib (AV-951) worked synergistically to inhibit cell growth in PLX4720-resistant melanoma cell lines harboring BRAF V600E in culture (%%PUBMED:26461489%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[28645859],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":6241,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"INU-152","efficacy_evidence":"In a preclinical study, INU-152 inhibited growth of colorectal cancer cell lines harboring BRAF V600E in culture, and reduced tumor growth in BRAF V600E-mutant colorectal cancer cell line xenograft models (%%PUBMED:28645859%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Vemurafenib","indication":"Erdheim-Chester disease","therapy_id":342,"normalized_cancer":"Erdheim-Chester Disease","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"Zelboraf (vemurafenib) is included in guidelines as preferred first-line or subsequent-line therapy for patients with Erdheim-Chester disease harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"predicted - sensitive","pub_med_references":[39376796],"normalized_drug":"Dabrafenib, Trametinib","indication":"lung adenocarcinoma","therapy_id":1066,"normalized_cancer":"Lung Adenocarcinoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, treatment with the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) resulted in a partial response ongoing for at least 73 months in an elderly patient with lung adenocarcinoma harboring BRAF V600E (%%PUBMED:39376796%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[38715777],"normalized_drug":"Dabrafenib, Trametinib","indication":"lung adenocarcinoma","therapy_id":1066,"normalized_cancer":"Lung Adenocarcinoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, treatment with the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) resulted in a partial response with a decrease in the size of the lung lesion in a patient with metastatic lung adenocarcinoma harboring BRAF V600E and germline BRCA L1908Rfs*2, who had previously progressed on several lines of therapy (%%PUBMED:38715777%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[36531075],"normalized_drug":"Dabrafenib, Trametinib","indication":"Her2-receptor negative breast cancer","therapy_id":1066,"normalized_cancer":"Invasive Breast Carcinoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) resulted in a complete response in the liver and bone lesions with a progression-free survival of 9 months in a patient with metastatic ERBB2 (HER2)-negative, hormone receptor-positive breast cancer harboring BRAF V600E (%%PUBMED:36531075%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[32029534],"normalized_drug":"Vemurafenib","indication":"histiocytic and dendritic cell cancer","therapy_id":342,"normalized_cancer":"Histiocytic and Dendritic Cell Neoplasms","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase II trial (VE-BASKET), responses were seen in patients with histiocytic neoplasms harboring BRAF V600E (n=27) when treated with Zelboraf (vemurafenib), including 15 patients with a partial response and 2 patients with a complete response (%%PUBMED:32029534%%; NCT01524978).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[19706763],"normalized_drug":"Refametinib","indication":"colorectal cancer","therapy_id":888,"normalized_cancer":"Colorectal 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culture","amp_tier":"NA"},{"response_type":"predicted - sensitive","pub_med_references":[31109800],"normalized_drug":"Dabrafenib","indication":"nephroblastoma","therapy_id":3,"normalized_cancer":"Wilms' Tumor","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a clinical case study, Tafinlar (dabrafenib) treatment resulted in a durable major response with a decrease in the pulmonary metastases in an adult patient with metastatic nephroblastoma harboring BRAF V600E (%%PUBMED:31109800%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[22389471],"normalized_drug":"Dabrafenib, Trametinib","indication":"melanoma","therapy_id":1066,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a preclinical study, Tafinlar (dabrafenib) in combination with Mekinist (trametinib) inhibited growth of melanoma cells harboring BRAF V600E in culture (%%PUBMED:22389471%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[28268064],"normalized_drug":"Dabrafenib, Trametinib","indication":"melanoma","therapy_id":1066,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a Phase II trial, BRAF V600E positive melanoma patients who progressed on treatment with BRAF inhibitors or the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) were treated again with the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) after 12 weeks off treatment, which resulted in a partial response in 35% (8/25) and stable disease in 40% (10/25) (%%PUBMED:28268064%%).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[25399551],"normalized_drug":"Dabrafenib, Trametinib","indication":"melanoma","therapy_id":1066,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a Phase III trial (COMBI-v) that supported FDA approval, the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) resulted in an improved overall survival rate at 12 months (72% vs 65%, HR=0.69, p=0.005), median progression-free survival (11.4 vs 7.3 months, HR=0.56, p<0.001), and objective response rate (64% vs 51%, p<0.001) compared to Zelboraf (vemurafenib) in melanoma patients harboring BRAF V600E or V600K (%%PUBMED:25399551%%; NCT01597908).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"FDA approved - On Companion Diagnostic","amp_tier":"I"},{"pub_med_references":[37838724],"response_type":"sensitive","indication":"melanoma","therapy_id":16290,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"ARCC4 + Dabrafenib","efficacy_evidence":"In a preclinical study, the addition of ARCC4 to Tafinlar (dabrafenib) treatment inhibited colony formation in melanoma cell lines harboring BRAF V600E in culture (%%PUBMED:37838724%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[34433654],"response_type":"predicted - sensitive","indication":"high grade glioma","therapy_id":7209,"normalized_cancer":"High-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"Belvarafenib","efficacy_evidence":"In a preclinical study, Belvarafenib (HM95573) treatment led to inhibition of cell viability in a patient-derived glioma cell line harboring BRAF V600E in culture (%%PUBMED:34433654%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"anaplastic astrocytoma","therapy_id":1066,"normalized_cancer":"Astrocytoma, IDH-Mutant, Grade 3","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Combination of Mekinist (trametinib) and Tafinlar (dabrafenib) is included in guidelines for patients with recurrent anaplastic gliomas harboring BRAF V600E, including anaplastic astrocytoma (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[25665005],"response_type":"sensitive","indication":"melanoma","therapy_id":3530,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Navitoclax + Vemurafenib","efficacy_evidence":"In a preclinical study, Navitoclax (ABT-263) enhanced the inhibitory effect of Zelboraf (vemurafenib) on human melanoma cells harboring BRAF V600E in culture (%%PUBMED:25665005%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[27312529],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":4536,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Selumetinib","efficacy_evidence":"In a preclinical study, Koselugo (selumetinib) and Erbitux (cetuximab) combination treatment inhibited survival of colorectal cancer cell lines harboring BRAF V600E in culture (%%PUBMED:27312529%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[34476331],"normalized_drug":"Dabrafenib, Trametinib","indication":"pancreatic cancer","therapy_id":1066,"normalized_cancer":"Pancreatic Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a retrospective analysis, treatment with the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) resulted in a partial response in two patients with pancreatic cancer harboring BRAF V600E, including one patient with a progression-free survival (PFS) of at least 2 years on third-line therapy and another patient with a PFS of 48 weeks on second-line therapy (%%PUBMED:34476331%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[33953400],"response_type":"predicted - sensitive","indication":"colorectal cancer","therapy_id":7209,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Belvarafenib","efficacy_evidence":"In a Phase I trial, Belvarafenib (HM95573) treatment in a colorectal cancer patient harboring BRAF V600E led to a tumor reduction of 39% after 8 weeks of treatment and a confirmed partial response at 12 weeks, and response to treatment was maintained for 8 weeks (%%PUBMED:33953400%%; NCT03118817).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[24398428],"normalized_drug":"Ganetespib","indication":"skin melanoma","therapy_id":745,"normalized_cancer":"Cutaneous Melanoma","evidence_type":"Actionable","therapy":"Ganetespib","efficacy_evidence":"In a preclinical study, the Hsp90 inhibitor Ganetespib destabilized BRAF, especially BRAF V600E, resulted in loss of cell viability in culture and antitumor effects in cell line xenograft models of melanoma (%%PUBMED:24398428%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"anaplastic thyroid carcinoma","therapy_id":1066,"normalized_cancer":"Anaplastic Thyroid Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Tafinlar (dabrafenib) and Mekinist (trametinib) combination therapy is included in guidelines for patients with advanced or metastatic thyroid gland anaplastic carcinoma harboring BRAF V600E (%%PUBMED:31549998%%, %%PUBMED:35491008%%; ESMO.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"anaplastic thyroid carcinoma","therapy_id":1066,"normalized_cancer":"Anaplastic Thyroid Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Tafinlar (dabrafenib) and Mekinist (trametinib) combination therapy is included in guidelines as neoadjuvant or systemic treatment for thyroid gland anaplastic carcinoma patients harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[27697975],"normalized_drug":"Dabrafenib, Trametinib","indication":"anaplastic thyroid carcinoma","therapy_id":1066,"normalized_cancer":"Anaplastic Thyroid Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, Tafinlar (dabrafenib) and Mekinist (trametinib) combination treatment resulted in a clinical and radiologic response that lasted for 9 months in an anaplastic thyroid cancer patient harboring BRAF V600E (%%PUBMED:27697975%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[35026411],"normalized_drug":"Dabrafenib, Trametinib","indication":"anaplastic thyroid carcinoma","therapy_id":1066,"normalized_cancer":"Anaplastic Thyroid Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a Phase II trial (ROAR) that supported FDA approval, the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) resulted in an overall response rate of 61% (20/33; 3 complete responses, 17 partial responses) in patients with anaplastic thyroid cancer harboring BRAF V600E, with 12-month duration of response rate of 50%, a median progression-free survival and overall survival of 6.7 and 14.5 months, respectively (%%PUBMED:35026411%%; NCT02034110).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"FDA approved - On Companion Diagnostic","amp_tier":"I"},{"pub_med_references":[26573800],"response_type":"sensitive","indication":"glioblastoma","therapy_id":5422,"normalized_cancer":"Glioblastoma, IDH-Wildtype","evidence_type":"Actionable","therapy":"BI2536 + PLX4720","efficacy_evidence":"In a preclinical study, the combination of BI 2536 and PLX4720 resulted in suppression of downstream signaling, increased apoptotic activity, inhibition of cell proliferation, and tumor growth suppression in glioblastoma cell line xenograft models harboring BRAF V600E (%%PUBMED:26573800%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[34337566],"response_type":"sensitive","indication":"melanoma","therapy_id":8304,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"ERAS-007","efficacy_evidence":"In a preclinical study, ERAS-007 (ASN007) treatment inhibited proliferation and Erk signaling in a melanoma cell line harboring BRAF V600E in culture, and inhibited tumor growth in patient-derived xenograft (PDX) models, including a Zelboraf (vemurafenib)-resistant PDX model (%%PUBMED:34337566%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Pdx & cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[32029534],"normalized_drug":"Vemurafenib","indication":"salivary gland cancer","therapy_id":342,"normalized_cancer":"Salivary Gland Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase II trial (VE-BASKET), a patient with salivary ductal carcinoma harboring BRAF V600E demonstrated a partial response when treated with Zelboraf (vemurafenib) (%%PUBMED:32029534%%; NCT01524978).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[26267534],"response_type":"sensitive","indication":"melanoma","therapy_id":2618,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"SCH772984","efficacy_evidence":"In a preclinical study, SCH772984 inhibited growth of melanoma cell lines harboring BRAF V600E in culture (%%PUBMED:26267534%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[25665005],"response_type":"sensitive","indication":"melanoma","therapy_id":3532,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Trametinib + TW-37","efficacy_evidence":"In a preclinical study, TW-37 enhanced the inhibitory effect of Mekinist (trametinib) on human melanoma cells harboring BRAF V600E in culture (%%PUBMED:25665005%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"response_type":"predicted - 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Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase II trial (VE-BASKET), Zelboraf (vemurafenib) treatment resulted in a response in patients with anaplastic thyroid carcinoma harboring BRAF V600E (n=12), including 1 patient with a complete response and 2 patients with a partial response (%%PUBMED:32029534%%; NCT01524978).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","normalized_drug":"Vemurafenib","indication":"ovarian cancer","therapy_id":342,"normalized_cancer":"Ovarian Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase II trial (MyPathway), Zelboraf (vemurafenib) treatment resulted in an objective response of 50% (2/4, 2 partial response) in patients with ovarian cancer harboring BRAF V600E, and stable disease lasting more than 120 days in 1 patient (%%PUBMED:29320312%%; NCT02091141).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[32029534],"normalized_drug":"Vemurafenib","indication":"ovarian cancer","therapy_id":342,"normalized_cancer":"Ovarian Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase II trial (VE-BASKET), responses were seen in ovarian cancer patients harboring BRAF V600E (n=4) when treated with Zelboraf (vemurafenib), including 2 patients with a partial response (%%PUBMED:32029534%%; NCT01524978).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[25665005],"response_type":"sensitive","indication":"melanoma","therapy_id":3531,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"TW-37 + Vemurafenib","efficacy_evidence":"In a preclinical study, TW-37 enhanced the inhibitory effect of Zelboraf (vemurafenib) on human melanoma cells harboring BRAF V600E in culture (%%PUBMED:25665005%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"response_type":"resistant","pub_med_references":[19001320],"normalized_drug":"Panitumumab","indication":"colorectal cancer","therapy_id":845,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Panitumumab","efficacy_evidence":"In a retrospective analysis, metastatic colorectal cancer patients harboring BRAF V600E demonstrated shorter progression-free survival (p=0.0107) and overall survival (p<0.0001) compared to patients with wild-type BRAF following Vectibix (panitumumab) or Erbitux (cetuximab) therapy with or without chemotherapy, and in a preclinical study, colorectal cancer cell lines harboring BRAF V600E were resistant to Vectibix (panitumumab) in culture (%%PUBMED:19001320%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Clinical Study","amp_tier":"II"},{"response_type":"resistant","pub_med_references":[25673558],"normalized_drug":"Panitumumab","indication":"colorectal cancer","therapy_id":845,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Panitumumab","efficacy_evidence":"In a meta-analysis, the addition of Erbitux (cetuximab) or Vectibix (panitumumab) to standard of care treatment with chemotherapy did not result in improved progression-free survival (HR=0.88; 95% CI, 0.67-1.14; p=0.33), overall survival (HR=0.91; 95% CI, 0.62-1.34; p=0.63), or objective response rate (relative risk=1.31; 95% CI, 0.83-2.08; p=0.25) in patients with advanced colorectal cancer harboring BRAF V600E (%%PUBMED:25673558%%).","cap_asco_evidence_level":"B","molecular_profile":"BRAF V600E","approval_status":"Clinical Study - Meta-analysis","amp_tier":"I"},{"response_type":"resistant","pub_med_references":[36307056],"normalized_drug":"Panitumumab","indication":"colorectal cancer","therapy_id":845,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Panitumumab","efficacy_evidence":"Vectibix (panitumumab), as a monotherapy, is not indicated for use in metastatic colorectal cancer patients with BRAF V600E (%%PUBMED:36307056%%; ESMO.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[26573800],"response_type":"decreased response","indication":"glioblastoma","therapy_id":1060,"normalized_cancer":"Glioblastoma, IDH-Wildtype","evidence_type":"Actionable","therapy":"PLX4720","efficacy_evidence":"In a preclinical study, a glioblastoma cell line harboring BRAF V600E demonstrated a decreased response to treatment with PLX4720, demonstrating increased viability of CD133 positive cells in culture and in xenograft models (%%PUBMED:26573800%%).","cap_asco_evidence_level":"NA","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"NA"},{"response_type":"sensitive","normalized_drug":"Cobimetinib, Vemurafenib","indication":"low grade glioma","therapy_id":1657,"normalized_cancer":"Low-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"Combination of Zelboraf (vemurafenib) and Cotellic (cobimetinib) is included in guidelines for patients with recurrent or progressive low grade glioma harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[27048246],"normalized_drug":"Dabrafenib, Trametinib","indication":"neuroendocrine tumor","therapy_id":1066,"normalized_cancer":"Gastrointestinal Neuroendocrine Tumor","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, Mekinist (trametinib) and Tafinlar (dabrafenib) combination treatment resulted in a rapid and sustained clinical response in a patient with a rectal neuroendocrine tumor harboring a BRAF V600E mutation (%%PUBMED:27048246%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"neuroendocrine tumor","therapy_id":1066,"normalized_cancer":"Gastrointestinal Neuroendocrine Tumor","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Mekinist (trametinib) and Tafinlar (dabrafenib) combination therapy is included in guidelines for patients with unresectable or metastatic extrapulmonary poorly differentiated neuroendocrine carcinoma, large or small cell carcinoma, or mixed neuroendocrine/non-neuroendocrine neoplasms harboring BRAF V600E who have progressed on or following prior treatment (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[34330842],"response_type":"sensitive","indication":"melanoma","therapy_id":6971,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"ASTX029","efficacy_evidence":"In a preclinical study, ASTX029 treatment reduced Erk and Rsk phosphorylation, induced cell-cycle arrest, and inhibited growth of a melanoma cell line harboring BRAF V600E in culture and inhibited tumor growth in cell line xenograft models, and was also effective against cells with acquired resistance to Zelboraf (vemurafenib) or Koselugo (selumetinib) (%%PUBMED:34330842%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[39399174],"normalized_drug":"Trametinib","indication":"diffuse leptomeningeal glioneuronal tumor","therapy_id":2,"normalized_cancer":"Miscellaneous Neuroepithelial Tumor","evidence_type":"Actionable","therapy":"Trametinib","efficacy_evidence":"In a clinical case study, Mekinist (trametinib) treatment resulted in a partial response in the brain and stable disease in the spine in a pediatric patient with diffuse leptomeningeal glioneuronal tumor harboring BRAF V600E (%%PUBMED:39399174%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"not predictive","pub_med_references":[29723688],"normalized_drug":"Atezolizumab","indication":"lung non-small cell carcinoma","therapy_id":1201,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Atezolizumab","efficacy_evidence":"In a retrospective analysis, non-small cell lung cancer patients harboring BRAF V600E did not demonstrate a significantly different response to treatment with either Keytruda (pembrolizumab), Opdivo (nivolumab), or Tecentriq (atezolizumab) compared to patients with BRAF non-V600E mutations, demonstrating an objective response rate of 25% (3/12) vs 33% (3/9) (p=1.0) and median progression-free survival of 3.7 months vs 4.1 months (p=0.37) (%%PUBMED:29723688%%).","cap_asco_evidence_level":"NA","molecular_profile":"BRAF V600E","approval_status":"Clinical Study - Cohort","amp_tier":"NA"},{"response_type":"sensitive","normalized_drug":"Vemurafenib","indication":"high grade glioma","therapy_id":342,"normalized_cancer":"High-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"Zelboraf (vemurafenib) is included in guidelines as adjuvant therapy for pediatric patients with diffuse high-grade gliomas harboring BRAF V600E, or as a preferred regimen for patients with recurrent or progressive disease (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[32029534],"normalized_drug":"Vemurafenib","indication":"high grade glioma","therapy_id":342,"normalized_cancer":"High-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase II trial (VE-BASKET), responses were seen in glioma patients harboring BRAF V600E (n=24) when treated with Zelboraf (vemurafenib), including 1 patient with a complete response and 5 patients with a partial response (%%PUBMED:32029534%%; NCT01524978).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[30351999],"normalized_drug":"Vemurafenib","indication":"high grade glioma","therapy_id":342,"normalized_cancer":"High-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase II trial (VE-BASKET), Zelboraf (vemurafenib) treatment resulted in an objective response rate of 25% (6/24, 1 complete response, 5 partial responses) in patients with gliomas harboring BRAF V600E, with a median progression free survival of 5.5-months, a median overall survival of 28.2 months (%%PUBMED:30351999%%; NCT01524978).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[24859340],"normalized_drug":"Vemurafenib","indication":"ameloblastoma","therapy_id":342,"normalized_cancer":"Head and Neck Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a preclinical study, Zelboraf (vemurafenib) inhibited viability of an ameloblastoma cell line harboring BRAF V600E in culture (%%PUBMED:24859340%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[35689405],"normalized_drug":"Vemurafenib","indication":"ameloblastoma","therapy_id":342,"normalized_cancer":"Head and Neck Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a preclinical study, Zelboraf (vemurafenib) inhibited viability of ameloblastoma cell lines harboring BRAF V600E in culture (%%PUBMED:35689405%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Vemurafenib","indication":"skin melanoma","therapy_id":342,"normalized_cancer":"Cutaneous Melanoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"Zelboraf (vemurafenib) therapy is included in guidelines for cutaneous melanoma patients with unresectable or metastatic disease harboring BRAF V600 activating mutations, such as BRAF V600E, in cases where BRAF/MEK inhibitor combination therapy is contraindicated (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","normalized_drug":"Dabrafenib","indication":"skin melanoma","therapy_id":3,"normalized_cancer":"Cutaneous Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"Tafinlar (dabrafenib) therapy is included in guidelines for cutaneous melanoma patients with unresectable or metastatic disease harboring BRAF V600 activating mutations, such as BRAF V600E, in cases where BRAF/MEK inhibitor combination therapy is contraindicated (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[33568355],"response_type":"predicted - sensitive","indication":"colon adenocarcinoma","therapy_id":11477,"normalized_cancer":"Colon Adenocarcinoma","evidence_type":"Actionable","therapy":"Dabrafenib + Regorafenib + Trametinib","efficacy_evidence":"In a clinical case study, combination treatment with Stivarga (regorafenib), Tafinlar (dabrafenib), and Mekinist (trametinib) in a patient with colon adenocarcinoma harboring BRAF V600E led to stable disease, and treatment continued for eight months, at which time some disease progression was observed (%%PUBMED:33568355%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[34818649],"response_type":"predicted - sensitive","indication":"triple-receptor negative breast cancer","therapy_id":12792,"normalized_cancer":"Invasive Breast Carcinoma","evidence_type":"Actionable","therapy":"Nab-paclitaxel + Vemurafenib","efficacy_evidence":"In a clinical case study, Zelboraf (vemurafenib) and Abraxane (nab-paclitaxel) combination treatment resulted in regression of some metastatic pulmonary lesions and a progression-free survival of 4.4 months in a patient with triple-negative breast cancer harboring BRAF V600E, but a biopsy in lesions that progressed showed acquisition of additional mutations in PDGFRB, NF2, GRM3, MLH1, FOXA1, LRP1B, and AR amplification (%%PUBMED:34818649%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[27217440],"response_type":"predicted - sensitive","indication":"high grade glioma","therapy_id":4902,"normalized_cancer":"High-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"Everolimus + PLX4720","efficacy_evidence":"In a preclinical study, Afinitor (everolimus) and PLX4720 synergistically inhibited growth and induced apoptosis in glioma cell lines in culture (%%PUBMED:27217440%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[36343387],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":14549,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Trametinib + Valproic acid","efficacy_evidence":"In a preclinical study, the combination of Mekinist (trametinib) and Valproic acid resulted in greater apoptotic activity compared to either agent alone in a colorectal cancer cell line harboring BRAF V600E in culture (%%PUBMED:36343387%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[29343524],"response_type":"sensitive","indication":"melanoma","therapy_id":6995,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"RAF709","efficacy_evidence":"In a preclinical study, RAF709 inhibited Erk signaling and proliferation of melanoma cells harboring BRAF V600E in culture (%%PUBMED:29343524%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","normalized_drug":"Ulixertinib","indication":"central nervous system cancer","therapy_id":997,"normalized_cancer":"CNS/Brain Cancer","evidence_type":"Actionable","therapy":"Ulixertinib","efficacy_evidence":"In a Phase II trial (APEC1621J), Ulixertinib (BVD-523) treatment resulted in a 6-month progression-free survival rate of 37% but no objective response in pediatric and young adult patients with advanced solid tumors harboring MAPK pathway activation, however, a patient with glioneuronal tumor harboring a BRAF V600E achieved prolonged stable disease and remained on treatment for 9 cycles (J Clin Oncol 40, no. 16_suppl (June 01, 2022) 3009; NCT03698994).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Cobimetinib, Vemurafenib","indication":"anaplastic oligodendroglioma","therapy_id":1657,"normalized_cancer":"Oligodendroglioma, IDH-mutant, and 1p/19q-Codeleted","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"Combination of Zelboraf (vemurafenib) and Cotellic (cobimetinib) is included in guidelines for patients with recurrent anaplastic gliomas harboring BRAF V600E, including anaplastic oligodendroglioma (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[37326340],"response_type":"sensitive","indication":"colorectal carcinoma","therapy_id":4034,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Gedatolisib + Palbociclib","efficacy_evidence":"In a preclinical study, the combination of Ibrance (palbociclib) and Gedatolisib (PF-05212384) synergistically inhibited growth of a colorectal carcinoma cell line harboring BRAF V600E in culture (%%PUBMED:37326340%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[39087485],"response_type":"no benefit","indication":"melanoma","therapy_id":17373,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"RGT-018","efficacy_evidence":"In a preclinical study, RGT-018 did not inhibit proliferation of melanoma cells harboring BRAF V600E in 3D culture (%%PUBMED:39087485%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[36343387],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":14548,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Entinostat + Trametinib","efficacy_evidence":"In a preclinical study, the combination of Mekinist (trametinib) and Entinostat (MS-275) resulted in greater apoptotic activity compared to either agent alone in a colorectal cancer cell line harboring BRAF V600E in culture (%%PUBMED:36343387%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[33461766],"normalized_drug":"Dabrafenib, Trametinib","indication":"brain glioblastoma multiforme","therapy_id":1066,"normalized_cancer":"Glioblastoma, IDH-Wildtype","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, Tafinlar (dabrafenib) and Mekinist (trametinib) combination therapy resulted in tumor shrinkage after 2 months in a patient with epithelioid glioblastoma multiforme harboring BRAF V600E, who had progressed after resection, radiotherapy, and chemotherapy, and following an interruption in therapy due to toxicity demonstrated a partial response and remained progression-free for 19 months, prior to progressing 29 months after initiation of therapy (%%PUBMED:33461766%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[36638198],"response_type":"predicted - sensitive","indication":"Advanced Solid Tumor","therapy_id":1710,"normalized_cancer":"All Solid Tumors","evidence_type":"Actionable","therapy":"Erlotinib + Vemurafenib","efficacy_evidence":"In a Phase Ib/II trial (EVICT), the combination of Zelboraf (vemurafenib) and Tarceva (erlotinib) resulted in an overall response rate of 43% (3/7), a clinical benefit rate of 100%, and a median PFS of 5.5 months in patients with advanced solid tumors other tan colorectal cancer harboring BRAF V600E (%%PUBMED:36638198%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[22389471],"response_type":"sensitive","indication":"melanoma","therapy_id":3027,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"GSK2126458 + Trametinib","efficacy_evidence":"In a preclinical study, Mekinist (trametinib) in combination with Omipalisib (GSK2126458) inhibited growth of melanoma cell lines harboring BRAF V600E in culture (%%PUBMED:22389471%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"lung non-small cell carcinoma","therapy_id":6765,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"LTT462 + LXH 254","efficacy_evidence":"In a Phase Ib trial, LTT462 and LXH 254 combination therapy was well tolerated and resulted in an unconfirmed partial response (PR) in 4% (2/49) and stable disease (SD) in 33% (16/49) of patients with advanced or metastatic KRAS- or BRAF-mutant non-small cell lung cancer, with 1 patient harboring BRAF V600E achieving an unconfirmed PR and 1 achieving SD with over 25% tumor reduction (Ann Oncol 31 (suppl 4):S881-S882; NCT02974725).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[33824136],"response_type":"no benefit","indication":"melanoma","therapy_id":11754,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"RM-018","efficacy_evidence":"In a preclinical study, RM-018 did not inhibit growth of melanoma cells harboring BRAF V600E in culture (%%PUBMED:33824136%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"colon cancer","therapy_id":13708,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"ABM-1310 + Cetuximab","efficacy_evidence":"In a preclinical study, combination treatment with ABM-1310 and Erbitux (cetuximab) led to inhibition of tumor growth in a colon cancer cell line xenograft model harboring BRAF V600E (Cancer Res (2020) 80 (16_Supplement): 4038).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[26916115],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":3709,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"BI 882370 + Trametinib","efficacy_evidence":"In a preclinical study, colorectal cancer cells harboring BRAF V600E were sensitive to the combination of BI 882370 and Mekinist (trametinib) in xenograft models, resulting in tumor growth inhibition and partial tumor regression (%%PUBMED:26916115%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[37040395],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":11094,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Encorafenib + Fluorouracil + Leucovorin + Oxaliplatin","efficacy_evidence":"In a preclinical study, treatment with the combination of Erbitux (cetuximab), Braftovi (encorafenib), and FOLFOX resulted in increased tumor growth inhibition and survival compared to Erbitux (cetuximab) plus Braftovi (encorafenib) or FOLFOX alone in colorectal cancer cell line xenograft models harboring BRAF V600E (%%PUBMED:37040395%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[39863775],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":11094,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Encorafenib + Fluorouracil + Leucovorin + Oxaliplatin","efficacy_evidence":"In a Phase III trial (BREAKWATER) that supported FDA approval, Braftovi (encorafenib) in combination with Erbitux (cetuximab) and mFOLFOX6 significantly improved objective response rate (60.9%, 67/110 vs 40.0%, 44/110, OR 2.443, p=0.0008) compared to standard of care in patients with metastatic colorectal cancer harboring BRAF V600E, with median duration of response of 13.9 vs 11.1 mo, and overall survival was not estimable vs 14.6 mo (HR 0.47) (%%PUBMED:39863775%%; NCT04607421).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"FDA approved - On Companion Diagnostic","amp_tier":"I"},{"pub_med_references":[36759733],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":15050,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Gefitinib + PLX4720 + Saracatinib","efficacy_evidence":"In a preclinical study, the combination of PLX4720, Iressa (gefitinib), and Saracatinib (AZD0530) inhibited tumor growth in colorectal cancer cell line xenograft models harboring BRAF V600E to a greater degree than the combinations of PLX4720 and Iressa (gefitinib) or PLX4720 and Saracatinib (AZD0530) (%%PUBMED:36759733%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[27048246],"response_type":"predicted - sensitive","indication":"neuroendocrine tumor","therapy_id":4234,"normalized_cancer":"Gastrointestinal Neuroendocrine Tumor","evidence_type":"Actionable","therapy":"Trametinib + Vemurafenib","efficacy_evidence":"In a clinical case study, Mekinist (trametinib) and Zelboraf (vemurafenib) combination treatment resulted in a rapid and sustained clinical response in a patient with a rectal neuroendocrine tumor harboring a BRAF V600E mutation (%%PUBMED:27048246%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[32758030],"normalized_drug":"Trametinib","indication":"Advanced Solid Tumor","therapy_id":2,"normalized_cancer":"All Solid Tumors","evidence_type":"Actionable","therapy":"Trametinib","efficacy_evidence":"In a Phase II trial (NCI-MATCH), Mekinist (trametinib) treatment resulted in an objective response rate of 37.9% (11/29) in patients with BRAF V600E positive advanced solid tumors other than melanoma, thyroid cancer, or colorectal cancer, with a median duration of response of 25.1 months, and a disease control rate of 75.9% (22/29) (%%PUBMED:32758030%%; NCT02465060).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[23733758],"normalized_drug":"Vemurafenib","indication":"lung non-small cell carcinoma","therapy_id":342,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a clinical case study, a non-small cell lung cancer patient harboring a BRAF V600E mutation had a complete response after treatment with Zelboraf (vemurafenib) (%%PUBMED:23733758%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[26200454],"normalized_drug":"Vemurafenib","indication":"lung non-small cell carcinoma","therapy_id":342,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a retrospective analysis, non-small cell lung cancer patients harboring BRAF V600E achieved an overall response rate of 54% (13/24, 2 complete responses, 11 partial responses, and 10 with stable disease) and a disease control rate of 96% following treatment with Zelboraf (vemurafenib) (%%PUBMED:26200454%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Clinical Study","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Vemurafenib","indication":"lung non-small cell carcinoma","therapy_id":342,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase II trial (MyPathway), Zelboraf (vemurafenib) treatment resulted in an objective response of 43% (6/14, 1 complete response, 5 partial response) in patients with non-small cell lung cancer harboring BRAF V600E, and stable disease lasting more than 120 days in 2 patients (%%PUBMED:29320312%%; NCT02091141).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Vemurafenib","indication":"lung non-small cell carcinoma","therapy_id":342,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"Zelboraf (vemurafenib) is included in guidelines as a first-line therapy for advanced or metastatic non-small cell lung cancer patients harboring BRAF V600E mutations who can not tolerate the combination of Mekinist (trametinib) and Tafinlar (dabrafenib) (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[32029534],"normalized_drug":"Vemurafenib","indication":"lung non-small cell carcinoma","therapy_id":342,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase II trial (VE-BASKET), responses were seen in patients with non-small cell lung cancer harboring BRAF V600E (n=63) when treated with Zelboraf (vemurafenib), including 23 patients with a partial response (%%PUBMED:32029534%%; NCT01524978).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"gallbladder cancer","therapy_id":1066,"normalized_cancer":"Gallbladder Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Tafinlar (dabrafenib) in combination with Mekinist (trametinib) is included in guidelines as subsequent-line therapy for patients with biliary cancer harboring BRAF V600E, including gallbladder cancer (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[27488531],"response_type":"conflicting","indication":"melanoma","therapy_id":849,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Mirdametinib","efficacy_evidence":"In a preclinical study, a melanoma cell line xenograft model harboring BRAF V600E treated with Gomekli (mirdametinib) demonstrated stable tumor growth, but by day 44, growth ensued and thus, demonstrated no benefit (%%PUBMED:27488531%%).","cap_asco_evidence_level":"NA","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"NA"},{"pub_med_references":[26267534],"response_type":"conflicting","indication":"melanoma","therapy_id":849,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Mirdametinib","efficacy_evidence":"In a preclinical study, Gomekli (mirdametinib) inhibited growth of melanoma cell lines harboring BRAF V600E in culture (%%PUBMED:26267534%%).","cap_asco_evidence_level":"NA","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"NA"},{"pub_med_references":[25422890],"response_type":"conflicting","indication":"melanoma","therapy_id":849,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Mirdametinib","efficacy_evidence":"In a preclinical study, Gomekli (mirdametinib) treatment induced cell cycle arrest and inhibited growth of melanoma cells harboring BRAF V600E in culture (%%PUBMED:25422890%%).","cap_asco_evidence_level":"NA","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"NA"},{"response_type":"predicted - sensitive","pub_med_references":[32206360],"normalized_drug":"Dabrafenib, Trametinib","indication":"breast metaplastic carcinoma","therapy_id":1066,"normalized_cancer":"Metaplastic Breast Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, treatment with the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) resulted in a partial response in a patient with metaplastic breast cancer harboring BRAF V600E, however, progression occurred after 8 weeks (%%PUBMED:32206360%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[38728872],"response_type":"sensitive","indication":"melanoma","therapy_id":2149,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Ravoxertinib","efficacy_evidence":"In a preclinical study, Ravoxertinib (GDC-0994) inhibited viability and colony formation in melanoma cell lines harboring BRAF V600E in culture (%%PUBMED:38728872%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[36622773],"response_type":"sensitive","indication":"melanoma","therapy_id":14824,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + DS03090629","efficacy_evidence":"In a preclinical study, the combination of DS03090629 and Tafinlar (dabrafenib) inhibited Erk phosphorylation and proliferation in a melanoma cell line harboring BRAF V600E in culture and induced tumor regression in a cell line xenograft model (%%PUBMED:36622773%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[23629727],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":4657,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Pimasertib + Regorafenib","efficacy_evidence":"In a preclinical study, Pimasertib (MSC1936369B) and Stivarga (regorafenib) synergistically inhibited proliferation of colorectal cancer cells harboring BRAF V600E in culture (%%PUBMED:23629727%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[20538618],"response_type":"sensitive","indication":"Advanced Solid Tumor","therapy_id":884,"normalized_cancer":"All Solid Tumors","evidence_type":"Actionable","therapy":"RAF265","efficacy_evidence":"In a preclinical study, RAF265 inhibited Erk phosphorylation and cell proliferation in BRAF V600E expressing cells in culture (%%PUBMED:20538618%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[27080216,27283860,28919011],"normalized_drug":"Dabrafenib, Trametinib","indication":"lung non-small cell carcinoma","therapy_id":1066,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a Phase II trial that supported FDA approval, treatment with the combination of Mekinist (trametinib) and Tafinlar (dabrafenib) in patients with non-small cell lung cancer harboring BRAF V600E resulted in an overall response rate of 66.7% (38/57) in previously treated patients and 64% (23/36) in untreated patients, versus 33% (26/78) treated with Tafinlar (dabrafenib) alone (%%PUBMED:27080216%%, %%PUBMED:27283860%%, %%PUBMED:28919011%%; NCT01336634).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"FDA approved - On Companion Diagnostic","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[39615406],"normalized_drug":"Dabrafenib, Trametinib","indication":"lung non-small cell carcinoma","therapy_id":1066,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Combination of Mekinist (trametinib) and Tafinlar (dabrafenib) is included in the Pan-Asian Guidelines Adaptation (PAGA) for advanced and metastatic non-small cell lung cancer patients harboring BRAF V600E (%%PUBMED:39615406%%; ESMO.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"lung non-small cell carcinoma","therapy_id":1066,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Combination of Mekinist (trametinib) and Tafinlar (dabrafenib) is included in guidelines as a first-line or subsequent therapy for advanced or metastatic non-small cell lung cancer patients harboring BRAF V600E mutations (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","normalized_drug":"Cobimetinib, Vemurafenib","indication":"glioblastoma","therapy_id":1657,"normalized_cancer":"Glioblastoma, IDH-Wildtype","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"Combination of Zelboraf (vemurafenib) and Cotellic (cobimetinib) is included in guidelines for patients with recurrent glioblastoma harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[31217909],"normalized_drug":"Cobimetinib, Vemurafenib","indication":"glioblastoma","therapy_id":1657,"normalized_cancer":"Glioblastoma, IDH-Wildtype","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"In a clinical case study, a patient with epithelioid glioblastoma harboring BRAF V600E continued to response as Cotellic (cobimetinib) was added to Zelboraf (vemurafenib) treatment (%%PUBMED:31217909%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[36967525],"normalized_drug":"Vemurafenib","indication":"ovarian serous cystadenocarcinoma","therapy_id":342,"normalized_cancer":"Serous Ovarian Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a clinical case study, Zelboraf (vemurafenib) treatment resulted in a complete radiological response that lasted for 3 years in a patient with low-grade serous cystadenocarcinoma of the ovary harboring BRAF V600E (%%PUBMED:36967525%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[27669459],"response_type":"sensitive","indication":"papillary thyroid carcinoma","therapy_id":2011,"normalized_cancer":"Papillary Thyroid Cancer","evidence_type":"Actionable","therapy":"RO5126766","efficacy_evidence":"In a preclinical study, RO5126766 inhibited Mek signaling and increased radioiodide uptake and response in transgenic animal models of papillary thyroid carcinoma driven by BRAF V600E (%%PUBMED:27669459%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[33669326],"normalized_drug":"Cobimetinib, Vemurafenib","indication":"cholangiocarcinoma","therapy_id":1657,"normalized_cancer":"Cholangiocarcinoma","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"In a clinical case study, Zelboraf (vemurafenib) and Cotellic (cobimetinib) combination treatment resulted in reduction of the pulmonary nodules and hepatic lesions 6 months after treatment initiation in a patient with metastatic cholangiocarcinoma harboring BRAF V600E, who maintained a stable disease and remained on treatment at 20 months (%%PUBMED:33669326%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[38096472],"normalized_drug":"Cobimetinib, Vemurafenib","indication":"cholangiocarcinoma","therapy_id":1657,"normalized_cancer":"Cholangiocarcinoma","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"In a Phase II trial (TAPUR), Zelboraf (vemurafenib) and Cotellic (cobimetinib) combination therapy resulted in a partial response in a patient with cholangiocarcinoma harboring BRAF V600E (%%PUBMED:38096472%%; NCT02693535).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[32816843],"response_type":"predicted - resistant","indication":"colorectal cancer","therapy_id":8871,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"BI-3406","efficacy_evidence":"In a preclinical study, BI-3406 treatment failed to inhibit growth of colorectal cancer cells harboring BRAF V600E in culture (%%PUBMED:32816843%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[27924459],"response_type":"sensitive","indication":"melanoma","therapy_id":5122,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Doxorubicin + PLX4720","efficacy_evidence":"In a preclinical study, the combination of PLX4720 and Adriamycin (doxorubicin) resulted in antitumor efficacy in a melanoma cell line harboring BRAF V600E, demonstrating decreased cell survival and increased apoptotic activity in xenograft models, and inhibition of cell growth in culture (%%PUBMED:27924459%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[27222538],"normalized_drug":"Trametinib","indication":"thyroid cancer","therapy_id":2,"normalized_cancer":"Thyroid Cancer","evidence_type":"Actionable","therapy":"Trametinib","efficacy_evidence":"In a preclinical study, Mekinist (trametinib) inhibited growth of both parental thyroid cancer cell lines harboring BRAF V600E and those acquired Sprycel (dasatinib)-resistance in culture (%%PUBMED:27222538%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[34433654],"response_type":"predicted - sensitive","indication":"high grade glioma","therapy_id":12678,"normalized_cancer":"High-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"Vemurafenib + ZM336372","efficacy_evidence":"In a preclinical study, combination treatment with Zelboraf (vemurafenib) and ZM336372 treatment led to inhibition of cell growth in a patient-derived glioma cell line harboring BRAF V600E in culture (%%PUBMED:34433654%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Patient cell culture","amp_tier":"II"},{"pub_med_references":[37504287],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":15636,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"SJ-C1044","efficacy_evidence":"In a preclinical study, SJ-C1044 decreased growth in a colorectal cancer cell line harboring BRAF V600E in culture and inhibited tumor growth in a cell line xenograft model (%%PUBMED:37504287%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"pancreatic adenocarcinoma","therapy_id":1066,"normalized_cancer":"Pancreatic Adenocarcinoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Tafinlar (dabrafenib) and Mekinist (trametinib) combination therapy is included in guidelines as first-line therapy for pancreatic adenocarcinoma patients harboring BRAF V600E with locally advanced disease (category 2A) with good (ECOG 0-1) or intermediate (ECOG 2) performance status, as first-line therapy in patients metastatic disease (category 2B) disease, and as subsequent-line therapy for patients with locally advanced, recurrent, or metastatic disease (category 2A) (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[27222538],"response_type":"sensitive","indication":"thyroid cancer","therapy_id":4600,"normalized_cancer":"Thyroid Cancer","evidence_type":"Actionable","therapy":"Dasatinib + Selumetinib","efficacy_evidence":"In a preclinical study, Sprycel (dasatinib) and Koselugo (selumetinib) synergistically inhibited proliferation and induced apoptosis in both parental thyroid cancer cell lines harboring BRAF V600E and those acquired Sprycel (dasatinib)-resistance in culture (%%PUBMED:27222538%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"resistant","normalized_drug":"Cetuximab","indication":"rectum cancer","therapy_id":694,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab","efficacy_evidence":"Erbitux (cetuximab), as a monotherapy, is not indicated for use in rectum cancer patients with BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"unknown","indication":"lung non-small cell carcinoma","therapy_id":10383,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"unspecified immune checkpoint inhibitor","efficacy_evidence":"In a retrospective clinical study, patients with non-small cell lung cancer harboring rare targetable drivers (RTD) (BRAF, ERBB2/3, RET, MET, ROS1, NTRK) who received immune checkpoint inhibitors (ICI) achieved longer median overall survival (mOS) (32 vs 13 mo, p=0.01) compared to those who did not receive ICI, mOS was not reached in patients harboring BRAF V600E (n=5) mutations, although RTD type was not associated with OS in a univariate analysis (%%PUBMED:30268448%%).","cap_asco_evidence_level":"NA","molecular_profile":"BRAF V600E","approval_status":"Clinical Study - Cohort","amp_tier":"NA"},{"response_type":"predicted - sensitive","pub_med_references":[37981300],"normalized_drug":"Cetuximab, Encorafenib","indication":"colon neuroendocrine neoplasm","therapy_id":1916,"normalized_cancer":"Gastrointestinal Neuroendocrine Tumors","evidence_type":"Actionable","therapy":"Cetuximab + Encorafenib","efficacy_evidence":"In a clinical case study, treatment with the combination of Erbitux (cetuximab) and Braftovi (encorafenib) resulted in reduced liver metastasis and a progression-free survival of 14 months in a patient with colorectal neuroendocrine carcinoma harboring BRAF V600E (%%PUBMED:37981300%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[27523909],"response_type":"sensitive","indication":"melanoma","therapy_id":4281,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"SB590885","efficacy_evidence":"In a preclinical study, SB590885 inhibited proliferation of melanoma cell lines harboring either monomeric BRAF V600E or dimeric isoform of V600E which conferred Zelboraf (vemurafenib)-resistance in culture (%%PUBMED:27523909%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"no benefit","pub_med_references":[35363510],"normalized_drug":"Selumetinib","indication":"Advanced Solid Tumor","therapy_id":913,"normalized_cancer":"All Solid Tumors","evidence_type":"Actionable","therapy":"Selumetinib","efficacy_evidence":"In a Phase II trial (Pediatric MATCH), Koselugo (selumetinib) treatment was tolerated but did not result in an objective response in pediatric patients with advanced solid tumors including high-grade glioma (n=8) and rhabdomyosarcoma (n=7) harboring MAPK pathway alterations including BRAF V600E (n=2), activating KRAS (n=8)/HRAS (n=1)/NRAS (n=3) or inactivating NF1 (n=7) mutations, with a 6-month progression-free survival of 15% (3/20) and 3 stable disease as best response (%%PUBMED:35363510%%; NCT03213691).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[33537843],"normalized_drug":"Dabrafenib, 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therapy resulted in stable disease, and the patient continued to demonstrate stable disease at least 16 months after initiation of therapy (%%PUBMED:29632053%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"glioblastoma","therapy_id":1066,"normalized_cancer":"Glioblastoma, IDH-Wildtype","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Combination of Mekinist (trametinib) and Tafinlar (dabrafenib) is included in guidelines for patients with recurrent glioblastoma harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[32923904],"normalized_drug":"Dabrafenib, Trametinib","indication":"glioblastoma","therapy_id":1066,"normalized_cancer":"Glioblastoma, IDH-Wildtype","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, Mekinist (trametinib) and Tafinlar (dabrafenib) combination treatment resulted in a complete resolution of symptoms and radiographic partial response after the first treatment in a patient with glioblastoma harboring BRAF V600E whose disease progressed on PLX8394 treatment, and a complete response after 11 months of treatment, CDKN2A/B loss and CHEK2 T367fs were also identified in the tumor (%%PUBMED:32923904%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[31345255],"normalized_drug":"Dabrafenib, Trametinib","indication":"glioblastoma","therapy_id":1066,"normalized_cancer":"Glioblastoma, IDH-Wildtype","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, combination therapy of Tafinlar (dabrafenib) and Mekinist (trametinib) resulted in improved clinical symptoms in a patient with epithelioid glioblastoma harboring BRAF V600E, and treatment of the patient's cells resulted in decreased cell viability, reduced phosphorylation of Mek and Erk, increased apoptotic activity compared to either agent alone, and cell cycle arrest in culture, and led to tumor growth suppression in the patient-derived xenograft (PDX) model (%%PUBMED:31345255%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[31217909],"normalized_drug":"Dabrafenib, Trametinib","indication":"glioblastoma","therapy_id":1066,"normalized_cancer":"Glioblastoma, IDH-Wildtype","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, Mekinist (trametinib) and Tafinlar (dabrafenib) combination treatment resulted in significant clinical improvement in a patient with epithelioid glioblastoma harboring BRAF V600E, however, her disease progressed after 3 months of therapy (%%PUBMED:31217909%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[34838156],"normalized_drug":"Dabrafenib, Trametinib","indication":"glioblastoma","therapy_id":1066,"normalized_cancer":"Glioblastoma, IDH-Wildtype","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a Phase II trial (ROAR), Tafinlar (dabrafenib) and Mekinist (trametinib) combination treatment resulted in an objective response in 32% (10/31, 2 complete responses, 8 partial responses) and stable disease in 19% (6/31) of patients with glioblastoma harboring BRAF V600E (%%PUBMED:34838156%%; NCT02034110).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"pub_med_references":[27312529],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":4541,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Dabrafenib + Trametinib","efficacy_evidence":"In a preclinical study, combination therapy consisting of Erbitux (cetuximab), Tafinlar (dabrafenib), and Mekinist (trametinib) inhibited survival of colorectal cancer cell lines harboring BRAF V600E in culture (%%PUBMED:27312529%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[20531415,26603897],"response_type":"sensitive","indication":"melanoma","therapy_id":3306,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"SBI-0640756","efficacy_evidence":"In a preclinical study, SBI-0640756 inhibited proliferation and Akt/mTOR signaling in human melanoma cell lines harboring BRAF V600E in culture (%%PUBMED:26603897%%, %%PUBMED:20531415%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[20531415,26603897],"response_type":"sensitive","indication":"melanoma","therapy_id":3308,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"BI-69A11","efficacy_evidence":"In a preclinical study, BI-69A11 inhibited proliferation and Akt/mTOR signaling in human melanoma cell lines harboring BRAF V600E in culture (%%PUBMED:26603897%%, %%PUBMED:20531415%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[28714990],"response_type":"decreased response","indication":"melanoma","therapy_id":6430,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + SCH772984 + Trametinib","efficacy_evidence":"In a preclinical study, combination of Tafinlar (dabrafenib), SCH772984, and Mekinist (trametinib) resulted in durable inhibition of Erk signaling and proliferation of melanoma cells overexpressing BRAF V600E in culture (%%PUBMED:28714990%%).","cap_asco_evidence_level":"NA","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"NA"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"pilocytic astrocytoma","therapy_id":1066,"normalized_cancer":"Pilocytic Astrocytoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Combination of Mekinist (trametinib) and Tafinlar (dabrafenib) is included in guidelines as an adjuvant treatment for patients with pilocytic astrocytoma harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[39399174],"normalized_drug":"Dabrafenib, Trametinib","indication":"pilocytic astrocytoma","therapy_id":1066,"normalized_cancer":"Pilocytic Astrocytoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, the addition of Mekinist (trametinib) to treatment with Tafinlar (dabrafenib) resulted in a partial response in 3 pediatric patients with suprasellar pilocytic astrocytoma harboring BRAF V600E who all previously progressed on Tafinlar (dabrafenib) treatment alone (%%PUBMED:39399174%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[33568355],"response_type":"sensitive","indication":"melanoma","therapy_id":11477,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + Regorafenib + Trametinib","efficacy_evidence":"In a preclinical study, combination treatment with Stivarga (regorafenib), Tafinlar (dabrafenib), and Mekinist (trametinib) in a melanoma cell line harboring BRAF V600E resulted in suppression of colony formation in culture, and suppressed tumor growth in patient-derived xenograft (PDX) models (%%PUBMED:33568355%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Pdx & cell culture","amp_tier":"II"},{"pub_med_references":[26810733],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":6368,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"EBI-907","efficacy_evidence":"In a preclinical study, EBI-907 inhibited BRAF and ERK signaling, resulted in growth inhibition of colorectal cancer cells harboring BRAF V600E in culture and in cell line xenograft models (%%PUBMED:26810733%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[37164118],"response_type":"sensitive","indication":"Advanced Solid Tumor","therapy_id":15389,"normalized_cancer":"All Solid Tumors","evidence_type":"Actionable","therapy":"IHMT-RAF-128","efficacy_evidence":"In a preclinical study, IHMT-RAF-128 inhibited proliferation of a cell line expressing BRAF V600E in culture (%%PUBMED:37164118%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[30036245],"normalized_drug":"Dabrafenib, Trametinib","indication":"colon neuroendocrine neoplasm","therapy_id":1066,"normalized_cancer":"Gastrointestinal Neuroendocrine Tumors","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, treatment with the combination of Mekinist (trametinib) and Tafinlar (dabrafenib) resulted in a clinical improvement and reduction of the primary tumor as well as the metastatic lesions in a cecal neuroendocrine carcinoma patient harboring BRAF V600E (%%PUBMED:30036245%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[38716076],"normalized_drug":"Dabrafenib, Trametinib","indication":"colon neuroendocrine neoplasm","therapy_id":1066,"normalized_cancer":"Gastrointestinal Neuroendocrine Tumors","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical study, second-line treatment with the combination of Mekinist (trametinib) and Tafinlar (dabrafenib) resulted in a partial response in two patients with a neuroendocrine carcinoma of the colon harboring BRAF V600E, with progression-free survival of 6 months in one patient and 4 months in the second patient (%%PUBMED:38716076%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[37808191],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":9644,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Tunlametinib","efficacy_evidence":"In a preclinical study, Tunlametinib (HL-085) inhibited viability of a colorectal cancer cell line harboring BRAF V600E in culture and inhibited tumor growth in a cell line xenograft model (%%PUBMED:37808191%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[30833748],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":11211,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Chloroquine + Trametinib","efficacy_evidence":"In a preclinical study, combination treatment with Mekinist (trametinib) and Chloroquine resulted in tumor regression in a colorectal cancer patient-derived xenograft (PDX) model harboring BRAF V600E (%%PUBMED:30833748%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[27480103],"normalized_drug":"Cobimetinib, Vemurafenib","indication":"melanoma","therapy_id":1657,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"In a Phase III trial (coBRIM) that supported FDA approval, treatment with the combination of Zelboraf (vemurafenib) and Cotellic (cobimetinib) resulted in an improved progression-free survival of 12.3 months, compared to 7.2 months with Zelboraf (vemurafenib) plus placebo, among patients with BRAF V600-mutated metastatic melanoma, and BRAF V600E and BRAF V600K are on the companion diagnostic (%%PUBMED:27480103%%; NCT01689519).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"FDA approved - On Companion Diagnostic","amp_tier":"I"},{"response_type":"sensitive","normalized_drug":"Dabrafenib","indication":"papillary thyroid carcinoma","therapy_id":3,"normalized_cancer":"Papillary Thyroid Cancer","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"Tafinlar (dabrafenib) is included in guidelines for patients with recurrent, advanced, or metastatic thyroid papillary carcinoma harboring BRAF V600E for whom clinical trials are not available or appropriate (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[25549723],"normalized_drug":"Dabrafenib","indication":"papillary thyroid carcinoma","therapy_id":3,"normalized_cancer":"Papillary Thyroid Cancer","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a clinical study, Tafinlar (dabrafenib) treatment stimulated radioiodine uptake in 60% (6/10) of patients with metastatic iodine-refractory papillary thyroid cancer harboring BRAF V600E (%%PUBMED:25549723%%; NCT01534897).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Clinical Study - Cohort","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"melanoma","therapy_id":17152,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Binimetinib + PLX8394","efficacy_evidence":"In a preclinical study, treatment with the combination of Mektovi (binimetinib) and PLX8394 inhibited viability of melanoma cells harboring BRAF V600E in culture (Cancer Res (2024) 84 (6_Supplement): 4609).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[39143272],"normalized_drug":"Dabrafenib, Trametinib","indication":"craniopharyngioma","therapy_id":1066,"normalized_cancer":"Sellar Tumor","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, treatment with the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) resulted in a partial response and progression-free survival of 1040 days in a patient with craniopharyngioma harboring BRAF V600E (%%PUBMED:39143272%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[38096472],"normalized_drug":"Cobimetinib, Vemurafenib","indication":"Advanced Solid Tumor","therapy_id":1657,"normalized_cancer":"All Solid Tumors","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"In a Phase II trial (TAPUR), treatment with the combination of Zelboraf (vemurafenib) and Cotellic (cobimetinib) resulted in an objective response rate of 57% (16/28, 2 complete responses (CR), 14 partial responses (PR)) and a disease control rate (CR + PR + stable disease at 16 wks (SD16+)) of 68% in patients with advanced solid tumors harboring BRAF mutations, with 2 CR, 13 PR, and 2 SD16+ in a total of 26 patients harboring BRAF V600E (%%PUBMED:38096472%%; NCT02693535).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"pub_med_references":[30264293],"response_type":"sensitive","indication":"melanoma","therapy_id":1011,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"E6201","efficacy_evidence":"In a Phase I trial, a patient with metastatic melanoma and brain metastasis harboring BRAF V600E demonstrated an ongoing near complete response with an overall survival of more than 8 years, and preclinical analysis of melanoma cell lines harboring homozygous or heterozygous BRAF V600E in culture were sensitive to treatment with E6201 (%%PUBMED:30264293%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[24448821],"response_type":"sensitive","indication":"melanoma","therapy_id":1011,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"E6201","efficacy_evidence":"In a preclinical study, E6201 inhibited Mapk pathway activation and proliferation of melanoma cell lines harboring BRAF V600E mutation in culture (%%PUBMED:24448821%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[27362227],"response_type":"no benefit","indication":"melanoma","therapy_id":4504,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"SHP099","efficacy_evidence":"In a preclinical study, SHP099 did not inhibit proliferation or ERK activation in a melanoma cell line harboring BRAF V600E in culture (%%PUBMED:27362227%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"stomach cancer","therapy_id":1066,"normalized_cancer":"Esophageal/Stomach Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Tafinlar (dabrafenib) and Mekinist (trametinib) combination therapy is included in guidelines as second-line or subsequent therapy for patients with unresectable locally advanced, recurrent, or metastatic gastric cancer harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[36343387],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":14547,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Mocetinostat + Trametinib","efficacy_evidence":"In a preclinical study, the combination of Mekinist (trametinib) and Mocetinostat (MGCD0103) resulted in greater apoptotic activity compared to either agent alone in a colorectal cancer cell line harboring BRAF V600E in culture (%%PUBMED:36343387%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[22319199],"response_type":"sensitive","indication":"melanoma","therapy_id":1002,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"RXDX-105","efficacy_evidence":"In preclinical studies, CEP-32496 (RXDX-105) reduced tumor volume and promoted tumor regression in xenograft models of a BRAF V600E mutant human melanoma cell line (%%PUBMED:22319199%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[23242808],"response_type":"sensitive","indication":"melanoma","therapy_id":3124,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"S3I-201","efficacy_evidence":"In a preclinical study, S3I-201 inhibited cell invasion and Stat3 signaling in human melanoma cell lines harboring BRAF V600E that are resistant to Braf inhibition in culture (%%PUBMED:23242808%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[27217440],"response_type":"predicted - sensitive","indication":"high grade glioma","therapy_id":1061,"normalized_cancer":"High-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"PLX4720 + Selumetinib","efficacy_evidence":"In a preclinical study, Koselugo (selumetinib) and PLX4720 synergistically inhibited growth and induced apoptosis in glioma cell lines in culture, resulted in prolonged survival in cell line xenograft models (%%PUBMED:27217440%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"sensitive","indication":"colon cancer","therapy_id":9562,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Encorafenib + Panitumumab","efficacy_evidence":"Braftovi (encorafenib) in combination with Vectibix (panitumumab) is included in guidelines as primary or subsequent therapy for patients with colon cancer harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[33318037],"response_type":"sensitive","indication":"melanoma","therapy_id":11345,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Lifirafenib + Trametinib","efficacy_evidence":"In a preclinical study, the combination treatment of Mekinist (trametinib) and Lifirafenib (BGB-283) led to greater inhibition of growth in melanoma cell lines harboring BRAF V600E in culture compared to either treatment alone (%%PUBMED:33318037%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[30351999],"normalized_drug":"Vemurafenib","indication":"pilocytic astrocytoma","therapy_id":342,"normalized_cancer":"Pilocytic Astrocytoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase II trial (VE-BASKET), Zelboraf (vemurafenib) treatment resulted in a partial response in a patient with pilocytic astrrocytoma harboring BRAF V600E who stayed on treatment for 15.3 months (%%PUBMED:30351999%%; NCT01524978).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[36622773],"response_type":"predicted - sensitive","indication":"melanoma","therapy_id":14819,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"DS03090629","efficacy_evidence":"In a preclinical study, DS03090629 inhibited Erk and Mek phosphorylation and proliferation in a melanoma cell line harboring BRAF V600E in culture and led to tumor stasis in a cell line xenograft model (%%PUBMED:36622773%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[32758030],"normalized_drug":"Trametinib","indication":"intrahepatic cholangiocarcinoma","therapy_id":2,"normalized_cancer":"Intrahepatic Cholangiocarcinoma","evidence_type":"Actionable","therapy":"Trametinib","efficacy_evidence":"In a Phase II trial (NCI-MATCH), Mekinist (trametinib) treatment resulted in an objective response rate of 37.9% (11/29) in patients with advanced solid tumors harboring BRAF V600E, of 4 patients with intrahepatic cholangiocarcinoma, 3 achieved a partial response, with individual progression-free survival of 12.8, 9.1, and 29.4 months (%%PUBMED:32758030%%; NCT02465060).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[34330842],"response_type":"sensitive","indication":"colorectal adenocarcinoma","therapy_id":6971,"normalized_cancer":"Colorectal Adenocarcinoma","evidence_type":"Actionable","therapy":"ASTX029","efficacy_evidence":"In a preclinical study, ASTX029 treatment reduced Erk and Rsk phosphorylation and inhibited growth of colorectal adenocarcinoma cell lines harboring BRAF V600E in culture, and inhibited tumor growth and induced tumor regression in cell line xenograft models (%%PUBMED:34330842%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"predicted - 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for patients with advanced or metastatic non-small cell lung cancer with BRAF V600E mutations who can not tolerate the combination of Mekinist (trametinib) and Tafinlar (dabrafenib) (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[27080216],"normalized_drug":"Dabrafenib","indication":"lung non-small cell carcinoma","therapy_id":3,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a Phase II trial, 33% (26/78) of previously treated non-small cell lung carcinoma patients harboring BRAF V600E demonstrated an overall response, which included all partial responses, when treated with Tafinlar (dabrafenib) while 67% (4/6) receiving Tafinlar (dabrafenib) as a first-line treatment achieved partial responses (%%PUBMED:27080216%%; NCT01336634).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"pub_med_references":[25665005],"response_type":"sensitive","indication":"lung non-small cell carcinoma","therapy_id":1386,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Navitoclax + Trametinib","efficacy_evidence":"In a preclinical study, Navitoclax (ABT-263) enhanced the inhibitory effect of Mekinist (trametinib) on human non-small cell lung cancer cells harboring BRAF V600E in culture (%%PUBMED:25665005%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[26916115],"response_type":"sensitive","indication":"melanoma","therapy_id":3709,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"BI 882370 + Trametinib","efficacy_evidence":"In a preclinical study, xenograft models of melanoma harboring BRAF V600E treated with the combination of BI 882370 and Mekinist (trametinib) demonstrated tumor regression with no regrowth during the 5 weeks of treatment (%%PUBMED:26916115%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"colorectal cancer","therapy_id":10113,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"JSI-1187","efficacy_evidence":"In a preclinical study, JSI-1187 treatment in a colorectal cancer cell line harboring BRAF V600E led to inhibition of cell proliferation in culture, and tumor regression and dose-dependent tumor growth inhibition in a cell line xenograft model (Cancer Res 2020;80(16 Suppl):Abstract nr 4188).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[22448344],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":1709,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Gefitinib + Vemurafenib","efficacy_evidence":"In a preclinical study, the combination of Zelboraf (vemurafenib) and Iressa (gefitinib) decreased the number of viable colorectal cancer cells harboring a BRAF V600E mutation in cell culture (%%PUBMED:22448344%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[25665005],"response_type":"sensitive","indication":"colon cancer","therapy_id":3530,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Navitoclax + Vemurafenib","efficacy_evidence":"In a preclinical study, Navitoclax (ABT-263) enhanced the inhibitory effect of Zelboraf (vemurafenib) on human colon cancer cells harboring BRAF V600E in culture (%%PUBMED:25665005%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[33917428],"response_type":"sensitive","indication":"melanoma","therapy_id":16090,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"SIJ777","efficacy_evidence":"In a preclinical study, SIJ777 inhibited Mek, Erk, and Akt phosphorylation, proliferation, migration, and invasion, and induced apoptosis in melanoma cell lines harboring BRAF V600E in culture (%%PUBMED:33917428%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"ampulla of Vater adenocarcinoma","therapy_id":1066,"normalized_cancer":"Ampullary Carcinoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Tafinlar (dabrafenib) and Mekinist (trametinib) combination therapy is included in guidelines as first-line therapy with good (ECOG 0-1; category 3) or poor (category 2B) performance status, or as subsequent therapy (category 2A), for metastatic ampullary adenocarcinoma patients harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[33355204],"response_type":"predicted - sensitive","indication":"melanoma","therapy_id":4442,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"LXH 254","efficacy_evidence":"In a preclinical study, a melanoma cell line harboring BRAF V600E was sensitive to treatment with LXH254, demonstrating inhibition of cell proliferation in culture, and inhibition of tumor growth and tumor regression in a cell line xenograft model of melanoma (%%PUBMED:33355204%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[23242808],"normalized_drug":"Saracatinib","indication":"melanoma","therapy_id":912,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Saracatinib","efficacy_evidence":"In a preclinical study, saracatinib inhibited proliferation of human melanoma cell lines harboring BRAF V600E that are resistant to Braf inhibition in culture (%%PUBMED:23242808%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[30559419],"response_type":"sensitive","indication":"melanoma","therapy_id":6245,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"BGB659","efficacy_evidence":"In a preclinical study, BGB659 treatment inhibited Erk phosphorylation and reduced proliferation of a melanoma cells harboring either monomeric BRAF V600E or dimeric isoform (p61) of V600E in culture (%%PUBMED:30559419%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[29247021],"normalized_drug":"Ulixertinib","indication":"lung cancer","therapy_id":997,"normalized_cancer":"Lung Cancer","evidence_type":"Actionable","therapy":"Ulixertinib","efficacy_evidence":"In a Phase I trial, treatment with Ulixertinib (BVD-523) resulted in a partial response in two patients with lung cancer each harboring BRAF V600E (%%PUBMED:29247021%%; NCT01781429).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[19706763],"normalized_drug":"Refametinib","indication":"melanoma","therapy_id":888,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Refametinib","efficacy_evidence":"In a preclinical study, Refametinib (BAY86-9766) inhibited growth of melanoma cell lines harboring BRAF V600E in culture and suppressed tumor growth in cell line xenograft models (%%PUBMED:19706763%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[27523909],"response_type":"sensitive","indication":"melanoma","therapy_id":3300,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"TAK-632","efficacy_evidence":"In a preclinical study, TAK-632 inhibited proliferation of melanoma cell lines harboring either monomeric BRAF V600E or dimeric isoform of V600E which conferred Zelboraf (vemurafenib)-resistance in culture (%%PUBMED:27523909%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[30559419],"response_type":"sensitive","indication":"melanoma","therapy_id":3300,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"TAK-632","efficacy_evidence":"In a preclinical study, TAK-632 treatment inhibited Erk phosphorylation and reduced proliferation of a melanoma cells harboring either monomeric BRAF V600E or dimeric isoform (p61) of V600E in culture (%%PUBMED:30559419%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"extrahepatic bile duct carcinoma","therapy_id":1066,"normalized_cancer":"Extrahepatic Cholangiocarcinoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Tafinlar (dabrafenib) in combination with Mekinist (trametinib) is included in guidelines as subsequent-line therapy for patients with biliary cancer harboring BRAF V600E, including extrahepatic cholangiocarcinoma (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[20538618],"response_type":"sensitive","indication":"Advanced Solid Tumor","therapy_id":1060,"normalized_cancer":"All Solid Tumors","evidence_type":"Actionable","therapy":"PLX4720","efficacy_evidence":"In a preclinical study, PLX4720 inhibited Erk phosphorylation and cell proliferation of transformed cells expression BRAF V600E in culture (%%PUBMED:20538618%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[36759733],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":15044,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Celecoxib + Gefitinib + Trametinib + Vemurafenib","efficacy_evidence":"In a preclinical study, the addition of Celecoxib to the combination of Zelboraf (vemurafenib), Mekinist (trametinib), and Iressa (gefitinib) synergistically inhibited viability in colorectal cancer cell lines harboring BRAF V600E in culture (%%PUBMED:36759733%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[33537843],"response_type":"predicted - sensitive","indication":"endometrial adenocarcinoma","therapy_id":12031,"normalized_cancer":"Endometrial Carcinoma","evidence_type":"Actionable","therapy":"Dabrafenib + Rabeprazole + Rifampin + Trametinib","efficacy_evidence":"In a Phase I trial, the addition of Mekinist (trametinib) to combination treatment with Tafinlar (dabrafenib), Rabeprazole, and Rifampin resulted in a maintained radiographic response of lung metastases and stable pelvic mass size in a patient with metastatic endometrial adenocarcinoma harboring BRAF V600E, which lasted for 12 months (%%PUBMED:33537843%%; NCT01954043).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[31744895],"response_type":"sensitive","indication":"melanoma","therapy_id":4588,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"LY3214996","efficacy_evidence":"In a preclinical study, LY3214996 treatment in a melanoma cell line harboring BRAF V600E led to decreased cell proliferation in culture, and inhibition of tumor growth in a cell line xenograft model (%%PUBMED:31744895%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[31386052],"normalized_drug":"Vemurafenib","indication":"pleomorphic xanthoastrocytoma","therapy_id":342,"normalized_cancer":"Pleomorphic Xanthoastrocytoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a clinical case study, Zelboraf (vemurafenib) treatment resulted in a complete intracranial response 2 months after treatment in a patient with anaplastic pleomorphic xanthoastrocytoma harboring BRAF V600E, although the disease progressed 1 month later (%%PUBMED:31386052%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[30351999],"normalized_drug":"Vemurafenib","indication":"pleomorphic xanthoastrocytoma","therapy_id":342,"normalized_cancer":"Pleomorphic Xanthoastrocytoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase II trial (VE-BASKET), Zelboraf (vemurafenib) treatment resulted in an objective response rate of 42.9% (3/7, 1 complete response, 2 partial responses) and a clinical benefit rate of 57% in patients with pleomorphic xanthoastrocytoma harboring BRAF V600E, with a median progression-free survival of 5.7 months, and median overall survival not reached (%%PUBMED:30351999%%; NCT01524978).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[32523649],"normalized_drug":"Vemurafenib","indication":"pleomorphic xanthoastrocytoma","therapy_id":342,"normalized_cancer":"Pleomorphic Xanthoastrocytoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase I trial (PNOC-002), Zelboraf (vemurafenib) treatment was tolerable and resulted in 1 complete response, 5 partial responses, and 13 stable disease in 19 pediatric patients with recurrent low grade gliomas harboring BRAF V600E, including 1 complete response and 1 stable disease among 2 patients with pleomorphic xanthroastrocytoma (%%PUBMED:32523649%%; NCT01748149).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[25665005],"response_type":"sensitive","indication":"lung non-small cell carcinoma","therapy_id":3531,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"TW-37 + Vemurafenib","efficacy_evidence":"In a preclinical study, TW-37 enhanced the inhibitory effect of Zelboraf (vemurafenib) on human non-small cell lung cancer cells harboring BRAF V600E in culture (%%PUBMED:25665005%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[26466569],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":4606,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"PLX7904","efficacy_evidence":"In a preclinical study, PLX7904 inhibited survival of colorectal cancer cells harboring BRAF V600E in culture and demonstrated anti-tumor activity in cell line xenograft models (%%PUBMED:26466569%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[26490654],"normalized_drug":"Vemurafenib","indication":"ovary serous adenocarcinoma","therapy_id":342,"normalized_cancer":"Serous Ovarian Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a clinical case study, Zelboraf (vemurafenib) treatment resulted in a partial response lasting more than 21 months in a patient with low grade serous ovarian adenocarcinoma harboring BRAF V600E (%%PUBMED:26490654%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[27523909],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":4607,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"PLX4720 + TAK-632","efficacy_evidence":"In a preclinical study, PLX4720 and TAK-632 combination treatment resulted in durable inhibition of Erk signaling and tumor growth in xenograft models of colorectal cancer cells harboring BRAF V600E (%%PUBMED:27523909%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[27924459],"response_type":"sensitive","indication":"melanoma","therapy_id":5118,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Imatinib + PLX4720","efficacy_evidence":"In a preclinical study, the combination of Gleevec (imatinib) and PLX4720 enhanced antitumor efficacy of melanoma cells harboring BRAF V600E, demonstrating decreased cell survival in xenograft models, and decreased phosphorylation of Mapk1 in culture (%%PUBMED:27924459%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[37326340],"response_type":"no benefit","indication":"colorectal carcinoma","therapy_id":1823,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Mirdametinib + Palbociclib","efficacy_evidence":"In a preclinical study, the combination of Ibrance (palbociclib) and Gomekli (mirdametinib) demonstrated antagonism in a colorectal carcinoma cell line harboring BRAF V600E in culture (%%PUBMED:37326340%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[29621181],"normalized_drug":"Dabrafenib","indication":"glioblastoma","therapy_id":3,"normalized_cancer":"Glioblastoma, IDH-Wildtype","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a clinical case study, a previously treated pediatric patient with epithelioid glioblastoma harboring BRAF V600E demonstrated stable disease for 10 months when treated with Tafinlar (dabrafenib) (%%PUBMED:29621181%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[36759733],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":15047,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Celecoxib + Dabrafenib + Panitumumab + Trametinib","efficacy_evidence":"In a preclinical study, the addition of Celecoxib to the combination of Tafinlar (dabrafenib), Mekinist (trametinib), and Vectibix (panitumumab) inhibited tumor growth and induced tumor regression in colorectal cancer patient-derived xenograft (PDX) models harboring BRAF V600E (%%PUBMED:36759733%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Encorafenib","indication":"colorectal cancer","therapy_id":796,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Encorafenib","efficacy_evidence":"In a Phase I trial, Encorafenib (LGX818) showed activity in patients with advanced metastatic colorectal cancer harboring a BRAF V600E mutation, resulting in a median progression-free survival of 4 months and a best response of stable disease in 66.7% (12/18) (Ann Oncol (2014) 25 (suppl 4): iv182-iv183).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase I","amp_tier":"II"},{"pub_med_references":[28719152],"response_type":"predicted - sensitive","indication":"melanoma","therapy_id":884,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"RAF265","efficacy_evidence":"In a Phase I trial, treatment with RAF265 in melanoma patients resulted in an objective response rate of 12.1% (8/66), including a partial response in four patients harboring BRAF V600E, two partial responses and one complete response in patients with wild-type BRAF, and one complete response in a patient with unknown mutational status (%%PUBMED:28719152%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[28939558],"normalized_drug":"Ulixertinib","indication":"melanoma","therapy_id":997,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Ulixertinib","efficacy_evidence":"In a preclinical study, Ulixertinib (BVD-523) inhibited Erk signaling in melanoma cells harboring BRAF V600E, resulted in cell cycle arrest in culture and tumor growth inhibition in cell line xenograft models (%%PUBMED:28939558%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[38820503],"normalized_drug":"Dabrafenib, Trametinib","indication":"acinar cell carcinoma","therapy_id":1066,"normalized_cancer":"Acinar Cell Carcinoma of the Pancreas","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, treatment with the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) resulted in near complete metabolic remission at 5 months and persistent complete metabolic remission at 12 months in a patient with metastatic acinar cell carcinoma of unknown primary harboring BRAF V600E (%%PUBMED:38820503%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - 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vemurafenib/PLX4720-resistant cells harboring distinct BRAF V600E splice variants (%%PUBMED:24422853%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[38593698],"response_type":"sensitive","indication":"papillary thyroid carcinoma","therapy_id":17831,"normalized_cancer":"Papillary Thyroid Cancer","evidence_type":"Actionable","therapy":"AZD1208 + Vemurafenib","efficacy_evidence":"In a preclinical study, treatment with the combination of Zelboraf (vemurafenib) and AZD1208 synergistically inhibited viability and colony formation of papillary thyroid carcinoma cell lines harboring BRAF V600E in culture (%%PUBMED:38593698%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[38565920],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":16825,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + IAG933 + LTT462","efficacy_evidence":"In a preclinical study, treatment with the combination of IAG933, Tafinlar (dabrafenib), and LTT462 inhibited proliferation of colorectal cancer cell lines harboring BRAF V600E in culture and resulted in greater tumor growth inhibition compared to either agent alone in a cell line xenograft model (%%PUBMED:38565920%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[35882450],"response_type":"sensitive","indication":"pleomorphic xanthoastrocytoma","therapy_id":14718,"normalized_cancer":"Pleomorphic Xanthoastrocytoma","evidence_type":"Actionable","therapy":"Navitoclax + Ulixertinib","efficacy_evidence":"In a preclinical study, the combination of Ulixertinib (BVD-523) and Navitoclax (ABT-263) synergistically induced apoptosis in a pleomorphic xanthoastrocytoma cell line harboring BRAF V600E in culture, and improved the partial response rate compared to either drug alone in a zebrafish xenograft model (%%PUBMED:35882450%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib","indication":"oncocytic carcinoma of the thyroid","therapy_id":3,"normalized_cancer":"Hurthle Cell Thyroid Cancer","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"Tafinlar (dabrafenib) is included in guidelines for patients with recurrent, advanced, or metastatic thyroid Hurthle cell carcinoma harboring BRAF V600E for whom clinical trials are not available or appropriate (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"predicted - sensitive","pub_med_references":[38814411],"normalized_drug":"Dabrafenib, Trametinib","indication":"pancreatic endocrine carcinoma","therapy_id":1066,"normalized_cancer":"Pancreatic Neuroendocrine Carcinoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, treatment with the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) resulted in a partial response lasting at least 15 months in a patient with unresectable, metastatic pancreatic neuroendocrine carcinoma harboring BRAF V600E (%%PUBMED:38814411%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[33979489],"response_type":"predicted - sensitive","indication":"hairy cell leukemia","therapy_id":11942,"normalized_cancer":"Hairy Cell Leukemia","evidence_type":"Actionable","therapy":"Ruxolitinib + Vemurafenib","efficacy_evidence":"In a Phase II trial (HCL-PG03), combined Zelboraf (vemurafenib) and Jakafi (ruxolitinib) therapy in relapsed or refractory hairy cell leukemia patients with BRAF V600E demonstrated safety, and led to complete response (CR) in 87% (26/30) of patients, including 17 (65%) with negative minimal residual disease, a progression-free survival rate of 78% at a median follow-up of 37 months, and a relapse-free survival rate of 85% in the 26 patients with a CR at a median follow-up of 34 months (%%PUBMED:33979489%%).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"melanoma","therapy_id":7465,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"BGB3245","efficacy_evidence":"In a Phase I trial, BGB3245 treatment demonstrated manageable safety and resulted in a disease control rate of 48% (16/33,1 complete response, 5 confirmed partial responses (PR), 2 unconfirmed PR, and 8 stable disease > 24 weeks) in patients with advanced solid tumors harboring MAPK pathway alterations, including 1 complete response and 1 confirmed partial response in patients with melanoma harboring BRAF V600E (Cancer Res (2023) 83 (8_Supplement): CT031).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[32758030],"normalized_drug":"Trametinib","indication":"ovarian serous carcinoma","therapy_id":2,"normalized_cancer":"Serous Ovarian Cancer","evidence_type":"Actionable","therapy":"Trametinib","efficacy_evidence":"In a Phase II trial (NCI-MATCH), Mekinist (trametinib) treatment resulted in an objective response rate of 37.9% (11/29) in patients with advanced solid tumors harboring BRAF V600E, of 5 patients with low grade serous ovarian carcinoma, 4 achieved a partial response (PR), 1 had stable disease, 3 of the PRs lasted over 12 months (%%PUBMED:32758030%%; NCT02465060).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[37808191],"response_type":"sensitive","indication":"melanoma","therapy_id":15985,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Tunlametinib + Vemurafenib","efficacy_evidence":"In a preclinical study, treatment with the combination of Tunlametinib (HL-085) and Zelboraf (vemurafenib) synergistically inhibited proliferation of a melanoma cell line harboring BRAF V600E in culture, and synergistically inhibited tumor growth in a cell line xenograft model (%%PUBMED:37808191%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[26573800],"response_type":"sensitive","indication":"glioblastoma","therapy_id":676,"normalized_cancer":"Glioblastoma, IDH-Wildtype","evidence_type":"Actionable","therapy":"BI2536","efficacy_evidence":"In a preclinical study, a glioblastoma cell line harboring BRAF V600E demonstrated sensitivity to BI2536 in culture (%%PUBMED:26573800%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[36702949],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":6023,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Spartalizumab + Trametinib","efficacy_evidence":"In a Phase II trial, the combination of Spartalizumab (PDR001), Tafinlar (dabrafenib), and Mekinist (trametinib) was well tolerated and resulted in a confirmed objective response rate of 24.3% (9/37, 2 complete responses), disease control rate of 70.3% (26/37), median progression-free survival of 4.3 months, median duration of response of 7.4 months, and median overall survival of 13.6 months in patients with metastatic colorectal cancer harboring BRAF V600E (%%PUBMED:36702949%%; NCT03668431).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"pub_med_references":[31937621],"response_type":"sensitive","indication":"thyroid cancer","therapy_id":10186,"normalized_cancer":"Thyroid Cancer","evidence_type":"Actionable","therapy":"Ponatinib + Vemurafenib","efficacy_evidence":"In a preclinical study, Iclusig (ponatinib) and Zelboraf (vemurafenib) treatment synergistically inhibited proliferation of thyroid cancer cells harboring BRAF V600E in culture (%%PUBMED:31937621%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[33976643],"normalized_drug":"Vemurafenib","indication":"triple-receptor negative breast cancer","therapy_id":342,"normalized_cancer":"Invasive Breast Carcinoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a clinical case study, Zelboraf (vemurafenib) treatment resulted in a partial response in the lung lesion lasting at least 19 months in a patient with metastatic triple-negative breast cancer harboring BRAF V600E (%%PUBMED:33976643%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[33318037],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":11345,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Lifirafenib + Trametinib","efficacy_evidence":"In a preclinical study, the combination treatment of Mekinist (trametinib) and Lifirafenib (BGB-283) led to greater inhibition of growth in a colorectal cancer cell line harboring BRAF V600E in culture compared to either treatment alone (%%PUBMED:33318037%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[23629727],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":1659,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Pimasertib + Sorafenib","efficacy_evidence":"In a preclinical study, Pimasertib (MSC1936369B) and Nexavar (sorafenib) synergistically inhibited proliferation of colorectal cancer cells harboring BRAF V600E in culture (%%PUBMED:23629727%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[27924459],"response_type":"sensitive","indication":"melanoma","therapy_id":5121,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"PLX4720 + Vorinostat","efficacy_evidence":"In a preclinical study, the combination of PLX4720 and Zolinza (vorinostat) resulted in antitumor efficacy in a melanoma cell line harboring BRAF V600E, demonstrating decreased cell survival and increased apoptotic activity in xenograft models, and decreased Rb phosphorylation in culture (%%PUBMED:27924459%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"follicular thyroid carcinoma","therapy_id":1066,"normalized_cancer":"Follicular Thyroid Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"The combination of Tafinlar (dabrafenib) and Mekinist (trametinib) is included in guidelines for patients with follicular thyroid carcinoma harboring BRAF V600E who have progressed on therapy and have no further treatment options (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[36198029],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":14530,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Pyrvinium + Vemurafenib","efficacy_evidence":"In a preclinical study, combination treatment with Zelboraf (vemurafenib) and Pyrvinium resulted in decreased viability in colorectal cancer cell lines harboring BRAF V600E in culture, and led to synergistic inhibition of tumor growth in a cell line xenograft model (%%PUBMED:36198029%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[35882450],"response_type":"predicted - sensitive","indication":"pleomorphic xanthoastrocytoma","therapy_id":12793,"normalized_cancer":"Pleomorphic Xanthoastrocytoma","evidence_type":"Actionable","therapy":"Trametinib + Ulixertinib","efficacy_evidence":"In a preclinical study, the combination of Ulixertinib (BVD-523) and Mekinist (trametinib) had a synergistic effect on the induction of apoptosis 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and those acquired Sprycel (dasatinib)-resistance in culture (%%PUBMED:27222538%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Binimetinib, Encorafenib","indication":"lung non-small cell carcinoma","therapy_id":1100,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Binimetinib + Encorafenib","efficacy_evidence":"Combination of Braftovi (encorafenib) and Mektovi (binimetinib) is included in guidelines as a first-line or subsequent therapy for advanced or metastatic non-small cell lung cancer patients harboring BRAF V600E mutations (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[37270692],"normalized_drug":"Binimetinib, Encorafenib","indication":"lung non-small cell 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treatment with Cotellic (cobimetinib) and Zelboraf (vemurafenib) (%%PUBMED:35046062%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[26438159],"response_type":"sensitive","indication":"melanoma","therapy_id":903,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"RO4987655","efficacy_evidence":"In a preclinical study, RO4987655 inhibited proliferation of melanoma cells harboring BRAF V600E in culture (%%PUBMED:26438159%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[39121480],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":9079,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Tazemetostat + Trametinib","efficacy_evidence":"In a preclinical study, the addition of Tazverik (tazemetostat) sensitized a colorectal cancer cell line harboring BRAF V600E to Mekinist (trametinib) treatment in culture, resulting in decreased cell proliferation (%%PUBMED:39121480%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[36343387],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":14550,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Panobinostat + Vemurafenib","efficacy_evidence":"In a preclinical study, the combination of Zelboraf (vemurafenib) and Farydak (panobinostat) resulted in greater apoptotic activity compared to either agent alone in a colorectal cancer cell line harboring BRAF V600E in culture (%%PUBMED:36343387%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - 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Zelboraf (vemurafenib), Iressa (gefitinib), and Sprycel (dasatinib) synergistically inhibited viability in colorectal cancer cell lines harboring BRAF V600E in culture and resulted in greater tumor growth inhibition and tumor regression in patient-derived xenograft (PDX) models to a greater degree than the doublet combinations of Zelboraf (vemurafenib) and Iressa (gefitinib) or Zelboraf (vemurafenib) and Sprycel (dasatinib) (%%PUBMED:36759733%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Pdx & cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[30181415],"normalized_drug":"Dabrafenib","indication":"colon neuroendocrine neoplasm","therapy_id":3,"normalized_cancer":"Gastrointestinal Neuroendocrine Tumors","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a clinical case study, Tafinlar (dabrafenib) treatment of a patient with recurrent neuroendocrine carcinoma of the colon harboring a BRAF V600E mutation resulted in stable disease for 6 months before disease progression (%%PUBMED:30181415%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[20531415,26603897],"response_type":"sensitive","indication":"melanoma","therapy_id":3307,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"SBI-0640726","efficacy_evidence":"In a preclinical study, SBI-0640726 inhibited proliferation and Akt/mTOR signaling in human melanoma cell lines harboring BRAF V600E in culture (%%PUBMED:26603897%%, %%PUBMED:20531415%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[28425764],"normalized_drug":"Dabrafenib, Trametinib","indication":"papillary craniopharyngioma","therapy_id":1066,"normalized_cancer":"Craniopharyngioma, Papillary 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(n=113) resulted in improved median overall survival (8.4 vs 5.4 months, HR=0.60, p<0.001), confirmed response rate (20% vs 2%, p<0.001), and median progression-free survival (4.2 vs 1.5 months, HR=0.40, p<0.001) compared to control (n=107) in patients with metastatic colorectal cancer harboring BRAF V600E (%%PUBMED:31566309%%; NCT02928224).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"FDA approved - On Companion Diagnostic","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[39255538],"normalized_drug":"Cetuximab, Encorafenib","indication":"colorectal cancer","therapy_id":1916,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Encorafenib","efficacy_evidence":"In a retrospective analysis, real-world treatment with Erbitux (cetuximab) and Braftovi (encorafenib) with or without Mektovi (binimetinib) led to an objective response rate (ORR) of 32.2% (57/201, 2 complete responses (CR)), disease control rate of 71.2% (126/201), median progression-free survival of 4.5 months, and median overall survival of 9.2 months in metastatic colorectal cancer patients with BRAF V600E, with an ORR of 32% (50/180, 1 CR) in patients treated with doublet therapy (%%PUBMED:39255538%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Clinical Study","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[36307056],"normalized_drug":"Cetuximab, Encorafenib","indication":"colorectal cancer","therapy_id":1916,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Encorafenib","efficacy_evidence":"Braftovi (encorafenib) in combination with Erbitux (cetuximab) is included in guidelines as second-line or subsequent therapy for patients with metastatic colorectal cancer harboring BRAF V600E (%%PUBMED:36307056%%; ESMO.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF 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mutations (%%PUBMED:16880785%%, %%PUBMED:22394203%%).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"pub_med_references":[18287029],"response_type":"sensitive","indication":"colon cancer","therapy_id":1060,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"PLX4720","efficacy_evidence":"In a preclinical study, PLX4720 inhibited growth of colon cancer cells harboring BRAF V600E in culture and in cell line xenograft models (%%PUBMED:18287029%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[24885690],"normalized_drug":"Sorafenib","indication":"colorectal cancer","therapy_id":920,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Sorafenib","efficacy_evidence":"In a preclinical study, colorectal cancer cell lines harboring a BRAF V600E mutation were sensitive to Nexavar (sorafenib) in culture (%%PUBMED:24885690%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[28939558],"normalized_drug":"Ulixertinib","indication":"colorectal cancer","therapy_id":997,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Ulixertinib","efficacy_evidence":"In a preclinical study, Ulixertinib (BVD-523) inhibited Erk signaling in colorectal cancer cells harboring BRAF V600E, resulted in cell cycle arrest in culture and tumor growth inhibition in cell line xenograft models (%%PUBMED:28939558%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[39190425],"normalized_drug":"Vemurafenib","indication":"histiocytosis","therapy_id":342,"normalized_cancer":"Histiocytosis","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a clinical study, Zelboraf (vemurafenib) treatment resulted in complete remission in 2 pediatric patients with Langerhans cell histiocytosis harboring BRAF V600E (%%PUBMED:39190425%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"Squamous Cell Carcinoma of Unknown Primary","therapy_id":1066,"normalized_cancer":"Squamous Cell Carcinoma, NOS","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"The combination of Tafinlar (dabrafenib) and Mekinist (trametinib) is included in guidelines for patients with squamous cell carcinoma of unknown primary harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[29118233],"response_type":"not applicable","indication":"hairy cell leukemia","therapy_id":1776,"normalized_cancer":"Hairy Cell Leukemia","evidence_type":"Diagnostic","therapy":"N/A","efficacy_evidence":"BRAF V600E is diagnostic and aids in distinguishing classic hairy cell leukemia (cHCL) from variant hairy cell leukemia (HCLv) and other B-cell lymphomas and leukemias (%%PUBMED:29118233%%, NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[18794803],"response_type":"predicted - sensitive","indication":"melanoma","therapy_id":2427,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"U0126","efficacy_evidence":"In a preclinical study, U0126 treatment inhibited Erk phosphorylation and reduced growth of melanoma cells harboring BRAF V600E in culture (%%PUBMED:18794803%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"not predictive","pub_med_references":[29723688],"normalized_drug":"Pembrolizumab","indication":"lung non-small cell carcinoma","therapy_id":1447,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Pembrolizumab","efficacy_evidence":"In a retrospective analysis, non-small cell lung cancer patients harboring BRAF V600E did not demonstrate a significantly different response to treatment with either Keytruda (pembrolizumab), Opdivo (nivolumab), or Tecentriq (atezolizumab), compared to patients with BRAF non-V600E mutations, demonstrating an objective response rate of 25% (3/12) vs 33% (3/9) (p=1.0) and median progression-free survival of 3.7 months vs 4.1 months (p=0.37) (%%PUBMED:29723688%%).","cap_asco_evidence_level":"NA","molecular_profile":"BRAF V600E","approval_status":"Clinical Study - Cohort","amp_tier":"NA"},{"pub_med_references":[39626159],"response_type":"predicted - sensitive","indication":"colon cancer","therapy_id":1992,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Panitumumab + Trametinib","efficacy_evidence":"In a clinical study, treatment with the combination of Vectibix (panitumumab), Tafinlar (dabrafenib), and Mekinist (trametinib) resulted in a clinical response in a pediatric patient with colon cancer harboring BRAF V600E, as well as TP53 G245S, SMAD4 S504R, and PTEN loss, with decreased liver metastases and reduction in CA-19-9 and BRAF V600E VAF levels in the cell free DNA (%%PUBMED:39626159%%; NCT02688517).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[36825105],"normalized_drug":"Dabrafenib, Trametinib","indication":"IDH-wildtype glioblastoma","therapy_id":1066,"normalized_cancer":"Glioblastoma, IDH-Wildtype","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, Tafinlar (dabrafenib) and Mekinist (trametinib) combination therapy resulted in a partial response lasting 9 months in a patient with metastatic MGMT unmethylated, IDH-wildtype glioblastoma harboring BRAF V600E along with amplification of MYC and TERT and loss of CDKN2A/B (%%PUBMED:36825105%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[28645859],"response_type":"sensitive","indication":"melanoma","therapy_id":6241,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"INU-152","efficacy_evidence":"In a preclinical study, INU-152 reduced MEK and ERK phosphorylation and growth of a melanona cell line harboring BRAF V600E in culture, and inhibited tumor growth in xenograft models (%%PUBMED:28645859%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"melanoma","therapy_id":10113,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"JSI-1187","efficacy_evidence":"In a preclinical study, JSI-1187 treatment in a melanoma cell line harboring BRAF V600E led to inhibition of cell proliferation in culture, and tumor growth inhibition in a cell line xenograft model (Cancer Res 2020;80(16 Suppl):Abstract nr 4188).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[32758030],"normalized_drug":"Trametinib","indication":"histiocytic sarcoma","therapy_id":2,"normalized_cancer":"Histiocytic Sarcoma","evidence_type":"Actionable","therapy":"Trametinib","efficacy_evidence":"In a Phase II trial (NCI-MATCH), Mekinist (trametinib) treatment resulted in an objective response rate of 37.9% (11/29) in patients with advanced solid tumors harboring BRAF V600E, 1 patient with histiocytic sarcoma of the brain achieved a partial response with an ongoing progression-free survival at 20.9 months (%%PUBMED:32758030%%; NCT02465060).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[39392364],"normalized_drug":"Binimetinib, Encorafenib","indication":"glomus tumor","therapy_id":1100,"normalized_cancer":"Soft Tissue Cancer","evidence_type":"Actionable","therapy":"Binimetinib + Encorafenib","efficacy_evidence":"In a clinical case study, treatment with the combination of Mektovi (binimetinib) and Braftovi (encorafenib) resulted in a complete response lasting more than 2 years in a patient with metastatic malignant glomus tumor harboring BRAF V600E (%%PUBMED:39392364%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[23629727],"normalized_drug":"Pimasertib","indication":"colorectal cancer","therapy_id":871,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Pimasertib","efficacy_evidence":"In a preclinical study, Pimasertib (MSC1936369B) inhibited proliferation of colorectal cancer cells harboring BRAF V600E in culture (%%PUBMED:23629727%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[37838724],"response_type":"sensitive","indication":"melanoma","therapy_id":16289,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"AZD3514 + Dabrafenib","efficacy_evidence":"In a preclinical study, the addition of AZD3514 to Tafinlar (dabrafenib) treatment inhibited colony formation in melanoma cell lines harboring BRAF V600E in culture (%%PUBMED:37838724%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[36343387],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":14545,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Trametinib + Vorinostat","efficacy_evidence":"In a preclinical study, the combination of Mekinist (trametinib) and Zolinza (vorinostat) resulted in greater apoptotic activity compared to either agent alone in a colorectal cancer cell line harboring BRAF V600E in culture (%%PUBMED:36343387%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[36343387],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":14546,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Romidepsin + Trametinib","efficacy_evidence":"In a preclinical study, the combination of Mekinist (trametinib) and Istodax (romidepsin) resulted in greater apoptotic activity compared to either agent alone in a colorectal cancer cell line harboring BRAF V600E in culture (%%PUBMED:36343387%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[30559419],"normalized_drug":"Plx8394","indication":"melanoma","therapy_id":1041,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"PLX8394","efficacy_evidence":"In a preclinical study, PLX8394 treatment inhibited Erk phosphorylation and reduced proliferation of melanoma cells harboring either monomeric BRAF V600E or dimeric isoform (p61) of V600E in culture (%%PUBMED:30559419%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"no benefit","pub_med_references":[27312529],"normalized_drug":"Vemurafenib","indication":"colorectal cancer","therapy_id":342,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a preclinical study, colorectal cancer cell lines harboring BRAF V600E demonstrated decreased response to Zelboraf (vemurafenib) in culture (%%PUBMED:27312529%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"no benefit","pub_med_references":[26460303],"normalized_drug":"Vemurafenib","indication":"colorectal cancer","therapy_id":342,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase II trial, Zelboraf (vemurafenib) did not demonstrate meaningful clinical activity as a single agent, resulted in partial response in 5% (1/21) and stable disease in 33% (7/21) of patients with metastatic colorectal cancer harboring BRAF V600E (%%PUBMED:26460303%%; NCT00405587).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"response_type":"no benefit","pub_med_references":[22281684],"normalized_drug":"Vemurafenib","indication":"colorectal cancer","therapy_id":342,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a preclinical study, colorectal cancer cell lines harboring BRAF V600E were not sensitive to growth inhibition by Zelboraf (vemurafenib) in culture or xenograft models, due to feedback activation of EGFR signaling (%%PUBMED:22281684%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[34178685],"normalized_drug":"Dabrafenib, Trametinib","indication":"lung papillary adenocarcinoma","therapy_id":1066,"normalized_cancer":"Lung Adenocarcinoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, Tafinlar (dabrafenib) and Mekinist (trametinib) combination treatment resulted in regression of the lesions in the chest, abdomen and brain in a patient with lung papillary carcinoma harboring BRAF V600E but progression was observed 3 months later (%%PUBMED:34178685%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[33537843],"normalized_drug":"Dabrafenib, Trametinib","indication":"intrahepatic cholangiocarcinoma","therapy_id":1066,"normalized_cancer":"Intrahepatic Cholangiocarcinoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, combination treatment with Tafinlar (dabrafenib) and Mekinist (trametinib) in a patient with intrahepatic cholangiocarcinoma harboring BRAF V600E who progressed on chemotherapy led to stable disease at 6 weeks, improvement of lung and liver lesions at 12 weeks after treatment, and response was maintained until disease progression in the liver was observed at 10 months (%%PUBMED:33537843%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[38109210],"normalized_drug":"Dabrafenib, Trametinib","indication":"intrahepatic cholangiocarcinoma","therapy_id":1066,"normalized_cancer":"Intrahepatic Cholangiocarcinoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a Phase II trial (NCI-MATCH), treatment with the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) resulted in an objective response rate of 38% in patients with advanced solid tumors harboring BRAF V600E, with a significantly greater tumor shrinkage observed in patients (n=4) with intrahepatic cholangiocarcinoma compared to the trial average ( -60% vs -35%, P=0.016) (%%PUBMED:38109210%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"intrahepatic cholangiocarcinoma","therapy_id":1066,"normalized_cancer":"Intrahepatic Cholangiocarcinoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Tafinlar (dabrafenib) in combination with Mekinist (trametinib) is included in guidelines as subsequent-line therapy for patients with biliary cancer harboring BRAF V600E, including intrahepatic cholangiocarcinoma (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[24983357],"response_type":"sensitive","indication":"melanoma","therapy_id":2960,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Navitoclax + PLX4720","efficacy_evidence":"In a preclinical study, PLX4720 and navitoclax (ABT-263) worked synergistically to inhibit growth and increase apoptosis of BRAF V600E mutant melanoma cells in culture and in xenografts (%%PUBMED:24983357%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[30323086],"normalized_drug":"Dabrafenib, Trametinib","indication":"salivary gland carcinoma","therapy_id":1066,"normalized_cancer":"Salivary Carcinoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case report, combined Tafinlar (dabrafenib) and Mekinist (trametinib) treatment of a patient with salivary duct carcinoma harboring BRAF V600E resulted in a reduction of metastatic lesions and stable disease lasting 13 months followed by disease progression (%%PUBMED:30323086%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"colorectal cancer","therapy_id":16367,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Encorafenib + IMM-6-415","efficacy_evidence":"In a preclinical study, treatment with the combination of Braftovi (encorafenib) and IMM-6-415 resulted in increased tumor growth inhibition compared to the combination of Mektovi (binimetinib) and Braftovi (encorafenib) in a cell line xenograft model of colorectal cancer harboring BRAF V600E (Mol Cancer Ther (2023) 22 (12_Supplement): A093).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[32758030],"normalized_drug":"Trametinib","indication":"lung adenocarcinoma","therapy_id":2,"normalized_cancer":"Lung Adenocarcinoma","evidence_type":"Actionable","therapy":"Trametinib","efficacy_evidence":"In a Phase II trial (NCI-MATCH), Mekinist (trametinib) treatment resulted in an objective response rate of 37.9% (11/29) in patients with advanced solid tumors harboring BRAF V600E, of 4 patients with lung adenocarcinoma, 1 achieved a partial response with an ongoing progression-free survival (PFS) at 32.5 mo, 3 patients had stable disease for 15.6, 6.6, and 3.6 mo, and an additional unevaluable patient achieved an 81% reduction of measured lesions and a PFS of 12.7 mo (%%PUBMED:32758030%%; NCT02465060).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[37417899],"normalized_drug":"Vemurafenib","indication":"synovial sarcoma","therapy_id":342,"normalized_cancer":"Synovial Sarcoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a clinical case study, Zelboraf (vemurafenib) resulted in a partial response after 4 months of treatment in a patient with intrathoracic synovial sarcoma harboring SS18-SSX1 (e10:e6) and BRAF V600E (%%PUBMED:37417899%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Cetuximab, Encorafenib","indication":"colon cancer","therapy_id":1916,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Encorafenib","efficacy_evidence":"Braftovi (encorafenib) in combination with Erbitux (cetuximab) is included in guidelines as primary or subsequent therapy for patients with colon cancer harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[40373261],"normalized_drug":"Cetuximab, Encorafenib","indication":"colon cancer","therapy_id":1916,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Encorafenib","efficacy_evidence":"In a clinical case study, neoadjuvant treatment with the combination of Braftovi (encorafenib) and Erbitux (cetuximab) resulted in tumor reduction in 2 patients with locally advanced, right-sided colon cancer harboring BRAF V600E (%%PUBMED:40373261%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[38343359],"normalized_drug":"Binimetinib, Encorafenib","indication":"papillary thyroid carcinoma","therapy_id":1100,"normalized_cancer":"Papillary Thyroid Cancer","evidence_type":"Actionable","therapy":"Binimetinib + Encorafenib","efficacy_evidence":"In a Phase II trial, Mektovi (binimetinib) plus Braftovi (encorafenib) demonstrated safety in patients with BRAF V600E-mutant thyroid cancer and resulted in an objective response rate (ORR) of 54.5% (12/22, 12 partial responses (PR)), with an ORR of 47.1% (8/17, 8 PR) and a disease control rate of 100% (17/17) in the differentiated thyroid cancer cohort (all papillary thyroid cancer), and median duration of response, progression-free survival, and overall survival were not reached (%%PUBMED:38343359%%).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"pub_med_references":[33229459],"response_type":"no benefit","indication":"uveal melanoma","therapy_id":11307,"normalized_cancer":"Uveal Melanoma","evidence_type":"Actionable","therapy":"YM-254890","efficacy_evidence":"In a preclinical study, transformed mouse melanocytes expressing BRAF V600E were insensitive to treatment with YM-254890 (%%PUBMED:33229459%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[38565920],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":16826,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + IAG933 + Trametinib","efficacy_evidence":"In a preclinical study, the combination of IAG933, Tafinlar (dabrafenib), and Mekinist (trametinib) inhibited proliferation of colorectal cancer cell lines harboring BRAF V600E in culture (%%PUBMED:38565920%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[38343359],"normalized_drug":"Binimetinib, Encorafenib","indication":"thyroid cancer","therapy_id":1100,"normalized_cancer":"Thyroid Cancer","evidence_type":"Actionable","therapy":"Binimetinib + Encorafenib","efficacy_evidence":"In a Phase II trial, treatment with Mektovi (binimetinib) plus Braftovi (encorafenib) demonstrated safety and activity in patients with BRAF V600E-mutant thyroid cancer, regardless of histological subtype, resulting in an objective response rate of 54.5% (12/22, 12 partial responses), disease control rate of 100% (22/22), and 12-month rate of ongoing response of 90.9%, and median duration of response, median progression-free survival, and median overall survival were not reached (%%PUBMED:38343359%%).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[38096472],"normalized_drug":"Cobimetinib, Vemurafenib","indication":"breast cancer","therapy_id":1657,"normalized_cancer":"Breast Cancer","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"In a Phase II trial (TAPUR), Zelboraf (vemurafenib) and Cotellic (cobimetinib) combination therapy resulted in a complete response that lasted 170 days and 2 partial responses out of 4 patients with advanced breast cancer harboring BRAF V600E (%%PUBMED:38096472%%; NCT02693535).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"melanoma","therapy_id":16367,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Encorafenib + IMM-6-415","efficacy_evidence":"In a preclinical study, treatment with the combination of Braftovi (encorafenib) and IMM-6-415 resulted in increased tumor growth inhibition compared to the combination of Mektovi (binimetinib) and Braftovi (encorafenib) in a cell line xenograft model of melanoma harboring BRAF V600E (Mol Cancer Ther (2023) 22 (12_Supplement): A093).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"resistant","normalized_drug":"Panitumumab","indication":"rectum cancer","therapy_id":845,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Panitumumab","efficacy_evidence":"Vectibix (panitumumab), as a monotherapy, is not indicated for use in rectum cancer patients with BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[22735384],"normalized_drug":"Dabrafenib","indication":"melanoma","therapy_id":3,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a Phase III clinical trial (BREAK-3) that supported FDA approval, Tafinlar (dabrafenib) improved median progression-free survival compared to Deticene (dacarbazine) (5.1 vs 2.7 months, HR=0.3, p<0.0001) in patients with BRAF V600E positive melanoma (%%PUBMED:22735384%%; NCT01227889).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"FDA approved - On Companion Diagnostic","amp_tier":"I"},{"pub_med_references":[25500121],"response_type":"sensitive","indication":"melanoma","therapy_id":3106,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"CCT241161","efficacy_evidence":"In a preclinical study, CCT241161 inhibited growth of a human melanoma cell line harboring BRAF V600E in culture, and induced tumor regression in several BRAF V600E-mutant melanoma patient-derived xenograft models (%%PUBMED:25500121%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"pub_med_references":[33568355],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":11477,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Regorafenib + Trametinib","efficacy_evidence":"In a preclinical study, combination treatment with Stivarga (regorafenib), Tafinlar (dabrafenib), and Mekinist (trametinib) in colorectal cancer cell lines harboring BRAF V600E resulted in suppression of colony formation in culture, and inhibition of tumor growth in a cell line xenograft model (%%PUBMED:33568355%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[27924459],"response_type":"sensitive","indication":"melanoma","therapy_id":5119,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Alpelisib + PLX4720","efficacy_evidence":"In a preclinical study, the combination of Alpelisib (BYL719) and PLX4720 enhanced antitumor activity in a melanoma cell line harboring BRAF V600E, demonstrating decreased cell survival and increased apoptotic activity in xenograft models, and decreased Akt signaling in culture (%%PUBMED:27924459%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[31937621],"response_type":"sensitive","indication":"thyroid cancer","therapy_id":10185,"normalized_cancer":"Thyroid Cancer","evidence_type":"Actionable","therapy":"PLX4720 + Ponatinib","efficacy_evidence":"In a preclinical study, Iclusig (ponatinib) and PLX4720 treatment demonstrated synergy, and inhibited Erk, Mek, and c-jun phosphorylation, reduced cell proliferation, colony formation, and migration, and induced apoptosis in thyroid cancer cells harboring BRAF V600E and in PLX4720-resistant cells harboring BRAF V600E in culture, and inhibited tumor growth, reduced lung and liver metastases, and increased survival in cell line xenograft models (%%PUBMED:31937621%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[33043759],"normalized_drug":"Binimetinib, Encorafenib","indication":"ovarian serous carcinoma","therapy_id":1100,"normalized_cancer":"Serous Ovarian Cancer","evidence_type":"Actionable","therapy":"Binimetinib + Encorafenib","efficacy_evidence":"In a clinical case study, Braftovi (encorafenib) and Mektovi (binimetinib) combination therapy resulted in durable stable disease lasting at least 3.5 years in a patient with low-grade serous ovarian carcinoma harboring BRAF V600E, who was previously treated with the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) (%%PUBMED:33043759%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[32029534],"normalized_drug":"Vemurafenib","indication":"cholangiocarcinoma","therapy_id":342,"normalized_cancer":"Cholangiocarcinoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase II trial (VE-BASKET), responses were seen in patients with cholangiocarcinoma harboring BRAF V600E (n=9) when treated with Zelboraf (vemurafenib), including 2 patients with a partial response (%%PUBMED:32029534%%; NCT01524978).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[37352476],"response_type":"no benefit","indication":"colorectal cancer","therapy_id":2184,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Fluorouracil + Irinotecan + Leucovorin + Oxaliplatin","efficacy_evidence":"In a Phase II trial (FIRE-4.5), the combination of Erbitux (cetuximab) with FOLFOXIRI as first-line therapy did not result in an improved objective response rate (ORR) compared to Avastin (bevacizumab) with FOLFOXIRI, with an ORR of 50.8% (30/59) vs 66.7% (20/30) (P=0.92), a median progression-free survival of 7.6 vs 12.4 months (P=0.003), and a median overall survival of 15.2 vs 22.9 months (P=0.14), respectively, in metastatic colorectal cancer patients harboring BRAF V600E (%%PUBMED:37352476%%).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"response_type":"sensitive","indication":"colorectal cancer","therapy_id":1718,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Panitumumab","efficacy_evidence":"In a Phase Ib/II trial, treatment with the combination of Vectibix (panitumumab) and Tafinlar (dabrafenib) resulted in stable disease in 7/8 colorectal cancer patients harboring a BRAF V600E mutation (J Clin Oncol 32:5s, 2014 (suppl; abstr 3515)).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase Ib/II","amp_tier":"II"},{"pub_med_references":[29431699],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":1718,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Panitumumab","efficacy_evidence":"In a Phase I trial, combination therapy consisting of Tafinlar (dabrafenib) and Vectibix (panitumumab) resulted in an overall response rate of 10% (2/20, 1 complete response, 1 partial response), stable disease in 80% (16/20), and a median progression-free survival of 3.5 months in patients with BRAF V600E colorectal cancer (%%PUBMED:29431699%%; NCT01750918).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase I","amp_tier":"II"},{"response_type":"sensitive","indication":"appendix adenocarcinoma","therapy_id":9562,"normalized_cancer":"Appendiceal Adenocarcinoma","evidence_type":"Actionable","therapy":"Encorafenib + Panitumumab","efficacy_evidence":"Braftovi (encorafenib) in combination with Vectibix (panitumumab) is included in guidelines for patients with advanced or metastatic appendiceal adenocarcinoma harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[36921494],"response_type":"no benefit","indication":"colorectal cancer","therapy_id":15623,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Fluorouracil + Leucovorin + Vemurafenib","efficacy_evidence":"In a Phase II trial (MODUL), patients with metastatic colorectal cancer harboring BRAF V600E did not demonstrate improved progression-free survival when treated with the combination of Zelboraf (vemurafenib), Erbitux (cetuximab), Adrucil (fluorouracil), and Wellcovorin (leucovorin) compared to the control treatment of Avastin (bevacizumab) with a fluoropyrimidine (HR=0.95 and P=0.872) (%%PUBMED:36921494%%; NCT02291289).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"pub_med_references":[25873592],"response_type":"sensitive","indication":"melanoma","therapy_id":1059,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"BI-847325","efficacy_evidence":"In a preclinical study, treatment with BI-847325 resulted in decreased expression of Mcl-1 and Mek, and inhibited growth of melanoma cell lines harboring BRAF V600E in culture, and inhibited tumor growth in xenograft models of BRAF V600E-positive melanoma, including models with BRAF-inhibitor resistance (%%PUBMED:25873592%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[15294323,25500121],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":3105,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"CCT196969","efficacy_evidence":"In a preclinical study, CCT196969 inhibited growth of BRAF-mutant colorectal cancer cell lines in culture (%%PUBMED:25500121%%), which have been reported to harbor BRAF V600E (%%PUBMED:15294323%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[26573800],"response_type":"conflicting","indication":"glioblastoma","therapy_id":849,"normalized_cancer":"Glioblastoma, IDH-Wildtype","evidence_type":"Actionable","therapy":"Mirdametinib","efficacy_evidence":"In a preclinical study, a glioblastoma cell line harboring BRAF V600E demonstrated a decreased response to treatment with Gomekli (mirdametinib), demonstrating increased viability of CD133 positive cells in culture (%%PUBMED:26573800%%).","cap_asco_evidence_level":"NA","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"NA"},{"pub_med_references":[38714355],"response_type":"conflicting","indication":"glioblastoma","therapy_id":849,"normalized_cancer":"Glioblastoma, IDH-Wildtype","evidence_type":"Actionable","therapy":"Mirdametinib","efficacy_evidence":"In a preclinical study, Gomekli (mirdametinib) inhibited growth of glioblastoma cell lines harboring BRAF V600E in culture (%%PUBMED:38714355%%).","cap_asco_evidence_level":"NA","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"NA"},{"pub_med_references":[25665005],"response_type":"sensitive","indication":"lung non-small cell carcinoma","therapy_id":3532,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Trametinib + TW-37","efficacy_evidence":"In a preclinical study, TW-37 enhanced the inhibitory effect of Mekinist (trametinib) on human non-small cell lung cancer cells harboring BRAF V600E in culture (%%PUBMED:25665005%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[30351999],"normalized_drug":"Vemurafenib","indication":"ganglioglioma","therapy_id":342,"normalized_cancer":"Ganglioglioma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase II trial (VE-BASKET), Zelboraf (vemurafenib) treatment resulted in a partial response in a patient with anaplastic ganglioglioma harboring BRAF V600E who stayed on treatment for 13.8 months (%%PUBMED:30351999%%; NCT01524978).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"skin melanoma","therapy_id":1066,"normalized_cancer":"Cutaneous Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Tafinlar (dabrafenib) and Mekinist (trametinib) combination therapy is included in guidelines for cutaneous melanoma patients harboring a BRAF V600 mutation, such as BRAF V600E, as neoadjuvant or adjuvant therapy for stage III disease and as systemic therapy for patients with unresectable or metastatic disease (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"predicted - sensitive","indication":"melanoma","therapy_id":13809,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"CFT1946","efficacy_evidence":"In a Phase I trial, CFT1946 treatment demonstrated safety and preliminary activity in patients with advanced solid tumors (n=25) including melanoma (40%), colorectal cancer (40%), non-small cell lung cancer (8%), and other non-CNS tumors harboring BRAF V600E (n=22), V600K (n=2), or V600R (n=1), with 1 unconfirmed partial response (uPR) and 7 stable diseases in efficacy evaluable patients (n=14) at data cutoff, and 1 additional uPR after data cutoff (Ann Oncol (2024) 35 (Suppl_2): S490-S491; NCT05668585).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase I","amp_tier":"II"},{"pub_med_references":[33568355],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":11479,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + RAF709 + Trametinib","efficacy_evidence":"In a preclinical study, combination treatment with RAF709, Tafinlar (dabrafenib), and Mekinist (trametinib) in colorectal cancer cell lines harboring BRAF V600E resulted in suppression of colony formation in culture (%%PUBMED:33568355%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[26916115],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":3711,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"BI 882370 + Cetuximab","efficacy_evidence":"In a preclinical study, colorectal cancer cells harboring BRAF V600E were sensitive to the combination of BI 882370 and Erbitux (cetuximab) in xenograft models, resulting in tumor growth inhibition and partial tumor regression (%%PUBMED:26916115%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[25500121],"response_type":"sensitive","indication":"melanoma","therapy_id":3105,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"CCT196969","efficacy_evidence":"In a preclinical study, CCT196969 inhibited growth of a human melanoma cell line harboring BRAF V600E in culture, and induced tumor regression in several BRAF V600E-mutant melanoma patient-derived xenograft models (%%PUBMED:25500121%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"pub_med_references":[31618628],"response_type":"sensitive","indication":"melanoma","therapy_id":3105,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"CCT196969","efficacy_evidence":"In a preclinical study, CCT196969 treatment inhibited viability of a melanoma cell line harboring BRAF V600E in culture (%%PUBMED:31618628%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"melanoma","therapy_id":15222,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"PHI-501","efficacy_evidence":"In a preclinical study, PHI-501 inhibited growth and migration and induced apoptosis in a melanoma cell line harboring BRAF V600E and induced dose-dependent tumor growth inhibition in a cell line xenograft model (Cancer Res (2023) 83 (7_Supplement): 1627).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[34969785],"normalized_drug":"Dabrafenib, Trametinib","indication":"lung combined large cell neuroendocrine carcinoma","therapy_id":1066,"normalized_cancer":"Large Cell Neuroendocrine Carcinoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, treatment with the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) resulted in a partial response after 10 weeks in a patient with combined large cell neuroendocrine carcinoma harboring BRAF V600E, who remained recurrence-free for at least a year (%%PUBMED:34969785%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[36759733],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":15049,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Dasatinib + Gefitinib + PLX4720","efficacy_evidence":"In a preclinical study, the combination of PLX4720, Iressa (gefitinib), and Sprycel (dasatinib) inhibited tumor growth in colorectal cancer cell line xenograft models harboring BRAF V600E to a greater degree than the combinations of PLX4720 and Iressa (gefitinib) or PLX4720 and Sprycel (dasatinib) (%%PUBMED:36759733%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[37403699],"response_type":"decreased response","indication":"melanoma","therapy_id":5891,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Toripalimab-tpzi","efficacy_evidence":"In a retrospective analysis, real-world treatment with either Keytruda (pembrolizumab) or Loqtorz (toripalimab-tpzi) resulted in a median disease-free survival of 17 months in melanoma patients harboring BRAF V600E compared to 32 months in patients with wild-type BRAF, NRAS, and KIT (p=0.022) (%%PUBMED:37403699%%).","cap_asco_evidence_level":"NA","molecular_profile":"BRAF V600E","approval_status":"Clinical Study","amp_tier":"NA"},{"pub_med_references":[36759733],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":15046,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Celecoxib + Dabrafenib + Trametinib","efficacy_evidence":"In a preclinical study, the addition of Celecoxib to the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) inhibited tumor growth and induced tumor regression in colorectal cancer patient-derived xenograft (PDX) models harboring BRAF V600E (%%PUBMED:36759733%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"pub_med_references":[29431699],"response_type":"predicted - sensitive","indication":"colorectal cancer","therapy_id":1992,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Panitumumab + Trametinib","efficacy_evidence":"In a Phase I trial, combination therapy consisting of Tafinlar (dabrafenib), Vectibix (panitumumab), and Mekinist (trametinib) resulted in an overall response rate of 21% (19/91, 1 complete response, 18 partial response), stable disease in 65% (59/91), and a median progression-free survival of 4.2 months in patients with BRAF V600E colorectal cancer (%%PUBMED:29431699%%; NCT01750918).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase I","amp_tier":"II"},{"pub_med_references":[37269335],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":15326,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Binimetinib + Encorafenib + PF-07284892","efficacy_evidence":"In a preclinical study, the combination of PF-07284892, Mektovi (binimetinib), and Braftovi (encorafenib) inhibited Erk phosphorylation in colorectal cancer cells harboring BRAF V600E in culture and induced tumor regression in a cell line xenograft model (%%PUBMED:37269335%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib","indication":"follicular thyroid carcinoma","therapy_id":3,"normalized_cancer":"Follicular Thyroid Cancer","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"Tafinlar (dabrafenib) is included in guidelines for patients with recurrent, advanced, or metastatic thyroid follicular carcinoma harboring BRAF V600E for whom clinical trials are not available or appropriate (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[33537843],"response_type":"predicted - sensitive","indication":"endometrial adenocarcinoma","therapy_id":1302,"normalized_cancer":"Endometrial Carcinoma","evidence_type":"Actionable","therapy":"Dabrafenib + Rabeprazole + Rifampin","efficacy_evidence":"In a Phase I trial, combination treatment with Tafinlar (dabrafenib), Rabeprazole, and Rifampin in a patient with metastatic endometrial adenocarcinoma harboring BRAF V600E, that recurred 11 years after original diagnosis and was refractory to treatment with chemotherapy, led to reduction of lung metastases and pelvic tissue mass at three months, but a slight increase in pelvic mass was observed at six months (%%PUBMED:33537843%%; NCT01954043).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","normalized_drug":"Vemurafenib","indication":"larynx cancer","therapy_id":342,"normalized_cancer":"Head and Neck Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase II trial (MyPathway), Zelboraf (vemurafenib) treatment resulted in complete response in a patient with larynx cancer harboring BRAF V600E (%%PUBMED:29320312%%; NCT02091141).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[38691346],"response_type":"predicted - sensitive","indication":"high grade glioma","therapy_id":13603,"normalized_cancer":"High-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"Binimetinib + PF-07799933","efficacy_evidence":"In a Phase I trial, the addition of Mektovi (binimetinib) to treatment with PF-07799933 resulted in a partial response in a patient with high grade glioma harboring BRAF V600E (%%PUBMED:38691346%%; NCT05355701).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[36198029],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":14531,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Axitinib + Vemurafenib","efficacy_evidence":"In a preclinical study, combination treatment with Zelboraf (vemurafenib) and Inlyta (axitinib) resulted in decreased cell viability in colorectal cancer cell lines harboring BRAF V600E in culture, and led to synergistic inhibition of tumor growth in cell line xenograft models (%%PUBMED:36198029%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[23942066],"normalized_drug":"Selumetinib","indication":"colorectal cancer","therapy_id":913,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Selumetinib","efficacy_evidence":"In a preclinical study, Koselugo (selumetinib) decreased tumor growth in a cell line xenograft model of colorectal cancer harboring BRAF V600E (%%PUBMED:23942066%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[30559419],"response_type":"sensitive","indication":"melanoma","therapy_id":3268,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"LY3009120","efficacy_evidence":"In a preclinical study, LY3009120 treatment inhibited Erk phosphorylation and reduced proliferation of a melanoma cells harboring either monomeric BRAF V600E or dimeric isoform (p61) of V600E in culture (%%PUBMED:30559419%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","indication":"melanoma","therapy_id":3268,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"LY3009120","efficacy_evidence":"In a preclinical study, LY3009120 inhibited growth, downstream MAPK signaling and soft agar growth in human melanoma cell lines harboring BRAF V600E in culture (%%PUBMED:26343583%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[39461261],"response_type":"predicted - sensitive","indication":"pancreatic ductal adenocarcinoma","therapy_id":4886,"normalized_cancer":"Pancreatic Adenocarcinoma","evidence_type":"Actionable","therapy":"Binimetinib + Cetuximab + Encorafenib","efficacy_evidence":"In a clinical case study, third-line treatment with the combination of Mektovi (binimetinib), Erbitux (cetuximab), and Braftovi (encorafenib) resulted in a partial response with a 74% decrease in primary tumor size in a patient with metastatic pancreatic ductal adenocarcinoma harboring BRAF V600E (%%PUBMED:39461261%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[38894534],"response_type":"sensitive","indication":"melanoma","therapy_id":17245,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"DSR6434 + unspecified PD-1 antibody + Vemurafenib","efficacy_evidence":"In a preclinical study, treatment with the combination of Zelboraf (vemurafenib), DSR6434, and an anti-PD-1 antibody induced tumor regression and resulted in prolonged progression-free survival compared to either of the doublet combination therapies in a syngeneic mouse model of melanoma harboring BRAF V600E (%%PUBMED:38894534%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"response_type":"sensitive","indication":"rectum cancer","therapy_id":9562,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Encorafenib + Panitumumab","efficacy_evidence":"Braftovi (encorafenib) in combination with Vectibix (panitumumab) is included in guidelines as primary or subsequent therapy for patients with rectal cancer harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","indication":"colon cancer","therapy_id":11094,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Encorafenib + Fluorouracil + Leucovorin + Oxaliplatin","efficacy_evidence":"Braftovi (encorafenib) in combination with Erbitux (cetuximab) and FOLFOX is included in guidelines as initial (category 2A) or subsequent-line (category 2B) therapy for patients with advanced or metastatic colon cancer harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[33229459],"response_type":"no benefit","indication":"skin melanoma","therapy_id":11307,"normalized_cancer":"Cutaneous Melanoma","evidence_type":"Actionable","therapy":"YM-254890","efficacy_evidence":"In a preclinical study, YM-254890 treatment did not inhibit cell viability of a cutaneous melanoma cell line harboring BRAF V600E in culture (%%PUBMED:33229459%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib","indication":"Erdheim-Chester disease","therapy_id":3,"normalized_cancer":"Erdheim-Chester Disease","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"Tafinlar (dabrafenib) is included in guidelines as first-line or subsequent-line therapy for patients with Erdheim-Chester disease harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"predicted - sensitive","pub_med_references":[34232949],"normalized_drug":"Vemurafenib","indication":"IDH-wildtype glioblastoma","therapy_id":342,"normalized_cancer":"Glioblastoma, IDH-Wildtype","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a clinical case study, Zelboraf (vemurafenib) treatment resulted in disease stability over 15 months in a patient with epithelioid glioblastoma harboring BRAF V600E, who previously progressed on conventional treatment options (%%PUBMED:34232949%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"esophagus squamous cell carcinoma","therapy_id":1066,"normalized_cancer":"Esophageal Squamous Cell Carcinoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Tafinlar (dabrafenib) and Mekinist (trametinib) combination therapy is included in guidelines as second-line or subsequent therapy for patients with locally advanced, recurrent, or metastatic esophageal squamous cell carcinoma harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[15294323,25500121],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":3106,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"CCT241161","efficacy_evidence":"In a preclinical study, CCT241161 inhibited growth of colorectal cancer cell lines harboring BRAF V600E in culture (%%PUBMED:25500121%%, %%PUBMED:15294323%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"response_type":"resistant","pub_med_references":[36307056],"normalized_drug":"Cetuximab","indication":"colorectal cancer","therapy_id":694,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab","efficacy_evidence":"Erbitux (cetuximab), as a monotherapy, is not indicated for use in metastatic colorectal cancer patients with BRAF V600E (%%PUBMED:36307056%%; ESMO.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"resistant","pub_med_references":[25673558],"normalized_drug":"Cetuximab","indication":"colorectal cancer","therapy_id":694,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab","efficacy_evidence":"In a meta-analysis, the addition of Erbitux (cetuximab) or Vectibix (panitumumab) to standard of care treatment with chemotherapy did not result in improved progression-free survival (HR=0.88; 95% CI, 0.67-1.14; p=0.33), overall survival (HR=0.91; 95% CI, 0.62-1.34; p=0.63), or objective response rate (relative risk=1.31; 95% CI, 0.83-2.08; p=0.25) in patients with advanced colorectal cancer harboring BRAF V600E (%%PUBMED:25673558%%).","cap_asco_evidence_level":"B","molecular_profile":"BRAF V600E","approval_status":"Clinical Study - Meta-analysis","amp_tier":"I"},{"response_type":"resistant","pub_med_references":[19001320],"normalized_drug":"Cetuximab","indication":"colorectal cancer","therapy_id":694,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab","efficacy_evidence":"In a retrospective analysis, metastatic colorectal cancer patients harboring BRAF V600E demonstrated shorter progression-free survival (p=0.0107) and overall survival (p<0.0001) compared to patients with wild-type BRAF following Vectibix (panitumumab) or Erbitux (cetuximab) therapy with or without chemotherapy, and in a preclinical study, colorectal cancer cell lines harboring BRAF V600E were resistant to Erbitux (cetuximab) in culture (%%PUBMED:19001320%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Clinical Study","amp_tier":"II"},{"pub_med_references":[39391046],"response_type":"predicted - sensitive","indication":"Cancer of Unknown Primary","therapy_id":8515,"normalized_cancer":"Cancer of Unknown Primary","evidence_type":"Actionable","therapy":"Binimetinib + Cetuximab","efficacy_evidence":"In a clinical case study, treatment with the combination of Mektovi (binimetinib) and Erbitux (cetuximab) resulted in a significant but brief response in all lesions in a patient with metastatic cancer of unknown primary harboring BRAF V600E (%%PUBMED:39391046%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[38795180],"response_type":"sensitive","indication":"thyroid cancer","therapy_id":17198,"normalized_cancer":"Thyroid Cancer","evidence_type":"Actionable","therapy":"PLX4720 + Sorafenib","efficacy_evidence":"In a preclinical study, treatment with the combination of PLX4720 and Nexavar (sorafenib) inhibited proliferation of thyroid cancer cell lines harboring BRAF V600E in culture and resulted in greater tumor growth inhibition than PLX4720 alone in a cell line xenograft model (%%PUBMED:38795180%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"no benefit","pub_med_references":[27488531],"normalized_drug":"Palbociclib","indication":"melanoma","therapy_id":850,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Palbociclib","efficacy_evidence":"In a preclinical study, treatment with Ibrance (palbociclib) in a melanoma cell line xenograft model harboring BRAF V600E resulted in no benefit, demonstrating low but continuous growth (%%PUBMED:27488531%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[27312529],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":4544,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + SCH772984","efficacy_evidence":"In a preclinical study, combination therapy consisting of Tafinlar (dabrafenib) and SCH772984 inhibited survival of colorectal cancer cell lines harboring BRAF V600E in culture (%%PUBMED:27312529%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[27222538],"response_type":"sensitive","indication":"thyroid cancer","therapy_id":4601,"normalized_cancer":"Thyroid Cancer","evidence_type":"Actionable","therapy":"Dasatinib + SCH772984","efficacy_evidence":"In a preclinical study, Sprycel (dasatinib) and SCH772984 synergistically inhibited proliferation and induced apoptosis in both parental thyroid cancer cell lines harboring BRAF V600E and those acquired Sprycel (dasatinib)-resistance in culture (%%PUBMED:27222538%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[26208524],"normalized_drug":"Lifirafenib","indication":"colorectal cancer","therapy_id":4025,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Lifirafenib","efficacy_evidence":"In a preclinical study, Lifirafenib (BGB-283) inhibited Braf phosphorylation and cell proliferation in colorectal cancer cell lines harboring BRAF V600E in culture, and resulted in partial tumor regression in both cell line and patient-derived xenograft models (%%PUBMED:26208524%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Pdx & cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"lung non-small cell carcinoma","therapy_id":10701,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Lifirafenib + Mirdametinib","efficacy_evidence":"In a Phase Ib trial, Lifirafenib (BGB-283) and Gomekli (mirdametinib) combination treatment demonstrated safety and activity in patients with advanced solid tumors harboring MAPK pathway alterations, resulting in an objective response rate of 27.8% (15/54, 1 complete and 14 partial responses), including an objective response in a patient with non-small cell lung cancer harboring BRAF V600E (Cancer Res (2023) 83 (8_Supplement): CT033).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase I","amp_tier":"II"},{"pub_med_references":[38728872],"response_type":"sensitive","indication":"anaplastic thyroid carcinoma","therapy_id":2149,"normalized_cancer":"Anaplastic Thyroid Cancer","evidence_type":"Actionable","therapy":"Ravoxertinib","efficacy_evidence":"In a preclinical study, Ravoxertinib (GDC-0994) inhibited viability and colony formation and induced cell cycle arrest in an anaplastic thyroid carcinoma cell line harboring BRAF V600E in culture, and inhibited tumor growth in a cell line xenograft model (%%PUBMED:38728872%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"sensitive","indication":"melanoma","therapy_id":5827,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"ASN003","efficacy_evidence":"In a preclinical study, a melanoma xenograft model harboring BRAF V600E demonstrated tumor regression when treated with ASN003 (Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr B100).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[26267534],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":849,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Mirdametinib","efficacy_evidence":"In a preclinical study, Gomekli (mirdametinib) inhibited growth of colorectal cancer cell lines harboring BRAF V600E in culture (%%PUBMED:26267534%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[39399174],"normalized_drug":"Dabrafenib","indication":"desmoplastic infantile ganglioglioma / desmoplastic infantile astrocytoma","therapy_id":3,"normalized_cancer":"Primary Neuroepithelial Tumor","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a clinical case study, Tafinlar (dabrafenib) treatment resulted in a partial response with resolution of ascites in a pediatric patient with suprasellar metastatic desmoplastic infantile astrocytoma harboring BRAF V600E (%%PUBMED:39399174%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[23792568],"response_type":"predicted - sensitive","indication":"colon cancer","therapy_id":6209,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Sorafenib","efficacy_evidence":"In a clinical case study, a patient with metastatic colon cancer harboring BRAF V600E demonstrated mixed radiographic response with slight progression in some locations and stable disease in other locations for 7 months following treatment with the combination of Nexavar (sorafenib) and Erbitux (cetuximab) (%%PUBMED:23792568%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[32923904],"normalized_drug":"Plx8394","indication":"glioblastoma","therapy_id":1041,"normalized_cancer":"Glioblastoma, IDH-Wildtype","evidence_type":"Actionable","therapy":"PLX8394","efficacy_evidence":"In a clinical case study, PLX8394 treatment resulted in a radiographic partial response and complete resolution of symptoms for 7 months in a patient with glioblastoma harboring BRAF V600E, CDKN2A/B loss and CHEK2 T367fs were also identified in the tumor (%%PUBMED:32923904%%; NCT02428712).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[33537843],"normalized_drug":"Dabrafenib, Trametinib","indication":"cholangiocarcinoma","therapy_id":1066,"normalized_cancer":"Cholangiocarcinoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, combination treatment with Tafinlar (dabrafenib) and Mekinist (trametinib) in a patient with metastatic cholangiocarcinoma harboring BRAF V600E who progressed on chemotherapy led to a sustained metabolic response for six months (%%PUBMED:33537843%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[33568355],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":11478,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + LXH 254 + Trametinib","efficacy_evidence":"In a preclinical study, combination treatment with LXH 254, Tafinlar (dabrafenib), and Mekinist (trametinib) in colorectal cancer cell lines harboring BRAF V600E resulted in suppression of colony formation in culture, and inhibition of tumor growth in a cell line xenograft model (%%PUBMED:33568355%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[26140595],"response_type":"predicted - sensitive","indication":"Advanced Solid Tumor","therapy_id":5443,"normalized_cancer":"All Solid Tumors","evidence_type":"Actionable","therapy":"PF-00477736 + PF3644022","efficacy_evidence":"In a preclinical study, Chk1 inhibitor PF-477736 and MK2 inhibitor PF3644022 synergistically inhibited growth of transformed cells over expressing BRAF V600E in culture, while single agent inhibition had no effect (%%PUBMED:26140595%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[22281684],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":6208,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + PLX4720","efficacy_evidence":"In a preclinical study, the combination of PLX4720 and Erbitux (cetuximab) inhibited tumor growth in colorectal cancer cell line xenograft models harboring BRAF V600E (%%PUBMED:22281684%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[21464044],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":1708,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Lapatinib + Panobinostat","efficacy_evidence":"In a preclinical study, Tykerb (lapatinib) and Faridak (panobinostat) worked synergistically to inhibit growth of BRAF V600E mutant colorectal cancer cells in culture (%%PUBMED:21464044%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"colon cancer","therapy_id":13709,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"ABM-1310 + Binimetinib","efficacy_evidence":"In a preclinical study, combination treatment with ABM-1310 and Mektovi (binimetinib) led to inhibition of tumor growth in a colon cancer cell line xenograft model harboring BRAF V600E (Cancer Res (2020) 80 (16_Supplement): 4038).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[27924459],"response_type":"sensitive","indication":"melanoma","therapy_id":5120,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Erlotinib + PLX4720","efficacy_evidence":"In a preclinical study, the combination of PLX4720 and Tarceva (erlotinib) resulted in antitumor efficacy in a melanoma cell line harboring BRAF V600E, demonstrating decreased cell survival and increased apoptotic activity in xenograft models and culture (%%PUBMED:27924459%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[32182156],"normalized_drug":"Lifirafenib","indication":"ovarian serous carcinoma","therapy_id":4025,"normalized_cancer":"Serous Ovarian Cancer","evidence_type":"Actionable","therapy":"Lifirafenib","efficacy_evidence":"In a Phase I trial, Lifirafenib (BGB-283) treatment demonstrated safety and resulted in partial response (PR) in 15.1% (8/53) of advanced solid tumor patients harboring a BRAF mutation, including 1 patient with BRAF V600E-mutant low-grade serous ovarian cancer (%%PUBMED:32182156%%; NCT02610361).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[37643378],"normalized_drug":"Dabrafenib, Trametinib","indication":"high grade glioma","therapy_id":1066,"normalized_cancer":"High-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a Phase II trial, Tafinlar (dabrafenib) and Mekinist (trametinib) combination treatment resulted in an overall response rate of 56.1% (23/41; 12 complete, 11 partial responses), a clinical benefit rate of 65.9% (27/41), median duration of response of 22.2 months, median progression-free survival of 9.0 months, and median overall survival of 32.8 months in pediatric patients with relapsed or refractory high-grade glioma harboring BRAF V600E (%%PUBMED:37643378%%; NCT02684058).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"high grade glioma","therapy_id":1066,"normalized_cancer":"High-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Tafinlar (dabrafenib) in combination with Mekinist (trametinib) is included in guidelines as adjuvant therapy for pediatric patients with diffuse high-grade gliomas harboring BRAF V600E, or as a preferred regimen for patients with recurrent or progressive disease (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[34838156],"normalized_drug":"Dabrafenib, Trametinib","indication":"high grade glioma","therapy_id":1066,"normalized_cancer":"High-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a Phase II trial (ROAR), Tafinlar (dabrafenib) and Mekinist (trametinib) combination treatment resulted in an objective response rate of 33% (15/45, 3 complete responses, 12 partial responses) in patients with high-grade glioma harboring BRAF V600E, with a median duration of response of 36.9 months, a median progression-free survival of 3.8 months, and an overall survival of 17.6 months (%%PUBMED:34838156%%; NCT02034110).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[39399174],"normalized_drug":"Dabrafenib, Trametinib","indication":"high grade glioma","therapy_id":1066,"normalized_cancer":"High-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, treatment with the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) resulted in a partial response in a pediatric patient with posterior fossa high grade glioma harboring BRAF V600E and deletion of CDKN2A (%%PUBMED:39399174%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[38096472],"normalized_drug":"Cobimetinib, Vemurafenib","indication":"colon neuroendocrine neoplasm","therapy_id":1657,"normalized_cancer":"Gastrointestinal Neuroendocrine Tumors","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"In a Phase II trial (TAPUR), Zelboraf (vemurafenib) and Cotellic (cobimetinib) combination therapy resulted in a partial response in a patient with neuroendocrine carcinoma of the colon harboring BRAF V600E (%%PUBMED:38096472%%; NCT02693535).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[29573941],"normalized_drug":"Binimetinib, Encorafenib","indication":"melanoma","therapy_id":1100,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Binimetinib + Encorafenib","efficacy_evidence":"In a Phase III (COLUMBUS) trial that supported FDA approval, Braftovi (encorafenib) in combination with Mektovi (binimetinib) demonstrated improved tolerability profile and efficacy, resulted in a progression-free survival of 14.9 months in patients with advanced melanoma harboring BRAF V600E/K mutations, comparing to 7.3 months in the Zelboraf (vemurafenib) group (HR=0.54, p<0.0001) (%%PUBMED:29573941%%; NCT01909453), and both BRAF V600E and V600K are on the companion diagnostic.","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"FDA approved - On Companion Diagnostic","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[30219628],"normalized_drug":"Binimetinib, Encorafenib","indication":"melanoma","therapy_id":1100,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Binimetinib + Encorafenib","efficacy_evidence":"In a Phase III (COLUMBUS) trial that supported FDA approval, Braftovi (encorafenib) in combination with Mektovi (binimetinib) resulted in a median overall survival (OS) of 33.6 months, a 1-year OS rate of 77.5%, and a 2-year OS rate of 57.7% in patients with advanced melanoma harboring BRAF V600E/K mutations compared to a median OS of 16.9 months and 1- and 2-year OS rates of 63.1% and 43.2%, respectively, in the Zelboraf (vemurafenib) treated group (%%PUBMED:30219628%%; NCT01909453).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"FDA approved - On Companion Diagnostic","amp_tier":"I"},{"pub_med_references":[29431699],"response_type":"no benefit","indication":"colorectal cancer","therapy_id":1991,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Panitumumab + Trametinib","efficacy_evidence":"In a Phase I trial, combination therapy consisting of Vectibix (panitumumab) and Mekinist (trametinib) resulted in an overall response rate of 0% (0/31), stable disease in 55% (17/31), and a median progression-free survival of 2.6 months in patients with BRAF V600E colorectal cancer (%%PUBMED:29431699%%; NCT01750918).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase I","amp_tier":"II"},{"pub_med_references":[26461489],"response_type":"sensitive","indication":"melanoma","therapy_id":1061,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"PLX4720 + Selumetinib","efficacy_evidence":"In a preclinical study, PLX4720 and Koselugo (selumetinib) worked synergistically to inhibit cell growth in PLX4720-resistant melanoma cell lines harboring BRAF V600E in culture (%%PUBMED:26461489%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[31151904],"normalized_drug":"Selumetinib","indication":"childhood pilocytic astrocytoma","therapy_id":913,"normalized_cancer":"Pilocytic Astrocytoma","evidence_type":"Actionable","therapy":"Selumetinib","efficacy_evidence":"In a Phase I trial, Koselugo (selumetinib) treatment resulted in a sustained partial response (PR) in 36% (9/25) and stable disease in 36% (9/25) of pediatric patients with pilocytic astrocytoma harboring KIAA1549-BRAF (n=18) or BRAF V600E (n=7), with a 2-year progression-free survival of 70%, and 29% (2/7) of the patients harboring BRAF V600E achieved PR (%%PUBMED:31151904%%; NCT01089101).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase I","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[22663011],"normalized_drug":"Trametinib","indication":"melanoma","therapy_id":2,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Trametinib","efficacy_evidence":"In a Phase III trial (METRIC) that supported FDA approval, Mekinist (trametinib) treatment, as compared to Deticine (dacarbazine) or Taxol (paclitaxel) treatment, resulted in improved progression-free survival of 4.8 months versus 1.5 months and an overall six month survival rate of 81% versus 67% in patients with BRAF V600E/K-positive metastatic melanoma (%%PUBMED:22663011%%; NCT01245062).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"FDA approved - On Companion Diagnostic","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[36608320],"normalized_drug":"Binimetinib, Encorafenib","indication":"multiple myeloma","therapy_id":1100,"normalized_cancer":"Plasma Cell Myeloma","evidence_type":"Actionable","therapy":"Binimetinib + Encorafenib","efficacy_evidence":"In a Phase II trial (BIRMA), Mektovi (binimetinib) plus Braftovi (encorafenib) treatment demonstrated safety and efficacy in relapsed/refractory multiple myeloma patients with BRAF V600E, with an overall response rate of 83% (10/12, 1 complete response (CR), 2 near-CR, 6 very good partial responses (PR), and 1 PR), a median duration of response of 4.8 mo, a median progression-free survival of 5.6 mo, and a median overall survival not reached but 66% at 12 mo and 55% at 24 mo (%%PUBMED:36608320%%; NCT02834364).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"pub_med_references":[38728872],"response_type":"sensitive","indication":"papillary thyroid carcinoma","therapy_id":2149,"normalized_cancer":"Papillary Thyroid Cancer","evidence_type":"Actionable","therapy":"Ravoxertinib","efficacy_evidence":"In a preclinical study, Ravoxertinib (GDC-0994) inhibited viability and colony formation in papillary thyroid carcinoma cell lines harboring BRAF V600E in culture (%%PUBMED:38728872%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[26637369],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":4083,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"DT01 + Fluorouracil + Oxaliplatin","efficacy_evidence":"In a preclinical study, DT01 increased sensitivity of human colorectal cancer (CRC) cells harboring BRAF V600E to Eloxatin (oxaliplatin) and Adrucil (5-fluorouracil), and the combination resulted in decreased liver tumor growth in CRC cell line xenograft metastasis models (%%PUBMED:26637369%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[18519791],"response_type":"sensitive","indication":"melanoma","therapy_id":10820,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"C6-ceramide nanoliposome + Sorafenib","efficacy_evidence":"In a preclinical study, Nexavar (sorafenib) treatment in combination with C6-ceramide nanoliposome inhibited Mek and Akt phosphorylation, led to enhanced apoptosis and inhibition of proliferation, and synergistically reduced viability of melanoma cells harboring BRAF V600E in culture, and enhanced inhibition of tumor growth in a cell line xenograft model (%%PUBMED:18519791%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[36759733],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":15048,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Celecoxib + Encorafenib + Panitumumab","efficacy_evidence":"In a preclinical study, the addition of Celecoxib to the combination of Braftovi (encorafenib) and Vectibix (panitumumab) inhibited tumor growth and induced tumor regression in colorectal cancer patient-derived xenograft (PDX) models harboring BRAF V600E to a greater degree than the combination of Braftovi (encorafenib) and Vectibix (panitumumab) (%%PUBMED:36759733%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[38096472],"normalized_drug":"Cobimetinib, Vemurafenib","indication":"ovarian cancer","therapy_id":1657,"normalized_cancer":"Ovarian Cancer","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"In a Phase II trial (TAPUR), Zelboraf (vemurafenib) and Cotellic (cobimetinib) combination therapy resulted in one complete response lasting 5 weeks, 2 partial responses, and 1 with stable disease lasting more than 16 weeks out of 6 patients with advanced ovarian cancer harboring BRAF V600E (%%PUBMED:38096472%%; NCT02693535).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[27222538],"response_type":"sensitive","indication":"thyroid cancer","therapy_id":4599,"normalized_cancer":"Thyroid Cancer","evidence_type":"Actionable","therapy":"Dasatinib + Trametinib","efficacy_evidence":"In a preclinical study, Sprycel (dasatinib) and Mekinist (trametinib) synergistically inhibited proliferation and induced apoptosis in both parental thyroid cancer cell lines harboring BRAF V600E and those acquired Sprycel (dasatinib)-resistance in culture (%%PUBMED:27222538%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Vemurafenib","indication":"follicular thyroid carcinoma","therapy_id":342,"normalized_cancer":"Follicular Thyroid Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"Zelboraf (vemurafenib) is included in guidelines for patients with recurrent, advanced, or metastatic thyroid follicular carcinoma harboring BRAF V600E for whom clinical trials are not available or appropriate (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"decreased response","pub_med_references":[30630828],"normalized_drug":"Nivolumab","indication":"melanoma","therapy_id":1312,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Nivolumab","efficacy_evidence":"In a retrospective analysis, patients with melanoma harboring BRAF V600E (n=84) had decreased response rates (29% vs. 53%, p=0.059), progression-free survival (2.7 vs. 19 months, p=0.049), and overall survival (11.7 vs. 20.4 months, p=0.081) relative to patients with BRAF V600K (n=19) when treated with Keytruda (pembrolizumab) (n=62 and 17 for BRAF V600E and V600K, respectively) or Opdivo (nivolumab) (n=22 and 2 for BRAF V600E and V600K, respectively) (%%PUBMED:30630828%%).","cap_asco_evidence_level":"NA","molecular_profile":"BRAF V600E","approval_status":"Clinical Study - Cohort","amp_tier":"NA"},{"response_type":"sensitive","pub_med_references":[19018267],"normalized_drug":"Ci-1040","indication":"ovarian cancer","therapy_id":699,"normalized_cancer":"Ovarian Cancer","evidence_type":"Actionable","therapy":"CI-1040","efficacy_evidence":"In a preclinical study, CI-1040 inhibited growth of a human ovarian cancer cell line harboring BRAF V600E in culture, and inhibited tumor growth in xenograft models (%%PUBMED:19018267%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[32238401],"normalized_drug":"Dabrafenib, Trametinib","indication":"epithelial predominant Wilms' tumor","therapy_id":1066,"normalized_cancer":"Wilms' Tumor","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, Tafinlar (dabrafenib) and Mekinist (trametinib) combination therapy resulted in a complete radiographic response 4 months after treatment initiation that was maintained for at least 12 months in a pediatric patient with metastatic epithelial-predominant Wilms tumor harboring BRAF V600E (%%PUBMED:32238401%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Cobimetinib, Vemurafenib","indication":"pilocytic astrocytoma","therapy_id":1657,"normalized_cancer":"Pilocytic Astrocytoma","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"Zelboraf (vemurafenib) and Cotellic (cobimetinib) combination therapy is included in guidelines as an adjuvant treatment for patients with pilocytic astrocytoma harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"predicted - sensitive","pub_med_references":[29880583],"normalized_drug":"Dabrafenib","indication":"ganglioglioma","therapy_id":3,"normalized_cancer":"Ganglioglioma","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a clinical case study, Tafinlar (dabrafenib) treatment resulted in partial response 8 weeks after therapy initiation in a pediatric patient with anaplastic ganglioglioma harboring BRAF V600E, but disease progression occurred at 40 weeks due to acquired resistance (%%PUBMED:29880583%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[31502039],"normalized_drug":"Dabrafenib","indication":"ganglioglioma","therapy_id":3,"normalized_cancer":"Ganglioglioma","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a clinical study, Tafinlar (dabrafenib) treatment resulted in symptomatic improvement and clinical efficacy in three pediatric patients with brainstem ganglioglioma harboring BRAF V600E, with decreased tumor volume and treatment continuing for at least 5.5 years in one patient, a significant partial response in another patient, and a partial response in a third patient with tumor regression and ongoing response for at least 2 years (%%PUBMED:31502039%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[39399174],"normalized_drug":"Dabrafenib","indication":"ganglioglioma","therapy_id":3,"normalized_cancer":"Ganglioglioma","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a clinical case study, Tafinlar (dabrafenib) treatment resulted in a partial response in two pediatric patients with ganglioglioma (1 suprasellar ganglioglioma, 1 cervicomedullary ganglioglioma) harboring BRAF V600E (%%PUBMED:39399174%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[34433654],"response_type":"no benefit","indication":"high grade glioma","therapy_id":1728,"normalized_cancer":"High-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"ZM336372","efficacy_evidence":"In a preclinical study, ZM336372 treatment did not lead to inhibition of cell growth in a patient-derived glioma cell line harboring BRAF V600E in culture (%%PUBMED:34433654%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Patient cell culture","amp_tier":"II"},{"response_type":"no benefit","indication":"melanoma","therapy_id":10333,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Cobimetinib + Pembrolizumab + Vemurafenib","efficacy_evidence":"In a Phase I trial, combination of Cotellic (cobimetinib), Zelboraf (vemurafenib), and Keytruda (pembrolizumab) resulted in unreached median progression-free survival and overall survival in patients with advanced melanoma harboring BRAF V600E or V600K mutations, however, the trial was closed due to high incidence of dose-limiting toxicity and decreased health utility at 1 year (J Clin Oncol 39, no. 15_suppl, abstract e21506; NCT02818023).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase I","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[32029534],"normalized_drug":"Vemurafenib","indication":"Advanced Solid Tumor","therapy_id":342,"normalized_cancer":"All Solid Tumors","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase II trial (VE-BASKET), Zelboraf (vemurafenib) treatment resulted in an objective response rate of 33% (56/172) in patients with advanced solid tumors harboring BRAF V600E, including 5 patients with a complete response and 51 patients with a partial response, and led a duration of response of 13.1 months, a progression-free survival of 5.8 months, and an overall survival of 17.6 months (%%PUBMED:32029534%%; NCT01524978).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Vemurafenib","indication":"Advanced Solid Tumor","therapy_id":342,"normalized_cancer":"All Solid Tumors","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase II trial (MyPathway), Zelboraf (vemurafenib) treatment resulted in an objective response of 46% (12/26, 2 complete response, 10 partial response) in patients with advanced solid tumors harboring BRAF V600E, but only 4% (1/23, 1 partial response) in patients harboring non-V600 BRAF mutations (%%PUBMED:29320312%%; NCT02091141).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"pub_med_references":[31618628],"response_type":"sensitive","indication":"melanoma","therapy_id":1034,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Tovorafenib","efficacy_evidence":"In a preclinical study, Ojemda (tovorafenib) treatment inhibited viability of a melanoma cell line harboring BRAF V600E in culture (%%PUBMED:31618628%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[35382161],"normalized_drug":"Cobimetinib, Vemurafenib","indication":"pancreatic ductal adenocarcinoma","therapy_id":1657,"normalized_cancer":"Pancreatic Adenocarcinoma","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"In a clinical case study, combination treatment with Cotellic (cobimetinib) and Zelboraf (vemurafenib) led to a partial response after 1 month of treatment in a microsatellite stable pancreatic ductal adenocarcinoma patient with BRAF V600E and amplification of FGFR1 and NOTCH2, with significant decrease in hepatic metastatic lesions and undetectable lung lesions at 6 months, and a progression-free survival of at least 6 months (%%PUBMED:35382161%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"colorectal cancer","therapy_id":18577,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"RG6344","efficacy_evidence":"In a Phase I trial, RG6344 treatment was well tolerated and demonstrated preliminary activity in patients with advanced solid tumors harboring BRAF V600E (n=64), including melanoma (n=11) and colorectal cancer (n=51), with an objective response rate of 25% (Cancer Res (2025) 85 (8_Supplement_2): CT017).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase I","amp_tier":"II"},{"pub_med_references":[35145907],"response_type":"predicted - sensitive","indication":"pancreatic ductal adenocarcinoma","therapy_id":4234,"normalized_cancer":"Pancreatic Adenocarcinoma","evidence_type":"Actionable","therapy":"Trametinib + Vemurafenib","efficacy_evidence":"In a clinical case study, Zelboraf (vemurafenib) and Mekinist (trametinib) combination treatment resulted in decreased tumor markers in a patient with pancreatic ductal adenocarcinoma harboring BRAF V600E, as well as a germline ATM mutation, and the patient received 13 months of combination therapy and was followed for 24 months (%%PUBMED:35145907%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[28611205],"response_type":"predicted - sensitive","indication":"colorectal cancer","therapy_id":6337,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"LSN3074753","efficacy_evidence":"In a preclinical study, LSN3074753 demonstrated modest efficacy in patient-derived xenograft models of colorectal cancer harboring BRAF V600E, resulted in tumor growth inhibition or regression, but relapse upon discontinuation of treatment (%%PUBMED:28611205%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[32758030],"normalized_drug":"Trametinib","indication":"peritoneal serous papillary adenocarcinoma","therapy_id":2,"normalized_cancer":"Peritoneal Serous Carcinoma","evidence_type":"Actionable","therapy":"Trametinib","efficacy_evidence":"In a Phase II trial (NCI-MATCH), Mekinist (trametinib) treatment resulted in an objective response rate of 37.9% (11/29) in patients with advanced solid tumors harboring BRAF V600E, 1 patient with mucinous-papillary serous adenocarcinoma of the peritoneum achieved a partial response (%%PUBMED:32758030%%; NCT02465060).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[26466569],"response_type":"sensitive","indication":"melanoma","therapy_id":4606,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"PLX7904","efficacy_evidence":"In a preclinical study, PLX7904 inhibited survival of melanoma cell lines harboring monomeric BRAF V600E as well as cells harboring the Zelboraf (vemurafenib)-resistant dimeric BRAF V600E in culture (%%PUBMED:26466569%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Cobimetinib, Vemurafenib","indication":"ganglioglioma","therapy_id":1657,"normalized_cancer":"Ganglioglioma","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"Zelboraf (vemurafenib) and Cotellic (cobimetinib) combination therapy is included in guidelines as an adjuvant treatment for patients with ganglioglioma harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"predicted - sensitive","indication":"melanoma","therapy_id":11379,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"PF-07284890","efficacy_evidence":"In a preclinical study, PF-07284890 treatment led to inhibition of tumor growth, tumor regression, and survival benefit in an intracranial model, and tumor growth inhibition in a subcutaneous cell line xenograft model of melanoma harboring BRAF V600E (Cancer Res 2021;81(13_Suppl):Abstract nr 1473).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[26918217],"normalized_drug":"Vemurafenib","indication":"renal cell carcinoma","therapy_id":342,"normalized_cancer":"Renal Cell Carcinoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a clinical case study, a patient with metastatic renal cell carcinoma harboring BRAF V600E demonstrated a partial response following treatment with Zelboraf (vemurafenib) (%%PUBMED:26918217%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"gastrointestinal stromal tumor","therapy_id":1066,"normalized_cancer":"Gastrointestinal Stromal Tumor","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Tafinlar (dabrafenib) in combination with Mekinist (trametinib) is included in guidelines as neoadjuvant therapy for patients with resectable disease and as first-line systemic therapy for patients with unresectable or metastatic gastrointestinal stromal tumor (GIST) harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[37040395],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":11093,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Encorafenib + Fluorouracil + Irinotecan + Leucovorin","efficacy_evidence":"In a preclinical study, treatment with the combination of Erbitux (cetuximab), Braftovi (encorafenib), and FOLFIRI resulted in increased tumor growth inhibition and tumor regression compared to Erbitux (cetuximab) plus Braftovi (encorafenib) or FOLFIRI alone in patient-derived xenograft (PDX) models of colorectal cancer harboring BRAF V600E and increased survival and tumor growth inhibition in cell line xenograft models (%%PUBMED:37040395%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"pub_med_references":[38691346],"response_type":"predicted - sensitive","indication":"melanoma","therapy_id":13603,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Binimetinib + PF-07799933","efficacy_evidence":"In a Phase I trial, treatment with the combination of PF-07799933 and Mektovi (binimetinib) resulted in a partial response in 2 patients with melanoma harboring BRAF V600E and stable disease in 1 patient (%%PUBMED:38691346%%; NCT05355701).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[31158244],"normalized_drug":"Vemurafenib","indication":"pancreatic endocrine carcinoma","therapy_id":342,"normalized_cancer":"Pancreatic Neuroendocrine Carcinoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a clinical case study, a patient with pancreatic endocrine carcinoma found to harbor BRAF V600E demonstrated stable disease and some tumor shrinkage when treated with Zelboraf (vemurafenib) (%%PUBMED:31158244%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[32234759],"response_type":"sensitive","indication":"melanoma","therapy_id":12556,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"KRT-232 + Navitoclax","efficacy_evidence":"In a preclinical study, the combination of KRT-232 (AMG 232) and Navitoclax (ABT-263) resulted in a greater response than either drug alone in patient-derived xenograft (PDX) models of melanoma harboring BRAF V600E, leading to tumor regression (%%PUBMED:32234759%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[38885476],"normalized_drug":"Binimetinib, Encorafenib","indication":"malignant fibrous histiocytoma","therapy_id":1100,"normalized_cancer":"Undifferentiated Pleomorphic Sarcoma/Malignant Fibrous Histiocytoma/High-Grade Spindle Cell Sarcoma","evidence_type":"Actionable","therapy":"Binimetinib + Encorafenib","efficacy_evidence":"In a clinical case study, treatment with the combination of Mektovi (binimetinib) and Braftovi (encorafenib) resulted in a clinical response after two months in a patient with angiomatoid fibrous histiocytoma harboring BRAF V600E, along with EWSR1-CREB1 (e7:e7), and in a preclinical study, combination treatment with Mektovi (binimetinib) and Braftovi (encorafenib) inhibited viability of cells in culture (%%PUBMED:38885476%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[29701552],"normalized_drug":"Dabrafenib","indication":"papillary craniopharyngioma","therapy_id":3,"normalized_cancer":"Craniopharyngioma, Papillary Type","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a clinical case study, Tafinlar (dabrafenib) treatment resulted in decreased size of the cystic and solid enhancing components of the tumor in a patient with papillary craniopharyngioma harboring BRAF V600E, with stable disease continuing 1 year after discontinuation of treatment (%%PUBMED:29701552%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[31666933],"normalized_drug":"Dabrafenib","indication":"papillary craniopharyngioma","therapy_id":3,"normalized_cancer":"Craniopharyngioma, Papillary Type","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a clinical case study, Tafinlar (dabrafenib) treatment resulted in a complete response of the solid internal nodular enhancement and symptom improvement in a patient with papillary craniopharyngioma harboring BRAF V600E (%%PUBMED:31666933%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[26603897],"response_type":"sensitive","indication":"melanoma","therapy_id":3309,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"SBI-755199","efficacy_evidence":"In a preclinical study, SBI-755199 induced cell death in human melanoma cell lines harboring BRAF V600E in culture (%%PUBMED:26603897%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[28984141],"normalized_drug":"Dabrafenib, Trametinib","indication":"anaplastic pleomorphic xanthoastrocytoma","therapy_id":1066,"normalized_cancer":"Anaplastic Pleomorphic Xanthoastrocytoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, Mekinist (trametinib) and Tafinlar (dabrafenib) combination treatment resulted in an ongoing partial response 8 months after initiation of treatment in a patient with anaplastic pleomorphic xanthoastrocytoma harboring BRAF V600E, and a near complete response after 3 months of treatment in another patient with relapsed disease (%%PUBMED:28984141%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"colorectal cancer","therapy_id":10114,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + JSI-1187","efficacy_evidence":"In a preclinical study, combination treatment with Tafinlar (dabrafenib) and JSI-1187 led to synergistic inhibition of tumor growth in a colorectal cancer cell line xenograft model harboring BRAF V600E (Cancer Res 2020;80(16 Suppl):Abstract nr 4188).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[34330842],"response_type":"sensitive","indication":"melanoma","therapy_id":12570,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"ASTX029 + Vemurafenib","efficacy_evidence":"In a preclinical study, combination treatment with ASTX029 and Zelboraf (vemurafenib) resulted in decreased viability of melanoma cells harboring BRAF V600E compared to either agent alone in culture (%%PUBMED:34330842%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[27488531],"response_type":"sensitive","indication":"melanoma","therapy_id":1823,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Mirdametinib + Palbociclib","efficacy_evidence":"In a preclinical study, the combination treatment of Gomekli (mirdametinib) and Ibrance (palbociclib) resulted in significant tumor regression in melanoma cell line xenograft models harboring BRAF V600E and demonstrated a 56% (5/9) complete response rate (%%PUBMED:27488531%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[33229459],"response_type":"no benefit","indication":"skin melanoma","therapy_id":11309,"normalized_cancer":"Cutaneous Melanoma","evidence_type":"Actionable","therapy":"Trametinib + YM-254890","efficacy_evidence":"In a preclinical study, combination treatment with YM-254890 and Mekinist (trametinib) did not result in synergistic inhibition of cell viability of a cutaneous melanoma cell line harboring BRAF V600E in culture (%%PUBMED:33229459%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Cobimetinib, Vemurafenib","indication":"skin melanoma","therapy_id":1657,"normalized_cancer":"Cutaneous Melanoma","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"Zelboraf (vemurafenib) and Cotellic (cobimetinib) combination therapy is included in cutaneous melanoma guidelines for patients with metastatic or unresectable disease harboring a BRAF V600 activating mutation (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"predicted - sensitive","indication":"melanoma","therapy_id":13736,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"IMM-1-104","efficacy_evidence":"In a preclinical study, IMM-1-104 treatment led to tumor growth inhibition in a cell line xenograft model of melanoma harboring BRAF V600E (Mol Cancer Ther 2021;20(12 Suppl):Abstract nr P252).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[39121480],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":17844,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Encorafenib + Tazemetostat","efficacy_evidence":"In a preclinical study, the addition of Tazverik (tazemetostat) sensitized a colorectal cancer cell line harboring BRAF V600E to Braftovi (encorafenib) treatment in culture, resulting in decreased cell proliferation (%%PUBMED:39121480%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Cobimetinib, Vemurafenib","indication":"pleomorphic xanthoastrocytoma","therapy_id":1657,"normalized_cancer":"Pleomorphic Xanthoastrocytoma","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"Zelboraf (vemurafenib) and Cotellic (cobimetinib) combination therapy is included in guidelines as an adjuvant treatment for patients with pleomorphic xanthoastrocytoma harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[22180495],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":10745,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Capecitabine + Vemurafenib","efficacy_evidence":"In a preclinical study, Zelboraf (vemurafenib) treatment in combination with Xeloda (capecitabine) enhanced tumor growth inhibition and increased survival in a cell line xenograft model of colorectal cancer harboring BRAF V600E (%%PUBMED:22180495%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[37164118],"response_type":"sensitive","indication":"melanoma","therapy_id":15389,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"IHMT-RAF-128","efficacy_evidence":"In a preclinical study, IHMT-RAF-128 inhibited proliferation and induced cell cycle arrest and apoptosis in melanoma cell lines harboring BRAF V600E in culture and inhibited tumor growth in a cell line xenograft model (%%PUBMED:37164118%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[21325073,24042735],"normalized_drug":"Gedatolisib","indication":"colon cancer","therapy_id":1040,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Gedatolisib","efficacy_evidence":"In a preclinical study, Gedatolisib (PKI-587) inhibited Braf V600E in vitro and inhibited growth of human colon cancer cells harboring BRAF V600E in culture (%%PUBMED:21325073%%, %%PUBMED:24042735%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[33537843],"normalized_drug":"Dabrafenib, Trametinib","indication":"pancreatic acinar cell adenocarcinoma","therapy_id":1066,"normalized_cancer":"Acinar Cell Carcinoma of the Pancreas","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, combination treatment with Tafinlar (dabrafenib) and Mekinist (trametinib) in a patient with pancreatic acinar cell carcinoma harboring BRAF V600E who had previously progressed on chemotherapy led to a response at 8 weeks, and ongoing clinical and radiological response was still observed at 32 months of treatment (%%PUBMED:33537843%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[32843432],"normalized_drug":"Dabrafenib, Trametinib","indication":"pancreatic acinar cell adenocarcinoma","therapy_id":1066,"normalized_cancer":"Acinar Cell Carcinoma of the Pancreas","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) resulted in near complete remission allowing for debulking surgery and disease control for 12 months in a patient with metastatic pancreatic acinar cell carcinoma harboring BRAF V600E, along with germline PALB2 R414* (%%PUBMED:32843432%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"ganglioglioma","therapy_id":1066,"normalized_cancer":"Ganglioglioma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Combination of Mekinist (trametinib) and Tafinlar (dabrafenib) is included in guidelines as an adjuvant treatment for patients with ganglioglioma harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[38446982],"normalized_drug":"Binimetinib, Encorafenib","indication":"high grade glioma","therapy_id":1100,"normalized_cancer":"High-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"Binimetinib + Encorafenib","efficacy_evidence":"In a Phase II trial, treatment with the combination of Mektovi (binimetinib) and Braftovi (encorafenib) demonstrated safety and activity in patients with high grade glioma harboring BRAF V600E, resulting in a radiographic response rate of 60% (3/5, 1 complete and 2 partial responses), with stable disease in 1 patient, a median duration of response of 10 months, a median progression-free survival of 9.4 months, and a median overall survival of 14.6 months (%%PUBMED:38446982%%; NCT03973918).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"not predictive","pub_med_references":[29723688],"normalized_drug":"Nivolumab","indication":"lung non-small cell carcinoma","therapy_id":1312,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Nivolumab","efficacy_evidence":"In a retrospective analysis, non-small cell lung cancer patients harboring BRAF V600E did not demonstrate a significantly different response to treatment with either Keytruda (pembrolizumab), Opdivo (nivolumab), or Tecentriq (atezolizumab), compared to patients with BRAF non-V600E mutations, demonstrating an objective response rate of 25% (3/12) vs 33% (3/9) (p=1.0) and median progression-free survival of 3.7 months vs 4.1 months (p=0.37) (%%PUBMED:29723688%%).","cap_asco_evidence_level":"NA","molecular_profile":"BRAF V600E","approval_status":"Clinical Study - Cohort","amp_tier":"NA"},{"pub_med_references":[22319199],"response_type":"sensitive","indication":"colon carcinoma","therapy_id":1002,"normalized_cancer":"Bowel Cancer","evidence_type":"Actionable","therapy":"RXDX-105","efficacy_evidence":"In preclinical studies, CEP-32496 (RXDX-105) reduced tumor volume and promoted tumor regression in xenograft models of a BRAF V600E mutant human colon carcinoma cell line (%%PUBMED:22319199%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[36157689],"normalized_drug":"Dabrafenib, Trametinib","indication":"spermatic cord cancer","therapy_id":1066,"normalized_cancer":"Soft Tissue Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, treatment with the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) resulted in a regression of the lung metastasis and progression-free survival of 6.5 months in a patient with undifferentiated sarcoma of the spermatic cord harboring BRAF V600E (%%PUBMED:36157689%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"small intestine adenocarcinoma","therapy_id":1066,"normalized_cancer":"Small Intestinal Carcinoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Tafinlar (dabrafenib) in combination with Mekinist (trametinib) is included in guidelines for patients with advanced or metastatic small bowel adenocarcinoma harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[37733309],"normalized_drug":"Dabrafenib, Trametinib","indication":"low grade glioma","therapy_id":1066,"normalized_cancer":"Low-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a Phase II trial that supported FDA approval, Mekinist (trametinib) plus Tafinlar (dabrafenib) significantly improved overall response rate (47% vs 11%, risk ratio 4.31, p<0.001), clinical benefit rate (86% vs 46%), median progression-free survival (PFS, 20.1 vs 7.4 months, p<0.001, HR 0.31), and 12-month PFS rate (67% vs 26%) compared to standard chemotherapy in pediatric patients of 1 year and older with low-grade glioma harboring BRAF V600E (%%PUBMED:37733309%%; NCT02684058).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"FDA approved","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[34838156],"normalized_drug":"Dabrafenib, Trametinib","indication":"low grade glioma","therapy_id":1066,"normalized_cancer":"Low-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a Phase II trial (ROAR), Tafinlar (dabrafenib) and Mekinist (trametinib) combination treatment resulted in an objective response rate of 69% (9/13, 1 complete response, 6 partial responses, 2 minor responses) in patients with low-grade glioma harboring BRAF V600E, with median duration of response, median progression-free survival, and overall survival time unreached (%%PUBMED:34838156%%; NCT02034110).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"low grade glioma","therapy_id":1066,"normalized_cancer":"Low-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Combination of Mekinist (trametinib) and Tafinlar (dabrafenib) is included in guidelines for patients with recurrent or progressive low grade glioma harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"low grade glioma","therapy_id":1066,"normalized_cancer":"Low-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a Phase I/II trial (Study X2101), Tafinlar (dabrafenib) and Mekinist (trametinib) combination treatment demonstrated manageable toxicity and resulted in an objective response rate of 25% (9/36, 1 complete response, 8 partial responses) and stable disease in 67% (24/36) of pediatric patients with pretreated low-grade glioma harboring BRAF V600E (J Clin Oncol 38, no. 15_suppl (May 20, 2020) 10506; NCT02124772).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase Ib/II","amp_tier":"II"},{"pub_med_references":[25665005],"response_type":"sensitive","indication":"lung non-small cell carcinoma","therapy_id":3530,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Navitoclax + Vemurafenib","efficacy_evidence":"In a preclinical study, Navitoclax (ABT-263) enhanced the inhibitory effect of Zelboraf (vemurafenib) on human non-small cell lung cancer cells harboring BRAF V600E in culture (%%PUBMED:25665005%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"low grade glioma","therapy_id":14102,"normalized_cancer":"Low-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"FCN-159","efficacy_evidence":"In a Phase II trial, FCN-159 treatment was well tolerated and resulted in 6 partial responses, 9 minor responses, and 7 with stable disease in 22 pediatric patients with low-grade glioma harboring BRAF V600E (12/23), KIAA1549-BRAF (8/23), or NF1 mutations (3/23) (Ann Oncol (2023) 34 (suppl_2): S391-S392).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"pub_med_references":[18287029],"response_type":"sensitive","indication":"melanoma","therapy_id":1060,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"PLX4720","efficacy_evidence":"In a preclinical study, PLX4720 inhibited growth of melanoma cells harboring BRAF V600E in culture and in cell line xenograft models (%%PUBMED:18287029%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"pleomorphic xanthoastrocytoma","therapy_id":1066,"normalized_cancer":"Pleomorphic Xanthoastrocytoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Mekinist (trametinib) and Tafinlar (dabrafenib) combination therapy is included in guidelines as an adjuvant treatment for patients with pleomorphic xanthoastrocytoma harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[29632053],"normalized_drug":"Dabrafenib, Trametinib","indication":"pleomorphic xanthoastrocytoma","therapy_id":1066,"normalized_cancer":"Pleomorphic Xanthoastrocytoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, Mekinist (trametinib) and Tafinlar (dabrafenib) combination treatment resulted in clinical benefit that lasted for more than 14 months in a patient with pleomorphic xanthoastrocytoma harboring BRAF V600E (%%PUBMED:29632053%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[37729428],"response_type":"sensitive","indication":"melanoma","therapy_id":16204,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Encorafenib + Talazoparib","efficacy_evidence":"In a preclinical study, treatment with the combination of Talzenna (talazoparib) and Braftovi (encorafenib) synergistically inhibited viability of patient-derived melanoma spheroids harboring BRAF V600E in culture (%%PUBMED:37729428%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Patient cell culture","amp_tier":"II"},{"pub_med_references":[27312529],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":4525,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Dabrafenib","efficacy_evidence":"In a preclinical study, combination therapy consisting of Erbitux (cetuximab) and Tafinlar (dabrafenib) inhibited survival of colorectal cancer cell lines harboring BRAF V600E in culture (%%PUBMED:27312529%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[20538618],"normalized_drug":"Ci-1040","indication":"Advanced Solid Tumor","therapy_id":699,"normalized_cancer":"All Solid Tumors","evidence_type":"Actionable","therapy":"CI-1040","efficacy_evidence":"In a preclinical study, CI-1040 (PD184352) inhibited Erk phosphorylation and growth of transformed cells expressing BRAF V600E in culture (%%PUBMED:20538618%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[23629727],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":4656,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Everolimus + Pimasertib","efficacy_evidence":"In a preclinical study, Pimasertib (MSC1936369B) and Afinitor (everolimus) synergistically inhibited proliferation of colorectal cancer cells harboring BRAF V600E in culture (%%PUBMED:23629727%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[28351928],"response_type":"sensitive","indication":"melanoma","therapy_id":1260,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Encorafenib + Ribociclib","efficacy_evidence":"In a Phase Ib/II trial, Encorafenib (LGX818) and Kisqali (ribociclib) combination treatment resulted in confirmed partial response in 7.1% (2/28), unconfirmed partial response in 10.7% (3/28), and stable disease in 35.7% (10/28) of patients with melanoma harboring BRAF V600E (%%PUBMED:28351928%%).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase Ib/II","amp_tier":"II"},{"pub_med_references":[24398428],"response_type":"sensitive","indication":"melanoma","therapy_id":1684,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Ganetespib + TAK-733","efficacy_evidence":"In a preclinical study, treatment with the Hsp90 inhibitor Ganetespib in combination with the MEK1/2 inhibitor TAK-733 resulted in tumor regression in Zelboraf (vemurafenib)-resistant cell line xenograft models of melanoma harboring BRAF V600E (%%PUBMED:24398428%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[34433654],"response_type":"sensitive","indication":"high grade glioma","therapy_id":12676,"normalized_cancer":"High-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"LY3009120 + Vemurafenib","efficacy_evidence":"In a preclinical study, combination treatment with Zelboraf (vemurafenib) and LY3009120 treatment led to greater inhibition of cell growth compared to either agent alone in a patient-derived glioma cell line harboring BRAF V600E in culture (%%PUBMED:34433654%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Patient cell culture","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[22048237],"normalized_drug":"Selumetinib","indication":"melanoma","therapy_id":913,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Selumetinib","efficacy_evidence":"In a Phase II trial, a favorable response rate to Koselugo (selumetinib) was observed in mutant BRAF but not BRAF wild-type melanoma patients (%%PUBMED:22048237%%).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"pub_med_references":[32816843],"response_type":"predicted - resistant","indication":"melanoma","therapy_id":8871,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"BI-3406","efficacy_evidence":"In a preclinical study, BI-3406 treatment failed to inhibit growth of KRAS wild-type melanoma cells harboring BRAF V600E in culture and in cell line xenograft models (%%PUBMED:32816843%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[36759733],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":15043,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Celecoxib + Vemurafenib","efficacy_evidence":"In a preclinical study, the combination of Zelboraf (vemurafenib) and Celecoxib synergistically inhibited viability in colorectal cancer cell lines harboring BRAF V600E in culture (%%PUBMED:36759733%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Ulixertinib","indication":"glioblastoma","therapy_id":997,"normalized_cancer":"Glioblastoma, IDH-Wildtype","evidence_type":"Actionable","therapy":"Ulixertinib","efficacy_evidence":"In an expanded access program (ULI-EAP-100), Ulixertinib (BVD-523) treatment resulted in clinical benefit in a patient with glioblastoma harboring BRAF V600E who stayed on treatment for 128 days (J Clin Oncol 40, no. 16_suppl (June 01, 2022) e15101; NCT04566393).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[29247021],"normalized_drug":"Ulixertinib","indication":"glioblastoma","therapy_id":997,"normalized_cancer":"Glioblastoma, IDH-Wildtype","evidence_type":"Actionable","therapy":"Ulixertinib","efficacy_evidence":"In a Phase I trial, treatment with Ulixertinib (BVD-523) resulted in a partial response in a patient with glioblastoma harboring BRAF V600E (%%PUBMED:29247021%%; NCT01781429).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[38728872],"response_type":"sensitive","indication":"melanoma","therapy_id":16940,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Ravoxertinib + Vemurafenib","efficacy_evidence":"In a preclinical study, treatment with the combination of Ravoxertinib (GDC-0994) and Zelboraf (vemurafenib) resulted in additive effects, with decreased growth of a melanoma cell line harboring BRAF V600E in culture (%%PUBMED:38728872%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"anaplastic oligodendroglioma","therapy_id":1066,"normalized_cancer":"Oligodendroglioma, IDH-mutant, and 1p/19q-Codeleted","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Combination of Mekinist (trametinib) and Tafinlar (dabrafenib) is included in guidelines for patients with recurrent anaplastic gliomas harboring BRAF V600E, including anaplastic oligodendroglioma (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"oncocytic carcinoma of the thyroid","therapy_id":1066,"normalized_cancer":"Hurthle Cell Thyroid Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"The combination of Tafinlar (dabrafenib) and Mekinist (trametinib) is included in guidelines for patients with thyroid Hurthle cell carcinoma harboring BRAF V600E who have progressed on therapy and have no further treatment options (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[26768652],"response_type":"not applicable","indication":"colon adenocarcinoma","therapy_id":1776,"normalized_cancer":"Colon Adenocarcinoma","evidence_type":"Emerging","therapy":"N/A","efficacy_evidence":"In a post-hoc analysis of a Phase III trial, BRAF V600E mutations in colon adenocarcinoma patients with microsatellite stable tumors were associated with a shorter disease-free survival and overall survival compared to those patients with microsatellite instability tumors, suggesting that BRAF V600E may serve as a future prognostic biomarker in this patient population (%%PUBMED:26768652%%).","cap_asco_evidence_level":"NA","molecular_profile":"BRAF V600E","approval_status":"Phase III","amp_tier":"NA"},{"pub_med_references":[27523909],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":3300,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"TAK-632","efficacy_evidence":"In a preclinical study, TAK-632 inhibited proliferation of colorectal cancer cells harboring BRAF V600E in culture (%%PUBMED:27523909%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[27048951],"response_type":"sensitive","indication":"melanoma","therapy_id":4232,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"DETD-35 + Vemurafenib","efficacy_evidence":"In a preclinical study, DETD-35 and Zelboraf (vemurafenib) synergistically inhibited proliferation and colony formation of melanoma cells harboring BRAF V600E in culture and reduced tumor size in xenograft models (%%PUBMED:27048951%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Atezolizumab, Cobimetinib, Vemurafenib","indication":"skin melanoma","therapy_id":4825,"normalized_cancer":"Cutaneous Melanoma","evidence_type":"Actionable","therapy":"Atezolizumab + Cobimetinib + Vemurafenib","efficacy_evidence":"Zelboraf (vemurafenib) plus Cotellic (cobimetinib) in combination with an immune checkpoint inhibitor, such as Tecentriq (atezolizumab), is included in guidelines as second-line or subsequent therapy (category 2A) for patients with metastatic or unresectable cutaneous melanoma harboring a BRAF V600 mutation, such as BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[36759733],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":15045,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Celecoxib + Trametinib + Vemurafenib","efficacy_evidence":"In a preclinical study, the addition of Celecoxib to the combination of Zelboraf (vemurafenib) and Mekinist (trametinib) synergistically inhibited viability in colorectal cancer cell lines harboring BRAF V600E in culture (%%PUBMED:36759733%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[23242808],"response_type":"sensitive","indication":"melanoma","therapy_id":3131,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Gefitinib + PLX4720","efficacy_evidence":"In a preclinical study, Iressa (gefitinib) in combination with PLX4720 inhibited proliferation and tumorigenicity in human melanoma cell line harboring BRAF V600E and resistant to Braf inhibition in culture and in animal models (%%PUBMED:23242808%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[38565920],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":16824,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + IAG933","efficacy_evidence":"In a preclinical study, the combination of IAG933 and Tafinlar (dabrafenib) inhibited proliferation of colorectal cancer cell lines harboring BRAF V600E in culture (%%PUBMED:38565920%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[39399174],"normalized_drug":"Dabrafenib","indication":"pleomorphic xanthoastrocytoma","therapy_id":3,"normalized_cancer":"Pleomorphic Xanthoastrocytoma","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a clinical case study, Tafinlar (dabrafenib) treatment resulted in 1 partial response and 1 stable disease in 2 patients with tempero-parietal pleomorphic xanthoastrocytoma harboring BRAF V600E and CDKN2A deletion (%%PUBMED:39399174%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[26267534],"response_type":"sensitive","indication":"melanoma","therapy_id":3769,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"DEL-22379","efficacy_evidence":"In a preclinical study, DEL-22379 inhibited growth of melanoma cells harboring BRAF V600E with high levels of ERK dimerization in culture and inhibited tumor progression in melanoma xenograft models harboring BRAF V600E (%%PUBMED:26267534%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[32029534],"normalized_drug":"Vemurafenib","indication":"sarcoma","therapy_id":342,"normalized_cancer":"Sarcoma, NOS","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase II trial (VE-BASKET), responses were seen in sarcoma patients harboring BRAF V600E (n=6) when treated with Zelboraf (vemurafenib), including 1 patient with a complete response and 1 patient with a partial response (%%PUBMED:32029534%%; NCT01524978).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"resistant","normalized_drug":"Panitumumab","indication":"colon cancer","therapy_id":845,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Panitumumab","efficacy_evidence":"Vectibix (panitumumab), as a monotherapy, is not indicated for use in colon cancer patients with BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[37269335],"response_type":"predicted - sensitive","indication":"colorectal cancer","therapy_id":11417,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Encorafenib + PF-07284892","efficacy_evidence":"In a clinical case study, the combination of PF-07284892, Erbitux (cetuximab), and Braftovi (encorafenib) resulted in a 30% tumor reduction in a colorectal cancer patient harboring BRAF V600E, who remained on treatment for 6 months, and the combination inhibited tumor growth in a cell line xenograft model (%%PUBMED:37269335%%; NCT04800822).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"salivary gland cancer","therapy_id":1066,"normalized_cancer":"Salivary Gland Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Tafinlar (dabrafenib) and Mekinist (trametinib) combination therapy is included in guidelines (category 2A) for patients with recurrent, unresectable, or metastatic salivary gland tumors harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[21639808,28961848],"normalized_drug":"Vemurafenib","indication":"melanoma","therapy_id":342,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase III trial (BRIM-3) that supported FDA approval, Zelboraf (vemurafenib), as compared to Deticene (dacarbazine), resulted in an improved overall survival (OS) (13.6 vs 9.7 months, HR=0.81, p=0.03) in patients with BRAF V600E-positive metastatic melanoma, with estimated OS rates of 56%, 30%, 21%, and 17% at 1, 2, 3, and 4 years, respectively (%%PUBMED:28961848%%, %%PUBMED:21639808%%; NCT01006980), and BRAF V600E is included on the companion diagnostic (FDA.gov).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"FDA approved - On Companion Diagnostic","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[20818844],"normalized_drug":"Vemurafenib","indication":"melanoma","therapy_id":342,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase I trial, Zelboraf (vemurafenib) treatment resulted in an overall response rate of 81% (26/32; 2 complete responses, 24 partial responses), and inhibition of tumor Erk and Ccnd1, and reduced cell proliferation in metastatic melanoma patients harboring BRAF V600E (%%PUBMED:20818844%%; NCT00215605).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase I","amp_tier":"II"},{"response_type":"no benefit","pub_med_references":[30181415],"normalized_drug":"Binimetinib","indication":"colon neuroendocrine neoplasm","therapy_id":807,"normalized_cancer":"Gastrointestinal Neuroendocrine Tumors","evidence_type":"Actionable","therapy":"Binimetinib","efficacy_evidence":"In Phase II trial, Mektovi (binimetinib) therapy in a patient with recurrent neuroendocrine carcinoma of the colon harboring a BRAF V600E mutation who had previously progressed on Tafinlar (dabrafenib) resulted in disease progression after two cycles (%%PUBMED:30181415%%; NCT01885195).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"melanoma","therapy_id":16364,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"IMM-6-415","efficacy_evidence":"In a preclinical study, IMM-6-415 treatment inhibited tumor growth in a cell line xenograft model of melanoma harboring BRAF V600E (Mol Cancer Ther (2023) 22 (12_Supplement): A093).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[35882450],"normalized_drug":"Ulixertinib","indication":"pleomorphic xanthoastrocytoma","therapy_id":997,"normalized_cancer":"Pleomorphic Xanthoastrocytoma","evidence_type":"Actionable","therapy":"Ulixertinib","efficacy_evidence":"In a preclinical study, Ulixertinib (BVD-523) reduced metabolic activity and inhibited MAPK pathway activity in a pleomorphic xanthoastrocytoma cell line harboring BRAF V600E in culture, and inhibited tumor growth and improved survival compared to vehicle (48.5 days vs 30 days, respectively) in a xenograft model (%%PUBMED:35882450%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"esophagus adenocarcinoma","therapy_id":1066,"normalized_cancer":"Esophageal Adenocarcinoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Tafinlar (dabrafenib) and Mekinist (trametinib) combination therapy is included in guidelines as second-line or subsequent therapy for patients with locally advanced, recurrent, or metastatic esophageal adenocarcinoma harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[27217440],"response_type":"predicted - sensitive","indication":"high grade glioma","therapy_id":4901,"normalized_cancer":"High-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"Everolimus + Selumetinib","efficacy_evidence":"In a preclinical study, Koselugo (selumetinib) and Afinitor (everolimus) synergistically inhibited growth and induced apoptosis in glioma cell lines in culture, resulted in prolonged survival in cell line xenograft models (%%PUBMED:27217440%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[23365119],"response_type":"sensitive","indication":"thyroid cancer","therapy_id":1707,"normalized_cancer":"Thyroid Cancer","evidence_type":"Actionable","therapy":"Lapatinib + Vemurafenib","efficacy_evidence":"In a preclinical study, the combination of Tykerb (lapatinib) and Zelboraf (vemurafenib) inhibited growth of thyroid cancer cells harboring a BRAF V600E mutation in culture and in BRAF-mutant mouse models of thyroid cancer (%%PUBMED:23365119%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"response_type":"predicted - 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patient with gastrointestinal stromal tumor harboring BRAF V600E (%%PUBMED:38756640%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[23470635],"normalized_drug":"Dabrafenib","indication":"gastrointestinal stromal tumor","therapy_id":3,"normalized_cancer":"Gastrointestinal Stromal Tumor","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a clinical case study, Tafinlar (dabrafenib) treatment resulted in a 20% decrease in tumor size after 24 weeks in a patient with a gastrointestinal stromal tumor harboring BRAF V600E (%%PUBMED:23470635%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[38096472],"normalized_drug":"Cobimetinib, Vemurafenib","indication":"breast malignant phyllodes tumor","therapy_id":1657,"normalized_cancer":"Malignant Phyllodes Tumor of the Breast","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"In a Phase II trial (TAPUR), Zelboraf (vemurafenib) and Cotellic (cobimetinib) combination therapy resulted in a partial response in a patient with a phyllodes tumor of the breast harboring BRAF V600E (%%PUBMED:38096472%%; NCT02693535).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[27048951],"response_type":"sensitive","indication":"melanoma","therapy_id":4230,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"DETD-35","efficacy_evidence":"In a preclinical study, DETD-35 inhibited proliferation and colony formation of melanoma cells harboring BRAF V600E in culture and reduced tumor size in xenograft models (%%PUBMED:27048951%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[16273091],"response_type":"sensitive","indication":"colon cancer","therapy_id":849,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Mirdametinib","efficacy_evidence":"In a preclinical study, Gomekli (mirdametinib) demonstrated antitumor activity against BRAF V600E colon cancer cell line xenografts (%%PUBMED:16273091%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[34337566],"response_type":"sensitive","indication":"diffuse large B-cell lymphoma","therapy_id":8304,"normalized_cancer":"Diffuse Large B-Cell Lymphoma, NOS","evidence_type":"Actionable","therapy":"ERAS-007","efficacy_evidence":"In a preclinical study, ERAS-007 (ASN007) treatment inhibited proliferation of diffuse large B-cell lymphoma cells harboring BRAF V600E in culture (%%PUBMED:34337566%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"cholangiocarcinoma","therapy_id":7465,"normalized_cancer":"Cholangiocarcinoma","evidence_type":"Actionable","therapy":"BGB3245","efficacy_evidence":"In a Phase I trial, BGB3245 treatment demonstrated manageable safety and resulted in a disease control rate of 48% (16/33,1 complete response, 5 confirmed partial responses (PR), 2 unconfirmed PR, and 8 stable disease > 24 weeks) in patients with advanced solid tumors harboring MAPK pathway alterations, including a partial response in a patient with cholangiocarcinoma harboring BRAF V600E (Cancer Res (2023) 83 (8_Supplement): CT031).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[20538618],"response_type":"sensitive","indication":"Advanced Solid Tumor","therapy_id":4281,"normalized_cancer":"All Solid Tumors","evidence_type":"Actionable","therapy":"SB590885","efficacy_evidence":"In a preclinical study, SB590885 inhibited inhibited Erk phosphorylation and cell proliferation of transformed cells expression BRAF V600E in culture (%%PUBMED:20538618%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"response_type":"sensitive","indication":"skin melanoma","therapy_id":1449,"normalized_cancer":"Cutaneous Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + Pembrolizumab + Trametinib","efficacy_evidence":"Tafinlar (dabrafenib) plus Mekinist (trametinib) in combination with an immune checkpoint inhibitor, such as Keytruda (pembrolizumab), is included in guidelines as second-line or subsequent therapy (category 2A) for patients with metastatic or unresectable cutaneous melanoma harboring a BRAF V600 mutation, such as BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[27297867],"response_type":"sensitive","indication":"melanoma","therapy_id":4604,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"PAC-1 + Vemurafenib","efficacy_evidence":"In a preclinical study, the combination of PAC-1 and Zelboraf (vemurafenib) resulted in a synergistic effect when treating melanoma cells harboring BRAF V600E in culture and xenograft models, demonstrating increased apoptosis and decreased tumor volume (%%PUBMED:27297867%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[26267534],"response_type":"sensitive","indication":"colorectal adenocarcinoma","therapy_id":3769,"normalized_cancer":"Colorectal Adenocarcinoma","evidence_type":"Actionable","therapy":"DEL-22379","efficacy_evidence":"In a preclinical study, DEL-22379 inhibited tumor growth in a colorectal adenocarcinoma patient-derived xenograft model harboring BRAF V600E (%%PUBMED:26267534%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"melanoma","therapy_id":18577,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"RG6344","efficacy_evidence":"In a Phase I trial, RG6344 treatment was well tolerated and demonstrated preliminary activity in patients with advanced solid tumors harboring BRAF V600E (n=64), including melanoma (n=11) and colorectal cancer (n=51), with an objective response rate of 25% (Cancer Res (2025) 85 (8_Supplement_2): CT017).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[33273059],"response_type":"sensitive","indication":"melanoma","therapy_id":11152,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"AZD0364","efficacy_evidence":"In a preclinical study, AZD0364 (ATG-017) inhibited cell growth, decreased phosphorylation of Erk target genes, and increased expression of apoptosis markers in melanoma cells harboring BRAF V600E in culture, and resulted in tumor regression in cell line xenograft models (%%PUBMED:33273059%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[37325052],"response_type":"sensitive","indication":"thyroid cancer","therapy_id":10505,"normalized_cancer":"Thyroid Cancer","evidence_type":"Actionable","therapy":"SHP099 + Vemurafenib","efficacy_evidence":"In a preclinical study, the combination of Zelboraf (vemurafenib) and SHP099 inhibited proliferation and induced cell cycle arrest in Zelboraf (vemurafenib)-resistant thyroid cancer cell lines harboring BRAF V600E in culture and inhibited tumor growth in a cell line xenograft model (%%PUBMED:37325052%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[35882450],"response_type":"sensitive","indication":"pleomorphic xanthoastrocytoma","therapy_id":14715,"normalized_cancer":"Pleomorphic Xanthoastrocytoma","evidence_type":"Actionable","therapy":"Binimetinib + Ulixertinib","efficacy_evidence":"In a preclinical study, the combination of Ulixertinib (BVD-523) and Mektovi (binimetinib) inhibited proliferation and had a synergistic effect on induction of apoptosis and inhibition of MAPK pathway activity in a pleomorphic xanthoastrocytoma cell line harboring BRAF V600E in culture, and improved the progressive disease/partial response ratio compared to either drug alone in a zebrafish xenograft model (%%PUBMED:35882450%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[36011019],"normalized_drug":"Dabrafenib","indication":"triple-receptor negative breast cancer","therapy_id":3,"normalized_cancer":"Invasive Breast Carcinoma","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a preclinical study, Tafinlar (dabrafenib) treatment inhibited Mapk signaling and viability in a triple-negative breast cancer cell line harboring BRAF V600E in culture (%%PUBMED:36011019%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[30867592],"normalized_drug":"Cobimetinib","indication":"lymphatic system cancer","therapy_id":1004,"normalized_cancer":"Lymphatic Cancer","evidence_type":"Actionable","therapy":"Cobimetinib","efficacy_evidence":"In a Phase II trial, treatment with Cotellic (cobimetinib) in patients with histiocytic neoplasms resulted in a PET overall response rate of 89% (16/18), with complete response in 72% (13/18) and partial response in 17% (3/18), and resulted in stable disease in 6% (1/18) of patients, including 1 partial response and 3 complete responses in 4 patients with Erdheim-Chester disease harboring BRAF V600E (%%PUBMED:30867592%%; NCT01953926).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"ovary epithelial cancer","therapy_id":1066,"normalized_cancer":"Ovarian Epithelial Tumor","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Tafinlar (dabrafenib) and Mekinist (trametinib) combination therapy is included in guidelines as systemic therapy for patients with recurrent epithelial ovarian, fallopian tube, or primary peritoneal cancer harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","normalized_drug":"Cetuximab, Encorafenib","indication":"rectum cancer","therapy_id":1916,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Encorafenib","efficacy_evidence":"Braftovi (encorafenib) in combination with Erbitux (cetuximab) is included in guidelines as primary or subsequent therapy for patients with rectal cancer harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[32523649],"normalized_drug":"Vemurafenib","indication":"childhood low-grade glioma","therapy_id":342,"normalized_cancer":"Low-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase I trial (PNOC-002), Zelboraf (vemurafenib) treatment was tolerable and resulted in 1 complete response, 5 partial responses, and 13 stable disease in 19 pediatric patients with recurrent low grade gliomas harboring BRAF V600E, including pilocytic astrocytoma (n=10), ganglioglioma (n=5), pleomorphic xanthroastrocytoma (n=2), fibrillary astrocytoma (n=1), and astrocytoma not otherwise specified (n=1) (%%PUBMED:32523649%%; NCT01748149).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase I","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[25309914],"normalized_drug":"Trametinib","indication":"colorectal cancer","therapy_id":2,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Trametinib","efficacy_evidence":"In a preclinical study, colorectal cancer cells harboring a BRAF V600E mutation had increased sensitivity to Mekinist (trametinib) compared to other colorectal cancer lines in culture (%%PUBMED:25309914%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"melanoma","therapy_id":1449,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + Pembrolizumab + Trametinib","efficacy_evidence":"In a Phase II trial (IMPemBra), Keytruda (pembrolizumab) in combination with short-term or intermittent Tafinlar (dabrafenib) plus Mekinist (trametinib) resulted in improved median progression-free survival compared to Keytruda (pembrolizumab) monotherapy (27.0 vs 10.6 mo, p=0.13) in patients with treatment-naive advanced melanoma harboring BRAF V600E (n=26) or V600K (n=6) mutations (J Clin Oncol 38: 2020 (suppl; abstr 10021); NCT02625337).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"response_type":"resistant","pub_med_references":[39626159],"normalized_drug":"Vemurafenib","indication":"colon cancer","therapy_id":342,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a preclinical study, mouse colon cancer organoids harboring BRAF V600E were resistant to Zelboraf (vemurafenib) in culture (%%PUBMED:39626159%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"resistant","normalized_drug":"Cetuximab","indication":"colon cancer","therapy_id":694,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab","efficacy_evidence":"Erbitux (cetuximab), as a monotherapy, is not indicated for use in colon cancer patients with BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[21170960],"normalized_drug":"Regorafenib","indication":"colorectal cancer","therapy_id":890,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Regorafenib","efficacy_evidence":"In a preclinical study, Stivarga (regorafenib) inhibited proliferation of colorectal cancer cells harboring BRAF V600E in culture and suppressed angiogenesis and tumor growth in cell line xenograft models (%%PUBMED:21170960%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[32818466,34838156],"normalized_drug":"Dabrafenib, Trametinib","indication":"Advanced Solid Tumor","therapy_id":1066,"normalized_cancer":"All Solid Tumors","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In 3 Phase II trials (ROAR, NCI-MATCH, X2101) that supported FDA approval, Tafinlar (dabrafenib) and Mekinist (trametinib) combination therapy demonstrated safety and efficacy in adult and pediatric (6 years or older) patients with advanced solid tumors harboring BRAF V600E (%%PUBMED:34838156%%, %%PUBMED:32818466%%, J Clin Oncol 37, no. 15_suppl (May 20, 2019) 3002, J Clin Oncol 38, no. 15_suppl (May 20, 2020) 10506; NCT02034110, NCT02465060, NCT02124772).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"FDA approved","amp_tier":"I"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"Advanced Solid Tumor","therapy_id":1066,"normalized_cancer":"All Solid Tumors","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a Phase II trial (NCI-MATCH), Tafinlar (dabrafenib) and Mekinist (trametinib) combination therapy resulted in an objective response rate of 33.3% (11/33) in patients with advanced solid tumors other than melanoma, thyroid, colorectal, and lung cancer harboring BRAF V600E, with a median duration of response of 12 months, median progression-free survival of 9.4 months, and median overall survival not reached (J Clin Oncol 37, no. 15_suppl (May 20, 2019) 3002; NCT02465060).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[24885690],"normalized_drug":"Dabrafenib","indication":"colorectal cancer","therapy_id":3,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a preclinical study, colorectal cancer cell lines harboring a BRAF V600E mutation had increased sensitivity to Tafinlar (dabrafenib) in culture compared to cell lines with wild-type BRAF (%%PUBMED:24885690%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"response_type":"predicted - 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and Zelboraf (vemurafenib) led to greater levels of caspase-3 activity and apoptosis in melanoma cells harboring BRAF V600E when compared to Zelboraf (vemurafenib) and Mekinist (trametinib) treatment without PAC-1 (%%PUBMED:27297867%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Cetuximab, Encorafenib","indication":"appendix adenocarcinoma","therapy_id":1916,"normalized_cancer":"Appendiceal Adenocarcinoma","evidence_type":"Actionable","therapy":"Cetuximab + Encorafenib","efficacy_evidence":"Braftovi (encorafenib) in combination with Erbitux (cetuximab) is included in guidelines for patients with advanced or metastatic appendiceal adenocarcinoma harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[39018564],"normalized_drug":"Encorafenib","indication":"pseudomyxoma peritonei","therapy_id":796,"normalized_cancer":"Peritoneal Cancer","evidence_type":"Actionable","therapy":"Encorafenib","efficacy_evidence":"In a preclinical study, Braftovi (encorafenib) inhibited viability and induced apoptosis in a patient-derived pseudomyxoma peritonei cell line harboring BRAF V600E in culture and inhibited tumor growth and improved survival of a patient-derived xenograft (PDX) model (%%PUBMED:39018564%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Pdx & cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"colorectal cancer","therapy_id":16364,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"IMM-6-415","efficacy_evidence":"In a preclinical study, IMM-6-415 treatment inhibited tumor growth in a cell line xenograft model of colorectal cancer harboring BRAF V600E (Mol Cancer Ther (2023) 22 (12_Supplement): A093).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"colorectal cancer","therapy_id":17152,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Binimetinib + PLX8394","efficacy_evidence":"In a preclinical study, treatment with the combination of Mektovi (binimetinib) and PLX8394 inhibited viability of colorectal cancer cells harboring BRAF V600E in culture (Cancer Res (2024) 84 (6_Supplement): 4609).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[36108341],"normalized_drug":"Dabrafenib, Trametinib","indication":"hairy cell leukemia","therapy_id":1066,"normalized_cancer":"Hairy Cell Leukemia","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a Phase II trial (ROAR), treatment with the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) demonstrated safety and resulted in an overall response rate of 89.1% (49/55; 36 complete responses, 13 partial responses) in patients with heavily pretreated recurrent/refractory hairy cell leukemia harboring BRAF V600E, with 24-month duration of response, progression-free-survival, and overall survival rates of 97.7%, 94.4% and 94.5%, respectively (%%PUBMED:36108341%%; NCT02034110).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"pub_med_references":[26267534],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":2618,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"SCH772984","efficacy_evidence":"In a preclinical study, SCH772984 inhibited growth of colorectal cancer cell lines harboring BRAF V600E in culture (%%PUBMED:26267534%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[38960393],"response_type":"predicted - sensitive","indication":"skin melanoma","therapy_id":4754,"normalized_cancer":"Cutaneous Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + Nivolumab + Trametinib","efficacy_evidence":"In a clinical case study, treatment with the combination of Mekinist (trametinib), Tafinlar (dabrafenib), and Opdivo (nivolumab) resulted in a partial response in the leptomeningeal disease on the spine and the extracranial melanoma, with the intracranial lesions remaining stable after 6 months, in a patient with cutaneous melanoma harboring BRAF V600E, and a follow-up at least 7 years following diagnosis demonstrated complete remission (%%PUBMED:38960393%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[36713531],"normalized_drug":"Vemurafenib","indication":"hairy cell leukemia","therapy_id":342,"normalized_cancer":"Hairy Cell Leukemia","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a clinical case study, Zelboraf (vemurafenib) treatment resulted in complete resolution of the brain lesions after 3 months of treatment, decreased spleen size, and resolution of leukemic retinopathy in a patient with hairy cell leukemia harboring BRAF V600E (%%PUBMED:36713531%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[26352686],"normalized_drug":"Vemurafenib","indication":"hairy cell leukemia","therapy_id":342,"normalized_cancer":"Hairy Cell Leukemia","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In two Phase II clinical studies, patients with refractory hairy cell leukemia harboring BRAF V600E responded to Zelboraf (vemurafenib) with overall response rates of 96% (25/26) and 100% (24/24) as well as complete response rates of 35% (9/26) and 42% (10/24) with median follow up times of 8 and 12 weeks, respectively (%%PUBMED:26352686%%).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"pub_med_references":[25665005],"response_type":"sensitive","indication":"colon cancer","therapy_id":1386,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Navitoclax + Trametinib","efficacy_evidence":"In a preclinical study, Navitoclax (ABT-263) enhanced the inhibitory effect of Mekinist (trametinib) on human colon cancer cells harboring BRAF V600E in culture (%%PUBMED:25665005%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[22180495],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":10746,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Bevacizumab + Capecitabine + Vemurafenib","efficacy_evidence":"In a preclinical study, Zelboraf (vemurafenib) treatment when combined with Xeloda (capecitabine) and Avastin (bevacizumab) enhanced tumor growth inhibition and increased survival in a cell line xenograft model of colorectal cancer harboring BRAF V600E (%%PUBMED:22180495%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"predicted - sensitive","normalized_drug":"Ulixertinib","indication":"pancreatic ductal adenocarcinoma","therapy_id":997,"normalized_cancer":"Pancreatic Adenocarcinoma","evidence_type":"Actionable","therapy":"Ulixertinib","efficacy_evidence":"In an expanded access program (ULI-EAP-100), Ulixertinib (BVD-523) treatment resulted in clinical benefit in a patient with pancreatic ductal adenocarcinoma harboring BRAF V600E who stayed on treatment for 413 days (J Clin Oncol 40, no. 16_suppl (June 01, 2022) e15101; NCT04566393).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[39399174],"normalized_drug":"Dabrafenib","indication":"anaplastic pleomorphic xanthoastrocytoma","therapy_id":3,"normalized_cancer":"Anaplastic Pleomorphic Xanthoastrocytoma","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a clinical case study, Tafinlar (dabrafenib) treatment resulted in a partial response in a patient with tempero-parietal anaplastic pleomorphic xanthoastrocytoma harboring BRAF V600E (%%PUBMED:39399174%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[36343387],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":14544,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Panobinostat + Trametinib","efficacy_evidence":"In a preclinical study, the combination of Mekinist (trametinib) and Farydak (panobinostat) synergistically inhibited cell viability and induced apoptosis in a colorectal cancer cell line harboring BRAF V600E in culture (%%PUBMED:36343387%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[26438159],"response_type":"sensitive","indication":"melanoma","therapy_id":2011,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"RO5126766","efficacy_evidence":"In a preclinical study, RO5126766 inhibited proliferation of melanoma cells harboring BRAF V600E in culture (%%PUBMED:26438159%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[25422890],"response_type":"sensitive","indication":"melanoma","therapy_id":2011,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"RO5126766","efficacy_evidence":"In a preclinical study, RO5126766 (VS-6766) treatment induced cell cycle arrest, decreased Mek and Erk phosphorylation, and inhibited growth of melanoma cells harboring BRAF V600E in culture (%%PUBMED:25422890%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[34337566],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":8304,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"ERAS-007","efficacy_evidence":"In a preclinical study, ERAS-007 (ASN007) treatment inhibited cell proliferation and Erk signaling in colorectal cancer cell lines harboring BRAF V600E in culture, and induced tumor regression in two patient-derived xenograft (PDX) models (%%PUBMED:34337566%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Pdx & cell culture","amp_tier":"II"},{"response_type":"sensitive","indication":"rectum cancer","therapy_id":18195,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Encorafenib + Fluorouracil + Leucovorin + Oxaliplatin + Panitumumab","efficacy_evidence":"Braftovi (encorafenib) in combination with Vectibix (panitumumab) and FOLFOX is included in guidelines as initial (category 2A) or subsequent-line (category 2B) therapy for patients with advanced or metastatic rectal cancer harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[38976815],"normalized_drug":"Vemurafenib","indication":"childhood pilocytic astrocytoma","therapy_id":342,"normalized_cancer":"Pilocytic Astrocytoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a clinical case study, Zelboraf (vemurafenib) treatment resulted in a partial response in a pediatric patient with pilocytic astrocytoma harboring BRAF V600E (%%PUBMED:38976815%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[32523649],"normalized_drug":"Vemurafenib","indication":"childhood pilocytic astrocytoma","therapy_id":342,"normalized_cancer":"Pilocytic Astrocytoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase I trial (PNOC-002), Zelboraf (vemurafenib) treatment was tolerable and resulted in 1 complete response, 5 partial responses, and 13 stable disease in 19 pediatric patients with recurrent low grade gliomas harboring BRAF V600E, including pilocytic astrocytoma (n=10), ganglioglioma (n=5), pleomorphic xanthroastrocytoma (n=2), fibrillary astrocytoma (n=1), and astrocytoma NOS (n=1) (%%PUBMED:32523649%%; NCT01748149).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase I","amp_tier":"II"},{"pub_med_references":[19276360],"response_type":"sensitive","indication":"melanoma","therapy_id":1095,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"GDC0879","efficacy_evidence":"In a preclinical study, GDC0879 inhibited survival of melanoma cell lines harboring BRAF V600E in cell culture, cell line xenograft and patient-derived xenograft (PDX) models (%%PUBMED:19276360%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Pdx & cell culture","amp_tier":"II"},{"response_type":"sensitive","indication":"rectum cancer","therapy_id":11094,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Encorafenib + Fluorouracil + Leucovorin + Oxaliplatin","efficacy_evidence":"Braftovi (encorafenib) in combination with Erbitux (cetuximab) and FOLFOX is included in guidelines as initial (category 2A) or subsequent-line (category 2B) therapy for patients with advanced or metastatic rectal cancer harboring BRAF V600E (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[38489728],"normalized_drug":"Vemurafenib","indication":"papillary thyroid carcinoma","therapy_id":342,"normalized_cancer":"Papillary Thyroid Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a clinical case study, Zelboraf (vemurafenib) treatment resulted in a partial response with approximately 90% tumor shrinkage and a progression-free survival of 10 months in a patient with metastatic papillary thyroid carcinoma harboring BRAF V600E (%%PUBMED:38489728%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[27460442],"normalized_drug":"Vemurafenib","indication":"papillary thyroid carcinoma","therapy_id":342,"normalized_cancer":"Papillary Thyroid Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase II trial, Zelboraf (vemurafenib) treatment resulted in a partial response in 38.5% (10/26) of patients with metastatic or unresectable, radioactive iodine-refractory papillary thyroid carcinoma harboring BRAF V600E that were multikinase inhibitor-naive, with a disease control rate of 73%, and a median progression-free survival of 18.2 months (%%PUBMED:27460442%%; NCT01286753).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E","approval_status":"Phase II","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[20818844],"normalized_drug":"Vemurafenib","indication":"papillary thyroid carcinoma","therapy_id":342,"normalized_cancer":"Papillary Thyroid Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase I trial, Zelboraf (vemurafenib) treatment resulted in a complete or partial response in three papillary thyroid carcinoma patients harboring BRAF V600E, with one patient having a response that lasted for 8 months who remained progression-free for 12 months, and another two patients having a stable disease that lasted for 11 and 13 months, respectively (%%PUBMED:20818844%%; NCT00215605).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Vemurafenib","indication":"papillary thyroid carcinoma","therapy_id":342,"normalized_cancer":"Papillary Thyroid Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"Zelboraf (vemurafenib) is included in guidelines for patients with recurrent, advanced, or metastatic thyroid papillary carcinoma harboring BRAF V600E for whom clinical trials are not available or appropriate (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[36011019],"normalized_drug":"Trametinib","indication":"triple-receptor negative breast cancer","therapy_id":2,"normalized_cancer":"Invasive Breast Carcinoma","evidence_type":"Actionable","therapy":"Trametinib","efficacy_evidence":"In a preclinical study, Mekinist (trametinib) treatment inhibited Mapk signaling and viability in a triple-negative breast cancer cell line harboring BRAF V600E in culture (%%PUBMED:36011019%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - resistant","pub_med_references":[34433654],"normalized_drug":"Dabrafenib","indication":"high grade glioma","therapy_id":3,"normalized_cancer":"High-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a preclinical study, NF1 knockdown in glioma cell lines harboring BRAF V600E led to decreased inhibition of cell growth and decreased apoptosis on treatment with Tafinlar (dabrafenib) in culture (%%PUBMED:34433654%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NF1 dec exp","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[34433654],"normalized_drug":"Dabrafenib, Trametinib","indication":"high grade glioma","therapy_id":1066,"normalized_cancer":"High-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a preclinical study, the addition of Mekinist (trametinib) to Tafinlar (dabrafenib) treatment overcame resistance to Tafinlar (dabrafenib) in glioma cell lines harboring BRAF V600E and a knockdown of NF1 in culture (%%PUBMED:34433654%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NF1 dec exp","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"resistant","pub_med_references":[23288408],"normalized_drug":"Selumetinib","indication":"melanoma","therapy_id":913,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Selumetinib","efficacy_evidence":"In a preclinical study, inhibition of NF1 in a BRAF V600E melanoma cell line conferred resistance to MEK inhibitor Koselugo (selumetinib) through sustained MAPK pathway activation (%%PUBMED:23288408%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NF1 dec exp","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[23288408],"response_type":"sensitive","indication":"melanoma","therapy_id":4351,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"VX-11e","efficacy_evidence":"In a preclinical study, inhibition of NF1 in a melanoma cell line harboring a BRAF V600E mutation did not affect sensitivity to the ERK inhibitor VX-11e (%%PUBMED:23288408%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NF1 dec exp","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[23288408],"response_type":"resistant","indication":"melanoma","therapy_id":1095,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"GDC0879","efficacy_evidence":"In a preclinical study, shRNA knockdown of NF1 in a BRAF V600E melanoma cell line confered resistance to the RAF inhibitor GDC0879 through 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RAF inhibitor PLX4720 through sustained MAPK pathway activation (%%PUBMED:23288408%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NF1 dec exp","approval_status":"Preclinical","amp_tier":"II"},{"response_type":"resistant","pub_med_references":[23288408],"normalized_drug":"Vemurafenib","indication":"melanoma","therapy_id":342,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a preclinical study, the shRNA knockdown of NF1 in a BRAF V600E melanoma cell line confers resistance to RAF inhibitor Zelboraf (vemurafenib) through sustained MAPK pathway activation (%%PUBMED:23288408%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NF1 dec exp","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[23288408],"response_type":"decreased response","indication":"melanoma","therapy_id":1061,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"PLX4720 + 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(%%PUBMED:23178117%%).","therapy":"Selumetinib","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Preclinical","normalized_drug":"Selumetinib","pub_med_references":[23178117],"molecular_profile":"BRAF V600E MED12 dec exp","profile_array":[{"type":"M1","gene":"V600E"}],"response_type":"resistant"},{"therapy_id":342,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a preclinical study, knock down of MED12 expression in BRAF V600E melanoma cell lines resulted in resistance to Zelboraf (vemurafenib) or Koselugo (selumetinib) (%%PUBMED:23178117%%).","therapy":"Vemurafenib","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Preclinical - Cell culture","normalized_drug":"Vemurafenib","pub_med_references":[23178117],"molecular_profile":"BRAF V600E MED12 dec 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(talazoparib) and Tafinlar (dabrafenib) synergistically inhibited viability of patient-derived melanoma spheroids harboring BRAF V600E and NRAS Q61K in culture (%%PUBMED:37729428%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NRAS Q61K","approval_status":"Preclinical - Patient cell culture","amp_tier":"II"},{"pub_med_references":[22351686],"response_type":"sensitive","indication":"melanoma","therapy_id":970,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"XL888","efficacy_evidence":"In a preclinical study, treatment with XL888 resulted in increased apoptosis and decreased growth of Zelboraf (vemurafenib)-resistant melanoma cells harboring BRAF V600E along with NRAS Q61K in cell culture (%%PUBMED:22351686%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NRAS Q61K","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[37729428],"response_type":"sensitive","indication":"melanoma","therapy_id":16209,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + Talazoparib + Trametinib","efficacy_evidence":"In a preclinical study, treatment with the combination of Talzenna (talazoparib), Tafinlar (dabrafenib), and Mekinist (trametinib) inhibited tumor growth and improved survival compared to controls in a melanoma patient-derived xenograft (PDX) model harboring BRAF V600E and NRAS Q61K (%%PUBMED:37729428%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NRAS Q61K","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[37729428],"normalized_drug":"Talazoparib","indication":"melanoma","therapy_id":682,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Talazoparib","efficacy_evidence":"In a preclinical study, Talzenna (talazoparib) treatment inhibited tumor growth and led to improved survival compared to controls in a melanoma patient-derived xenograft (PDX) model harboring BRAF V600E and NRAS Q61K (%%PUBMED:37729428%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NRAS Q61K","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"pub_med_references":[38691346],"response_type":"predicted - sensitive","indication":"lung non-small cell carcinoma","therapy_id":13602,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"PF-07799933","efficacy_evidence":"In a preclinical study, PF-07799933 inhibited Erk phosphorylation in melanoma cells harboring BRAF V600E and NRAS Q61K in culture (%%PUBMED:38691346%%).","cap_asco_evidence_level":"NA","molecular_profile":"BRAF V600E NRAS Q61K","approval_status":"Preclinical - Biochemical","amp_tier":"NA"},{"response_type":"predicted - 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culture (%%PUBMED:36622773%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NRAS Q61K","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[28951457],"response_type":"predicted - resistant","indication":"colorectal cancer","therapy_id":1717,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Panitumumab + Vemurafenib","efficacy_evidence":"In a clinical case study, a patient with BRAF V600E colorectal cancer developed progressive disease after a partial response lasting 40 weeks to Vectibix (panitumumab) and Zelboraf (vemurafenib) combination treatment, NRAS Q61K was identified as an acquired mutation at the time of progression (%%PUBMED:28951457%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NRAS Q61K","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[36622773],"response_type":"predicted - 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(%%PUBMED:37729428%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NRAS Q61K","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[22389471],"normalized_drug":"Dabrafenib, Trametinib","indication":"melanoma","therapy_id":1066,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a preclinical study, Talfinlar (dabrafenib) in combination with Mekinist (trametinib) resulted in improved growth inhibition of melanoma cell lines harboring BRAF V600E and NRAS Q61K in culture, compared to either agent alone (%%PUBMED:22389471%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NRAS Q61K","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[34330842],"response_type":"sensitive","indication":"melanoma","therapy_id":6971,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"ASTX029","efficacy_evidence":"In a preclinical study, ASTX029 treatment reduced Erk and Rsk phosphorylation and inhibited growth of a melanoma cell line harboring BRAF V600E and expressing NRAS Q61K in culture (%%PUBMED:34330842%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NRAS Q61K","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[37729428],"response_type":"sensitive","indication":"melanoma","therapy_id":16206,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Encorafenib + Olaparib","efficacy_evidence":"In a preclinical study, treatment with the combination of Lynparza (olaparib) and Braftovi (encorafenib) synergistically inhibited viability of patient-derived melanoma spheroids harboring BRAF V600E and NRAS Q61K in culture (%%PUBMED:37729428%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NRAS Q61K","approval_status":"Preclinical - Patient cell 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signaling (%%PUBMED:22389471%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NRAS Q61K","approval_status":"Preclinical","amp_tier":"II"},{"response_type":"resistant","pub_med_references":[36622773],"normalized_drug":"Dabrafenib","indication":"melanoma","therapy_id":3,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a preclinical study, a melanoma cell line harboring BRAF V600E and expressing NRAS Q61K was resistant to Tafinlar (dabrafenib) in culture (%%PUBMED:36622773%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NRAS Q61K","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - resistant","pub_med_references":[29631033],"normalized_drug":"Dabrafenib, Trametinib","indication":"lung adenocarcinoma","therapy_id":1066,"normalized_cancer":"Lung Adenocarcinoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, a breast cancer patient with metastatic lung adenocarcinoma harboring BRAF V600E developed progressive disease after initial response to Tafinlar (dabrafenib) and Mekinist (trametinib) combination therapy, and NRAS Q61K was identified as an acquired mutation after disease progression (%%PUBMED:29631033%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NRAS Q61K","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"resistant","pub_med_references":[34376578],"normalized_drug":"Vemurafenib","indication":"melanoma","therapy_id":342,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a clinical case study, a melanoma patient harboring BRAF V600E experienced progressive disease after response to treatment Zelboraf (vemurafenib), and was found to have acquired NRAS Q61K (%%PUBMED:34376578%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NRAS Q61K","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"resistant","pub_med_references":[21107323],"normalized_drug":"Vemurafenib","indication":"melanoma","therapy_id":342,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a preclinical study, a NRAS Q61K mutation conferred resistance to Zelboraf (vemurafenib) in melanoma cells harboring BRAF V600E in culture (%%PUBMED:21107323%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NRAS Q61K","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[37729428],"response_type":"sensitive","indication":"melanoma","therapy_id":16204,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Encorafenib + Talazoparib","efficacy_evidence":"In a preclinical study, treatment with the combination of Talzenna (talazoparib) and Braftovi (encorafenib) synergistically inhibited viability of patient-derived melanoma spheroids harboring BRAF V600E and NRAS Q61K in culture (%%PUBMED:37729428%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NRAS Q61K","approval_status":"Preclinical - Patient cell culture","amp_tier":"II"},{"pub_med_references":[37729428],"response_type":"sensitive","indication":"melanoma","therapy_id":16207,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Encorafenib + Rucaparib","efficacy_evidence":"In a preclinical study, treatment with the combination of Rubraca (rucaparib) and Braftovi (encorafenib) synergistically inhibited viability of patient-derived melanoma spheroids harboring BRAF V600E and NRAS Q61K in culture (%%PUBMED:37729428%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NRAS Q61K","approval_status":"Preclinical - Patient cell 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PDGFRB in cell culture and in xenograft models (%%PUBMED:22351686%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E PDGFRB over exp","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"resistant","pub_med_references":[28986383],"normalized_drug":"Vemurafenib","indication":"melanoma","therapy_id":342,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a preclinical study, a melanoma cell line harboring BRAF V600E and overexpressing Pdgfrb demonstrated resistance to Zelboraf (vemurafenib) in culture (%%PUBMED:28986383%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E PDGFRB over exp","approval_status":"Preclinical - Cell 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(%%PUBMED:28986383%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E PDGFRB over exp","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[22351686],"response_type":"sensitive","profile_array":[{"type":"M1","gene":"V600E"}],"indication":"melanoma","therapy_id":970,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"XL888","efficacy_evidence":"In a preclinical study, treatment with XL888 resulted in increased apoptosis and decreased growth of Zelboraf (vemurafenib)-resistant melanoma cells harboring a BRAF V600E mutation and over expression of MAP3K8 (COT) in cell culture (%%PUBMED:22351686%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E MAP3K8 over exp","approval_status":"Preclinical","amp_tier":"II"},{"therapy_id":342,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a preclinical study, a melanoma cell line harboring BRAF V600E and overexpressing Map3k8 demonstrated resistance to Zelboraf (vemurafenib) in culture (%%PUBMED:28986383%%).","therapy":"Vemurafenib","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Preclinical - Cell culture","normalized_drug":"Vemurafenib","pub_med_references":[28986383],"molecular_profile":"BRAF V600E MAP3K8 over exp","profile_array":[{"type":"M1","gene":"V600E"}],"response_type":"resistant"},{"pub_med_references":[23737487],"response_type":"resistant","indication":"melanoma","therapy_id":1060,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"PLX4720","efficacy_evidence":"In a preclinical study, expression of RAF1 G361A conferred resistance to PLX4720 in human melanoma cells harboring BRAF V600E in culture (%%PUBMED:23737487%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E RAF1 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- Cell culture","amp_tier":"II"},{"pub_med_references":[27312529],"response_type":"resistant","indication":"colorectal cancer","therapy_id":1711,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Vemurafenib","efficacy_evidence":"In a preclinical study, colorectal cancer cells harboring BRAF V600E that acquired a KRAS A146T mutation and subsequent resistance to Erbitux (cetuximab) and Encorafenib (LGX818) combination treatment were resistant to combination therapy consisting of Erbitux (cetuximab) and Zelboraf (vemurafenib) in culture (%%PUBMED:27312529%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E KRAS A146T","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"resistant","pub_med_references":[27312529],"normalized_drug":"Cetuximab, Encorafenib","indication":"colorectal cancer","therapy_id":1916,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + 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inhibited viability of a melanoma cell line harboring BRAF V600E and expressing MAP2K1 K57T in culture (%%PUBMED:36442478%%).","therapy":"Dabrafenib + Trametinib","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Preclinical - Cell culture","normalized_drug":"Dabrafenib, Trametinib","pub_med_references":[36442478],"molecular_profile":"BRAF V600E MAP2K1 K57T","profile_array":[{"type":"M1","gene":"V600E"}],"response_type":"sensitive"},{"therapy_id":342,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a preclinical study, a melanoma cell line harboring BRAF V600E and expressing MAP2K1 K57T was resistant to Zelboraf (vemurafenib) in culture (%%PUBMED:36442478%%).","therapy":"Vemurafenib","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Preclinical - Cell culture","normalized_drug":"Vemurafenib","pub_med_references":[36442478],"molecular_profile":"BRAF V600E MAP2K1 K57T","profile_array":[{"type":"M1","gene":"V600E"}],"response_type":"resistant"},{"therapy_id":796,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a preclinical study, a melanoma cell line harboring BRAF V600E and expressing MAP2K1 K57T was resistant to Braftovi (encorafenib) in culture (%%PUBMED:36442478%%).","therapy":"Encorafenib","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Preclinical - Cell culture","normalized_drug":"Encorafenib","pub_med_references":[36442478],"molecular_profile":"BRAF V600E MAP2K1 K57T","profile_array":[{"type":"M1","gene":"V600E"}],"response_type":"resistant"},{"therapy_id":1100,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a preclinical study, the combination of Braftovi (encorafenib) and Mektovi (binimetinib) synergistically inhibited viability of a melanoma cell line harboring BRAF V600E and expressing MAP2K1 K57T in culture (%%PUBMED:36442478%%).","therapy":"Binimetinib + Encorafenib","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Preclinical - Cell culture","normalized_drug":"Binimetinib, Encorafenib","pub_med_references":[36442478],"molecular_profile":"BRAF V600E MAP2K1 K57T","profile_array":[{"type":"M1","gene":"V600E"}],"response_type":"sensitive"},{"therapy_id":3,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a preclinical study, a melanoma cell line harboring BRAF V600E and expressing MAP2K1 K57T was resistant to Tafinlar (dabrafenib) in culture (%%PUBMED:36442478%%).","therapy":"Dabrafenib","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Preclinical - Cell culture","normalized_drug":"Dabrafenib","pub_med_references":[36442478],"molecular_profile":"BRAF V600E MAP2K1 K57T","profile_array":[{"type":"M1","gene":"V600E"}],"response_type":"resistant"},{"therapy_id":807,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a preclinical study, a melanoma cell line harboring BRAF V600E and expressing MAP2K1 K57T was resistant to Mektovi (binimetinib) in culture (%%PUBMED:36442478%%).","therapy":"Binimetinib","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Preclinical - Cell culture","normalized_drug":"Binimetinib","pub_med_references":[36442478],"molecular_profile":"BRAF V600E MAP2K1 K57T","profile_array":[{"type":"M1","gene":"V600E"}],"response_type":"resistant"},{"therapy_id":1657,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a clinical case study, a patient with hairy cell leukemia harboring BRAF V600E who relapsed after initial response to Zelboraf (vemurafenib) and was found to have acquired multiple clones with Mek/Erk activating mutations, including MAP2K1 K57T, demonstrated a sustained response greater than 12 months to combined Zelboraf (vemurafenib) and Cotellic (cobimetinib) treatment (%%PUBMED:30341394%%).","therapy":"Cobimetinib + Vemurafenib","evidence_type":"Actionable","normalized_cancer":"Hairy Cell Leukemia","indication":"refractory hairy cell leukemia","approval_status":"Case Reports/Case Series","normalized_drug":"Cobimetinib, Vemurafenib","pub_med_references":[30341394],"molecular_profile":"BRAF V600E MAP2K1 K57T","profile_array":[{"type":"M1","gene":"V600E"}],"response_type":"predicted - sensitive"},{"pub_med_references":[36921494],"response_type":"predicted - resistant","profile_array":[{"type":"M1","gene":"V600E"}],"indication":"colorectal cancer","therapy_id":15623,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Fluorouracil + Leucovorin + Vemurafenib","efficacy_evidence":"In a Phase II trial (MODUL), a patient with metastatic colorectal cancer harboring BRAF V600E was found to have acquired MAP2K1 K57T prior to progression on treatment with the combination of Zelboraf (vemurafenib), Erbitux (cetuximab), Adrucil (fluorouracil), and Wellcovorin (leucovorin) (%%PUBMED:36921494%%; NCT02291289).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E MAP2K1 K57T","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"therapy_id":660,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a retrospective analysis, BRAF V600E was identified at the time of progression on Tagrisso (osimertinib) treatment in a non-small cell lung cancer patient harboring an EGFR exon 19 deletion mutation (%%PUBMED:37806383%%).","therapy":"Osimertinib","evidence_type":"Actionable","normalized_cancer":"Non-Small Cell Lung Cancer","indication":"lung non-small cell carcinoma","approval_status":"Case Reports/Case Series","normalized_drug":"Osimertinib","pub_med_references":[37806383],"molecular_profile":"BRAF V600E EGFR exon 19 del","profile_array":[{"type":"exon del","number":19,"gene":"EGFR"}],"response_type":"predicted - resistant"},{"therapy_id":660,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a clinical study, a patient with non-small cell lung cancer harboring EGFR T790M and an EGFR exon 19 deletion developed progressive disease on treatment with Tagrisso (osimertinib) and was found to have acquired BRAF V600E and lost EGFR T790M in the post-progression liquid and tissue biopsies (%%PUBMED:39317868%%).","therapy":"Osimertinib","evidence_type":"Actionable","normalized_cancer":"Non-Small Cell Lung Cancer","indication":"lung non-small cell carcinoma","approval_status":"Case Reports/Case Series","normalized_drug":"Osimertinib","pub_med_references":[39317868],"molecular_profile":"BRAF V600E EGFR exon 19 del","profile_array":[{"type":"exon del","number":19,"gene":"EGFR"}],"response_type":"predicted - 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Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Osimertinib + Trametinib","efficacy_evidence":"In a retrospective analysis, treatment with the combination of Tafinlar (dabrafenib), Mekinist (trametinib), and Tagrisso (Osimertinib) resulted in an objective response rate of 61.5% (8/13, all partial responses) and disease control rate of 92.3% (12/13) in non-small cell lung cancer patients harboring EGFR L858R (n=4) or an exon 19 deletion (n=9) and acquired BRAF V600E (%%PUBMED:39507030%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E EGFR exon 19 del","approval_status":"Clinical Study","amp_tier":"II"},{"therapy_id":660,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a clinical case study, Tagrisso (osimertinib) treatment resulted in stable disease with treatment ongoing for at least 12 months in a patient with lung adenocarcinoma harboring BRAF V600E and an EGFR Exon 19 deletion (%%PUBMED:38529368%%).","therapy":"Osimertinib","evidence_type":"Actionable","normalized_cancer":"Lung Adenocarcinoma","indication":"lung adenocarcinoma","approval_status":"Case Reports/Case Series","normalized_drug":"Osimertinib","pub_med_references":[38529368],"molecular_profile":"BRAF V600E EGFR exon 19 del","profile_array":[{"type":"exon del","number":19,"gene":"EGFR"}],"response_type":"predicted - sensitive"},{"therapy_id":1309,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a Phase I trial, a lung adenocarcinoma patient harboring an EGFR exon 19 deletion and EGFR T790M demonstrated a partial response to treatment with Nazartinib (CO-1686), but developed progression in the liver after 11 months, and a post-progression biopsy identified the EGFR exon 19 deletion without EGFR T790M, and emergence of BRAF V600E (%%PUBMED:30123863%%; NCT02108964).","therapy":"Nazartinib","evidence_type":"Actionable","normalized_cancer":"Lung Adenocarcinoma","indication":"lung adenocarcinoma","approval_status":"Case Reports/Case Series","normalized_drug":"Nazartinib","pub_med_references":[30123863],"molecular_profile":"BRAF V600E EGFR exon 19 del","profile_array":[{"type":"exon del","number":19,"gene":"EGFR"}],"response_type":"predicted - resistant"},{"response_type":"predicted - sensitive","pub_med_references":[30181415],"normalized_drug":"Dabrafenib, Trametinib","indication":"colon neuroendocrine neoplasm","therapy_id":1066,"normalized_cancer":"Gastrointestinal Neuroendocrine Tumors","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, combination Tafinlar (dabrafenib) and Mekinist (trametinib) therapy in a patient with Platinol (cisplatin)-resistant metastatic neuroendocrine carcinoma of the colon harboring BRAF V600E and TP53 H214R mutations and amplifications of FLT3 and CDK8 resulted in decreased disease burden with a clinical benefit for 5 months before disease progression (%%PUBMED:30181415%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E CDK8 amp FLT3 amp TP53 H214R","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - resistant","pub_med_references":[30181415],"normalized_drug":"Dabrafenib, Trametinib","indication":"colon neuroendocrine neoplasm","therapy_id":1066,"normalized_cancer":"Gastrointestinal Neuroendocrine Tumors","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, a patient with Platinol (cisplatin)-resistant metastatic neuroendocrine carcinoma of the colon harboring BRAF V600E and TP53 H214R mutations and amplifications of FLT3 and CDK8 who had an initial response to combination Tafinlar (dabrafenib) and Mekinist (trametinib) therapy was found to have acquired an ARID1B Q123* mutation upon disease progression (%%PUBMED:30181415%%).","cap_asco_evidence_level":"D","molecular_profile":"ARID1B Q123* BRAF V600E CDK8 amp FLT3 amp TP53 H214R","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[30867592],"normalized_drug":"Cobimetinib","indication":"lymphatic system cancer","therapy_id":1004,"normalized_cancer":"Lymphatic Cancer","evidence_type":"Actionable","therapy":"Cobimetinib","efficacy_evidence":"In a Phase II trial, treatment with Cotellic (cobimetinib) in patients with histiocytic neoplasms resulted in a PET overall response rate of 89% (16/18), with complete response in 72% (13/18) and partial response in 17% (3/18), and resulted in stable disease in 6% (1/18) of patients, including a complete response in a patient with Langerhans cell histiocytosis harboring BRAF V600E, KRAS G13C, and NRAS G12D (%%PUBMED:30867592%%; NCT01953926).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E KRAS G13C NRAS G12D","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[28951457],"response_type":"predicted - resistant","indication":"colorectal cancer","therapy_id":1917,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Alpelisib + Cetuximab + Encorafenib","efficacy_evidence":"In a clinical case study, a patient with BRAF V600E colorectal cancer developed progressive disease after a partial response lasting 24 weeks to Alpelisib (BYL719), Erbitux (cetuximab), and Braftovi (encorafenib) combination treatment, BRAF V47_D380del (reported as deletion of exons 2-8) was identified as an acquired mutation in peritoneal metastasis at the time of progression (%%PUBMED:28951457%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V47_D380del BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"resistant","pub_med_references":[29605720],"normalized_drug":"Vemurafenib","indication":"melanoma","therapy_id":342,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a preclinical study, expression of BRAF V47_D380del in a melanoma cell line harboring BRAF V600E conferred resistance to Zelboraf (vemurafenib) in culture (%%PUBMED:29605720%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V47_D380del BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - resistant","pub_med_references":[39282524],"normalized_drug":"Binimetinib, Encorafenib","indication":"melanoma","therapy_id":1100,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Binimetinib + Encorafenib","efficacy_evidence":"In a clinical case study, NRAS G13R with progressively increasing variant allele frequency was identified in the circulating tumor DNA of a patient with metastatic melanoma harboring BRAF V600E who progressed on treatment with the combination of Mektovi (binimetinib) and Braftovi (encorafenib) (%%PUBMED:39282524%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NRAS G13R","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[28951457],"response_type":"predicted - sensitive","indication":"colorectal cancer","therapy_id":8106,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"BGB659 + Cetuximab","efficacy_evidence":"In a preclinical study, BGB659 and Erbitux (cetuximab) combination treatment resulted in sustained inhibition of Mek and Erk phosphorylation, lead to tumor regression in patient-derived xenograft models of colorectal cancer harboring BRAF V600E and NRAS G13R (%%PUBMED:28951457%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NRAS G13R","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"pub_med_references":[28951457],"response_type":"predicted - resistant","indication":"colorectal cancer","therapy_id":1917,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Alpelisib + Cetuximab + Encorafenib","efficacy_evidence":"In a clinical case study, a patient with BRAF V600E colorectal cancer developed progressive disease after a partial response lasting 24 weeks to Alpelisib (BYL719), Erbitux (cetuximab), and Braftovi (encorafenib) combination treatment, NRAS G13R was identified as an acquired mutation in liver metastasis at the time of progression (%%PUBMED:28951457%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NRAS G13R","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[28951457],"response_type":"predicted - resistant","indication":"colorectal cancer","therapy_id":1917,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Alpelisib + Cetuximab + Encorafenib","efficacy_evidence":"In a clinical case study, a patient with BRAF V600E colorectal cancer developed progressive disease after a partial response lasting 18 weeks to Alpelisib (BYL719), Erbitux (cetuximab), and Braftovi (encorafenib) combination treatment, KRAS G12A was identified as an acquired mutation at the time of progression (%%PUBMED:28951457%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E KRAS G12A","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[28951457],"response_type":"predicted - resistant","profile_array":[{"type":"M1","gene":"amp"}],"indication":"colorectal cancer","therapy_id":1717,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Panitumumab + Vemurafenib","efficacy_evidence":"In a clinical case study, a patient with BRAF V600E colorectal cancer developed progressive disease after achieving stable disease for 32 weeks with Vectibix (panitumumab) and Zelboraf (vemurafenib) combination treatment, KRAS and MET amplification were identified as acquired alterations at the time of progression (%%PUBMED:28951457%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E KRAS amp MET amp","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[28951457],"response_type":"predicted - resistant","indication":"colorectal cancer","therapy_id":1717,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Panitumumab + Vemurafenib","efficacy_evidence":"In a clinical case study, a patient with BRAF V600E colorectal cancer developed progressive disease after achieving stable disease for 16 weeks with Vectibix (panitumumab) and Zelboraf (vemurafenib) combination treatment, NRAS amplification was identified as an acquired alteration at the time of progression (%%PUBMED:28951457%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NRAS amp","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[28951457],"response_type":"resistant","indication":"colorectal cancer","therapy_id":1711,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Vemurafenib","efficacy_evidence":"In a preclinical study, overexpression of wild-type KRAS in colorectal cancer cell lines harboring BRAF V600E induced Ras activation and Braf/Craf dimerization, conferred resistance to Erbitux (cetuximab) and Zelboraf (vemurafenib) combination treatment in culture and in cell line xenograft models (%%PUBMED:28951457%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E KRAS over exp","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[28951457],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":8106,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"BGB659 + Cetuximab","efficacy_evidence":"In a preclinical study, BGB659 and Erbitux (cetuximab) combination treatment demonstrated enhanced inhibition of Erk phosphorylation and growth in BRAF V600E colorectal cancer cell lines overexpressing Nras in culture (%%PUBMED:28951457%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NRAS over exp","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[28951457],"response_type":"resistant","indication":"colorectal cancer","therapy_id":1711,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Vemurafenib","efficacy_evidence":"In a preclinical study, overexpression of wild-type NRAS in colorectal cancer cell lines harboring BRAF V600E induced Ras activation and Braf/Craf dimerization, conferred resistance to Erbitux (cetuximab) and Zelboraf (vemurafenib) combination treatment in culture and in cell line xenograft models (%%PUBMED:28951457%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NRAS over exp","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[27325282],"response_type":"predicted - resistant","profile_array":[{"type":"M1","gene":"V600E"}],"indication":"rectum mucinous adenocarcinoma","therapy_id":1717,"normalized_cancer":"Mucinous Adenocarcinoma of the Colon and Rectum","evidence_type":"Actionable","therapy":"Panitumumab + Vemurafenib","efficacy_evidence":"In a clinical case study, a patient with microsatellite-stable mucinous rectal cancer harboring BRAF V600E eventually developed resistance to Vectibix (panitumumab) and Zelboraf (vemurafenib) combination therapy, potentially due to acquiring amplification of MET (%%PUBMED:27325282%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E MET amp","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[39313594],"response_type":"predicted - resistant","profile_array":[{"type":"M1","gene":"V600E"}],"indication":"colorectal cancer","therapy_id":4886,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Binimetinib + Cetuximab + Encorafenib","efficacy_evidence":"In a Phase III (BEACON CRC) trial, MET amplification was identified in end-of-treatment ctDNA samples in 19.6% (22/112) of patients with colorectal cancer harboring BRAF V600E following treatment with the combination of Braftovi (encorafenib), Mektovi (binimetinib), and Erbitux (cetuximab) (%%PUBMED:39313594%%; NCT02928224).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E MET amp","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[34994629],"response_type":"predicted - sensitive","profile_array":[{"type":"M1","gene":"V600E"}],"indication":"colon cancer","therapy_id":1338,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Capmatinib + Encorafenib","efficacy_evidence":"In a clinical case study, a patient with left-sided colon cancer harboring BRAF V600E and MET amplification (copy number 31), who had progressed on prior lines of therapy, experienced rapid clinical improvement and a partial metabolic and morphologic response following treatment with the combination of Tabrecta (capmatinib) and Braftovi (encorafenib), until progression after 14 weeks of treatment (%%PUBMED:34994629%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E MET amp","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"therapy_id":1916,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a clinical case study, MET amplification was identified in a patient with rectal adenocarcinoma harboring BRAF V600E after the disease progressed on Braftovi (encorafenib) and Erbitux (cetuximab) treatment (%%PUBMED:35820242%%).","therapy":"Cetuximab + Encorafenib","evidence_type":"Actionable","normalized_cancer":"Rectal Adenocarcinoma","indication":"rectum adenocarcinoma","approval_status":"Case Reports/Case Series","normalized_drug":"Cetuximab, Encorafenib","pub_med_references":[35820242],"molecular_profile":"BRAF V600E MET amp","profile_array":[{"type":"M1","gene":"V600E"}],"response_type":"predicted - resistant"},{"pub_med_references":[27325282],"response_type":"predicted - sensitive","profile_array":[{"type":"M1","gene":"V600E"}],"indication":"rectum mucinous adenocarcinoma","therapy_id":4648,"normalized_cancer":"Mucinous Adenocarcinoma of the Colon and Rectum","evidence_type":"Actionable","therapy":"Crizotinib + Vemurafenib","efficacy_evidence":"In a clinical case study, a patient with microsatellite-stable mucinous rectal cancer harboring BRAF V600E and acquired MET amplification responded to the combination treatment of Xalkori (crizotinib) and Zelboraf (vemurafenib), resulting in a rapid clinical and metabolic response (%%PUBMED:27325282%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E MET amp","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"therapy_id":1916,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a Phase III (BEACON CRC) trial, MET amplification was identified in end-of-treatment ctDNA samples in 17.0% (19/112) of patients with colorectal cancer harboring BRAF V600E following treatment with the combination of Braftovi (encorafenib) and Erbitux (cetuximab) (%%PUBMED:39313594%%; NCT02928224).","therapy":"Cetuximab + Encorafenib","evidence_type":"Actionable","normalized_cancer":"Colorectal Cancer","indication":"colorectal cancer","approval_status":"Case Reports/Case Series","normalized_drug":"Cetuximab, Encorafenib","pub_med_references":[39313594],"molecular_profile":"BRAF V600E MET amp","profile_array":[{"type":"M1","gene":"V600E"}],"response_type":"predicted - resistant"},{"pub_med_references":[35820242],"response_type":"predicted - sensitive","profile_array":[{"type":"M1","gene":"V600E"}],"indication":"rectum adenocarcinoma","therapy_id":4648,"normalized_cancer":"Rectal Adenocarcinoma","evidence_type":"Actionable","therapy":"Crizotinib + Vemurafenib","efficacy_evidence":"In a clinical case study, Zelboraf (vemurafenib) and Xalkori (crizotinib) combination treatment resulted in early radiologic tumor shrinkage in a patient with rectal adenocarcinoma harboring BRAF V600E and MET amplification, however, the tumor progressed after two months (%%PUBMED:35820242%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E MET amp","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[27325282],"response_type":"predicted - resistant","profile_array":[{"type":"M1","gene":"V600E"}],"indication":"colorectal cancer","therapy_id":1917,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Alpelisib + Cetuximab + Encorafenib","efficacy_evidence":"In a preclinical study, emergence of MET amplification was detected in colorectal cancer cells harboring BRAF V600E that acquired resistance to Alpelisib (BYL719), Erbitux (cetuximab), and Braftovi (encorafenib) combination treatment in culture (%%PUBMED:27325282%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E MET amp","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[27325282],"response_type":"predicted - sensitive","profile_array":[{"type":"M1","gene":"V600E"}],"indication":"colorectal cancer","therapy_id":4648,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Crizotinib + Vemurafenib","efficacy_evidence":"In a preclinical study, Xalkori (crizotinib) and Zelboraf (vemurafenib) combination treatment inhibited growth of colorectal cancer cells harboring BRAF V600E and overexpressing Met in culture (%%PUBMED:27325282%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E MET over exp","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[39626159],"response_type":"sensitive","profile_array":[{"type":"M1","gene":"V600E"}],"indication":"colon cancer","therapy_id":17952,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Crizotinib + Erlotinib + Vemurafenib","efficacy_evidence":"In a preclinical study, the addition of Xalkori (crizotinib) to treatment with the combination of Tarceva (erlotinib) and Zelboraf (vemurafenib) inhibited viability in mouse colon cancer organoids harboring BRAF V600E with overexpression of MET in culture (%%PUBMED:39626159%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E MET over exp","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[27325282],"response_type":"resistant","profile_array":[{"type":"M1","gene":"V600E"}],"indication":"colorectal cancer","therapy_id":1717,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Panitumumab + Vemurafenib","efficacy_evidence":"In a preclinical study, overexpressing Met in colorectal cancer cells harboring BRAF V600E conferred resistance to Vectibix (panitumumab) and Zelboraf (vemurafenib) combination treatment in culture (%%PUBMED:27325282%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E MET over exp","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[39626159],"response_type":"resistant","profile_array":[{"type":"M1","gene":"V600E"}],"indication":"colon cancer","therapy_id":1710,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Erlotinib + Vemurafenib","efficacy_evidence":"In a preclinical study, colon cancer organoids harboring BRAF V600E and overexpressing MET were resistant to treatment with the combination of Zelboraf (vemurafenib) and Tarceva (erlotinib) in culture (%%PUBMED:39626159%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E MET over exp","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"lung non-small cell carcinoma","therapy_id":8472,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Osimertinib","efficacy_evidence":"In a clinical case study, a patient with advanced non-small cell lung cancer who lost EGFR T790M, but still harbors EGFR E746_A750del and acquired BRAF V600E demonstrated an improved metabolic response when treated with the combination therapy of Tafinlar (dabrafenib) and Tagrisso (osimertinib) (Journal of Clinical Oncology, 2019, 37, no. 15_suppl).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E EGFR E746_A750del","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - resistant","normalized_drug":"Dabrafenib, Trametinib","indication":"lung non-small cell carcinoma","therapy_id":1066,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, a patient with advanced non-small cell lung cancer who lost EGFR T790M, but still harbors EGFR E746_A750del and acquired BRAF V600E demonstrated continued progression while being treated with the combination therapy of Tafinlar (dabrafenib) and Mekinist (trametinib) (Journal of Clinical Oncology, 2019, 37, no. 15_suppl).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E EGFR E746_A750del","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[39555453],"response_type":"predicted - resistant","indication":"lung adenocarcinoma","therapy_id":6979,"normalized_cancer":"Lung Adenocarcinoma","evidence_type":"Actionable","therapy":"Furmonertinib","efficacy_evidence":"In a clinical case study, a lung adenocarcinoma patient harboring EGFR E746_A750del progressed on treatment with Furmonertinib (alflutinib) and was found to have acquired BRAF V600E (%%PUBMED:39555453%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E EGFR E746_A750del","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[40082212],"response_type":"predicted - sensitive","indication":"lung adenocarcinoma","therapy_id":12100,"normalized_cancer":"Lung Adenocarcinoma","evidence_type":"Actionable","therapy":"Dabrafenib + Osimertinib + Trametinib","efficacy_evidence":"In a clinical case study, treatment with the combination of Tagrisso (osimertinib), Mekinist (trametinib), and Tafinlar (dabrafenib) resulted in a partial response with a total reduction in the target lesion diameters of 30.9% and a progression-free survival ongoing at 13 months in a patient with metastatic lung adenocarcinoma harboring EGFR E746_A750del and BRAF V600E (%%PUBMED:40082212%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E EGFR E746_A750del","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[37533438],"response_type":"predicted - sensitive","indication":"lung adenocarcinoma","therapy_id":12100,"normalized_cancer":"Lung Adenocarcinoma","evidence_type":"Actionable","therapy":"Dabrafenib + Osimertinib + Trametinib","efficacy_evidence":"In a clinical case study, the combination of Tagrisso (osimertinib), Mekinist (trametinib), and Tafinlar (dabrafenib) resulted in disease control lasting 8 months, with complete response in the brain, in a patient with metastatic lung adenocarcinoma and leptomeningeal metastasis harboring BRAF V600E and EGFR E746_A750del (%%PUBMED:37533438%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E EGFR E746_A750del","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[39555453],"normalized_drug":"Dabrafenib, Trametinib","indication":"lung adenocarcinoma","therapy_id":1066,"normalized_cancer":"Lung Adenocarcinoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, treatment with the combination of Mekinist (trametinib) and Tafinlar (dabrafenib) resulted in a partial remission and improvement in the pleural effusion and liver metastasis in a lung adenocarcinoma patient harboring EGFR E746_A750del and BRAF V600E (%%PUBMED:39555453%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E EGFR E746_A750del","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - resistant","pub_med_references":[36849494],"normalized_drug":"Osimertinib","indication":"lung non-small cell carcinoma","therapy_id":660,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Osimertinib","efficacy_evidence":"In a Phase III trial (FLAURA), BRAF V600E was identified at the time of progression on Tagrisso (osimertinib) in a patient with non-small cell lung cancer harboring EGFR E746_A750del (%%PUBMED:36849494%%; NCT02296125).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E EGFR E746_A750del","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[31217909],"response_type":"predicted - sensitive","indication":"glioblastoma","therapy_id":4129,"normalized_cancer":"Glioblastoma, IDH-Wildtype","evidence_type":"Actionable","therapy":"Palbociclib + Vemurafenib","efficacy_evidence":"In a clinical case study, Ibrance (palbociclib) in combination with Zelboraf (vemurafenib) resulted in clinical improvement and stable disease in a patient with epithelioid glioblastoma harboring BRAF V600E and homozygous deletion of CDKN2A and CDKN2B, however, his disease progressed after 10 weeks on treatment (%%PUBMED:31217909%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E CDKN2A del CDKN2B del","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[31085763],"normalized_drug":"Cabozantinib","indication":"papillary thyroid carcinoma","therapy_id":998,"normalized_cancer":"Papillary Thyroid Cancer","evidence_type":"Actionable","therapy":"Cabozantinib","efficacy_evidence":"In a clinical case study, a papillary thyroid carcinoma patient with BRAF V600E who progressed on the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) was found to have an acquired KRAS G12V mutation, and was subsequently treated with Cometriq (Cabometyx, cabozantinib), resulting in a partial response with target lesion reduction of 45% (%%PUBMED:31085763%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E KRAS G12V","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - resistant","pub_med_references":[31085763],"normalized_drug":"Dabrafenib, Trametinib","indication":"papillary thyroid carcinoma","therapy_id":1066,"normalized_cancer":"Papillary Thyroid Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, a papillary thyroid carcinoma patient with BRAF V600E who progressed on the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) was found to have an acquired KRAS G12V mutation (%%PUBMED:31085763%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E KRAS G12V","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - resistant","pub_med_references":[31406350],"normalized_drug":"Dabrafenib, Trametinib","indication":"pancreatic cancer","therapy_id":1066,"normalized_cancer":"Pancreatic Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, a patient with pancreatic cancer harboring CTRC-NTRK1 and BRAF V600E treated with a combination of Tafinlar (dabrafenib) and Mekinist (trametinib) demonstrated tumor regression, but later showed radiographical progression and was found to have acquired KRAS G12D (%%PUBMED:31406350%%).","cap_asco_evidence_level":"D","molecular_profile":"CTRC - NTRK1 BRAF V600E KRAS G12D","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - resistant","pub_med_references":[31406350],"normalized_drug":"Larotrectinib","indication":"pancreatic cancer","therapy_id":2650,"normalized_cancer":"Pancreatic Cancer","evidence_type":"Actionable","therapy":"Larotrectinib","efficacy_evidence":"In a clinical case study, a patient with pancreatic cancer harboring CTRC-NTRK1 progressed on Vitrakvi (larotrectinib) treatment, showing acquisition of BRAF V600E via biopsy testing and BRAF V600E and KRAS G12D via cell-free DNA testing (%%PUBMED:31406350%%).","cap_asco_evidence_level":"D","molecular_profile":"CTRC - NTRK1 BRAF V600E KRAS G12D","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - resistant","pub_med_references":[31406350],"normalized_drug":"Selitrectinib","indication":"pancreatic cancer","therapy_id":5917,"normalized_cancer":"Pancreatic Cancer","evidence_type":"Actionable","therapy":"Selitrectinib","efficacy_evidence":"In a clinical case study, a patient with pancreatic cancer harboring CTRC-NTRK1, BRAF V600E, and KRAS G12D demonstrated resistance to treatment with Selitrectinib (LOXO-195) (%%PUBMED:31406350%%).","cap_asco_evidence_level":"D","molecular_profile":"CTRC - NTRK1 BRAF V600E KRAS G12D","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[31406350],"response_type":"predicted - sensitive","indication":"pancreatic cancer","therapy_id":8908,"normalized_cancer":"Pancreatic Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Larotrectinib + Trametinib","efficacy_evidence":"In a preclinical study, a patient-derived xenograft (PDX) model with pancreatic cancer harboring CTRC-NTRK1, BRAF V600E, and KRAS G12D demonstrated greater tumor growth inhibition when treated with a combination of Tafinlar (dabrafenib), Mekinist (trametinib), and Vitrakvi (larotrectinib) versus a combination of Tafinlar (dabrafenib) and Mekinst (trametinib) only (%%PUBMED:31406350%%).","cap_asco_evidence_level":"D","molecular_profile":"CTRC - NTRK1 BRAF V600E KRAS G12D","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"response_type":"resistant","pub_med_references":[31406350],"normalized_drug":"Selitrectinib","indication":"pancreatic cancer","therapy_id":5917,"normalized_cancer":"Pancreatic Cancer","evidence_type":"Actionable","therapy":"Selitrectinib","efficacy_evidence":"In a preclinical study, a pancreatic cancer cell line harboring TPR-NTRK1 and NTRK1 G595R, and expressing BRAF V600E demonstrated resistance to treatment with Selitrectinib (LOXO-195) in culture (%%PUBMED:31406350%%).","cap_asco_evidence_level":"D","molecular_profile":"TPR - NTRK1 NTRK1 G595R BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[31406350],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":8909,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Selitrectinib + Trametinib","efficacy_evidence":"In a preclinical study, the combination therapy of Tafinlar (dabrafenib), Mekinist (trametinib), and Selitrectinib (LOXO-195) in a colorectal cancer cell line harboring LMNA-NTRK1 and NTRK1 G595R and expressing BRAF V600E demonstrated tumor growth suppression and inhibition of Akt, Erk, and Mek signaling in culture (%%PUBMED:31406350%%).","cap_asco_evidence_level":"D","molecular_profile":"LMNA - NTRK1 NTRK1 G595R BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - resistant","pub_med_references":[31605106],"normalized_drug":"Dabrafenib, Trametinib","indication":"pancreatic ductal adenocarcinoma","therapy_id":1066,"normalized_cancer":"Pancreatic Adenocarcinoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, a pancreatic ductal adenocarcinoma patient harboring CTRC-NTRK1 and BRAF V600E demonstrated progression when treated with the combination therapy of Tafinlar (dabrafenib) and Mekinist (trametinib) (%%PUBMED:31605106%%).","cap_asco_evidence_level":"D","molecular_profile":"CTRC - NTRK1 BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - resistant","pub_med_references":[31605106],"normalized_drug":"Larotrectinib","indication":"pancreatic ductal adenocarcinoma","therapy_id":2650,"normalized_cancer":"Pancreatic Adenocarcinoma","evidence_type":"Actionable","therapy":"Larotrectinib","efficacy_evidence":"In a clinical case study, a pancreatic ductal adenocarcinoma patient harboring CTRC-NTRK1 initially responded to Vitrakvi (larotrectinib), but then progressed after 6 months, and was subsequently found to have acquired BRAF V600E (%%PUBMED:31605106%%).","cap_asco_evidence_level":"D","molecular_profile":"CTRC - NTRK1 BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[31406350],"response_type":"predicted - sensitive","indication":"pancreatic cancer","therapy_id":8918,"normalized_cancer":"Pancreatic Cancer","evidence_type":"Actionable","therapy":"Larotrectinib + Trametinib","efficacy_evidence":"In a preclinical study, the combination therapy of Vitrakvi (larotrectinib) and Mekinist (trametinib) resulted in delayed tumor growth in a Vitrakvi (larotrectinib)-resistant patient-derived xenograft (PDX) model with pancreatic cancer harboring CTRC-NTRK1 and BRAF V600E, but led to controlled tumor growth for 1 month and tumor regression at 3 months in the PDX model with only CTRC-NTRK1, which subsequently revealed a low variant allele frequency for BRAF V600E (%%PUBMED:31406350%%).","cap_asco_evidence_level":"D","molecular_profile":"CTRC - NTRK1 BRAF V600E","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"response_type":"predicted - resistant","pub_med_references":[31605106],"normalized_drug":"Selitrectinib","indication":"pancreatic ductal adenocarcinoma","therapy_id":5917,"normalized_cancer":"Pancreatic Adenocarcinoma","evidence_type":"Actionable","therapy":"Selitrectinib","efficacy_evidence":"In a clinical case study, a pancreatic ductal adenocarcinoma patient harboring CTRC-NTRK1 and BRAF V600E progressed when treated with Selitrectinib (LOXO-195) (%%PUBMED:31605106%%).","cap_asco_evidence_level":"D","molecular_profile":"CTRC - NTRK1 BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"therapy_id":1312,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a clinical case study, a patient with melanoma harboring BRAF V600E developed progressive disease after 12 weeks of Tafinlar (dabrafenib) and Mekinist (trametinib) combination treatment, and progressed again after 106 weeks on anti-PD1 therapy including Opdivo (nivolumab) (90 weeks) followed by Keytruda (pembrolizumab), B2M V5Lfs*30, LRP1B W1344*, MAP2K2 F133L, NF2 Y66*, and TP53 C238F were identified in the post-progression biopsy in addition to BRAF V600E (%%PUBMED:31082388%%).","therapy":"Nivolumab","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Case Reports/Case Series","normalized_drug":"Nivolumab","pub_med_references":[31082388],"molecular_profile":"B2M V5Lfs*30 BRAF V600E LRP1B W1344* MAP2K2 F133L NF2 Y66* TP53 C238F","profile_array":[{"type":"M1","gene":"W1344*"}],"response_type":"predicted - resistant"},{"therapy_id":1066,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a clinical case study, a patient with melanoma harboring BRAF V600E developed progressive disease after 12 weeks of Tafinlar (dabrafenib) and Mekinist (trametinib) combination treatment, and progressed again after 106 weeks on anti-PD1 therapy including Opdivo (nivolumab) (90 weeks) followed by Keytruda (pembrolizumab), B2M V5Lfs*30, LRP1B W1344*, MAP2K2 F133L, NF2 Y66*, and TP53 C238F were identified in the post-progression biopsy in addition to BRAF V600E (%%PUBMED:31082388%%).","therapy":"Dabrafenib + Trametinib","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Case Reports/Case Series","normalized_drug":"Dabrafenib, Trametinib","pub_med_references":[31082388],"molecular_profile":"B2M V5Lfs*30 BRAF V600E LRP1B W1344* MAP2K2 F133L NF2 Y66* TP53 C238F","profile_array":[{"type":"M1","gene":"W1344*"}],"response_type":"predicted - resistant"},{"therapy_id":1447,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a clinical case study, a patient with melanoma harboring BRAF V600E developed progressive disease after 12 weeks of Tafinlar (dabrafenib) and Mekinist (trametinib) combination treatment, and progressed again after 106 weeks on anti-PD1 therapy including Opdivo (nivolumab) (90 weeks) followed by Keytruda (pembrolizumab), B2M V5Lfs*30, LRP1B W1344*, MAP2K2 F133L, NF2 Y66*, and TP53 C238F were identified in the post-progression biopsy in addition to BRAF V600E (%%PUBMED:31082388%%).","therapy":"Pembrolizumab","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Case Reports/Case Series","normalized_drug":"Pembrolizumab","pub_med_references":[31082388],"molecular_profile":"B2M V5Lfs*30 BRAF V600E LRP1B W1344* MAP2K2 F133L NF2 Y66* TP53 C238F","profile_array":[{"type":"M1","gene":"W1344*"}],"response_type":"predicted - resistant"},{"response_type":"predicted - sensitive","pub_med_references":[32007138],"normalized_drug":"Dabrafenib, Trametinib","indication":"melanoma","therapy_id":1066,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a Phase III (COMBI-AD) trial, Tafinlar (dabrafenib) and Mekinist (trametinib) combination therapy compared to placebo resulted in more benefit (HR=0.49, p<0.0001) in TMB low patients with resected melanoma harboring BRAF V600E or V600K, than in TMB high (HR=0.75, p=0.27) patients, however, TMB was not associated with relapse-free survival in the combination treatment group (%%PUBMED:32007138%%; NCT01682083).","cap_asco_evidence_level":"B","molecular_profile":"BRAF V600E TMB low","approval_status":"Phase III","amp_tier":"I"},{"response_type":"resistant","pub_med_references":[30143629],"normalized_drug":"Dabrafenib, Trametinib","indication":"melanoma","therapy_id":1066,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a preclinical study, decreased Sirt6 expression through siRNA knockdown resulted in activation of IGF-1R/AKT pathway, conferred resistance to Tafinlar (dabrafenib) and Mekinist (trametinib) combination treatment in melanoma cell lines and patient-derived melanoma cells harboring BRAF V600E in culture (%%PUBMED:30143629%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E SIRT6 dec exp","approval_status":"Preclinical - Patient cell culture","amp_tier":"II"},{"response_type":"resistant","pub_med_references":[30143629],"normalized_drug":"Vemurafenib","indication":"melanoma","therapy_id":342,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a preclinical study, decreased Sirt6 expression was identified in cells derived from patients with melanoma harboring BRAF V600E at times of disease progression while on Zelboraf (vemurafenib), and melanoma cell lines harboring BRAF V600E and with decreased Sirt6 expression through siRNA knockdown were resistance to Zelboraf (vemurafenib) in cell line xenograft models (%%PUBMED:30143629%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E SIRT6 dec exp","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"resistant","pub_med_references":[30143629],"normalized_drug":"Dabrafenib","indication":"melanoma","therapy_id":3,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a preclinical study, decreased Sirt6 expression through siRNA knockdown resulted in activation of IGF-1R/AKT pathway, conferred resistance to Tafinlar (dabrafenib) in melanoma cell lines and patient-derived melanoma cells harboring BRAF V600E in culture (%%PUBMED:30143629%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E SIRT6 dec exp","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[30143629],"response_type":"sensitive","indication":"melanoma","therapy_id":9382,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + Linsitinib","efficacy_evidence":"In a preclinical study, combination of Tafinlar (dabrafenib) and Linsitinib (OSI-906) enhanced inhibition of Igf1r and Akt phosphorylation, led to apoptosis and reduced proliferation in BRAF V600E melanoma cells with decreased Sirt6 expression via siRNA knockdown in culture, and tumor regression in cell line xenograft models (%%PUBMED:30143629%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E SIRT6 dec exp","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"resistant","pub_med_references":[29605720],"normalized_drug":"Vemurafenib","indication":"melanoma","therapy_id":342,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a preclinical study, a melanoma cell line harboring BRAF V600E was found to have BRAF V47_D380del and BCORL1 Q1076H mutations after acquiring resistance to Zelboraf (vemurafenib), and expression of BRAF V47_D380del and BCORL1 Q1076H in a BRAF V600E-positive melanoma cell line resulted in decreased sensitivity to Zelboraf (vemurafenib) in culture 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patient harboring BRAF V600E, CDK4 R24C, and MYC amplification resulted in disease progression after 2.3 months following an initial partial response (%%PUBMED:31980996%%).","therapy":"Vemurafenib","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Case Reports/Case Series","normalized_drug":"Vemurafenib","pub_med_references":[31980996],"molecular_profile":"BRAF V600E CDK4 R24C MYC amp","profile_array":[{"type":"M1","gene":"R24C"}],"response_type":"predicted - resistant"},{"response_type":"predicted - resistant","pub_med_references":[31980996],"normalized_drug":"Vemurafenib","indication":"melanoma","therapy_id":342,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a clinical case study, Zelboraf (vemurafenib) treatment resulted in disease progression within two months in a metastatic melanoma patient harboring BRAF V600E, ATM deletion, and PAX5 deletion 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a metastatic melanoma patient harboring BRAF V600E, MITF G6R, and MYC T259I (%%PUBMED:31980996%%).","therapy":"Dabrafenib","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Case Reports/Case Series","normalized_drug":"Dabrafenib","pub_med_references":[31980996],"molecular_profile":"BRAF V600E MITF G6R MYC T259I","profile_array":[{"type":"M1","gene":"V600E"}],"response_type":"predicted - resistant"},{"response_type":"predicted - resistant","pub_med_references":[31980996],"normalized_drug":"Vemurafenib","indication":"melanoma","therapy_id":342,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a clinical case study, Zelboraf (vemurafenib) treatment resulted in disease progression within 2 months following an initial partial response in a metastatic melanoma patient harboring BRAF V600E, BRAF S602T, NF1 P1951S, and PAX5 deletion (%%PUBMED:31980996%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E BRAF S602T NF1 P1951S PAX5 del","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[31925410],"response_type":"resistant","profile_array":[{"type":"M1","gene":"V600E"}],"indication":"melanoma","therapy_id":4351,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"VX-11e","efficacy_evidence":"In a preclinical study, expression of MAPK1 L107E in melanoma cells harboring BRAF V600E conferred resistance to VX-11e treatment in culture (%%PUBMED:31925410%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E MAPK1 L107E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"therapy_id":699,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a preclinical study, expression of MAP2K1 I99T in melanoma cells harboring BRAF V600E conferred resistance to CI-1040 (PD184352) treatment in culture (%%PUBMED:19915144%%).","therapy":"CI-1040","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Preclinical - Cell culture","normalized_drug":"Ci-1040","pub_med_references":[19915144],"molecular_profile":"BRAF V600E MAP2K1 I99T","profile_array":[{"type":"M1","gene":"V600E"}],"response_type":"resistant"},{"therapy_id":2,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a preclinical study, melanoma cells harboring BRAF V600E and expressing MAP2K1 I99T demonstrated resistance to Mekinist (trametinib) treatment in culture (%%PUBMED:31925410%%).","therapy":"Trametinib","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Preclinical - Cell culture","normalized_drug":"Trametinib","pub_med_references":[31925410],"molecular_profile":"BRAF V600E MAP2K1 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(%%PUBMED:31925410%%).","therapy":"Dabrafenib","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Preclinical - Cell culture","normalized_drug":"Dabrafenib","pub_med_references":[31925410],"molecular_profile":"BRAF V600E MAP2K1 I99T","profile_array":[{"type":"M1","gene":"V600E"}],"response_type":"resistant"},{"therapy_id":3,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a preclinical study, melanoma cells harboring BRAF V600E and expressing MAP2K1 I99G demonstrated resistance to Tafinlar (dabrafenib) treatment in culture (%%PUBMED:31925410%%).","therapy":"Dabrafenib","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Preclinical - Cell culture","normalized_drug":"Dabrafenib","pub_med_references":[31925410],"molecular_profile":"BRAF V600E MAP2K1 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(%%PUBMED:31925410%%).","therapy":"Dabrafenib","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Preclinical - Cell culture","normalized_drug":"Dabrafenib","pub_med_references":[31925410],"molecular_profile":"BRAF V600E MAP2K1 I99M","profile_array":[{"type":"M1","gene":"V600E"}],"response_type":"sensitive"},{"therapy_id":2,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a preclinical study, melanoma cells harboring BRAF V600E and expressing MAP2K1 I99M demonstrated sensitivity to Mekinist (trametinib) treatment similar to cells expressing wild-type MAP2K1 in culture (%%PUBMED:31925410%%).","therapy":"Trametinib","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Preclinical - Cell culture","normalized_drug":"Trametinib","pub_med_references":[31925410],"molecular_profile":"BRAF V600E MAP2K1 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inhibit colony formation and reduce Erk activation in a melanoma cell line harboring BRAF V600E that was found to have acquired a STAG2 D193N mutation in culture (%%PUBMED:27500726%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E STAG2 D193N","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[23031422],"normalized_drug":"Dabrafenib","indication":"melanoma","therapy_id":3,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a clinical case study, a patient with rapidly growing malignant melanoma harboring BRAF V600E and V600M achieved a 60% reduction in tumor size 1 week following treatment with Tafinlar (dabrafenib), and the tumor completely disappeared 1 month after beginning treatment (%%PUBMED:23031422%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E BRAF V600M","approval_status":"Case Reports/Case 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study, a patient with metastatic giant sarcomatoid melanoma harboring BRAF V600E and CDKN2A R80* achieved a partial response following four months of treatment with the combination of Tafinlar (dabrafenib) and Mekinist (trametinib), and reached a complete response with regression of lung and bone metastases after one year of treatment (%%PUBMED:32922664%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E CDKN2A R80*","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"resistant","pub_med_references":[36622773],"normalized_drug":"Dabrafenib, Trametinib","indication":"melanoma","therapy_id":1066,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a preclinical study, a melanoma cell line overexpressing BRAF V600E was resistant to the combination of Mekinist (trametinib) and Tafinlar (dabrafenib) in culture (%%PUBMED:36622773%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E BRAF over exp","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"resistant","pub_med_references":[30559419],"normalized_drug":"Vemurafenib","indication":"melanoma","therapy_id":342,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a preclinical study, a cell line xenograft model of melanoma overexpressing BRAF V600E demonstrated resistance to Zelboraf (vemurafenib) treatment (%%PUBMED:30559419%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E BRAF over exp","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[36622773],"response_type":"sensitive","indication":"melanoma","therapy_id":14824,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + DS03090629","efficacy_evidence":"In a preclinical study, the combination of DS03090629 and Tafinlar (dabrafenib) inhibited Erk phosphorylation and proliferation in a melanoma cell line overexpressing BRAF V600E in culture and induced tumor regression in a cell line xenograft model (%%PUBMED:36622773%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E BRAF over exp","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"resistant","pub_med_references":[36622773],"normalized_drug":"Dabrafenib","indication":"melanoma","therapy_id":3,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a preclinical study, a melanoma cell line overexpressing BRAF V600E was resistant to Tafinlar (dabrafenib) in culture (%%PUBMED:36622773%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E BRAF over exp","approval_status":"Preclinical - Cell 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(%%PUBMED:36622773%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E BRAF over exp","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[30559419],"normalized_drug":"Plx8394","indication":"melanoma","therapy_id":1041,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"PLX8394","efficacy_evidence":"In a preclinical study, PLX8394 treatment inhibited Erk signaling and reduced tumor growth in a Zelboraf (vemurafenib)-resistant cell line xenograft model of melanoma overexpressing BRAF V600E (%%PUBMED:30559419%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E BRAF over exp","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[32816843],"response_type":"predicted - resistant","indication":"colorectal cancer","therapy_id":8871,"normalized_cancer":"Colorectal 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Adenocarcinoma","evidence_type":"Actionable","therapy":"Pembrolizumab","efficacy_evidence":"In a clinical case study, a patient with CD274 (PD-L1)-positive (IHC = 90% of tumor cells) metastatic lung adenocarcinoma who progressed after an 18-month response to Tafinlar (dabrafenib) treatment based on the presence of BRAF V600E, was then treated with Keytruda (pembrolizumab) for two cycles, and achieved an early response and remained progression-free 7 months after initiating immunotherapy (%%PUBMED:29142786%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E CD274 pos","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[29142786],"normalized_drug":"Dabrafenib","indication":"lung adenocarcinoma","therapy_id":3,"normalized_cancer":"Lung Adenocarcinoma","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a clinical case study, a patient with CD274 (PD-L1)-positive (IHC = 90% of tumor cells) metastatic lung adenocarcinoma harboring BRAF V600E achieved a partial response to treatment with Tafinlar (dabrafenib) and remained stable with improved performance status for 18 months until disease progression, and subsequently achieved a response to Keytruda (pembrolizumab) treatment (%%PUBMED:29142786%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E CD274 pos","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[39036436],"response_type":"predicted - sensitive","indication":"glioblastoma","therapy_id":17805,"normalized_cancer":"Glioblastoma, IDH-Wildtype","evidence_type":"Actionable","therapy":"Binimetinib + Encorafenib + Nivolumab + Temozolomide","efficacy_evidence":"In a clinical case study, the addition of Mektovi (binimetinib) and Braftovi (encorafenib) to treatment with the combination of Opdivo (nivolumab) and Temodar (temozolomide) resulted in a complete response after 6 months in a patient with CD274 (PD-L1), PDCD1 (PD-1)-positive glioblastoma harboring BRAF V600E, and the patient remained progression-free for at least 20 months while on treatment (%%PUBMED:39036436%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E CD274 pos","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[32859654],"normalized_drug":"Dabrafenib, Trametinib","indication":"lung non-small cell carcinoma","therapy_id":1066,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical study, combination treatment with Tafinlar (dabrafenib) and Mekinist (trametinib) resulted in stable disease as best response in a non-small cell lung cancer patient harboring BRAF V600E, tested in tissue and plasma, and AKT1 E17K, tested in plasma only (%%PUBMED:32859654%%).","cap_asco_evidence_level":"D","molecular_profile":"AKT1 E17K BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[32859654],"normalized_drug":"Vemurafenib","indication":"lung non-small cell carcinoma","therapy_id":342,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a clinical study, Zelboraf (vemurafenib) resulted in a partial response for 3.7 months in a non-small cell lung cancer patient harboring BRAF V600E, tested in tissue and plasma, and ERBB2 (HER2) amplification, tested in plasma only (%%PUBMED:32859654%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E ERBB2 amp","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[32859654],"normalized_drug":"Vemurafenib","indication":"lung non-small cell carcinoma","therapy_id":342,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a clinical study, Zelboraf (vemurafenib) treatment resulted in stable disease for 3.3 months in a non-small cell lung cancer patient harboring BRAF V600E, tested in tissue and plasma, and FGFR2 A553D, tested in plasma only (%%PUBMED:32859654%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E FGFR2 A553D","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[32859654],"normalized_drug":"Dabrafenib, Trametinib","indication":"lung non-small cell carcinoma","therapy_id":1066,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical study, combination treatment with Tafinlar (dabrafenib) and Mekinist (trametinib) resulted in stable disease as best response in a non-small cell lung cancer patient harboring BRAF V600E, tested in plasma and tissue, and NTRK3 P612T, tested in plasma only (%%PUBMED:32859654%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NTRK3 P612T","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[32859654],"normalized_drug":"Vemurafenib","indication":"lung non-small cell carcinoma","therapy_id":342,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a clinical study, Zelboraf (vemurafenib) treatment resulted in stable disease for 6.4 months in a non-small cell lung cancer patient harboring BRAF V600E, tested in tissue and plasma, and PIK3CA E545K, tested in plasma only (%%PUBMED:32859654%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E PIK3CA E545K","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - 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Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical study, a non-small cell lung cancer patient harboring BRAF V600E, tested in tissue, and IDH1 R132C, tested in plasma, demonstrated disease progression when treated with the combination of Tafinlar (dabrafenib) and Mekinist (trametinib), and was found, via circulating tumor DNA testing, to have acquired KRAS G12V, KRAS Q61R, U2AF1 R156H (%%PUBMED:32859654%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E IDH1 R132C KRAS G12V KRAS Q61R U2AF1 R156H","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - resistant","pub_med_references":[32859654],"normalized_drug":"Dabrafenib, Trametinib","indication":"lung non-small cell carcinoma","therapy_id":1066,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical study, a non-small cell lung cancer patient harboring BRAF V600E demonstrated disease progression when treated with the combination of Tafinlar (dabrafenib) and Mekinist (trametinib), and was found, via circulating tumor DNA testing, to have acquired U2AF1 Q157P (%%PUBMED:32859654%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E U2AF1 Q157P","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[33824136],"response_type":"resistant","indication":"pancreatic ductal adenocarcinoma","therapy_id":7769,"normalized_cancer":"Pancreatic Adenocarcinoma","evidence_type":"Actionable","therapy":"Adagrasib","efficacy_evidence":"In a preclinical study, Krazati (adagrasib) failed to inhibit phosphorylation of Erk and Rsk in pancreatic ductal adenocarcinoma cells expressing BRAF V600E and KRAS G12C in culture (%%PUBMED:33824136%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E KRAS G12C","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[37611121],"response_type":"predicted - resistant","indication":"large cell neuroendocrine carcinoma","therapy_id":10876,"normalized_cancer":"Large Cell Neuroendocrine Carcinoma","evidence_type":"Actionable","therapy":"Divarasib","efficacy_evidence":"In a Phase I trial, BRAF V600E was identified in the post-progression circulating tumor DNA of a patient with lung large cell neuroendocrine carcinoma harboring KRAS G12C who previously responded to treatment with Divarasib (GDC-6036) (%%PUBMED:37611121%%; NCT04449874).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E KRAS G12C","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - resistant","pub_med_references":[36967525],"normalized_drug":"Cobimetinib, Vemurafenib","indication":"ovarian serous cystadenocarcinoma","therapy_id":1657,"normalized_cancer":"Serous Ovarian Cancer","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"In a clinical case study, a patient with low-grade serous cystadenocarcinoma of the ovary harboring BRAF V600E demonstrated progressive disease on treatment with the combination of Zelboraf (vemurafenib) and Cotellic (cobimetinib) and was found to have acquired KRAS G12C (%%PUBMED:36967525%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E KRAS G12C","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[34161704],"response_type":"predicted - resistant","profile_array":[{"type":"M1","gene":"H95R"}],"indication":"colorectal cancer","therapy_id":7769,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Adagrasib","efficacy_evidence":"In a Phase Ib/II trial, a colorectal cancer patient harboring KRAS G12C who initially responded to treatment with Krazati (adagrasib) progressed and through circulating tumor DNA testing was found to have acquired several mutations including KRAS H95Q, KRAS H95R, KRAS G12R/D/V, KRAS G13D, KRAS Q61H, MAP2K1 K57N/T, CCDC6-RET, and BRAF V600E (%%PUBMED:34161704%%; NCT03785249).","cap_asco_evidence_level":"D","molecular_profile":"CCDC6 - RET BRAF V600E KRAS G12C KRAS G12R KRAS G12V KRAS G13D KRAS Q61H KRAS H95Q KRAS H95R MAP2K1 K57N MAP2K1 K57T","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[34161704],"response_type":"predicted - resistant","indication":"lung adenocarcinoma","therapy_id":7769,"normalized_cancer":"Lung Adenocarcinoma","evidence_type":"Actionable","therapy":"Adagrasib","efficacy_evidence":"In a Phase Ib/II trial, a lung adenocarcinoma patient harboring KRAS G12C who initially responded to treatment with Krazati (adagrasib) progressed and through circulating tumor DNA testing was found to have acquired several mutations including KRAS G12V/W, KRAS R68S, KRAS H95D, and BRAF V600E (%%PUBMED:34161704%%; NCT03785249).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E KRAS G12C KRAS G12V KRAS G12W KRAS R68S KRAS H95D","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[33953400],"response_type":"predicted - resistant","indication":"melanoma","therapy_id":7209,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Belvarafenib","efficacy_evidence":"In a Phase I trial, a melanoma patient harboring BRAF V600E initially demonstrated stable disease on treatment with Belvarafenib (HM95573), however, later developed disease progression likely due to the acquisition of a secondary resistance mutation ARAF P462L (%%PUBMED:33953400%%; NCT03118817).","cap_asco_evidence_level":"D","molecular_profile":"ARAF P462L BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[33953400],"response_type":"predicted - resistant","indication":"melanoma","therapy_id":7209,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Belvarafenib","efficacy_evidence":"In a Phase I trial, a melanoma patient harboring BRAF V600E initially demonstrated stable disease on treatement with Belvarafenib (HM95573), however, later developed disease progression likely due to the acquisition of a secondary resistance mutation ARAF G377R, and expression of ARAF G377R in a melanoma cell line harboring BRAF V600E conferred resistance to Belvarafenib (HM95573) in culture (%%PUBMED:33953400%%; NCT03118817).","cap_asco_evidence_level":"D","molecular_profile":"ARAF G377R BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[33953400],"response_type":"predicted - resistant","indication":"nephroblastoma","therapy_id":7209,"normalized_cancer":"Wilms' Tumor","evidence_type":"Actionable","therapy":"Belvarafenib","efficacy_evidence":"In a Phase I trial, a nephroblastoma patient harboring BRAF V600E initially demonstrated stable disease on treatment with Belvarafenib (HM95573), however, later developed disease progression likely due to the acquisition of a secondary resistance mutation, ARAF G387N (%%PUBMED:33953400%%; NCT03118817).","cap_asco_evidence_level":"D","molecular_profile":"ARAF G387N BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[33953400],"response_type":"predicted - resistant","indication":"melanoma","therapy_id":7209,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Belvarafenib","efficacy_evidence":"In a preclinical study, a melanoma cell line harboring BRAF V600E and expressing ARAF G387N was resistant to treatment with Belvarafenib (HM95573) in culture (%%PUBMED:33953400%%).","cap_asco_evidence_level":"D","molecular_profile":"ARAF G387N BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[31744895],"response_type":"predicted - sensitive","indication":"melanoma","therapy_id":4588,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"LY3214996","efficacy_evidence":"In a preclinical study, a melanoma cell line harboring BRAF V600E, BRAF V600M, BRAF V600K and NF1 loss was sensitive to treatment with LY3214996 in culture, demonstrating decreased cell proliferation (%%PUBMED:31744895%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E BRAF V600K BRAF V600M NF1 loss","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[33947696],"response_type":"predicted - resistant","indication":"melanoma","therapy_id":4129,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Palbociclib + Vemurafenib","efficacy_evidence":"In a preclinical study, Ibrance (palbociclib) and Zelboraf (vemurafenib) combination therapy in a melanoma cell line harboring BRAF V600E, CDKN2A loss, RB1 expression, and decreased expression of CHEK2 via siRNA resulted in increased cell proliferation and p-ERK levels compared to treated cells without decreased expression of CHEK2 in culture (%%PUBMED:33947696%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E CDKN2A loss CHEK2 dec exp RB1 pos","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - resistant","pub_med_references":[33709535],"normalized_drug":"Infigratinib","indication":"intrahepatic cholangiocarcinoma","therapy_id":674,"normalized_cancer":"Intrahepatic Cholangiocarcinoma","evidence_type":"Actionable","therapy":"Infigratinib","efficacy_evidence":"In a preclinical study, expression of BRAF V600E in an intrahepatic cholangiocarcinoma cell line harboring FGFR2-PPHLN1 conferred resistance to treatment with Infigratinib (BGJ398) in culture (%%PUBMED:33709535%%).","cap_asco_evidence_level":"D","molecular_profile":"FGFR2 - PPHLN1 BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - resistant","pub_med_references":[34376578],"normalized_drug":"Cobimetinib, 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combination therapy with Zelboraf (vemurafenib) and Cotellic (cobimetinib), likely due to acquisition of NRAS G12V and a loss of one copy of CDKN2A (%%PUBMED:34376578%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E CDKN2A loss NRAS G12V","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - resistant","pub_med_references":[38617091],"normalized_drug":"Osimertinib","indication":"lung adenocarcinoma","therapy_id":660,"normalized_cancer":"Lung Adenocarcinoma","evidence_type":"Actionable","therapy":"Osimertinib","efficacy_evidence":"In a clinical case study, BRAF V600E was identified in post-progression biopsy in a patient with metastatic lung adenocarcinoma harboring EGFR E746_A750del and EGFR T790M, who previously achieved stable disease with Tagrisso (osimertinib) treatment (%%PUBMED:38617091%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E EGFR E746_A750del EGFR T790M","approval_status":"Case Reports/Case 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Adenocarcinoma","evidence_type":"Actionable","therapy":"Osimertinib + Vemurafenib","efficacy_evidence":"In a clinical case study, the combination of Tagrisso (osimertinib) and Zelboraf (vemurafenib) resulted in stable disease and improvement of clinical symptoms in a lung adenocarcinoma patient harboring EGFR E746_A750del, EGFR T790M, and BRAF V600E (%%PUBMED:32693944%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E EGFR E746_A750del EGFR T790M","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"resistant","pub_med_references":[31925410],"normalized_drug":"Dabrafenib","indication":"melanoma","therapy_id":3,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a preclinical study, melanoma cells harboring BRAF V600E and expressing BRAF I463W or expressing BRAF V600E and I463W in cis demonstrated resistance to Tafinlar (dabrafenib) treatment in culture (%%PUBMED:31925410%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF I463W BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"resistant","pub_med_references":[31925410],"normalized_drug":"Dabrafenib","indication":"melanoma","therapy_id":3,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a preclinical study, expression of BRAF L485S in melanoma cells harboring BRAF V600E conferred resistance to Tafinlar (dabrafenib) treatment in culture (%%PUBMED:31925410%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF L485S BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"therapy_id":3,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a preclinical study, expression of MAP2K1 S218D and S222D in melanoma cells harboring BRAF V600E conferred resistance to Tafinlar (dabrafenib) treatment in culture (%%PUBMED:31925410%%).","therapy":"Dabrafenib","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Preclinical - Cell culture","normalized_drug":"Dabrafenib","pub_med_references":[31925410],"molecular_profile":"BRAF V600E MAP2K1 S218D MAP2K1 S222D","profile_array":[{"type":"M1","gene":"V600E"}],"response_type":"resistant"},{"therapy_id":699,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a preclinical study, expression of MAP2K1 L115R in melanoma cells harboring BRAF V600E conferred resistance to CI-1040 (PD184352) treatment in culture (%%PUBMED:19915144%%).","therapy":"CI-1040","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Preclinical - Cell culture","normalized_drug":"Ci-1040","pub_med_references":[19915144],"molecular_profile":"BRAF V600E MAP2K1 L115R","profile_array":[{"type":"M1","gene":"V600E"}],"response_type":"resistant"},{"pub_med_references":[19915144],"response_type":"resistant","profile_array":[{"type":"M1","gene":"V600E"}],"indication":"melanoma","therapy_id":1060,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"PLX4720","efficacy_evidence":"In a preclinical study, expression of MAP2K1 L115R in melanoma cells harboring BRAF V600E conferred resistance to PLX4720 treatment in culture (%%PUBMED:19915144%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E MAP2K1 L115R","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"therapy_id":913,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a preclinical study, expression of MAP2K1 L115R in melanoma cells harboring BRAF V600E conferred resistance to Koselugo (selumetinib) treatment in culture (%%PUBMED:19915144%%).","therapy":"Selumetinib","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Preclinical - Cell culture","normalized_drug":"Selumetinib","pub_med_references":[19915144],"molecular_profile":"BRAF V600E MAP2K1 L115R","profile_array":[{"type":"M1","gene":"V600E"}],"response_type":"resistant"},{"response_type":"resistant","pub_med_references":[34433654],"normalized_drug":"Vemurafenib","indication":"high grade glioma","therapy_id":342,"normalized_cancer":"High-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a preclinical study, a glioma cell line harboring BRAF V600E developed resistance after prolonged exposure to Zelboraf (vemurafenib) in culture, and was subsequently found to have acquired ERRFI1 S251* (%%PUBMED:34433654%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E ERRFI1 S251*","approval_status":"Preclinical - Cell 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harboring BRAF V600E was found to have acquired KRAS Q61H prior to progression on treatment with the combination of Zelboraf (vemurafenib), Erbitux (cetuximab), Adrucil (fluorouracil), and Wellcovorin (leucovorin) (%%PUBMED:36921494%%; NCT02291289).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E KRAS Q61H","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[32669268],"response_type":"predicted - resistant","indication":"colon adenocarcinoma","therapy_id":1331,"normalized_cancer":"Colon Adenocarcinoma","evidence_type":"Actionable","therapy":"Cetuximab + Irinotecan + Vemurafenib","efficacy_evidence":"In a clinical case study, BRAF V47_M438del (reported as deletion of exons 2-10) was identified in the post-progression biopsy of a patient with colon adenocarcinoma harboring BRAF V600E, who previously responded to the combination of Captosar (irinotecan), Erbitux (cetuximab), and Zelboraf (vemurafenib) (%%PUBMED:32669268%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V47_M438del BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[33580193],"response_type":"predicted - sensitive","indication":"lung adenocarcinoma","therapy_id":12100,"normalized_cancer":"Lung Adenocarcinoma","evidence_type":"Actionable","therapy":"Dabrafenib + Osimertinib + Trametinib","efficacy_evidence":"In a clinical case study, a patient with metastatic lung adenocarcinoma harboring EGFR E746_A750del, EGFR T790M, BRAF V600E, and PIK3CA E545K, who had previously progressed on Tagrisso (osimertinib), demonstrated a partial response in the lung and bones and complete response in the lymph nodes with clinical improvement following treatment with the combination of Tagrisso (osimertinib), Tafinlar (dabrafenib), and Mekinist (trametinib) (%%PUBMED:33580193%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E EGFR E746_A750del EGFR T790M PIK3CA 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expressing RAC1 P29S were resistant to Mekinist (trametinib) in culture (%%PUBMED:25056119%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E RAC1 P29S","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[25056119],"response_type":"resistant","indication":"melanoma","therapy_id":1060,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"PLX4720","efficacy_evidence":"In a preclinical study, melanoma cells harboring BRAF V600E and expressing RAC1 P29S were resistant to PLX4720 in a cell line xenograft model, resulting in persistent tumor growth and decreased overall survival (%%PUBMED:25056119%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E RAC1 P29S","approval_status":"Preclinical - Cell line 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a colorectal cancer cell line harboring LMNA-NTRK1 and expressing BRAF V600E resulted in tumor growth suppression and inhibition of Akt, Erk, and Mek signaling in culture (%%PUBMED:31406350%%).","cap_asco_evidence_level":"D","molecular_profile":"LMNA - NTRK1 BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[37972659],"response_type":"sensitive","indication":"cholangiocarcinoma","therapy_id":16054,"normalized_cancer":"Cholangiocarcinoma","evidence_type":"Actionable","therapy":"Futibatinib + Trametinib","efficacy_evidence":"In a preclinical study, treatment with the combination of Lytgobi (futibatinib) and Mekinist (trametinib) treatment synergistically decreased survival in a cholangiocyte cell line expressing FGFR2-BICC1 and BRAF V600E in culture (%%PUBMED:37972659%%).","cap_asco_evidence_level":"D","molecular_profile":"FGFR2 - BICC1 BRAF V600E","approval_status":"Preclinical - Cell 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treatment synergistically decreased survival in a cholangiocyte cell line expressing FGFR2-BICC1 and BRAF V600E in culture (%%PUBMED:37972659%%).","cap_asco_evidence_level":"D","molecular_profile":"FGFR2 - BICC1 BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[37972659],"response_type":"sensitive","indication":"cholangiocarcinoma","therapy_id":16055,"normalized_cancer":"Cholangiocarcinoma","evidence_type":"Actionable","therapy":"Futibatinib + TAS-117","efficacy_evidence":"In a preclinical study, treatment with the combination of Lytgobi (futibatinib) and TAS-117 treatment synergistically decreased survival in a cholangiocyte cell line expressing FGFR2-BICC1 and BRAF V600E in culture (%%PUBMED:37972659%%).","cap_asco_evidence_level":"D","molecular_profile":"FGFR2 - BICC1 BRAF V600E","approval_status":"Preclinical - Cell 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(%%PUBMED:37729428%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NRAS Q61R","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[37729428],"normalized_drug":"Dabrafenib, Trametinib","indication":"melanoma","therapy_id":1066,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a preclinical study, treatment with the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) moderately inhibited tumor growth in a melanoma patient-derived xenograft (PDX) model harboring BRAF V600E and NRAS Q61R (%%PUBMED:37729428%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NRAS Q61R","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"pub_med_references":[37729428],"response_type":"sensitive","indication":"melanoma","therapy_id":16205,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Binimetinib + 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(%%PUBMED:37729428%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NRAS Q61R","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"pub_med_references":[37729428],"response_type":"sensitive","indication":"melanoma","therapy_id":16204,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Encorafenib + Talazoparib","efficacy_evidence":"In a preclinical study, treatment with the combination of Talzenna (talazoparib) and Braftovi (encorafenib) synergistically inhibited viability of patient-derived melanoma spheroids harboring BRAF V600E and NRAS Q61R in culture (%%PUBMED:37729428%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NRAS Q61R","approval_status":"Preclinical - Patient cell 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controls in a melanoma patient-derived xenograft (PDX) model harboring BRAF V600E and NRAS Q61R (%%PUBMED:37729428%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NRAS Q61R","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"pub_med_references":[37729428],"response_type":"sensitive","indication":"melanoma","therapy_id":16205,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Binimetinib + Encorafenib + Talazoparib","efficacy_evidence":"In a preclinical study, treatment with the combination of Talzenna (talazoparib), Braftovi (encorafenib), and Mektovi (binimetinib) synergistically inhibited viability of patient-derived melanoma spheroids harboring BRAF V600E and NRAS Q61H in culture (%%PUBMED:37729428%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E NRAS Q61H","approval_status":"Preclinical - Patient cell 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cancer cell line harboring BRAF V600E and PIK3CA E542k to Sprycel (dasatinib) and Mekinist (trametinib) combination treatment in culture (%%PUBMED:37713162%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E PIK3CA E542K","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[37713162],"response_type":"resistant","indication":"anaplastic thyroid carcinoma","therapy_id":4599,"normalized_cancer":"Anaplastic Thyroid Cancer","evidence_type":"Actionable","therapy":"Dasatinib + Trametinib","efficacy_evidence":"In a preclinical study, an anaplastic thyroid cancer cell line harboring BRAF V600E and PIK3CA E542K was resistant to the combination of Sprycel (dasatinib) and Mekinist (trametinib) in culture (%%PUBMED:37713162%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E PIK3CA E542K","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[37713162],"response_type":"sensitive","indication":"anaplastic thyroid carcinoma","therapy_id":16262,"normalized_cancer":"Anaplastic Thyroid Cancer","evidence_type":"Actionable","therapy":"GSK2334470 + Trametinib","efficacy_evidence":"In a preclinical study, the addition of GSK2334470 sensitized an anaplastic thyroid cancer cell line harboring BRAF V600E and PIK3CA E542K to Mekinist (trametinib) treatment as demonstrated by a reduction in viability in culture (%%PUBMED:37713162%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E PIK3CA E542K","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[37713162],"response_type":"resistant","indication":"anaplastic thyroid carcinoma","therapy_id":4599,"normalized_cancer":"Anaplastic Thyroid Cancer","evidence_type":"Actionable","therapy":"Dasatinib + Trametinib","efficacy_evidence":"In a preclinical study, an anaplastic thyroid cancer cell line harboring BRAF V600E and PIK3CA N1044S was resistant to the combination of Sprycel (dasatinib) and Mekinist (trametinib) in culture (%%PUBMED:37713162%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E PIK3CA N1044S","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[37713162],"response_type":"sensitive","indication":"anaplastic thyroid carcinoma","therapy_id":16262,"normalized_cancer":"Anaplastic Thyroid Cancer","evidence_type":"Actionable","therapy":"GSK2334470 + Trametinib","efficacy_evidence":"In a preclinical study, the addition of GSK2334470 sensitized an anaplastic thyroid cancer cell line harboring BRAF V600E and PIK3CA N1044S to Mekinist (trametinib) treatment as demonstrated by a reduction in viability in culture (%%PUBMED:37713162%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E PIK3CA N1044S","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[37713162],"response_type":"resistant","indication":"anaplastic thyroid carcinoma","therapy_id":16264,"normalized_cancer":"Anaplastic Thyroid Cancer","evidence_type":"Actionable","therapy":"Dasatinib + MK2206 + Trametinib","efficacy_evidence":"In a preclinical study, the addition of MK2206 did not sensitize an anaplastic thyroid cancer cell line harboring BRAF V600E and PIK3CA N1044S to Sprycel (dasatinib) and Mekinist (trametinib) combination treatment in culture (%%PUBMED:37713162%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E PIK3CA N1044S","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[37713162],"response_type":"sensitive","profile_array":[{"type":"M1","gene":"PIK3CA"}],"indication":"anaplastic thyroid carcinoma","therapy_id":4599,"normalized_cancer":"Anaplastic Thyroid Cancer","evidence_type":"Actionable","therapy":"Dasatinib + Trametinib","efficacy_evidence":"In a preclinical study, the combination of Sprycel (dasatinib) and Mekinist (trametinib) inhibited viability of an anaplastic thyroid cancer cell line harboring BRAF V600E and PIK3CA M1043I in culture (%%PUBMED:37713162%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E PIK3CA M1043I","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[37713162],"response_type":"sensitive","indication":"papillary thyroid carcinoma","therapy_id":4599,"normalized_cancer":"Papillary Thyroid Cancer","evidence_type":"Actionable","therapy":"Dasatinib + Trametinib","efficacy_evidence":"In a preclinical study, the combination of Sprycel (dasatinib) and Mekinist (trametinib) inhibited viability of a papillary thyroid cancer cell line harboring BRAF V600E and PIK3CA E542K and W11C in culture (%%PUBMED:37713162%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E PIK3CA W11C PIK3CA E542K","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"resistant","pub_med_references":[37838724],"normalized_drug":"Dabrafenib, Trametinib","indication":"melanoma","therapy_id":1066,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a preclinical study, melanoma cell lines harboring BRAF V600E with AR overexpression were resistant to the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) in culture (%%PUBMED:37838724%%).","cap_asco_evidence_level":"D","molecular_profile":"AR over exp BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[37838724],"normalized_drug":"Azd3514","indication":"melanoma","therapy_id":2826,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"AZD3514","efficacy_evidence":"In a preclinical study, AZD3514 inhibited proliferation and induced cell death in BRAF inhibitor-resistant melanoma cell lines with AR overexpression and harboring BRAF V600E in culture and decreased tumor growth in a cell line xenograft model and syngeneic mouse model (%%PUBMED:37838724%%).","cap_asco_evidence_level":"D","molecular_profile":"AR over exp BRAF V600E","approval_status":"Preclinical","amp_tier":"II"},{"response_type":"resistant","pub_med_references":[37838724],"normalized_drug":"Dabrafenib","indication":"melanoma","therapy_id":3,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a preclinical study, melanoma cell lines harboring BRAF V600E demonstrated resistance to Tafinlar (dabrafenib), and were found to have increased AR expression (%%PUBMED:37838724%%).","cap_asco_evidence_level":"D","molecular_profile":"AR over exp BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[37838724],"response_type":"sensitive","indication":"melanoma","therapy_id":15932,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"ARCC4","efficacy_evidence":"In a preclinical study, ARCC4 inhibited proliferation and induced cell death in BRAF inhibitor-resistant melanoma cell lines with AR overexpression and harboring BRAF V600E in culture (%%PUBMED:37838724%%).","cap_asco_evidence_level":"D","molecular_profile":"AR over exp BRAF V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - resistant","pub_med_references":[38229767],"normalized_drug":"Lorlatinib","indication":"lung adenocarcinoma","therapy_id":869,"normalized_cancer":"Lung Adenocarcinoma","evidence_type":"Actionable","therapy":"Lorlatinib","efficacy_evidence":"In a clinical case study, BRAF V600E and ALK V1180L were identified in a post-progression biopsy in a lung adenocarcinoma patient harboring HIP1-ALK who progressed on third-line treatment with Lorbrena (lorlatinib) (%%PUBMED:38229767%%).","cap_asco_evidence_level":"D","molecular_profile":"HIP1 - ALK ALK V1180L BRAF V600E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - 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G12R was identified in post-progression biopsy in a patient with metastatic colon adenocarcinoma harboring BRAF V600E who previously responded to Zelboraf (vemurafenib) treatment (%%PUBMED:30036146%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E KRAS G12R","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[37611121],"response_type":"predicted - resistant","indication":"colorectal cancer","therapy_id":10876,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Divarasib","efficacy_evidence":"In a Phase I trial, KRAS G12V, KRAS G12A, KRAS G12D, KRAS Y96D, KRAS A146T, BRAF V600E, and KRAS amplification were identified in the post-progression circulating tumor DNA of a patient with colorectal cancer harboring KRAS G12C who previously responded to treatment with Divarasib (GDC-6036) (%%PUBMED:37611121%%; NCT04449874).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E KRAS G12A KRAS G12C KRAS G12D KRAS G12V KRAS Y96D KRAS A146T KRAS amp","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[38429896],"normalized_drug":"Dabrafenib, Trametinib","indication":"lung adenocarcinoma","therapy_id":1066,"normalized_cancer":"Lung Adenocarcinoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, second-line treatment with the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) resulted in a clinical response lasting at least 5 years in a patient with lung adenocarcinoma harboring BRAF V600E and high CD274 (PD-L1) expression (TPS=100%) who did not respond to first-line Keytruda (pembrolizumab) (%%PUBMED:38429896%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E CD274 over exp","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[39507030],"response_type":"sensitive","indication":"lung non-small cell 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acquired BRAF V600E (%%PUBMED:35952324%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E EGFR L858R","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[34707694],"normalized_drug":"Dabrafenib, Trametinib","indication":"lung adenocarcinoma","therapy_id":1066,"normalized_cancer":"Lung Adenocarcinoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a clinical case study, treatment with the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) resulted in a partial response after 24 days in a patient with metastatic lung adenocarcinoma harboring EGFR L858R and BRAF V600E (%%PUBMED:34707694%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E EGFR L858R","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - resistant","pub_med_references":[34707694],"normalized_drug":"Afatinib","indication":"lung 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V600E (%%PUBMED:38449561%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E EGFR L858R","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[38711893],"response_type":"predicted - sensitive","profile_array":[{"type":"M1","gene":"V600E"}],"indication":"colon adenocarcinoma","therapy_id":16933,"normalized_cancer":"Colon Adenocarcinoma","evidence_type":"Actionable","therapy":"Crizotinib + Regorafenib + Tislelizumab","efficacy_evidence":"In a clinical case study, treatment with the combination of Tevimbra (tislelizumab), Stivarga (regorafenib), and Xalkori (crizotinib) resulted in a partial response in the primary tumor and liver metastases in a patient with metastatic colon adenocarcinoma harboring BRAF V600E, MET amplification, and TPM4-ALK (%%PUBMED:38711893%%).","cap_asco_evidence_level":"D","molecular_profile":"TPM4 - ALK BRAF V600E MET amp","approval_status":"Case Reports/Case 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melanoma patient harboring BRAF V600E who was treated with Zelboraf (vemurafenib) (%%PUBMED:22113612%%).","therapy":"Vemurafenib","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Case Reports/Case Series","normalized_drug":"Vemurafenib","pub_med_references":[22113612],"molecular_profile":"BRAF del exon4-8 BRAF V600E","profile_array":[{"type":"del exon","number":4,"gene":"BRAF"}],"response_type":"predicted - resistant"},{"pub_med_references":[38691346],"response_type":"sensitive","profile_array":[{"type":"del exon","number":4,"gene":"BRAF"}],"indication":"melanoma","therapy_id":13603,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Binimetinib + PF-07799933","efficacy_evidence":"In a preclinical study, treatment with the combination of PF-07799933 and Mektovi (binimetinib) resulted in tumor regression in a patient-derived xenograft (PDX) model of melanoma harboring BRAF V600E and a BRAF exon 4-8 deletion variant (reported as p61 splice variant) (%%PUBMED:38691346%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF del exon4-8 BRAF V600E","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"therapy_id":1066,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a clinical case study, a BRAF exon 4-8 deletion variant (reported as p61) was identified in the post-progression plasma ctDNA of two patients with metastatic melanoma harboring BRAF V600E who previously responded to treatment with the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) (%%PUBMED:33216826%%).","therapy":"Dabrafenib + Trametinib","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Case Reports/Case Series","normalized_drug":"Dabrafenib, Trametinib","pub_med_references":[33216826],"molecular_profile":"BRAF del exon4-8 BRAF V600E","profile_array":[{"type":"del exon","number":4,"gene":"BRAF"}],"response_type":"predicted - 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melanoma patient harboring BRAF V600E who was treated with Zelboraf (vemurafenib) (%%PUBMED:22113612%%).","therapy":"Vemurafenib","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Case Reports/Case Series","normalized_drug":"Vemurafenib","pub_med_references":[22113612],"molecular_profile":"BRAF del exon2-8 BRAF V600E","profile_array":[{"type":"del exon","number":2,"gene":"BRAF"}],"response_type":"predicted - resistant"},{"therapy_id":342,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a clinical case study, a deletion of BRAF exons 4-10 was identified in the post-progression biopsy of a melanoma patient harboring BRAF V600E who was treated with Zelboraf (vemurafenib) (%%PUBMED:22113612%%).","therapy":"Vemurafenib","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Case Reports/Case 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proliferation and synergistically decreased viability in a patient-derived colorectal cancer cell line harboring BRAF V600E and PTEN R173C (%%PUBMED:39145064%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E PTEN R173C","approval_status":"Preclinical - Patient cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[39500140],"normalized_drug":"Dabrafenib, Trametinib","indication":"melanoma","therapy_id":1066,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a retrospective analysis, treatment with the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) resulted in a partial response with an overall survival of 51.1 months and a duration of treatment of 4.1 months in a melanoma patient harboring BRAF V600E and IDH1 R132C (%%PUBMED:39500140%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E IDH1 R132C","approval_status":"Case Reports/Case 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cancer","therapy_id":4525,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Dabrafenib","efficacy_evidence":"In a preclinical study, a colorectal cancer cell line harboring BRAF V600E and expressing EGFR S464L was resistant to treatment with the combination of Tafinlar (dabrafenib) and Erbitux (cetuximab) in culture (%%PUBMED:39424923%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E EGFR S464L","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[39424923],"response_type":"resistant","profile_array":[{"type":"M1","gene":"V600E"}],"indication":"colorectal cancer","therapy_id":4525,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Dabrafenib","efficacy_evidence":"In a preclinical study, Tafinlar (dabrafenib) and Erbitux (cetuximab) combination treatment inhibited senescence in a colorectal cancer cell line harboring BRAF V600E and expressing MAP2K1 Y130C in culture (%%PUBMED:39424923%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E MAP2K1 Y130C","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[39424923],"response_type":"resistant","profile_array":[{"type":"M1","gene":"V600E"}],"indication":"colorectal cancer","therapy_id":4525,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Dabrafenib","efficacy_evidence":"In a preclinical study, Tafinlar (dabrafenib) and Erbitux (cetuximab) combination treatment increased growth of a colorectal cancer cell line harboring BRAF V600E and expressing MAP2K2 Y134H in culture (%%PUBMED:39424923%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E MAP2K2 Y134H","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"therapy_id":2,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a preclinical study, Mekinist (trametinib) treatment increased growth of a colorectal 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(%%PUBMED:39424923%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E MAP2K1 S194P","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"resistant","pub_med_references":[39574163],"normalized_drug":"Vemurafenib","indication":"melanoma","therapy_id":342,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a preclinical study, melanoma cells harboring BRAF V600E and overexpressing PDE4D were resistant to Zelboraf (vemurafenib) in culture (%%PUBMED:39574163%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E PDE4D over exp","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[39574163],"response_type":"resistant","indication":"melanoma","therapy_id":17922,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Roflumilast + Vemurafenib","efficacy_evidence":"In a preclinical study, melanoma cells harboring BRAF V600E and overexpressing PDE4D were resistant to the combination of Roflumilast and Zelboraf (vemurafenib) in culture (%%PUBMED:39574163%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E PDE4D over exp","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"resistant","pub_med_references":[39574163],"normalized_drug":"Cobimetinib","indication":"melanoma","therapy_id":1004,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Cobimetinib","efficacy_evidence":"In a preclinical study, melanoma cells harboring BRAF V600E and overexpressing PDE4D were resistant to Cotellic (cobimetinib) in culture (%%PUBMED:39574163%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E PDE4D over exp","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - resistant","pub_med_references":[39611930],"normalized_drug":"Trastuzumab","indication":"Her2-receptor positive breast 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NCT02688517).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E BRAF amp MET amp","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - resistant","pub_med_references":[37806383],"normalized_drug":"Osimertinib","indication":"lung non-small cell carcinoma","therapy_id":660,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Osimertinib","efficacy_evidence":"In a retrospective analysis, BRAF V600E and FGFR3 K650E were identified at the time of progression on Tagrisso (osimertinib) treatment in a non-small cell lung cancer patient harboring EGFR L858R (%%PUBMED:37806383%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E EGFR L858R FGFR3 K650E","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[34376578],"response_type":"predicted - 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melanoma harboring BRAF V600E, NRAS G12V, and CDKN2A copy number loss (%%PUBMED:34376578%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E CDKN2A del NRAS G12V","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"therapy_id":698,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a retrospective analysis of a Phase III trial (J-ALEX), BRAF V600E was identified in the post-progression cell-free DNA of a patient with non-small lung cancer with ALK rearrangement who progressed on treatment with Alecensa (alectinib) (%%PUBMED:40912045%%).","therapy":"Alectinib","evidence_type":"Actionable","normalized_cancer":"Non-Small Cell Lung Cancer","indication":"lung non-small cell carcinoma","approval_status":"Case Reports/Case Series","normalized_drug":"Alectinib","pub_med_references":[40912045],"molecular_profile":"ALK rearrange BRAF V600E","profile_array":[{"type":"rearrange","gene":"ALK"}],"response_type":"predicted - 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V600E","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"resistant","pub_med_references":[40481178],"normalized_drug":"Vemurafenib","indication":"colorectal cancer","therapy_id":342,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a preclinical study, Src-overexpressing colorectal cancer cell lines harboring BRAF V600E were resistant to Zelboraf (vemurafenib) in culture (%%PUBMED:40481178%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E SRC over exp","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"resistant","pub_med_references":[40481178],"normalized_drug":"Encorafenib","indication":"colorectal cancer","therapy_id":796,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Encorafenib","efficacy_evidence":"In a preclinical study, Src-overexpressing colorectal cancer cell lines harboring BRAF V600E were resistant to Braftovi (encorafenib) in culture (%%PUBMED:40481178%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E SRC over exp","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - resistant","pub_med_references":[36849494],"normalized_drug":"Osimertinib","indication":"lung non-small cell carcinoma","therapy_id":660,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Osimertinib","efficacy_evidence":"In a Phase III trial (FLAURA), EGFR C797S, BRAF V600E, and PIK3CA H1047R were identified at the time of progression on Tagrisso (osimertinib) in a patient with non-small cell lung cancer harboring EGFR E746_A750del (%%PUBMED:36849494%%; NCT02296125).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E EGFR E746_A750del EGFR C797S PIK3CA H1047R","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"predicted - 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patients with unresectable, BRAF inhibitor naive, metastatic melanoma harboring BRAF V600E (n=20) or V600K (n=1) resulted in complete and partial responses in 15% (3/20) and 60% (12/20) of evaluable patients, respectively, a 9.2-month median progression free survival, and a 34.6-month overall survival (%%PUBMED:29674508%%).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E/K","approval_status":"Phase I","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Vemurafenib","indication":"skin melanoma","therapy_id":342,"normalized_cancer":"Cutaneous Melanoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"Zelboraf (vemurafenib) therapy is included in cutaneous melanoma guidelines for patients with metastatic or unresectable disease harboring a BRAF V600 activating mutation (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E/K","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[22663011],"normalized_drug":"Trametinib","indication":"melanoma","therapy_id":2,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Trametinib","efficacy_evidence":"In a Phase III trial (METRIC) that supported FDA approval, Mekinist (trametinib) treatment, as compared to Deticine (dacarbazine) or Taxol (paclitaxel) treatment, resulted in improved progression-free survival of 4.8 months versus 1.5 months and an overall six month survival rate of 81% versus 67% in patients with BRAF V600E/K positive metastatic melanoma (%%PUBMED:22663011%%; NCT01245062).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E/K","approval_status":"FDA approved - On Companion Diagnostic","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[22805292],"normalized_drug":"Trametinib","indication":"melanoma","therapy_id":2,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Trametinib","efficacy_evidence":"In a Phase I trial, Mekinist (trametinib) resulted in complete response in 7% (2/30), partial response in 33% (10/30), and stable disease in 37% (11/30) of BRAF-mutant melanoma patients (%%PUBMED:22805292%%; NCT00687622).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E/K","approval_status":"Phase I","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[27480103],"normalized_drug":"Cobimetinib, Vemurafenib","indication":"melanoma","therapy_id":1657,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"In a Phase III trial (coBRIM) that supported FDA approval, treatment with the combination of Zelboraf (vemurafenib) and Cotellic (cobimetinib) resulted in an improved progression-free survival of 12.3 months, compared to 7.2 months with Zelboraf (vemurafenib) plus placebo, among patients with BRAF V600-mutated metastatic melanoma, and BRAF V600E and BRAF V600K are on the companion diagnostic (%%PUBMED:27480103%%; NCT01689519).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E/K","approval_status":"FDA approved - On Companion Diagnostic","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[33020646],"normalized_drug":"Dabrafenib, Trametinib","indication":"melanoma","therapy_id":1066,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a Phase II trial (S1320), intermittent dosing (3-week-off, 5-week-on) of Tafinlar (dabrafenib) and Mekinist (trametinib) did not improve median progression-free survival (5.5 v 9.0 months; HR=1.36, p=0.064, two-sided alpha=0.2) compared to continuous dosing in melanoma patients harboring BRAF V600E or V600K, and there were no significant differences in median overall survival, treatment response, or toxicity between the two treatment groups (%%PUBMED:33020646%%; NCT02196181).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600E/K","approval_status":"Phase II","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[25399551],"normalized_drug":"Dabrafenib, Trametinib","indication":"melanoma","therapy_id":1066,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a Phase III trial (COMBI-v) that supported FDA approval, the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) resulted in an improved overall survival rate at 12 months (72% vs 65%, HR=0.69, p=0.005), median progression-free survival (11.4 vs 7.3 months, HR=0.56, p<0.001), and objective response rate (64% vs 51%, p<0.001) compared to Zelboraf (vemurafenib) in melanoma patients harboring BRAF V600E or V600K (%%PUBMED:25399551%%; NCT01597908).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E/K","approval_status":"FDA approved - On Companion Diagnostic","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[28891408],"normalized_drug":"Dabrafenib, Trametinib","indication":"melanoma","therapy_id":1066,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a Phase III trial (COMBI-AD) that supported FDA approval, adjuvant treatment with the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) resulted in an improved estimated 3-year relapse-free survival rate (58% vs 39%, HR=0.47, P<0.001) and 3-year overall survival rate (86% vs 77%, HR=0.57; 95% CI, 0.42 to 0.79, P=0.0006) compared to placebo in stage III melanoma patients harboring BRAF V600E or V600K mutations (%%PUBMED:28891408%%; NCT01682083).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E/K","approval_status":"FDA approved - On Companion Diagnostic","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[30959471],"normalized_drug":"Binimetinib, Encorafenib","indication":"skin melanoma","therapy_id":1100,"normalized_cancer":"Cutaneous Melanoma","evidence_type":"Actionable","therapy":"Binimetinib + Encorafenib","efficacy_evidence":"Braftovi (encorafenib) in combination with Mektovi (binimetinib) is included in guidelines as first-line and second-line therapy for patients with metastatic or unresectable cutaneous melanoma harboring BRAF V600E or V600K mutations (%%PUBMED:30959471%%; NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E/K","approval_status":"Guideline","amp_tier":"I"},{"response_type":"predicted - sensitive","pub_med_references":[32182156],"normalized_drug":"Lifirafenib","indication":"melanoma","therapy_id":4025,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Lifirafenib","efficacy_evidence":"In a Phase I trial, Lifirafenib (BGB-283) treatment resulted in partial response in 15.1% (8/53) of solid tumor patients with BRAF mutations, including 5 of 23 patients with melanoma harboring BRAF V600E or V600K overall, and in the dose expansion phase 57.1% (4/7) patient with BRAF V600-mutant melanoma had a partial response (%%PUBMED:32182156%%; NCT02610361).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600E/K","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[29573941],"normalized_drug":"Binimetinib, Encorafenib","indication":"melanoma","therapy_id":1100,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Binimetinib + Encorafenib","efficacy_evidence":"In a Phase III (COLUMBUS) trial that supported FDA approval, Braftovi (encorafenib) in combination with Mektovi (binimetinib) demonstrated improved tolerability profile and efficacy, resulted in a progression-free survival of 14.9 months in patients with advanced melanoma harboring BRAF V600E/K mutations, comparing to 7.3 months in the Zelboraf (vemurafenib) group (HR=0.54, p<0.0001) (%%PUBMED:29573941%%; NCT01909453) and both BRAF V600E and V600K are on the companion diagnostic.","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E/K","approval_status":"FDA approved - On Companion Diagnostic","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[30219628],"normalized_drug":"Binimetinib, Encorafenib","indication":"melanoma","therapy_id":1100,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Binimetinib + Encorafenib","efficacy_evidence":"In a Phase III (COLUMBUS) trial that supported FDA approval, Braftovi (encorafenib) in combination with Mektovi (binimetinib) resulted in a median overall survival (OS) of 33.6 months, a 1-year OS rate of 77.5%, and a 2-year OS rate of 57.7% in patients with advanced melanoma harboring BRAF V600E/K mutations compared to a median OS of 16.9 months and 1- and 2-year OS rates of 63.1% and 43.2%, respectively, in the Zelboraf (vemurafenib) treated group (%%PUBMED:30219628%%; NCT01909453).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600E/K","approval_status":"FDA approved - On Companion Diagnostic","amp_tier":"I"},{"pub_med_references":[27974663],"response_type":"predicted - sensitive","profile_array":[{"type":"act mut","gene":"BRAF"}],"indication":"colorectal cancer","therapy_id":12380,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"VX-11e + WEHI-539","efficacy_evidence":"In a preclinical study, inhibition of Erk signaling by VX-11e sensitized colorectal cancer cell lines harboring KRAS or BRAF activating mutations to WEHI-539 in culture (%%PUBMED:27974663%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF act mut","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"therapy_id":1041,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a preclinical study, PLX8394 had been shown to block survival and growth of vemurafenib/PLX4720-resistant cells harboring distinct BRAF activating mutations (%%PUBMED:24422853%%).","therapy":"PLX8394","evidence_type":"Actionable","normalized_cancer":"All Solid Tumors","indication":"Advanced Solid Tumor","approval_status":"Preclinical","normalized_drug":"Plx8394","pub_med_references":[24422853],"molecular_profile":"BRAF act mut","profile_array":[{"type":"act mut","gene":"BRAF"}],"response_type":"sensitive"},{"response_type":"sensitive","profile_array":[{"type":"act mut","gene":"BRAF"}],"normalized_drug":"Binimetinib, Encorafenib","indication":"Advanced Solid Tumor","therapy_id":1100,"normalized_cancer":"All Solid Tumors","evidence_type":"Actionable","therapy":"Binimetinib + Encorafenib","efficacy_evidence":"In a Phase Ib/II trial, Mektovi (binimetinib), in combination with Encorafenib (LGX818), demonstrated safety and efficacy in patients with BRAF mutant advanced solid tumors (J Clin Oncol 31, 2013 (suppl; abstr 9029)).","cap_asco_evidence_level":"C","molecular_profile":"BRAF act mut","approval_status":"Phase Ib/II","amp_tier":"II"},{"pub_med_references":[27974663],"response_type":"no benefit","profile_array":[{"type":"act mut","gene":"BRAF"}],"indication":"colorectal cancer","therapy_id":12379,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Venetoclax + VX-11e","efficacy_evidence":"In a preclinical study, inhibition of Erk signaling by VX-11e did not sensitize colorectal cancer cell lines harboring KRAS or BRAF activating mutations to Venclexta (venetoclax) in culture (%%PUBMED:27974663%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF act mut","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[29343524],"response_type":"sensitive","profile_array":[{"type":"act mut","gene":"BRAF"}],"indication":"lung non-small cell carcinoma","therapy_id":6995,"normalized_cancer":"Non-Small Cell Lung 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(%%PUBMED:37074042%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF act mut","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"therapy_id":1004,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a preclinical study, Cobimetinib (GDC-0973) induced cell death in human melanoma cell lines harboring BRAF activating mutations in culture and inhibited tumor growth in xenograft models (%%PUBMED:22084396%%).","therapy":"Cobimetinib","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Preclinical - Cell line xenograft","normalized_drug":"Cobimetinib","molecular_profile":"BRAF act mut","profile_array":[{"type":"act mut","gene":"BRAF"}],"response_type":"sensitive"},{"therapy_id":920,"amp_tier":"II","cap_asco_evidence_level":"C","efficacy_evidence":"In a Phase II study, Nexavar (sorafenib) displayed negligible efficacy in melanoma patients with BRAF mutations (%%PUBMED:16880785%%, %%PUBMED:22394203%%).","therapy":"Sorafenib","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Phase II","normalized_drug":"Sorafenib","pub_med_references":[16880785,22394203],"molecular_profile":"BRAF act mut","profile_array":[{"type":"act mut","gene":"BRAF"}],"response_type":"no benefit"},{"therapy_id":1627,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a systematic review, an analysis of several clinical trials demonstrated Opdivo (nivolumab) plus Yervoy (ipilimumab) resulted in improved overall survival (OS) compared to BRAF plus MEK inhibitor in BRAF-mutant advanced melanoma patients when considering the entire study period, and analysis of the period beginning 12 months after treatment initiation demonstrated significantly greater OS and progression-free survival (%%PUBMED:33556898%%; NCT01844505, NCT01584648, NCT01597908, NCT01909453, NCT01689519).","therapy":"Ipilimumab + 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with the triple combination of Tafinlar (dabrafenib), Mekinist (trametinib), and Vectibix (panitumumab) resulted in an objective response rate (ORR) of 21% and median progression-free survival (mPFS) of 4.2 mo, compared with 0% ORR and mPFS of 2.6 mo with Mekinist (trametinib) plus Vectibix (panitumumab), and 10% ORR and mPFS of 3.5 mo with Tafinlar (dabrafenib) plus Vectibix (panitumumab) in patients with BRAF-mutant colorectal cancer (%%PUBMED:27770002%%; NCT01750918).","cap_asco_evidence_level":"C","molecular_profile":"BRAF mutant","approval_status":"Phase Ib/II","amp_tier":"II"},{"therapy_id":2,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a preclinical study, Mekinist (trametinib) inhibited growth of lung adenocarcinoma cells harboring mutant BRAF in culture (%%PUBMED:26343583%%).","therapy":"Trametinib","evidence_type":"Actionable","normalized_cancer":"Lung Adenocarcinoma","indication":"lung 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(%%PUBMED:27307593%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF mutant","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"therapy_id":2,"amp_tier":"II","cap_asco_evidence_level":"C","efficacy_evidence":"In a Phase II trial (NCI-MATCH), Mekinist (trametinib) treatment did not demonstrate clinical activity in patients with advanced solid tumors or lymphoma harboring BRAF fusion (n=1) or non-V600 mutations (n=31), resulted in a partial response in 3% (1/32) and stable disease in 31% (10/32) of the patients, with a median progression-free survival of 1.8 months, and a median overall survival of 5.7 months (%%PUBMED:31924734%%; NCT02465060).","therapy":"Trametinib","evidence_type":"Actionable","normalized_cancer":"All Solid Tumors","indication":"Advanced Solid Tumor","approval_status":"Phase II","normalized_drug":"Trametinib","pub_med_references":[31924734],"molecular_profile":"BRAF mutant","profile_array":[{"type":"mutant","gene":"BRAF"}],"response_type":"no 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(%%PUBMED:30268448%%).","cap_asco_evidence_level":"NA","molecular_profile":"BRAF mutant","approval_status":"Clinical Study - Cohort","amp_tier":"NA"},{"pub_med_references":[26351322],"response_type":"sensitive","profile_array":[{"type":"mutant","gene":"BRAF"}],"indication":"colorectal cancer","therapy_id":4791,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"AZ628 + Selumetinib","efficacy_evidence":"In a preclinical study, Koselugo (selumetinib) and AZ628 synergistically inhibited Mapk signaling and cell proliferation in BRAF mutant colorectal cancer cell lines in culture (%%PUBMED:26351322%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF mutant","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","profile_array":[{"type":"mutant","gene":"BRAF"}],"indication":"Advanced Solid Tumor","therapy_id":1034,"normalized_cancer":"All Solid 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(%%PUBMED:27307593%%).","therapy":"Buparlisib","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Preclinical - Cell line xenograft","normalized_drug":"Buparlisib","pub_med_references":[27307593],"molecular_profile":"BRAF mutant","profile_array":[{"type":"mutant","gene":"BRAF"}],"response_type":"sensitive"},{"response_type":"predicted - sensitive","profile_array":[{"type":"mutant","gene":"BRAF"}],"indication":"pancreatic cancer","therapy_id":5747,"normalized_cancer":"Pancreatic Cancer","evidence_type":"Actionable","therapy":"KO-947","efficacy_evidence":"In a preclinical study, KO-947 inhibited Erk signaling and induced tumor regression in patient-derived xenograft models of BRAF-mutant pancreatic cancer (Cancer Res 2017;77(13 Suppl):Abstract nr 5168).","cap_asco_evidence_level":"D","molecular_profile":"BRAF mutant","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"response_type":"not 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months in BRAF inhibitor-pretreated patients (%%PUBMED:28611198%%; NCT01436656).","therapy":"Encorafenib","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Phase I","normalized_drug":"Encorafenib","pub_med_references":[28611198],"molecular_profile":"BRAF mutant","profile_array":[{"type":"mutant","gene":"BRAF"}],"response_type":"sensitive"},{"response_type":"predicted - sensitive","profile_array":[{"type":"mutant","gene":"BRAF"}],"normalized_drug":"Binimetinib, Encorafenib","indication":"Advanced Solid Tumor","therapy_id":1100,"normalized_cancer":"All Solid Tumors","evidence_type":"Actionable","therapy":"Binimetinib + Encorafenib","efficacy_evidence":"In a Phase II trial (BEAVER), Mektovi (binimetinib) and Braftovi (encorafenib) combination therapy demonstrated safety and preliminary efficacy in advanced solid tumor patients harboring BRAF non-V600E mutations including class 1 (n=1), class 2 (n=4), and class 3 (n=5), with an objective response rate of 22% (2/9) and a partial response in a patient with ampullary cancer harboring BRAF D594G and an unconfirmed PR in a melanoma patient harboring BRAF G469S (Annals of Oncology 32 (2021): S596; NCT03839342).","cap_asco_evidence_level":"C","molecular_profile":"BRAF mutant","approval_status":"Phase II","amp_tier":"II"},{"response_type":"predicted - sensitive","profile_array":[{"type":"mutant","gene":"BRAF"}],"indication":"stomach carcinoma","therapy_id":5747,"normalized_cancer":"Stomach Adenocarcinoma","evidence_type":"Actionable","therapy":"KO-947","efficacy_evidence":"In a preclinical study, KO-947 inhibited Erk signaling and induced tumor regression in patient-derived xenograft models of BRAF-mutant gastric carcinoma (Cancer Res 2017;77(13 Suppl):Abstract nr 5168).","cap_asco_evidence_level":"D","molecular_profile":"BRAF mutant","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"response_type":"predicted - 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complete response in 33% (1/3) and partial response in 67% (2/3) of BRAFi-nau00efve melanoma patients harboring BRAF mutations (J Clin Oncol 33, 2015 (suppl; abstr 9076)).","cap_asco_evidence_level":"C","molecular_profile":"BRAF mutant","approval_status":"Phase I","amp_tier":"II"},{"pub_med_references":[27307593],"response_type":"sensitive","profile_array":[{"type":"mutant","gene":"BRAF"}],"indication":"melanoma","therapy_id":1337,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Buparlisib + Encorafenib","efficacy_evidence":"In a preclinical study, the combination of Buparlisib (BKM120) and Encorafenib (LGX818) resulted in improved cell growth inhibition compared to either agent alone in a metastatic melanoma cell line harboring a BRAF mutation in culture (%%PUBMED:27307593%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF mutant","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - 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(%%PUBMED:27760111%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF mutant","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[29423521],"response_type":"predicted - resistant","profile_array":[{"type":"mutant","gene":"BRAF"}],"indication":"colorectal cancer","therapy_id":931,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"SYM004","efficacy_evidence":"In a preclinical study, patient-derived xenograft (PDX) models of colorectal cancer harboring KRAS, NRAS or BRAF mutations demonstrated poor response to SYM004 treatment compared to wild-type models (%%PUBMED:29423521%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF mutant","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"response_type":"sensitive","profile_array":[{"type":"mutant","gene":"BRAF"}],"indication":"melanoma","therapy_id":4865,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"S63845 + 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(%%PUBMED:26343583%%).","therapy":"Trametinib","evidence_type":"Actionable","normalized_cancer":"Colorectal Cancer","indication":"colorectal cancer","approval_status":"Preclinical","normalized_drug":"Trametinib","molecular_profile":"BRAF mutant","profile_array":[{"type":"mutant","gene":"BRAF"}],"response_type":"resistant"},{"pub_med_references":[31645440],"response_type":"no benefit","profile_array":[{"type":"mutant","gene":"BRAF"}],"indication":"Advanced Solid Tumor","therapy_id":3268,"normalized_cancer":"All Solid Tumors","evidence_type":"Actionable","therapy":"LY3009120","efficacy_evidence":"In a Phase I trial, LY3009120 did not achieve expected pharmacodynamic effects, resulted in stable disease as best overall response in 5 of 12 patients with advanced or metastatic cancer harboring BRAF mutations (%%PUBMED:31645440%%; NCT02014116).","cap_asco_evidence_level":"D","molecular_profile":"BRAF mutant","approval_status":"Case Reports/Case 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three melanoma patients all harboring a BRAF mutation (%%PUBMED:29247021%%; NCT01781429).","therapy":"Ulixertinib","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Case Reports/Case Series","normalized_drug":"Ulixertinib","pub_med_references":[29247021],"molecular_profile":"BRAF mutant","profile_array":[{"type":"mutant","gene":"BRAF"}],"response_type":"predicted - sensitive"},{"therapy_id":913,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a Phase II trial, 5 out of 6 patients with advanced melanoma exhibiting a response to Koselugo (selumetinib) had BRAF-mutant tumors (%%PUBMED:22048237%%).","therapy":"Selumetinib","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Case Reports/Case Series","normalized_drug":"Selumetinib","pub_med_references":[22048237],"molecular_profile":"BRAF 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mutant","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"therapy_id":2,"amp_tier":"II","cap_asco_evidence_level":"C","efficacy_evidence":"In a Phase II trial (NCI-MATCH), Mekinist (trametinib) treatment did not demonstrate clinical activity in patients with advanced solid tumors or lymphoma harboring BRAF fusion (n=1) or non-V600 mutations (n=31), resulted in a partial response in 3% (1/32) and stable disease in 31% (10/32) of the patients, with a median progression-free survival of 1.8 months, and a median overall survival of 5.7 months (%%PUBMED:31924734%%; NCT02465060).","therapy":"Trametinib","evidence_type":"Actionable","normalized_cancer":"Lymphoid Neoplasm","indication":"lymphoma","approval_status":"Phase II","normalized_drug":"Trametinib","pub_med_references":[31924734],"molecular_profile":"BRAF mutant","profile_array":[{"type":"mutant","gene":"BRAF"}],"response_type":"no benefit"},{"pub_med_references":[27488531],"response_type":"sensitive","profile_array":[{"type":"mutant","gene":"BRAF"}],"indication":"melanoma","therapy_id":1368,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Palbociclib + Trametinib","efficacy_evidence":"In a preclinical study, a melanoma cell line harboring a BRAF mutation demonstrated greater sensitivity to the combination treatment of Mekinist (trametinib) and Ibrance (palbociclib) in culture when compared to either agent alone (%%PUBMED:27488531%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF mutant","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","profile_array":[{"type":"mutant","gene":"BRAF"}],"indication":"lung non-small cell carcinoma","therapy_id":5248,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"unspecified PD-L1 antibody","efficacy_evidence":"In a clinical study, mutant BRAF correlated with prolonged duration on immune checkpoint inhibitor therapy compared to wild-type BRAF in non-small cell lung cancer patients (Ann Oncol 2017, Vol 28, Suppl 5, Abstract #1138PD).","cap_asco_evidence_level":"C","molecular_profile":"BRAF mutant","approval_status":"Clinical Study - Cohort","amp_tier":"II"},{"response_type":"decreased response","profile_array":[{"type":"mutant","gene":"BRAF"}],"indication":"Advanced Solid Tumor","therapy_id":1050,"normalized_cancer":"All Solid Tumors","evidence_type":"Actionable","therapy":"XL147","efficacy_evidence":"In a preclinical study, tumor cell lines harboring BRAF mutations demonstrated limited sensitivity to XL147 treatment in culture (%%PUBMED:25637314%%).","cap_asco_evidence_level":"NA","molecular_profile":"BRAF mutant","approval_status":"Preclinical","amp_tier":"NA"},{"pub_med_references":[29343524],"response_type":"sensitive","profile_array":[{"type":"mutant","gene":"BRAF"}],"indication":"Advanced Solid Tumor","therapy_id":6995,"normalized_cancer":"All Solid Tumors","evidence_type":"Actionable","therapy":"RAF709","efficacy_evidence":"In a preclinical study, cancer cell lines harboring BRAF mutations demonstrated increased sensitivity to RAF709 compared to BRAF wild-type cells in culture (%%PUBMED:29343524%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF mutant","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[23039341],"response_type":"sensitive","profile_array":[{"type":"mutant","gene":"BRAF"}],"indication":"melanoma","therapy_id":3911,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"E6201 + LY294002","efficacy_evidence":"In a preclinical study, E6201 and LY294002 synergistically inhibited proliferation of melanoma cell lines harboring BRAF mutations in culture, regardless of PTEN mutation status (%%PUBMED:23039341%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF mutant","approval_status":"Preclinical","amp_tier":"II"},{"pub_med_references":[28611205],"response_type":"predicted - sensitive","profile_array":[{"type":"mutant","gene":"BRAF"}],"indication":"colorectal cancer","therapy_id":6337,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"LSN3074753","efficacy_evidence":"In a preclinical study, LSN3074753 resulted in a disease control rate of 8.3% (1/12) in BRAF mutant patient-derived xenograft models of colorectal cancer (%%PUBMED:28611205%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF mutant","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"response_type":"predicted - sensitive","profile_array":[{"type":"mutant","gene":"BRAF"}],"indication":"colorectal cancer","therapy_id":8094,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"SY-5609","efficacy_evidence":"In a preclinical study, SY-5609 treatment resulted in 90% or more tumor growth inhibition or tumor regression in 50% (5/10) of patient-derived xenograft (PDX) models of colorectal cancer harboring BRAF mutations (J Clin Oncol 38: 2020 (suppl; abstr 3585)).","cap_asco_evidence_level":"D","molecular_profile":"BRAF mutant","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"therapy_id":913,"amp_tier":"II","cap_asco_evidence_level":"C","efficacy_evidence":"In a Phase I study, Koselugo (selumetinib) demonstrated an increase in iodine uptake and retention in a subgroup of patients with thyroid cancer that was refractory to radioiodine, including patients with BRAF and NRAS mutations (%%PUBMED:23406027%%).","therapy":"Selumetinib","evidence_type":"Actionable","normalized_cancer":"Thyroid Cancer","indication":"thyroid cancer","approval_status":"Phase I","normalized_drug":"Selumetinib","pub_med_references":[23406027],"molecular_profile":"BRAF mutant","profile_array":[{"type":"mutant","gene":"BRAF"}],"response_type":"predicted - sensitive"},{"therapy_id":1041,"amp_tier":"II","cap_asco_evidence_level":"D","efficacy_evidence":"In a preclinical study, PLX8394 blocked survival and growth of vemurafenib/PLX4720-resistant melanoma cells harboring BRAF V600E splice variants in culture (%%PUBMED:24422853%%).","therapy":"PLX8394","evidence_type":"Actionable","normalized_cancer":"Melanoma","indication":"melanoma","approval_status":"Preclinical","normalized_drug":"Plx8394","pub_med_references":[24422853],"molecular_profile":"BRAF mutant","profile_array":[{"type":"mutant","gene":"BRAF"}],"response_type":"sensitive"},{"therapy_id":890,"amp_tier":"II","cap_asco_evidence_level":"C","efficacy_evidence":"In a Phase II clinical trial (PREVIUM), Stivarga (regorafenib) treatment resulted in 0% (0/15) 6-month progression free survival (PFS), a 2.2-month median PFS, and a median overall survival of 3.3 months in metastatic colorectal cancer patients with KRAS (n=9), NRAS (n=3) or BRAF (n=2) mutations who failed first line therapy; however, the trial was terminated early due to poor accrual (%%PUBMED:30120161%%; NCT02175654).","therapy":"Regorafenib","evidence_type":"Actionable","normalized_cancer":"Colorectal Cancer","indication":"colorectal cancer","approval_status":"Phase II","normalized_drug":"Regorafenib","pub_med_references":[30120161],"molecular_profile":"BRAF mutant","profile_array":[{"type":"mutant","gene":"BRAF"}],"response_type":"no benefit"},{"pub_med_references":[37219686],"response_type":"sensitive","profile_array":[{"type":"mutant","gene":"BRAF"}],"indication":"melanoma","therapy_id":1034,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Tovorafenib","efficacy_evidence":"In a Phase I trial, Ojemda (tovorafenib) treatment resulted in stable disease in 23% (5/22) of patients with advanced solid tumors in the dose escalation phase, an objective response rate of 15% (10/68) in the dose expansion phase with responses in 50% (8/16) of patients with RAF and MEK inhibitor-naive BRAF-mutant melanoma, an overall median duration of response of 6.0 months, and a median progression-free survival of 1.9 months (%%PUBMED:37219686%%; NCT01425008).","cap_asco_evidence_level":"C","molecular_profile":"BRAF mutant","approval_status":"Phase I","amp_tier":"II"},{"response_type":"sensitive","profile_array":[{"type":"mutant","gene":"BRAF"}],"indication":"melanoma","therapy_id":1034,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Tovorafenib","efficacy_evidence":"In a preclinical study, Ojemda (tovorafenib) demonstrated efficacy in BRAF mutant xenograft models of melanoma and colorectal cancer (J Clin Oncol 31, 2013 (suppl; abstr e13529)).","cap_asco_evidence_level":"D","molecular_profile":"BRAF mutant","approval_status":"Preclinical - Cell line xenograft","amp_tier":"II"},{"pub_med_references":[28611205],"response_type":"sensitive","profile_array":[{"type":"mutant","gene":"BRAF"}],"indication":"colorectal cancer","therapy_id":6338,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + LSN3074753","efficacy_evidence":"In a preclinical study, LSN3074753 and Erbitux (cetuximab) synergistically inhibited tumor growth in patient-derived xenograft models of colorectal cancer harboring BRAF mutations, resulted in a disease control rate of 41.7% (5/12) (%%PUBMED:28611205%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF mutant","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"pub_med_references":[33020648],"response_type":"predicted - sensitive","indication":"melanoma","therapy_id":6023,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + Spartalizumab + Trametinib","efficacy_evidence":"In a Phase III trial (COMBI-i), the combination of Tafinlar (dabrafenib), Mekinist (trametinib), and Spartalizumab (PDR001) resulted in an objective response rate of 78% (28/36, 16 complete, 12 partial), disease control rate of 94% (34/36), and median progression-free survival of 23 months in patients with BRAF V600-mutant metastatic melanoma, including 29 patients (81%) harboring BRAF V600E and 4 patients (11%) harboring BRAF V600K (%%PUBMED:33020648%%; NCT02967692).","cap_asco_evidence_level":"B","molecular_profile":"BRAF V600X","approval_status":"Phase III","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[30285222],"normalized_drug":"Dabrafenib, Trametinib","indication":"lung non-small cell carcinoma","therapy_id":1066,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"The combination of Tafinlar (dabrafenib) and Mekinist (trametinib) is included in guidelines as first-line therapy for patients with metastatic non-small cell lung cancer harboring a BRAF V600 mutation, or as subsequent therapy in patients harboring BRAF V600 mutations that have not received prior BRAF/MEK inhibitor therapy (%%PUBMED:30285222%%; ESMO.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600X","approval_status":"Guideline","amp_tier":"I"},{"response_type":"predicted - sensitive","pub_med_references":[31506385],"normalized_drug":"Dabrafenib","indication":"Advanced Solid Tumor","therapy_id":3,"normalized_cancer":"All Solid Tumors","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a Phase I trial (BRF116013), Tafinlar (dabrafenib) treatment was well tolerated and demonstrated preliminary efficacy, resulted in a median duration of treatment of 75.6 week in pediatric patients with BRAF V600-mutant advanced solid tumors, including low-grade (n=15) and high-grade (n=8) gliomas, Langerhans cell histiocytosis (n=2), neuroblastoma (n=1), and papillary thyroid cancer (n=1) (%%PUBMED:31506385%%; NCT01677741).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600X","approval_status":"Phase I","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[26287849],"normalized_drug":"Vemurafenib","indication":"thyroid cancer","therapy_id":342,"normalized_cancer":"Thyroid Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase II trial, treatment with Zelboraf (vemurafenib) resulted in an overall response rate of 29% (2/7), with 1 complete response and 1 partial response, in patients with anaplastic thyroid cancer patients with BRAF V600 mutations (%%PUBMED:26287849%%; NCT01524978).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600X","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[31171876],"response_type":"sensitive","indication":"melanoma","therapy_id":1216,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Atezolizumab + Vemurafenib","efficacy_evidence":"In a Phase Ib trial, the combination therapy of Tecentriq (atezolizumab) and Zelboraf (vemurafenib) in patients with metastatic melanoma harboring a BRAF V600 mutation resulted in a best objective response rate of 76.5% (13/17), with a complete response in 17.6% (3/17), a median progression-free survival of 10.9 months, a median overall survival of 46.2 months, and median duration of confirmed response of 10.6 months (%%PUBMED:31171876%%; NCT01656642).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600X","approval_status":"Phase Ib/II","amp_tier":"II"},{"response_type":"sensitive","indication":"subependymal giant cell astrocytoma","therapy_id":1034,"normalized_cancer":"Low-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"Tovorafenib","efficacy_evidence":"Ojemda (tovorafenib) is included in guidelines (category 2A) for patients with recurrent or progressive circumscribed glioma, including subependymal giant cell astrocytoma, harboring BRAF fusions, rearrangements, or BRAF V600 mutations (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600X","approval_status":"Guideline","amp_tier":"I"},{"response_type":"predicted - sensitive","pub_med_references":[32182156],"normalized_drug":"Lifirafenib","indication":"Advanced Solid Tumor","therapy_id":4025,"normalized_cancer":"All Solid Tumors","evidence_type":"Actionable","therapy":"Lifirafenib","efficacy_evidence":"In a Phase I trial, Lifirafenib (BGB-283) treatment demonstrated safety and resulted in partial response (PR) in 15.1% (8/53) of advanced solid tumor patients harboring a BRAF mutation, including 5 patients with BRAF V600E/K-mutant melanoma, 2 patients with BRAF V600E-mutant thyroid cancer, and 1 patient with BRAF V600E-mutant low-grade serous ovarian carcinoma, complete response in 1.9% (1/53), in a patient with melanoma, and stable disease in 50.9% (27/53) (%%PUBMED:32182156%%; NCT02610361).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600X","approval_status":"Phase I","amp_tier":"II"},{"pub_med_references":[37978284],"response_type":"sensitive","indication":"childhood low-grade glioma","therapy_id":1034,"normalized_cancer":"Low-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"Tovorafenib","efficacy_evidence":"In a Phase II trial (FIREFLY-1) that supported FDA approval, Ojemda (tovorafenib) was well tolerated and resulted in an overall response rate (ORR) per RAPNO criteria of 51% (39/76, 28 partial and 11 minor responses), clinical benefit rate (CBR) of 82% (62/76), and median duration of response of 13.8 mo in pediatric patients with low-grade glioma harboring BRAF fusions, rearrangements, or BRAF V600 mutations, with an ORR of 50% (6/12) in patients harboring BRAF V600E (%%PUBMED:37978284%%; NCT04775485).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600X","approval_status":"FDA approved","amp_tier":"I"},{"response_type":"sensitive","normalized_drug":"Dabrafenib, Trametinib","indication":"skin melanoma","therapy_id":1066,"normalized_cancer":"Cutaneous Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"Tafinlar (dabrafenib) and Mekinist (trametinib) combination therapy is included in guidelines as neoadjuvant or adjuvant therapy for stage III disease and as second-line or subsequent therapy for patients with metastatic or unresectable cutaneous melanoma harboring a BRAF V600 mutation (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600X","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[39550033],"normalized_drug":"Dabrafenib, Trametinib","indication":"skin melanoma","therapy_id":1066,"normalized_cancer":"Cutaneous Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"BRAF inhibitor plus MEK inhibitor combination therapy, such as Tafinlar (dabrafenib) plus Mekinist (trametinib), is included in guidelines for cutaneous melanoma patients with unresectable or metastatic disease harboring a BRAF V600 mutation (%%PUBMED:39550033%%; ESMO.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600X","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[24265152],"response_type":"sensitive","indication":"melanoma","therapy_id":4653,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"MK2206 + Trametinib","efficacy_evidence":"In a preclinical study, the combination of MK2206 and Mekinist (trametinib) inhibited growth of BRAF V600-mutant melanoma cell lines in culture, with increased efficacy over either agent alone (%%PUBMED:24265152%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600X","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"pub_med_references":[24265152],"response_type":"sensitive","indication":"melanoma","therapy_id":3773,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Selumetinib + Vemurafenib","efficacy_evidence":"In a preclinical study, the combination of Koselugo (selumetinib) and Zelboraf (vemurafenib) inhibited growth of BRAF V600-mutant melanoma cell lines in culture, with increased efficacy over either agent alone (%%PUBMED:24265152%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600X","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[31959346],"normalized_drug":"Vemurafenib","indication":"lung non-small cell carcinoma","therapy_id":342,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase II trial, Zelboraf (vemurafenib) treatment resulted in a objective response rate of 44.8% (43/96), median duration of response of 6.4 months, median progression-free survival of 5.2 months, and median overall survival of 10 months in non-small cell lung cancer patients with BRAF V600 mutations (%%PUBMED:31959346%%; NCT02304809).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600X","approval_status":"Phase II","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[26287849],"normalized_drug":"Vemurafenib","indication":"lung non-small cell carcinoma","therapy_id":342,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase II trial, treatment with Zelboraf (vemurafenib) resulted in an overall response rate of 42% (8/19, 8 partial responses) in patients with non-small cell lung cancer harboring BRAF V600 mutations, with a median progression-free survival of 7.3 months (%%PUBMED:26287849%%; NCT01524978}.","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600X","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Vemurafenib","indication":"skin melanoma","therapy_id":342,"normalized_cancer":"Cutaneous Melanoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"Zelboraf (vemurafenib) therapy is included in guidelines for patients with unresectable or metastatic cutaneous melanoma harboring BRAF V600 activating mutations, in cases where BRAF/MEK inhibitor combination therapy is contraindicated (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600X","approval_status":"Guideline","amp_tier":"I"},{"response_type":"predicted - sensitive","indication":"melanoma","therapy_id":11201,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Binimetinib + Encorafenib + Pembrolizumab","efficacy_evidence":"In a Phase I trial (IMMU-Target), Mektovi (binimetinib), Braftovi (encorafenib), and Keytruda (pembrolizumab) demonstrated safety and preliminary efficacy in treatment naive patients with advanced melanoma harboring BRAF V600 mutations, resulting in an overall response rate of 64% (9/14), with a 12-month progression-free survival rate of 37.5% (n=8) and 60% (n=6) at the two tested dose levels, respectively (J Clin Oncol 39, no. 15_suppl (May 20, 2021) 9532; NCT02902042).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600X","approval_status":"Phase I","amp_tier":"II"},{"response_type":"predicted - sensitive","normalized_drug":"Cobimetinib, Vemurafenib","indication":"lung non-small cell carcinoma","therapy_id":1657,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"In a Phase II trial, treatment with the combination of Zelboraf (vemurafenib) and Cotellic (cobimetinib) resulted in an objective response rate (ORR) of 50% (18/36), median progression-free survival of 7.9 months, and overall survival of 15.9 months in patients with advanced solid tumors harboring a BRAF V600 mutation and an ORR of 42% (10/24) in treatment-naive patients with non-small cell lung cancer harboring a BRAF V600 mutation (Ann Oncol (2024) 35 (Suppl_2): S498).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600X","approval_status":"Phase II","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Cobimetinib, Vemurafenib","indication":"skin melanoma","therapy_id":1657,"normalized_cancer":"Cutaneous Melanoma","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"Zelboraf (vemurafenib) and Cotellic (cobimetinib) combination therapy is included in guidelines as a second-line or subsequent therapy for patients with metastatic or unresectable cutaneous melanoma harboring a BRAF V600 activating mutation (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600X","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[39550033],"normalized_drug":"Cobimetinib, Vemurafenib","indication":"skin melanoma","therapy_id":1657,"normalized_cancer":"Cutaneous Melanoma","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"BRAF inhibitor plus MEK inhibitor combination therapy, such as Cotellic (cobimetinib) plus Zelboraf (vemurafenib), is included in guidelines for cutaneous melanoma patients with unresectable or metastatic disease harboring a BRAF V600 mutation (%%PUBMED:39550033%%; ESMO.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600X","approval_status":"Guideline","amp_tier":"I"},{"response_type":"predicted - sensitive","pub_med_references":[40411977],"normalized_drug":"Binimetinib, Encorafenib","indication":"melanoma","therapy_id":1100,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Binimetinib + Encorafenib","efficacy_evidence":"In a retrospective analysis, real-world treatment with the combination of Mektovi (binimetinib) and Braftovi (encorafenib) demonstrated activity in melanoma patients with brain metastases harboring a BRAF V600 mutation, with an objective response rate of 69.4% (125/180, 4 complete and 121 partial responses), median progression-free survival of 5.5 months, and median overall survival of 11.9 months (%%PUBMED:40411977%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600X","approval_status":"Clinical Study","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[31811016],"normalized_drug":"Dabrafenib","indication":"ganglioglioma","therapy_id":3,"normalized_cancer":"Ganglioglioma","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a Phase I/II trial, Tafinlar (dabrafenib) treatment resulted in a partial response in a pediatric patient with BRAF V600-mutant ganglioglioma (%%PUBMED:31811016%%; NCT01677741).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600X","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[24265152],"response_type":"sensitive","indication":"melanoma","therapy_id":1974,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Buparlisib + Trametinib","efficacy_evidence":"In a preclinical study, the combination of Buparlisib (BKM120) and Mekinist (trametinib) inhibited growth of BRAF V600-mutant melanoma cell lines in culture, with increased efficacy over either agent alone (%%PUBMED:24265152%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600X","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"melanoma","therapy_id":4754,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + Nivolumab + Trametinib","efficacy_evidence":"In a Phase II trial, combination of Tafinlar (dabrafenib), Mekinist (trametinib), and Opdivo (nivolumab) resulted in an objective response rate (ORR) of 92% (24/27, 3 CR, 21 PR) in patients with MEK inhibitor-naive, BRAF V600-mutated melanoma, with a median progression-free survival of 8.5 mos, ORR was 88% (14/16) and 100% (10/10) in PD1 refractory or naive patients, 57% (4/7) of patients with brain metastasis achieved intracranial response (J Clin Oncol 39, no. 15_suppl (May 20, 2021) 9520; NCT02910700).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600X","approval_status":"Phase II","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"lung non-small cell carcinoma","therapy_id":15985,"normalized_cancer":"Non-Small Cell Lung Cancer","evidence_type":"Actionable","therapy":"Tunlametinib + Vemurafenib","efficacy_evidence":"In a Phase I trial, the combination of Tunlametinib (HL-085) and Zelboraf (vemurafenib) demonstrated safety and resulted in an objective response rate of 60.6% (20/33), a median duration of response of 11.3 months, and a median progression free survival of 11.7 months in patients with advanced non-small cell lung cancer harboring a BRAF V600 mutation (Ann Oncol (2023) 34 (suppl_2): S790; NCT03781219).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600X","approval_status":"Phase I","amp_tier":"II"},{"pub_med_references":[26287849],"response_type":"sensitive","indication":"colorectal cancer","therapy_id":1711,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Cetuximab + Vemurafenib","efficacy_evidence":"In a Phase II trial, treatment with the combination of Zelboraf (vemurafenib) and Erbitux (cetuximab) resulted in an overall response rate of 4% (1/26), stable disease in 69% (18/26), and a median progression-free survival of 3.7 months in patients with BRAF V600-mutant colorectal cancer (%%PUBMED:26287849%%; NCT01524978).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600X","approval_status":"Phase II","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[36130145],"normalized_drug":"Ipilimumab, Nivolumab","indication":"melanoma","therapy_id":1627,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Ipilimumab + Nivolumab","efficacy_evidence":"In a retrospective analysis, melanoma patients harboring BRAF V600 mutations (V600E/K/R/D or V600_K601delinsE) treated with the combination of Yervoy (ipilimumab) and Opdivo (nivolumab) demonstrated significantly improved median progression-free survival (10.1 vs 5.2 months; P=0.0057) and median overall survival (not reached vs 16.9 months; P<0.0001) compared to patients without BRAF V600 mutations (%%PUBMED:36130145%%).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600X","approval_status":"Clinical Study - Cohort","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Dabrafenib","indication":"skin melanoma","therapy_id":3,"normalized_cancer":"Cutaneous Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"Tafinlar (dabrafenib) therapy is included in guidelines for patients with unresectable or metastatic cutaneous melanoma harboring BRAF V600 activating mutations, in cases where BRAF/MEK inhibitor combination therapy is contraindicated (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600X","approval_status":"Guideline","amp_tier":"I"},{"response_type":"predicted - sensitive","pub_med_references":[26287849],"normalized_drug":"Vemurafenib","indication":"cholangiocarcinoma","therapy_id":342,"normalized_cancer":"Cholangiocarcinoma","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase II trial, treatment with Zelboraf (vemurafenib) resulted in partial response in 12% (1/8) and stable disease in 50% (4/8) of cholangiocarcinoma patients with BRAF V600 mutations (%%PUBMED:26287849%%; NCT01524978).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600X","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"pub_med_references":[24265152],"response_type":"sensitive","indication":"melanoma","therapy_id":4234,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Trametinib + Vemurafenib","efficacy_evidence":"In a preclinical study, the combination of Mekinist (trametinib) and Zelboraf (vemurafenib) inhibited growth of BRAF V600-mutant melanoma cell lines in culture, with increased efficacy over either agent alone (%%PUBMED:24265152%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600X","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[31811016],"normalized_drug":"Dabrafenib","indication":"low grade glioma","therapy_id":3,"normalized_cancer":"Low-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"Dabrafenib","efficacy_evidence":"In a Phase I/II trial, Tafinlar (dabrafenib) treatment was well tolerated and demonstrated preliminary efficacy, resulted in an objective response rate of 44% (14/32, 1 complete response, 13 partial response) and a disease control rate of 78% (25/32), with a median duration of response of 26 months in pediatric patients with BRAF V600-mutant low-grade gliomas (%%PUBMED:31811016%%; NCT01677741).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600X","approval_status":"Phase Ib/II","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[29188284],"normalized_drug":"Vemurafenib","indication":"Erdheim-Chester disease","therapy_id":342,"normalized_cancer":"Erdheim-Chester Disease","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase II trial (VE-BASKET) that supported FDA approval, Zelboraf (vemurafenib) treatment resulted in an objective response rate of 54.5% (12/22, 1 complete and 11 partial responses) in patients with Erdheim-Chester disease harboring BRAF V600 mutations, with a 2-year progression-free survival rate of 83% and 2-year overall survival rate of 95% (%%PUBMED:29188284%%; NCT01524978).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600X","approval_status":"FDA approved","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[23414587],"normalized_drug":"Binimetinib","indication":"melanoma","therapy_id":807,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Binimetinib","efficacy_evidence":"In a Phase II trial, Mektovi (binimetinib) treatment resulted in a partial response in 20% (8/41) of melanoma patients harboring BRAF V600 mutations, including V600E (33/41), V600K (5/41), and V600R (1/41) (%%PUBMED:23414587%%; NCT01320085).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600X","approval_status":"Phase II","amp_tier":"II"},{"response_type":"predicted - sensitive","pub_med_references":[36375115],"normalized_drug":"Trametinib","indication":"low grade glioma","therapy_id":2,"normalized_cancer":"Low-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"Trametinib","efficacy_evidence":"In a Phase I/II trial, Mekinist (trametinib) treatment demonstrated a manageable safety profile in pediatric patients with BRAF V600-mutant low grade glioma, and resulted in an objective response rate of 15.4% (2/13, all partial responses), a clinical benefit rate of 61.5% (8/13), a median progression-free survival of 16.4 months, and median duration of response not reached (%%PUBMED:36375115%%; NCT02124772).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600X","approval_status":"Phase Ib/II","amp_tier":"II"},{"response_type":"predicted - sensitive","normalized_drug":"Plx8394","indication":"Advanced Solid Tumor","therapy_id":1041,"normalized_cancer":"All Solid Tumors","evidence_type":"Actionable","therapy":"PLX8394","efficacy_evidence":"In a Phase I/II trial, PLX8394 treatment resulted in a partial response in 39% (9/23) of patients with MAPK inhibitor-naive advanced solid tumors (excluding colorectal cancer) harboring BRAF V600X with a median duration of response of 32 months, and resulted in a partial response in 18% (3/17) and stable disease in 29% of patients previously treated with a MAPK inhibitor (J Clin Oncol 41, 2023 (suppl 16; abstr 3006); NCT02428712).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600X","approval_status":"Phase Ib/II","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[39550033],"normalized_drug":"Binimetinib, Encorafenib","indication":"skin melanoma","therapy_id":1100,"normalized_cancer":"Cutaneous Melanoma","evidence_type":"Actionable","therapy":"Binimetinib + Encorafenib","efficacy_evidence":"BRAF inhibitor plus MEK inhibitor combination therapy, such as Mektovi (binimetinib) plus Braftovi (encorafenib), is included in guidelines for cutaneous melanoma patients with unresectable or metastatic disease harboring a BRAF V600 mutation (%%PUBMED:39550033%%; ESMO.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600X","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","normalized_drug":"Binimetinib, Encorafenib","indication":"skin melanoma","therapy_id":1100,"normalized_cancer":"Cutaneous Melanoma","evidence_type":"Actionable","therapy":"Binimetinib + Encorafenib","efficacy_evidence":"Mektovi (binimetinib) and Braftovi (encorafenib) combination therapy is included in guidelines as a second-line or subsequent therapy for patients with metastatic or unresectable cutaneous melanoma harboring a BRAF V600 activating mutation (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600X","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[35022320],"response_type":"predicted - sensitive","indication":"melanoma","therapy_id":9169,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + Hydroxychloroquine + Trametinib","efficacy_evidence":"In a Phase I/II trial (BAMM), the combination of Tafinlar (dabrafenib), Mekinist (trametinib), and Plaquenil (hydroxychloroquine sulfate) resulted in a 1-year progression-free survival (PFS) rate of 48.2%, a median PFS of 11.2 mo, a response rate (RR) of 85% (29/34, 14 complete, 15 partial responses), and median overall survival (OS) of 26.5 mo in patients with advanced BRAF V600-mutant melanoma, RR, mPFS, and OS were 88%, 7.3, and 22 mo in patients with elevated LDH (n=16) (%%PUBMED:35022320%%; NCT02257424).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600X","approval_status":"Phase Ib/II","amp_tier":"II"},{"response_type":"sensitive","indication":"pilocytic astrocytoma","therapy_id":1034,"normalized_cancer":"Pilocytic Astrocytoma","evidence_type":"Actionable","therapy":"Tovorafenib","efficacy_evidence":"Ojemda (tovorafenib) is included in guidelines (category 2A) for patients with recurrent or progressive circumscribed glioma, including pilocytic astrocytoma, harboring BRAF fusions, rearrangements, or BRAF V600 mutations (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600X","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[24265152],"response_type":"sensitive","indication":"melanoma","therapy_id":1322,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Buparlisib + Vemurafenib","efficacy_evidence":"In a preclinical study, the combination of Buparlisib (BKM120) and Zelboraf (vemurafenib) inhibited growth of BRAF V600-mutant melanoma cell lines in culture, with increased efficacy over either agent alone (%%PUBMED:24265152%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600X","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","indication":"skin melanoma","therapy_id":1449,"normalized_cancer":"Cutaneous Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + Pembrolizumab + Trametinib","efficacy_evidence":"Tafinlar (dabrafenib) plus Mekinist (trametinib) in combination with an immune checkpoint inhibitor, such as Keytruda (pembrolizumab), is included in guidelines as second-line or subsequent therapy (category 2A) for patients with metastatic or unresectable cutaneous melanoma harboring a BRAF V600 mutation (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600X","approval_status":"Guideline","amp_tier":"I"},{"response_type":"predicted - sensitive","pub_med_references":[36375115],"normalized_drug":"Dabrafenib, Trametinib","indication":"low grade glioma","therapy_id":1066,"normalized_cancer":"Low-Grade Glioma, NOS","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a Phase I/II trial, Mekinist (trametinib) and Tafinlar (dabrafenib) combination treatment demonstrated a manageable safety profile in pediatric patients with BRAF V600-mutant low-grade glioma, and resulted in an objective response rate of 25% (9/36, all partial responses), a clinical benefit rate of 88.9% (32/36), a median duration of response of 33.6 months, and a median progression-free survival of 36.9 months (%%PUBMED:36375115%%; NCT02124772).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600X","approval_status":"Phase Ib/II","amp_tier":"II"},{"response_type":"no benefit","pub_med_references":[26287849],"normalized_drug":"Vemurafenib","indication":"colorectal cancer","therapy_id":342,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Vemurafenib","efficacy_evidence":"In a Phase II trial, treatment with Zelboraf (vemurafenib) in colorectal cancer patients with BRAF V600 mutations did not result in clinical benefit, with no patients achieving response, and 50% (5/10) demonstrating progressive disease (%%PUBMED:26287849%%; NCT01524978).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600X","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[26811525],"normalized_drug":"Dabrafenib, Trametinib","indication":"melanoma","therapy_id":1066,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + Trametinib","efficacy_evidence":"In a Phase I/II clinical trial, patients with BRAF V600 mutant melanoma (n=78) treated with the combination of Tafinlar (dabrafenib) and Mekinist (trametinib) had a median overall survival of greater than 2 years (%%PUBMED:26811525%%).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600X","approval_status":"Phase Ib/II","amp_tier":"II"},{"response_type":"sensitive","indication":"melanoma","therapy_id":5827,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"ASN003","efficacy_evidence":"In a preclinical study, melanoma patient derived xenograft (PDX) model harboring a BRAF V600 mutation demonstrated antitumor activity when treated with ASN003 (J Clin Oncol 35, 2017 (suppl; abstr e14102)).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600X","approval_status":"Preclinical - Pdx","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"brain cancer","therapy_id":9125,"normalized_cancer":"Primary Brain Tumor","evidence_type":"Actionable","therapy":"ABM-1310","efficacy_evidence":"In a Phase I trial, ABM-1310 treatment was well tolerated and resulted in preliminary antitumor activity with 3 partial responses and 8 stable disease among 13 patients with brain tumors harboring BRAF V600 mutations, including a partial response in a patient with glioblastoma and 2 partial responses in patients with pleomorphic xanthoastrocytoma (Ann Oncol (2024) 35 (suppl_2): S411; NCT05892653).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600X","approval_status":"Phase I","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"colorectal cancer","therapy_id":15985,"normalized_cancer":"Colorectal Cancer","evidence_type":"Actionable","therapy":"Tunlametinib + Vemurafenib","efficacy_evidence":"In a Phase I trial, the combination of Tunlametinib (HL-085) and Zelboraf (vemurafenib) demonstrated safety and resulted in an objective response rate of 25.0% (6/24), a median duration of response of 5.5 months, and a median progression free survival of 6.2 months in patients with advanced colorectal cancer harboring a BRAF V600 mutation (Ann Oncol (2023) 34 (suppl_2): S790; NCT03781219).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600X","approval_status":"Phase I","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[27480103],"normalized_drug":"Cobimetinib, Vemurafenib","indication":"melanoma","therapy_id":1657,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"In a Phase III trial, combination treatment with Zelboraf (vemurafenib) and Cotellic (cobimetinib) resulted in an improved progression-free survival of 12.3 months compared to 7.2 months with Zelboraf (vemurafenib) alone among patients with BRAF V600-mutated metastatic melanoma (%%PUBMED:27480103%%; NCT01689519).","cap_asco_evidence_level":"B","molecular_profile":"BRAF V600X","approval_status":"Phase III","amp_tier":"I"},{"pub_med_references":[24265152],"response_type":"sensitive","indication":"melanoma","therapy_id":4635,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"MK2206 + Vemurafenib","efficacy_evidence":"In a preclinical study, the combination of MK2206 and Zelboraf (vemurafenib) inhibited growth of BRAF V600-mutant melanoma cell lines in culture, with increased efficacy over either agent alone (%%PUBMED:24265152%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600X","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"sensitive","normalized_drug":"Atezolizumab, Cobimetinib, Vemurafenib","indication":"skin melanoma","therapy_id":4825,"normalized_cancer":"Cutaneous Melanoma","evidence_type":"Actionable","therapy":"Atezolizumab + Cobimetinib + Vemurafenib","efficacy_evidence":"Zelboraf (vemurafenib) plus Cotellic (cobimetinib) in combination with an immune checkpoint inhibitor, such as Tecentriq (atezolizumab), is included in guidelines as second-line or subsequent therapy (category 2A) for patients with metastatic or unresectable cutaneous melanoma harboring a BRAF V600 mutation (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600X","approval_status":"Guideline","amp_tier":"I"},{"pub_med_references":[24265152],"response_type":"sensitive","indication":"melanoma","therapy_id":4652,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Buparlisib + Selumetinib","efficacy_evidence":"In a preclinical study, the combination of Buparlisib (BKM120) and Koselugo (selumetinib) inhibited growth of BRAF V600-mutant melanoma cell lines in culture, with increased efficacy over either agent alone (%%PUBMED:24265152%%).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600X","approval_status":"Preclinical - Cell culture","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"Advanced Solid Tumor","therapy_id":9125,"normalized_cancer":"All Solid Tumors","evidence_type":"Actionable","therapy":"ABM-1310","efficacy_evidence":"In a Phase I trial, ABM-1310 treatment was tolerated and demonstrated preliminary efficacy in patients with advanced solid tumors harboring BRAF V600X, resulting in 2 partial responses (1 pleomorphic xanthroastrocytoma, 1 glioblastoma) and 8 stable diseases among 16 evaluable patients (J Clin Oncol 41, 2023 (suppl 16; abstr 3098); NCT04190628).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600X","approval_status":"Phase I","amp_tier":"II"},{"response_type":"predicted - sensitive","normalized_drug":"Cobimetinib, Vemurafenib","indication":"Advanced Solid Tumor","therapy_id":1657,"normalized_cancer":"All Solid Tumors","evidence_type":"Actionable","therapy":"Cobimetinib + Vemurafenib","efficacy_evidence":"In a Phase II trial, treatment with the combination of Zelboraf (vemurafenib) and Cotellic (cobimetinib) resulted in an objective response rate (ORR) of 50% (18/36), median progression-free survival of 7.9 months, and overall survival of 15.9 months in patients with advanced solid tumors harboring a BRAF V600 mutation and an ORR of 42% (10/24) in treatment-naive patients with non-small cell lung cancer harboring a BRAF V600 mutation (Ann Oncol (2024) 35 (Suppl_2): S498).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600X","approval_status":"Phase II","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"Advanced Solid Tumor","therapy_id":11782,"normalized_cancer":"All Solid Tumors","evidence_type":"Actionable","therapy":"Belvarafenib + Cobimetinib","efficacy_evidence":"In a Phase Ib trial, combination treatment with Belvarafenib (HM95573) and Cotellic (cobimetinib) was well-tolerated and demonstrated safety, and led to a confirmed partial response in 33.3% (3/9) solid tumor patients harboring BRAF V600 mutations (Annals of Oncology 32 (2021): S595; NCT03284502).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600X","approval_status":"Phase I","amp_tier":"II"},{"response_type":"predicted - sensitive","indication":"melanoma","therapy_id":15373,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"ABM-1310 + Cobimetinib","efficacy_evidence":"In a Phase I trial, the combination of ABM-1310 and Cotellic (cobimetinib) was tolerated and demonstrated preliminary efficacy in patients with advanced solid tumors harboring BRAF V600X, resulting in 1 partial response in a patient with melanoma and 1 stable disease among 3 evaluable patients (J Clin Oncol 41, 2023 (suppl 16; abstr 3098); NCT04190628).","cap_asco_evidence_level":"D","molecular_profile":"BRAF V600X","approval_status":"Case Reports/Case Series","amp_tier":"II"},{"response_type":"sensitive","indication":"pleomorphic xanthoastrocytoma","therapy_id":1034,"normalized_cancer":"Pleomorphic Xanthoastrocytoma","evidence_type":"Actionable","therapy":"Tovorafenib","efficacy_evidence":"Ojemda (tovorafenib) is included in guidelines (category 2A) for patients with recurrent or progressive circumscribed glioma, including pleomorphic xanthoastrocytoma, harboring BRAF fusions, rearrangements, or BRAF V600 mutations (NCCN.org).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600X","approval_status":"Guideline","amp_tier":"I"},{"response_type":"sensitive","indication":"melanoma","therapy_id":1453,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Dabrafenib + KRT-232 + Trametinib","efficacy_evidence":"In a Phase I trial, the combination therapy of KRT-232 (AMG 232), Mekinist (trametinib), and Tafinlar (dabrafenib) in 6 patients with metastatic cutaneous melanoma harboring a BRAF V600 mutation resulted in 4 patients with a partial response and 2 patients with stable disease, and of the 6 patients, all experienced tumor reduction (J Clin Oncol 35, 2017 (suppl; abstr 2575)).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600X","approval_status":"Phase I","amp_tier":"II"},{"response_type":"sensitive","pub_med_references":[32534646],"normalized_drug":"Atezolizumab, Cobimetinib, Vemurafenib","indication":"melanoma","therapy_id":4825,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Atezolizumab + Cobimetinib + Vemurafenib","efficacy_evidence":"In a Phase III trial (IMspire150) that supported FDA approval, addition of Tecentriq (atezolizumab) to Zelboraf (vemurafenib) and Cotellic (cobimetinib) combination therapy significantly improved progression-free survival (15.1 vs 10.6 months, HR=0.78, p=0.025) compared to control in patients with advanced or metastatic melanoma harboring BRAF V600 mutations (%%PUBMED:32534646%%; NCT02908672).","cap_asco_evidence_level":"A","molecular_profile":"BRAF V600X","approval_status":"FDA approved","amp_tier":"I"},{"response_type":"sensitive","pub_med_references":[31171876],"normalized_drug":"Atezolizumab, Cobimetinib, Vemurafenib","indication":"melanoma","therapy_id":4825,"normalized_cancer":"Melanoma","evidence_type":"Actionable","therapy":"Atezolizumab + Cobimetinib + Vemurafenib","efficacy_evidence":"In a Phase Ib trial, the combination therapy of Tecentriq (atezolizumab), Zelboraf (vemurafenib), and Cotellic (cobimetinib) in patients with metastatic melanoma harboring a BRAF V600 mutation resulted in a best objective response rate of 71.8% (28/39), with a complete response in 20.5% (8/39), a median progression-free survival of 12.9 months, a median overall survival not yet reached, and median duration of confirmed response of 17.4 months (%%PUBMED:31171876%%; NCT01656642).","cap_asco_evidence_level":"C","molecular_profile":"BRAF V600X","approval_status":"Phase Ib/II","amp_tier":"II"}],"gene_variant_descriptions":[{"pub_med_references":[15035987,18697864],"description":"BRAF V600E (previously reported as V599E) lies within the activation segment of the kinase domain of the Braf protein (PMID: 15035987). V600E confers a gain of function to the Braf protein as demonstrated by increased Braf kinase activity, downstream signaling, and the ability to transform cells in culture (PMID: 15035987, PMID: 29533785, PMID: 18697864)."}],"protein_effect":"gain of function","cap_asco_evidence_level":null,"polymorphism":null,"transforming_activity":true,"associated_with_drug_resistance":null}],"phastcons100way":[{"version":"14-Apr-2021","conservation_score":["1.000"]}],"phylop100way":[{"version":"13-Apr-2021","conservation_score":["9.201"]}],"maxentscan":null,"variant_pubmed_automap":[{"version":"22-Jul-2025","pub_med_references":[15009715,15277467,15294323,15342696,15356020,15694309,15735849,15781663,15782118,15811117,15902486,15947100,15947103,15948115,15948220,15998781,16001072,16007166,16021577,16024606,16079850,16123397,16143123,16219636,16219715,16266992,16268813,16299399,16361694,16403224,16410717,16452550,16487015,16540682,16551863,16557238,16567964,16601293,16606457,16647954,16691193,16702958,16757326,16757355,16772349,16801397,16818621,16818623,16873291,16880785,16890795,16896265,16918957,16932068,16964246,16964379,16983703,17001349,17006850,17044028,17054470,17065421,17082247,17087942,17096326,17101316,17119056,17148775,17159251,17159915,17186541,17199440,17199737,17260021,17273161,17293392,17295241,17298986,17299132,17312306,17317846,17355635,17363500,17374713,17381488,17387744,17409425,17415708,17427169,17429154,17440063,17453004,17453358,17464312,17465858,17478764,17488796,17510423,17518771,17520704,17542667,17545526,17566669,17641411,17685465,17693984,17696195,17696956,17714762,17717450,17721188,17724477,17727338,17785355,17824790,17854396,17868408,17878251,17914558,17942460,17950780,17956956,17962436,17962726,17972530,17974567,17989125,18006922,18032947,18056475,18058267,18061181,18070147,18089783,18096441,18098337,18186519,18227705,18235983,18280030,18283163,18287029,18310286,18310287,18310288,18360353,18383861,18393366,18403637,18408659,18426810,18428050,18451216,18451217,18462259,18470905,18473997,18491251,18519771,18524847,18556776,18559533,18591935,18615679,18615680,18621636,18628431,18631381,18636014,18644254,18669866,18676742,18676837,18676857,18679422,18682506,18697864,18710471,18715233,18718023,18753363,18757433,18778891,18782444,18790768,18794153,18794803,18798261,18806830,18829479,18840924,18945298,18985043,19001320,19010912,19014278,19016743,19033861,19034577,19040996,19055826,19066305,19076977,19079609,19087308,19088048,19126563,19147753,19152441,19156774,19158841,19159571,19169486,19190079,19190105,19190129,19200582,19207009,19208736,19213871,19269016,19274086,19276360,19289622,19338646,19342899,19351826,19355825,19358278,19363522,19370505,19371126,19383316,19383812,19389934,19393416,19398955,19404918,19414674,19415957,19424571,19430299,19440799,19441164,19474002,19475551,19498322,19500021,19534623,19547661,19561230,19561646,19572146,19574281,19582761,19603018,19626635,19627734,19637313,19652585,19659611,19663727,19669908,19672964,19693938,19710001,19724275,19738388,19745699,19752400,19765726,19850689,19855373,19861538,19878585,19880792,19881948,19883729,19893009,19903742,19913280,19913317,19919630,19931546,19936769,19949877,19959686,20001715,20012784,20023270,20025539,20027224,20068183,20102720,20130576,20149136,20156809,20162668,20171085,20177422,20179705,20186005,20187782,20197478,20200438,20230995,20233436,20299678,20300843,20367313,20369307,20381446,20393746,20406109,20410389,20412787,20413299,20417091,20417200,20425073,20447069,20459574,20470206,20472680,20473281,20473912,20485284,20489114,20494973,20496269,20501503,20518413,20519626,20531415,20543822,20551059,20551065,20564403,20570909,20576522,20605766,20607744,20607849,20616366,20630094,20631031,20635392,20640859,20645028,20647301,20652698,20668238,20670148,20674547,20679909,20682701,20716222,20730472,20735442,20806365,20818844,20837233,20854070,20857202,20924129,20925915,20926530,20942773,20944096,20945104,20952593,20953721,20959475,20962618,20972475,21048359,21049459,21051014,21081656,21098728,21102416,21107323,21113787,21131838,21131919,21134548,21134562,21136722,21167555,21169256,21179278,21185263,21190184,21190444,21199003,21206909,21220306,21221869,21224857,21227391,21239517,21249150,21251608,21263251,21274720,21279555,21289333,21295327,21307665,21315413,21326296,21343559,21349766,21351275,21352266,21354060,21355020,21358618,21385081,21412762,21430505,21430779,21430780,21431280,21436632,21441079,21447722,21447745,21449767,21455633,21457162,21458265,21479234,21483012,21496703,21498916,21505227,21511245,21512141,21516079,21519026,21521301,21526955,21527556,21527587,21554046,21558395,21568726,21570823,21587258,21594703,21609347,21610151,21615873,21615881,21635872,21636552,21638088,21639808,21653734,21659424,21660283,21663470,21666714,21671463,21681432,21693616,21694724,21707687,21708284,21716161,21717063,21726664,21730105,21733000,21733555,21738740,21743435,21750866,21770473,21774961,21788131,21791485,21793228,21795305,21796448,21802280,21803329,21818706,21825258,21826256,21826673,21827678,21844014,21859834,21862261,21875464,21879273,21882184,21884820,21889780,21897114,21900390,21903858,21905615,21906875,21910720,21937738,21940036,21943394,21945875,21948220,21979329,21995398,2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+##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##PEDIGREE= +##PEDIGREE= +##PEDIGREE= +##PEDIGREE= +##PEDIGREE= +##PEDIGREE= +##PEDIGREE= +##PEDIGREE= +##PEDIGREE= +##PEDIGREE= +##PEDIGREE= +##PEDIGREE= +##PEDIGREE= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12877 +chr1 126113 . C A . PASS MTD=isaac_strelka,bwa_freebayes,bwa_platypus,bwa_gatk;KM=17.27;KFP=0;KFF=0 GT 1|1 +chr1 535131 . T G . PASS MTD=bwa_freebayes,bwa_gatk;KM=6.33;KFP=0;KFF=0 GT 1|0 +chr1 567239 . CG C . PASS MTD=isaac_strelka,bwa_platypus,bwa_gatk;KM=11.15;KFP=0;KFF=0 GT 1|1 +chr1 570254 . A G . PASS MTD=bwa_gatk;KM=14.00;KFP=0;KFF=0 GT 1|0 +chr1 592368 . A G . PASS MTD=bwa_freebayes;KM=12.67;KFP=0;KFF=0 GT 1|0 +chr1 610426 . A G . PASS MTD=bwa_freebayes;KM=6.67;KFP=0;KFF=0 GT 1|0 +chr1 628140 . T C . PASS MTD=bwa_freebayes;KM=5.00;KFP=0;KFF=0 GT 0|1 +chr1 645605 . T A . PASS MTD=bwa_gatk;KM=14.77;KFP=0;KFF=0 GT 1|1 +chr1 649192 . A T . PASS MTD=bwa_freebayes,bwa_gatk;KM=8.00;KFP=0;KFF=0 GT 0|1 +chr1 662414 . C T . PASS MTD=bwa_gatk;KM=6.71;KFP=0;KFF=0 GT 0|1 +chr1 662622 . G A . PASS MTD=isaac_strelka,bwa_freebayes,bwa_platypus,bwa_gatk;KM=9.86;KFP=0;KFF=0 GT 0|1 +chr1 662857 . G A . PASS MTD=bwa_gatk;KM=6.95;KFP=0;KFF=0 GT 1|0 +chr1 663097 . G C . PASS MTD=bwa_platypus,bwa_gatk;KM=11.32;KFP=0;KFF=0 GT 1|0 +chr1 665266 . T C . PASS MTD=bwa_freebayes,bwa_gatk;KM=9.29;KFP=0;KFF=0 GT 0|1 +chr1 672232 . C T . PASS MTD=bwa_freebayes,bwa_gatk;KM=12.14;KFP=0;KFF=0 GT 0|1 +chr1 693731 . A G . PASS MTD=bwa_freebayes,bwa_platypus,bwa_gatk;KM=12.11;KFP=0;KFF=0 GT 0|1 +chr1 693823 . G C . PASS MTD=bwa_freebayes,bwa_gatk;KM=9.86;KFP=0;KFF=0 GT 0|1 +chr1 703255 . C T . PASS MTD=bwa_freebayes;KM=6.50;KFP=0;KFF=0 GT 1|0 +chr1 704367 . T C . PASS MTD=isaac_strelka,bwa_freebayes,bwa_platypus,bwa_gatk;KM=2.69;KFP=2;KFF=0 GT 1|1 +chr1 706368 . A G . PASS MTD=bwa_platypus,bwa_gatk;KM=9.37;KFP=0;KFF=0 GT 1|0 diff --git a/tests/test_cli.py b/tests/test_cli.py new file mode 100644 index 0000000..745a0ac --- /dev/null +++ b/tests/test_cli.py @@ -0,0 +1,451 @@ +import argparse +import logging +from typing import Any +from unittest.mock import MagicMock, patch + +import pytest + +from varsome_api.cli.utils import ( + build_base_parser, + configure_logging, + parse_request_parameters, + validate_batch_args, + validate_file_args, +) +from varsome_api.cli.varsome_api_annotate_vcf import ( + build_parser as build_annotate_parser, +) +from varsome_api.cli.varsome_api_annotate_vcf import ( + validate_args as validate_annotate_args, +) +from varsome_api.cli.varsome_api_run import ( + _iter_variants_from_file, + build_parser, + lookup_from_file, + lookup_query, + validate_args, +) +from varsome_api.client import BatchResult + + +class TestParseRequestParameters: + """Verify ``parse_request_parameters`` behaviour.""" + + def test_returns_none_when_input_is_none(self) -> None: + assert parse_request_parameters(None) is None + + def test_returns_none_for_empty_list(self) -> None: + assert parse_request_parameters([]) is None + + def test_parses_single_key_value_pair(self) -> None: + result = parse_request_parameters(["add-all-data=1"]) + assert result == {"add-all-data": "1"} + + def test_parses_multiple_key_value_pairs(self) -> None: + result = parse_request_parameters( + ["add-all-data=1", "expand-pubmed-articles=0"] + ) + assert result == {"add-all-data": "1", "expand-pubmed-articles": "0"} + + def test_skips_malformed_entries_and_warns(self) -> None: + """Entries without ``=`` are skipped with a logged warning.""" + with patch("varsome_api.cli.utils.logger") as mock_logger: + result = parse_request_parameters(["bad_param", "good=1"]) + assert result == {"good": "1"} + mock_logger.warning.assert_called_once() + assert "bad_param" in mock_logger.warning.call_args[0][1] + + def test_returns_none_when_all_entries_malformed(self) -> None: + with patch("varsome_api.cli.utils.logger"): + result = parse_request_parameters(["nope", "alsobad"]) + assert result is None + + +class TestBuildBaseParser: + """Verify the shared base argument parser is configured correctly.""" + + def test_requires_api_key(self) -> None: + parser = build_base_parser("test") + with pytest.raises(SystemExit): + parser.parse_args([]) + + def test_defaults_with_api_key(self) -> None: + parser = build_base_parser("test") + args = parser.parse_args(["-k", "mykey"]) + assert args.k == "mykey" + assert args.g == "hg19" + assert args.p == ["add-ACMG-annotation=1"] + assert args.u is None + assert args.t == 5 + assert args.m == 100 + assert args.verbose is False + + def test_all_base_flags(self) -> None: + parser = build_base_parser("test") + args = parser.parse_args( + [ + "-k", + "mykey", + "-g", + "hg38", + "-p", + "add-all-data=1", + "-u", + "https://staging-api.varsome.com", + "-t", + "10", + "-m", + "150", + "-v", + ] + ) + assert args.k == "mykey" + assert args.g == "hg38" + assert args.p == ["add-all-data=1"] + assert args.u == "https://staging-api.varsome.com" + assert args.t == 10 + assert args.m == 150 + assert args.verbose is True + + def test_multiple_request_parameters(self) -> None: + parser = build_base_parser("test") + args = parser.parse_args( + ["-k", "mykey", "-p", "add-all-data=1", "expand-pubmed=0"] + ) + assert args.p == ["add-all-data=1", "expand-pubmed=0"] + + +class TestBuildParser: + """Verify the argument parser is configured correctly.""" + + def test_requires_api_key(self) -> None: + parser = build_parser() + with pytest.raises(SystemExit): + parser.parse_args(["-q", "chr1:100:A:T"]) + + def test_defaults(self) -> None: + parser = build_parser() + args = parser.parse_args(["-k", "mykey", "-q", "chr1:100:A:T"]) + assert args.g == "hg19" + assert args.q == ["chr1:100:A:T"] + assert args.k == "mykey" + assert args.i is None + assert args.o is None + assert args.t == 5 + assert args.m == 100 + assert args.p == ["add-ACMG-annotation=1"] + + def test_all_flags(self) -> None: + parser = build_parser() + args = parser.parse_args( + [ + "-k", + "mykey", + "-g", + "hg38", + "-q", + "v1", + "v2", + "-p", + "add-all-data=1", + "-o", + "out.json", + "-u", + "https://staging-api.varsome.com", + "-t", + "10", + "-m", + "150", + ] + ) + assert args.k == "mykey" + assert args.g == "hg38" + assert args.q == ["v1", "v2"] + assert args.p == ["add-all-data=1"] + assert args.o == "out.json" + assert args.u == "https://staging-api.varsome.com" + assert args.t == 10 + assert args.m == 150 + + +class TestValidateArgs: + """Verify CLI argument validation.""" + + def test_both_q_and_i_exits(self) -> None: + parser = build_parser() + args = parser.parse_args( + ["-k", "mykey", "-q", "chr1:100:A:T", "-i", "file.txt"] + ) + with pytest.raises(SystemExit): + validate_args(args) + + def test_neither_q_nor_i_exits(self) -> None: + parser = build_parser() + args = parser.parse_args(["-k", "mykey"]) + with pytest.raises(SystemExit): + validate_args(args) + + def test_missing_input_file_exits(self) -> None: + parser = build_parser() + args = parser.parse_args(["-k", "mykey", "-i", "/nonexistent/file.txt"]) + with pytest.raises(SystemExit): + validate_args(args) + + def test_output_file_already_exists_exits(self, tmp_path: Any) -> None: + existing = tmp_path / "exists.json" + existing.write_text("{}") + parser = build_parser() + args = parser.parse_args(["-k", "mykey", "-q", "v1", "-o", str(existing)]) + with pytest.raises(SystemExit): + validate_args(args) + + def test_valid_query_passes(self) -> None: + parser = build_parser() + args = parser.parse_args(["-k", "mykey", "-q", "chr1:100:A:T"]) + validate_args(args) # should not raise + + def test_valid_input_file_passes(self, tmp_path: Any) -> None: + f = tmp_path / "variants.txt" + f.write_text("chr1:100:A:T\n") + parser = build_parser() + args = parser.parse_args(["-k", "mykey", "-i", str(f)]) + validate_args(args) # should not raise + + +async def _async_gen_from_list(items: list[Any]) -> Any: + """Yield items from a list as an async generator.""" + for item in items: + yield item + + +class TestIterVariantsFromFile: + """Verify ``_iter_variants_from_file`` streams lines correctly.""" + + async def test_yields_all_non_empty_lines(self, tmp_path: Any) -> None: + f = tmp_path / "variants.txt" + f.write_text("v1\nv2\nv3\n") + + result = [v async for v in _iter_variants_from_file(str(f))] + + assert result == ["v1", "v2", "v3"] + + async def test_skips_blank_lines(self, tmp_path: Any) -> None: + f = tmp_path / "variants.txt" + f.write_text("v1\n\nv2\n\n\nv3\n") + + result = [v async for v in _iter_variants_from_file(str(f))] + + assert result == ["v1", "v2", "v3"] + + async def test_strips_leading_and_trailing_whitespace(self, tmp_path: Any) -> None: + f = tmp_path / "variants.txt" + f.write_text(" v1 \n\tv2\t\n v3\n") + + result = [v async for v in _iter_variants_from_file(str(f))] + + assert result == ["v1", "v2", "v3"] + + async def test_yields_nothing_for_blank_only_file(self, tmp_path: Any) -> None: + f = tmp_path / "blank.txt" + f.write_text("\n\n \n") + + result = [v async for v in _iter_variants_from_file(str(f))] + + assert not result + + async def test_yields_nothing_for_empty_file(self, tmp_path: Any) -> None: + f = tmp_path / "empty.txt" + f.write_text("") + + result = [v async for v in _iter_variants_from_file(str(f))] + + assert not result + + async def test_preserves_file_order(self, tmp_path: Any) -> None: + variants = [f"chr{i}:100:A:T" for i in range(1, 6)] + f = tmp_path / "ordered.txt" + f.write_text("\n".join(variants) + "\n") + + result = [v async for v in _iter_variants_from_file(str(f))] + + assert result == variants + + +class TestLookupQuery: + """Verify ``lookup_query`` delegates correctly to the async API.""" + + async def test_single_query_calls_alookup(self) -> None: + api = MagicMock() + api.abatch_lookup = MagicMock( + return_value=_async_gen_from_list( + [ + BatchResult( + variants=["chr1:100:A:T"], + response=[{"variant_id": "123"}], + ) + ] + ) + ) + + result = lookup_query( + api, + ["chr1:100:A:T"], + request_parameters=None, + ref_genome="hg19", + max_requests=5, + ) + + result_list = [item async for item in result] + + api.abatch_lookup.assert_called_once_with( + ["chr1:100:A:T"], params=None, ref_genome="hg19", max_requests=5 + ) + assert result_list == [{"variant_id": "123"}] + + async def test_batch_query_calls_abatch_lookup(self) -> None: + api = MagicMock() + api.abatch_lookup = MagicMock( + return_value=_async_gen_from_list( + [ + BatchResult( + variants=["v1", "v2"], + response=[{"id": "1"}, {"id": "2"}], + ) + ] + ) + ) + + result = lookup_query( + api, + ["v1", "v2"], + request_parameters=None, + ref_genome="hg38", + max_requests=5, + ) + + result_list = [item async for item in result] + api.abatch_lookup.assert_called_once_with( + ["v1", "v2"], params=None, ref_genome="hg38", max_requests=5 + ) + assert result_list == [{"id": "1"}, {"id": "2"}] + + +class TestLookupFromFile: + """Verify ``lookup_from_file`` reads the file and calls the async API.""" + + async def test_batch_lookup(self, tmp_path: Any) -> None: + f = tmp_path / "vars.txt" + f.write_text("v1\nv2\n") + api = MagicMock() + api.abatch_lookup = MagicMock( + return_value=_async_gen_from_list( + [ + BatchResult( + variants=["v1", "v2"], + response=[{"id": "1"}, {"id": "2"}], + ) + ] + ) + ) + + result = lookup_from_file( + api, + str(f), + request_parameters=None, + ref_genome="hg19", + max_requests=5, + ) + + result_list = [item async for item in result] + assert result_list == [{"id": "1"}, {"id": "2"}] + api.abatch_lookup.assert_called_once() + + +class TestBuildAnnotateParser: + """Verify the annotate_vcf argument parser is configured correctly.""" + + def test_requires_api_key_and_input(self) -> None: + parser = build_annotate_parser() + with pytest.raises(SystemExit): + parser.parse_args([]) + + def test_requires_input_file(self) -> None: + parser = build_annotate_parser() + with pytest.raises(SystemExit): + parser.parse_args(["-k", "mykey"]) + + def test_defaults(self) -> None: + parser = build_annotate_parser() + args = parser.parse_args(["-k", "mykey", "-i", "input.vcf"]) + assert args.k == "mykey" + assert args.i == "input.vcf" + assert args.g == "hg19" + assert args.o is None + assert args.t == 5 + assert args.p == ["add-ACMG-annotation=1"] + assert args.verbose is False + + def test_all_flags(self) -> None: + parser = build_annotate_parser() + args = parser.parse_args( + [ + "-k", + "mykey", + "-i", + "input.vcf", + "-o", + "output.vcf", + "-g", + "hg38", + "-t", + "10", + "-p", + "add-all-data=1", + "-u", + "https://staging-api.varsome.com", + "-v", + ] + ) + assert args.k == "mykey" + assert args.i == "input.vcf" + assert args.o == "output.vcf" + assert args.g == "hg38" + assert args.t == 10 + assert args.p == ["add-all-data=1"] + assert args.u == "https://staging-api.varsome.com" + assert args.verbose is True + + +class TestValidateAnnotateArgs: + """Verify annotate_vcf argument validation.""" + + def test_exits_when_input_file_missing(self) -> None: + parser = build_annotate_parser() + args = parser.parse_args(["-k", "mykey", "-i", "/nonexistent/input.vcf"]) + with pytest.raises(SystemExit): + validate_annotate_args(args) + + def test_exits_when_output_file_exists(self, tmp_path: Any) -> None: + inp = tmp_path / "input.vcf" + inp.write_text("##fileformat=VCFv4.1\n") + out = tmp_path / "output.vcf" + out.write_text("existing data") + parser = build_annotate_parser() + args = parser.parse_args(["-k", "mykey", "-i", str(inp), "-o", str(out)]) + with pytest.raises(SystemExit): + validate_annotate_args(args) + + def test_passes_with_valid_input_file(self, tmp_path: Any) -> None: + inp = tmp_path / "input.vcf" + inp.write_text("##fileformat=VCFv4.1\n") + parser = build_annotate_parser() + args = parser.parse_args(["-k", "mykey", "-i", str(inp)]) + validate_annotate_args(args) # should not raise + + def test_passes_with_valid_input_and_new_output(self, tmp_path: Any) -> None: + inp = tmp_path / "input.vcf" + inp.write_text("##fileformat=VCFv4.1\n") + out = tmp_path / "new_output.vcf" + parser = build_annotate_parser() + args = parser.parse_args(["-k", "mykey", "-i", str(inp), "-o", str(out)]) + validate_annotate_args(args) # should not raise diff --git a/tests/test_client.py b/tests/test_client.py index bfcf0ed..745535f 100644 --- a/tests/test_client.py +++ b/tests/test_client.py @@ -1,165 +1,500 @@ -# Copyright 2018 Saphetor S.A. -# -# Licensed under the Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.apache.org/licenses/LICENSE-2.0 -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. - - -import os - -import unittest -from tempfile import NamedTemporaryFile - -try: - unittest.TestCase.subTest -except AttributeError: - import unittest2 as unittest - - -from vcf.parser import _Info, _encode_type -from varsome_api.client import VarSomeAPIClient, VarSomeAPIException -from varsome_api.models.variant import AnnotatedVariant -from varsome_api.vcf import VCFAnnotator as BaseVCFAnnotator, vcf_reader - -API_KEY = os.getenv("VARSOME_API_KEY", None) -BASE_DIR = os.path.dirname(os.path.dirname(os.path.abspath(__file__))) -VARIANTS_CSV_FILE = os.path.join(BASE_DIR, "tests", "variants.csv") -VARIANTS_VCF_FILE = os.path.join(BASE_DIR, "tests", "variants.vcf") - - -class TestApiClient(unittest.TestCase): - def __init__(self, methodName="runTest"): - super().__init__(methodName) - self.client = VarSomeAPIClient(API_KEY) - with open(VARIANTS_CSV_FILE) as f: - self.variants_to_lookup = f.read().splitlines() - if API_KEY is None: - # just get 5 variants without an API key tests might fail with 429 - self.variants_to_lookup = self.variants_to_lookup[:5] - else: - self.variants_to_lookup = self.variants_to_lookup[:50] - - def test_schema(self): - """Check we receive the response schema back""" - self.assertIsNotNone(self.client.schema()) - self.client.session.close() - - def test_404(self): - """Check we can raise VarSomeAPIException""" - with self.assertRaises(VarSomeAPIException) as ve: - self.client.lookup("chrM:410:A:T", ref_genome="hg64") - test_exception = ve.exception - self.assertEqual(test_exception.status, 404) - self.client.session.close() - - def test_get_lookup_hg19(self): - """Check we can do plain get requests""" - for i, variant in enumerate(self.variants_to_lookup): - with self.subTest(i=i): - result = self.client.lookup( - variant, - ref_genome="hg19", - params={"add-all-data": 1, "expand-pubmed-articles": 0}, - ) - self.assertIsNotNone(result) - self.assertTrue("variant_id" in result) - self.client.session.close() - - def test_batch_lookup_hg19(self): - """Check we can do batch requests""" - results = self.client.batch_lookup( - self.variants_to_lookup, - ref_genome="hg19", - params={"add-all-data": 1, "expand-pubmed-articles": 0}, - raise_exceptions=True, +import asyncio +from collections.abc import AsyncGenerator, Callable +from typing import Any +from unittest.mock import AsyncMock, MagicMock, patch + +import aiohttp +import pytest + +from varsome_api.client import ( + DEFAULT_API_URL, + DEFAULT_HEADERS, + BatchResult, + VarSomeAPIClient, + VarSomeAPIClientBase, +) +from varsome_api.exceptions import VarSomeAPIException + + +def _build_mock_session(status: int, json_data: Any) -> MagicMock: + """Return a ``MagicMock`` aiohttp session whose request yields *json_data*. + Args: + status: HTTP status code the mock response should report. + json_data: The value returned by ``response.json()``. + Returns: + A ``MagicMock`` that mimics an ``aiohttp.ClientSession``. + """ + mock_resp = AsyncMock() + mock_resp.status = status + mock_resp.json = AsyncMock(return_value=json_data) + cm = MagicMock() + cm.__aenter__ = AsyncMock(return_value=mock_resp) + cm.__aexit__ = AsyncMock(return_value=False) + session = MagicMock() + session.request = MagicMock(return_value=cm) + return session + + +class TestBatchResult: + """Verify the ``BatchResult`` dataclass behaviour.""" + + def test_stores_variants_and_response(self) -> None: + variants = ["chr1:100:A:T", "chr2:200:G:C"] + response = [{"chromosome": "chr1"}, {"chromosome": "chr2"}] + result = BatchResult(variants=variants, response=response) + assert result.variants == variants + assert result.response == response + + def test_correlates_errors_with_input(self) -> None: + """When the API returns an error without the original variant, + callers can still identify the batch that caused it.""" + variants = ["chr1:100:A:T", "chr7:BAD:X:Y"] + response = [ + {"chromosome": "chr1", "original_variant": "chr1:100:A:T"}, + {"error": "Invalid variant format"}, + ] + result = BatchResult(variants=variants, response=response) + errors = [r for r in result.response if "error" in r] + assert len(errors) == 1 + assert result.variants == variants + + +class TestVarSomeAPIClientBaseInit: + """Verify ``VarSomeAPIClientBase`` initialization and header configuration.""" + + def test_default_api_url(self) -> None: + client = VarSomeAPIClientBase(api_key="key123") + assert client.api_url == DEFAULT_API_URL + + def test_custom_api_url(self) -> None: + client = VarSomeAPIClientBase(api_key="key123", api_url="https://custom.api") + assert client.api_url == "https://custom.api" + + def test_auth_header_set_when_key_provided(self) -> None: + client = VarSomeAPIClientBase(api_key="mytoken") + assert client._headers["Authorization"] == "Token mytoken" + + def test_no_auth_header_without_key(self) -> None: + client = VarSomeAPIClientBase() + assert "Authorization" not in client._headers + + def test_headers_contain_defaults(self) -> None: + client = VarSomeAPIClientBase() + for key, value in DEFAULT_HEADERS.items(): + assert client._headers[key] == value + + +class TestVarSomeAPIClientBaseContextManager: + """Verify ``VarSomeAPIClientBase`` async context manager behaviour.""" + + async def test_aenter_creates_session(self) -> None: + """``__aenter__`` must create an open ``aiohttp.ClientSession``.""" + client = VarSomeAPIClientBase(api_key="test") + await client.__aenter__() + try: + assert client._session is not None + assert not client._session.closed + finally: + await client.__aexit__(None, None, None) + + async def test_aexit_closes_and_clears_session(self) -> None: + """``__aexit__`` must close the session and set ``_session`` to ``None``.""" + async with VarSomeAPIClientBase(api_key="test") as client: + assert client._session is not None + assert client._session is None + + async def test_aexit_noop_when_session_is_none(self) -> None: + """``__aexit__`` must be a no-op when ``_session`` is already ``None``.""" + client = VarSomeAPIClientBase() + assert client._session is None + await client.__aexit__(None, None, None) # must not raise + assert client._session is None + + +class TestVarSomeAPIClientBaseMakeRequest: + """Verify ``VarSomeAPIClientBase._make_request`` HTTP handling.""" + + async def test_get_returns_json_response(self) -> None: + session = _build_mock_session(200, {"chromosome": "chr1"}) + result = await VarSomeAPIClientBase._make_request( + session, path="/lookup/chr1:100:A:T", method="GET" ) - self.assertEqual(len(results), len(self.variants_to_lookup)) - self.client.session.close() - - -class TestApiResponse(unittest.TestCase): - def __init__(self, methodName="runTest"): - super().__init__(methodName) - client = VarSomeAPIClient(API_KEY, max_variants_per_batch=1000) - with open(VARIANTS_CSV_FILE) as f: - self.variants_to_lookup = f.read().splitlines() - self.results = client.batch_lookup( - self.variants_to_lookup, - ref_genome="hg19", - params={"add-all-data": 1, "expand-pubmed-articles": 0}, - raise_exceptions=True, + assert result == {"chromosome": "chr1"} + session.request.assert_called_once_with( + "GET", url="/lookup/chr1:100:A:T", params=None ) - client.session.close() - - def test_result_is_not_none(self): - """Check result is not None""" - for i, result in enumerate(self.results): - with self.subTest(i=i): - self.assertIsNotNone(result) - - def test_result_has_variant_id(self): - """Check result includes variant_id""" - for i, result in enumerate(self.results): - with self.subTest(i=i): - self.assertTrue("variant_id" in result) - - def test_variant_chromosome_result_chromosome(self): - """Check that the requested chromosome is the same as the one returned""" - for i, result in enumerate(self.results): - with self.subTest(i=i): - chromosome = self.variants_to_lookup[i].split(":")[0] - self.assertEqual(result["chromosome"], chromosome) - - def test_result_wrapper(self): - """Check that we can wrap the result in a json model""" - for i, result in enumerate(self.results): - with self.subTest(i=i): - annotated_variant = AnnotatedVariant(**result) - self.assertEqual(annotated_variant.chromosome, result["chromosome"]) - self.assertIsNotNone(annotated_variant.pos) - self.assertEqual(result["pos"], annotated_variant.pos) - - -class VCFAnnotator(BaseVCFAnnotator): - def annotate_record(self, record, variant_result, original_variant): - record.INFO["gnomad_genomes_AN"] = variant_result.gnomad_genomes_an - return record - - def add_vcf_header_info(self, vcf_template): - vcf_template.infos["gnomad_genomes_AN"] = _Info( - "gnomad_genomes_AN", - ".", - "Integer", - "GnomAD genomes allele number value", - None, - None, - _encode_type("Integer"), + + async def test_post_forwards_json_and_headers(self) -> None: + """POST with json body and custom headers passes them through correctly.""" + session = _build_mock_session(200, [{"id": "v1"}]) + result = await VarSomeAPIClientBase._make_request( + session, + path="/lookup/batch/hg19", + method="POST", + json={"variants": ["v1"]}, + headers={"Content-Type": "application/json"}, ) + assert result == [{"id": "v1"}] + _, call_kwargs = session.request.call_args + assert call_kwargs["json"] == {"variants": ["v1"]} + assert call_kwargs["headers"] == {"Content-Type": "application/json"} + + async def test_optional_json_and_headers_omitted_when_not_supplied(self) -> None: + """``json`` and ``headers`` must not appear in the request when absent.""" + session = _build_mock_session(200, {}) + await VarSomeAPIClientBase._make_request(session, path="/lookup/chr1:100:A:T") + _, call_kwargs = session.request.call_args + assert "json" not in call_kwargs + assert "headers" not in call_kwargs + + async def test_error_status_raises_varsome_exception(self) -> None: + """HTTP 4xx/5xx responses must raise ``VarSomeAPIException``.""" + session = _build_mock_session(400, {"detail": "bad request"}) + with pytest.raises(VarSomeAPIException) as exc_info: + await VarSomeAPIClientBase._make_request( + session, path="/lookup/bad", method="GET" + ) + assert exc_info.value.status == 400 + + @pytest.mark.parametrize( + ("exc_class", "expected_fragment"), + [ + (aiohttp.ServerTimeoutError, "timed out"), + (aiohttp.ClientConnectionError, "Connection failure"), + (aiohttp.ClientError, "Unknown error"), + ], + ids=["timeout", "connection_error", "generic_client_error"], + ) + async def test_aiohttp_transport_errors_wrapped( + self, + exc_class: type[aiohttp.ClientError], + expected_fragment: str, + ) -> None: + """aiohttp transport errors must be re-raised as ``VarSomeAPIException``.""" + session = MagicMock() + session.request = MagicMock(side_effect=exc_class()) + with pytest.raises(VarSomeAPIException) as exc_info: + await VarSomeAPIClientBase._make_request( + session, path="/lookup/chr1:100:A:T", method="GET" + ) + assert expected_fragment in str(exc_info.value) + + +class TestVarSomeAPIClientBaseGet: + """Verify ``VarSomeAPIClientBase.get``.""" + + async def test_returns_response(self) -> None: + """``get`` must delegate to ``_make_request`` and return its result.""" + expected: dict[str, Any] = {"chromosome": "chr1"} + client = VarSomeAPIClientBase(api_key="test") + with patch.object( + type(client), "_make_request", new=AsyncMock(return_value=expected) + ): + result = await client.get("/lookup/chr1:100:A:T") + assert result == expected + + async def test_passes_params(self) -> None: + """Query parameters must be forwarded to ``_make_request``.""" + client = VarSomeAPIClientBase(api_key="test") + mock_request = AsyncMock(return_value={}) + with patch.object(type(client), "_make_request", new=mock_request): + await client.get("/lookup/chr1:100:A:T", params={"expand": "1"}) + _, kwargs = mock_request.call_args + assert kwargs.get("params") == {"expand": "1"} + assert kwargs.get("method") == "GET" + + +class TestVarSomeAPIClientBasePost: + """Verify ``VarSomeAPIClientBase.post``.""" + + async def test_returns_response(self) -> None: + """``post`` must delegate to ``_make_request`` and return its result.""" + expected: dict[str, Any] = {"ok": True} + client = VarSomeAPIClientBase(api_key="test") + with patch.object( + type(client), "_make_request", new=AsyncMock(return_value=expected) + ): + result = await client.post( + "/lookup/batch/hg19", json_data={"variants": ["v1"]} + ) + assert result == expected + + async def test_forwards_json_data(self) -> None: + """``json_data`` must be passed as ``json`` with a JSON content-type header.""" + client = VarSomeAPIClientBase(api_key="test") + mock_request = AsyncMock(return_value={}) + with patch.object(type(client), "_make_request", new=mock_request): + await client.post("/lookup/batch/hg19", json_data={"variants": ["v1"]}) + _, kwargs = mock_request.call_args + assert kwargs.get("method") == "POST" + assert kwargs.get("json") == {"variants": ["v1"]} + assert kwargs.get("headers") == {"Content-Type": "application/json"} + + +class TestVarSomeAPIClientInit: + """Verify ``VarSomeAPIClient``-specific initialisation.""" + + def test_default_max_variants_per_batch(self) -> None: + client = VarSomeAPIClient() + assert client.max_variants_per_batch == 200 + + def test_custom_max_variants_per_batch(self) -> None: + client = VarSomeAPIClient(max_variants_per_batch=50) + assert client.max_variants_per_batch == 50 + + def test_inherits_base_auth_header(self) -> None: + client = VarSomeAPIClient(api_key="mytoken") + assert client._headers["Authorization"] == "Token mytoken" + + def test_inherits_base_api_url(self) -> None: + client = VarSomeAPIClient(api_url="https://custom.api") + assert client.api_url == "https://custom.api" + + +class TestVarSomeAPIClientLookup: + """Verify ``VarSomeAPIClient.alookup`` and its sync wrapper ``lookup``.""" + + async def test_alookup_returns_annotation(self) -> None: + """``alookup`` must return the JSON annotation dict from the API.""" + expected: dict[str, Any] = {"chromosome": "chr1", "position": 100} + client = VarSomeAPIClient(api_key="test") + with patch.object(client, "get", new=AsyncMock(return_value=expected)): + result = await client.alookup("chr1:100:A:T", ref_genome="hg19") + assert result == expected + + async def test_alookup_constructs_correct_url(self) -> None: + """URL must follow the pattern ``/lookup//``.""" + client = VarSomeAPIClient(api_key="test") + mock_get = AsyncMock(return_value={}) + with patch.object(client, "get", new=mock_get): + await client.alookup("chr1:100:A:T", ref_genome="hg19") + mock_get.assert_called_once_with("/lookup/chr1:100:A:T/hg19", params=None) + + async def test_alookup_forwards_params(self) -> None: + """Optional query params must be forwarded unchanged to ``get``.""" + client = VarSomeAPIClient(api_key="test") + mock_get = AsyncMock(return_value={}) + with patch.object(client, "get", new=mock_get): + await client.alookup( + "chr1:100:A:T", + params={"exclude-source-databases": "gnomad-genomes"}, + ref_genome="hg38", + ) + _, kwargs = mock_get.call_args + assert kwargs.get("params") == {"exclude-source-databases": "gnomad-genomes"} + + def test_lookup_is_sync_wrapper_around_alookup(self) -> None: + """``lookup`` must block and return the same result as ``alookup``.""" + expected: dict[str, Any] = {"chromosome": "chr19"} + client = VarSomeAPIClient(api_key="test") + with patch.object(client, "get", new=AsyncMock(return_value=expected)): + result = client.lookup("chr19:20082943:1:G", ref_genome="hg19") + assert result == expected + + +class TestVarSomeAPIClientBatchProducer: + """Verify ``VarSomeAPIClient._batch_producer`` chunking behaviour.""" + + @pytest.mark.parametrize( + ("batch_size", "items", "expected"), + [ + (2, ["v1", "v2", "v3", "v4"], [["v1", "v2"], ["v3", "v4"]]), + (2, ["v1", "v2", "v3"], [["v1", "v2"], ["v3"]]), + (10, [], []), + (10, ["v1"], [["v1"]]), + (3, ["v1", "v2", "v3"], [["v1", "v2", "v3"]]), + ], + ids=[ + "exact_multiples", + "remainder", + "empty_list", + "single_element", + "batch_equals_length", + ], + ) + async def test_sync_iterable_chunking( + self, + batch_size: int, + items: list[str], + expected: list[list[str]], + ) -> None: + """Sync iterables are split into batches of at most *batch_size* items.""" + client = VarSomeAPIClient(max_variants_per_batch=batch_size) + queue: asyncio.Queue = asyncio.Queue() + await client._batch_producer(items, queue) + batches: list[list[str]] = [] + while not queue.empty(): + item = queue.get_nowait() + if item is None: + break + batches.append(list(item)) + assert batches == expected + + async def test_async_iterable_chunked_correctly(self) -> None: + """Async generators are chunked identically to sync iterables.""" + + async def async_variants() -> AsyncGenerator[str, None]: + for v in ["v1", "v2", "v3", "v4", "v5"]: + yield v + + client = VarSomeAPIClient(max_variants_per_batch=2) + queue: asyncio.Queue = asyncio.Queue() + await client._batch_producer(async_variants(), queue) + batches: list[list[str]] = [] + while not queue.empty(): + item = queue.get_nowait() + if item is None: + break + batches.append(list(item)) + assert batches == [["v1", "v2"], ["v3", "v4"], ["v5"]] + + async def test_async_iterable_final_partial_batch_flushed(self) -> None: + """The trailing partial batch must always be put on the queue.""" + + async def async_variants() -> AsyncGenerator[str, None]: + for v in ["a", "b", "c"]: + yield v + + client = VarSomeAPIClient(max_variants_per_batch=10) + queue: asyncio.Queue = asyncio.Queue() + await client._batch_producer(async_variants(), queue) + items: list[Any] = [] + while not queue.empty(): + items.append(queue.get_nowait()) + assert items[-1] is None + assert items[:-1] == [["a", "b", "c"]] + + +class TestVarSomeAPIClientBatchWorker: + """Verify ``VarSomeAPIClient._batch_worker`` request dispatching.""" + + async def test_successful_batch_put_on_result_queue( + self, make_fake_request: Callable + ) -> None: + """A successful request must place a ``BatchResult`` on the result queue.""" + fake = make_fake_request(lambda batch: [{"id": v} for v in batch]) + client = VarSomeAPIClient(api_key="test") + session = MagicMock() + request_queue: asyncio.Queue = asyncio.Queue() + result_queue: asyncio.Queue = asyncio.Queue() + await request_queue.put(["v1", "v2"]) + await request_queue.put(None) + with patch.object(type(client), "_make_request", side_effect=fake): + await client._batch_worker( + session, request_queue, result_queue, "/lookup/batch/hg19", None + ) + result = result_queue.get_nowait() + assert isinstance(result, BatchResult) + assert result.variants == ["v1", "v2"] + + async def test_failed_batch_puts_exception_on_result_queue(self) -> None: + """On ``VarSomeAPIException``, the exception must be enqueued, not re-raised.""" + exc = VarSomeAPIException(500, "Server Error") + + async def failing_request(_session: Any, **kwargs: Any) -> Any: + raise exc + + client = VarSomeAPIClient(api_key="test") + session = MagicMock() + request_queue: asyncio.Queue = asyncio.Queue() + result_queue: asyncio.Queue = asyncio.Queue() + await request_queue.put(["v1", "v2"]) + await request_queue.put(None) + with patch.object(type(client), "_make_request", side_effect=failing_request): + await client._batch_worker( + session, request_queue, result_queue, "/lookup/batch/hg19", None + ) + queued = result_queue.get_nowait() + assert isinstance(queued, VarSomeAPIException) + assert queued is exc + + +class TestVarSomeAPIClientBatchLookup: + """Verify ``VarSomeAPIClient.abatch_lookup`` and its sync wrapper ``batch_lookup``.""" + + async def test_yields_batch_results(self, make_fake_request: Callable) -> None: + """Each yielded item must be a ``BatchResult`` covering at most *batch_size* variants.""" + variants = ["v1", "v2", "v3", "v4", "v5"] + mock_responses = { + ("v1", "v2"): [{"id": "1"}, {"id": "2"}], + ("v3", "v4"): [{"id": "3"}, {"id": "4"}], + ("v5",): [{"id": "5"}], + } + fake = make_fake_request(lambda batch: mock_responses[tuple(batch)]) + client = VarSomeAPIClient(api_key="test", max_variants_per_batch=2) + async with client: + with patch.object(type(client), "_make_request", side_effect=fake): + results = [ + r + async for r in client.abatch_lookup( + variants, ref_genome="hg19", max_requests=1 + ) + ] + assert len(results) == 3 + for result in results: + assert isinstance(result, BatchResult) + assert len(result.variants) <= 2 + all_variants = [v for r in results for v in r.variants] + assert sorted(all_variants) == sorted(variants) + + async def test_batch_response_paired_with_input( + self, make_fake_request: Callable + ) -> None: + """Each ``BatchResult.response`` must correspond to its ``.variants``.""" + variants = ["chr1:100:A:T", "chr2:200:G:C"] + fake = make_fake_request(lambda batch: [{"original_variant": v} for v in batch]) + client = VarSomeAPIClient(api_key="test", max_variants_per_batch=10) + async with client: + with patch.object(type(client), "_make_request", side_effect=fake): + results = [ + r async for r in client.abatch_lookup(variants, ref_genome="hg19") + ] + assert len(results) == 1 + assert results[0].variants == variants + assert results[0].response == [ + {"original_variant": "chr1:100:A:T"}, + {"original_variant": "chr2:200:G:C"}, + ] + + async def test_accepts_async_generator(self, make_fake_request: Callable) -> None: + """``abatch_lookup`` must accept an async generator in place of a list.""" + + async def async_variants() -> AsyncGenerator[str, None]: + for v in ["v1", "v2", "v3"]: + yield v + + fake = make_fake_request(lambda batch: [{"id": v} for v in batch]) + client = VarSomeAPIClient(api_key="test", max_variants_per_batch=2) + with patch.object(type(client), "_make_request", side_effect=fake): + results = [ + r + async for r in client.abatch_lookup(async_variants(), ref_genome="hg19") + ] + all_variants = [v for r in results for v in r.variants] + assert sorted(all_variants) == ["v1", "v2", "v3"] + + async def test_propagates_batch_exception(self) -> None: + """A failed batch must raise ``VarSomeAPIException`` to the caller.""" + + async def failing_request(_session: Any, **kwargs: Any) -> Any: + raise VarSomeAPIException(500, "Server Error") + client = VarSomeAPIClient(api_key="test", max_variants_per_batch=10) + with patch.object(type(client), "_make_request", side_effect=failing_request): + with pytest.raises(VarSomeAPIException): + async for _ in client.abatch_lookup(["v1", "v2"], ref_genome="hg19"): + pass -class TestVcfAnnotator(unittest.TestCase): - def __init__(self, methodName="runTest"): - super().__init__(methodName) - self.annotator = VCFAnnotator(API_KEY) - - def test_annotate_vcf(self): - """Check that we can annotate a vcf file""" - output_vcf_file = NamedTemporaryFile(delete=False) - output_vcf_file.close() - self.annotator.annotate(VARIANTS_VCF_FILE, output_vcf_file.name) - with vcf_reader( - filename=output_vcf_file.name, strict_whitespace=True - ) as reader: - self.assertTrue("gnomad_genomes_AN" in reader.infos) - for i, record in enumerate(reader): - with self.subTest(i=i): - self.assertTrue("gnomad_genomes_AN" in record.INFO) - self.annotator.session.close() + def test_batch_lookup_sync_collects_all_results( + self, make_fake_request: Callable + ) -> None: + """``batch_lookup`` must return a flat list of all ``BatchResult`` objects.""" + variants = ["v1", "v2"] + fake = make_fake_request(lambda batch: [{"id": v} for v in batch]) + client = VarSomeAPIClient(api_key="test", max_variants_per_batch=10) + with patch.object(type(client), "_make_request", side_effect=fake): + results = client.batch_lookup(variants, ref_genome="hg19") + assert len(results) == 1 + assert isinstance(results[0], BatchResult) + assert results[0].variants == variants + assert results[0].response == [{"id": "v1"}, {"id": "v2"}] diff --git a/tests/test_exception.py b/tests/test_exception.py new file mode 100644 index 0000000..919f191 --- /dev/null +++ b/tests/test_exception.py @@ -0,0 +1,31 @@ +import pytest + +from varsome_api.exceptions import VarSomeAPIException + + +class TestVarSomeAPIException: + """Verify the custom API exception behaviour.""" + + @pytest.mark.parametrize( + ("status", "response", "expected_fragments"), + [ + (400, "Bad input", ["400", "Bad input"]), + (500, None, ["500", "Internal Server Error"]), + (None, "Connection refused", ["Connection refused"]), + (None, None, ["Unknown error"]), + ], + ids=["status_and_response", "status_only", "none_status", "no_info"], + ) + def test_str_representation( + self, + status: int | None, + response: str | None, + expected_fragments: list[str], + ) -> None: + exc = VarSomeAPIException(status, response) + for fragment in expected_fragments: + assert fragment in str(exc) + + def test_repr(self) -> None: + exc = VarSomeAPIException(404) + assert repr(exc) == "VarSomeAPIException(status=404)" diff --git a/tests/test_models.py b/tests/test_models.py new file mode 100644 index 0000000..6348886 --- /dev/null +++ b/tests/test_models.py @@ -0,0 +1,483 @@ +import json +from pathlib import Path +from typing import Any + +import pytest + +from varsome_api.models.slim.annotation import AnnotatedVariant as SlimAnnotatedVariant +from varsome_api.models.variant import AnnotatedVariant + +BASE_DIR = Path(__file__).resolve().parent +FIXTURES_DIR = BASE_DIR / "fixtures" +GERMLINE_FIXTURE = FIXTURES_DIR / "example_response_germline.json" +AMP_FIXTURE = FIXTURES_DIR / "example_response_amp.json" + + +@pytest.fixture(scope="module") +def germline_data() -> dict[str, Any]: + """Load the germline example response as a raw dict.""" + with GERMLINE_FIXTURE.open() as f: + return json.load(f) + + +@pytest.fixture(scope="module") +def amp_data() -> dict[str, Any]: + """Load the AMP example response as a raw dict.""" + with AMP_FIXTURE.open() as f: + return json.load(f) + + +@pytest.fixture(scope="module") +def germline_variant(germline_data: dict[str, Any]) -> AnnotatedVariant: + """Deserialize the germline fixture into an AnnotatedVariant.""" + return AnnotatedVariant(**germline_data) + + +@pytest.fixture(scope="module") +def amp_variant(amp_data: dict[str, Any]) -> AnnotatedVariant: + """Deserialize the AMP fixture into an AnnotatedVariant.""" + return AnnotatedVariant(**amp_data) + + +class TestDeserialization: + """Verify that example responses can be completely deserialized.""" + + def test_germline_response_deserializes( + self, germline_variant: AnnotatedVariant + ) -> None: + assert germline_variant is not None + + def test_amp_response_deserializes(self, amp_variant: AnnotatedVariant) -> None: + assert amp_variant is not None + + def test_empty_dict_produces_default_variant(self) -> None: + """An empty dict should produce a valid instance with all None fields.""" + v = AnnotatedVariant() + assert v.chromosome is None + assert v.pos is None + + def test_extra_fields_accepted(self) -> None: + """Unknown keys must not cause a validation error.""" + v = AnnotatedVariant( + chromosome="chr1", + some_future_database=[{"version": "1.0", "score": 42}], + ) + assert v.chromosome == "chr1" + assert v.some_future_database == [{"version": "1.0", "score": 42}] + + +class TestCoreFields: + """Check that core fields are parsed from both fixtures.""" + + @pytest.mark.parametrize("fixture", ["germline_variant", "amp_variant"]) + def test_chromosome(self, fixture: str, request: pytest.FixtureRequest) -> None: + v: AnnotatedVariant = request.getfixturevalue(fixture) + assert v.chromosome == "chr7" + + @pytest.mark.parametrize("fixture", ["germline_variant", "amp_variant"]) + def test_pos(self, fixture: str, request: pytest.FixtureRequest) -> None: + v: AnnotatedVariant = request.getfixturevalue(fixture) + assert v.pos == 140453136 + + @pytest.mark.parametrize("fixture", ["germline_variant", "amp_variant"]) + def test_ref_alt(self, fixture: str, request: pytest.FixtureRequest) -> None: + v: AnnotatedVariant = request.getfixturevalue(fixture) + assert v.ref == "A" + assert v.alt == "T" + + @pytest.mark.parametrize("fixture", ["germline_variant", "amp_variant"]) + def test_variant_type(self, fixture: str, request: pytest.FixtureRequest) -> None: + v: AnnotatedVariant = request.getfixturevalue(fixture) + assert v.variant_type == "SNV" + + @pytest.mark.parametrize("fixture", ["germline_variant", "amp_variant"]) + def test_cytobands(self, fixture: str, request: pytest.FixtureRequest) -> None: + v: AnnotatedVariant = request.getfixturevalue(fixture) + assert v.cytobands == "7q34" + + +class TestConvenienceProperties: + """Verify the computed helper properties on AnnotatedVariant.""" + + def test_genes(self, germline_variant: AnnotatedVariant) -> None: + assert sorted(germline_variant.genes) == ["BRAF"] + + def test_refseq_genes_not_empty(self, germline_variant: AnnotatedVariant) -> None: + assert len(germline_variant.refseq_genes) > 0 + assert all(g == "BRAF" for g in germline_variant.refseq_genes) + + def test_ensembl_genes_not_empty(self, germline_variant: AnnotatedVariant) -> None: + assert len(germline_variant.ensembl_genes) > 0 + assert all(g == "BRAF" for g in germline_variant.ensembl_genes) + + def test_rs_ids(self, germline_variant: AnnotatedVariant) -> None: + assert germline_variant.rs_ids == ["rs113488022"] + + def test_gnomad_exomes_af(self, germline_variant: AnnotatedVariant) -> None: + af = germline_variant.gnomad_exomes_af + assert af is not None + assert af > 0 + + def test_gnomad_exomes_an(self, germline_variant: AnnotatedVariant) -> None: + assert germline_variant.gnomad_exomes_an == 251260 + + def test_gnomad_genomes_af_none_when_absent( + self, germline_variant: AnnotatedVariant + ) -> None: + assert germline_variant.gnomad_genomes_af is None + + def test_gnomad_genomes_an_none_when_absent( + self, germline_variant: AnnotatedVariant + ) -> None: + assert germline_variant.gnomad_genomes_an is None + + def test_acmg_verdict(self, germline_variant: AnnotatedVariant) -> None: + assert germline_variant.acmg_verdict == "Pathogenic" + + def test_acmg_rules(self, germline_variant: AnnotatedVariant) -> None: + rules = germline_variant.acmg_rules + assert rules is not None + assert "PS3" in rules + assert "PM1" in rules + + +class TestGermlineDataSources: + """Verify presence and basic structure of data sources in the germline fixture.""" + + def test_regions_present(self, germline_variant: AnnotatedVariant) -> None: + assert germline_variant.regions is not None + + def test_refseq_transcripts(self, germline_variant: AnnotatedVariant) -> None: + assert germline_variant.refseq_transcripts is not None + assert len(germline_variant.refseq_transcripts) == 1 + + def test_ensembl_transcripts(self, germline_variant: AnnotatedVariant) -> None: + assert germline_variant.ensembl_transcripts is not None + assert len(germline_variant.ensembl_transcripts) == 1 + + def test_gnomad_exomes(self, germline_variant: AnnotatedVariant) -> None: + assert germline_variant.gnomad_exomes is not None + assert len(germline_variant.gnomad_exomes) == 1 + + def test_ncbi_dbsnp(self, germline_variant: AnnotatedVariant) -> None: + assert germline_variant.ncbi_dbsnp is not None + assert len(germline_variant.ncbi_dbsnp) > 0 + + def test_ncbi_clinvar2(self, germline_variant: AnnotatedVariant) -> None: + assert germline_variant.ncbi_clinvar2 is not None + assert len(germline_variant.ncbi_clinvar2) > 0 + + def test_dbnsfp(self, germline_variant: AnnotatedVariant) -> None: + assert germline_variant.dbnsfp is not None + assert len(germline_variant.dbnsfp) > 0 + + def test_acmg_annotation(self, germline_variant: AnnotatedVariant) -> None: + assert germline_variant.acmg_annotation is not None + assert germline_variant.acmg_annotation.verdict is not None + + def test_alpha_missense(self, germline_variant: AnnotatedVariant) -> None: + assert germline_variant.alpha_missense is not None + assert len(germline_variant.alpha_missense) > 0 + + def test_cadd(self, germline_variant: AnnotatedVariant) -> None: + assert germline_variant.cadd is not None + assert len(germline_variant.cadd) > 0 + + def test_pharmgkb(self, germline_variant: AnnotatedVariant) -> None: + assert germline_variant.pharmgkb is not None + assert len(germline_variant.pharmgkb) > 0 + + def test_publications(self, germline_variant: AnnotatedVariant) -> None: + assert germline_variant.publications is not None + + def test_saphetor_known_pathogenicity( + self, germline_variant: AnnotatedVariant + ) -> None: + assert germline_variant.saphetor_known_pathogenicity is not None + assert len(germline_variant.saphetor_known_pathogenicity) > 0 + + def test_cancer_hotspots(self, germline_variant: AnnotatedVariant) -> None: + assert germline_variant.cancer_hotspots is not None + assert len(germline_variant.cancer_hotspots) > 0 + + def test_cbio_portal(self, germline_variant: AnnotatedVariant) -> None: + assert germline_variant.cbio_portal is not None + assert len(germline_variant.cbio_portal) > 0 + + def test_jax_ckb(self, germline_variant: AnnotatedVariant) -> None: + assert germline_variant.jax_ckb is not None + assert len(germline_variant.jax_ckb) > 0 + + def test_lumc_lovd(self, germline_variant: AnnotatedVariant) -> None: + assert germline_variant.lumc_lovd is not None + assert len(germline_variant.lumc_lovd) > 0 + + def test_wustl_civic(self, germline_variant: AnnotatedVariant) -> None: + assert germline_variant.wustl_civic is not None + assert len(germline_variant.wustl_civic) > 0 + + def test_sanger_cosmic_licensed(self, germline_variant: AnnotatedVariant) -> None: + assert germline_variant.sanger_cosmic_licensed is not None + assert len(germline_variant.sanger_cosmic_licensed) > 0 + + +class TestAmpDataSources: + """Verify AMP-specific sources that are absent from the germline fixture.""" + + def test_amp_annotation_present(self, amp_variant: AnnotatedVariant) -> None: + assert amp_variant.amp_annotation is not None + + def test_oncokb_present(self, amp_variant: AnnotatedVariant) -> None: + assert amp_variant.oncokb is not None + assert len(amp_variant.oncokb) > 0 + + def test_germline_lacks_amp_annotation( + self, germline_variant: AnnotatedVariant + ) -> None: + assert germline_variant.amp_annotation is None + + def test_germline_lacks_oncokb(self, germline_variant: AnnotatedVariant) -> None: + assert germline_variant.oncokb is None + + +class TestConveniencePropertiesEdgeCases: + """Verify convenience properties handle empty / missing data gracefully.""" + + def test_genes_empty_when_no_transcripts(self) -> None: + v = AnnotatedVariant() + assert v.genes == [] + + def test_refseq_genes_empty_when_no_transcripts(self) -> None: + v = AnnotatedVariant() + assert v.refseq_genes == [] + + def test_ensembl_genes_empty_when_no_transcripts(self) -> None: + v = AnnotatedVariant() + assert v.ensembl_genes == [] + + def test_rs_ids_empty_when_no_dbsnp(self) -> None: + v = AnnotatedVariant() + assert v.rs_ids == [] + + def test_gnomad_exomes_af_none_when_empty(self) -> None: + v = AnnotatedVariant() + assert v.gnomad_exomes_af is None + + def test_gnomad_genomes_af_none_when_empty(self) -> None: + v = AnnotatedVariant() + assert v.gnomad_genomes_af is None + + def test_gnomad_exomes_an_none_when_empty(self) -> None: + v = AnnotatedVariant() + assert v.gnomad_exomes_an is None + + def test_gnomad_genomes_an_none_when_empty(self) -> None: + v = AnnotatedVariant() + assert v.gnomad_genomes_an is None + + def test_acmg_verdict_none_when_no_annotation(self) -> None: + v = AnnotatedVariant() + assert v.acmg_verdict is None + + def test_acmg_rules_empty_when_no_annotation(self) -> None: + v = AnnotatedVariant() + assert v.acmg_rules == [] + + +@pytest.fixture(scope="module") +def slim_germline_variant(germline_data: dict[str, Any]) -> SlimAnnotatedVariant: + """Deserialize the germline fixture into a SlimAnnotatedVariant.""" + return SlimAnnotatedVariant(**germline_data) + + +@pytest.fixture(scope="module") +def slim_amp_variant(amp_data: dict[str, Any]) -> SlimAnnotatedVariant: + """Deserialize the AMP fixture into a SlimAnnotatedVariant.""" + return SlimAnnotatedVariant(**amp_data) + + +class TestSlimDeserialization: + """Verify that SlimAnnotatedVariant deserializes fixtures without errors.""" + + def test_germline_deserializes( + self, slim_germline_variant: SlimAnnotatedVariant + ) -> None: + assert slim_germline_variant is not None + + def test_amp_deserializes(self, slim_amp_variant: SlimAnnotatedVariant) -> None: + assert slim_amp_variant is not None + + def test_empty_dict_produces_default(self) -> None: + v = SlimAnnotatedVariant() + assert v.chromosome is None + assert v.pos is None + + def test_extra_fields_are_discarded(self) -> None: + """Undeclared keys must be silently ignored (not stored).""" + v = SlimAnnotatedVariant( + chromosome="chr1", + dbnsfp=[{"version": "4.9a"}], + sanger_cosmic=[{"version": "100"}], + ) + assert v.chromosome == "chr1" + assert not hasattr(v, "dbnsfp") + assert not hasattr(v, "sanger_cosmic") + + +class TestSlimCoreFields: + """Verify core fields on the slim model match the full model.""" + + @pytest.mark.parametrize("fixture", ["slim_germline_variant", "slim_amp_variant"]) + def test_chromosome(self, fixture: str, request: pytest.FixtureRequest) -> None: + v: SlimAnnotatedVariant = request.getfixturevalue(fixture) + assert v.chromosome == "chr7" + + @pytest.mark.parametrize("fixture", ["slim_germline_variant", "slim_amp_variant"]) + def test_pos(self, fixture: str, request: pytest.FixtureRequest) -> None: + v: SlimAnnotatedVariant = request.getfixturevalue(fixture) + assert v.pos == 140453136 + + @pytest.mark.parametrize("fixture", ["slim_germline_variant", "slim_amp_variant"]) + def test_ref_alt(self, fixture: str, request: pytest.FixtureRequest) -> None: + v: SlimAnnotatedVariant = request.getfixturevalue(fixture) + assert v.ref == "A" + assert v.alt == "T" + + +class TestSlimConvenienceProperties: + """Convenience properties from the mixin must work on the slim model.""" + + def test_genes(self, slim_germline_variant: SlimAnnotatedVariant) -> None: + assert sorted(slim_germline_variant.genes) == ["BRAF"] + + def test_refseq_genes_not_empty( + self, slim_germline_variant: SlimAnnotatedVariant + ) -> None: + assert len(slim_germline_variant.refseq_genes) > 0 + assert all(g == "BRAF" for g in slim_germline_variant.refseq_genes) + + def test_ensembl_genes_not_empty( + self, slim_germline_variant: SlimAnnotatedVariant + ) -> None: + assert len(slim_germline_variant.ensembl_genes) > 0 + assert all(g == "BRAF" for g in slim_germline_variant.ensembl_genes) + + def test_rs_ids(self, slim_germline_variant: SlimAnnotatedVariant) -> None: + assert slim_germline_variant.rs_ids == ["rs113488022"] + + def test_gnomad_exomes_af( + self, slim_germline_variant: SlimAnnotatedVariant + ) -> None: + af = slim_germline_variant.gnomad_exomes_af + assert af is not None + assert float(af) > 0 + + def test_gnomad_exomes_an( + self, slim_germline_variant: SlimAnnotatedVariant + ) -> None: + assert slim_germline_variant.gnomad_exomes_an == 251260 + + def test_acmg_verdict(self, slim_germline_variant: SlimAnnotatedVariant) -> None: + assert slim_germline_variant.acmg_verdict == "Pathogenic" + + def test_acmg_rules(self, slim_germline_variant: SlimAnnotatedVariant) -> None: + rules = slim_germline_variant.acmg_rules + assert rules is not None + assert "PS3" in rules + assert "PM1" in rules + + +class TestSlimMatchesFullModel: + """Verify that convenience properties return identical values on both models.""" + + def test_genes_match( + self, + germline_variant: AnnotatedVariant, + slim_germline_variant: SlimAnnotatedVariant, + ) -> None: + assert sorted(germline_variant.genes) == sorted(slim_germline_variant.genes) + + def test_rs_ids_match( + self, + germline_variant: AnnotatedVariant, + slim_germline_variant: SlimAnnotatedVariant, + ) -> None: + assert germline_variant.rs_ids == slim_germline_variant.rs_ids + + def test_gnomad_exomes_af_match( + self, + germline_variant: AnnotatedVariant, + slim_germline_variant: SlimAnnotatedVariant, + ) -> None: + assert ( + germline_variant.gnomad_exomes_af == slim_germline_variant.gnomad_exomes_af + ) + + def test_gnomad_exomes_an_match( + self, + germline_variant: AnnotatedVariant, + slim_germline_variant: SlimAnnotatedVariant, + ) -> None: + assert ( + germline_variant.gnomad_exomes_an == slim_germline_variant.gnomad_exomes_an + ) + + def test_gnomad_genomes_af_match( + self, + germline_variant: AnnotatedVariant, + slim_germline_variant: SlimAnnotatedVariant, + ) -> None: + assert ( + germline_variant.gnomad_genomes_af + == slim_germline_variant.gnomad_genomes_af + ) + + def test_acmg_verdict_match( + self, + germline_variant: AnnotatedVariant, + slim_germline_variant: SlimAnnotatedVariant, + ) -> None: + assert germline_variant.acmg_verdict == slim_germline_variant.acmg_verdict + + def test_acmg_rules_match( + self, + germline_variant: AnnotatedVariant, + slim_germline_variant: SlimAnnotatedVariant, + ) -> None: + assert germline_variant.acmg_rules == slim_germline_variant.acmg_rules + + +class TestSlimEdgeCases: + """Verify slim model handles empty / missing data gracefully.""" + + def test_genes_empty_when_no_transcripts(self) -> None: + v = SlimAnnotatedVariant() + assert v.genes == [] + + def test_rs_ids_empty_when_no_dbsnp(self) -> None: + v = SlimAnnotatedVariant() + assert v.rs_ids == [] + + def test_gnomad_exomes_af_none_when_empty(self) -> None: + v = SlimAnnotatedVariant() + assert v.gnomad_exomes_af is None + + def test_gnomad_genomes_af_none_when_empty(self) -> None: + v = SlimAnnotatedVariant() + assert v.gnomad_genomes_af is None + + def test_gnomad_exomes_an_none_when_empty(self) -> None: + v = SlimAnnotatedVariant() + assert v.gnomad_exomes_an is None + + def test_gnomad_genomes_an_none_when_empty(self) -> None: + v = SlimAnnotatedVariant() + assert v.gnomad_genomes_an is None + + def test_acmg_verdict_none_when_no_annotation(self) -> None: + v = SlimAnnotatedVariant() + assert v.acmg_verdict is None + + def test_acmg_rules_empty_when_no_annotation(self) -> None: + v = SlimAnnotatedVariant() + assert v.acmg_rules == [] diff --git a/tests/test_sync.py b/tests/test_sync.py new file mode 100644 index 0000000..efb80c3 --- /dev/null +++ b/tests/test_sync.py @@ -0,0 +1,87 @@ +import asyncio + +import pytest + +from varsome_api._sync import run_sync, sync_wrapper + + +class TestRunSync: + """Verify that ``run_sync`` correctly executes coroutines.""" + + def test_returns_coroutine_result(self) -> None: + """A simple coroutine result should be returned to the caller.""" + + async def greet() -> str: + return "hello" + + assert run_sync(greet()) == "hello" + + def test_propagates_exceptions(self) -> None: + """Exceptions raised inside the coroutine must propagate.""" + + async def boom() -> None: + raise ValueError("kaboom") + + with pytest.raises(ValueError, match="kaboom"): + run_sync(boom()) + + def test_works_with_await_chains(self) -> None: + """Coroutines that await other coroutines should work transparently.""" + + async def add(a: int, b: int) -> int: + await asyncio.sleep(0) + return a + b + + async def pipeline() -> int: + x = await add(1, 2) + y = await add(x, 3) + return y + + assert run_sync(pipeline()) == 6 + + async def test_fallback_when_loop_is_running(self) -> None: + """When called from within a running loop, must still work via thread fallback.""" + + async def inner() -> int: + return 42 + + assert run_sync(inner()) == 42 + + +class TestSyncWrapper: + """Verify that ``sync_wrapper`` produces a working synchronous wrapper.""" + + def test_wraps_coroutine_function(self) -> None: + async def afetch(url: str) -> str: + return f"response from {url}" + + fetch = sync_wrapper(afetch) + assert fetch("https://example.com") == "response from https://example.com" + + def test_preserves_function_name(self) -> None: + async def afetch(url: str) -> str: + return url + + fetch = sync_wrapper(afetch) + assert fetch.__name__ == "afetch" + assert fetch.__wrapped__ is afetch # type: ignore[attr-defined] + + def test_propagates_exceptions(self) -> None: + async def fail() -> None: + raise RuntimeError("oops") + + sync_fail = sync_wrapper(fail) + with pytest.raises(RuntimeError, match="oops"): + sync_fail() + + def test_works_as_unbound_method(self) -> None: + """sync_wrapper(async_method) works correctly when assigned as a class attr.""" + + class Greeter: + async def agreet(self, name: str) -> str: + return f"hi {name}" + + greet = sync_wrapper(agreet) + + g = Greeter() + assert g.greet("world") == "hi world" diff --git a/tests/test_vcf.py b/tests/test_vcf.py new file mode 100644 index 0000000..b19a6b7 --- /dev/null +++ b/tests/test_vcf.py @@ -0,0 +1,549 @@ +import os +from pathlib import Path +from typing import Any +from unittest.mock import MagicMock, patch + +import pysam +import pytest + +from varsome_api.models.slim.annotation import AnnotatedVariant as SlimAnnotatedVariant +from varsome_api.models.variant import AnnotatedVariant +from varsome_api.vcf import AnnotationResult +from varsome_api.vcf import BatchResult as VcfBatchResult +from varsome_api.vcf import VCFAnnotator + +FIXTURES_DIR = Path(__file__).parent / "fixtures" +VARIANTS_VCF = str(FIXTURES_DIR / "variants.vcf") + + +class TestAnnotationResult: + """Verify the ``AnnotationResult`` dataclass.""" + + def test_stores_all_fields(self) -> None: + result = AnnotationResult( + total_variants=5, + filtered_out_variants=[("v1", {"filtered_out": "reason"})], + variants_with_errors=[("v2", {"error": "bad"})], + ) + assert result.total_variants == 5 + assert len(result.filtered_out_variants) == 1 + assert len(result.variants_with_errors) == 1 + + +class TestReadHeaderFromVcf: + """Verify that ``_read_header_from_vcf`` reads only the header.""" + + def test_returns_header_object(self) -> None: + header = VCFAnnotator._read_header_from_vcf(VARIANTS_VCF) + assert isinstance(header, pysam.VariantHeader) + + def test_header_contains_contigs(self) -> None: + header = VCFAnnotator._read_header_from_vcf(VARIANTS_VCF) + contig_names = list(header.contigs) + assert "chr1" in contig_names + + def test_header_contains_info_fields(self) -> None: + header = VCFAnnotator._read_header_from_vcf(VARIANTS_VCF) + assert "KM" in header.info + + +class TestReadVariantsFromVcf: + """Verify that ``_read_variants_from_vcf`` yields the expected variant tuples.""" + + async def test_yields_all_variants(self) -> None: + """All variants with ALT alleles should be yielded.""" + annotator = VCFAnnotator(max_variants_per_batch=100, max_requests=1) + header = VCFAnnotator._read_header_from_vcf(VARIANTS_VCF) + + items = [ + item + async for item in annotator._read_variants_from_vcf(VARIANTS_VCF, header) + ] + # The test VCF has 20 variants with ALT alleles + assert len(items) == 20 + + async def test_yields_valid_variant_strings(self) -> None: + """Each variant string should be a valid chrom:pos:ref:alt string.""" + annotator = VCFAnnotator(max_variants_per_batch=100, max_requests=1) + header = VCFAnnotator._read_header_from_vcf(VARIANTS_VCF) + + variant_strings = [ + variant_str + async for variant_str, _ in annotator._read_variants_from_vcf( + VARIANTS_VCF, header + ) + ] + for variant_str in variant_strings: + parts = variant_str.split(":") + assert len(parts) == 4, f"Invalid variant string: {variant_str}" + assert parts[0], "Contig is empty" + assert parts[1].isdigit(), "Position is not numeric" + + async def test_yields_variant_records(self) -> None: + """Each yielded record should be a pysam VariantRecord.""" + annotator = VCFAnnotator(max_variants_per_batch=100, max_requests=1) + header = VCFAnnotator._read_header_from_vcf(VARIANTS_VCF) + + records = [ + record + async for _, record in annotator._read_variants_from_vcf( + VARIANTS_VCF, header + ) + ] + for record in records: + assert isinstance(record, pysam.VariantRecord) + + async def test_empty_vcf_yields_nothing(self, tmp_path: Path) -> None: + """A VCF with only a header and no records should yield nothing.""" + vcf_path = tmp_path / "empty.vcf" + header = pysam.VariantHeader() + header.add_sample("SAMPLE1") + header.contigs.add("1") + with pysam.VariantFile(str(vcf_path), "w", header=header): + pass # write only the header + + annotator = VCFAnnotator(max_variants_per_batch=10, max_requests=1) + read_header = VCFAnnotator._read_header_from_vcf(str(vcf_path)) + + items = [ + item + async for item in annotator._read_variants_from_vcf( + str(vcf_path), read_header + ) + ] + assert not items + + +class TestConstructVariantFromRecord: + """Verify variant string construction from VCF records.""" + + def test_returns_variant_strings_for_records_with_alt(self) -> None: + with pysam.VariantFile(VARIANTS_VCF, "r") as reader: + for record in reader: + result = VCFAnnotator._construct_variant_from_record(record) + if record.alleles and len(record.alleles) >= 2: + alt = record.alleles[1] + if alt not in (None, "."): + assert len(result) >= 1 + + def test_returns_empty_for_no_alleles(self) -> None: + """Records with fewer than 2 alleles return an empty list.""" + mock_record = MagicMock() + mock_record.alleles = ("A",) + result = VCFAnnotator._construct_variant_from_record(mock_record) + assert result == [] + + @pytest.mark.parametrize("ref_allele", [None, ".", ""]) + def test_does_not_return_empty_for_no_ref(self, ref_allele) -> None: + """Records with no reference allele should not be filtered out.""" + mock_record = MagicMock() + mock_record.alleles = (ref_allele, "T") + mock_record.contig = "1" + mock_record.pos = 100 + result = VCFAnnotator._construct_variant_from_record(mock_record) + assert len(result) == 1 + assert result[0][0] == "1:100::T" + + @pytest.mark.parametrize("alt_allele", [None, ".", ""]) + def test_does_not_return_empty_for_no_alt(self, alt_allele) -> None: + """Records with no ALT allele should not be filtered out.""" + mock_record = MagicMock() + mock_record.alleles = ("A", alt_allele) + mock_record.contig = "1" + mock_record.pos = 100 + result = VCFAnnotator._construct_variant_from_record(mock_record) + assert len(result) == 1 + assert result[0][0] == "1:100:A:" + + def test_returns_empty_for_none_alleles(self) -> None: + mock_record = MagicMock() + mock_record.alleles = None + result = VCFAnnotator._construct_variant_from_record(mock_record) + assert result == [] + + +class TestProcessRequest: + """Verify batch result processing.""" + + def test_counts_annotated_variants(self) -> None: + annotator = VCFAnnotator(max_variants_per_batch=10) + mock_writer = MagicMock() + + mock_record = MagicMock(spec=pysam.VariantRecord) + mock_record.info = {} + + batch_result = VcfBatchResult( + variants=["1:100:A:T"], + records=[mock_record], + response=[ + { + "original_variant": "1:100:A:T", + "chromosome": "1", + "pos": 100, + "ref": "A", + "alt": "T", + } + ], + ) + + count, filtered, errors = annotator._process_request(batch_result, mock_writer) + assert count == 1 + assert filtered == [] + assert errors == [] + mock_writer.write.assert_called_once() + + def test_tracks_filtered_variants(self) -> None: + annotator = VCFAnnotator(max_variants_per_batch=10) + mock_writer = MagicMock() + + batch_result = VcfBatchResult( + variants=["1:100:A:T"], + records=[MagicMock(spec=pysam.VariantRecord)], + response=[{"filtered_out": "Frequency less than 0.01"}], + ) + + count, filtered, errors = annotator._process_request(batch_result, mock_writer) + assert count == 0 + assert len(filtered) == 1 + assert filtered[0][0] == "1:100:A:T" + assert "filtered_out" in filtered[0][1] + + def test_tracks_errored_variants(self) -> None: + annotator = VCFAnnotator(max_variants_per_batch=10) + mock_writer = MagicMock() + + batch_result = VcfBatchResult( + variants=["1:100:A:T"], + records=[MagicMock(spec=pysam.VariantRecord)], + response=[{"error": "Invalid variant"}], + ) + + count, filtered, errors = annotator._process_request(batch_result, mock_writer) + assert count == 0 + assert filtered == [] + assert len(errors) == 1 + assert errors[0][0] == "1:100:A:T" + + def test_mixed_results(self) -> None: + """A batch with success, filtered, and error entries.""" + annotator = VCFAnnotator(max_variants_per_batch=10) + mock_writer = MagicMock() + + mock_record = MagicMock(spec=pysam.VariantRecord) + mock_record.info = {} + + batch_result = VcfBatchResult( + variants=["1:100:A:T", "1:200:G:C", "1:300:A:G"], + records=[ + mock_record, + MagicMock(spec=pysam.VariantRecord), + MagicMock(spec=pysam.VariantRecord), + ], + response=[ + { + "original_variant": "1:100:A:T", + "chromosome": "1", + "pos": 100, + "ref": "A", + "alt": "T", + }, + {"filtered_out": "reason"}, + {"error": "bad"}, + ], + ) + + count, filtered, errors = annotator._process_request(batch_result, mock_writer) + assert count == 1 + assert len(filtered) == 1 + assert len(errors) == 1 + + +async def _async_gen_from_list(items: list[Any]) -> Any: + """Yield items from a list as an async generator.""" + for item in items: + yield item + + +class TestAnnotateVariantsAndWriteToVcf: + """Verify the annotation pipeline reads all variants then annotates.""" + + async def test_read_variants_from_vcf_is_called(self, tmp_path: Path) -> None: + """The pipeline should call _read_variants_from_vcf during annotation.""" + annotator = VCFAnnotator( + api_key="test", + max_variants_per_batch=2, + max_requests=1, + ) + output = str(tmp_path / "output.vcf") + header = VCFAnnotator._read_header_from_vcf(VARIANTS_VCF) + + read_called = False + original_method = annotator._read_variants_from_vcf + + def tracking_read(input_vcf_file: str, vcf_header: pysam.VariantHeader) -> Any: + # Flag is set at call time (before iterating), not inside the body. + nonlocal read_called + read_called = True + return original_method(input_vcf_file, vcf_header) + + with ( + patch.object( + annotator, + "_read_variants_from_vcf", + tracking_read, + ), + patch.object( + annotator, + "abatch_lookup", + return_value=_async_gen_from_list([]), + ), + ): + await annotator._annotate_variants_and_write_to_vcf( + VARIANTS_VCF, header, output + ) + + assert read_called + + async def test_returns_annotated_count(self, tmp_path: Path) -> None: + """The method returns a 3-tuple of (annotated_count, filtered, errors).""" + annotator = VCFAnnotator( + api_key="test", + max_variants_per_batch=100, + max_requests=1, + ) + output = str(tmp_path / "output.vcf") + header = VCFAnnotator._read_header_from_vcf(VARIANTS_VCF) + + mock_batch_result = VcfBatchResult(variants=[], records=[], response=[]) + + with patch.object( + annotator, + "abatch_lookup", + return_value=_async_gen_from_list([mock_batch_result]), + ): + total_annotated, filtered, errors = ( + await annotator._annotate_variants_and_write_to_vcf( + VARIANTS_VCF, header, output + ) + ) + + assert total_annotated == 0 # mock returns empty batches + assert filtered == [] + assert errors == [] + + async def test_default_output_file_name(self, tmp_path: Path) -> None: + """When output_vcf_file is None, it defaults to input + .annotated.vcf.""" + # Create a simple VCF in tmp_path so the annotated output goes there too + vcf_path = tmp_path / "test.vcf" + header = pysam.VariantHeader() + header.add_sample("S1") + header.contigs.add("1") + with pysam.VariantFile(str(vcf_path), "w", header=header) as w: + pass + + annotator = VCFAnnotator( + api_key="test", + max_variants_per_batch=100, + max_requests=1, + ) + read_header = VCFAnnotator._read_header_from_vcf(str(vcf_path)) + + with patch.object( + annotator, + "abatch_lookup", + return_value=_async_gen_from_list([]), + ): + await annotator._annotate_variants_and_write_to_vcf( + str(vcf_path), read_header, None + ) + + expected_output = f"{str(vcf_path)}.annotated.vcf" + assert os.path.isfile(expected_output) + + async def test_passes_all_variant_keys_to_batch_lookup( + self, tmp_path: Path + ) -> None: + """All variant keys from _read_variants_from_vcf are sent to abatch_lookup.""" + annotator = VCFAnnotator( + api_key="test", + max_variants_per_batch=2, + max_requests=1, + ) + output = str(tmp_path / "output.vcf") + header = VCFAnnotator._read_header_from_vcf(VARIANTS_VCF) + + captured_variants: list[str] = [] + + async def mock_abatch_lookup(variants: Any, **kwargs: Any) -> Any: + # Consume the async generator to capture the variant strings + async for variant_str, _record in variants: + captured_variants.append(variant_str) + if False: + yield # make this an async generator + + with patch.object(annotator, "abatch_lookup", mock_abatch_lookup): + await annotator._annotate_variants_and_write_to_vcf( + VARIANTS_VCF, header, output + ) + + # All 20 variants should have been passed through the generator + assert len(captured_variants) == 20 + + +class TestAannotate: + """Verify the public async annotation entry point.""" + + async def test_raises_for_missing_file(self) -> None: + annotator = VCFAnnotator(api_key="test") + with pytest.raises(FileNotFoundError): + await annotator.aannotate("/nonexistent/file.vcf") + + async def test_returns_annotation_result(self, tmp_path: Path) -> None: + """End-to-end: reads file, calls API, returns AnnotationResult.""" + annotator = VCFAnnotator( + api_key="test", + max_variants_per_batch=100, + max_requests=1, + ) + output = str(tmp_path / "annotated.vcf") + + mock_batch_result = VcfBatchResult(variants=[], records=[], response=[]) + + with patch.object( + annotator, + "abatch_lookup", + return_value=_async_gen_from_list([mock_batch_result]), + ): + result = await annotator.aannotate(VARIANTS_VCF, output) + + assert isinstance(result, AnnotationResult) + assert result.total_variants == 0 + assert result.filtered_out_variants == [] + assert result.variants_with_errors == [] + + async def test_all_variants_passed_to_batch_lookup(self, tmp_path) -> None: + """Verify all variants from the VCF are processed through abatch_lookup.""" + annotator = VCFAnnotator( + api_key="test", + max_variants_per_batch=3, + max_requests=2, + ) + + captured_variants: list[str] = [] + output = str(tmp_path / "annotated.vcf") + + async def mock_abatch_lookup(variants: Any, **kwargs: Any) -> Any: + async for variant_str, _record in variants: + captured_variants.append(variant_str) + if False: + yield # make this an async generator + + with patch.object(annotator, "abatch_lookup", mock_abatch_lookup): + await annotator.aannotate(VARIANTS_VCF, output) + + # All 20 variants should have been passed through the generator + assert len(captured_variants) == 20 + + +class TestAnnotateSync: + """Verify the synchronous ``annotate`` wrapper.""" + + def test_sync_wrapper_exists(self) -> None: + """The sync wrapper should be a callable attribute.""" + assert callable(VCFAnnotator.annotate) + + def test_sync_raises_for_missing_file(self) -> None: + annotator = VCFAnnotator(api_key="test") + with pytest.raises(FileNotFoundError): + annotator.annotate("/nonexistent/file.vcf") + + +class TestAddVcfHeaderInfo: + """Verify that ``add_vcf_header_info`` adds expected INFO fields.""" + + def test_adds_required_info_fields(self) -> None: + annotator = VCFAnnotator(max_variants_per_batch=10) + header = pysam.VariantHeader() + annotator.add_vcf_header_info(header) + expected_fields = [ + "genes", + "gnomad_exomes_AF", + "gnomad_genomes_AF", + "acmg_verdict", + "acmg_rules", + "original_variant", + ] + for field in expected_fields: + assert field in header.info, f"Missing INFO field: {field}" + + +class TestVariantModel: + """Verify the ``variant_model`` class attribute extension point.""" + + def test_default_variant_model_is_slim(self) -> None: + assert VCFAnnotator.variant_model is SlimAnnotatedVariant + + def test_can_override_to_full_annotated_variant(self) -> None: + """Subclass can switch back to the full model for more fields.""" + + class FullAnnotator(VCFAnnotator): + variant_model = AnnotatedVariant + + assert FullAnnotator.variant_model is AnnotatedVariant + + def test_custom_variant_model_is_used_for_deserialization(self) -> None: + """A subclass can set variant_model to a slim Pydantic model.""" + from pydantic import BaseModel, ConfigDict + + class SlimVariant(BaseModel): + model_config = ConfigDict(extra="ignore") + original_variant: str | None = None + custom_score: float | None = None + chromosome: str | None = None + pos: int | None = None + ref: str | None = None + alt: str | None = None + + class SlimAnnotator(VCFAnnotator): + variant_model = SlimVariant + + def annotate_record(self, record, variant_result, original_variant): + if variant_result.custom_score is not None: + record.info["custom_score"] = variant_result.custom_score + + def add_vcf_header_info(self, header): + header.info.add("custom_score", "1", "Float", "Custom score") + + annotator = SlimAnnotator(max_variants_per_batch=10) + mock_writer = MagicMock() + mock_record = MagicMock(spec=pysam.VariantRecord) + mock_record.info = {} + + batch_result = VcfBatchResult( + variants=["1:100:A:T"], + records=[mock_record], + response=[ + { + "custom_score": 0.95, + "original_variant": "1:100:A:T", + "chromosome": "1", + "pos": 100, + "ref": "A", + "alt": "T", + "gnomad_exomes": [{"version": "4.1", "af": 0.001}], + "dbnsfp": [{"version": "4.9a"}], + } + ], + ) + + count, filtered, errors = annotator._process_request(batch_result, mock_writer) + assert count == 1 + mock_writer.write.assert_called_once() + # Verify the slim model was used (extra fields were ignored). + assert not hasattr( + SlimVariant( + original_variant="x", + gnomad_exomes=[{"version": "4.1"}], # type: ignore[call-arg] + ), + "gnomad_exomes", + ) diff --git a/tests/variants.csv b/tests/variants.csv deleted file mode 100644 index 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-chr11:65636053:T:C -chr9:734679:G:T -chr11:55157433:GT:G -chr14:47372973:C:T -chr2:34525514:T:C -chr17:78765219:A:G -chr6:130809232:T:C -chr10:90964145:C:T -chr11:47570396:C:A -chr11:121232811:A:G -chr2:140246353:A:G -chrX:15996576:AT:A -chr12:124219791:C:T -chr1:240493636:G:C -chr15:40937727:C:T -chr8:98569494:C:G -chrX:87104324:G:T -chr3:48377611:G:C -chr9:90607127:G:C -chr8:70901834:C:T -chr3:66662225:A:T -chr6:14852052:A:G -chr16:15523463:G:T -chr6:32549935:C:G -chr8:23174044:T:C -chr14:98059593:T:C -chr8:143762932:G:A -chr11:78516320:T:TCTCCCCACCCTCCACACCCCACCCCTCATTCTTCCCCACCCCCACTCCTCCTCCACCCACCCTTC -chr1:52812631:G:T -chr4:68904834:T:G -chr20:34688762:G:T -chrX:106510764:G:T -chr5:38958167:A:G -chr3:78676422:G:A -chr7:128043612:CA:C -chr7:57657805:T:A -chr3:9069747:A:G -chr6:88498308:G:T -chr1:119716734:A:C -chr12:94783104:C:A -chr2:29676067:G:GCAA -chr2:150261562:G:T -chr21:40669898:G:A -chr21:11111721:C:T -chr5:58288004:G:A -chr5:147498849:C:T -chrX:93763745:G:T -chr4:153969414:T:C -chr4:69040870:G:A -chr15:79032469:C:T -chr10:2096399:G:A -chr5:132339445:C:T -chr18:7262939:A:G -chr1:53430603:T:G -chr6:65859520:C:T -chr7:61975440:G:A -chr1:53513178:A:C -chr12:122198200:C:CA -chr10:87619446:A:G -chr3:65685325:G:T -chr8:3141555:A:G -chrX:92410936:G:A -chr16:87584748:G:A -chrX:70348344:G:A -chr8:90995019:C:T -chr12:88787112:C:T diff --git a/tests/variants.vcf b/tests/variants.vcf deleted file mode 100644 index 906a5b4..0000000 --- a/tests/variants.vcf +++ /dev/null @@ -1,156 +0,0 @@ -##fileformat=VCFv4.1 -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[reads.bam] read_buffer_size=null phone_home=NO_ET read_filter=[] intervals=[chr22:42020321-42527953] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL reference_sequence=/data/reference/ucsc/hg19/ucsc.hg19.fasta rodBind=[] nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=CALCULATE_AS_NECESSARY baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=2 num_cpu_threads=null num_io_threads=null num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false logging_level=INFO log_to_file=gatk.log help=false genotype_likelihoods_model=SNP p_nonref_model=EXACT heterozygosity=0.001 pcr_error_rate=1.0E-4 genotyping_mode=DISCOVERY output_mode=EMIT_VARIANTS_ONLY standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 computeSLOD=false alleles=(RodBinding name= source=UNBOUND) min_base_quality_score=17 max_deletion_fraction=0.15 multiallelic=false max_alternate_alleles=5 min_indel_count_for_genotyping=5 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10.0 indelGapOpenPenalty=45.0 indelHaplotypeSize=80 bandedIndel=false indelDebug=false ignoreSNPAlleles=false dbsnp=(RodBinding name=dbsnp source=/data/reference/dbSNP_132/dbsnp_132.hg19.vcf) out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_mismatching_base_and_quals=false" -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##reference=file:///data/reference/ucsc/hg19/ucsc.hg19.fasta -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT BLANK NA12878 NA12891 NA12892 NA19238 NA19239 NA19240 -chr22 42522392 rs28371738 G A 2951.95 . AC=2;AF=0.143;AN=14;BaseQRankSum=0.375;DB;DP=1506;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=123.5516;MQ=253.92;MQ0=0;MQRankSum=0.685;QD=5.90;ReadPosRankSum=0.590 GT:AD:DP:GQ:PL 0/0:6,0:6:18.04:0,18,211 0/1:138,107:250:99:1961,0,3049 0/1:169,77:250:99:1038,0,3533 0/0:249,0:250:99:0,600,5732 0/0:248,1:250:99:0,627,6191 0/0:250,0:250:99:0,615,5899 0/0:250,0:250:99:0,579,5674 -chr22 42522613 rs1135840 G C 11611.03 . AC=6;AF=0.429;AN=14;BaseQRankSum=16.289;DB;DP=1518;DS;Dels=0.03;FS=0.000;HRun=0;HaplotypeScore=142.5716;MQ=242.46;MQ0=0;MQRankSum=2.010;QD=9.16;ReadPosRankSum=-1.731 GT:AD:DP:GQ:PL 0/1:13,4:17:62.64:63,0,296 0/1:118,127:246:99:2396,0,1719 0/0:241,0:244:99:0,459,4476 0/1:161,85:246:99:1489,0,2353 0/1:110,132:242:99:2561,0,1488 0/1:106,135:242:99:2613,0,1389 0/1:116,126:243:99:2489,0,1537 -chr22 42522755 . C G 36.98 . AC=1;AF=0.071;AN=14;BaseQRankSum=-14.866;DP=1527;DS;Dels=0.01;FS=0.000;HRun=0;HaplotypeScore=253.4254;MQ=197.36;MQ0=2;MQRankSum=-10.810;QD=0.15;ReadPosRankSum=-17.244 GT:AD:DP:GQ:PL 0/0:26,1:27:51.08:0,51,570 0/0:208,40:248:99:0,236,4169 0/0:192,56:249:99:0,114,4292 0/1:179,66:245:75.42:75,0,3683 0/0:214,32:246:99:0,172,4235 0/0:200,49:249:61.05:0,61,4049 0/0:195,50:246:32.07:0,32,3757 -chr22 42523003 rs116917064 A G 7113.55 . AC=8;AF=0.571;AN=14;BaseQRankSum=6.026;DB;DP=1433;DS;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=101.7894;MQ=182.04;MQ0=0;MQRankSum=-2.501;QD=4.96;ReadPosRankSum=8.294 GT:AD:DP:GQ:PL 0/1:10,2:12:0.62:1,0,257 1/1:9,173:183:99:2385,273,0 0/1:153,95:249:99:355,0,2355 0/1:140,110:250:99:1334,0,2242 0/1:164,85:249:99:1070,0,2279 0/1:160,90:250:99:1245,0,2300 0/1:156,81:238:99:724,0,2764 -chr22 42523077 . A G 54.31 . AC=1;AF=0.071;AN=14;BaseQRankSum=-0.563;DP=1521;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=54.8434;MQ=164.04;MQ0=1;MQRankSum=-2.419;QD=2.59;ReadPosRankSum=-1.229 GT:AD:DP:GQ:PL 0/1:17,4:21:92.74:93,0,533 0/0:249,1:250:99:0,544,6985 0/0:250,0:250:99:0,577,6968 0/0:248,2:250:99:0,605,7687 0/0:248,1:249:99:0,583,7300 0/0:246,2:249:99:0,626,7473 0/0:248,1:249:99:0,594,7553 -chr22 42523209 rs28371730 T C 15556.89 . AC=8;AF=0.571;AN=14;BaseQRankSum=3.458;DB;DP=1509;DS;Dels=0.01;FS=0.000;HRun=0;HaplotypeScore=120.8206;MQ=221.07;MQ0=0;MQRankSum=-4.945;QD=10.31;ReadPosRankSum=0.639 GT:AD:DP:GQ:PL 0/1:3,6:9:99:154,0,101 1/1:6,237:247:99:4532,308,0 0/1:130,117:248:99:1399,0,3147 0/1:112,129:244:99:2641,0,2556 0/1:115,127:247:99:2320,0,2526 0/1:115,128:248:99:2546,0,2520 0/1:143,104:249:99:1965,0,3288 -chr22 42523211 rs2004511 T C 2445.52 . AC=2;AF=0.143;AN=14;BaseQRankSum=10.587;DB;DP=1509;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=102.7564;MQ=221.50;MQ0=0;MQRankSum=-6.926;QD=4.89;ReadPosRankSum=2.057 GT:AD:DP:GQ:PL 0/0:9,0:9:24.06:0,24,289 0/1:136,113:250:99:1384,0,2176 0/1:146,104:250:99:1108,0,2809 0/0:247,3:250:99:0,439,5546 0/0:245,2:249:99:0,459,5316 0/0:248,2:250:99:0,459,5404 0/0:248,1:250:99:0,533,6069 -chr22 42523409 rs1985842 G T 6801.90 . AC=6;AF=0.429;AN=14;BaseQRankSum=20.509;DB;DP=1454;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=150.8967;MQ=200.12;MQ0=0;MQRankSum=4.472;QD=5.65;ReadPosRankSum=9.396 GT:AD:DP:GQ:PL 0/1:1,3:4:25.84:53,0,26 0/1:153,95:249:99:1597,0,1798 0/0:245,4:250:99:0,336,4079 0/1:168,82:250:99:1339,0,1880 0/1:147,103:250:99:1522,0,1805 0/1:156,94:250:99:1341,0,2322 0/1:129,71:201:99:949,0,2082 -chr22 42523805 rs28371725 C T 1637.33 . AC=1;AF=0.071;AN=14;BaseQRankSum=-0.379;DB;DP=1516;DS;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=77.2321;MQ=226.05;MQ0=0;MQRankSum=2.862;QD=6.55;ReadPosRankSum=0.064 GT:AD:DP:GQ:PL 0/0:16,0:16:39.09:0,39,475 0/0:248,1:249:99:0,613,7187 0/1:132,116:248:99:1676,0,2916 0/0:248,0:248:99:0,625,7171 0/0:248,2:250:99:0,604,7252 0/0:250,0:250:99:0,631,7426 0/0:248,1:249:99:0,584,6964 -chr22 42523943 rs16947 A G 23661.10 . AC=8;AF=0.571;AN=14;BaseQRankSum=4.602;DB;DP=1514;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=38.3217;MQ=238.64;MQ0=0;MQRankSum=2.485;QD=15.63;ReadPosRankSum=3.749 GT:AD:DP:GQ:PL 0/1:9,5:14:99:163,0,303 1/1:3,246:250:99:8092,667,0 0/1:129,116:246:99:3190,0,2852 0/1:149,98:247:99:2429,0,3588 0/1:129,118:247:99:3267,0,3052 0/1:122,123:245:99:3428,0,3052 0/1:124,119:244:99:3092,0,2845 -chr22 42524150 . C G 3758.65 . AC=8;AF=0.571;AN=14;BaseQRankSum=24.314;DP=1506;DS;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=172.5901;MQ=242.92;MQ0=0;MQRankSum=11.537;QD=2.50;ReadPosRankSum=-9.185 GT:AD:DP:GQ:PL 1/1:3,3:6:5.98:46,6,0 0/1:161,88:250:99:708,0,300 0/1:161,88:250:99:635,0,308 0/1:160,90:250:99:658,0,229 0/1:180,69:250:99:478,0,113 0/1:176,73:250:99:530,0,271 0/1:170,79:249:99:704,0,133 -chr22 42524435 rs1807313 T A 5252.25 . AC=3;AF=0.214;AN=14;BaseQRankSum=-0.192;DB;DP=1526;DS;Dels=0.01;FS=0.000;HRun=1;HaplotypeScore=152.3866;MQ=242.06;MQ0=0;MQRankSum=1.923;QD=9.99;ReadPosRankSum=3.008 GT:AD:DP:GQ:PL 0/1:7,19:26:99:456,0,195 0/0:250,0:250:99:0,698,8167 0/0:246,2:249:99:0,673,7735 0/0:248,2:250:99:0,685,7919 0/0:250,0:250:99:0,688,7814 0/1:120,126:247:99:2539,0,3250 0/1:131,110:246:99:2257,0,3278 -chr22 42524696 rs58440431 T C 6423.61 . AC=2;AF=0.143;AN=14;BaseQRankSum=3.119;DB;DP=1509;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=53.0005;MQ=230.78;MQ0=0;MQRankSum=2.825;QD=12.85;ReadPosRankSum=2.051 GT:AD:DP:GQ:PL 0/0:9,0:9:27.08:0,27,351 0/1:132,116:250:99:3341,0,3914 0/1:141,108:250:99:3082,0,3917 0/0:248,1:250:99:0,692,8578 0/0:250,0:250:99:0,743,8836 0/0:247,2:250:99:0,695,8726 0/0:249,1:250:99:0,699,8650 -chr22 42524947 rs3892097 C T 731.18 . AC=2;AF=0.143;AN=14;BaseQRankSum=0.602;DB;DP=1495;DS;Dels=0.01;FS=0.000;HRun=1;HaplotypeScore=154.5421;MQ=217.65;MQ0=0;MQRankSum=4.304;QD=1.47;ReadPosRankSum=1.019 GT:AD:DP:GQ:PL 0/0:3,0:3:8.99:0,9,89 0/1:108,75:244:99:403,0,1684 0/1:125,74:242:99:375,0,2335 0/0:227,1:249:99:0,460,5036 0/0:226,1:247:99:0,448,4884 0/0:192,1:247:99:0,400,4405 0/0:194,1:247:99:0,405,4694 -chr22 42525132 rs1058164 G C 14639.91 . AC=5;AF=0.357;AN=14;BaseQRankSum=4.944;DB;DP=1508;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=38.1229;MQ=207.02;MQ0=6;MQRankSum=2.510;QD=11.71;ReadPosRankSum=0.306 GT:AD:DP:GQ:PL 0/0:8,0:8:24.05:0,24,309 0/1:125,125:250:99:3147,0,3294 0/0:245,1:248:99:0,549,7172 0/1:139,109:248:99:2470,0,3232 0/1:136,107:243:99:2545,0,3408 0/1:116,130:247:99:3206,0,2926 0/1:122,124:247:99:3271,0,3300 -chr22 42525772 rs28371706 G A 7552.52 . AC=4;AF=0.286;AN=14;BaseQRankSum=12.028;DB;DP=1506;DS;Dels=0.01;FS=0.000;HRun=0;HaplotypeScore=89.8512;MQ=222.09;MQ0=0;MQRankSum=5.200;QD=9.99;ReadPosRankSum=2.275 GT:AD:DP:GQ:PL 0/1:4,2:6:29.34:29,0,147 0/0:249,0:249:99:0,592,6835 0/0:249,1:250:99:0,590,7041 0/0:248,0:248:99:0,652,7316 0/1:126,120:248:99:2668,0,2833 0/1:134,113:247:99:2453,0,2485 0/1:137,113:250:99:2403,0,2988 -chr22 42525798 rs28371705 G C 1954.58 . AC=2;AF=0.143;AN=14;BaseQRankSum=6.229;DB;DP=1509;DS;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=36.0442;MQ=228.55;MQ0=0;MQRankSum=0.852;QD=3.91;ReadPosRankSum=6.520 GT:AD:DP:GQ:PL 0/0:9,0:9:27.08:0,27,342 0/1:164,85:250:99:981,0,3519 0/1:171,79:250:99:1020,0,3665 0/0:249,1:250:99:0,526,6474 0/0:249,1:250:99:0,550,6481 0/0:248,2:250:99:0,542,6933 0/0:250,0:250:99:0,604,7282 -chr22 42525811 rs28371704 T C 3688.26 . AC=2;AF=0.143;AN=14;BaseQRankSum=4.752;DB;DP=1510;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=36.9902;MQ=210.28;MQ0=0;MQRankSum=2.309;QD=7.38;ReadPosRankSum=6.262 GT:AD:DP:GQ:PL 0/0:10,0:10:27.06:0,27,333 0/1:163,86:249:99:1958,0,3391 0/1:167,78:245:99:1730,0,3945 0/0:248,1:249:99:0,542,6887 0/0:246,1:247:99:0,550,6569 0/0:247,1:250:99:0,548,6954 0/0:249,1:250:99:0,557,7079 -chr22 42525821 rs28371703 G T 3940.90 . AC=2;AF=0.143;AN=14;BaseQRankSum=4.652;DB;DP=1510;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=34.0483;MQ=210.28;MQ0=0;MQRankSum=2.924;QD=7.88;ReadPosRankSum=5.487 GT:AD:DP:GQ:PL 0/0:10,0:10:24.08:0,24,317 0/1:164,85:250:99:2033,0,3659 0/1:167,79:249:99:1907,0,4271 0/0:249,1:250:99:0,565,7321 0/0:249,1:250:99:0,545,7102 0/0:248,2:250:99:0,536,7254 0/0:249,0:250:99:0,605,7633 -chr22 42525952 rs71328650 C A 5872.92 . AC=7;AF=0.500;AN=14;BaseQRankSum=25.986;DB;DP=1505;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=144.2979;MQ=173.55;MQ0=0;MQRankSum=3.660;QD=4.68;ReadPosRankSum=7.152 GT:AD:DP:GQ:PL 1/1:2,3:5:6:53,6,0 0/1:132,117:250:99:1397,0,702 0/0:248,1:250:99:0,245,2219 0/1:166,83:250:99:1151,0,934 0/1:164,86:250:99:1070,0,1147 0/1:170,80:250:99:1009,0,1141 0/1:162,87:250:99:1194,0,1085 -chr22 42526049 . C G 8544.41 . AC=10;AF=0.714;AN=14;BaseQRankSum=-8.121;DP=1505;DS;Dels=0.01;FS=0.000;HRun=0;HaplotypeScore=241.7335;MQ=162.18;MQ0=2;MQRankSum=-1.399;QD=6.81;ReadPosRankSum=2.132 GT:AD:DP:GQ:PL 1/1:0,5:5:3:26,3,0 0/1:86,162:248:99:1053,0,1167 0/0:235,12:248:99:0,378,3886 0/1:108,137:245:99:782,0,1662 1/1:3,242:245:99:2351,264,0 1/1:5,245:250:99:2193,222,0 1/1:4,242:246:99:2140,240,0 -chr22 42526449 . T A 151.47 . AC=1;AF=0.071;AN=14;BaseQRankSum=2.662;DP=1226;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=41.2083;MQ=240.47;MQ0=0;MQRankSum=0.578;QD=4.89;ReadPosRankSum=3.611 GT:AD:DP:GQ:PL 0/1:23,8:31:99:190,0,694 0/0:188,0:190:99:0,478,5376 0/0:187,0:187:99:0,493,5322 0/0:247,0:249:99:0,634,6728 0/0:185,0:185:99:0,487,5515 0/0:202,0:202:99:0,520,5857 0/0:181,1:182:99:0,440,5362 -chr22 42526484 rs28371699 A C 4220.99 . AC=6;AF=0.429;AN=14;BaseQRankSum=-17.855;DB;DP=1532;DS;Dels=0.02;FS=0.000;HRun=0;HaplotypeScore=136.8893;MQ=233.92;MQ0=0;MQRankSum=3.448;QD=3.29;ReadPosRankSum=-2.663 GT:AD:DP:GQ:PL 0/1:16,15:31:99:238,0,428 0/1:112,135:247:99:796,0,1908 0/0:227,13:241:99:0,433,4747 0/1:108,133:242:99:588,0,2014 0/1:90,154:245:99:1055,0,1892 0/1:112,131:246:99:741,0,2222 0/1:108,137:246:99:803,0,2266 -chr22 42526549 rs56011157 C T 14276.31 . AC=8;AF=0.571;AN=14;BaseQRankSum=17.750;DB;DP=1537;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=87.3394;MQ=231.34;MQ0=0;MQRankSum=4.781;QD=9.29;ReadPosRankSum=7.463 GT:AD:DP:GQ:PL 0/1:22,15:37:99:251,0,330 1/1:23,227:250:99:5404,430,0 0/1:151,98:250:99:1878,0,2475 0/1:153,97:250:99:1769,0,2410 0/1:149,100:250:99:1792,0,2569 0/1:164,84:250:99:1440,0,2646 0/1:149,98:248:99:1742,0,2601 -chr22 42526561 rs28695233 G T 4524.61 . AC=7;AF=0.500;AN=14;BaseQRankSum=9.714;DB;DP=1538;DS;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=98.8415;MQ=220.45;MQ0=0;MQRankSum=9.430;QD=3.02;ReadPosRankSum=7.682 GT:AD:DP:GQ:PL 0/0:22,15:38:15.74:0,16,609 1/1:4,240:249:99:2685,237,0 0/1:142,108:250:99:505,0,3133 0/1:138,109:249:99:521,0,3281 0/1:150,99:249:99:336,0,3601 0/1:153,93:250:99:194,0,3695 0/1:148,97:249:99:283,0,3093 -chr22 42526562 rs75276289 G C 3780.51 . AC=6;AF=0.429;AN=14;BaseQRankSum=15.200;DB;DP=1540;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=116.4370;MQ=215.67;MQ0=0;MQRankSum=9.072;QD=2.52;ReadPosRankSum=10.863 GT:AD:DP:GQ:PL 0/0:25,15:40:17.73:0,18,633 0/1:50,199:250:99:1522,0,283 0/1:143,106:250:99:600,0,2844 0/1:143,107:250:99:605,0,3002 0/1:151,99:250:99:432,0,3352 0/1:157,93:250:99:254,0,3483 0/1:149,99:248:99:368,0,2999 -chr22 42526567 rs76312385 G A 434.33 . AC=1;AF=0.071;AN=14;BaseQRankSum=18.089;DB;DP=1540;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=89.3746;MQ=219.80;MQ0=0;MQRankSum=6.196;QD=1.74;ReadPosRankSum=7.564 GT:AD:DP:GQ:PL 0/0:22,18:40:4.68:0,5,427 0/1:34,215:250:56.26:473,0,56 0/0:142,108:250:20.78:0,21,2288 0/0:142,108:250:49.48:0,49,2451 0/0:152,97:250:99:0,210,2801 0/0:150,100:250:34.96:0,35,2515 0/0:148,102:250:77.19:0,77,2590 -chr22 42526571 rs74644586 C G 339.60 . AC=1;AF=0.071;AN=14;BaseQRankSum=-11.480;DB;DP=1540;DS;Dels=0.02;FS=0.000;HRun=4;HaplotypeScore=93.3402;MQ=218.52;MQ0=0;MQRankSum=3.709;QD=1.36;ReadPosRankSum=6.322 GT:AD:DP:GQ:PL 0/0:22,18:40:36.46:0,36,689 0/1:4,232:239:30.49:378,0,30 0/0:138,110:249:99:0,295,4017 0/0:137,111:249:99:0,250,4041 0/0:147,97:245:99:0,321,4348 0/0:150,97:247:99:0,358,4657 0/0:144,101:247:99:0,275,4123 -chr22 42526573 rs1080996 T G 12579.34 . AC=8;AF=0.571;AN=14;BaseQRankSum=6.163;DB;DP=1540;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=76.6550;MQ=224.49;MQ0=0;MQRankSum=1.355;QD=8.17;ReadPosRankSum=5.794 GT:AD:DP:GQ:PL 0/1:22,18:40:99:200,0,668 1/1:4,244:248:99:5175,439,0 0/1:136,110:250:99:1862,0,3521 0/1:136,113:249:99:1734,0,3677 0/1:144,99:250:99:1119,0,3818 0/1:150,99:250:99:1196,0,4178 0/1:145,104:250:99:1293,0,3628 -chr22 42526580 rs1080995 G C 16619.47 . AC=8;AF=0.571;AN=14;BaseQRankSum=7.991;DB;DP=1541;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=56.1489;MQ=221.29;MQ0=0;MQRankSum=2.223;QD=10.78;ReadPosRankSum=4.443 GT:AD:DP:GQ:PL 0/1:22,19:41:99:335,0,664 1/1:15,234:250:99:5895,337,0 0/1:137,113:250:99:2421,0,3301 0/1:134,116:250:99:2262,0,3430 0/1:144,105:250:99:1929,0,3421 0/1:148,101:250:99:1778,0,3867 0/1:142,108:250:99:1999,0,3334 -chr22 42526634 . T C 32.60 . AC=1;AF=0.071;AN=14;BaseQRankSum=1.147;DP=1225;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=50.0151;MQ=240.65;MQ0=0;MQRankSum=1.151;QD=1.30;ReadPosRankSum=1.276 GT:AD:DP:GQ:PL 0/1:21,4:25:71.04:71,0,702 0/0:187,2:189:99:0,481,6080 0/0:233,0:233:99:0,667,7351 0/0:230,0:230:99:0,667,7394 0/0:174,1:175:99:0,446,5469 0/0:194,2:196:99:0,498,6239 0/0:174,0:175:99:0,511,5894 -chr22 42526679 . G C 60.60 . AC=1;AF=0.071;AN=14;BaseQRankSum=-12.425;DP=1525;DS;Dels=0.09;FS=0.000;HRun=1;HaplotypeScore=331.3182;MQ=215.48;MQ0=0;MQRankSum=-14.680;QD=0.24;ReadPosRankSum=-13.323 GT:AD:DP:GQ:PL 0/0:23,0:23:66.17:0,66,829 0/1:175,56:232:99:99,0,4273 0/0:199,26:226:76.45:0,76,5104 0/0:196,37:233:41.98:0,42,5109 0/0:170,47:218:99:0,162,4505 0/0:188,36:224:99:0,230,4974 0/0:177,47:225:99:0,167,4592 -chr22 42526694 rs1065852 G A 4420.63 . AC=2;AF=0.143;AN=14;BaseQRankSum=8.566;DB;DP=1529;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=117.6833;MQ=214.96;MQ0=0;MQRankSum=5.852;QD=8.84;ReadPosRankSum=1.454 GT:AD:DP:GQ:PL 0/0:29,0:29:81.24:0,81,1040 0/1:136,114:250:99:2333,0,3170 0/1:145,104:250:99:2087,0,2794 0/0:250,0:250:99:0,586,6963 0/0:247,2:250:99:0,497,6185 0/0:248,2:250:99:0,544,6640 0/0:250,0:250:99:0,571,6444 -chr22 42527471 rs28633410 T C 26831.16 . AC=10;AF=0.833;AN=12;BaseQRankSum=-1.092;DB;DP=1501;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=79.3853;MQ=176.86;MQ0=0;MQRankSum=-2.644;QD=17.89;ReadPosRankSum=2.185 GT:AD:DP:GQ:PL ./. 1/1:1,249:250:99:5741,478,0 0/1:102,148:250:99:3026,0,1748 0/1:115,132:250:99:2716,0,1896 1/1:1,249:250:99:5040,392,0 1/1:1,248:250:99:5109,427,0 1/1:4,245:249:99:5199,306,0 -chr22 42527533 rs28624811 A G 13619.46 . AC=7;AF=0.583;AN=12;BaseQRankSum=-8.893;DB;DP=1501;DS;Dels=0.01;FS=0.000;HRun=1;HaplotypeScore=86.1948;MQ=179.18;MQ0=0;MQRankSum=0.472;QD=9.08;ReadPosRankSum=0.778 GT:AD:DP:GQ:PL ./. 1/1:2,241:243:99:4171,416,0 0/1:113,132:245:99:2000,0,2018 0/1:120,126:246:99:1781,0,1970 0/1:131,118:249:99:1885,0,1784 0/1:122,126:248:99:1893,0,1807 0/1:122,127:249:99:1890,0,2119 -chr22 42527793 rs1080989 C T 3454.66 . AC=2;AF=0.167;AN=12;BaseQRankSum=-3.007;DB;DP=1074;DS;Dels=0.01;FS=0.000;HRun=1;HaplotypeScore=75.7865;MQ=209.00;MQ0=0;MQRankSum=3.014;QD=9.36;ReadPosRankSum=0.618 GT:AD:DP:GQ:PL ./. 0/1:72,90:162:99:1699,0,1767 0/1:103,96:202:99:1756,0,2532 0/0:188,0:188:99:0,526,5889 0/0:160,0:160:99:0,457,4983 0/0:197,0:198:99:0,544,6100 0/0:156,0:156:99:0,439,5041 -chr22 42527891 . T A 109.83 . AC=5;AF=0.417;AN=12;BaseQRankSum=11.235;DP=1500;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=638.4601;MQ=166.82;MQ0=0;MQRankSum=1.444;QD=0.09;ReadPosRankSum=0.839 GT:AD:DP:GQ:PL ./. 0/1:238,7:248:13.70:14,0,38 0/0:246,3:250:5.97:0,6,45 0/1:239,11:250:31.42:31,0,54 0/1:232,16:250:49.09:49,0,76 0/1:233,14:249:52.10:52,0,53 0/1:238,11:250:12.71:13,0,36 diff --git a/tox.ini b/tox.ini deleted file mode 100644 index 98e5c3b..0000000 --- a/tox.ini +++ /dev/null @@ -1,9 +0,0 @@ -# content of: tox.ini , put in same dir as setup.py -[tox] -envlist = py33,py34,py35,py36,py37,py38,py39,py310 - -[testenv] -deps = pytest -passenv = VARSOME_API_KEY -commands = - pytest diff --git a/varsome_api/__init__.py b/varsome_api/__init__.py index e69de29..27fdca4 100755 --- a/varsome_api/__init__.py +++ b/varsome_api/__init__.py @@ -0,0 +1 @@ +__version__ = "0.0.3" diff --git a/varsome_api/_sync.py b/varsome_api/_sync.py new file mode 100644 index 0000000..3de48aa --- /dev/null +++ b/varsome_api/_sync.py @@ -0,0 +1,54 @@ +import asyncio +import functools +from collections.abc import Callable, Coroutine +from concurrent.futures import ThreadPoolExecutor +from typing import Any, TypeVar + +T = TypeVar("T") + +_SYNC_EXECUTOR = ThreadPoolExecutor(max_workers=4) + + +def run_sync(coro: Coroutine[Any, Any, T]) -> T: + """Run an async coroutine from synchronous code and return its result. + + Args: + coro: The coroutine to execute. + + Returns: + The value returned by the coroutine. + + Raises: + Any exception raised inside the coroutine is re-raised. + """ + try: + asyncio.get_running_loop() + except RuntimeError: + return asyncio.run(coro) + + future = _SYNC_EXECUTOR.submit(asyncio.run, coro) + return future.result() + + +def sync_wrapper(async_fn: Callable[..., Coroutine[Any, Any, T]]) -> Callable[..., T]: + """Return a synchronous function that calls *async_fn* via :func:`run_sync`. + + Useful as a decorator or factory for building sync counterparts of + async methods:: + + class Client: + async def alookup(self, query: str) -> dict: ... + lookup = sync_wrapper(alookup) + + Args: + async_fn: The async function or unbound method to wrap. + + Returns: + A synchronous wrapper that forwards all arguments to *async_fn*. + """ + + @functools.wraps(async_fn) + def wrapper(*args: Any, **kwargs: Any) -> T: + return run_sync(async_fn(*args, **kwargs)) + + return wrapper diff --git a/varsome_api/cli/__init__.py b/varsome_api/cli/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/varsome_api/cli/utils.py b/varsome_api/cli/utils.py new file mode 100644 index 0000000..4fb440d --- /dev/null +++ b/varsome_api/cli/utils.py @@ -0,0 +1,248 @@ +"""Shared CLI utility helpers used across VarSome API command-line tools.""" + +import argparse +import json +import logging +import os +import sys +from collections.abc import AsyncIterable +from typing import IO, Any + +from varsome_api.constants import REFERENCE_GENOMES +from varsome_api.log import logger + +MAX_CONCURRENT_REQUESTS = 20 +MAX_VARIANTS_PER_BATCH = 200 +DEFAULT_REQUESTS = 5 +DEFAULT_VARIANTS_PER_BATCH = 100 +VARSOME_API_URL_CHOICES = [ + "https://api.varsome.com", + "https://stable-api.varsome.com", + "https://staging-api.varsome.com", +] +DEFAULT_PARAMETER = ["add-ACMG-annotation=1"] + + +def build_base_parser(description: str) -> argparse.ArgumentParser: + """Build an argument parser pre-loaded with common VarSome API CLI flags. + + Adds the following arguments common to all VarSome CLI tools: + + * ``-k`` — API key (required) + * ``-g`` — reference genome (default ``hg19``) + * ``-p`` — request parameters (``key=value`` pairs) + * ``-u`` — custom API host URL + * ``-t`` — max concurrent API requests (default ``5``) + * ``-m`` — max variants per batch request (default ``100``) + * ``-v`` / ``--verbose`` — enable debug logging + + Callers should extend the returned parser with command-specific arguments + before calling ``parse_args()``. + + Args: + description: Description text shown in ``--help`` output. + + Returns: + An ``ArgumentParser`` with common arguments already registered. + """ + parser = argparse.ArgumentParser(description=description) + parser.add_argument( + "-k", + help="Your key to the API", + type=str, + metavar="API Key", + required=True, + ) + parser.add_argument( + "-g", + help="Reference genome either hg19 or hg38", + type=str, + choices=REFERENCE_GENOMES, + metavar="Reference Genome", + required=False, + default=REFERENCE_GENOMES[0], + ) + parser.add_argument( + "-p", + help=( + "Request parameters e.g. add-ACMG-annotation=1. " + "Check https://api.varsome.com/docs/variants/ query parameters " + "for available parameters" + ), + type=str, + metavar="Request Params", + required=False, + default=DEFAULT_PARAMETER, + nargs="+", + ) + parser.add_argument( + "-u", + help=( + f"Use specific VarSome API host url " + f"among: {', '.join(VARSOME_API_URL_CHOICES)}" + ), + type=str, + choices=VARSOME_API_URL_CHOICES, + required=False, + metavar="VarSome API host url", + ) + parser.add_argument( + "-t", + help="Maximum number of concurrent API requests", + type=int, + default=DEFAULT_REQUESTS, + required=False, + metavar="Max concurrent requests", + ) + parser.add_argument( + "-m", + help="Maximum number of variants to send per batch request", + type=int, + default=DEFAULT_VARIANTS_PER_BATCH, + required=False, + metavar="Max variants per batch", + ) + parser.add_argument( + "-v", + "--verbose", + help="Enable verbose (debug) logging output", + action="store_true", + default=False, + ) + return parser + + +def validate_file_args( + *, + input_file: str | None = None, + output_file: str | None = None, +) -> None: + """Validate input and output file arguments common to all CLI tools. + + Exits the process with an error message when validation fails. + + Args: + input_file: Path to an input file. When provided, the file must + exist on disk. + output_file: Path to an output file. When provided, the file must + **not** already exist (to avoid accidental overwrites). + + Raises: + SystemExit: When any file validation check fails. + """ + if input_file is not None and not os.path.exists(input_file): + sys.stderr.write(f"File {input_file} does not exist\n") + sys.exit(1) + if output_file is not None and os.path.exists(output_file): + sys.stderr.write(f"File {output_file} already exists\n") + sys.exit(1) + + +def validate_batch_args(args: argparse.Namespace) -> None: + """Validate and clamp the ``-t`` and ``-m`` batch arguments in-place. + + Ensures ``-t`` (max concurrent requests) is between 1 and + :data:`MAX_CONCURRENT_REQUESTS` and ``-m`` (max variants per batch) + does not exceed :data:`MAX_VARIANTS_PER_BATCH`. Values outside the + allowed range are clamped with a logged warning. + + Args: + args: Parsed CLI arguments (modified in-place). + """ + if args.t < 1: + logger.warning("Concurrency must be at least 1, setting it to 1.") + args.t = 1 + if args.t > MAX_CONCURRENT_REQUESTS: + logger.warning( + "Maximum number of concurrent requests is capped at %d. " + "Setting it to %d.", + MAX_CONCURRENT_REQUESTS, + MAX_CONCURRENT_REQUESTS, + ) + args.t = MAX_CONCURRENT_REQUESTS + if args.m > MAX_VARIANTS_PER_BATCH: + logger.warning( + "Maximum number of variants per request is capped at %d. " + "Setting it to %d.", + MAX_VARIANTS_PER_BATCH, + MAX_VARIANTS_PER_BATCH, + ) + args.m = MAX_VARIANTS_PER_BATCH + + +def configure_logging(*, verbose: bool = False) -> None: + """Configure logging for CLI entry points. + + Sets up a ``StreamHandler`` on the ``varsome_api_client`` logger with a + human-readable format. The level defaults to ``INFO`` and switches to + ``DEBUG`` when *verbose* is ``True``. + + Args: + verbose: When ``True``, set the log level to ``DEBUG``. + """ + level = logging.DEBUG if verbose else logging.INFO + logger = logging.getLogger("varsome_api_client") + logger.setLevel(level) + handler = logging.StreamHandler() + handler.setLevel(level) + formatter = logging.Formatter( + "%(asctime)s - %(name)s - %(levelname)s - %(message)s" + ) + handler.setFormatter(formatter) + logger.addHandler(handler) + + +def parse_request_parameters(raw_params: list[str] | None) -> dict[str, str] | None: + """Parse key=value CLI parameters into a dictionary. + + Each element in *raw_params* is expected to be a string of the form + ``"key=value"``. Malformed entries (missing ``=``) are reported and skipped. + + Args: + raw_params: List of ``"key=value"`` strings as collected by + argparse ``nargs="+"``, or ``None`` if the flag was not used. + + Returns: + A dict mapping parameter names to their values, or ``None`` when + *raw_params* is ``None`` or empty. + """ + if not raw_params: + return None + parameters: dict[str, str] = {} + for param in raw_params: + parts = param.split("=", maxsplit=1) + if len(parts) != 2: + logger.warning( + "Ignoring malformed parameter (expected key=value): %s", param + ) + continue + parameters[parts[0]] = parts[1] + return parameters or None + + +async def stream_json_output( + results: AsyncIterable[dict[str, Any]], + output_file: str | None = None, + *, + stream: IO[str] | None = None, +) -> None: + """Stream JSON Lines output (one JSON object per line) from an async iterable. + + Writes results immediately as they arrive from the async iterable, + avoiding accumulation of large result sets in memory. + + Args: + results: Async iterable of JSON-serializable dicts. + output_file: When provided, write to this file path. Otherwise use stream. + stream: Writable text stream. Defaults to ``sys.stdout``. + """ + if output_file: + with open(output_file, "w") as fp: + async for item in results: + fp.write(json.dumps(item, sort_keys=True)) + fp.write("\n") + else: + stream = stream or sys.stdout + async for item in results: + stream.write(json.dumps(item, sort_keys=True)) + stream.write("\n") diff --git a/varsome_api/cli/varsome_api_annotate_vcf.py b/varsome_api/cli/varsome_api_annotate_vcf.py new file mode 100755 index 0000000..b07dd84 --- /dev/null +++ b/varsome_api/cli/varsome_api_annotate_vcf.py @@ -0,0 +1,101 @@ +#!/usr/bin/env python3 +"""CLI tool for annotating a VCF file via the VarSome API.""" + +import argparse +import asyncio +import time + +from varsome_api.cli.utils import ( + build_base_parser, + configure_logging, + parse_request_parameters, + validate_batch_args, + validate_file_args, +) +from varsome_api.log import logger +from varsome_api.vcf import VCFAnnotator + + +def build_parser() -> argparse.ArgumentParser: + """Build and return the argument parser for ``varsome_api_annotate_vcf``. + + Extends the shared base parser with VCF-annotation-specific arguments: + ``-i`` (input VCF) and ``-o`` (output VCF). + + Returns: + Configured ``ArgumentParser`` ready for ``parse_args()``. + """ + parser = build_base_parser("VCF Annotator command line") + parser.add_argument( + "-i", + help="Path to vcf file", + type=str, + metavar="Input VCF File", + required=True, + ) + parser.add_argument( + "-o", + help="Path to output vcf file", + type=str, + metavar="Output VCF File", + required=False, + ) + return parser + + +def validate_args(args: argparse.Namespace) -> None: + """Validate file-related and batch argument constraints for VCF annotation. + + Args: + args: Parsed CLI arguments. + + Raises: + SystemExit: When any validation check fails. + """ + validate_batch_args(args) + validate_file_args(input_file=args.i, output_file=args.o) + + +async def annotate() -> None: + """Parse CLI arguments and run the async VCF annotation pipeline.""" + args = build_parser().parse_args() + configure_logging(verbose=args.verbose) + validate_args(args) + request_parameters = parse_request_parameters(args.p) + + vcf_annotator = VCFAnnotator( + api_key=args.k, + api_url=args.u, + ref_genome=args.g, + request_parameters=request_parameters, + max_requests=args.t, + max_variants_per_batch=args.m, + ) + async with vcf_annotator: + start = time.monotonic() + result = await vcf_annotator.aannotate(args.i, args.o) + elapsed = time.monotonic() - start + for variant, filtered in result.filtered_out_variants: + logger.info( + "Filtered out variant %s: %s", + variant, + filtered.get("filtered_out", filtered), + ) + for variant, errored in result.variants_with_errors: + logger.error( + "Error for variant %s: %s", + variant, + errored.get("error", errored), + ) + logger.info( + "Annotated %d variant(s) in %.2f seconds. " + "Filtered out %d variant(s). Errors in %d variant(s)", + result.total_variants, + elapsed, + len(result.filtered_out_variants), + len(result.variants_with_errors), + ) + + +def main() -> None: + asyncio.run(annotate()) diff --git a/varsome_api/cli/varsome_api_run.py b/varsome_api/cli/varsome_api_run.py new file mode 100755 index 0000000..639f16d --- /dev/null +++ b/varsome_api/cli/varsome_api_run.py @@ -0,0 +1,267 @@ +#!/usr/bin/env python3 +"""CLI tool for performing single or batch variant lookups via the VarSome API.""" + +import argparse +import asyncio +import sys +import time +from collections.abc import AsyncGenerator, AsyncIterable +from typing import Any + +from varsome_api.cli.utils import ( + build_base_parser, + configure_logging, + parse_request_parameters, + stream_json_output, + validate_batch_args, + validate_file_args, +) +from varsome_api.client import VarSomeAPIClient +from varsome_api.constants import DEFAULT_REF_GENOME, RefGenome +from varsome_api.log import logger + + +def build_parser() -> argparse.ArgumentParser: + """Build and return the argument parser for ``varsome_api_run``. + + Extends the shared base parser with lookup-specific arguments: + ``-q`` (query), ``-i`` (input file), and ``-o`` (output file). + + Returns: + Configured ``ArgumentParser`` ready for ``parse_args()``. + """ + parser = build_base_parser("Sample VarSome API calls") + parser.add_argument( + "-q", + help=( + "Query to lookup in the API e.g. " + "chr19:20082943:1:G or in case of batch request " + "e.g. chr15-73027478-T-C rs113488022. " + "Don't use it together with the -i option" + ), + type=str, + metavar="Query", + required=False, + nargs="+", + ) + parser.add_argument( + "-i", + help=( + "Path to text file with variants. " + "It should include one variant per line. Don't use it " + "together with the -q option" + ), + type=str, + metavar="Text/CSV File one line per variant", + required=False, + ) + parser.add_argument( + "-o", + help="Path to output file to store variant annotations", + type=str, + metavar="Output File with json entries", + required=False, + ) + return parser + + +def validate_args(args: argparse.Namespace) -> None: + """Validate mutually-exclusive and required argument constraints. + + Args: + args: Parsed CLI arguments. + + Raises: + SystemExit: When any validation check fails. + """ + if args.q and args.i: + sys.stderr.write( + "Don't specify -i and -q options together. Use only one of them\n" + ) + sys.exit(1) + if not args.q and not args.i: + sys.stderr.write("Please either specify -i or -q options\n") + sys.exit(1) + validate_batch_args(args) + validate_file_args(input_file=args.i, output_file=args.o) + + +async def _stream_batch_results( + api: VarSomeAPIClient, + variants: list[str] | AsyncIterable[str], + *, + request_parameters: dict[str, str] | None, + ref_genome: RefGenome = DEFAULT_REF_GENOME, + max_requests: int = 5, +) -> AsyncGenerator[dict[str, Any], None]: + """Stream annotation results as they arrive, logging warnings and errors. + + Yields individual response items as they come in from the API, avoiding + accumulation of large result sets in memory. + + Args: + api: An initialised VarSome API client. + variants: Variant query strings to look up. + request_parameters: Optional additional API query parameters. + ref_genome: Reference genome identifier (``"hg19"`` or ``"hg38"``). + max_requests: Maximum number of concurrent API requests. + + Yields: + Individual annotation result dicts as they arrive. + """ + async for batch_result in api.abatch_lookup( + variants, + params=request_parameters, + ref_genome=ref_genome, + max_requests=max_requests, + ): + for idx, response_item in enumerate(batch_result.response): + variant_string = batch_result.variants[idx] + if "filtered_out" in response_item: + logger.warning( + "Variant filtered out: %s — %s", + variant_string, + response_item.get("filtered_out"), + ) + elif "error" in response_item: + logger.error( + "Error for variant %s: %s", + variant_string, + response_item.get("error"), + ) + yield response_item + + +def lookup_query( + api: VarSomeAPIClient, + query: list[str], + *, + request_parameters: dict[str, str] | None, + ref_genome: RefGenome = DEFAULT_REF_GENOME, + max_requests: int = 5, +) -> AsyncGenerator[dict[str, Any], None]: + """Perform a single or batch variant lookup from CLI query arguments. + + Args: + api: An initialised VarSome API client. + query: One or more variant query strings. + request_parameters: Optional additional API query parameters. + ref_genome: Reference genome identifier (``"hg19"`` or ``"hg38"``). + max_requests: Maximum number of concurrent API requests. + + Returns: + An async generator that yields annotation result dicts. + """ + + return _stream_batch_results( + api, + query, + request_parameters=request_parameters, + ref_genome=ref_genome, + max_requests=max_requests, + ) + + +async def lookup_from_file( + api: VarSomeAPIClient, + input_file: str, + *, + request_parameters: dict[str, str] | None, + ref_genome: RefGenome = DEFAULT_REF_GENOME, + max_requests: int = 5, +) -> AsyncGenerator[dict[str, Any], None]: + """Stream results for variants read from a text file. + + Variants are streamed from the file line by line to avoid loading the + entire file into memory. Results are yielded as they arrive from the API. + + Args: + api: An initialised VarSome API client. + input_file: Path to a text file with one variant per line. + request_parameters: Optional additional API query parameters. + ref_genome: Reference genome identifier. + max_requests: Maximum number of concurrent API requests. + + Yields: + Annotation result dicts as they arrive from the API. + + Raises: + SystemExit: When the file contains no variants. + """ + with open(input_file) as _f: + if not any(line.strip() for line in _f): + sys.stderr.write(f"No variants found in file {input_file}\n") + sys.exit(1) + + async for result in _stream_batch_results( + api, + _iter_variants_from_file(input_file), + request_parameters=request_parameters, + ref_genome=ref_genome, + max_requests=max_requests, + ): + yield result + + +async def _iter_variants_from_file(input_file: str) -> AsyncGenerator[str, None]: + """Yield non-empty variant strings from a text file one line at a time. + + Args: + input_file: Path to a text file with one variant per line. + + Yields: + Stripped, non-empty variant strings in file order. + """ + with open(input_file) as f: + for line in f: + if stripped := line.strip(): + yield stripped + + +async def run() -> None: + """Async entry point that drives the full CLI workflow. + + Parses command-line arguments, performs variant lookups via the VarSome API, + and streams JSON results to stdout or an output file. + """ + parser = build_parser() + args = parser.parse_args() + configure_logging(verbose=args.verbose) + validate_args(args) + + request_parameters = parse_request_parameters(args.p) + + async with VarSomeAPIClient( + args.k, api_url=args.u, max_variants_per_batch=args.m + ) as api: + try: + start = time.monotonic() + result_stream = ( + lookup_query( + api, + args.q, + request_parameters=request_parameters, + ref_genome=args.g, + max_requests=args.t, + ) + if args.q + else lookup_from_file( + api, + args.i, + request_parameters=request_parameters, + ref_genome=args.g, + max_requests=args.t, + ) + ) + await stream_json_output(result_stream, args.o) + + elapsed = time.monotonic() - start + logger.info("Variant annotation completed in %.2f seconds", elapsed) + except Exception as e: + sys.stderr.write(f"{e}\n") + sys.exit(1) + + +def main() -> None: + """Entry point for the ``varsome_api_run`` CLI command.""" + asyncio.run(run()) diff --git a/varsome_api/client.py b/varsome_api/client.py index 09ca33c..056f59c 100755 --- a/varsome_api/client.py +++ b/varsome_api/client.py @@ -1,232 +1,460 @@ -# Copyright 2018 Saphetor S.A. -# -# Licensed under the Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.apache.org/licenses/LICENSE-2.0 -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. - import asyncio -import concurrent.futures -import logging -import os -import re -from itertools import chain - -import requests -from requests.exceptions import HTTPError, Timeout, ConnectionError, RequestException - - -class VarSomeAPIException(Exception): - ERROR_CODES = { - 400: "Bad request. A parameter you have passed is not valid, or something in your request is wrong", - 401: "Not Authorized: either you need to provide authentication credentials, or the credentials provided aren't" - " valid.", - 403: "Bad Request: your request is invalid, and we'll return an error message that tells you why. This is the " - "status code returned if you've exceeded the rate limit (see below).", - 404: "Not Found: either you're requesting an invalid URI or the resource in question doesn't exist", - 500: "Internal Server Error: we did something wrong.", - 501: "Not implemented.", - 502: "Bad Gateway: returned if VariantAPI is down or being upgraded.", - 503: "Service Unavailable: the VariantAPI servers are up, but are overloaded with requests. Try again later.", - 504: "Gateway Timeout", - } - - def __init__(self, status, response=None): - self.status = status - self.response = response - - def __str__(self): - return "%s (%s)" % ( - self.status, - self.ERROR_CODES.get(self.status, "Unknown error.") - if self.response is None - else self.response, - ) - - def __repr__(self): - return "%s(status=%s)" % (self.__class__.__name__, self.status) - - -class VarSomeAPIClientBase(object): - _api_url = "https://api.varsome.com" - _accepted_methods = ("GET", "POST") - - def __init__(self, api_key=None, logger=None, api_url=None): - if logger is None: - BASE_DIR = os.path.dirname(os.path.dirname(os.path.abspath(__file__))) - logger = logging.getLogger(__name__) - logger.setLevel(logging.DEBUG) - formatter = logging.Formatter( - "%(asctime)s - %(name)s - %(levelname)s - %(message)s" +import contextlib +import functools +import time +from collections.abc import AsyncGenerator, Callable +from dataclasses import dataclass +from typing import Any, AsyncIterable, Iterable, Literal + +import aiohttp + +from varsome_api import __version__ +from varsome_api._sync import run_sync, sync_wrapper +from varsome_api.constants import DEFAULT_REF_GENOME, RefGenome +from varsome_api.exceptions import VarSomeAPIException +from varsome_api.log import logger + +DEFAULT_HEADERS = { + "Accept": "application/json", + "Accept-Encoding": "gzip, deflate, br, zstd", + "User-Agent": f"VarSomeApiClientPython/{__version__}", +} + +DEFAULT_API_URL = "https://api.varsome.com" + + +@dataclass(frozen=True, slots=True, kw_only=True) +class BatchResult: + """Pairs an input variant batch with the corresponding API response. + + Allows callers to correlate which variants were sent in a particular + batch request with the response returned by the API. This is + especially useful when the response contains errors that omit the + original variant identifier. + + Attributes: + variants: The variant strings sent in this batch request. + response: The parsed JSON response from the API for this batch. + """ + + variants: list[str] + response: list[dict[str, Any]] + + +def _log_request_time(func: Callable) -> Callable: + """Decorator that logs the wall-clock time of an async request. + + Expects the wrapped function to receive ``path`` and ``method`` keyword + arguments. For POST requests carrying a ``json`` payload with a + ``"variants"`` key the number of variants in the batch is logged; + GET requests are logged as a single-variant lookup. + + Args: + func: The async function to wrap. + + Returns: + An async wrapper that logs elapsed time and variant count after + the call completes. + """ + + @functools.wraps(func) + async def wrapper(*args: Any, **kwargs: Any) -> Any: + start_time = time.monotonic() + path = kwargs.get("path", "") + method = kwargs.get("method", "GET") + json_body = kwargs.get("json") + if method == "POST" and isinstance(json_body, dict): + variant_count = len(json_body.get("variants", [])) + else: + variant_count = 1 + try: + return await func(*args, **kwargs) + finally: + elapsed = time.monotonic() - start_time + logger.debug( + "Request on %s took %.2f seconds (%d variant(s))", + path, + elapsed, + variant_count, ) - ch = logging.StreamHandler() - ch.setLevel(logging.DEBUG) - ch.setFormatter(formatter) - logger.addHandler(ch) - if api_url is not None: - self._api_url = api_url - self.logger = logger - self.api_key = api_key - self._headers = { - "Accept": "application/json", - "user-agent": "VarSomeApiClientPython/2.0", + + return wrapper + + +class VarSomeAPIClientBase: + """Base client for the VarSome API providing HTTP session and request handling. + + Can be used as an async context manager to maintain a persistent session + across multiple requests:: + + async with VarSomeAPIClientBase(api_key="...") as client: + await client.get("/lookup/chr7-140453136-A-T") + await client.get("/lookup/chr19-20082943-1-G") + + When used without the context manager, each ``get``/``post`` call creates + and closes its own session automatically. + """ + + def __init__( + self, + api_key: str | None = None, + api_url: str | None = None, + ) -> None: + self.api_url = api_url or DEFAULT_API_URL + self._headers = DEFAULT_HEADERS.copy() + if api_key is not None: + self._headers["Authorization"] = f"Token {api_key}" + self._session: aiohttp.ClientSession | None = None + + async def __aenter__(self) -> "VarSomeAPIClientBase": + self._session = aiohttp.ClientSession(self.api_url, headers=self._headers) + return self + + async def __aexit__( + self, + exc_type: type[BaseException] | None, + exc_val: BaseException | None, + exc_tb: Any, + ) -> None: + if self._session is not None: + await self._session.close() + self._session = None + + def _create_session(self) -> aiohttp.ClientSession: + """Create a new ``aiohttp.ClientSession`` bound to the API base URL.""" + return aiohttp.ClientSession(self.api_url, headers=self._headers) + + @contextlib.asynccontextmanager + async def _ensure_session(self) -> AsyncGenerator[aiohttp.ClientSession, None]: + """Yield the persistent session if open, otherwise a temporary one. + + When the client is used as an async context manager, the existing + session is reused. Otherwise, a fresh session is created and closed + at the end of the ``async with`` block. + """ + if self._session is not None and not self._session.closed: + yield self._session + else: + async with self._create_session() as session: + yield session + + @staticmethod + @_log_request_time + async def _make_request( + session: aiohttp.ClientSession, + *, + path: str, + method: Literal["GET", "POST"] = "GET", + params: dict[str, Any] | None = None, + json: dict[str, Any] | None = None, + headers: dict[str, str] | None = None, + ) -> dict[str, Any]: + """Execute an HTTP request against the VarSome API. + + This is a generic request executor. Callers are responsible for + passing method-specific arguments (e.g. ``json`` and ``headers`` + for POST requests). + + Args: + session: An active aiohttp client session. + path: The API endpoint path (appended to the session base URL). + method: HTTP method, either ``"GET"`` or ``"POST"``. + params: Optional query-string parameters. + json: Optional JSON-serializable body payload. + headers: Optional extra headers to merge into the request. + + Returns: + The parsed JSON response as a dictionary. + + Raises: + VarSomeAPIException: On HTTP error status codes, timeouts, or + connection failures. + """ + request_kwargs: dict[str, Any] = { + "url": path, + "params": params, } - if self.api_key is not None: - self._headers["Authorization"] = "Token " + self.api_key - self.session = requests.Session() - self.session.headers.update(self._headers) - - def _make_request(self, path, method="GET", params=None, json_data=None): - if method not in self._accepted_methods: - raise VarSomeAPIException("", "Unsupported method %s" % method) + if json is not None: + request_kwargs["json"] = json + if headers is not None: + request_kwargs["headers"] = headers try: - if method == "GET": - r = self.session.get(self._api_url + path, params=params, stream=True) - if method == "POST": - if json_data is None: - raise RuntimeError("You need to provide a post request body") - r = self.session.post( - self._api_url + path, - params=params, - json=json_data, - headers={"Content-Type": "application/json"}, - stream=True, - ) - self.logger.info("Time between request and response %s" % r.elapsed) - self.logger.info("Content length %s" % len(r.content)) - r.raise_for_status() - return r - except HTTPError as e: - response = e.response - if response.status_code in VarSomeAPIException.ERROR_CODES: - error_message = "Unexpected error" - if r.headers["Content-Type"] == "application/json": - error_message = response.json().get("detail", None) - raise VarSomeAPIException(response.status_code, error_message) - raise VarSomeAPIException("", "Unknown http error %s" % e) - except Timeout as e: - raise VarSomeAPIException("", "Request timed out %s" % e) - except ConnectionError as e: + async with session.request(method, **request_kwargs) as response: + if response.status in VarSomeAPIException.ERROR_CODES: + error_message = await response.json() + raise VarSomeAPIException(response.status, error_message) + return await response.json() + except aiohttp.ServerTimeoutError as e: + raise VarSomeAPIException(None, f"Request timed out {e}") from e + except aiohttp.ClientConnectionError as e: raise VarSomeAPIException( - "", "Connection failure or connection refused %s" % e + None, f"Connection failure or connection refused {e}" + ) from e + except aiohttp.ClientError as e: + raise VarSomeAPIException(None, f"Unknown error {e}") from e + + async def get( + self, + path: str, + params: dict[str, Any] | None = None, + ) -> dict[str, Any]: + """Perform an async GET request against the API. + + Args: + path: The API endpoint path. + params: Optional query-string parameters. + + Returns: + The parsed JSON response as a dictionary. + + Raises: + VarSomeAPIException: On HTTP error status codes, timeouts, or + connection failures. + """ + async with self._ensure_session() as session: + return await self._make_request( + session, + path=path, + method="GET", + params=params, ) - except RequestException as e: - raise VarSomeAPIException("", "Unknown error %s" % e) - def get(self, path, params=None): - response = self._make_request(path, "GET", params=params) - return response.json() + async def post( + self, + path: str, + params: dict[str, Any] | None = None, + json_data: dict[str, Any] | None = None, + ) -> dict[str, Any]: + """Perform an async POST request against the API. - def post(self, path, params=None, json_data=None, raise_exceptions=True): - # handle api errors in batch requests. - try: - response = self._make_request( - path, "POST", params=params, json_data=json_data + Args: + path: The API endpoint path. + params: Optional query-string parameters. + json_data: Optional JSON body payload. + + Returns: + The parsed JSON response as a dictionary. + + Raises: + VarSomeAPIException: On HTTP error status codes, timeouts, or + connection failures. + """ + async with self._ensure_session() as session: + return await self._make_request( + session, + path=path, + method="POST", + params=params, + json=json_data, + headers={"Content-Type": "application/json"}, ) - return response.json() - except VarSomeAPIException as e: - if raise_exceptions: - raise e - self.logger.error(e) - return [ - { - "error": "Could not annotate variant %s because " - "request failed with %s" % (variant, e) - } - for variant in json_data["variants"] - ] class VarSomeAPIClient(VarSomeAPIClientBase): - schema_lookup_path = "/lookup/schema" + """High-level client for single and batch variant lookups via the VarSome API.""" + lookup_path = "/lookup/%s" ref_genome_lookup_path = lookup_path + "/%s" batch_lookup_path = "/lookup/batch/%s" def __init__( - self, api_key=None, logger=None, api_url=None, max_variants_per_batch=200 - ): - super(VarSomeAPIClient, self).__init__(api_key, logger, api_url) - self.max_variants_per_batch = max_variants_per_batch + self, + api_key: str | None = None, + api_url: str | None = None, + max_variants_per_batch: int = 200, + ) -> None: + """Initialise the variant lookup client. - @staticmethod - def query_is_variant_id(query): - """ - Query may be a variat identifier developed by Saphetor - :param query: - :return: + Args: + api_key: Optional API authentication token. + api_url: Optional custom API base URL. + max_variants_per_batch: Maximum number of variants sent in a + single batch POST request. Must be a positive integer. """ - return re.search(r"^\d{20}$", str(query)) + super().__init__(api_key, api_url) + self.max_variants_per_batch = max_variants_per_batch + + async def alookup( + self, + query: str, + params: dict[str, Any] | None = None, + ref_genome: RefGenome = DEFAULT_REF_GENOME, + ) -> dict[str, Any]: + """Look up annotations for a single variant asynchronously. - def schema(self): - return self.get(self.schema_lookup_path) + Args: + query: Variant representation (e.g. ``"chr19:20082943:1:G"``). + params: Optional HTTP GET parameters. Refer to + https://api.varsome.com/docs/variants/ for available parameters. + ref_genome: Reference genome (``"hg19"`` or ``"hg38"``). - def lookup(self, query, params=None, ref_genome=None): + Returns: + A dictionary of variant annotations. Refer to + https://api.varsome.com/docs/variants/ for the response schema. """ + url = self.ref_genome_lookup_path % (query, ref_genome) + return await self.get(url, params=params) + + lookup = sync_wrapper(alookup) + + async def _batch_producer( + self, variants: Iterable[str] | AsyncIterable[str], queue: asyncio.Queue + ) -> None: + """Add batches of variants to the request queue.""" + batch = [] + if isinstance(variants, AsyncIterable): + async for variant in variants: + batch.append(variant) + if len(batch) >= self.max_variants_per_batch: + await queue.put(batch) + batch = [] + else: + for variant in variants: + batch.append(variant) + if len(batch) >= self.max_variants_per_batch: + await queue.put(batch) + batch = [] + if batch: + await queue.put(batch) + await queue.put(None) + + async def _batch_worker( + self, + session: aiohttp.ClientSession, + request_queue: asyncio.Queue, + result_queue: asyncio.Queue, + url, + params, + ) -> None: + """Consume batches of variants from the request + queue and send them to the API.""" + while True: + batch = await request_queue.get() + if batch is None: + request_queue.task_done() + break + try: + response = await self._make_request( + session, + path=url, + method="POST", + params=params, + json={"variants": batch}, + headers={"Content-Type": "application/json"}, + ) + await result_queue.put(BatchResult(variants=batch, response=response)) + except VarSomeAPIException as e: + await result_queue.put(e) + finally: + request_queue.task_done() + + async def abatch_lookup( + self, + variants: Iterable[str] | AsyncIterable[str] | AsyncGenerator[Any, None], + params: dict[str, Any] | None = None, + ref_genome: RefGenome = DEFAULT_REF_GENOME, + max_requests: int = 5, + ) -> AsyncGenerator[BatchResult, None]: + """Look up annotations for a list of variants asynchronously in batches. + + Splits variants into batches of *max_variants_per_batch* and sends + them concurrently via POST requests. Concurrency is bounded by + *max_requests* worker tasks — at most that many HTTP requests are + in-flight at any given time. + + Each yielded ``BatchResult`` pairs the original variant strings with + the API response, allowing callers to correlate inputs with outputs — + especially useful when the response omits the original variant + identifier. - :param query: variant representation - :param params: dictionary of key value pairs for http GET parameters. Refer to the api documentation - of https://api.varsome.com for examples - :param ref_genome: reference genome (hg19 or hg38 or None) default for requests with no ref genome is hg19 - :return:dictionary of annotations. refer to https://api.varsome.com/lookup/schema for dictionary properties + Args: + variants: Variant strings to look up (sync or async iterable). + params: Optional dictionary of query parameters. + ref_genome: Reference genome, either ``"hg19"`` or ``"hg38"``. + max_requests: Maximum number of concurrent HTTP requests. + + Yields: + A ``BatchResult`` for each batch, in completion order. + + Raises: + VarSomeAPIException: If any batch request fails. All remaining + in-flight requests are cancelled, and the exception is + propagated. """ - url = self.lookup_path % query - if ref_genome is not None and not self.query_is_variant_id(query): - url = self.ref_genome_lookup_path % (query, ref_genome) - return self.get(url, params=params) + url = self.batch_lookup_path % ref_genome + request_queue = asyncio.Queue(maxsize=max_requests * 2) + response_queue: asyncio.Queue[BatchResult | Exception | None] = asyncio.Queue() + + async with self._ensure_session() as session: + producer_task = asyncio.create_task( + self._batch_producer(variants, request_queue) + ) + workers = [ + asyncio.create_task( + self._batch_worker( + session, request_queue, response_queue, url, params + ) + ) + for _ in range(max_requests) + ] + + async def wrap_up(): + await producer_task + await request_queue.join() + await response_queue.put(None) + + wrap_up_task = asyncio.create_task(wrap_up()) + + try: + while True: + result = await response_queue.get() + if result is None: + break + if isinstance(result, Exception): + raise result + yield result + finally: + producer_task.cancel() + wrap_up_task.cancel() + for w in workers: + w.cancel() + await asyncio.gather( + producer_task, wrap_up_task, *workers, return_exceptions=True + ) def batch_lookup( self, - variants, - params=None, - ref_genome="hg19", - max_threads=3, - raise_exceptions=False, - ): - """ + variants: list[str], + params: dict[str, Any] | None = None, + ref_genome: RefGenome = DEFAULT_REF_GENOME, + max_requests: int = 5, + ) -> list[BatchResult]: + """Synchronous wrapper around :meth:`abatch_lookup`. + + Collects every batch result into a list and returns it. - :param variants: list of variant representations - :param params: dictionary of key value pairs for http GET parameters. Refer to the api documentation - of https://api.varsome.com for examples - :param ref_genome: reference genome (hg19 or hg38) - :param max_threads: how many concurrent requests to make - (max_variants_per_batch has to be less than len(variants) param to have any effect) - :raise_exceptions: If a post request should raise an exception True, thus terminating the whole process or if it - should proceed to let the process continue - :return: list of dictionaries with annotations per variant refer to https://api.varsome.com/lookup/schema - for dictionary properties + Args: + variants: List of variant strings to look up. + params: Optional dictionary of query parameters. + ref_genome: Reference genome, either "hg19" or "hg38". + max_requests: Maximum number of concurrent requests. + + Returns: + A list of ``BatchResult`` objects, one per batch. + + Raises: + VarSomeAPIException: If any batch request fails. """ - @asyncio.coroutine - def batch(batch_executor): - batch_loop = asyncio.get_event_loop() - futures = [ - batch_loop.run_in_executor( - batch_executor, - self.post, - self.batch_lookup_path % ref_genome, - params, - {"variants": queries}, - raise_exceptions, + async def _collect() -> list[BatchResult]: + return [ + result + async for result in self.abatch_lookup( + variants, + params=params, + ref_genome=ref_genome, + max_requests=max_requests, ) - for queries in [ - variants[x : x + self.max_variants_per_batch] - for x in range(0, len(variants), self.max_variants_per_batch) - ] ] - responses = yield from asyncio.gather(*futures) - return responses - - # Create a limited thread pool. - executor = concurrent.futures.ThreadPoolExecutor( - max_workers=max_threads, - ) - loop = asyncio.get_event_loop() - return list(chain.from_iterable(loop.run_until_complete(batch(executor)))) + + return run_sync(_collect()) diff --git a/varsome_api/constants.py b/varsome_api/constants.py new file mode 100644 index 0000000..edda1bf --- /dev/null +++ b/varsome_api/constants.py @@ -0,0 +1,5 @@ +from typing import Literal, get_args + +RefGenome = Literal["hg19", "hg38"] +DEFAULT_REF_GENOME = "hg19" +REFERENCE_GENOMES = get_args(RefGenome) diff --git a/varsome_api/exceptions.py b/varsome_api/exceptions.py new file mode 100644 index 0000000..01dc1a5 --- /dev/null +++ b/varsome_api/exceptions.py @@ -0,0 +1,73 @@ +class VarSomeAPIException(Exception): + """Exception raised for VarSome API errors. + + For HTTP errors, *status* is the integer status code and *response* + is the parsed JSON body (if available). For connection-level errors + (timeouts, refused connections) *status* is ``None`` and *response* + carries a human-readable description. + + Attributes: + status: HTTP status code, or ``None`` for connection-level errors. + response: Optional response body / error description from the API. + """ + + ERROR_CODES: dict[int, str] = { + 400: ( + "Bad Request: a parameter you have passed is not valid, " + "or something in your request is wrong." + ), + 401: ( + "Unauthorized: authentication credentials are missing or invalid. " + "Please provide a valid API token." + ), + 403: ( + "Forbidden: you are authenticated but do not have permission " + "to access this resource." + ), + 404: ( + "Not Found: either you're requesting an invalid URI or the " + "resource in question doesn't exist." + ), + 429: ( + "Too Many Requests: you have exceeded the allowed request rate. " + "Please wait before retrying." + ), + 500: "Internal Server Error: an unexpected error occurred on the server.", + 501: ( + "Not Implemented: the requested feature or endpoint is not " + "supported by the API." + ), + 502: ( + "Bad Gateway: the upstream API is unreachable or returned an " + "invalid response." + ), + 503: ( + "Service Unavailable: the upstream API is temporarily unable to " + "handle the request, possibly due to overload. Try again later." + ), + 504: ( + "Gateway Timeout: the upstream API did not respond in time. " + "Try again later." + ), + } + + def __init__( + self, + status: int | None, + response: object = None, + ) -> None: + self.status = status + self.response = response + super().__init__(str(self)) + + def __str__(self) -> str: + if self.response is not None: + detail = self.response + elif self.status is not None: + detail = self.ERROR_CODES.get(self.status, "Unknown error.") + else: + detail = "Unknown error." + return f"{self.status} ({detail})" + + def __repr__(self) -> str: + return f"{self.__class__.__name__}(status={self.status!r})" diff --git a/varsome_api/log.py b/varsome_api/log.py new file mode 100644 index 0000000..e75b7b0 --- /dev/null +++ b/varsome_api/log.py @@ -0,0 +1,4 @@ +import logging + +logger = logging.getLogger("varsome_api_client") +logger.addHandler(logging.NullHandler()) diff --git a/varsome_api/models/__init__.py b/varsome_api/models/__init__.py index 139597f..b0c271b 100755 --- a/varsome_api/models/__init__.py +++ b/varsome_api/models/__init__.py @@ -1,2 +1,9 @@ +from varsome_api.models.variant import ( # noqa: F401 + AnnotatedVariant, + AnnotatedVariantPropertiesMixin, +) - +__all__ = [ + "AnnotatedVariant", + "AnnotatedVariantPropertiesMixin", +] diff --git a/varsome_api/models/annotation.py b/varsome_api/models/annotation.py new file mode 100644 index 0000000..554a781 --- /dev/null +++ b/varsome_api/models/annotation.py @@ -0,0 +1,2629 @@ +from decimal import Decimal +from typing import Any + +from pydantic import AnyUrl, BaseModel, ConfigDict, Field + + +class _GeneratedBase(BaseModel): + """Common base for all generated models. + + Allows extra fields from the API that are not yet in the schema + and coerces strings to numbers (the OpenAPI schema sometimes types + numeric fields as ``string``). + """ + + model_config = ConfigDict(extra="allow") + + +class UniprotRegionItem(_GeneratedBase): + absolute_positon: int | None = None + amino_acid: str | None = None + chromo: str | None = None + colour: str | None = None + description: str | None = None + length: int | None = None + position: int | None = None + protein: str | None = None + type: str | None = None + pub_med_references: list[int | None] | None = None + + +class UniprotRegions(_GeneratedBase): + version: str | None = None + items: list[UniprotRegionItem] | None = None + + +class SubmissionDisease(_GeneratedBase): + symbols: list[str | None] | None = None + normalized_disease: list[str | None] | None = None + names: list[str | None] | None = None + normalized_cancer: list[str | None] | None = None + + +class Submission(_GeneratedBase): + submitter_name: str | None = None + submitter_date: int | None = None + review_description: str | None = None + review_status: str | None = None + review_date: int | None = None + submission_description: list[str | None] | None = None + accession_id: str | None = None + clinical_significance: list[str | None] | None = None + diseases: list[SubmissionDisease] | None = None + method: str | None = None + date_updated: str | None = None + origin: str | None = None + + +class AccessionDisease(_GeneratedBase): + pub_med_references: list[int | None] | None = None + symbols: list[str | None] | None = None + normalized_cancer: list[str | None] | None = None + keyword: str | None = None + disease_mechanism: str | None = None + normalized_disease: list[str | None] | None = None + names: list[str | None] | None = None + + +class Accession(_GeneratedBase): + variation_id: int | None = None + submissions: list[Submission] | None = None + review_stars: int | None = None + review_description: str | None = None + allele_id: int | None = None + submission_description: list[str | None] | None = None + accession_id: str | None = None + clinical_significance: list[str | None] | None = None + date_created: str | None = None + diseases: list[AccessionDisease] | None = None + title: str | None = None + review_status: str | None = None + review_date: str | None = None + + +class Clinvarregionjson(_GeneratedBase): + accessions: list[Accession] | None = None + acmg_class: str | None = None + allele_id: int | None = None + clinical_significance: list[str | None] | None = None + date_created: str | None = None + last_evaluation: str | None = None + names: list[str | None] | None = None + num_submissions: int | None = None + num_submitters: int | None = None + review_stars: int | None = None + review_status: str | None = None + type: str | None = None + variation_id: int | None = None + + +class OverlapData(_GeneratedBase): + predicted_pathogenicity: str | None = None + known_cnv_pathogenicity: str | None = None + overlap_fraction: float | None = None + overlapping_exons: int | None = None + total_variant_exons: int | None = None + overlapping_genes: int | None = None + total_variant_genes: int | None = None + variant_contains_cnv: bool | None = None + type: str | None = None + size_similarity: float | None = None + overlapping_genes_indices: str | None = None + overlapping_genes_names: str | None = None + + +class ClinvarCnvItem(_GeneratedBase): + clinvarregionjson: Clinvarregionjson | None = None + absolute_positon: int | None = None + chromo: str | None = None + length: int | None = None + position: int | None = None + overlap_data: OverlapData | None = None + + +class Clinvarcnv(_GeneratedBase): + version: str | None = None + items: list[ClinvarCnvItem] | None = None + + +class DecipherVariantJson(_GeneratedBase): + contribution: str | None = None + genotype: str | None = None + inheritance: str | None = None + mean_ratio: float | None = None + normalized_phenotype: list[str | None] | None = None + pathogenicity: str | None = None + phenotypes: list[str | None] | None = None + variant_class: str | None = None + variant_type: str | None = None + + +class DecipherItem(_GeneratedBase): + json_: DecipherVariantJson | None = Field(None, alias="json") + absolute_positon: int | None = None + chromo: str | None = None + colour: str | None = None + length: int | None = None + position: int | None = None + overlap_data: OverlapData | None = None + + +class Decipher(_GeneratedBase): + version: str | None = None + items: list[DecipherItem] | None = None + + +class NcbiDbVarItem(_GeneratedBase): + ac: int | None = None + af: int | None = None + clnacc: str | None = None + clnsig: str | None = None + desc: str | None = None + experiment: int | None = None + links: str | None = None + origin: str | None = None + regionid: str | None = None + svlen: str | None = None + svtype: str | None = None + absolute_positon: int | None = None + chromo: str | None = None + clinical_source: str | None = None + length: int | None = None + position: int | None = None + overlap_data: OverlapData | None = None + + +class NcbiDbVar(_GeneratedBase): + version: str | None = None + items: list[NcbiDbVarItem] | None = None + + +class ExacCnvItem(_GeneratedBase): + absolute_positon: int | None = None + chromo: str | None = None + colour: str | None = None + exac_population: str | None = None + length: int | None = None + position: int | None = None + quality: int | None = None + + +class ExacCnv(_GeneratedBase): + version: str | None = None + items: list[ExacCnvItem] | None = None + + +class Observations(_GeneratedBase): + observed_gains: int | None = None + observed_losses: int | None = None + samplesize: int | None = None + + +class Dgvregionjson(_GeneratedBase): + accession: str | None = None + observations: Observations | None = None + pubmedids: int | None = None + sv_type: str | None = None + + +class TcagDgvItem(_GeneratedBase): + dgvregionjson: Dgvregionjson | None = None + absolute_positon: int | None = None + chromo: str | None = None + length: int | None = None + position: int | None = None + overlap_data: OverlapData | None = None + + +class TcagDgv(_GeneratedBase): + version: str | None = None + items: list[TcagDgvItem] | None = None + + +class ClingenRegionItem(_GeneratedBase): + pub_med_references: list[int | None] | None = None + triplosensitivity_description: str | None = None + haploinsufficiency_description: str | None = None + haploinsufficiency_score: int | None = None + position: int | None = None + chromo: str | None = None + absolute_positon: int | None = None + length: int | None = None + triplosensitivity_score: int | None = None + isca_id: str | None = None + isca_region_name: str | None = None + + +class ClingenRegions(_GeneratedBase): + version: str | None = None + items: list[ClingenRegionItem] | None = None + + +class ClingenCnvItem(_GeneratedBase): + colour: str | None = None + description: str | None = None + length: int | None = None + absolute_positon: int | None = None + chromo: str | None = None + position: int | None = None + overlap_data: OverlapData | None = None + + +class ClingenCnvs(_GeneratedBase): + version: str | None = None + items: list[ClingenCnvItem] | None = None + + +class Expressions(_GeneratedBase): + adipose_subcutaneous: float | None = None + adipose_visceral_omentum: float | None = None + adrenal_gland: float | None = None + artery_aorta: float | None = None + artery_coronary: float | None = None + artery_tibial: float | None = None + bladder: float | None = None + brain_amygdala: float | None = None + brain_anterior_cingulate_cortex_ba24: float | None = None + brain_caudate_basal_ganglia: float | None = None + brain_cerebellar_hemisphere: float | None = None + brain_cerebellum: float | None = None + brain_cortex: float | None = None + brain_frontal_cortex_ba9: float | None = None + brain_hippocampus: float | None = None + brain_hypothalamus: float | None = None + brain_nucleus_accumbens_basal_ganglia: float | None = None + brain_putamen_basal_ganglia: float | None = None + brain_spinal_cord_cervical_c_1: float | None = None + brain_substantia_nigra: float | None = None + breast_mammary_tissue: float | None = None + cells_cultured_fibroblasts: float | None = None + cells_ebv_transformed_lymphocytes: float | None = None + cervix_ectocervix: float | None = None + cervix_endocervix: float | None = None + colon_sigmoid: float | None = None + colon_transverse: float | None = None + esophagus_gastroesophageal_junction: float | None = None + esophagus_mucosa: float | None = None + esophagus_muscularis: float | None = None + fallopian_tube: float | None = None + heart_atrial_appendage: float | None = None + heart_left_ventricle: float | None = None + kidney_cortex: float | None = None + kidney_medulla: float | None = None + liver: float | None = None + lung: float | None = None + minor_salivary_gland: float | None = None + muscle_skeletal: float | None = None + nerve_tibial: float | None = None + ovary: float | None = None + pancreas: float | None = None + pituitary: float | None = None + prostate: float | None = None + skin_not_sun_exposed_suprapubic: float | None = None + skin_sun_exposed_lower_leg: float | None = None + small_intestine_terminal_ileum: float | None = None + spleen: float | None = None + stomach: float | None = None + testis: float | None = None + thyroid: float | None = None + uterus: float | None = None + vagina: float | None = None + whole_blood: float | None = None + + +class GeneModelPositions(_GeneratedBase): + chromosome: str | None = None + end: int | None = None + start: int | None = None + strand: str | None = None + + +class GenePositions(_GeneratedBase): + chromosome: str | None = None + end: int | None = None + start: int | None = None + strand: str | None = None + + +class GtExJsonData(_GeneratedBase): + exon_id: str | None = None + exon_number: str | None = None + expressions: Expressions | None = None + gencode_id: str | None = None + gene: str | None = None + gene_model_positions: GeneModelPositions | None = None + gene_positions: GenePositions | None = None + + +class NihGtexItem(_GeneratedBase): + gt_ex_json_data: GtExJsonData | None = Field(None, alias="GTExJsonData") + absolute_positon: int | None = None + chromo: str | None = None + length: int | None = None + position: int | None = None + + +class NihGtex(_GeneratedBase): + version: str | None = None + items: list[NihGtexItem] | None = None + + +class IraMHallLabItem(_GeneratedBase): + end: str | None = None + svlen: str | None = None + svtype: str | None = None + absolute_positon: int | None = None + chromo: str | None = None + length: int | None = None + position: int | None = None + overlap_data: OverlapData | None = None + + +class IraMHallLab(_GeneratedBase): + version: str | None = None + items: list[IraMHallLabItem] | None = None + + +class ChildrenMercyItem(_GeneratedBase): + end: str | None = None + svlen: str | None = None + svtype: str | None = None + absolute_positon: int | None = None + chromo: str | None = None + length: int | None = None + position: int | None = None + overlap_data: OverlapData | None = None + + +class ChildrenMercyResearchInstitute(_GeneratedBase): + version: str | None = None + items: list[ChildrenMercyItem] | None = None + + +class TcagConradEstd20Item(_GeneratedBase): + end: str | None = None + svlen: str | None = None + svtype: str | None = None + absolute_positon: int | None = None + chromo: str | None = None + length: int | None = None + position: int | None = None + overlap_data: OverlapData | None = None + + +class TcagConradEstd20(_GeneratedBase): + version: str | None = None + items: list[TcagConradEstd20Item] | None = None + + +class HprcItem(_GeneratedBase): + end: str | None = None + svlen: str | None = None + svtype: str | None = None + absolute_positon: int | None = None + chromo: str | None = None + length: int | None = None + position: int | None = None + overlap_data: OverlapData | None = None + + +class Hprc(_GeneratedBase): + version: str | None = None + items: list[HprcItem] | None = None + + +class Regions(_GeneratedBase): + uniprot_regions: UniprotRegions | None = None + clinvarcnv: Clinvarcnv | None = None + decipher: Decipher | None = None + ncbi_db_var: NcbiDbVar | None = Field(None, alias="ncbi_dbVar") + exac_cnv: ExacCnv | None = Field(None, alias="exacCNV") + gnomad_sv: dict[str, Any] | None = None + tcag_dgv: TcagDgv | None = None + clingen_regions: ClingenRegions | None = None + clingen_cnvs: ClingenCnvs | None = None + nih_gtex: NihGtex | None = None + ira_m_hall_lab: IraMHallLab | None = None + children_mercy_research_institute: ChildrenMercyResearchInstitute | None = None + tcag_conrad_estd20: TcagConradEstd20 | None = None + hprc: Hprc | None = None + + +class TranscriptItem(_GeneratedBase): + name: str | None = None + strand: str | None = None + coding_impact: str | None = None + function: list[Any] | None = None + hgvs: str | None = None + hgvs_p1: str | None = None + hgvs_p3: str | None = None + location: str | None = None + coding_location: str | None = None + canonical: bool | None = False + gene_symbol: str | None = None + splice_distance: str | None = None + ensembl_support_level: str | None = None + ensembl_appris: str | None = None + mane_select: str | None = None + mane_plus: str | None = None + uniprot_id: str | None = None + + +class RefseqTranscript(_GeneratedBase): + items: list[TranscriptItem] | None = None + version: str | None = None + + +class EnsemblTranscript(_GeneratedBase): + items: list[TranscriptItem] | None = None + version: str | None = None + + +class BroadExacItem(_GeneratedBase): + version: str | None = None + ac: int | None = None + an: int | None = None + ac_adj: str | None = None + an_adj: str | None = None + af: float | None = None + ac_afr: int | None = None + ac_amr: int | None = None + ac_asj: int | None = None + ac_eas: int | None = None + ac_fin: int | None = None + ac_nfe: int | None = None + ac_oth: int | None = None + ac_sas: int | None = None + ac_male: int | None = None + ac_female: int | None = None + hom: int | None = None + hemi: int | None = None + ac_hom: str | None = None + ac_hemi: str | None = None + an_afr: int | None = None + an_amr: int | None = None + an_asj: int | None = None + an_eas: int | None = None + an_fin: int | None = None + an_nfe: int | None = None + an_oth: int | None = None + an_sas: int | None = None + an_male: int | None = None + an_female: int | None = None + hom_afr: int | None = None + hom_amr: int | None = None + hom_asj: int | None = None + hom_eas: int | None = None + hom_fin: int | None = None + hom_nfe: int | None = None + hom_oth: int | None = None + hom_sas: int | None = None + hom_male: int | None = None + hom_female: int | None = None + hemi_afr: int | None = None + hemi_amr: int | None = None + hemi_asj: int | None = None + hemi_eas: int | None = None + hemi_fin: int | None = None + hemi_nfe: int | None = None + hemi_oth: int | None = None + hemi_sas: int | None = None + af_afr: float | None = None + af_amr: float | None = None + af_asj: float | None = None + af_eas: float | None = None + af_fin: float | None = None + af_nfe: float | None = None + af_oth: float | None = None + af_sas: float | None = None + af_male: float | None = None + af_female: float | None = None + indel_original_representation: str | None = None + + +class GnomadExome(_GeneratedBase): + version: str | None = None + filter: str | None = None + ac: int | None = None + an: int | None = None + af: float | None = None + ac_afr: int | None = None + ac_amr: int | None = None + ac_ami: int | None = None + ac_asj: int | None = None + ac_eas: int | None = None + ac_eas_kor: int | None = None + ac_eas_jpn: int | None = None + ac_eas_oea: int | None = None + ac_fin: int | None = None + ac_nfe: int | None = None + ac_mid: int | None = None + ac_nfe_bgr: int | None = None + ac_nfe_est: int | None = None + ac_nfe_nwe: int | None = None + ac_nfe_onf: int | None = None + ac_nfe_seu: int | None = None + ac_nfe_swe: int | None = None + ac_oth: int | None = None + ac_sas: int | None = None + ac_afr_male: int | None = None + ac_amr_male: int | None = None + ac_ami_male: int | None = None + ac_asj_male: int | None = None + ac_eas_male: int | None = None + ac_fin_male: int | None = None + ac_nfe_male: int | None = None + ac_mid_male: int | None = None + ac_oth_male: int | None = None + ac_sas_male: int | None = None + ac_afr_female: int | None = None + ac_amr_female: int | None = None + ac_ami_female: int | None = None + ac_asj_female: int | None = None + ac_eas_female: int | None = None + ac_fin_female: int | None = None + ac_nfe_female: int | None = None + ac_mid_female: int | None = None + ac_oth_female: int | None = None + ac_sas_female: int | None = None + ac_male: int | None = None + ac_female: int | None = None + an_afr: int | None = None + an_amr: int | None = None + an_ami: int | None = None + an_asj: int | None = None + an_eas: int | None = None + an_eas_kor: int | None = None + an_eas_jpn: int | None = None + an_eas_oea: int | None = None + an_fin: int | None = None + an_nfe: int | None = None + an_mid: int | None = None + an_nfe_bgr: int | None = None + an_nfe_est: int | None = None + an_nfe_nwe: int | None = None + an_nfe_onf: int | None = None + an_nfe_seu: int | None = None + an_nfe_swe: int | None = None + an_oth: int | None = None + an_sas: int | None = None + an_afr_male: int | None = None + an_amr_male: int | None = None + an_ami_male: int | None = None + an_asj_male: int | None = None + an_eas_male: int | None = None + an_fin_male: int | None = None + an_nfe_male: int | None = None + an_mid_male: int | None = None + an_oth_male: int | None = None + an_sas_male: int | None = None + an_afr_female: int | None = None + an_amr_female: int | None = None + an_ami_female: int | None = None + an_asj_female: int | None = None + an_eas_female: int | None = None + an_fin_female: int | None = None + an_nfe_female: int | None = None + an_mid_female: int | None = None + an_oth_female: int | None = None + an_sas_female: int | None = None + an_male: int | None = None + an_female: int | None = None + nhomalt: int | None = None + nhomalt_afr: int | None = None + nhomalt_amr: int | None = None + nhomalt_ami: int | None = None + nhomalt_asj: int | None = None + nhomalt_eas: int | None = None + nhomalt_eas_kor: int | None = None + nhomalt_eas_jpn: int | None = None + nhomalt_eas_oea: int | None = None + nhomalt_fin: int | None = None + nhomalt_nfe: int | None = None + nhomalt_mid: int | None = None + nhomalt_nfe_bgr: int | None = None + nhomalt_nfe_est: int | None = None + nhomalt_nfe_nwe: int | None = None + nhomalt_nfe_onf: int | None = None + nhomalt_nfe_seu: int | None = None + nhomalt_nfe_swe: int | None = None + nhomalt_oth: int | None = None + nhomalt_sas: int | None = None + nhomalt_afr_male: int | None = None + nhomalt_amr_male: int | None = None + nhomalt_ami_male: int | None = None + nhomalt_asj_male: int | None = None + nhomalt_eas_male: int | None = None + nhomalt_fin_male: int | None = None + nhomalt_nfe_male: int | None = None + nhomalt_mid_male: int | None = None + nhomalt_oth_male: int | None = None + nhomalt_sas_male: int | None = None + nhomalt_afr_female: int | None = None + nhomalt_amr_female: int | None = None + nhomalt_ami_female: int | None = None + nhomalt_asj_female: int | None = None + nhomalt_eas_female: int | None = None + nhomalt_fin_female: int | None = None + nhomalt_nfe_female: int | None = None + nhomalt_mid_female: int | None = None + nhomalt_oth_female: int | None = None + nhomalt_sas_female: int | None = None + nhomalt_male: int | None = None + nhomalt_female: int | None = None + age_hist_het_under_30: int | None = None + age_hist_het_30_35: int | None = None + age_hist_het_35_40: int | None = None + age_hist_het_40_45: int | None = None + age_hist_het_45_50: int | None = None + age_hist_het_50_55: int | None = None + age_hist_het_55_60: int | None = None + age_hist_het_60_65: int | None = None + age_hist_het_65_70: int | None = None + age_hist_het_70_75: int | None = None + age_hist_het_75_80: int | None = None + age_hist_het_over_80: int | None = None + age_hist_hom_under_30: int | None = None + age_hist_hom_30_35: int | None = None + age_hist_hom_35_40: int | None = None + age_hist_hom_40_45: int | None = None + age_hist_hom_45_50: int | None = None + age_hist_hom_50_55: int | None = None + age_hist_hom_55_60: int | None = None + age_hist_hom_60_65: int | None = None + age_hist_hom_65_70: int | None = None + age_hist_hom_70_75: int | None = None + age_hist_hom_75_80: int | None = None + age_hist_hom_over_80: int | None = None + variant_type: str | None = Field( + None, + description="Only populated for multi-variants, possible values are: " + "multi-snv, multi-indel, or mixed", + ) + segdup: bool | None = Field( + None, + description="is set if the variant falls within a segmental duplication region", + ) + lcr: bool | None = None + original_variant: str | None = None + main_data: str | None = None + nonpar: int | None = None + + +class GnomadExomesCoverageItem(_GeneratedBase): + version: str | None = None + coverage_mean: list[Any] | None = None + coverage_median: list[Any] | None = None + coverage_20_frequency: list[Any] | None = None + + +class GnomadGenome(_GeneratedBase): + version: str | None = None + filter: str | None = None + ac: int | None = None + an: int | None = None + af: float | None = None + ac_afr: int | None = None + ac_amr: int | None = None + ac_ami: int | None = None + ac_asj: int | None = None + ac_eas: int | None = None + ac_eas_kor: int | None = None + ac_eas_jpn: int | None = None + ac_eas_oea: int | None = None + ac_fin: int | None = None + ac_nfe: int | None = None + ac_mid: int | None = None + ac_nfe_bgr: int | None = None + ac_nfe_est: int | None = None + ac_nfe_nwe: int | None = None + ac_nfe_onf: int | None = None + ac_nfe_seu: int | None = None + ac_nfe_swe: int | None = None + ac_oth: int | None = None + ac_sas: int | None = None + ac_afr_male: int | None = None + ac_amr_male: int | None = None + ac_ami_male: int | None = None + ac_asj_male: int | None = None + ac_eas_male: int | None = None + ac_fin_male: int | None = None + ac_nfe_male: int | None = None + ac_mid_male: int | None = None + ac_oth_male: int | None = None + ac_sas_male: int | None = None + ac_afr_female: int | None = None + ac_amr_female: int | None = None + ac_ami_female: int | None = None + ac_asj_female: int | None = None + ac_eas_female: int | None = None + ac_fin_female: int | None = None + ac_nfe_female: int | None = None + ac_mid_female: int | None = None + ac_oth_female: int | None = None + ac_sas_female: int | None = None + ac_male: int | None = None + ac_female: int | None = None + an_afr: int | None = None + an_amr: int | None = None + an_ami: int | None = None + an_asj: int | None = None + an_eas: int | None = None + an_eas_kor: int | None = None + an_eas_jpn: int | None = None + an_eas_oea: int | None = None + an_fin: int | None = None + an_nfe: int | None = None + an_mid: int | None = None + an_nfe_bgr: int | None = None + an_nfe_est: int | None = None + an_nfe_nwe: int | None = None + an_nfe_onf: int | None = None + an_nfe_seu: int | None = None + an_nfe_swe: int | None = None + an_oth: int | None = None + an_sas: int | None = None + an_afr_male: int | None = None + an_amr_male: int | None = None + an_ami_male: int | None = None + an_asj_male: int | None = None + an_eas_male: int | None = None + an_fin_male: int | None = None + an_nfe_male: int | None = None + an_mid_male: int | None = None + an_oth_male: int | None = None + an_sas_male: int | None = None + an_afr_female: int | None = None + an_amr_female: int | None = None + an_ami_female: int | None = None + an_asj_female: int | None = None + an_eas_female: int | None = None + an_fin_female: int | None = None + an_nfe_female: int | None = None + an_mid_female: int | None = None + an_oth_female: int | None = None + an_sas_female: int | None = None + an_male: int | None = None + an_female: int | None = None + nhomalt: int | None = None + nhomalt_afr: int | None = None + nhomalt_amr: int | None = None + nhomalt_ami: int | None = None + nhomalt_asj: int | None = None + nhomalt_eas: int | None = None + nhomalt_eas_kor: int | None = None + nhomalt_eas_jpn: int | None = None + nhomalt_eas_oea: int | None = None + nhomalt_fin: int | None = None + nhomalt_nfe: int | None = None + nhomalt_mid: int | None = None + nhomalt_nfe_bgr: int | None = None + nhomalt_nfe_est: int | None = None + nhomalt_nfe_nwe: int | None = None + nhomalt_nfe_onf: int | None = None + nhomalt_nfe_seu: int | None = None + nhomalt_nfe_swe: int | None = None + nhomalt_oth: int | None = None + nhomalt_sas: int | None = None + nhomalt_afr_male: int | None = None + nhomalt_amr_male: int | None = None + nhomalt_ami_male: int | None = None + nhomalt_asj_male: int | None = None + nhomalt_eas_male: int | None = None + nhomalt_fin_male: int | None = None + nhomalt_nfe_male: int | None = None + nhomalt_mid_male: int | None = None + nhomalt_oth_male: int | None = None + nhomalt_sas_male: int | None = None + nhomalt_afr_female: int | None = None + nhomalt_amr_female: int | None = None + nhomalt_ami_female: int | None = None + nhomalt_asj_female: int | None = None + nhomalt_eas_female: int | None = None + nhomalt_fin_female: int | None = None + nhomalt_nfe_female: int | None = None + nhomalt_mid_female: int | None = None + nhomalt_oth_female: int | None = None + nhomalt_sas_female: int | None = None + nhomalt_male: int | None = None + nhomalt_female: int | None = None + age_hist_het_under_30: int | None = None + age_hist_het_30_35: int | None = None + age_hist_het_35_40: int | None = None + age_hist_het_40_45: int | None = None + age_hist_het_45_50: int | None = None + age_hist_het_50_55: int | None = None + age_hist_het_55_60: int | None = None + age_hist_het_60_65: int | None = None + age_hist_het_65_70: int | None = None + age_hist_het_70_75: int | None = None + age_hist_het_75_80: int | None = None + age_hist_het_over_80: int | None = None + age_hist_hom_under_30: int | None = None + age_hist_hom_30_35: int | None = None + age_hist_hom_35_40: int | None = None + age_hist_hom_40_45: int | None = None + age_hist_hom_45_50: int | None = None + age_hist_hom_50_55: int | None = None + age_hist_hom_55_60: int | None = None + age_hist_hom_60_65: int | None = None + age_hist_hom_65_70: int | None = None + age_hist_hom_70_75: int | None = None + age_hist_hom_75_80: int | None = None + age_hist_hom_over_80: int | None = None + variant_type: str | None = Field( + None, + description="Only populated for multi-variants, " + "possible values are: multi-snv, multi-indel, or mixed", + ) + segdup: bool | None = Field( + None, + description="is set if the variant falls within " + "a segmental duplication region", + ) + lcr: bool | None = None + original_variant: str | None = None + main_data: str | None = None + nonpar: int | None = None + + +class GnomadGenomesCoverageItem(_GeneratedBase): + version: str | None = None + coverage_mean: list[Any] | None = None + coverage_median: list[Any] | None = None + coverage_20_frequency: list[Any] | None = None + + +class ThousandGenome(_GeneratedBase): + version: str | None = None + ac: list[int | None] | None = None + af: list[float | None] | None = None + an: list[int | None] | None = None + ns: list[int | None] | None = None + afr_af: list[float | None] | None = None + amr_af: list[float | None] | None = None + eas_af: list[float | None] | None = None + eur_af: list[float | None] | None = None + sas_af: list[float | None] | None = None + main_data: str | None = None + + +class GerpItem(_GeneratedBase): + version: str | None = None + gerp_nr: list[float | None] | None = None + gerp_rs: list[float | None] | None = None + + +class IsbKaviar3Item(_GeneratedBase): + version: str | None = None + ac: list[int | None] | None = None + an: list[int | None] | None = None + main_data: str | None = None + + +class DbnsfpItem(_GeneratedBase): + version: str | None = None + ensembl_proteinid: list[str | None] | None = None + ensembl_transcriptid: list[str | None] | None = None + mutationtaster_pred: list[str | None] | None = None + mutationtaster_score: list[float | None] | None = None + sift_score: list[float | None] | None = None + sift_pred: list[str | None] | None = None + phylop100way_vertebrate: list[float | None] | None = None + phylop46way_placental: list[float | None] | None = None + phylop46way_primate: list[float | None] | None = None + mutationtaster_converted_rankscore: list[float | None] | None = None + mutationassessor_pred: list[str | None] | None = None + mutationassessor_score: list[float | None] | None = None + mutationassessor_rankscore: list[float | None] | None = None + fathmm_mkl_coding_pred: list[str | None] | None = None + fathmm_mkl_coding_score: list[float | None] | None = None + fathmm_mkl_coding_rankscore: list[float | None] | None = None + fathmm_pred: list[str | None] | None = None + fathmm_score: list[float | None] | None = None + fathmm_converted_rankscore: list[float | None] | None = None + sift_converted_rankscore: list[float | None] | None = None + metasvm_pred: list[str | None] | None = None + metasvm_score: list[float | None] | None = None + metasvm_rankscore: list[float | None] | None = None + metalr_pred: list[str | None] | None = None + metalr_score: list[float | None] | None = None + metalr_rankscore: list[float | None] | None = None + provean_pred: list[str | None] | None = None + provean_score: list[float | None] | None = None + provean_converted_rankscore: list[float | None] | None = None + lrt_pred: list[str | None] | None = None + lrt_score: list[float | None] | None = None + lrt_converted_rankscore: list[float | None] | None = None + lrt_omega: list[float | None] | None = None + cadd_raw: list[float | None] | None = None + cadd_raw_rankscore: list[float | None] | None = None + cadd_phred: list[float | None] | None = None + gm12878_confidence_value: list[float | None] | None = None + gm12878_fitcons_score: list[float | None] | None = None + gm12878_fitcons_rankscore: list[float | None] | None = None + siphy_29way_logodds_rankscore: list[float | None] | None = None + siphy_29way_pi: list[float | None] | None = None + siphy_29way_logodds: float | None = None + phylop20way_mammalian: list[float | None] | None = None + phylop20way_mammalian_rankscore: list[float | None] | None = None + phylop100way_vertebrate_rankscore: list[float | None] | None = None + phastcons20way_mammalian: list[float | None] | None = None + phastcons20way_mammalian_rankscore: list[float | None] | None = None + phastcons100way_vertebrate: list[float | None] | None = None + phastcons100way_vertebrate_rankscore: list[float | None] | None = None + vest3_score: list[float | None] | None = None + vest3_rankscore: list[float | None] | None = None + aloft_confidence: list[str | None] | None = None + aloft_fraction_transcripts_affected: list[str | None] | None = None + aloft_pred: list[str | None] | None = None + aloft_prob_dominant: list[float | None] | None = None + aloft_prob_recessive: list[float | None] | None = None + aloft_prob_tolerant: list[float | None] | None = None + bstatistic: float | None = None + bstatistic_rankscore: float | None = None + deogen2_pred: list[str | None] | None = None + deogen2_rankscore: float | None = None + deogen2_score: list[float | None] | None = None + eigen_pc_phred_coding: float | None = None + eigen_pc_raw_coding: float | None = None + eigen_pc_raw_coding_rankscore: float | None = None + eigen_pred_coding: float | None = None + eigen_raw_coding: float | None = None + eigen_raw_coding_rankscore: float | None = None + fathmm_xf_coding_score: float | None = None + fathmm_xf_coding_rankscore: float | None = None + fathmm_xf_coding_pred: list[str | None] | None = None + integrated_confidence_value: int | None = None + integrated_fitcons_score: float | None = None + integrated_fitcons_rankscore: float | None = None + h1_hesc_confidence_value: int | None = None + h1_hesc_fitcons_score: float | None = None + h1_hesc_fitcons_rankscore: float | None = None + huvec_confidence_value: int | None = None + huvec_fitcons_score: float | None = None + huvec_fitcons_rankscore: float | None = None + phylop17way_primate: float | None = None + phylop17way_primate_rankscore: float | None = None + phylop30way_mammalian: float | None = None + phylop30way_mammalian_rankscore: float | None = None + phastcons17way_primate: float | None = None + phastcons17way_primate_rankscore: float | None = None + phastcons30way_mammalian: float | None = None + phastcons30way_mammalian_rankscore: float | None = None + polyphen2_hdiv_pred: list[str | None] | None = None + polyphen2_hdiv_rankscore: float | None = None + polyphen2_hdiv_score: list[float | None] | None = None + polyphen2_hvar_pred: list[str | None] | None = None + polyphen2_hvar_rankscore: float | None = None + polyphen2_hvar_score: list[float | None] | None = None + primateai_pred: list[str | None] | None = None + primateai_score: list[float | None] | None = None + primateai_rankscore: list[float | None] | None = None + mpc_score: list[float | None] | None = None + mpc_rankscore: float | None = None + mutpred_score: list[float | None] | None = None + mutpred_rankscore: float | None = None + mvp_score: list[float | None] | None = None + mvp_rankscore: float | None = None + sift4g_score: list[float | None] | None = None + sift4g_converted_rankscore: float | None = None + sift4g_pred: list[str | None] | None = None + revel_score: list[float | None] | None = None + revel_rankscore: float | None = None + list_s2_pred: list[str | None] | None = None + list_s2_score: list[float | None] | None = None + list_s2_rankscore: float | None = None + bayesdel_addaf_pred: list[str | None] | None = None + bayesdel_addaf_score: float | None = None + bayesdel_addaf_rankscore: float | None = None + bayesdel_noaf_pred: list[str | None] | None = None + bayesdel_noaf_score: float | None = None + bayesdel_noaf_rankscore: float | None = None + metarnn_pred: list[str | None] | None = None + metarnn_score: list[float | None] | None = None + metarnn_rankscore: float | None = None + m_cap_pred: list[str | None] | None = None + m_cap_score: float | None = None + m_cap_rankscore: float | None = None + dann_score: float | None = None + dann_rankscore: float | None = None + gmvp_score: list[float | None] | None = None + gmvp_rankscore: float | None = None + varity_r_score: list[float | None] | None = None + varity_r_rankscore: float | None = None + varity_er_score: list[float | None] | None = None + varity_er_rankscore: float | None = None + varity_r_loo_score: list[float | None] | None = None + varity_r_loo_rankscore: float | None = None + varity_er_loo_score: list[float | None] | None = None + varity_er_loo_rankscore: float | None = None + esm1b_score: list[float | None] | None = None + esm1b_converted_rankscore: float | None = None + esm1b_pred: list[str | None] | None = None + clinpred_score: float | None = None + clinpred_rankscore: float | None = None + clinpred_pred: list[str | None] | None = None + phactboost_score: list[float | None] | None = None + phactboost_rankscore: float | None = None + mutpred2_score: list[float | None] | None = None + mutpred2_rankscore: float | None = None + mutpred2_pred: list[str | None] | None = None + + +class DannSnv(_GeneratedBase): + version: str | None = None + dann_score: float | None = None + + +class DbnsfpDbscsnvItem(_GeneratedBase): + version: str | None = None + ada_score: list[float | None] | None = None + rf_score: list[float | None] | None = None + + +class NcbiDbsnpItem(_GeneratedBase): + version: str | None = None + rsid: list[int | None] | None = None + + +class SangerCosmicItem(_GeneratedBase): + version: str | None = None + primary_site: list[str | None] | None = None + pub_med_references: list[Any] | None = None + + +class CosmicPublicEntry(_GeneratedBase): + id: str | None = None + num_samples: int | None = None + is_consistent: bool | None = None + + +class SangerCosmicPublicItem(_GeneratedBase): + version: str | None = None + items: list[CosmicPublicEntry] | None = None + + +class DrugEntry(_GeneratedBase): + drug_name: str | None = None + somatic_status: str | None = None + zygosity: str | None = None + gene: str | None = None + transcript: str | None = None + census_gene: str | None = None + pub_med_references: list[Any] | None = None + histology_freq: list[Any] | None = None + tissue_freq: list[Any] | None = None + + +class CosmicLicensedEntry(_GeneratedBase): + entry_type: str | None = None + cosmic_id: list[Any] | None = None + pub_med_references: list[Any] | None = None + legacy_cosmic_id: list[str | None] | None = None + histology_freq: list[Any] | None = None + genome_wide_screen_freq: list[Any] | None = None + loh_freq: list[Any] | None = None + age_freq: list[Any] | None = None + zygosity_freq: list[Any] | None = None + tumour_origin_freq: list[Any] | None = None + somatic_status_freq: list[Any] | None = None + primary_site_freq: list[Any] | None = None + description: list[Any] | None = None + accession_number: list[Any] | None = None + fathmm_prediction: str | None = None + fathmm_score: float | None = None + num_entries: int | None = None + num_samples: int | None = None + gene: list[Any] | None = None + fathmm_mkl_coding_score: float | None = None + fathmm_mkl_coding_groups: str | None = None + fathmm_mkl_non_coding_score: float | None = None + fathmm_mkl_non_coding_groups: str | None = None + whole_exome_freq: list[Any] | None = None + whole_genome_reseq_freq: list[Any] | None = None + resistance_mutation: list[Any] | None = None + drug_entries: list[DrugEntry] | None = None + + +class SangerCosmicLicensedItem(_GeneratedBase): + version: str | None = None + items: list[CosmicLicensedEntry] | None = None + + +class NcbiClinvar2Item(_GeneratedBase): + version: str | None = None + review_status: str | None = None + review_stars: int | None = None + variation_id: int | None = None + num_submitters: int | None = None + pub_med_references: list[Any] | None = None + clinical_significance: list[Any] | None = None + last_evaluation: str | None = None + origin: list[Any] | None = None + accessions: list[Any] | None = None + main_data: str | None = None + names: list[Any] | None = None + variant_type: str | None = None + + +class ProjectCodeItem(_GeneratedBase): + key: str | None = None + value: int | None = None + + +class OncotreeCodeItem(_GeneratedBase): + key: str | None = None + value: int | None = None + + +class CancerNameItem(_GeneratedBase): + key: str | None = None + value: int | None = None + + +class CancerTypeItem(_GeneratedBase): + key: str | None = None + value: int | None = None + + +class TissueTypeItem(_GeneratedBase): + key: str | None = None + value: int | None = None + + +class IcgcSomaticItem(_GeneratedBase): + version: str | None = None + affected_donors: int | None = None + mutation_id: str | None = None + project_code: list[ProjectCodeItem] | None = None + project_count: int | None = None + tested_donors: int | None = None + total_donors: int | None = None + pub_med_references: list[Any] | None = None + oncotree_code: list[OncotreeCodeItem] | None = None + cancer_name: list[CancerNameItem] | None = None + cancer_type: list[CancerTypeItem] | None = None + tissue_type: list[TissueTypeItem] | None = None + + +class SexItem(_GeneratedBase): + key: str | None = None + value: int | None = None + + +class AgeFreqItem(_GeneratedBase): + key: str | None = None + value: int | None = None + + +class CountryItem(_GeneratedBase): + key: str | None = None + value: int | None = None + + +class PatientItem(_GeneratedBase): + key: str | None = None + value: int | None = None + + +class InheritanceItem(_GeneratedBase): + key: str | None = None + value: int | None = None + + +class GermlineCarrierItem(_GeneratedBase): + key: str | None = None + value: int | None = None + + +class AgeAtDiagnosi(_GeneratedBase): + key: str | None = None + value: int | None = None + + +class OsStatu(_GeneratedBase): + key: str | None = None + value: int | None = None + + +class IarcTp53GermlineItem(_GeneratedBase): + version: str | None = None + sex: list[SexItem] | None = None + age_freq: list[AgeFreqItem] | None = None + country: list[CountryItem] | None = None + hotspot: bool | None = None + effect: str | None = None + pub_med_references: list[Any] | None = None + total_samples: int | None = None + oncotree_code: list[OncotreeCodeItem] | None = None + cancer_name: list[CancerNameItem] | None = None + cancer_type: list[CancerTypeItem] | None = None + tissue_type: list[TissueTypeItem] | None = None + patient: list[PatientItem] | None = None + inheritance: list[InheritanceItem] | None = None + germline_carrier: list[GermlineCarrierItem] | None = None + age_at_diagnosis: list[AgeAtDiagnosi] | None = None + os_status: list[OsStatu] | None = None + unaffected: bool | None = None + + +class StageItem(_GeneratedBase): + key: str | None = None + value: int | None = None + + +class GradeItem(_GeneratedBase): + key: str | None = None + value: int | None = None + + +class InfectiousAgentItem(_GeneratedBase): + key: str | None = None + value: int | None = None + + +class SampleSourceItem(_GeneratedBase): + key: str | None = None + value: int | None = None + + +class RaceItem(_GeneratedBase): + key: str | None = None + value: int | None = None + + +class IarcTp53SomaticItem(_GeneratedBase): + version: str | None = None + sex: list[SexItem] | None = None + age_freq: list[AgeFreqItem] | None = None + country: list[CountryItem] | None = None + hotspot: bool | None = None + effect: str | None = None + pub_med_references: list[Any] | None = None + total_samples: int | None = None + oncotree_code: list[OncotreeCodeItem] | None = None + cancer_name: list[CancerNameItem] | None = None + cancer_type: list[CancerTypeItem] | None = None + tissue_type: list[TissueTypeItem] | None = None + structural_motif: str | None = None + stage: list[StageItem] | None = None + grade: list[GradeItem] | None = None + infectious_agent: list[InfectiousAgentItem] | None = None + sample_source: list[SampleSourceItem] | None = None + race: list[RaceItem] | None = None + mut_rate: float | None = None + + +class Evidences(_GeneratedBase): + pub_med_references: list[Any] | None = None + cosmic_study: list[Any] | None = None + + +class AssociationItem(_GeneratedBase): + disease: str | None = None + disease_description: str | None = None + disease_symbol: str | None = None + disease_alt_symbol: str | None = None + evidences: Evidences | None = None + + +class UniprotVariantEntry(_GeneratedBase): + annotation_id: str | None = None + protein_id: str | None = None + proteinname: str | None = None + somaticstatus: str | None = None + frequency: float | None = None + gene: str | None = None + clinicalsignificances: list[Any] | None = None + transcripts: list[Any] | None = None + association: list[AssociationItem] | None = None + siftscore: str | None = None + siftprediction: str | None = None + polyphenscore: str | None = None + polyphenprediction: str | None = None + evidences: Evidences | None = None + xrefs: dict[str, Any] | None = None + variant_type: str | None = None + disease: str | None = None + disease_symbol: str | None = None + disease_alt_symbol: str | None = None + bed_comments: str | None = None + pub_med_references: list[Any] | None = None + + +class UniprotVariant(_GeneratedBase): + version: str | None = None + items: list[UniprotVariantEntry] | None = None + + +class UoiDvdItem(_GeneratedBase): + version: str | None = None + comment: str | None = None + disease: str | None = None + pathogenicity: str | None = None + pub_med_references: list[Any] | None = None + + +class PmkbInterpretation(_GeneratedBase): + tier: int | None = None + definition: list[Any] | None = None + interpretations: str | None = None + tissues: list[Any] | None = None + tumour_types: list[Any] | None = None + disease_or_trait: str | None = None + pub_med_references: list[Any] | None = None + variants: list[Any] | None = None + + +class WeillCornellMedicinePmkbItem(_GeneratedBase): + version: str | None = None + items: list[PmkbInterpretation] | None = None + + +class AscoEntry(_GeneratedBase): + asco_citation_id: str | None = None + asco_abstract_id: str | None = None + + +class AssertionDetail(_GeneratedBase): + amp_category: str | None = None + assertion_civic_url: str | None = None + assertion_description: str | None = None + assertion_direction: str | None = None + assertion_id: str | None = None + assertion_summary: str | None = None + assertion_type: str | None = None + clinical_significance: str | None = None + disease: str | None = None + doid: str | None = None + drugs: list[str | None] | None = None + evidence_item_ids: list[str | None] | None = None + fda_companion_test: bool | None = None + gene: str | None = None + nccn_guideline: str | None = None + nccn_guideline_version: str | None = None + normalized_drug: list[str | None] | None = None + regulatory_approval: bool | None = None + + +class GroupDetails(_GeneratedBase): + description: str | None = None + variant_group_civic_url: str | None = None + + +class VariantGroup(_GeneratedBase): + group: str | None = None + group_details: GroupDetails | None = None + + +class VariantItem(_GeneratedBase): + gene: str | None = None + hgvs: str | None = None + variant_ids: list[str | None] | None = None + + +class CivicMolecularProfileDetail(_GeneratedBase): + evidence_item_ids: list[int | None] | None = None + name: str | None = None + summary: str | None = None + variant: list[VariantItem] | None = None + + +class MolecularProfile(_GeneratedBase): + molecular_profile: CivicMolecularProfileDetail | None = None + molecular_profile_civic_id: int | None = None + + +class CivicEvidenceEntry(_GeneratedBase): + asco_entry: AscoEntry | None = None + clinical_significance: str | None = None + disease: str | None = None + doid: str | None = None + drug_interaction_type: str | None = None + drugs: list[str | None] | None = None + entrez_id: str | None = None + evidence_civic_url: str | None = None + evidence_direction: str | None = None + evidence_level: str | None = None + evidence_statement: str | None = None + evidence_status: str | None = None + evidence_type: str | None = None + gene: str | None = None + gene_civic_url: str | None = None + last_review_date: str | None = None + nct_ids: list[str | None] | None = None + normalized_drug: list[str | None] | None = None + phenotypes: list[str | None] | None = None + pub_med_references: list[int | None] | None = None + rating: str | None = None + representative_transcript: str | None = None + transcripts: list[Any] | None = None + variant: str | None = None + variant_civic_url: str | None = None + variant_origin: str | None = None + variant_summary: str | None = None + assertion_details: list[AssertionDetail] | None = None + civic_variant_evidence_score: str | None = None + variant_groups: list[VariantGroup] | None = None + molecular_profile_civic_url: str | None = None + molecular_profiles: list[MolecularProfile] | None = None + + +class WustlCivicItem(_GeneratedBase): + version: str | None = None + items: list[CivicEvidenceEntry] | None = None + + +class GwasEntry(_GeneratedBase): + gwas_symbol: str | None = None + date: str | None = None + study: str | None = None + disease_or_trait: str | None = None + mapped_traits: list[Any] | None = None + mapped_trait_urls: list[Any] | None = None + strongest_snp_risk_allele: str | None = None + odds_ratio: float | None = None + p_value: str | None = None + confidence_range_95_low: float | None = None + confidence_range_95_high: float | None = None + confidence_comment: str | None = None + initial_sample_size: str | None = None + replication_sample_size: str | None = None + pub_med_references: list[Any] | None = None + + +class Gwa(_GeneratedBase): + version: str | None = None + items: list[GwasEntry] | None = None + + +class TumorStatu(_GeneratedBase): + key: str | None = None + value: int | None = None + + +class TumorTissueSiteItem(_GeneratedBase): + key: str | None = None + value: int | None = None + + +class PathTStageItem(_GeneratedBase): + key: str | None = None + value: int | None = None + + +class PathNStageItem(_GeneratedBase): + key: str | None = None + value: int | None = None + + +class PathMStageItem(_GeneratedBase): + key: str | None = None + value: int | None = None + + +class ClinTStageItem(_GeneratedBase): + key: str | None = None + value: int | None = None + + +class ClinNStageItem(_GeneratedBase): + key: str | None = None + value: int | None = None + + +class ClinMStageItem(_GeneratedBase): + key: str | None = None + value: int | None = None + + +class AjccPathologicTumorStageItem(_GeneratedBase): + key: str | None = None + value: int | None = None + + +class StudyNameItem(_GeneratedBase): + key: str | None = None + value: int | None = None + + +class PriorDxItem(_GeneratedBase): + key: str | None = None + value: int | None = None + + +class DrugItem(_GeneratedBase): + key: str | None = None + value: int | None = None + + +class MeasureOfResponseItem(_GeneratedBase): + key: str | None = None + value: int | None = None + + +class TherapyTypeItem(_GeneratedBase): + key: str | None = None + value: int | None = None + + +class RouteOfAdministrationItem(_GeneratedBase): + key: str | None = None + value: int | None = None + + +class TherapyOngoingItem(_GeneratedBase): + key: str | None = None + value: int | None = None + + +class ClinicalSignificanceItem(_GeneratedBase): + key: str | None = None + value: int | None = None + + +class NihGdcItem(_GeneratedBase): + version: str | None = None + sex: list[SexItem] | None = None + age_freq: list[AgeFreqItem] | None = None + os_status: list[OsStatu] | None = None + race: list[RaceItem] | None = None + tumor_status: list[TumorStatu] | None = None + tumor_tissue_site: list[TumorTissueSiteItem] | None = None + path_t_stage: list[PathTStageItem] | None = None + path_n_stage: list[PathNStageItem] | None = None + path_m_stage: list[PathMStageItem] | None = None + clin_t_stage: list[ClinTStageItem] | None = None + clin_n_stage: list[ClinNStageItem] | None = None + clin_m_stage: list[ClinMStageItem] | None = None + ajcc_pathologic_tumor_stage: list[AjccPathologicTumorStageItem] | None = None + total_samples: int | None = None + study_name: list[StudyNameItem] | None = None + prior_dx: list[PriorDxItem] | None = None + drug: list[DrugItem] | None = None + measure_of_response: list[MeasureOfResponseItem] | None = None + therapy_type: list[TherapyTypeItem] | None = None + route_of_administration: list[RouteOfAdministrationItem] | None = None + therapy_ongoing: list[TherapyOngoingItem] | None = None + clinical_significance: list[ClinicalSignificanceItem] | None = None + pub_med_references: list[Any] | None = None + oncotree_code: list[OncotreeCodeItem] | None = None + cancer_name: list[CancerNameItem] | None = None + cancer_type: list[CancerTypeItem] | None = None + tissue_type: list[TissueTypeItem] | None = None + + +class BravoItem(_GeneratedBase): + version: str | None = None + filter: str | None = None + ac: int | None = None + an: int | None = None + af: float | None = None + het: int | None = None + hom: int | None = None + ns: int | None = None + vrt: int | None = None + main_data: str | None = None + original_variant: str | None = None + + +class NcbiClinvar2AnnotationItem(_GeneratedBase): + functions: list[str | None] | None = None + coding_impact: str | None = None + acmg_confirmed: bool | None = None + acmg_class: str | None = None + acmg_reannotated: str | None = None + source: str | None = None + codon: int | None = None + gene_symbol: str | None = None + hgvs: str | None = None + transcript: str | None = None + review_status: str | None = None + submission_count: int | None = None + review_stars: int | None = None + accession_count: int | None = None + publication_count: int | None = None + clinical_significance: list[str | None] | None = None + pub_med_references: list[int | None] | None = None + possible_functional_studies: list[str | None] | None = None + disease_name: list[str | None] | None = None + is_conflicting: bool | None = None + submissions_b: int | None = None + submissions_p: int | None = None + submissions_vus: int | None = None + + +class SaphetorVarsomeAiVariantItem(_GeneratedBase): + functions: list[str | None] | None = None + coding_impact: str | None = None + acmg_confirmed: bool | None = None + acmg_class: str | None = None + acmg_reannotated: str | None = None + source: str | None = None + codon: int | None = None + gene_symbol: str | None = None + hgvs: str | None = None + transcript: str | None = None + original_variant: str | None = None + pub_med_references: list[Any] | None = None + + +class MitimpactItem(_GeneratedBase): + apogee: str | None = None + apogee_score: float | None = None + mitimpact_id: str | None = None + + +class ChopMitotipItem(_GeneratedBase): + functions: list[str | None] | None = None + coding_impact: str | None = None + acmg_confirmed: bool | None = None + acmg_class: str | None = None + acmg_reannotated: str | None = None + source: str | None = None + codon: int | None = None + gene_symbol: str | None = None + hgvs: str | None = None + transcript: str | None = None + count: float | None = None + mitotip_score: float | None = None + mitomap_status: str | None = None + percentage: float | None = None + quartile: str | None = None + + +class ChopMitomapItem(_GeneratedBase): + functions: list[str | None] | None = None + coding_impact: str | None = None + acmg_confirmed: bool | None = None + acmg_class: str | None = None + acmg_reannotated: str | None = None + source: str | None = None + codon: int | None = None + gene_symbol: str | None = None + hgvs: str | None = None + transcript: str | None = None + diseases: list[Any] | None = None + possible_functional_studies: list[str | None] | None = None + pub_med_references: list[int | None] | None = None + + +class SaphetorVarsomeCommentItem(_GeneratedBase): + functions: list[str | None] | None = None + coding_impact: str | None = None + acmg_confirmed: bool | None = None + acmg_class: str | None = None + acmg_reannotated: str | None = None + source: str | None = None + codon: int | None = None + gene_symbol: str | None = None + hgvs: str | None = None + transcript: str | None = None + comment: str | None = None + flagged_at_timestamp: str | None = None + id: int | None = None + saphetor_class: str | None = Field(None, alias="saphetorClass") + user_id: int | None = None + variant_id: int | None = None + is_lifted_over: bool | None = None + lifted_from: str | None = None + + +class SaphetorPubmeduserentryItem(_GeneratedBase): + functions: list[str | None] | None = None + coding_impact: str | None = None + acmg_confirmed: bool | None = None + acmg_class: str | None = None + acmg_reannotated: str | None = None + source: str | None = None + codon: int | None = None + gene_symbol: str | None = None + hgvs: str | None = None + transcript: str | None = None + pub_med_references: list[int | None] | None = None + pathogenicity: str | None = None + id: int | None = None + confirmed_by_functional_study: bool | None = Field( + None, alias="confirmedByFunctionalStudy" + ) + is_lifted_over: bool | None = None + lifted_from: str | None = None + + +class UniprotUniprotVariant(_GeneratedBase): + functions: list[str | None] | None = None + coding_impact: str | None = None + acmg_confirmed: bool | None = None + acmg_class: str | None = None + acmg_reannotated: str | None = None + source: str | None = None + codon: int | None = None + gene_symbol: str | None = None + hgvs: str | None = None + transcript: str | None = None + possible_functional_studies: list[int | None] | None = None + pub_med_references: list[int | None] | None = None + disease_name: list[str | None] | None = None + disease_symbol: list[str | None] | None = None + annotation_id: str | None = None + variant_type: str | None = None + disease: str | None = None + + +class Annotations(_GeneratedBase): + ncbi_clinvar2: list[NcbiClinvar2AnnotationItem] | None = None + saphetor_varsome_ai_variant: list[SaphetorVarsomeAiVariantItem] | None = None + mitimpact: list[MitimpactItem] | None = None + chop_mitotip: list[ChopMitotipItem] | None = None + chop_mitomap: list[ChopMitomapItem] | None = None + saphetor_varsome_comment: list[SaphetorVarsomeCommentItem] | None = None + saphetor_pubmeduserentry: list[SaphetorPubmeduserentryItem] | None = None + uniprot_uniprot_variants: list[UniprotUniprotVariant] | None = None + + +class KnownPathogenicityEntry(_GeneratedBase): + annotations: Annotations | None = None + + +class SaphetorKnownPathogenicityItem(_GeneratedBase): + version: str | None = None + items: list[KnownPathogenicityEntry] | None = None + + +class MitotipItem(_GeneratedBase): + count: float | None = None + mitotip_score: float | None = None + mitomap_status: str | None = None + percentage: float | None = None + quartile: str | None = None + + +class MitomapItem(_GeneratedBase): + version: str | None = None + ac: int | None = None + af: float | None = None + disease_status: str | None = None + diseases: list[Any] | None = None + heteroplasmy: str | None = None + homoplasmy: str | None = None + pub_med_references: list[Any] | None = None + main_data: str | None = None + + +class AlphaMissenseItem(_GeneratedBase): + version: str | None = None + main_data: str | None = None + alpha_missense_score: float | None = None + + +class ChemicalRelation(_GeneratedBase): + significant: bool | None = None + curator_notes: str | None = None + annotation_id: int | None = None + drug_variant_relation: str | None = None + pub_med_references: list[Any] | None = None + id: str | None = None + name: str | None = None + normalized_drug: list[str | None] | None = None + association: str | None = None + pharmacodynamic: bool | None = None + pharmacokinetic: bool | None = None + drug_label_annotations: list[Any] | None = None + + +class DiseaseRelation(_GeneratedBase): + pub_med_references: list[Any] | None = None + pharmacodynamic: bool | None = None + pharmacokinetic: bool | None = None + name: str | None = None + association: str | None = None + id: str | None = None + + +class EvidenceItem(_GeneratedBase): + summary: str | None = None + evidence_url: str | None = None + evidence_id: str | None = None + score: float | None = None + evidence_type: str | None = None + + +class ClinicalAnnotation(_GeneratedBase): + pub_med_references: list[Any] | None = None + url: str | None = None + annotation_text: list[Any] | None = None + evidence: list[EvidenceItem] | None = None + score: float | None = None + id: int | None = None + annotation_type: str | None = None + chemical_relations: list[Any] | None = None + level_of_evidence: str | None = None + + +class VariantInfoItem(_GeneratedBase): + url: AnyUrl | None = None + variant: str | None = None + variant_id: str | None = None + + +class PharmgkbItem(_GeneratedBase): + version: str | None = None + chemical_relations: list[ChemicalRelation] | None = None + disease_relations: list[DiseaseRelation] | None = None + clinical_annotations: list[ClinicalAnnotation] | None = None + variant_info: list[VariantInfoItem] | None = None + + +class TranscriptCandidate(_GeneratedBase): + canonical: bool | None = None + gene_id: int | None = None + gene_symbol: str | None = None + is_splicing: bool | None = None + name: str | None = None + coding_impact: str | None = None + blosum_score: int | None = None + total_coding_length: int | None = None + total_exon_length: int | None = None + user_specifier: bool | None = None + gene_transcript: str | None = None + + +class AcmgRules(_GeneratedBase): + approx_score: int | None = None + benign_score: int | None = None + benign_subscore: str | None = None + clinical_score: float | None = None + pathogenic_score: int | None = None + pathogenic_subscore: str | None = None + total_score: int | None = None + verdict: str | None = None + + +class AcmgVerdict(_GeneratedBase): + acmg_rules: AcmgRules | None = Field(None, alias="ACMG_rules") + classifications: list[str | None] | None = None + + +class AcmgClassification(_GeneratedBase): + name: str | None = None + met_criteria: bool | None = None + user_explain: list[str | None] | None = None + user_explain_failed: list[str | None] | None = None + strength: str | None = None + + +class AcmgSampleFindings(_GeneratedBase): + inheritance: str | None = None + phenotypes: str | None = None + disease: str | None = None + mode_of_inheritance: str | None = None + ethinicity: str | None = None + + +class ThrottlingInfo(_GeneratedBase): + throttling_msg: str | None = None + + +class Error(_GeneratedBase): + classifier: str | None = None + exception: str | None = None + + +class AcmgAnnotation(_GeneratedBase): + version_name: str | None = None + gene_symbol: str | None = None + transcript: str | None = None + transcript_reason: str | None = None + transcript_candidates: list[TranscriptCandidate] | None = None + coding_impact: str | None = None + blosum_score: int | None = None + verdict: AcmgVerdict | None = None + classifications: list[AcmgClassification] | None = None + gene_id: int | None = None + sample_findings: AcmgSampleFindings | None = None + throttling_info: ThrottlingInfo | None = None + errors: list[Error] | None = None + is_cancer_explain: str | None = None + + +class AmpVerdict(_GeneratedBase): + tier: str | None = None + approx_score: float | None = None + + +class UserExplain(_GeneratedBase): + tier_1: list[Any] | None = None + tier_2: list[Any] | None = None + tier_3: list[Any] | None = None + tier_4: list[Any] | None = None + + +class AmpClassification(_GeneratedBase): + name: str | None = None + tier: str | None = None + user_explain: UserExplain | None = None + total_samples: int | None = None + approx_score: float | None = None + + +class AmpSampleFindings(_GeneratedBase): + sex: str | None = None + inheritance: str | None = None + age: str | None = None + age_match: str | None = None + tissue_type_match: list[Any] | None = None + cancer_type_match: list[Any] | None = None + ethnic_frequency: str | None = None + + +class ApprovedTherapyDrug(_GeneratedBase): + drug_name: str | None = None + id: int | None = None + normalized_drug: str | None = None + + +class TherapyDescription(_GeneratedBase): + description: str | None = None + pub_med_references: list[int | None] | None = None + + +class ApprovedTherapy(_GeneratedBase): + approval_status: str | None = None + evidence_type: str | None = None + efficacy_evidence: str | None = None + response_type: str | None = None + amp_tier: str | None = None + cap_level: str | None = None + therapy: str | None = None + therapy_id: int | None = None + normalized_drug_name: str | None = None + indication: str | None = None + normalized_cancer: str | None = None + pub_med_references: list[int | None] | None = None + molecular_profile: str | None = None + approved_authorities: list[str | None] | None = None + drugs: list[ApprovedTherapyDrug] | None = None + therapy_descriptions: list[TherapyDescription] | None = None + + +class AmpAnnotation(_GeneratedBase): + version_name: str | None = None + verdict: AmpVerdict | None = None + classifications: list[AmpClassification] | None = None + sample_findings: AmpSampleFindings | None = None + approved_therapies: list[ApprovedTherapy] | None = None + throttling_info: ThrottlingInfo | None = None + errors: list[Error] | None = None + + +class DbnsfpPremiumItem(_GeneratedBase): + version: str | None = None + ensembl_proteinid: list[str | None] | None = None + ensembl_transcriptid: list[str | None] | None = None + polyphen2_hdiv_pred: list[str | None] | None = None + polyphen2_hdiv_rankscore: float | None = None + polyphen2_hdiv_score: list[float | None] | None = None + polyphen2_hvar_pred: list[str | None] | None = None + polyphen2_hvar_rankscore: float | None = None + polyphen2_hvar_score: list[float | None] | None = None + + +class CaddItem(_GeneratedBase): + version: str | None = None + cadd_score: float | None = None + + +class SampleIdItem(_GeneratedBase): + key: str | None = None + value: int | None = None + + +class SampleTypeItem(_GeneratedBase): + key: str | None = None + value: int | None = None + + +class MutationStatu(_GeneratedBase): + key: str | None = None + value: int | None = None + + +class ValidationStatu(_GeneratedBase): + key: str | None = None + value: int | None = None + + +class CenterItem(_GeneratedBase): + key: str | None = None + value: int | None = None + + +class OsMonth(_GeneratedBase): + key: str | None = None + value: int | None = None + + +class DfsMonth(_GeneratedBase): + key: str | None = None + value: int | None = None + + +class PfsStatu(_GeneratedBase): + key: str | None = None + value: int | None = None + + +class RadiationTherapyItem(_GeneratedBase): + key: str | None = None + value: int | None = None + + +class NewTumorEventAfterInitialTreatmentItem(_GeneratedBase): + key: str | None = None + value: int | None = None + + +class DssStatu(_GeneratedBase): + key: str | None = None + value: int | None = None + + +class SomaticStatusFreqItem(_GeneratedBase): + key: str | None = None + value: int | None = None + + +class CbioPortalItem(_GeneratedBase): + version: str | None = None + total_samples: int | None = None + sample_id: list[SampleIdItem] | None = None + sample_type: list[SampleTypeItem] | None = None + study_name: list[StudyNameItem] | None = None + mutation_status: list[MutationStatu] | None = None + validation_status: list[ValidationStatu] | None = None + center: list[CenterItem] | None = None + t_ref_count: int | None = None + t_alt_count: int | None = None + n_ref_count: int | None = None + n_alt_count: int | None = None + n_depth: int | None = None + t_depth: int | None = None + canonical: bool | None = None + hotspot: bool | None = None + ensp: str | None = None + ccds: str | None = None + cdsposition: str | None = None + cdnaposition: str | None = None + biotype: str | None = None + uniparc: str | None = None + pick: float | None = None + sex: list[SexItem] | None = None + age_freq: list[AgeFreqItem] | None = None + os_months: list[OsMonth] | None = None + os_status: list[OsStatu] | None = None + race: list[RaceItem] | None = None + tumor_status: list[TumorStatu] | None = None + dfs_months: list[DfsMonth] | None = None + path_t_stage: list[PathTStageItem] | None = None + pfs_status: list[PfsStatu] | None = None + radiation_therapy: list[RadiationTherapyItem] | None = None + path_n_stage: list[PathNStageItem] | None = None + path_m_stage: list[PathMStageItem] | None = None + new_tumor_event_after_initial_treatment: ( + list[NewTumorEventAfterInitialTreatmentItem] | None + ) = None + ajcc_pathologic_tumor_stage: list[AjccPathologicTumorStageItem] | None = None + dss_status: list[DssStatu] | None = None + prior_dx: list[PriorDxItem] | None = None + somatic_status_freq: list[SomaticStatusFreqItem] | None = None + grade: list[GradeItem] | None = None + pub_med_references: list[Any] | None = None + oncotree_code: list[OncotreeCodeItem] | None = None + cancer_name: list[CancerNameItem] | None = None + cancer_type: list[CancerTypeItem] | None = None + tissue_type: list[TissueTypeItem] | None = None + + +class SomaticItem(_GeneratedBase): + key: str | None = None + value: int | None = None + + +class CancerHotspot(_GeneratedBase): + version: str | None = None + total_samples: int | None = None + t_ref_count: int | None = None + t_alt_count: int | None = None + n_ref_count: int | None = None + n_alt_count: int | None = None + n_depth: int | None = None + t_depth: int | None = None + somatic: list[SomaticItem] | None = None + canonical: bool | None = None + ensp: str | None = None + ccds: str | None = None + cdsposition: str | None = None + cdnaposition: str | None = None + biotype: str | None = None + feature: str | None = None + uniparc: str | None = None + pick: float | None = None + pub_med_references: list[Any] | None = None + oncotree_code: list[OncotreeCodeItem] | None = None + cancer_name: list[CancerNameItem] | None = None + cancer_type: list[CancerTypeItem] | None = None + tissue_type: list[TissueTypeItem] | None = None + + +class JaxCkbItem(_GeneratedBase): + ckb_id: int | None = None + version: str | None = None + coding_impact: str | None = None + evidence: list[Any] | None = None + extended_evidence: list[Any] | None = None + gene_variant_descriptions: list[Any] | None = None + protein_effect: str | None = None + cap_asco_evidence_level: str | None = None + polymorphism: bool | None = None + transforming_activity: bool | None = None + associated_with_drug_resistance: bool | None = None + + +class Phastcons100wayItem(_GeneratedBase): + version: str | None = None + conservation_score: list[Decimal | None] | None = None + + +class Phylop100wayItem(_GeneratedBase): + version: str | None = None + conservation_score: list[Decimal | None] | None = None + + +class MaxentscanItem(_GeneratedBase): + version: str | None = None + maxentscan_score: list[float | None] | None = None + + +class GnomadMitoItem(_GeneratedBase): + version: str | None = None + filter: str | None = None + ac: int | None = None + an: int | None = None + af: float | None = None + ac_afr: int | None = None + ac_ami: int | None = None + ac_amr: int | None = None + ac_asj: int | None = None + ac_eas: int | None = None + ac_fin: int | None = None + ac_nfe: int | None = None + ac_oth: int | None = None + ac_sas: int | None = None + ac_mid: int | None = None + ac_hom: int | None = None + ac_het: int | None = None + ac_afr_hom: int | None = None + ac_ami_hom: int | None = None + ac_amr_hom: int | None = None + ac_asj_hom: int | None = None + ac_eas_hom: int | None = None + ac_fin_hom: int | None = None + ac_nfe_hom: int | None = None + ac_oth_hom: int | None = None + ac_sas_hom: int | None = None + ac_mid_hom: int | None = None + ac_afr_het: int | None = None + ac_ami_het: int | None = None + ac_amr_het: int | None = None + ac_asj_het: int | None = None + ac_eas_het: int | None = None + ac_fin_het: int | None = None + ac_nfe_het: int | None = None + ac_oth_het: int | None = None + ac_sas_het: int | None = None + ac_mid_het: int | None = None + an_afr: int | None = None + an_ami: int | None = None + an_amr: int | None = None + an_asj: int | None = None + an_eas: int | None = None + an_fin: int | None = None + an_nfe: int | None = None + an_oth: int | None = None + an_sas: int | None = None + an_mid: int | None = None + age_hist_het_under_30: int | None = None + age_hist_het_30_35: int | None = None + age_hist_het_35_40: int | None = None + age_hist_het_40_45: int | None = None + age_hist_het_45_50: int | None = None + age_hist_het_50_55: int | None = None + age_hist_het_55_60: int | None = None + age_hist_het_60_65: int | None = None + age_hist_het_65_70: int | None = None + age_hist_het_70_75: int | None = None + age_hist_het_75_80: int | None = None + age_hist_het_over_80: int | None = None + age_hist_hom_under_30: int | None = None + age_hist_hom_30_35: int | None = None + age_hist_hom_35_40: int | None = None + age_hist_hom_40_45: int | None = None + age_hist_hom_45_50: int | None = None + age_hist_hom_50_55: int | None = None + age_hist_hom_55_60: int | None = None + age_hist_hom_60_65: int | None = None + age_hist_hom_65_70: int | None = None + age_hist_hom_70_75: int | None = None + age_hist_hom_75_80: int | None = None + age_hist_hom_over_80: int | None = None + mitotip_score: float | None = None + mitotip_trna_prediction: str | None = None + pon_ml_probability_of_pathogenicity: float | None = None + pon_mt_trna_prediction: str | None = None + original_variant: str | None = None + main_data: str | None = None + + +class VariantPubmedAutomapItem(_GeneratedBase): + version: str | None = None + pub_med_references: list[int | None] | None = None + + +class DocmDisease(_GeneratedBase): + disease: str | None = None + doid: str | None = None + pub_med_references: list[Any] | None = None + tags: list[Any] | None = None + + +class DocmDrug(_GeneratedBase): + effect: str | None = None + evidence: str | None = None + pathway: str | None = None + source: str | None = None + status: str | None = None + therapeutic_context: str | None = None + pub_med_references: list[Any] | None = None + + +class WustlDocmItem(_GeneratedBase): + version: str | None = None + diseases: list[DocmDisease] | None = None + drugs: list[DocmDrug] | None = None + pub_med_references: list[Any] | None = None + hgvs: str | None = None + + +class EveScoreEntry(_GeneratedBase): + aa_change: str | None = None + class_75: str | None = None + current_variant: bool | None = None + eve_score: Decimal | None = None + + +class EveItem(_GeneratedBase): + version: str | None = None + items: list[list[EveScoreEntry]] | None = None + + +class Reference(_GeneratedBase): + pub_med_references: list[int | None] | None = None + reference_number: int | None = None + title: str | None = None + source: str | None = None + authors: str | None = None + + +class OmimPhenotypeEntry(_GeneratedBase): + description: str | None = None + mutations: str | None = None + omim_id: int | None = None + number: int | None = None + phenotype_name: str | None = None + alternative_phenotype_names: list[str | None] | None = None + references: list[Reference] | None = None + + +class OmimItem(_GeneratedBase): + version: str | None = None + items: list[OmimPhenotypeEntry] | None = None + + +class NihClingenVariant(_GeneratedBase): + version: str | None = None + approval_date: str | None = None + disease: str | None = None + evidence_met: list[str | None] | None = None + evidence_not_met: list[str | None] | None = None + expert_panel: str | None = None + guideline: str | None = None + mode_of_inheritance: str | None = None + mondo_id: str | None = None + pathogenicity: str | None = None + pub_med_references: list[int | None] | None = None + published_date: str | None = None + repo_link: str | None = None + retracted: str | None = None + summary: str | None = None + + +class Gene(_GeneratedBase): + gene_id: int | None = None + hgnc_id: int | None = None + gene_symbol: str | None = None + + +class Pathogenicity(_GeneratedBase): + clinical_classification_submitter: str | None = None + clinical_classification_curator: str | None = None + effect_submitter: str | None = None + effect_curator: str | None = None + effect_symbol: str | None = None + lovd_link: str | None = None + + +class LovdVariantInfoItem(_GeneratedBase): + variant_id: str | None = None + variant_notation: str | None = None + + +class Variant(_GeneratedBase): + comments: list[str | None] | None = None + is_current: bool | None = None + is_lifted_over: bool | None = None + lovd_link: str | None = None + pathogenicity: Pathogenicity | None = None + variant_info: list[LovdVariantInfoItem] | None = None + + +class Individual(_GeneratedBase): + comments: list[str | None] | None = None + gender: str | None = None + phenotypes: list[str | None] | None = None + pub_med_references: list[int | None] | None = None + variants: list[Variant] | None = None + + +class LumcLovdItem(_GeneratedBase): + version: str | None = None + genes: list[Gene] | None = None + individuals: list[Individual] | None = None + is_lifted_over: bool | None = None + pathogenicities: list[Pathogenicity] | None = None + + +class Abstract(_GeneratedBase): + abstract: str | None = None + link: str | None = None + + +class MainType(_GeneratedBase): + id: int | None = None + name: str | None = None + tumor_form: str | None = None + + +class TumorType(_GeneratedBase): + children: dict[str, Any] | None = None + code: str | None = None + color: str | None = None + id: int | None = None + level: int | None = None + main_type: MainType | None = None + name: str | None = None + parent: str | None = None + tissue: str | None = None + tumor_form: str | None = None + + +class DiagnosticImplication(_GeneratedBase): + abstracts: list[Abstract] | None = None + alterations: list[str | None] | None = None + description: str | None = None + level_of_evidence: str | None = None + pmids: list[str | None] | None = None + tumor_type: TumorType | None = None + + +class PrognosticTumorType(_GeneratedBase): + children: dict[str, Any] | None = None + code: str | None = None + color: str | None = None + id: int | None = None + level: int | None = None + main_type: MainType | None = None + name: str | None = None + parent: str | None = None + tissue: str | None = None + tumor_form: str | None = None + + +class PrognosticImplication(_GeneratedBase): + abstracts: list[Abstract] | None = None + alterations: list[str | None] | None = None + description: str | None = None + level_of_evidence: str | None = None + pmids: list[str | None] | None = None + tumor_type: PrognosticTumorType | None = None + + +class OncokbDrug(_GeneratedBase): + drug_name: str | None = None + ncit_code: str | None = None + + +class LevelAssociatedCancerType(_GeneratedBase): + children: dict[str, Any] | None = None + code: str | None = None + color: str | None = None + id: int | None = None + level: int | None = None + main_type: MainType | None = None + name: str | None = None + parent: str | None = None + tissue: str | None = None + tumor_form: str | None = None + + +class Treatment(_GeneratedBase): + abstracts: list[Abstract] | None = None + alterations: list[str | None] | None = None + description: str | None = None + approved_indications: list[Any] | None = None + drugs: list[OncokbDrug] | None = None + fda_level: str | None = None + level: str | None = None + level_associated_cancer_type: LevelAssociatedCancerType | None = None + pmids: list[str | None] | None = None + + +class OncokbItem(_GeneratedBase): + version: str | None = None + allele_exist: bool | None = None + diagnostic_implications: list[DiagnosticImplication] | None = None + diagnostic_summary: str | None = None + gene_exist: bool | None = None + gene_summary: str | None = None + highest_diagnostic_implication_level: str | None = None + highest_fda_level: str | None = None + highest_prognostic_implication_level: str | None = None + highest_resistance_level: str | None = None + highest_sensitive_level: str | None = None + hotspot: bool | None = None + last_update: str | None = None + mutation_effect: dict[str, Any] | None = None + oncogenic: str | None = None + other_significant_resistance_levels: list[str | None] | None = None + other_significant_sensitive_levels: list[str | None] | None = None + prognostic_implications: list[PrognosticImplication] | None = None + prognostic_summary: str | None = None + query: dict[str, Any] | None = None + treatments: list[Treatment] | None = None + tumor_type_summary: str | None = None + variant_exist: bool | None = None + variant_summary: str | None = None + variant_id: int | None = None + vus: bool | None = None + + +class SpliceVaultEntry(_GeneratedBase): + event_rank: int | None = None + exon_no: int | None = None + tx_id: str | None = None + gtex_sample_count: int | None = None + skipped_exons_id: str | None = None + splicing_event_class: str | None = None + sra_sample_count: int | None = None + ss_type: str | None = None + cryptic_distance: int | None = None + skipped_exons_count: int | None = None + gtex_max_uniq_map_reads: int | None = None + intropolis_sample_count: int | None = None + splice_junction_coordinates: str | None = None + missplicing_inframe: bool | None = None + + +class KncSpliceVaultItem(_GeneratedBase): + version: str | None = None + items: list[list[SpliceVaultEntry]] | None = None + + +class VariantSpecificDetail(_GeneratedBase): + classification: str | None = None + pubmedid: int | None = None + validation_doi: str | None = None + validation_metric1: str | None = None + validation_metric2: str | None = None + tissue: str | None = None + method: str | None = None + outcome: str | None = None + + +class SplicevardbJson(_GeneratedBase): + variant_specific_details: list[VariantSpecificDetail] | None = None + overall_validation_method: list[str | None] | None = None + overall_classification: str | None = None + hgvs_refseq: str | None = None + gene_symbol_list: str | None = None + locations: str | None = None + + +class CompbioSpliceVarDb(_GeneratedBase): + version: str | None = None + splicevardb_json: SplicevardbJson | None = None + + +class VariantVariantApi(_GeneratedBase): + original_variant: str | None = None + chromosome: str | None = None + alt: str | None = None + ref: str | None = None + pos: int | None = None + regions: Regions | None = None + variant_type: str | None = None + cytobands: str | None = None + refseq_transcripts: list[RefseqTranscript] | None = None + ensembl_transcripts: list[EnsemblTranscript] | None = None + broad_exac: list[BroadExacItem] | None = None + gnomad_exomes: list[GnomadExome] | None = None + gnomad_exomes_coverage: list[GnomadExomesCoverageItem] | None = None + gnomad_genomes: list[GnomadGenome] | None = None + gnomad_genomes_coverage: list[GnomadGenomesCoverageItem] | None = None + thousand_genomes: list[ThousandGenome] | None = None + gerp: list[GerpItem] | None = None + isb_kaviar3: list[IsbKaviar3Item] | None = None + dbnsfp: list[DbnsfpItem] | None = None + dann_snvs: list[DannSnv] | None = None + dbnsfp_dbscsnv: list[DbnsfpDbscsnvItem] | None = None + ncbi_dbsnp: list[NcbiDbsnpItem] | None = None + sanger_cosmic: list[SangerCosmicItem] | None = None + sanger_cosmic_public: list[SangerCosmicPublicItem] | None = None + sanger_cosmic_licensed: list[SangerCosmicLicensedItem] | None = None + ncbi_clinvar2: list[NcbiClinvar2Item] | None = None + icgc_somatic: list[IcgcSomaticItem] | None = None + iarc_tp53_germline: list[IarcTp53GermlineItem] | None = None + iarc_tp53_somatic: list[IarcTp53SomaticItem] | None = None + pub_med_articles: dict[str, Any] | None = None + publications: dict[str, Any] | None = None + publication_counts: list[Any] | None = None + uniprot_variants: list[UniprotVariant] | None = None + uoi_dvd: list[UoiDvdItem] | None = None + weill_cornell_medicine_pmkb: list[WeillCornellMedicinePmkbItem] | None = None + wustl_civic: list[WustlCivicItem] | None = None + gwas: list[Gwa] | None = None + nih_gdc: list[NihGdcItem] | None = None + bravo: list[BravoItem] | None = None + saphetor_known_pathogenicity: list[SaphetorKnownPathogenicityItem] | None = None + mitimpact: list[MitimpactItem] | None = None + mitotip: list[MitotipItem] | None = None + mitomap: list[MitomapItem] | None = None + alpha_missense: list[AlphaMissenseItem] | None = None + pharmgkb: list[PharmgkbItem] | None = None + acmg_annotation: AcmgAnnotation | None = None + amp_annotation: AmpAnnotation | None = None + not_subscribed_sources: dict[str, Any] | None = None + dbnsfp_premium: list[DbnsfpPremiumItem] | None = None + cadd: list[CaddItem] | None = None + cbio_portal: list[CbioPortalItem] | None = None + cancer_hotspots: list[CancerHotspot] | None = None + jax_ckb: list[JaxCkbItem] | None = None + phastcons100way: list[Phastcons100wayItem] | None = None + phylop100way: list[Phylop100wayItem] | None = None + maxentscan: list[MaxentscanItem] | None = None + gnomad_mito: list[GnomadMitoItem] | None = None + variant_pubmed_automap: list[VariantPubmedAutomapItem] | None = None + wustl_docm: list[WustlDocmItem] | None = None + eve: list[EveItem] | None = None + omim: list[OmimItem] | None = None + nih_clingen_variants: list[NihClingenVariant] | None = None + lumc_lovd: list[LumcLovdItem] | None = None + oncokb: list[OncokbItem] | None = None + knc_splice_vault: list[KncSpliceVaultItem] | None = None + compbio_splice_var_db: CompbioSpliceVarDb | None = None + + +class VariantVariantBatchRequestApi(_GeneratedBase): + variants: list[str | None] | None = Field(None, max_length=200, min_length=1) + variants_specs: dict[str, Any] | None = None + variants_transcripts: dict[str, Any] | None = None diff --git a/varsome_api/models/elements/__init__.py b/varsome_api/models/elements/__init__.py deleted file mode 100755 index c87dc37..0000000 --- a/varsome_api/models/elements/__init__.py +++ /dev/null @@ -1,16 +0,0 @@ -from .acmg import * -from .broad import * -from .dann import * -from .dbnsfp import * -from .gerp import * -from .gnomad import * -from .gwas import * -from .iarc import * -from .icgc import * -from .isb import * -from .ncbi import * -from .sanger import * -from .thousand_genomes import * -from .transcript import * -from .uniprot import * -from .wustl import * diff --git a/varsome_api/models/elements/acmg.py b/varsome_api/models/elements/acmg.py deleted file mode 100644 index 45a5cf5..0000000 --- a/varsome_api/models/elements/acmg.py +++ /dev/null @@ -1,56 +0,0 @@ -# Copyright 2018 Saphetor S.A. -# -# Licensed under the Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.apache.org/licenses/LICENSE-2.0 -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. - -from jsonmodels import models, fields - - -class ACMGClassification(models.Base): - met_criteria = fields.BoolField() - name = fields.StringField(help_text="ACMG Classification Name") - user_explain = fields.ListField( - items_types=(str,), - help_text="Criteria explanation", - required=False, - nullable=True, - ) - - -class ACMGRule(models.Base): - pathogenic_subscore = fields.StringField(required=False, nullable=True) - benign_subscore = fields.StringField(required=False, nullable=True) - verdict = fields.StringField(required=False, nullable=True) - - -class ACMGVerdict(models.Base): - classifications = fields.ListField( - items_types=(str,), - help_text="Classification names", - required=False, - nullable=True, - ) - ACMG_rules = fields.EmbeddedField(ACMGRule) - - -class ACMG(models.Base): - classifications = fields.ListField( - required=False, - items_types=(ACMGClassification,), - help_text="ACMG Classifications", - ) - verdict = fields.EmbeddedField( - ACMGVerdict, nullable=True, required=False, help_text="ACMG Verdict" - ) - coding_impact = fields.StringField(required=False, nullable=True) - transcript = fields.StringField(required=False, nullable=True) - transcript_reason = fields.StringField(required=False, nullable=True) diff --git a/varsome_api/models/elements/broad.py b/varsome_api/models/elements/broad.py deleted file mode 100755 index d1a0bf3..0000000 --- a/varsome_api/models/elements/broad.py +++ /dev/null @@ -1,194 +0,0 @@ -# Copyright 2018 Saphetor S.A. -# -# Licensed under the Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.apache.org/licenses/LICENSE-2.0 -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. - -from jsonmodels import models, fields - - -class ExAC(models.Base): - version = fields.StringField(help_text="Version") - ac = fields.IntField(help_text="Allele Count", required=False, nullable=True) - an = fields.IntField(help_text="Allele Number", required=False, nullable=True) - ac_adj = fields.FloatField(help_text="Allele Count", required=False, nullable=True) - an_adj = fields.FloatField(help_text="Allele Number", required=False, nullable=True) - af = fields.FloatField(help_text="Allele Frequency", required=False, nullable=True) - ac_afr = fields.IntField( - help_text="Allele Count African", required=False, nullable=True - ) - ac_amr = fields.IntField( - help_text="Allele Count American", required=False, nullable=True - ) - ac_asj = fields.IntField( - help_text="Allele Count Ashkenazi Jewish", required=False, nullable=True - ) - ac_eas = fields.IntField( - help_text="Allele Count East Asian", required=False, nullable=True - ) - ac_fin = fields.IntField( - help_text="Allele Count European (Finnish)", required=False, nullable=True - ) - ac_nfe = fields.IntField( - help_text="Allele Count European (Non-Finnish)", required=False, nullable=True - ) - ac_oth = fields.IntField( - help_text="Allele Count Other", required=False, nullable=True - ) - ac_sas = fields.IntField( - help_text="Allele Count South Asian", required=False, nullable=True - ) - ac_male = fields.IntField( - help_text="Allele Count Male", required=False, nullable=True - ) - ac_female = fields.IntField( - help_text="Allele Count Female", required=False, nullable=True - ) - hom = fields.IntField( - help_text="Number of Homozygotes", required=False, nullable=True - ) - hemi = fields.IntField( - help_text="Number of Hemizygotes", required=False, nullable=True - ) - ac_hom = fields.FloatField( - help_text="Number of Homozygotes", required=False, nullable=True - ) - ac_hemi = fields.FloatField( - help_text="Number of Hemizygotes", required=False, nullable=True - ) - an_afr = fields.IntField( - help_text="Allele Number African", required=False, nullable=True - ) - an_amr = fields.IntField( - help_text="Allele Number American", required=False, nullable=True - ) - an_asj = fields.IntField( - help_text="Allele Number Ashkenazi Jewish", required=False, nullable=True - ) - an_eas = fields.IntField( - help_text="Allele Number East Asian", required=False, nullable=True - ) - an_fin = fields.IntField( - help_text="Allele Number European (Finnish)", required=False, nullable=True - ) - an_nfe = fields.IntField( - help_text="Allele Number European (Non-Finnish)", required=False, nullable=True - ) - an_oth = fields.IntField( - help_text="Allele Number Other", required=False, nullable=True - ) - an_sas = fields.IntField( - help_text="Allele Number South Asian", required=False, nullable=True - ) - an_male = fields.IntField( - help_text="Allele Number Male", required=False, nullable=True - ) - an_female = fields.IntField( - help_text="Allele Number Female", required=False, nullable=True - ) - hom_afr = fields.IntField( - help_text="Number of Homozygotes African", required=False, nullable=True - ) - hom_amr = fields.IntField( - help_text="Number of Homozygotes American", required=False, nullable=True - ) - hom_asj = fields.IntField( - help_text="Number of Homozygotes Ashkenazi Jewish", - required=False, - nullable=True, - ) - hom_eas = fields.IntField( - help_text="Number of Homozygotes East Asian", required=False, nullable=True - ) - hom_fin = fields.IntField( - help_text="Number of Homozygotes European (Finnish)", - required=False, - nullable=True, - ) - hom_nfe = fields.IntField( - help_text="Number of Homozygotes European (Non-Finnish)", - required=False, - nullable=True, - ) - hom_oth = fields.IntField( - help_text="Number of Homozygotes Other", required=False, nullable=True - ) - hom_sas = fields.IntField( - help_text="Number of Homozygotes South Asian", required=False, nullable=True - ) - hom_male = fields.IntField( - help_text="Number of Homozygotes Male", required=False, nullable=True - ) - hom_female = fields.IntField( - help_text="Number of Homozygotes Female", required=False, nullable=True - ) - hemi_afr = fields.IntField( - help_text="Number of Hemizygotes African", required=False, nullable=True - ) - hemi_amr = fields.IntField( - help_text="Number of Hemizygotes American", required=False, nullable=True - ) - hemi_asj = fields.IntField( - help_text="Number of Hemizygotes Ashkenazi Jewish", - required=False, - nullable=True, - ) - hemi_eas = fields.IntField( - help_text="Number of Hemizygotes East Asian", required=False, nullable=True - ) - hemi_fin = fields.IntField( - help_text="Number of Hemizygotes European (Finnish)", - required=False, - nullable=True, - ) - hemi_nfe = fields.IntField( - help_text="Number of Hemizygotes European (Non-Finnish)", - required=False, - nullable=True, - ) - hemi_oth = fields.IntField( - help_text="Number of Hemizygotes Other", required=False, nullable=True - ) - hemi_sas = fields.IntField( - help_text="Number of Hemizygotes South Asian", required=False, nullable=True - ) - af_afr = fields.FloatField( - help_text="Allele Frequency African", required=False, nullable=True - ) - af_amr = fields.FloatField( - help_text="Allele Frequency American", required=False, nullable=True - ) - af_asj = fields.FloatField( - help_text="Allele Frequency Ashkenazi Jewish", required=False, nullable=True - ) - af_eas = fields.FloatField( - help_text="Allele Frequency East Asian", required=False, nullable=True - ) - af_fin = fields.FloatField( - help_text="Allele Frequency European (Finnish)", required=False, nullable=True - ) - af_nfe = fields.FloatField( - help_text="Allele Frequency European (Non-Finnish)", - required=False, - nullable=True, - ) - af_oth = fields.FloatField( - help_text="Allele Frequency Other", required=False, nullable=True - ) - af_sas = fields.FloatField( - help_text="Allele Frequency South Asian", required=False, nullable=True - ) - af_male = fields.FloatField( - help_text="Allele Frequency Male", required=False, nullable=True - ) - af_female = fields.FloatField( - help_text="Allele Frequency Female", required=False, nullable=True - ) diff --git a/varsome_api/models/elements/dann.py b/varsome_api/models/elements/dann.py deleted file mode 100755 index 20815e3..0000000 --- a/varsome_api/models/elements/dann.py +++ /dev/null @@ -1,22 +0,0 @@ -# Copyright 2018 Saphetor S.A. -# -# Licensed under the Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.apache.org/licenses/LICENSE-2.0 -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. - -from jsonmodels import models, fields - - -class DannSNVs(models.Base): - version = fields.StringField(help_text="Version") - dann_score = fields.FloatField( - help_text="DANN Score", required=False, nullable=True - ) diff --git a/varsome_api/models/elements/dbnsfp.py b/varsome_api/models/elements/dbnsfp.py deleted file mode 100755 index dc88b99..0000000 --- a/varsome_api/models/elements/dbnsfp.py +++ /dev/null @@ -1,223 +0,0 @@ -# Copyright 2018 Saphetor S.A. -# -# Licensed under the Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.apache.org/licenses/LICENSE-2.0 -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. - -from jsonmodels import models, fields - -from varsome_api.models.fields import NullableItemListField - - -class DbNSFP(models.Base): - version = fields.StringField(help_text="Version") - mutationtaster_pred = NullableItemListField( - items_types=(str,), help_text="MutationTaster Prediction", required=False - ) - mutationtaster_score = NullableItemListField( - items_types=(float,), - help_text="MutationTaster Accuracy", - required=False, - nullable=True, - ) - sift_score = NullableItemListField( - items_types=(float,), help_text="SIFT score", required=False, nullable=True - ) - sift_prediction = fields.StringField( - help_text="SIFT prediction", required=False, nullable=True - ) - phylop100way_vertebrate = NullableItemListField( - items_types=(float,), help_text="phyloP100way vertebrate", required=False - ) - phylop46way_placental = NullableItemListField( - items_types=(float,), help_text="phyloP46way placental", required=False - ) - phylop46way_primate = NullableItemListField( - items_types=(float,), help_text="phyloP46way primate", required=False - ) - mutationtaster_converted_rankscore = NullableItemListField( - items_types=(float,), - help_text="MutationTaster converted rankscore", - required=False, - nullable=True, - ) - mutationassessor_pred = NullableItemListField( - items_types=(str,), help_text="MutationAssessor prediction", required=False - ) - mutationassessor_score = NullableItemListField( - items_types=(float,), help_text="MutationAssessor score", required=False - ) - mutationassessor_score_rankscore = NullableItemListField( - items_types=(float,), - help_text="MutationAssessor rankscore", - required=False, - nullable=True, - ) - fathmm_mkl_coding_pred = NullableItemListField( - items_types=(str,), - help_text="FATHMM-MKL coding prediction", - required=False, - nullable=True, - ) - fathmm_mkl_coding_score = NullableItemListField( - items_types=(float,), help_text="FATHMM-MKL coding score", required=False - ) - fathmm_mkl_coding_rankscore = NullableItemListField( - items_types=(float,), - help_text="FATHMM-MKL coding rankscore", - required=False, - nullable=True, - ) - fathmm_pred = NullableItemListField( - items_types=(str,), help_text="FATHMM prediction", required=False, nullable=True - ) - fathmm_score = NullableItemListField( - items_types=(float,), help_text="FATHMM score", required=False - ) - fathmm_converted_rankscore = NullableItemListField( - items_types=(float,), - help_text="FATHMM converted rankscore", - required=False, - nullable=True, - ) - sift_converted_rankscore = NullableItemListField( - items_types=(float,), help_text="SIFT converted rankscore", required=False - ) - metasvm_pred = NullableItemListField( - items_types=(str,), help_text="MetaSVM prediction", required=False - ) - metasvm_score = NullableItemListField( - items_types=(float,), help_text="MetaSVM score", required=False, nullable=True - ) - metasvm_rankscore = NullableItemListField( - items_types=(float,), help_text="MetaSVM rankscore", required=False - ) - metalr_pred = NullableItemListField( - items_types=(str,), help_text="MetalR prediction", required=False, nullable=True - ) - metalr_score = NullableItemListField( - items_types=(float,), help_text="MetalR score", required=False, nullable=True - ) - metalr_rankscore = NullableItemListField( - items_types=(float,), - help_text="MetalR rankscore", - required=False, - nullable=True, - ) - provean_pred = NullableItemListField( - items_types=(str,), help_text="Provean prediction", required=False - ) - provean_score = NullableItemListField( - items_types=(float,), help_text="Provean score", required=False - ) - provean_converted_rankscore = NullableItemListField( - items_types=(float,), - help_text="Provean converted rankscore", - required=False, - nullable=True, - ) - lrt_pred = NullableItemListField( - items_types=(str,), help_text="LRT prediction", required=False, nullable=True - ) - lrt_score = NullableItemListField( - items_types=(float,), help_text="LRT score", required=False, nullable=True - ) - lrt_converted_rankscore = NullableItemListField( - items_types=(float,), help_text="LRT converted rankscore", required=False - ) - lrt_omega = NullableItemListField( - items_types=(float,), help_text="LRT Omega", required=False, nullable=True - ) - cadd_raw = NullableItemListField( - items_types=(float,), help_text="CADD raw score", required=False, nullable=True - ) - cadd_raw_rankscore = NullableItemListField( - items_types=(float,), help_text="CADD raw rankscore", required=False - ) - cadd_phred = NullableItemListField( - items_types=(float,), help_text="CADD phred", required=False, nullable=True - ) - gm12878_confidence_value = NullableItemListField( - items_types=(float,), - help_text="GM12878 fitCons confidence value", - required=False, - nullable=True, - ) - gm12878_fitcons_score = NullableItemListField( - items_types=(float,), help_text="GM12878 fitCons score", required=False - ) - gm12878_fitcons_score_rankscore = NullableItemListField( - items_types=(float,), - help_text="GM12878 fitCons rankscore", - required=False, - nullable=True, - ) - siphy_29way_logodds_rankscore = NullableItemListField( - items_types=(float,), - help_text="SiPhy29way logOdds rankscore", - required=False, - nullable=True, - ) - siphy_29way_pi = NullableItemListField( - items_types=(float,), help_text="SiPhy29way pi", required=False, nullable=True - ) - phylop20way_mammalian = NullableItemListField( - items_types=(float,), help_text="phyloP20way mammalian", required=False - ) - phylop20way_mammalian_rankscore = NullableItemListField( - items_types=(float,), - help_text="phyloP20way mammalian rankscore", - required=False, - nullable=True, - ) - phylop100way_vertebrate_rankscore = NullableItemListField( - items_types=(float,), - help_text="phyloP100way vertebrate rankscore", - required=False, - nullable=True, - ) - phastcons20way_mammalian = NullableItemListField( - items_types=(float,), help_text="phastCons20way mammalian", required=False - ) - phastcons20way_mammalian_rankscore = NullableItemListField( - items_types=(float,), - help_text="phastCons20way mammalian rankscore", - required=False, - nullable=True, - ) - phastcons100way_vertebrate = NullableItemListField( - items_types=(float,), - help_text="phastCons100way vertebrate", - required=False, - nullable=True, - ) - phastcons100way_vertebrate_rankscore = NullableItemListField( - items_types=(float,), - help_text="phastCons100way vertebrate rankscore", - required=False, - nullable=True, - ) - vest3_score = NullableItemListField( - items_types=(float,), help_text="VEST3 score", required=False - ) - vest3_rankscore = NullableItemListField( - items_types=(float,), help_text="VEST3 rankscore", required=False, nullable=True - ) - - -class DBscSNV(models.Base): - version = fields.StringField(help_text="Version") - ada_score = NullableItemListField( - items_types=(float,), help_text="ADA Score", required=False, nullable=True - ) - rf_score = NullableItemListField( - items_types=(float,), help_text="RF Score", required=False, nullable=True - ) diff --git a/varsome_api/models/elements/gerp.py b/varsome_api/models/elements/gerp.py deleted file mode 100755 index 5496569..0000000 --- a/varsome_api/models/elements/gerp.py +++ /dev/null @@ -1,31 +0,0 @@ -# Copyright 2018 Saphetor S.A. -# -# Licensed under the Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.apache.org/licenses/LICENSE-2.0 -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. - -from jsonmodels import models, fields - - -class Gerp(models.Base): - version = fields.StringField(help_text="Version") - gerp_nr = fields.ListField( - items_types=(float, type(None)), - required=False, - help_text="GERP NR", - nullable=True, - ) - gerp_rs = fields.ListField( - items_types=(float, type(None)), - required=False, - help_text="GERP RS", - nullable=True, - ) diff --git a/varsome_api/models/elements/gnomad.py b/varsome_api/models/elements/gnomad.py deleted file mode 100755 index 9bdfc94..0000000 --- a/varsome_api/models/elements/gnomad.py +++ /dev/null @@ -1,177 +0,0 @@ -# Copyright 2018 Saphetor S.A. -# -# Licensed under the Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.apache.org/licenses/LICENSE-2.0 -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. - -from jsonmodels import models, fields - - -class GnomADCoverage(models.Base): - version = fields.StringField(help_text="Version") - coverage_mean = fields.ListField( - help_text="Mean coverage", - items_types=(float, type(None)), - required=False, - nullable=True, - ) - coverage_median = fields.ListField( - help_text="Median coverage", - items_types=(float, type(None)), - required=False, - nullable=True, - ) - coverage_20_frequency = fields.ListField( - help_text="Proportion of samples with over 20x", - items_types=(float, type(None)), - required=False, - nullable=True, - ) - - -class GnomAD(models.Base): - version = fields.StringField(help_text="Version") - ac = fields.IntField(help_text="Allele Count", required=False, nullable=True) - an = fields.IntField(help_text="Allele Number", required=False, nullable=True) - ac_adj = fields.FloatField(help_text="Allele Count", required=False, nullable=True) - an_adj = fields.FloatField(help_text="Allele Number", required=False, nullable=True) - af = fields.FloatField(help_text="Allele Frequency", required=False, nullable=True) - ac_afr = fields.IntField( - help_text="Allele Count African", required=False, nullable=True - ) - ac_amr = fields.IntField( - help_text="Allele Count American", required=False, nullable=True - ) - ac_asj = fields.IntField( - help_text="Allele Count Ashkenazi Jewish", required=False, nullable=True - ) - ac_eas = fields.IntField( - help_text="Allele Count East Asian", required=False, nullable=True - ) - ac_fin = fields.IntField( - help_text="Allele Count European (Finnish)", required=False, nullable=True - ) - ac_nfe = fields.IntField( - help_text="Allele Count European (Non-Finnish)", required=False, nullable=True - ) - ac_oth = fields.IntField( - help_text="Allele Count Other", required=False, nullable=True - ) - ac_male = fields.IntField( - help_text="Allele Count Male", required=False, nullable=True - ) - ac_female = fields.IntField( - help_text="Allele Count Female", required=False, nullable=True - ) - hom = fields.IntField( - help_text="Number of Homozygotes", required=False, nullable=True - ) - hemi = fields.IntField( - help_text="Number of Hemizygotes", required=False, nullable=True - ) - ac_hom = fields.FloatField( - help_text="Number of Homozygotes", required=False, nullable=True - ) - ac_hemi = fields.FloatField( - help_text="Number of Hemizygotes", required=False, nullable=True - ) - an_afr = fields.IntField( - help_text="Allele Number African", required=False, nullable=True - ) - an_amr = fields.IntField( - help_text="Allele Number American", required=False, nullable=True - ) - an_asj = fields.IntField( - help_text="Allele Number Ashkenazi Jewish", required=False, nullable=True - ) - an_eas = fields.IntField( - help_text="Allele Number East Asian", required=False, nullable=True - ) - an_fin = fields.IntField( - help_text="Allele Number European (Finnish)", required=False, nullable=True - ) - an_nfe = fields.IntField( - help_text="Allele Number European (Non-Finnish)", required=False, nullable=True - ) - an_oth = fields.IntField( - help_text="Allele Number Other", required=False, nullable=True - ) - an_male = fields.IntField( - help_text="Allele Number Male", required=False, nullable=True - ) - an_female = fields.IntField( - help_text="Allele Number Female", required=False, nullable=True - ) - hom_afr = fields.IntField( - help_text="Number of Homozygotes African", required=False, nullable=True - ) - hom_amr = fields.IntField( - help_text="Number of Homozygotes American", required=False, nullable=True - ) - hom_asj = fields.IntField( - help_text="Number of Homozygotes Ashkenazi Jewish", - required=False, - nullable=True, - ) - hom_eas = fields.IntField( - help_text="Number of Homozygotes East Asian", required=False, nullable=True - ) - hom_fin = fields.IntField( - help_text="Number of Homozygotes European (Finnish)", - required=False, - nullable=True, - ) - hom_nfe = fields.IntField( - help_text="Number of Homozygotes European (Non-Finnish)", - required=False, - nullable=True, - ) - hom_oth = fields.IntField( - help_text="Number of Homozygotes Other", required=False, nullable=True - ) - hom_male = fields.IntField( - help_text="Number of Homozygotes Male", required=False, nullable=True - ) - hom_female = fields.IntField( - help_text="Number of Homozygotes Female", required=False, nullable=True - ) - af_afr = fields.FloatField( - help_text="Allele Frequency African", required=False, nullable=True - ) - af_amr = fields.FloatField( - help_text="Allele Frequency American", required=False, nullable=True - ) - af_asj = fields.FloatField( - help_text="Allele Frequency Ashkenazi Jewish", required=False, nullable=True - ) - af_eas = fields.FloatField( - help_text="Allele Frequency East Asian", required=False, nullable=True - ) - af_fin = fields.FloatField( - help_text="Allele Frequency European (Finnish)", required=False, nullable=True - ) - af_nfe = fields.FloatField( - help_text="Allele Frequency European (Non-Finnish)", - required=False, - nullable=True, - ) - af_oth = fields.FloatField( - help_text="Allele Frequency Other", required=False, nullable=True - ) - af_male = fields.FloatField( - help_text="Allele Frequency Male", required=False, nullable=True - ) - af_female = fields.FloatField( - help_text="Allele Frequency Female", required=False, nullable=True - ) - main_data = fields.StringField( - help_text="Main data point", required=False, nullable=True - ) diff --git a/varsome_api/models/elements/gwas.py b/varsome_api/models/elements/gwas.py deleted file mode 100755 index 2af7f2c..0000000 --- a/varsome_api/models/elements/gwas.py +++ /dev/null @@ -1,62 +0,0 @@ -# Copyright 2018 Saphetor S.A. -# -# Licensed under the Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.apache.org/licenses/LICENSE-2.0 -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. - -from jsonmodels import models, fields - - -class GWASDetails(models.Base): - gwas_symbol = fields.StringField( - help_text="GWAS symbol", required=False, nullable=True - ) - date = fields.StringField(help_text="Date", required=False, nullable=True) - study = fields.StringField(help_text="Study", required=False, nullable=True) - disease_or_trait = fields.StringField( - help_text="Disease or trait", required=False, nullable=True - ) - mapped_traits = fields.ListField( - items_types=(str,), help_text="Mapped trait", required=False, nullable=True - ) - mapped_trait_urls = fields.ListField( - items_types=(str,), help_text="Mapped trait URL", required=False, nullable=True - ) - strongest_snp_risk_allele = fields.StringField( - help_text="Strongest SNP risk allele", required=False, nullable=True - ) - odds_ratio = fields.FloatField( - help_text="Odds ratio", required=False, nullable=True - ) - p_value = fields.StringField(help_text="p value", required=False, nullable=True) - confidence_range_95_low = fields.FloatField( - help_text="Confidence range 95% low", required=False, nullable=True - ) - confidence_range_95_high = fields.FloatField( - help_text="Confidence range 95% high", required=False, nullable=True - ) - confidence_comment = fields.StringField( - help_text="Confidence comment", required=False, nullable=True - ) - initial_sample_size = fields.StringField( - help_text="Initial sample size", required=False, nullable=True - ) - replication_sample_size = fields.StringField( - help_text="Replication sample size", required=False, nullable=True - ) - pub_med_references = fields.ListField( - items_types=(int,), help_text="PubMed References", required=False, nullable=True - ) - - -class GWAS(models.Base): - version = fields.StringField(help_text="Version") - items = fields.ListField(help_text="Details", items_types=(GWASDetails,)) diff --git a/varsome_api/models/elements/iarc.py b/varsome_api/models/elements/iarc.py deleted file mode 100755 index a849fd8..0000000 --- a/varsome_api/models/elements/iarc.py +++ /dev/null @@ -1,77 +0,0 @@ -# Copyright 2018 Saphetor S.A. -# -# Licensed under the Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.apache.org/licenses/LICENSE-2.0 -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. - - -from jsonmodels import models, fields - - -class TP53GermlineDetails(models.Base): - age_at_diagnosis = fields.IntField( - help_text="Age at diagnosis", required=False, nullable=True - ) - country = fields.StringField(help_text="Country", required=False, nullable=True) - effect = fields.StringField(help_text="Effect", required=False, nullable=True) - familycase = fields.StringField( - help_text="Family case", required=False, nullable=True - ) - familycase_group = fields.StringField( - help_text="Family case group", required=False, nullable=True - ) - family_code = fields.StringField( - help_text="Family code", required=False, nullable=True - ) - generation = fields.StringField( - help_text="Generation", required=False, nullable=True - ) - morphology = fields.StringField( - help_text="Morphology", required=False, nullable=True - ) - sex = fields.StringField(help_text="Sex", required=False, nullable=True) - topography = fields.StringField( - help_text="Topography", required=False, nullable=True - ) - unaffected = fields.IntField(help_text="Unaffected", required=False, nullable=True) - - -class TP53SomaticDetails(models.Base): - age = fields.IntField(help_text="Age", required=False, nullable=True) - country = fields.StringField(help_text="Country", required=False, nullable=True) - effect = fields.StringField(help_text="Effect", required=False, nullable=True) - morphology = fields.StringField( - help_text="Morphology", required=False, nullable=True - ) - mut_rate = fields.IntField(help_text="Mutation rate", required=False, nullable=True) - pub_med_references = fields.ListField( - items_types=(int,), help_text="PubMed References", required=False, nullable=True - ) - sample_source = fields.StringField( - help_text="Sample source", required=False, nullable=True - ) - stage = fields.StringField(help_text="Stage", required=False, nullable=True) - structural_motif = fields.StringField( - help_text="Structural Motif", required=False, nullable=True - ) - topography = fields.StringField( - help_text="Topography", required=False, nullable=True - ) - - -class TP53Germline(models.Base): - version = fields.StringField(help_text="Version") - items = fields.ListField(help_text="Details", items_types=(TP53GermlineDetails,)) - - -class TP53Somatic(models.Base): - version = fields.StringField(help_text="Version") - items = fields.ListField(help_text="Details", items_types=(TP53SomaticDetails,)) diff --git a/varsome_api/models/elements/icgc.py b/varsome_api/models/elements/icgc.py deleted file mode 100755 index c58ac02..0000000 --- a/varsome_api/models/elements/icgc.py +++ /dev/null @@ -1,40 +0,0 @@ -# Copyright 2018 Saphetor S.A. -# -# Licensed under the Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.apache.org/licenses/LICENSE-2.0 -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. - -from jsonmodels import models, fields - - -class Occurrence(models.Base): - affected = fields.IntField( - required=False, nullable=True, help_text="Affected number" - ) - donors = fields.IntField(required=False, nullable=True, help_text="Donors number") - project = fields.StringField(required=False, nullable=True, help_text="Project") - - -class Somatic(models.Base): - version = fields.StringField(help_text="Version") - id = fields.StringField(help_text="ID", required=False, nullable=True) - occurrence = fields.ListField( - required=False, nullable=True, items_types=(Occurrence,), help_text="Occurrence" - ) - affected_donors = fields.IntField( - help_text="Affected Donors", required=False, nullable=True - ) - project_count = fields.IntField( - help_text="Project Count", required=False, nullable=True - ) - main_data = fields.StringField( - help_text="Main data point", required=False, nullable=True - ) diff --git a/varsome_api/models/elements/isb.py b/varsome_api/models/elements/isb.py deleted file mode 100755 index a128fa3..0000000 --- a/varsome_api/models/elements/isb.py +++ /dev/null @@ -1,26 +0,0 @@ -# Copyright 2018 Saphetor S.A. -# -# Licensed under the Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.apache.org/licenses/LICENSE-2.0 -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. - -from jsonmodels import models, fields - - -class Kaviar3(models.Base): - version = fields.StringField(help_text="Version") - ac = fields.ListField( - items_types=(int,), help_text="ac", required=False, nullable=True - ) - an = fields.ListField( - items_types=(int,), help_text="an", required=False, nullable=True - ) - main_data = fields.StringField(help_text="Main data point", required=False) diff --git a/varsome_api/models/elements/ncbi.py b/varsome_api/models/elements/ncbi.py deleted file mode 100755 index 8382232..0000000 --- a/varsome_api/models/elements/ncbi.py +++ /dev/null @@ -1,59 +0,0 @@ -# Copyright 2018 Saphetor S.A. -# -# Licensed under the Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.apache.org/licenses/LICENSE-2.0 -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. - -from jsonmodels import models, fields - -from varsome_api.models.fields import DictField - - -class DbSNP(models.Base): - version = fields.StringField(help_text="Version") - rsid = fields.ListField(items_types=(int,), help_text="RS ID") - - -class ClinVar2(models.Base): - version = fields.StringField(help_text="Version") - review_status = fields.StringField( - help_text="Review status", required=False, nullable=True - ) - review_stars = fields.IntField( - help_text="Review stars", required=False, nullable=True - ) - variation_id = fields.IntField( - help_text="Variation ID", required=False, nullable=True - ) - num_submitters = fields.IntField( - help_text="Number of submitters", required=False, nullable=True - ) - pub_med_references = fields.ListField( - items_types=(int,), help_text="PubMed references", required=False, nullable=True - ) - clinical_significance = fields.ListField( - items_types=(str,), - help_text="Clinical significance", - required=False, - nullable=True, - ) - last_evaluation = fields.StringField( - help_text="Last evaluation", required=False, nullable=True - ) - origin = fields.ListField( - items_types=(str,), help_text="Origin", required=False, nullable=True - ) - accessions = fields.ListField( - items_types=(dict,), help_text="Accessions", required=False, nullable=True - ) - main_data = fields.StringField( - help_text="Main data point", required=False, nullable=True - ) diff --git a/varsome_api/models/elements/sanger.py b/varsome_api/models/elements/sanger.py deleted file mode 100755 index 75abad2..0000000 --- a/varsome_api/models/elements/sanger.py +++ /dev/null @@ -1,215 +0,0 @@ -# Copyright 2018 Saphetor S.A. -# -# Licensed under the Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.apache.org/licenses/LICENSE-2.0 -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. - -from jsonmodels import models, fields - - -class Cosmic(models.Base): - version = fields.StringField(help_text="Version") - primary_site = fields.ListField( - items_types=(str,), help_text="Primary site", required=False, nullable=True - ) - pub_med_references = fields.ListField( - items_types=(int,), help_text="PUBMED References", required=False, nullable=True - ) - - -class CosmicLicensedDrugEntry(models.Base): - drug_name = fields.StringField(help_text="Drug name", required=False, nullable=True) - somatic_status = fields.StringField( - help_text="Somatic status", required=False, nullable=True - ) - zygosity = fields.StringField(help_text="Zygosity", required=False, nullable=True) - gene = fields.StringField(help_text="Gene", required=False, nullable=True) - transcript = fields.StringField( - help_text="Transcript", required=False, nullable=True - ) - census_gene = fields.StringField( - help_text="Census gene", required=False, nullable=True - ) - pub_med_references = fields.ListField( - items_types=(int,), help_text="PUBMED References", required=False, nullable=True - ) - histology_freq = fields.ListField( - items_types=(float,), - help_text="Histology frequency", - required=False, - nullable=True, - ) - tissue_freq = fields.ListField( - items_types=(float,), - help_text="Tissue frequency", - required=False, - nullable=True, - ) - - -class CosmicLicensedDetails(models.Base): - entry_type = fields.StringField( - help_text="Entry type", required=False, nullable=True - ) - cosmic_id = fields.ListField( - items_types=( - str, - dict, - ), - help_text="Cosmic ID", - required=False, - nullable=True, - ) - pub_med_references = fields.ListField( - items_types=(int,), help_text="PUBMED References", required=False, nullable=True - ) - histology_freq = fields.ListField( - items_types=(int, str, float), - help_text="Histology frequency", - required=False, - nullable=True, - ) - genome_wide_screen_freq = fields.ListField( - items_types=(int, str, float), - help_text="Histology frequency", - required=False, - nullable=True, - ) - loh_freq = fields.ListField( - items_types=(int, str, float), - help_text="LOH frequency", - required=False, - nullable=True, - ) - age_freq = fields.ListField( - items_types=(int, str, float), - help_text="Age frequency", - required=False, - nullable=True, - ) - zygosity_freq = fields.ListField( - items_types=(int, str, float), - help_text="Zygosity frequency", - required=False, - nullable=True, - ) - tumour_origin_freq = fields.ListField( - items_types=( - int, - str, - float, - ), - help_text="Tumour original frequency", - required=False, - nullable=True, - ) - somatic_status_freq = fields.ListField( - items_types=(int, str, float), - help_text="Somatic status frequency", - required=False, - nullable=True, - ) - primary_site_freq = fields.ListField( - items_types=(int, str, float), - help_text="Primary site frequency", - required=False, - nullable=True, - ) - description = fields.ListField( - items_types=(str,), help_text="Description", required=False, nullable=True - ) - accession_number = fields.ListField( - items_types=(str,), help_text="Accession number", required=False, nullable=True - ) - fathmm_prediction = fields.StringField( - help_text="FATHMM prediction", required=False, nullable=True - ) - fathmm_score = fields.FloatField( - help_text="FATHMM score", required=False, nullable=True - ) - num_entries = fields.IntField( - help_text="Number of entries", required=False, nullable=True - ) - num_samples = fields.IntField( - help_text="Number of samples", required=False, nullable=True - ) - gene = fields.ListField( - items_types=(str,), help_text="Gene", required=False, nullable=True - ) - - fathmm_mkl_coding_score = fields.FloatField( - help_text="FATHMM_MKL coding score", required=False, nullable=True - ) - fathmm_mkl_coding_groups = fields.StringField( - help_text="FATHMM_MKL coding groups", required=False, nullable=True - ) - fathmm_mkl_non_coding_score = fields.FloatField( - help_text="FATHMM_MKL non coding score", required=False, nullable=True - ) - fathmm_mkl_non_coding_groups = fields.StringField( - help_text="FATHMM_MKL non coding groups", required=False, nullable=True - ) - whole_exome_freq = fields.ListField( - items_types=( - str, - int, - float, - ), - help_text="Whole exome frequency", - required=False, - nullable=True, - ) - whole_genome_reseq_freq = fields.ListField( - items_types=( - str, - int, - float, - ), - help_text="Whole genome reseq frequency", - required=False, - nullable=True, - ) - - resistance_mutation = fields.ListField( - items_types=(str,), - help_text="Resistance mutation", - required=False, - nullable=True, - ) - drug_entries = fields.ListField( - items_types=(CosmicLicensedDrugEntry,), - help_text="Drug entries", - required=False, - nullable=True, - ) - - -class ComsicPublicDetails(models.Base): - num_samples = fields.IntField(help_text="Number of samples") - id = fields.StringField(help_text="Cosmic ID") - is_consistent = fields.BoolField( - help_text="Cosmic ID is consistent across databases" - ) - - -class CosmicPublic(models.Base): - version = fields.StringField(help_text="Version") - items = fields.ListField( - items_types=(ComsicPublicDetails,), - help_text="Details", - required=False, - nullable=True, - ) - - -class CosmicLicensed(models.Base): - version = fields.StringField(help_text="Version") - items = fields.ListField(items_types=(CosmicLicensedDetails,), help_text="Details") diff --git a/varsome_api/models/elements/thousand_genomes.py b/varsome_api/models/elements/thousand_genomes.py deleted file mode 100755 index 30629cb..0000000 --- a/varsome_api/models/elements/thousand_genomes.py +++ /dev/null @@ -1,67 +0,0 @@ -# Copyright 2018 Saphetor S.A. -# -# Licensed under the Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.apache.org/licenses/LICENSE-2.0 -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. - -from jsonmodels import models, fields - - -class ThousandGenomes(models.Base): - version = fields.StringField(help_text="Version") - ac = fields.ListField( - items_types=(int,), help_text="Allele Count", required=False, nullable=True - ) - af = fields.ListField( - items_types=(float,), - help_text="Allele Frequency", - required=False, - nullable=True, - ) - an = fields.ListField( - items_types=(int,), help_text="Allele Number", required=False, nullable=True - ) - ns = fields.ListField( - items_types=(int,), help_text="Number of Samples", required=False, nullable=True - ) - afr_af = fields.ListField( - items_types=(float,), - help_text="Allele Frequency African", - required=False, - nullable=True, - ) - amr_af = fields.ListField( - items_types=(float,), - help_text="Allele Frequency American", - required=False, - nullable=True, - ) - eas_af = fields.ListField( - items_types=(float,), - help_text="Allele Frequency East Asian", - required=False, - nullable=True, - ) - eur_af = fields.ListField( - items_types=(float,), - help_text="Allele Frequency European", - required=False, - nullable=True, - ) - sas_af = fields.ListField( - items_types=(float,), - help_text="Allele Frequency South Asian", - required=False, - nullable=True, - ) - main_data = fields.StringField( - help_text="Main data point", required=False, nullable=True - ) diff --git a/varsome_api/models/elements/transcript.py b/varsome_api/models/elements/transcript.py deleted file mode 100755 index 1194703..0000000 --- a/varsome_api/models/elements/transcript.py +++ /dev/null @@ -1,49 +0,0 @@ -# Copyright 2018 Saphetor S.A. -# -# Licensed under the Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.apache.org/licenses/LICENSE-2.0 -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. - - -from jsonmodels import models, fields - - -class TranscriptItem(models.Base): - name = fields.StringField(help_text="Transcript") - coding_impact = fields.StringField( - help_text="Coding impact", required=False, nullable=True - ) - function = fields.ListField( - help_text="Function", items_types=(str,), required=False, nullable=True - ) - hgvs = fields.StringField( - required=False, help_text="HGVS cDNA level", nullable=True - ) - hgvs_p1 = fields.StringField(required=False, nullable=True) - hgvs_p3 = fields.StringField(required=False, nullable=True) - hgvs_notation = fields.StringField( - help_text="HGVS notation", required=False, nullable=True - ) - location = fields.StringField(help_text="Location", required=False, nullable=True) - coding_location = fields.StringField( - help_text="Coding location", required=False, nullable=True - ) - canonical = fields.BoolField(help_text="Canonical", required=False, nullable=True) - gene_symbol = fields.StringField( - help_text="Gene symbol", required=False, nullable=True - ) - - -class Transcript(models.Base): - items = fields.ListField( - help_text="Transcripts", items_types=(TranscriptItem,), required=False - ) - version = fields.StringField(help_text="Version") diff --git a/varsome_api/models/elements/uniprot.py b/varsome_api/models/elements/uniprot.py deleted file mode 100755 index 0447526..0000000 --- a/varsome_api/models/elements/uniprot.py +++ /dev/null @@ -1,50 +0,0 @@ -# Copyright 2018 Saphetor S.A. -# -# Licensed under the Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.apache.org/licenses/LICENSE-2.0 -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. - - -from jsonmodels import models, fields - - -class UniprotVariantsDetails(models.Base): - annotation_id = fields.StringField( - help_text="Annotation ID", required=False, nullable=True - ) - protein_id = fields.StringField( - help_text="Protein ID", required=False, nullable=True - ) - bed_comments = fields.ListField( - help_text="Comments", items_types=(str,), required=False, nullable=True - ) - gene = fields.StringField(help_text="Gene", required=False, nullable=True) - variant_type = fields.StringField( - help_text="Variant type", required=False, nullable=True - ) - transcripts = fields.ListField( - help_text="Transcripts", items_types=(str,), required=False, nullable=True - ) - pub_med_references = fields.ListField( - help_text="PubMed References", items_types=(int,), required=False, nullable=True - ) - disease = fields.StringField(help_text="Disease", required=False, nullable=True) - disease_symbol = fields.StringField( - help_text="Disease symbol", required=False, nullable=True - ) - disease_alt_symbol = fields.StringField( - help_text="Disease alt symbol", required=False, nullable=True - ) - - -class UniprotVariants(models.Base): - version = fields.StringField(help_text="Version") - items = fields.ListField(help_text="Details", items_types=(UniprotVariantsDetails,)) diff --git a/varsome_api/models/elements/wustl.py b/varsome_api/models/elements/wustl.py deleted file mode 100755 index 343c03b..0000000 --- a/varsome_api/models/elements/wustl.py +++ /dev/null @@ -1,74 +0,0 @@ -# Copyright 2018 Saphetor S.A. -# -# Licensed under the Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.apache.org/licenses/LICENSE-2.0 -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. - -from jsonmodels import models, fields - - -class CivicDetails(models.Base): - variant = fields.StringField(help_text="Variant", required=False, nullable=True) - variant_summary = fields.StringField( - help_text="Variant summary", required=False, nullable=True - ) - variant_civic_url = fields.StringField( - help_text="Variant CIViC URL", required=False, nullable=True - ) - variant_origin = fields.StringField( - help_text="Variant origin", required=False, nullable=True - ) - pub_med_references = fields.ListField( - items_types=(int,), help_text="PubMed References", required=False, nullable=True - ) - clinical_significance = fields.StringField( - help_text="Clinical significance", required=False, nullable=True - ) - evidence_level = fields.StringField( - help_text="Evidence level", required=False, nullable=True - ) - evidence_statement = fields.StringField( - help_text="Evidence statement", required=False, nullable=True - ) - evidence_type = fields.StringField( - help_text="Evidence type", required=False, nullable=True - ) - evidence_status = fields.StringField( - help_text="Evidence status", required=False, nullable=True - ) - evidence_direction = fields.StringField( - help_text="Evidence direction", required=False, nullable=True - ) - evidence_civic_url = fields.StringField( - help_text="Evidence CIViC URL", required=False, nullable=True - ) - drugs = fields.ListField( - items_types=(str,), help_text="Drugs", required=False, nullable=True - ) - transcripts = fields.ListField( - items_types=(str,), help_text="Transcripts", required=False, nullable=True - ) - representative_transcript = fields.StringField( - help_text="Representative transcript", required=False, nullable=True - ) - disease = fields.StringField(help_text="Disease", required=False, nullable=True) - rating = fields.StringField(help_text="Rating", required=False, nullable=True) - gene = fields.StringField(help_text="Gene", required=False, nullable=True) - gene_civic_url = fields.StringField( - help_text="Gene CIViC URL", required=False, nullable=True - ) - entrez_id = fields.StringField(help_text="Entrez ID", required=False, nullable=True) - doid = fields.StringField(help_text="DOID", required=False, nullable=True) - - -class Civic(models.Base): - version = fields.StringField(help_text="Version") - items = fields.ListField(help_text="Details", items_types=(CivicDetails,)) diff --git a/varsome_api/models/fields.py b/varsome_api/models/fields.py deleted file mode 100755 index 5680874..0000000 --- a/varsome_api/models/fields.py +++ /dev/null @@ -1,45 +0,0 @@ -# Copyright 2018 Saphetor S.A. -# -# Licensed under the Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.apache.org/licenses/LICENSE-2.0 -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. - -from jsonmodels import fields - - -class DictField(fields.BaseField): - - types = (dict,) - - -class NullableItemListField(fields.ListField): - """ - A list field that accepts None as item types - """ - - def validate_single_value(self, item): - if item is None: - return - super().validate_single_value(item) - - def parse_value(self, values): - """Cast value to proper collection.""" - result = self.get_default_value() - - if not values: - return result - - if not isinstance(values, list): - return values - - return [ - self._cast_value(value) if value is not None else None for value in values - ] diff --git a/varsome_api/models/slim/__init__.py b/varsome_api/models/slim/__init__.py new file mode 100644 index 0000000..53f149b --- /dev/null +++ b/varsome_api/models/slim/__init__.py @@ -0,0 +1,21 @@ +from varsome_api.models.slim.annotation import ( # noqa: F401 + AcmgAnnotation, + AcmgRules, + AcmgVerdict, + AnnotatedVariant, + DbsnpItem, + GnomadFrequency, + Transcript, + TranscriptItem, +) + +__all__ = [ + "AcmgAnnotation", + "AcmgRules", + "AcmgVerdict", + "AnnotatedVariant", + "DbsnpItem", + "GnomadFrequency", + "Transcript", + "TranscriptItem", +] diff --git a/varsome_api/models/slim/annotation.py b/varsome_api/models/slim/annotation.py new file mode 100644 index 0000000..ed11f8d --- /dev/null +++ b/varsome_api/models/slim/annotation.py @@ -0,0 +1,73 @@ +from pydantic import BaseModel, ConfigDict, Field + +from varsome_api.models.variant import AnnotatedVariantPropertiesMixin + + +class _SlimBase(BaseModel): + """Common base for all slim models. + + ``extra="ignore"`` silently drops any key that is not declared + as a field. + """ + + model_config = ConfigDict(extra="ignore") + + +class GnomadFrequency(_SlimBase): + """Allele frequency and allele number from gnomAD (exomes or genomes).""" + + af: float | None = None + an: int | None = None + + +class AcmgRules(_SlimBase): + """ACMG rules verdict (innermost level).""" + + verdict: str | None = None + + +class AcmgVerdict(_SlimBase): + """ACMG verdict containing the rules object and classification list.""" + + acmg_rules: AcmgRules | None = Field(None, alias="ACMG_rules") + classifications: list[str | None] | None = None + + +class AcmgAnnotation(_SlimBase): + """Top-level ACMG annotation — only the verdict sub-tree.""" + + verdict: AcmgVerdict | None = None + + +class TranscriptItem(_SlimBase): + """Single transcript item — only the gene symbol is retained.""" + + gene_symbol: str | None = None + + +class Transcript(_SlimBase): + """Transcript list wrapper (shared by RefSeq and Ensembl).""" + + items: list[TranscriptItem] | None = None + + +class DbsnpItem(_SlimBase): + """dbSNP entry — only the RS-ID list.""" + + rsid: list[int | None] | None = None + + +class AnnotatedVariant(_SlimBase, AnnotatedVariantPropertiesMixin): + """Lightweight variant model for VCF annotation pipelines.""" + + original_variant: str | None = None + chromosome: str | None = None + pos: int | None = None + ref: str | None = None + alt: str | None = None + gnomad_exomes: list[GnomadFrequency] | None = None + gnomad_genomes: list[GnomadFrequency] | None = None + acmg_annotation: AcmgAnnotation | None = None + refseq_transcripts: list[Transcript] | None = None + ensembl_transcripts: list[Transcript] | None = None + ncbi_dbsnp: list[DbsnpItem] | None = None diff --git a/varsome_api/models/variant.py b/varsome_api/models/variant.py index 8227e08..9e4c129 100755 --- a/varsome_api/models/variant.py +++ b/varsome_api/models/variant.py @@ -1,193 +1,133 @@ -# Copyright 2018 Saphetor S.A. -# -# Licensed under the Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.apache.org/licenses/LICENSE-2.0 -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -from .elements import * - - -class AnnotatedVariant(models.Base): - """ - Base variant result definition model - Most fields are defined as list fields, even though they contain a single list item - This is due to the fact that VarSome API can return both current and old versions of databases - """ +from varsome_api.models.annotation import VariantVariantApi - chromosome = fields.StringField(help_text="Chromosome") - alt = fields.StringField(help_text="ALT Sequence", required=False, nullable=True) - ref = fields.StringField(help_text="REF Sequence", required=False, nullable=True) - pos = fields.IntField(help_text="Position") - variant_id = fields.StringField(help_text="Variant Id") - refseq_transcripts = fields.ListField( - required=False, items_types=(Transcript,), help_text="RefSeq Transcripts" - ) - ensembl_transcripts = fields.ListField( - required=False, items_types=(Transcript,), help_text="Ensembl Transcripts" - ) - broad_exac = fields.ListField(required=False, items_types=(ExAC,), help_text="ExAC") - gnomad_exomes = fields.ListField( - required=False, items_types=(GnomAD,), help_text="gnomAD Exomes (ExAC)" - ) - gnomad_exomes_coverage = fields.ListField( - required=False, - items_types=(GnomADCoverage,), - help_text="gnomAD exomes coverage", - ) - gnomad_genomes = fields.ListField( - required=False, items_types=(GnomAD,), help_text="gnomAD Genomes" - ) - gnomad_genomes_coverage = fields.ListField( - required=False, - items_types=(GnomADCoverage,), - help_text="gnomAD genomes coverage", - ) - thousand_genomes = fields.ListField( - required=False, items_types=(ThousandGenomes,), help_text="1000 Genomes" - ) - gerp = fields.ListField(required=False, items_types=(Gerp,), help_text="GERP") - isb_kaviar3 = fields.ListField( - required=False, items_types=(Kaviar3,), help_text="ISB Kaviar3" - ) - dbnsfp = fields.ListField(required=False, items_types=(DbNSFP,), help_text="dbNSFP") - dann_snvs = fields.ListField( - required=False, items_types=(DannSNVs,), help_text="DANN score" - ) - dbnsfp_dbscsnv = fields.ListField( - required=False, items_types=(DBscSNV,), help_text="dbNSFP dbscSNV" - ) - ncbi_dbsnp = fields.ListField( - required=False, items_types=(DbSNP,), help_text="dbSNP" - ) - sanger_cosmic = fields.ListField( - required=False, items_types=(Cosmic,), help_text="Sanger Cosmic" - ) - sanger_cosmic_public = fields.ListField( - required=False, items_types=(CosmicPublic,), help_text="Cosmic" - ) - sanger_cosmic_licensed = fields.ListField( - required=False, items_types=(CosmicLicensed,), help_text="Cosmic" - ) - ncbi_clinvar2 = fields.ListField( - required=False, items_types=(ClinVar2,), help_text="ClinVar2" - ) - icgc_somatic = fields.ListField( - required=False, items_types=(Somatic,), help_text="ICGC Somatic" - ) - iarc_tp53_germline = fields.ListField( - required=False, items_types=(TP53Germline,), help_text="IARC TP53 Germline" - ) - iarc_tp53_somatic = fields.ListField( - required=False, items_types=(TP53Somatic,), help_text="IARC TP53 Somatic" - ) - pub_med_articles = DictField(required=False, help_text="PUBMED Articles") - uniprot_variants = fields.ListField( - required=False, items_types=(UniprotVariants,), help_text="UniProt variants" - ) - wustl_civic = fields.ListField( - required=False, items_types=(Civic,), help_text="CIViC" - ) - gwas = fields.ListField(required=False, items_types=(GWAS,), help_text="GWAS") - acmg_annotation = fields.EmbeddedField( - ACMG, required=False, nullable=True, help_text="ACMG Annotations" - ) - @property - def genes(self): - """ +class AnnotatedVariantPropertiesMixin: + """Mixin providing convenience properties for variant annotation results. - :return: list of genes - """ - genes = [] + Expects the consuming class to declare the following attributes + (all ``None``-able): + + - ``refseq_transcripts`` / ``ensembl_transcripts`` — iterables whose + items expose ``.items`` containing objects with a ``.gene_symbol``. + - ``ncbi_dbsnp`` — iterable whose items expose ``.rsid`` (list of ints). + - ``gnomad_exomes`` / ``gnomad_genomes`` — iterables whose items + expose ``.af`` and ``.an``. + - ``acmg_annotation`` — object with ``.verdict.acmg_rules.verdict`` + and ``.verdict.classifications``. + """ + + @property + def genes(self) -> list[str]: + """Return the deduplicated union of RefSeq and Ensembl gene symbols.""" + genes: list[str] = [] genes.extend(self.refseq_genes) genes.extend(self.ensembl_genes) return list(set(genes)) @property - def refseq_genes(self): - """ - - :return: list of genes found in RefSeq transcripts - """ - genes = [] - for transcript in self.refseq_transcripts: - genes.extend( - [item.gene_symbol for item in transcript.items if item.gene_symbol] - ) + def refseq_genes(self) -> list[str]: + """Return gene symbols extracted from RefSeq transcripts.""" + genes: list[str] = [] + if self.refseq_transcripts: + for transcript in self.refseq_transcripts: + if transcript.items: + genes.extend( + item.gene_symbol + for item in transcript.items + if item.gene_symbol + ) return genes @property - def ensembl_genes(self): - """ - - :return: list of genes found in Ensembl transcripts - """ - genes = [] - for transcript in self.ensembl_transcripts: - genes.extend( - [item.gene_symbol for item in transcript.items if item.gene_symbol] - ) + def ensembl_genes(self) -> list[str]: + """Return gene symbols extracted from Ensembl transcripts.""" + genes: list[str] = [] + if self.ensembl_transcripts: + for transcript in self.ensembl_transcripts: + if transcript.items: + genes.extend( + item.gene_symbol + for item in transcript.items + if item.gene_symbol + ) return genes @property - def rs_ids(self): - """ - - :return: list of rsids (str) - """ - rs_ids = [] - for dbnsp_entry in self.ncbi_dbsnp: - rs_ids.extend(dbnsp_entry.rsid) - return ["rs%s" % rs_id for rs_id in rs_ids] + def rs_ids(self) -> list[str]: + """Return dbSNP RS identifiers prefixed with ``rs``.""" + rs_ids: list[int] = [] + if self.ncbi_dbsnp: + for dbsnp_entry in self.ncbi_dbsnp: + rs_ids.extend(dbsnp_entry.rsid) + return [f"rs{rs_id}" for rs_id in rs_ids] @property - def gnomad_exomes_af(self): - """ - Returns the gnomad exomes af value. - :return: float gnomad exomes af - """ - af = [gnomad_exomes.af for gnomad_exomes in self.gnomad_exomes] - return af[0] if af else None + def gnomad_exomes_af(self) -> float | str | None: + """Return the gnomAD exomes allele frequency, or None if unavailable.""" + if self.gnomad_exomes: + af = [entry.af for entry in self.gnomad_exomes if entry.af is not None] + return af[0] if af else None + return None @property - def gnomad_genomes_af(self): - """ - Returns the gnomad genomes af value. - :return: float gnomad genomes af - """ - af = [gnomad_genomes.af for gnomad_genomes in self.gnomad_genomes] - return af[0] if af else None + def gnomad_genomes_af(self) -> float | str | None: + """Return the gnomAD genomes allele frequency, or None if unavailable.""" + if self.gnomad_genomes: + af = [entry.af for entry in self.gnomad_genomes if entry.af is not None] + return af[0] if af else None + return None @property - def gnomad_exomes_an(self): - """ - - :return: int gnomad exomes an - """ - an = [gnomad_exomes.an for gnomad_exomes in self.gnomad_exomes] - return an[0] if an else None + def gnomad_exomes_an(self) -> int | None: + """Return the gnomAD exomes allele number, or None if unavailable.""" + if self.gnomad_exomes: + an = [entry.an for entry in self.gnomad_exomes if entry.an is not None] + return an[0] if an else None + return None @property - def gnomad_genomes_an(self): - """ - :return: int gnomad genomes an - """ - an = [gnomad_genomes.an for gnomad_genomes in self.gnomad_genomes] - return an[0] if an else None + def gnomad_genomes_an(self) -> int | None: + """Return the gnomAD genomes allele number, or None if unavailable.""" + if self.gnomad_genomes: + an = [entry.an for entry in self.gnomad_genomes if entry.an is not None] + return an[0] if an else None + return None @property - def acmg_verdict(self): - """ - :return: the acmg verdict for the variant - """ - acmg_annotation = self.acmg_annotation - if acmg_annotation is not None and acmg_annotation.verdict is not None: - return acmg_annotation.verdict.ACMG_rules.verdict + def acmg_verdict(self) -> str | None: + """Return the ACMG classification verdict string, or None.""" + if ( + self.acmg_annotation is not None + and self.acmg_annotation.verdict is not None + and self.acmg_annotation.verdict.acmg_rules is not None + ): + return self.acmg_annotation.verdict.acmg_rules.verdict return None + + @property + def acmg_rules(self) -> list[str]: + """Return the list of ACMG classification rule names, or an empty list.""" + if ( + self.acmg_annotation is not None + and self.acmg_annotation.verdict is not None + ): + return self.acmg_annotation.verdict.classifications + return [] + + +class AnnotatedVariant(VariantVariantApi, AnnotatedVariantPropertiesMixin): + """Variant annotation result with convenience accessors. + + All fields from the OpenAPI ``variant_VariantApi`` schema are + available as typed attributes. The computed ``@property`` methods + (provided by :class:`AnnotatedVariantPropertiesMixin`) offer + shortcuts for the most commonly needed derived values. + + This model validates **every** field the API returns (via + ``extra="allow"`` on the base). For performance-sensitive + pipelines, consider :class:`~varsome_api.models.slim.annotation.AnnotatedVariant` + which validates only the fields needed by the default + ``VCFAnnotator.annotate_record``, or use your own Pydantic model + """ + + pass diff --git a/varsome_api/vcf.py b/varsome_api/vcf.py index b2fb1eb..55328ca 100755 --- a/varsome_api/vcf.py +++ b/varsome_api/vcf.py @@ -1,262 +1,445 @@ -# Copyright 2018 Saphetor S.A. -# -# Licensed under the Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.apache.org/licenses/LICENSE-2.0 -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -import contextlib +from __future__ import annotations + +import asyncio import os -import time -from collections import OrderedDict +from dataclasses import dataclass +from typing import Any, AsyncGenerator -import vcf -from vcf.parser import _Info, _encode_type +import aiohttp +from pydantic import BaseModel +from varsome_api._sync import sync_wrapper +from varsome_api.client import BatchResult as _BaseBatchResult from varsome_api.client import VarSomeAPIClient -from varsome_api.models.variant import AnnotatedVariant +from varsome_api.constants import DEFAULT_REF_GENOME, RefGenome +from varsome_api.exceptions import VarSomeAPIException +from varsome_api.models.slim.annotation import AnnotatedVariant as SlimAnnotatedVariant +from varsome_api.models.variant import AnnotatedVariantPropertiesMixin, AnnotatedVariant + +try: + import pysam + + _PYSAM_AVAILABLE = True +except ImportError: + pysam = None # type: ignore[assignment] + _PYSAM_AVAILABLE = False -@contextlib.contextmanager -def vcf_writer(*args, **kwargs): - writer = vcf.Writer(*args, **kwargs) - yield writer - writer.close() +def _require_pysam() -> None: + """Raise ImportError with installation instructions if pysam is not installed. + Raises: + ImportError: When pysam is not present in the current environment, + with instructions for installing the ``vcf`` extra. + """ + if not _PYSAM_AVAILABLE: + raise ImportError( + "pysam is required for VCF support but is not installed.\n" + "Install it with: pip install 'varsome_api[vcf]'\n\n" + "See the developer guide." + ) -@contextlib.contextmanager -def vcf_reader(*args, **kwargs): - reader = vcf.Reader(*args, **kwargs) - yield reader - reader._reader.close() +@dataclass(frozen=True, slots=True, kw_only=True) +class AnnotationResult: + """Summary statistics returned after a VCF annotation run. -class VCFAnnotator(VarSomeAPIClient): + Attributes: + total_variants: Number of variants successfully annotated and + written to the output VCF. + filtered_out_variants: Pairs of ``(variant_string, response_dict)`` + for variants filtered out by the API. Each response dict + contains at least a ``"filtered_out"`` key with a reason string. + variants_with_errors: Pairs of ``(variant_string, response_dict)`` + for variants that encountered annotation errors. Each response + dict contains at least an ``"error"`` key. """ - VCFAnnotator will take an input vcf file parse it and produce an annotated vcf file + + total_variants: int + filtered_out_variants: list[tuple[str, dict[str, Any]]] + variants_with_errors: list[tuple[str, dict[str, Any]]] + + +@dataclass(frozen=True, slots=True, kw_only=True) +class BatchResult(_BaseBatchResult): + """Extends :class:`~varsome_api.client.BatchResult` with VCF records. + + Attributes: + records: The ``pysam.VariantRecord`` objects corresponding to each + variant, aligned by index with *variants* and *response*. """ + records: list[pysam.VariantRecord] + + +class VCFAnnotator(VarSomeAPIClient): + """Annotate a VCF file using the VarSome API. + + Reads an input VCF, sends variants in batches to the API, and writes + an annotated VCF with the results. + + Three class-level extension points control the annotation pipeline: + + ``variant_model`` + The Pydantic model used to deserialise each API response dict. + Defaults to + :class:`~varsome_api.models.slim.annotation.AnnotatedVariant`, + which declares only the fields consumed by the default + ``annotate_record`` implementation. Swap in the full + :class:`~varsome_api.models.variant.AnnotatedVariant` if you + need access to the complete API response, or use your own + Pydantic model for a custom field selection. + + ``annotate_record`` + Called once per variant to write INFO fields into the + ``pysam.VariantRecord``. The base implementation writes a + default set of annotations. Override this to customize which + fields appear in the output VCF. + + ``add_vcf_header_info`` + Called once before annotation begins to register INFO header + lines. Must declare every INFO key that ``annotate_record`` + writes. + + .. note:: + + If you override ``annotate_record`` to read additional API + fields that are **not** present on the default slim + ``AnnotatedVariant``, you must also set ``variant_model`` + to a model that includes those fields — either the full + ``AnnotatedVariant`` or a custom slim model of your own. + """ + + variant_model: type[BaseModel] = SlimAnnotatedVariant + def __init__( self, - api_key=None, - logger=None, - api_url=None, - max_variants_per_batch=1000, - ref_genome="hg19", - get_parameters=None, - max_threads=None, + api_key: str | None = None, + api_url: str | None = None, + max_variants_per_batch: int = 100, + ref_genome: RefGenome = DEFAULT_REF_GENOME, + request_parameters: dict[str, Any] | None = None, + max_requests: int = 1, ): - super().__init__(api_key, logger, api_url, max_variants_per_batch) + """Initialise the VCF annotator. + + Args: + api_key: Optional API authentication token. + api_url: Optional custom API base URL. + max_variants_per_batch: Number of variants per batch request. + ref_genome: Reference genome, either ``"hg19"`` or ``"hg38"``. + request_parameters: Optional dict of additional API query + parameters (e.g. ``{"add-all-data": "1"}``). + max_requests: Maximum number of concurrent API requests. + """ + super().__init__(api_key, api_url, max_variants_per_batch) + _require_pysam() self.ref_genome = ref_genome - self.get_parameters = get_parameters - self.total_variants = 0 - self.filtered_out_variants = 0 - self.variants_with_errors = 0 - self.max_threads = max_threads or 1 - if self.max_variants_per_batch > 3000 and self.max_threads > 1: - self.logger.warning( - "Having more than 1 thread with more than 3000 variants per batch may not be optimal" - ) + self.request_parameters = request_parameters + self.max_requests = max_requests or 1 - def _process_request(self, input_batch, writer): - start = time.time() - input_batch_variants = list(input_batch.keys()) - api_results = self.batch_lookup( - input_batch_variants, - params=self.get_parameters, - ref_genome=self.ref_genome, - max_threads=self.max_threads, - ) - duration = time.time() - start - self.logger.info( - "Annotated %s variants from a source of %s in %s" - % (len(api_results), len(input_batch), duration) - ) - self.logger.info("Writing to output vcf file") + def _process_request( + self, + batch_result: BatchResult, + writer: pysam.VariantFile, + ) -> tuple[int, list[tuple[str, dict[str, Any]]], list[tuple[str, dict[str, Any]]]]: + """Process a batch result and write annotated records to the output VCF. - for i, results in enumerate(api_results): - try: - record = input_batch[input_batch_variants[i]] - if results: - if "filtered_out" in results: - self.logger.info( - "%s: %s" - % (input_batch_variants[i], results["filtered_out"]) - ) - self.filtered_out_variants += 1 - continue - if "error" in results: - self.logger.error( - "%s: %s" % (input_batch_variants[i], results["error"]) - ) - self.variants_with_errors += 1 - continue - if results.get("variant_id"): - variant_result = AnnotatedVariant(**results) - record = self.annotate_record( - record, variant_result, input_batch_variants[i] - ) - writer.write_record(record) - else: - self.logger.error("%s: %s" % (input_batch_variants[i], results)) - self.variants_with_errors += 1 - except Exception as e: - self.logger.error("Result set error %s, %s" % (e, results)) - self.variants_with_errors += 1 - pass # log an exception.. - - def annotate_record(self, record, variant_result, original_variant): - """ - Method to annotate a record. You should override this with your own implementation - to include variant result properties you want in your output vcf - :param record: vcf record object - :param variant_result: AnnotatedVariant object - :param original_variant: The variant as present in the request - :return: annotated record object + Iterates over each variant in *batch_result* by index, skips + filtered-out or errored responses, deserialises valid responses via + ``self.variant_model``, and delegates to ``annotate_record`` before + writing the record. + + Args: + batch_result: A ``BatchResult`` whose ``variants``, ``records``, + and ``response`` lists are aligned by index. + writer: An open ``pysam.VariantFile`` in write mode. + + Returns: + A 3-tuple ``(annotated_count, filtered_variants, errored_variants)`` + where *filtered_variants* and *errored_variants* are lists of + ``(variant_string, response_dict)`` tuples for this batch. """ - record.INFO["variant_id"] = variant_result.variant_id - record.INFO["gene"] = ",".join(variant_result.genes) - record.INFO["gnomad_exomes_AF"] = variant_result.gnomad_exomes_af - record.INFO["gnomad_genomes_AF"] = variant_result.gnomad_genomes_af - acmg_verdict = variant_result.acmg_verdict - if acmg_verdict is not None: - acmg_verdict = acmg_verdict.replace(" ", "_") - record.INFO["acmg_verdict"] = acmg_verdict - record.INFO["original_variant"] = original_variant - record.REF = variant_result.ref or "." - record.ALT = [variant_result.alt] - record.POS = variant_result.pos - record.ID = ";".join(variant_result.rs_ids) or "." - return record - - def add_vcf_header_info(self, vcf_template): + annotated_count = 0 + filtered_variants: list[tuple[str, dict[str, Any]]] = [] + errored_variants: list[tuple[str, dict[str, Any]]] = [] + for idx, variant in enumerate(batch_result.variants): + annotated_variant = batch_result.response[idx] + vcf_record = batch_result.records[idx] + if "filtered_out" in annotated_variant: + filtered_variants.append((variant, annotated_variant)) + continue + if "error" in annotated_variant: + errored_variants.append((variant, annotated_variant)) + continue + variant_result = self.variant_model(**annotated_variant) + self.annotate_record( + vcf_record, variant_result, variant_result.original_variant + ) + writer.write(vcf_record) + annotated_count += 1 + return annotated_count, filtered_variants, errored_variants + + def annotate_record( + self, + record: pysam.VariantRecord, + variant_result: AnnotatedVariant, + original_variant: str, + ) -> None: + """Annotate a VCF record with API result data. + + This base implementation adds a default set of annotations + (genes, gnomAD frequencies, ACMG verdict/rules). + Override this method to customize which fields appear in your + output VCF. + + Values that are ``None`` are omitted from the INFO field to avoid + writing invalid VCF entries. ``ref``, ``alts``, and ``pos`` are + only updated when the API returns non-None values. + + Args: + record: The ``pysam.VariantRecord`` to annotate in-place. + variant_result: A variant model instance (``SlimAnnotatedVariant`` + by default). + original_variant: The variant string as sent in the request. """ - Adds vcf INFO headers for the annotated values provided - This is just a base method you need to override in your own implementation - depending on the annotations added through the annotate_record method - :param vcf_template: vcf reader object - :return: + scalar_info: dict[str, Any] = { + "gnomad_exomes_AF": variant_result.gnomad_exomes_af, + "gnomad_genomes_AF": variant_result.gnomad_genomes_af, + "acmg_verdict": variant_result.acmg_verdict, + "acmg_rules": variant_result.acmg_rules, + "genes": variant_result.genes, + "original_variant": original_variant, + } + for key, value in scalar_info.items(): + if value is not None: + record.info[key] = value + record.pos = variant_result.pos + ref_allele = variant_result.ref or "." + alt_allele = variant_result.alt or "." + record.alleles = (ref_allele, alt_allele) if alt_allele else (ref_allele,) + record.id = ";".join(variant_result.rs_ids) if variant_result.rs_ids else None + + def add_vcf_header_info(self, header: pysam.VariantHeader) -> None: + """Add INFO header lines for the annotated fields. + + This base implementation adds headers for the default annotations + written by ``annotate_record``. Override this method to match your + custom ``annotate_record`` implementation. + + Args: + header: The ``pysam.VariantHeader`` to add INFO lines to. """ - vcf_template.infos["variant_id"] = _Info( - "variant_id", - 1, - "Integer", - "Saphetor variant identifier", - None, - None, - _encode_type("Integer"), - ) - vcf_template.infos["gene"] = _Info( - "gene", - ".", - "String", - "Genes related to this variant", - None, - None, - _encode_type("String"), - ) - vcf_template.infos["gnomad_exomes_AF"] = _Info( + header.info.add("genes", ".", "String", "Genes related to this variant") + header.info.add( "gnomad_exomes_AF", - 1, + "1", "Float", "GnomAD exomes allele frequency value", - None, - None, - _encode_type("Float"), ) - vcf_template.infos["gnomad_genomes_AF"] = _Info( + header.info.add( "gnomad_genomes_AF", - 1, + "1", "Float", "GnomAD genomes allele frequency value", - None, - None, - _encode_type("Float"), - ) - vcf_template.infos["acmg_verdict"] = _Info( - "acmg_verdict", - ".", - "String", - "ACMG Classification Verdict", - None, - None, - _encode_type("String"), ) - vcf_template.infos["original_variant"] = _Info( + header.info.add("acmg_verdict", "1", "String", "ACMG Classification Verdict") + header.info.add("acmg_rules", ".", "String", "ACMG Classifications") + header.info.add( "original_variant", - ".", + "1", "String", "Variant as present in the request", - None, - None, - _encode_type("String"), ) - def annotate(self, input_vcf_file, output_vcf_file=None, template=None, **kwargs): + @staticmethod + def _construct_variant_from_record( + record: pysam.VariantRecord, + ) -> list[tuple[str, pysam.VariantRecord]]: + """Construct variant strings from a VCF record. + + For multi-allelic records, returns one ``(variant_string, record)`` + pair per supported ALT allele. + + Args: + record: A ``pysam.VariantRecord`` object. + + Returns: + A list of ``(variant_string, record)`` tuples for every + supported ALT allele, or an empty list when none are present. """ - :param input_vcf_file: The input vcf file to be annotated - :param output_vcf_file: The file to write annotations back if none input_vcf_file.annotated.vcf will be - generated instead - :param template: An alternate vcf file to use for vcf file headers. If none the input vcf file will - be used - :return: + alleles = record.alleles + if alleles is None or len(alleles) < 2: + return [] + + ref = alleles[0] if alleles[0] not in (None, ".") else "" + + results: list[tuple[str, pysam.VariantRecord]] = [] + for alt in alleles[1:]: + alt_value = alt if alt not in (None, ".") else "" + results.append( + ( + f"{record.contig}:{record.pos}:{ref}:{alt_value}", + record.copy(), + ) + ) + return results + + @staticmethod + def _read_header_from_vcf( + input_vcf_file: str, + ) -> pysam.VariantHeader: + """Read only the header from a VCF file without loading records. + + Args: + input_vcf_file: Path to the input VCF file. + + Returns: + A copy of the VCF header. """ - annotations_start = time.time() - if not os.path.isfile(input_vcf_file): - raise FileNotFoundError("%s does not exist" % input_vcf_file) + with pysam.VariantFile(input_vcf_file, "r") as reader: + return reader.header.copy() + + async def _read_variants_from_vcf( + self, + input_vcf_file: str, + vcf_header: pysam.VariantHeader, + ) -> AsyncGenerator[tuple[str, pysam.VariantRecord], Any]: + with pysam.VariantFile(input_vcf_file, "r") as reader: + for record in reader: + record.translate(vcf_header) + for variant_str, rec in self._construct_variant_from_record(record): + yield variant_str, rec + + async def _batch_producer( + self, + variants: AsyncGenerator[tuple[str, pysam.VariantRecord], Any], + queue: asyncio.Queue, + ) -> None: + batch = [] + async for variant_str, record in variants: + batch.append((variant_str, record)) + if len(batch) >= self.max_variants_per_batch: + await queue.put(batch) + batch = [] + if batch: + await queue.put(batch) + await queue.put(None) + + async def _batch_worker( + self, + session: aiohttp.ClientSession, + request_queue: asyncio.Queue, + result_queue: asyncio.Queue, + url, + params, + ) -> None: + """Consume batches of variants from the request + queue and send them to the API.""" + while True: + batch = await request_queue.get() + if batch is None: + request_queue.task_done() + break + variant_reprs, records = zip(*batch) + try: + response = await self._make_request( + session, + path=url, + method="POST", + params=params, + json={"variants": variant_reprs}, + headers={"Content-Type": "application/json"}, + ) + await result_queue.put( + BatchResult( + variants=variant_reprs, records=records, response=response + ) + ) + except VarSomeAPIException as e: + await result_queue.put(e) + finally: + request_queue.task_done() + + async def _annotate_variants_and_write_to_vcf( + self, + input_vcf_file: str, + vcf_header: pysam.VariantHeader, + output_vcf_file: str | None = None, + ) -> tuple[int, list[tuple[str, dict[str, Any]]], list[tuple[str, dict[str, Any]]]]: + """Read all variants, annotate them via the API, and write a VCF. + + Args: + input_vcf_file: Path to the input VCF file. + vcf_header: The VCF header to use for the output file. + output_vcf_file: Optional explicit output file path. When + *None*, defaults to ``{input_vcf_file}.annotated.vcf``. + + Returns: + A 3-tuple ``(total_annotated, filtered_variants, errored_variants)`` + where *filtered_variants* and *errored_variants* are accumulated + lists of ``(variant_string, response_dict)`` tuples across all + batches. + """ + self.add_vcf_header_info(vcf_header) if output_vcf_file is None: - output_vcf_file = "%s.annotated.vcf" % input_vcf_file - if template is None: - template = input_vcf_file - with vcf_reader( - filename=input_vcf_file, - strict_whitespace=kwargs.get("strict_whitespace", True), - ) as reader: - with vcf_reader( - filename=template, - strict_whitespace=kwargs.get("strict_whitespace", True), - ) as vcf_template: - self.add_vcf_header_info(vcf_template) - with vcf_writer(open(output_vcf_file, "w"), vcf_template) as writer: - input_batch = OrderedDict() - batch_limit = self.max_variants_per_batch * self.max_threads * 2 - for record in reader: - reference_sequence = record.REF - if reference_sequence is None or reference_sequence == ".": - reference_sequence = "" - for alt_seq in record.ALT: - if alt_seq is None or alt_seq == ".": - alt_seq = "" - requested_variant = "%s:%s:%s:%s" % ( - record.CHROM, - record.POS, - reference_sequence, - alt_seq, - ) - input_batch[requested_variant] = record - self.total_variants += 1 - if len(input_batch) < batch_limit: - continue - self._process_request(input_batch, writer) - # reset input batch - input_batch = OrderedDict() - # we may have some variants remaining if input batch is less than batch size - if len(input_batch) > 0: - self._process_request(input_batch, writer) - self.logger.info( - "Annotating %s variants in %s. " - "Filtered out %s. " - "Errors %s" - % ( - self.total_variants, - time.time() - annotations_start, - self.filtered_out_variants, - self.variants_with_errors, + output_vcf_file = f"{input_vcf_file}.annotated.vcf" + + total_annotated = 0 + all_filtered: list[tuple[str, dict[str, Any]]] = [] + all_errors: list[tuple[str, dict[str, Any]]] = [] + + with pysam.VariantFile(output_vcf_file, "w", header=vcf_header) as writer: + async for batch_result in self.abatch_lookup( + self._read_variants_from_vcf(input_vcf_file, vcf_header), + params=self.request_parameters, + ref_genome=self.ref_genome, + max_requests=self.max_requests, + ): + annotated, filtered, errors = self._process_request( + batch_result, + writer, + ) + total_annotated += annotated + all_filtered.extend(filtered) + all_errors.extend(errors) + + return total_annotated, all_filtered, all_errors + + async def aannotate( + self, + input_vcf_file: str, + output_vcf_file: str | None = None, + ) -> AnnotationResult: + """Asynchronously annotate a VCF file and write the results. + + Variants are streamed from the input VCF and sent to the API in + concurrent batches. + + Args: + input_vcf_file: Path to the input VCF file. + output_vcf_file: Path to the output VCF file. Defaults to + ``{input_vcf_file}.annotated.vcf``. + + Returns: + An ``AnnotationResult`` with counts of annotated, filtered-out, + and errored variants. + + Raises: + FileNotFoundError: If *input_vcf_file* does not exist. + """ + if not os.path.isfile(input_vcf_file): + raise FileNotFoundError(f"{input_vcf_file} does not exist") + header = self._read_header_from_vcf(input_vcf_file) + total_annotated, filtered_variants, errored_variants = ( + await self._annotate_variants_and_write_to_vcf( + input_vcf_file, header, output_vcf_file ) ) + return AnnotationResult( + total_variants=total_annotated, + filtered_out_variants=filtered_variants, + variants_with_errors=errored_variants, + ) + + annotate = sync_wrapper(aannotate) diff --git a/version.py b/version.py deleted file mode 100644 index e362c38..0000000 --- a/version.py +++ /dev/null @@ -1,3 +0,0 @@ -# Copyright (c) 2022. Saphetor S.A. All rights reserved. -# Confidential -__version__ = "0.0.1" \ No newline at end of file From 6b1b6a1c982a216e2e391436bd69018a2309638c Mon Sep 17 00:00:00 2001 From: Christos Kopanos Date: Sun, 29 Mar 2026 12:53:09 +0300 Subject: [PATCH 2/6] =?UTF-8?q?bump:=20version=200.0.3=20=E2=86=92=201.0.0?= =?UTF-8?q?b0?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .cz.toml | 3 ++- .github/workflows/python-tests.yml | 32 +++++++++++++++++++----------- CHANGELOG.md | 17 ++++++++++++++++ pyproject.toml | 2 +- varsome_api/__init__.py | 2 +- 5 files changed, 41 insertions(+), 15 deletions(-) diff --git a/.cz.toml b/.cz.toml index c513397..67ce01a 100644 --- a/.cz.toml +++ b/.cz.toml @@ -1,9 +1,10 @@ [tool.commitizen] name = "cz_github_jira_conventional" tag_format = "v$major.$minor.$patch$prerelease" -version = "0.0.3" +version = "1.0.0b0" version_files = [ "varsome_api/__init__.py:__version__", + "pyproject.toml:version", ] jira_base_url = "https://saphetor.atlassian.net" github_repo = "saphetor/varsome-api-client-python" diff --git a/.github/workflows/python-tests.yml b/.github/workflows/python-tests.yml index a8a320e..80c2c65 100644 --- a/.github/workflows/python-tests.yml +++ b/.github/workflows/python-tests.yml @@ -2,9 +2,9 @@ name: Python Tests on: push: - branches: [ main ] + branches: [ master ] pull_request: - branches: [ main ] + branches: [ master ] jobs: test: @@ -40,26 +40,34 @@ jobs: libssl-dev \ libdeflate-dev - - name: Load cached dependencies + - name: Install Poetry + uses: snok/install-poetry@v1 + with: + version: latest + virtualenvs-in-project: true + + - name: Load cached venv uses: actions/cache@v4 - id: cache-dependencies + id: cache-venv with: - path: ~/.cache/pip - key: pip-${{ runner.os }}-${{ matrix.python-version }}-${{ hashFiles('**/requirements.txt') }}-${{ hashFiles('**/requirements-dev.txt') }} + path: .venv + key: venv-${{ runner.os }}-${{ matrix.python-version }}-${{ hashFiles('**/poetry.lock') }} - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install -r requirements.txt - pip install -r requirements-dev.txt + run: poetry install --with dev - name: Run tests run: | - pytest -v --junitxml=pytest-report.xml + if [ "${{ matrix.python-version }}" = "3.13" ]; then + poetry run pytest -v --junitxml=pytest-report.xml --no-cov + else + poetry run pytest -v --junitxml=pytest-report.xml + fi - name: Publish Test Results + # Using EnricoMi/publish-unit-test-result-action@v2 uses: EnricoMi/publish-unit-test-result-action@v2 if: always() with: files: pytest-report.xml - check_name: "Python Test Results" + check_name: "Python Test Results (${{ matrix.python-version }})" diff --git a/CHANGELOG.md b/CHANGELOG.md index 8b13789..10a2a76 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1 +1,18 @@ +## v1.0.0b0 (2026-03-29) + +### BREAKING CHANGE + +- models/elements/* consolidated into models/annotation.py; +CLI moved from scripts/ to varsome_api/cli/ package; client and VCF +interfaces rewritten. [28370](https://github.com//saphetor/varsome-api-client-python/commit/28370e05c911398a3328c976e48d497610f11457) + +### Refactor + +- **[DEV-1896](https://saphetor.atlassian.net/browse/DEV-1896)**: complete rewrite of varsome-api-client-python v1 [28370](https://github.com//saphetor/varsome-api-client-python/commit/28370e05c911398a3328c976e48d497610f11457) + +## v0.0.2 (2024-03-26) + +### Feat + +- **[SP-4818](https://saphetor.atlassian.net/browse/SP-4818)**: #comment varsome api client updated to use commitizen [bba69](https://github.com//saphetor/varsome-api-client-python/commit/bba69f8fb1457954fecb3b17b8a2aa5ad22cb0d8) diff --git a/pyproject.toml b/pyproject.toml index 4e79c8a..be7dda6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "varsome_api" -version = "0.0.3" +version = "1.0.0b0" description = "A basic python api client implementation for https://api.varsome.com" authors = ["Saphetor S.A. "] readme = "README.md" diff --git a/varsome_api/__init__.py b/varsome_api/__init__.py index 27fdca4..c9bd737 100755 --- a/varsome_api/__init__.py +++ b/varsome_api/__init__.py @@ -1 +1 @@ -__version__ = "0.0.3" +__version__ = "1.0.0b0" From 0f60016fc3f479c5c016387c763baa0d5220f28f Mon Sep 17 00:00:00 2001 From: Christos Kopanos Date: Tue, 7 Apr 2026 15:20:47 +0300 Subject: [PATCH 3/6] refactor(DEV-1896): Update VarSomeAPIClient to support multiple query types Refactor the VarSomeAPIClient to handle queries for variants, genes, and CNVs. Additionally, the CLI tool and developer guide have been updated to reflect these changes --- README.md | 40 ++++- docs/developer-guide.md | 159 ++++++++++++++++--- examples/parquet/annotate_to_parquet.py | 2 +- tests/test_cli.py | 37 +++-- tests/test_client.py | 36 ++--- tests/test_vcf.py | 14 +- varsome_api/cli/utils.py | 24 +-- varsome_api/cli/varsome_api_run.py | 162 ++++++++++++------- varsome_api/client.py | 199 +++++++++++++++++------- varsome_api/constants.py | 4 + varsome_api/vcf.py | 17 +- 11 files changed, 498 insertions(+), 196 deletions(-) diff --git a/README.md b/README.md index d32a201..9227d90 100644 --- a/README.md +++ b/README.md @@ -18,12 +18,12 @@ If you need compatibility with Python 3.10 or earlier, use the previous release: ## What this library provides -- **`varsome_api_run`** — look up one or more variants and receive the full JSON - annotation response. +- **`varsome_api_run`** — look up one or more variants, genes, or CNVs and receive + the full JSON annotation response. - **`varsome_api_annotate_vcf`** — read a VCF file, annotate every variant via the VarSome API, and write an annotated output VCF. -- **`VarSomeAPIClient`** — a Python class for integrating variant annotation - directly into your own code (synchronous and async interfaces). +- **`VarSomeAPIClient`** — a Python class for integrating variant, gene, and CNV + annotation directly into your own code (synchronous and async interfaces). - **`VCFAnnotator`** — a customisable VCF annotation pipeline class for use in your own Python projects. @@ -140,6 +140,27 @@ varsome_api_run -g hg19 -k YOUR_API_KEY \ varsome_api_run -g hg19 -k YOUR_API_KEY -i variants.txt -o annotations.json -p add-all-data=1 ``` +### Look up gene information + +```bash +varsome_api_run -y genes -g hg19 -k YOUR_API_KEY -q BRCA1 TP53 +``` + +```bash +varsome_api_run -y genes -g hg19 -k YOUR_API_KEY -i genes.txt -o gene_annotations.json +``` + +### Look up CNV information + +```bash +varsome_api_run -y cnvs -g hg19 -k YOUR_API_KEY -q 'chr1:122:5235:DEL' 'chr1:100:L1254:DUP' +``` + +```bash +varsome_api_run -y cnvs -g hg19 -k YOUR_API_KEY -i cnvs.txt -o cnv_annotations.json +``` + + Output defaults to stdout. Use `-o` to write to a file. The output is always written in [JSON Lines](https://jsonlines.org) format — one JSON object per line — regardless of whether you write to a file or stdout. @@ -161,12 +182,21 @@ varsome_api_annotate_vcf -g hg19 -k YOUR_API_KEY -i input.vcf -o annotated.vcf - |------|-------------|---------| | `-k` | API key (required) | — | | `-g` | Reference genome: `hg19` or `hg38` | `hg19` | +| `-y` | Query type: `variants`, `genes`, or `cnvs` | `variants` | | `-p` | Request parameters as `key=value` pairs | `add-ACMG-annotation=1` | | `-u` | API server URL | `https://api.varsome.com` | | `-t` | Max concurrent requests (1–20) | `5` | -| `-m` | Max variants per batch request (1–200) | `100` | +| `-m` | Max items per batch request | `100` | | `-v` / `--verbose` | Enable debug-level logging | off | +> **Batch limits:** The `-m` parameter specifies the maximum number of items +> (variants or genes) per batch request. The API enforces per-environment limits: +> - **Live / Stable**: Variants: 200, Genes: 100 +> - **Staging**: Variants: 50, Genes: 10 +> +> If you exceed the environment's limit, the API will return an error. Adjust `-m` +> accordingly. CNV queries do not support batching and are always sent individually. + Run any tool with `--help` for the full option reference. --- diff --git a/docs/developer-guide.md b/docs/developer-guide.md index 25ecab3..2fda923 100644 --- a/docs/developer-guide.md +++ b/docs/developer-guide.md @@ -125,11 +125,18 @@ Requires **Python ≥ 3.11, < 3.15**. ## VarSomeAPIClient -### Single variant lookup (synchronous) +### Single lookup (synchronous) `lookup` is a synchronous convenience wrapper around the underlying async method. It returns a plain `dict` containing the full API JSON response. +The `query_type` parameter controls what type of lookup is performed: +- `"variants"` (default): variant lookup +- `"genes"`: gene symbol lookup +- `"cnvs"`: CNV query lookup + +#### Variant lookup + ```python from varsome_api.client import VarSomeAPIClient @@ -146,7 +153,42 @@ print(result["chromosome"]) print(result["gnomad_exomes"]) ``` -`api_key` is optional for single-variant lookups against public data. It is +#### Gene lookup + +```python +from varsome_api.client import VarSomeAPIClient + +api = VarSomeAPIClient(api_key="YOUR_API_KEY") + +result = api.lookup( + "BRCA1", + query_type="genes", + ref_genome="hg19", +) + +print(result) +``` + +#### CNV lookup + +```python +from varsome_api.client import VarSomeAPIClient + +api = VarSomeAPIClient(api_key="YOUR_API_KEY") + +result = api.lookup( + "chr1:122:5235:DEL", + query_type="cnvs", + ref_genome="hg19", +) + +print(result) +``` + +> **Note:** CNV queries do not support batch mode. Each CNV must be looked up +> individually via `lookup(..., query_type="cnvs")`. + +`api_key` is optional for single-item lookups against public data. It is required for batch lookups. To target a specific API server, pass `api_url`: @@ -160,9 +202,16 @@ api = VarSomeAPIClient( ### Batch lookup (synchronous) -`batch_lookup` sends variants in batches and returns a `list[BatchResult]`. -Each `BatchResult` pairs the submitted variant strings with the corresponding -API response list, aligned by index. +`batch_lookup` sends items (variants, genes, etc.) in batches and returns a +`list[BatchResult]`. Each `BatchResult` pairs the submitted query strings with +the corresponding API response list, aligned by index. + +The `query_type` parameter controls what type of batch lookup is performed: +- `"variants"` (default): variant batch lookup +- `"genes"`: gene symbol batch lookup +- `"cnvs"`: not supported for batch (CNVs must be queried individually) + +#### Batch variant lookup ```python from varsome_api.client import VarSomeAPIClient @@ -178,17 +227,46 @@ batch_results = api.batch_lookup( ) for batch in batch_results: - for i, variant_str in enumerate(batch.variants): + for i, query_string in enumerate(batch.queries): annotation = batch.response[i] if "error" in annotation: - print(f"{variant_str}: error — {annotation['error']}") + print(f"{query_string}: error — {annotation['error']}") elif "filtered_out" in annotation: - print(f"{variant_str}: filtered out — {annotation['filtered_out']}") + print(f"{query_string}: filtered out — {annotation['filtered_out']}") + else: + print(f"{query_string}: gnomad_exomes = {annotation.get('gnomad_exomes')}") +``` + +#### Batch gene lookup + +```python +from varsome_api.client import VarSomeAPIClient + +api = VarSomeAPIClient(api_key="YOUR_API_KEY") + +genes = ["BRCA1", "TP53", "EGFR"] + +batch_results = api.batch_lookup( + genes, + query_type="genes", + params={"add-source-databases": "cgd"}, + ref_genome="hg19", +) + +for batch in batch_results: + for i, gene_symbol in enumerate(batch.queries): + annotation = batch.response[i] + if "error" in annotation: + print(f"{gene_symbol}: error — {annotation['error']}") else: - print(f"{variant_str}: gnomad_exomes = {annotation.get('gnomad_exomes')}") + print(f"{gene_symbol}: {annotation}") ``` -`max_variants_per_batch` (default `200`) controls how many variants are sent per +> **Batch limits:** The API enforces different limits per environment: +> - **Live / Stable**: Variants: 200, Genes: 100 +> - **Staging**: Variants: 50, Genes: 10 + +`max_variants_per_batch` (default `200`) controls how many items are sent per POST request. `max_requests` (default `5`) controls the maximum number of concurrent HTTP requests: @@ -217,10 +295,11 @@ except VarSomeAPIException as e: ## Async interface -The client is async-native. The synchronous `lookup` / `batch_lookup` methods are -thin wrappers. Use the async interface directly for better performance in async code. +The client is async-native. The synchronous `lookup` / `batch_lookup` methods +are thin wrappers. Use the async interface directly for better performance in +async code. -### Single lookup +### Single item lookup ```python import asyncio @@ -228,6 +307,7 @@ from varsome_api.client import VarSomeAPIClient async def main(): async with VarSomeAPIClient(api_key="YOUR_API_KEY") as api: + # Variant lookup result = await api.alookup( "chr7-140453136-A-T", params={"add-source-databases": "gnomad-exomes"}, @@ -235,6 +315,22 @@ async def main(): ) print(result["chromosome"]) + # Gene lookup + result = await api.alookup( + "BRCA1", + query_type="genes", + ref_genome="hg19", + ) + print(result) + + # CNV lookup + result = await api.alookup( + "chr1:100:L1254:DUP", + query_type="cnvs", + ref_genome="hg19", + ) + print(result) + asyncio.run(main()) ``` @@ -245,7 +341,10 @@ call creates and closes its own session automatically. ### Batch lookup (async generator) `abatch_lookup` is an async generator that yields `BatchResult` objects as each -batch completes: +batch completes. The `query_type` parameter controls whether variants, genes, or +other query types are batch-processed. + +#### Batch variant lookup ```python import asyncio @@ -261,9 +360,33 @@ async def main(): ref_genome="hg19", max_requests=5, ): - for i, variant_str in enumerate(batch.variants): + for i, query_string in enumerate(batch.queries): annotation = batch.response[i] - print(variant_str, annotation.get("gnomad_exomes")) + print(query_string, annotation.get("gnomad_exomes")) + +asyncio.run(main()) +``` + +#### Batch gene lookup + +```python +import asyncio +from varsome_api.client import VarSomeAPIClient + +async def main(): + genes = ["BRCA1", "TP53", "EGFR"] + + async with VarSomeAPIClient(api_key="YOUR_API_KEY") as api: + async for batch in api.abatch_lookup( + genes, + query_type="genes", + ref_genome="hg19", + max_requests=5, + ): + for i, gene_symbol in enumerate(batch.queries): + annotation = batch.response[i] + print(gene_symbol, annotation) + asyncio.run(main()) ``` @@ -384,7 +507,7 @@ from varsome_api.vcf import VCFAnnotator annotator = VCFAnnotator( api_key="YOUR_API_KEY", ref_genome="hg19", - request_parameters={"add-all-data": "1"}, + request_parameters={"add-ACMG-annotation": "1"}, ) annotator.annotate("input.vcf", "annotated.vcf") ``` @@ -592,7 +715,7 @@ from varsome_api.models.slim.annotation import AnnotatedVariant api = VarSomeAPIClient(api_key="YOUR_API_KEY") for batch in api.batch_lookup(my_variants, params={...}, ref_genome="hg19"): - for i, variant_str in enumerate(batch.variants): + for i, query_string in enumerate(batch.queries): raw = batch.response[i] if "error" not in raw and "filtered_out" not in raw: variant = AnnotatedVariant(**raw) diff --git a/examples/parquet/annotate_to_parquet.py b/examples/parquet/annotate_to_parquet.py index 3bc5674..d0ebf51 100644 --- a/examples/parquet/annotate_to_parquet.py +++ b/examples/parquet/annotate_to_parquet.py @@ -96,7 +96,7 @@ def annotate_and_write( ) for batch in batch_results: - for i, variant_str in enumerate(batch.variants): + for i, variant_str in enumerate(batch.queries): raw: dict = batch.response[i] if "error" in raw: diff --git a/tests/test_cli.py b/tests/test_cli.py index 745a0ac..6cfb179 100644 --- a/tests/test_cli.py +++ b/tests/test_cli.py @@ -19,7 +19,7 @@ validate_args as validate_annotate_args, ) from varsome_api.cli.varsome_api_run import ( - _iter_variants_from_file, + _iter_queries_from_file, build_parser, lookup_from_file, lookup_query, @@ -219,13 +219,13 @@ async def _async_gen_from_list(items: list[Any]) -> Any: class TestIterVariantsFromFile: - """Verify ``_iter_variants_from_file`` streams lines correctly.""" + """Verify ``_iter_queries_from_file`` streams lines correctly.""" async def test_yields_all_non_empty_lines(self, tmp_path: Any) -> None: f = tmp_path / "variants.txt" f.write_text("v1\nv2\nv3\n") - result = [v async for v in _iter_variants_from_file(str(f))] + result = [v async for v in _iter_queries_from_file(str(f))] assert result == ["v1", "v2", "v3"] @@ -233,7 +233,7 @@ async def test_skips_blank_lines(self, tmp_path: Any) -> None: f = tmp_path / "variants.txt" f.write_text("v1\n\nv2\n\n\nv3\n") - result = [v async for v in _iter_variants_from_file(str(f))] + result = [v async for v in _iter_queries_from_file(str(f))] assert result == ["v1", "v2", "v3"] @@ -241,7 +241,7 @@ async def test_strips_leading_and_trailing_whitespace(self, tmp_path: Any) -> No f = tmp_path / "variants.txt" f.write_text(" v1 \n\tv2\t\n v3\n") - result = [v async for v in _iter_variants_from_file(str(f))] + result = [v async for v in _iter_queries_from_file(str(f))] assert result == ["v1", "v2", "v3"] @@ -249,7 +249,7 @@ async def test_yields_nothing_for_blank_only_file(self, tmp_path: Any) -> None: f = tmp_path / "blank.txt" f.write_text("\n\n \n") - result = [v async for v in _iter_variants_from_file(str(f))] + result = [v async for v in _iter_queries_from_file(str(f))] assert not result @@ -257,7 +257,7 @@ async def test_yields_nothing_for_empty_file(self, tmp_path: Any) -> None: f = tmp_path / "empty.txt" f.write_text("") - result = [v async for v in _iter_variants_from_file(str(f))] + result = [v async for v in _iter_queries_from_file(str(f))] assert not result @@ -266,7 +266,7 @@ async def test_preserves_file_order(self, tmp_path: Any) -> None: f = tmp_path / "ordered.txt" f.write_text("\n".join(variants) + "\n") - result = [v async for v in _iter_variants_from_file(str(f))] + result = [v async for v in _iter_queries_from_file(str(f))] assert result == variants @@ -280,7 +280,7 @@ async def test_single_query_calls_alookup(self) -> None: return_value=_async_gen_from_list( [ BatchResult( - variants=["chr1:100:A:T"], + queries=["chr1:100:A:T"], response=[{"variant_id": "123"}], ) ] @@ -290,6 +290,7 @@ async def test_single_query_calls_alookup(self) -> None: result = lookup_query( api, ["chr1:100:A:T"], + query_type="variants", request_parameters=None, ref_genome="hg19", max_requests=5, @@ -298,7 +299,11 @@ async def test_single_query_calls_alookup(self) -> None: result_list = [item async for item in result] api.abatch_lookup.assert_called_once_with( - ["chr1:100:A:T"], params=None, ref_genome="hg19", max_requests=5 + ["chr1:100:A:T"], + params=None, + ref_genome="hg19", + max_requests=5, + query_type="variants", ) assert result_list == [{"variant_id": "123"}] @@ -308,7 +313,7 @@ async def test_batch_query_calls_abatch_lookup(self) -> None: return_value=_async_gen_from_list( [ BatchResult( - variants=["v1", "v2"], + queries=["v1", "v2"], response=[{"id": "1"}, {"id": "2"}], ) ] @@ -318,6 +323,7 @@ async def test_batch_query_calls_abatch_lookup(self) -> None: result = lookup_query( api, ["v1", "v2"], + query_type="variants", request_parameters=None, ref_genome="hg38", max_requests=5, @@ -325,7 +331,11 @@ async def test_batch_query_calls_abatch_lookup(self) -> None: result_list = [item async for item in result] api.abatch_lookup.assert_called_once_with( - ["v1", "v2"], params=None, ref_genome="hg38", max_requests=5 + ["v1", "v2"], + params=None, + ref_genome="hg38", + max_requests=5, + query_type="variants", ) assert result_list == [{"id": "1"}, {"id": "2"}] @@ -341,7 +351,7 @@ async def test_batch_lookup(self, tmp_path: Any) -> None: return_value=_async_gen_from_list( [ BatchResult( - variants=["v1", "v2"], + queries=["v1", "v2"], response=[{"id": "1"}, {"id": "2"}], ) ] @@ -351,6 +361,7 @@ async def test_batch_lookup(self, tmp_path: Any) -> None: result = lookup_from_file( api, str(f), + query_type="variants", request_parameters=None, ref_genome="hg19", max_requests=5, diff --git a/tests/test_client.py b/tests/test_client.py index 745535f..e694e1e 100644 --- a/tests/test_client.py +++ b/tests/test_client.py @@ -38,25 +38,25 @@ def _build_mock_session(status: int, json_data: Any) -> MagicMock: class TestBatchResult: """Verify the ``BatchResult`` dataclass behaviour.""" - def test_stores_variants_and_response(self) -> None: - variants = ["chr1:100:A:T", "chr2:200:G:C"] + def test_stores_queries_and_response(self) -> None: + queries = ["chr1:100:A:T", "chr2:200:G:C"] response = [{"chromosome": "chr1"}, {"chromosome": "chr2"}] - result = BatchResult(variants=variants, response=response) - assert result.variants == variants + result = BatchResult(queries=queries, response=response) + assert result.queries == queries assert result.response == response def test_correlates_errors_with_input(self) -> None: - """When the API returns an error without the original variant, + """When the API returns an error without the original query, callers can still identify the batch that caused it.""" - variants = ["chr1:100:A:T", "chr7:BAD:X:Y"] + queries = ["chr1:100:A:T", "chr7:BAD:X:Y"] response = [ {"chromosome": "chr1", "original_variant": "chr1:100:A:T"}, {"error": "Invalid variant format"}, ] - result = BatchResult(variants=variants, response=response) + result = BatchResult(queries=queries, response=response) errors = [r for r in result.response if "error" in r] assert len(errors) == 1 - assert result.variants == variants + assert result.queries == queries class TestVarSomeAPIClientBaseInit: @@ -381,11 +381,11 @@ async def test_successful_batch_put_on_result_queue( await request_queue.put(None) with patch.object(type(client), "_make_request", side_effect=fake): await client._batch_worker( - session, request_queue, result_queue, "/lookup/batch/hg19", None + session, request_queue, result_queue, "/lookup/batch/hg19", None, "variants" ) result = result_queue.get_nowait() assert isinstance(result, BatchResult) - assert result.variants == ["v1", "v2"] + assert result.queries == ["v1", "v2"] async def test_failed_batch_puts_exception_on_result_queue(self) -> None: """On ``VarSomeAPIException``, the exception must be enqueued, not re-raised.""" @@ -402,7 +402,7 @@ async def failing_request(_session: Any, **kwargs: Any) -> Any: await request_queue.put(None) with patch.object(type(client), "_make_request", side_effect=failing_request): await client._batch_worker( - session, request_queue, result_queue, "/lookup/batch/hg19", None + session, request_queue, result_queue, "/lookup/batch/hg19", None, "variants" ) queued = result_queue.get_nowait() assert isinstance(queued, VarSomeAPIException) @@ -433,14 +433,14 @@ async def test_yields_batch_results(self, make_fake_request: Callable) -> None: assert len(results) == 3 for result in results: assert isinstance(result, BatchResult) - assert len(result.variants) <= 2 - all_variants = [v for r in results for v in r.variants] - assert sorted(all_variants) == sorted(variants) + assert len(result.queries) <= 2 + all_queries = [v for r in results for v in r.queries] + assert sorted(all_queries) == sorted(variants) async def test_batch_response_paired_with_input( self, make_fake_request: Callable ) -> None: - """Each ``BatchResult.response`` must correspond to its ``.variants``.""" + """Each ``BatchResult.response`` must correspond to its ``.queries``.""" variants = ["chr1:100:A:T", "chr2:200:G:C"] fake = make_fake_request(lambda batch: [{"original_variant": v} for v in batch]) client = VarSomeAPIClient(api_key="test", max_variants_per_batch=10) @@ -450,7 +450,7 @@ async def test_batch_response_paired_with_input( r async for r in client.abatch_lookup(variants, ref_genome="hg19") ] assert len(results) == 1 - assert results[0].variants == variants + assert results[0].queries == variants assert results[0].response == [ {"original_variant": "chr1:100:A:T"}, {"original_variant": "chr2:200:G:C"}, @@ -470,7 +470,7 @@ async def async_variants() -> AsyncGenerator[str, None]: r async for r in client.abatch_lookup(async_variants(), ref_genome="hg19") ] - all_variants = [v for r in results for v in r.variants] + all_variants = [v for r in results for v in r.queries] assert sorted(all_variants) == ["v1", "v2", "v3"] async def test_propagates_batch_exception(self) -> None: @@ -496,5 +496,5 @@ def test_batch_lookup_sync_collects_all_results( results = client.batch_lookup(variants, ref_genome="hg19") assert len(results) == 1 assert isinstance(results[0], BatchResult) - assert results[0].variants == variants + assert results[0].queries == variants assert results[0].response == [{"id": "v1"}, {"id": "v2"}] diff --git a/tests/test_vcf.py b/tests/test_vcf.py index b19a6b7..e2f4cd2 100644 --- a/tests/test_vcf.py +++ b/tests/test_vcf.py @@ -173,7 +173,7 @@ def test_counts_annotated_variants(self) -> None: mock_record.info = {} batch_result = VcfBatchResult( - variants=["1:100:A:T"], + queries=["1:100:A:T"], records=[mock_record], response=[ { @@ -197,7 +197,7 @@ def test_tracks_filtered_variants(self) -> None: mock_writer = MagicMock() batch_result = VcfBatchResult( - variants=["1:100:A:T"], + queries=["1:100:A:T"], records=[MagicMock(spec=pysam.VariantRecord)], response=[{"filtered_out": "Frequency less than 0.01"}], ) @@ -213,7 +213,7 @@ def test_tracks_errored_variants(self) -> None: mock_writer = MagicMock() batch_result = VcfBatchResult( - variants=["1:100:A:T"], + queries=["1:100:A:T"], records=[MagicMock(spec=pysam.VariantRecord)], response=[{"error": "Invalid variant"}], ) @@ -233,7 +233,7 @@ def test_mixed_results(self) -> None: mock_record.info = {} batch_result = VcfBatchResult( - variants=["1:100:A:T", "1:200:G:C", "1:300:A:G"], + queries=["1:100:A:T", "1:200:G:C", "1:300:A:G"], records=[ mock_record, MagicMock(spec=pysam.VariantRecord), @@ -314,7 +314,7 @@ async def test_returns_annotated_count(self, tmp_path: Path) -> None: output = str(tmp_path / "output.vcf") header = VCFAnnotator._read_header_from_vcf(VARIANTS_VCF) - mock_batch_result = VcfBatchResult(variants=[], records=[], response=[]) + mock_batch_result = VcfBatchResult(queries=[], records=[], response=[]) with patch.object( annotator, @@ -407,7 +407,7 @@ async def test_returns_annotation_result(self, tmp_path: Path) -> None: ) output = str(tmp_path / "annotated.vcf") - mock_batch_result = VcfBatchResult(variants=[], records=[], response=[]) + mock_batch_result = VcfBatchResult(queries=[], records=[], response=[]) with patch.object( annotator, @@ -520,7 +520,7 @@ def add_vcf_header_info(self, header): mock_record.info = {} batch_result = VcfBatchResult( - variants=["1:100:A:T"], + queries=["1:100:A:T"], records=[mock_record], response=[ { diff --git a/varsome_api/cli/utils.py b/varsome_api/cli/utils.py index 4fb440d..012b247 100644 --- a/varsome_api/cli/utils.py +++ b/varsome_api/cli/utils.py @@ -1,5 +1,3 @@ -"""Shared CLI utility helpers used across VarSome API command-line tools.""" - import argparse import json import logging @@ -12,7 +10,6 @@ from varsome_api.log import logger MAX_CONCURRENT_REQUESTS = 20 -MAX_VARIANTS_PER_BATCH = 200 DEFAULT_REQUESTS = 5 DEFAULT_VARIANTS_PER_BATCH = 100 VARSOME_API_URL_CHOICES = [ @@ -33,7 +30,7 @@ def build_base_parser(description: str) -> argparse.ArgumentParser: * ``-p`` — request parameters (``key=value`` pairs) * ``-u`` — custom API host URL * ``-t`` — max concurrent API requests (default ``5``) - * ``-m`` — max variants per batch request (default ``100``) + * ``-m`` — max items per batch request (default ``100``) * ``-v`` / ``--verbose`` — enable debug logging Callers should extend the returned parser with command-specific arguments @@ -96,11 +93,11 @@ def build_base_parser(description: str) -> argparse.ArgumentParser: ) parser.add_argument( "-m", - help="Maximum number of variants to send per batch request", + help="Maximum number of items to send per batch request", type=int, default=DEFAULT_VARIANTS_PER_BATCH, required=False, - metavar="Max variants per batch", + metavar="Max items per batch", ) parser.add_argument( "-v", @@ -139,12 +136,11 @@ def validate_file_args( def validate_batch_args(args: argparse.Namespace) -> None: - """Validate and clamp the ``-t`` and ``-m`` batch arguments in-place. + """Validate and clamp the ``-t`` batch argument in-place. Ensures ``-t`` (max concurrent requests) is between 1 and - :data:`MAX_CONCURRENT_REQUESTS` and ``-m`` (max variants per batch) - does not exceed :data:`MAX_VARIANTS_PER_BATCH`. Values outside the - allowed range are clamped with a logged warning. + :data:`MAX_CONCURRENT_REQUESTS`. Values outside the allowed range + are clamped with a logged warning. Args: args: Parsed CLI arguments (modified in-place). @@ -160,14 +156,6 @@ def validate_batch_args(args: argparse.Namespace) -> None: MAX_CONCURRENT_REQUESTS, ) args.t = MAX_CONCURRENT_REQUESTS - if args.m > MAX_VARIANTS_PER_BATCH: - logger.warning( - "Maximum number of variants per request is capped at %d. " - "Setting it to %d.", - MAX_VARIANTS_PER_BATCH, - MAX_VARIANTS_PER_BATCH, - ) - args.m = MAX_VARIANTS_PER_BATCH def configure_logging(*, verbose: bool = False) -> None: diff --git a/varsome_api/cli/varsome_api_run.py b/varsome_api/cli/varsome_api_run.py index 639f16d..b37e002 100755 --- a/varsome_api/cli/varsome_api_run.py +++ b/varsome_api/cli/varsome_api_run.py @@ -1,5 +1,5 @@ #!/usr/bin/env python3 -"""CLI tool for performing single or batch variant lookups via the VarSome API.""" +"""CLI tool for performing single or batch lookups (variants, genes, or CNVs) via the VarSome API.""" import argparse import asyncio @@ -17,7 +17,13 @@ validate_file_args, ) from varsome_api.client import VarSomeAPIClient -from varsome_api.constants import DEFAULT_REF_GENOME, RefGenome +from varsome_api.constants import ( + DEFAULT_QUERY_TYPE, + DEFAULT_REF_GENOME, + QueryType, + RefGenome, + QUERY_TYPES, +) from varsome_api.log import logger @@ -25,7 +31,8 @@ def build_parser() -> argparse.ArgumentParser: """Build and return the argument parser for ``varsome_api_run``. Extends the shared base parser with lookup-specific arguments: - ``-q`` (query), ``-i`` (input file), and ``-o`` (output file). + ``-q`` (query), ``-i`` (input file), ``-o`` (output file), and + ``-y`` (query type). Returns: Configured ``ArgumentParser`` ready for ``parse_args()``. @@ -34,9 +41,10 @@ def build_parser() -> argparse.ArgumentParser: parser.add_argument( "-q", help=( - "Query to lookup in the API e.g. " - "chr19:20082943:1:G or in case of batch request " - "e.g. chr15-73027478-T-C rs113488022. " + "Query to lookup in the API. Format depends on query type (-y): " + "variants: chr19:20082943:1:G or chr15-73027478-T-C; " + "genes: BRCA1 or TP53; cnvs: chr1:122:5235:DEL. " + "For batch requests, use multiple values. " "Don't use it together with the -i option" ), type=str, @@ -47,21 +55,34 @@ def build_parser() -> argparse.ArgumentParser: parser.add_argument( "-i", help=( - "Path to text file with variants. " - "It should include one variant per line. Don't use it " - "together with the -q option" + "Path to text file with queries (one per line). " + "Format depends on query type (-y): variants, genes, or CNV queries. " + "Don't use it together with the -q option" ), type=str, - metavar="Text/CSV File one line per variant", + metavar="Text/CSV File one line per query", required=False, ) parser.add_argument( "-o", - help="Path to output file to store variant annotations", + help="Path to output file to store results", type=str, metavar="Output File with json entries", required=False, ) + parser.add_argument( + "-y", + help=( + "Query type: 'variants', 'genes', or 'cnvs'. " + "Note: CNV queries do not support batch mode, each CNV is looked up individually. " + "Check documentation for batch limits per environment" + ), + type=str, + choices=QUERY_TYPES, + metavar="Query Type", + required=False, + default=DEFAULT_QUERY_TYPE, + ) return parser @@ -88,8 +109,9 @@ def validate_args(args: argparse.Namespace) -> None: async def _stream_batch_results( api: VarSomeAPIClient, - variants: list[str] | AsyncIterable[str], + queries: list[str] | AsyncIterable[str], *, + query_type: QueryType, request_parameters: dict[str, str] | None, ref_genome: RefGenome = DEFAULT_REF_GENOME, max_requests: int = 5, @@ -101,7 +123,8 @@ async def _stream_batch_results( Args: api: An initialised VarSome API client. - variants: Variant query strings to look up. + queries: Query strings (variants, genes, or CNV queries). + query_type: Type of query: 'variants', 'genes', or 'cnvs'. request_parameters: Optional additional API query parameters. ref_genome: Reference genome identifier (``"hg19"`` or ``"hg38"``). max_requests: Maximum number of concurrent API requests. @@ -109,53 +132,86 @@ async def _stream_batch_results( Yields: Individual annotation result dicts as they arrive. """ - async for batch_result in api.abatch_lookup( - variants, - params=request_parameters, - ref_genome=ref_genome, - max_requests=max_requests, - ): - for idx, response_item in enumerate(batch_result.response): - variant_string = batch_result.variants[idx] - if "filtered_out" in response_item: - logger.warning( - "Variant filtered out: %s — %s", - variant_string, - response_item.get("filtered_out"), - ) - elif "error" in response_item: - logger.error( - "Error for variant %s: %s", - variant_string, - response_item.get("error"), + if query_type == "cnvs": + # CNVs don't support batch mode, process each one individually + async for query in _ensure_async_iterable(queries): + try: + yield await api.alookup( + query, + params=request_parameters, + ref_genome=ref_genome, + query_type="cnvs", ) - yield response_item + except Exception as e: + logger.error("Error for CNV %s: %s", query, str(e)) + else: + # Variants and genes use batch mode + async for batch_result in api.abatch_lookup( + queries, + params=request_parameters, + ref_genome=ref_genome, + max_requests=max_requests, + query_type=query_type, + ): + item_type = "Gene" if query_type == "genes" else "Variant" + for idx, response_item in enumerate(batch_result.response): + query_string = batch_result.queries[idx] + if "filtered_out" in response_item: + logger.warning( + "%s filtered out: %s — %s", + item_type, + query_string, + response_item.get("filtered_out"), + ) + elif "error" in response_item: + logger.error( + "Error for %s %s: %s", + item_type.lower(), + query_string, + response_item.get("error"), + ) + yield response_item + + +async def _ensure_async_iterable( + queries: list[str] | AsyncIterable[str], +) -> AsyncGenerator[str, None]: + """Ensure that queries are yielded as an async iterable.""" + if isinstance(queries, list): + for query in queries: + yield query + else: + async for query in queries: + yield query def lookup_query( api: VarSomeAPIClient, query: list[str], *, + query_type: QueryType, request_parameters: dict[str, str] | None, ref_genome: RefGenome = DEFAULT_REF_GENOME, max_requests: int = 5, ) -> AsyncGenerator[dict[str, Any], None]: - """Perform a single or batch variant lookup from CLI query arguments. + """Perform a single or batch lookup from CLI query arguments. Args: api: An initialised VarSome API client. - query: One or more variant query strings. + query: One or more query strings. + query_type: Type of query: 'variants', 'genes', or 'cnvs'. request_parameters: Optional additional API query parameters. ref_genome: Reference genome identifier (``"hg19"`` or ``"hg38"``). max_requests: Maximum number of concurrent API requests. Returns: - An async generator that yields annotation result dicts. + An async generator that yields result dicts. """ return _stream_batch_results( api, query, + query_type=query_type, request_parameters=request_parameters, ref_genome=ref_genome, max_requests=max_requests, @@ -166,36 +222,32 @@ async def lookup_from_file( api: VarSomeAPIClient, input_file: str, *, + query_type: QueryType, request_parameters: dict[str, str] | None, ref_genome: RefGenome = DEFAULT_REF_GENOME, max_requests: int = 5, ) -> AsyncGenerator[dict[str, Any], None]: - """Stream results for variants read from a text file. + """Stream results for queries read from a text file. - Variants are streamed from the file line by line to avoid loading the + Queries are streamed from the file line by line to avoid loading the entire file into memory. Results are yielded as they arrive from the API. Args: api: An initialised VarSome API client. - input_file: Path to a text file with one variant per line. + input_file: Path to a text file with one query per line. + query_type: Type of query: 'variants', 'genes', or 'cnvs'. request_parameters: Optional additional API query parameters. ref_genome: Reference genome identifier. max_requests: Maximum number of concurrent API requests. Yields: - Annotation result dicts as they arrive from the API. - - Raises: - SystemExit: When the file contains no variants. + Result dicts as they arrive from the API. """ - with open(input_file) as _f: - if not any(line.strip() for line in _f): - sys.stderr.write(f"No variants found in file {input_file}\n") - sys.exit(1) async for result in _stream_batch_results( api, - _iter_variants_from_file(input_file), + _iter_queries_from_file(input_file), + query_type=query_type, request_parameters=request_parameters, ref_genome=ref_genome, max_requests=max_requests, @@ -203,14 +255,14 @@ async def lookup_from_file( yield result -async def _iter_variants_from_file(input_file: str) -> AsyncGenerator[str, None]: - """Yield non-empty variant strings from a text file one line at a time. +async def _iter_queries_from_file(input_file: str) -> AsyncGenerator[str, None]: + """Yield non-empty query strings from a text file one line at a time. Args: - input_file: Path to a text file with one variant per line. + input_file: Path to a text file with one query per line. Yields: - Stripped, non-empty variant strings in file order. + Stripped, non-empty query strings in file order. """ with open(input_file) as f: for line in f: @@ -221,7 +273,7 @@ async def _iter_variants_from_file(input_file: str) -> AsyncGenerator[str, None] async def run() -> None: """Async entry point that drives the full CLI workflow. - Parses command-line arguments, performs variant lookups via the VarSome API, + Parses command-line arguments, performs lookups via the VarSome API, and streams JSON results to stdout or an output file. """ parser = build_parser() @@ -240,6 +292,7 @@ async def run() -> None: lookup_query( api, args.q, + query_type=args.y, request_parameters=request_parameters, ref_genome=args.g, max_requests=args.t, @@ -248,6 +301,7 @@ async def run() -> None: else lookup_from_file( api, args.i, + query_type=args.y, request_parameters=request_parameters, ref_genome=args.g, max_requests=args.t, @@ -256,7 +310,7 @@ async def run() -> None: await stream_json_output(result_stream, args.o) elapsed = time.monotonic() - start - logger.info("Variant annotation completed in %.2f seconds", elapsed) + logger.info("Lookup completed in %.2f seconds", elapsed) except Exception as e: sys.stderr.write(f"{e}\n") sys.exit(1) diff --git a/varsome_api/client.py b/varsome_api/client.py index 056f59c..3be7176 100755 --- a/varsome_api/client.py +++ b/varsome_api/client.py @@ -10,7 +10,12 @@ from varsome_api import __version__ from varsome_api._sync import run_sync, sync_wrapper -from varsome_api.constants import DEFAULT_REF_GENOME, RefGenome +from varsome_api.constants import ( + DEFAULT_QUERY_TYPE, + DEFAULT_REF_GENOME, + QueryType, + RefGenome, +) from varsome_api.exceptions import VarSomeAPIException from varsome_api.log import logger @@ -25,19 +30,20 @@ @dataclass(frozen=True, slots=True, kw_only=True) class BatchResult: - """Pairs an input variant batch with the corresponding API response. + """Pairs a batch of queries with the corresponding API response. - Allows callers to correlate which variants were sent in a particular - batch request with the response returned by the API. This is - especially useful when the response contains errors that omit the - original variant identifier. + Allows callers to correlate which queries (variants, genes, CNVs, etc.) + were sent in a particular batch request with the response returned by + the API. This is especially useful when the response contains errors + that omit the original query identifier. Attributes: - variants: The variant strings sent in this batch request. + queries: The query strings sent in this batch request (variants, + genes, CNVs, or other query types). response: The parsed JSON response from the API for this batch. """ - variants: list[str] + queries: list[str] response: list[dict[str, Any]] @@ -251,11 +257,30 @@ async def post( class VarSomeAPIClient(VarSomeAPIClientBase): - """High-level client for single and batch variant lookups via the VarSome API.""" + """High-level client for single and batch lookups (variants, genes, or CNVs) via the VarSome API. - lookup_path = "/lookup/%s" - ref_genome_lookup_path = lookup_path + "/%s" - batch_lookup_path = "/lookup/batch/%s" + Supports querying variants, genes, and CNVs with a unified interface. + The query_type parameter controls endpoint selection and request/response handling. + """ + + # API endpoint paths + _ENDPOINTS = { + "variants": { + "single": "/lookup/%s/%s", # query, ref_genome + "batch": "/lookup/batch/%s", # ref_genome + "batch_key": "variants", + }, + "genes": { + "single": "/lookup/gene/%s/%s", # gene_symbol, ref_genome + "batch": "/lookup/genes/batch/%s", # ref_genome + "batch_key": "genes", + }, + "cnvs": { + "single": "/lookup/cnv/%s/%s", # query, ref_genome + "batch": None, # CNVs don't support batch + "batch_key": None, + }, + } def __init__( self, @@ -263,54 +288,96 @@ def __init__( api_url: str | None = None, max_variants_per_batch: int = 200, ) -> None: - """Initialise the variant lookup client. + """Initialise the lookup client. Args: api_key: Optional API authentication token. api_url: Optional custom API base URL. - max_variants_per_batch: Maximum number of variants sent in a + max_variants_per_batch: Maximum number of items sent in a single batch POST request. Must be a positive integer. """ super().__init__(api_key, api_url) self.max_variants_per_batch = max_variants_per_batch + @staticmethod + def _get_single_url( + query_type: QueryType, query: str, ref_genome: RefGenome + ) -> str: + """Build the single-item lookup URL for the given query type. + + Args: + query_type: Type of query: 'variants', 'genes', or 'cnvs'. + query: The query string (variant, gene symbol, or CNV query). + ref_genome: Reference genome identifier. + + Returns: + The formatted URL path. + """ + return VarSomeAPIClient._ENDPOINTS[query_type]["single"] % (query, ref_genome) + + @staticmethod + def _get_batch_url(query_type: QueryType, ref_genome: RefGenome) -> str | None: + """Build the batch lookup URL for the given query type. + + Args: + query_type: Type of query: 'variants', 'genes', or 'cnvs'. + ref_genome: Reference genome identifier. + + Returns: + The formatted URL path, or None if batch is not supported. + """ + batch_path = VarSomeAPIClient._ENDPOINTS[query_type]["batch"] + return batch_path % ref_genome if batch_path else None + + @staticmethod + def _get_batch_key(query_type: QueryType) -> str | None: + """Get the JSON key name for batch request payloads. + + Args: + query_type: Type of query: 'variants', 'genes', or 'cnvs'. + + Returns: + The key name (e.g., 'variants' or 'genes'), or None if batch is not supported. + """ + return VarSomeAPIClient._ENDPOINTS[query_type]["batch_key"] + async def alookup( self, query: str, params: dict[str, Any] | None = None, ref_genome: RefGenome = DEFAULT_REF_GENOME, + query_type: QueryType = DEFAULT_QUERY_TYPE, ) -> dict[str, Any]: - """Look up annotations for a single variant asynchronously. + """Look up annotations for a single item (variant, gene, or CNV) asynchronously. Args: - query: Variant representation (e.g. ``"chr19:20082943:1:G"``). - params: Optional HTTP GET parameters. Refer to - https://api.varsome.com/docs/variants/ for available parameters. + query: The query string (variant representation, gene symbol, or CNV query). + params: Optional HTTP GET parameters. ref_genome: Reference genome (``"hg19"`` or ``"hg38"``). + query_type: Type of query: 'variants', 'genes', or 'cnvs'. Returns: - A dictionary of variant annotations. Refer to - https://api.varsome.com/docs/variants/ for the response schema. + A dictionary of annotations. """ - url = self.ref_genome_lookup_path % (query, ref_genome) + url = self._get_single_url(query_type, query, ref_genome) return await self.get(url, params=params) lookup = sync_wrapper(alookup) async def _batch_producer( - self, variants: Iterable[str] | AsyncIterable[str], queue: asyncio.Queue + self, items: Iterable[str] | AsyncIterable[str], queue: asyncio.Queue ) -> None: - """Add batches of variants to the request queue.""" + """Add batches of items to the request queue.""" batch = [] - if isinstance(variants, AsyncIterable): - async for variant in variants: - batch.append(variant) + if isinstance(items, AsyncIterable): + async for item in items: + batch.append(item) if len(batch) >= self.max_variants_per_batch: await queue.put(batch) batch = [] else: - for variant in variants: - batch.append(variant) + for item in items: + batch.append(item) if len(batch) >= self.max_variants_per_batch: await queue.put(batch) batch = [] @@ -323,11 +390,20 @@ async def _batch_worker( session: aiohttp.ClientSession, request_queue: asyncio.Queue, result_queue: asyncio.Queue, - url, - params, + url: str, + params: dict[str, Any] | None, + batch_key: str, ) -> None: - """Consume batches of variants from the request - queue and send them to the API.""" + """Consume batches from the request queue and send them to the API. + + Args: + session: Active aiohttp client session. + request_queue: Queue of batches to process. + result_queue: Queue to put results/exceptions into. + url: The API endpoint URL. + params: Optional query parameters. + batch_key: The JSON key for the batch payload (e.g., 'variants' or 'genes'). + """ while True: batch = await request_queue.get() if batch is None: @@ -339,10 +415,10 @@ async def _batch_worker( path=url, method="POST", params=params, - json={"variants": batch}, + json={batch_key: batch}, headers={"Content-Type": "application/json"}, ) - await result_queue.put(BatchResult(variants=batch, response=response)) + await result_queue.put(BatchResult(queries=batch, response=response)) except VarSomeAPIException as e: await result_queue.put(e) finally: @@ -350,49 +426,61 @@ async def _batch_worker( async def abatch_lookup( self, - variants: Iterable[str] | AsyncIterable[str] | AsyncGenerator[Any, None], + items: Iterable[str] | AsyncIterable[str] | AsyncGenerator[Any, None], params: dict[str, Any] | None = None, ref_genome: RefGenome = DEFAULT_REF_GENOME, max_requests: int = 5, + query_type: QueryType = DEFAULT_QUERY_TYPE, ) -> AsyncGenerator[BatchResult, None]: - """Look up annotations for a list of variants asynchronously in batches. + """Look up annotations for a list of items asynchronously in batches. - Splits variants into batches of *max_variants_per_batch* and sends - them concurrently via POST requests. Concurrency is bounded by - *max_requests* worker tasks — at most that many HTTP requests are - in-flight at any given time. + Supports variants, genes, and CNVs (though CNVs don't support batch mode). + Splits items into batches of *max_variants_per_batch* and sends them + concurrently via POST requests. Concurrency is bounded by *max_requests* + worker tasks — at most that many HTTP requests are in-flight at any given time. - Each yielded ``BatchResult`` pairs the original variant strings with - the API response, allowing callers to correlate inputs with outputs — - especially useful when the response omits the original variant - identifier. + Each yielded ``BatchResult`` pairs the original query strings with + the API response, allowing callers to correlate inputs with outputs. Args: - variants: Variant strings to look up (sync or async iterable). + items: Query strings to look up (sync or async iterable). params: Optional dictionary of query parameters. ref_genome: Reference genome, either ``"hg19"`` or ``"hg38"``. max_requests: Maximum number of concurrent HTTP requests. + query_type: Type of query: 'variants', 'genes', or 'cnvs'. Yields: A ``BatchResult`` for each batch, in completion order. Raises: - VarSomeAPIException: If any batch request fails. All remaining - in-flight requests are cancelled, and the exception is - propagated. + VarSomeAPIException: If any batch request fails. All remaining + in-flight requests are cancelled, and the exception is propagated. """ - url = self.batch_lookup_path % ref_genome + batch_url = self._get_batch_url(query_type, ref_genome) + batch_key = self._get_batch_key(query_type) + + if batch_url is None or batch_key is None: + raise ValueError( + f"Query type '{query_type}' does not support batch operations. " + "Use single item lookups instead." + ) + request_queue = asyncio.Queue(maxsize=max_requests * 2) response_queue: asyncio.Queue[BatchResult | Exception | None] = asyncio.Queue() async with self._ensure_session() as session: producer_task = asyncio.create_task( - self._batch_producer(variants, request_queue) + self._batch_producer(items, request_queue) ) workers = [ asyncio.create_task( self._batch_worker( - session, request_queue, response_queue, url, params + session, + request_queue, + response_queue, + batch_url, + params, + batch_key, ) ) for _ in range(max_requests) @@ -424,20 +512,22 @@ async def wrap_up(): def batch_lookup( self, - variants: list[str], + items: list[str], params: dict[str, Any] | None = None, ref_genome: RefGenome = DEFAULT_REF_GENOME, max_requests: int = 5, + query_type: QueryType = DEFAULT_QUERY_TYPE, ) -> list[BatchResult]: """Synchronous wrapper around :meth:`abatch_lookup`. Collects every batch result into a list and returns it. Args: - variants: List of variant strings to look up. + items: List of query strings to look up (variants, genes, etc.). params: Optional dictionary of query parameters. ref_genome: Reference genome, either "hg19" or "hg38". max_requests: Maximum number of concurrent requests. + query_type: Type of query: 'variants', 'genes', or 'cnvs'. Returns: A list of ``BatchResult`` objects, one per batch. @@ -450,10 +540,11 @@ async def _collect() -> list[BatchResult]: return [ result async for result in self.abatch_lookup( - variants, + items, params=params, ref_genome=ref_genome, max_requests=max_requests, + query_type=query_type, ) ] diff --git a/varsome_api/constants.py b/varsome_api/constants.py index edda1bf..1b26ed5 100644 --- a/varsome_api/constants.py +++ b/varsome_api/constants.py @@ -3,3 +3,7 @@ RefGenome = Literal["hg19", "hg38"] DEFAULT_REF_GENOME = "hg19" REFERENCE_GENOMES = get_args(RefGenome) + +QueryType = Literal["variants", "genes", "cnvs"] +DEFAULT_QUERY_TYPE = "variants" +QUERY_TYPES = get_args(QueryType) diff --git a/varsome_api/vcf.py b/varsome_api/vcf.py index 55328ca..6e70366 100755 --- a/varsome_api/vcf.py +++ b/varsome_api/vcf.py @@ -66,7 +66,7 @@ class BatchResult(_BaseBatchResult): Attributes: records: The ``pysam.VariantRecord`` objects corresponding to each - variant, aligned by index with *variants* and *response*. + query, aligned by index with *queries* and *response*. """ records: list[pysam.VariantRecord] @@ -145,13 +145,13 @@ def _process_request( ) -> tuple[int, list[tuple[str, dict[str, Any]]], list[tuple[str, dict[str, Any]]]]: """Process a batch result and write annotated records to the output VCF. - Iterates over each variant in *batch_result* by index, skips + Iterates over each query in *batch_result* by index, skips filtered-out or errored responses, deserialises valid responses via ``self.variant_model``, and delegates to ``annotate_record`` before writing the record. Args: - batch_result: A ``BatchResult`` whose ``variants``, ``records``, + batch_result: A ``BatchResult`` whose ``queries``, ``records``, and ``response`` lists are aligned by index. writer: An open ``pysam.VariantFile`` in write mode. @@ -163,7 +163,7 @@ def _process_request( annotated_count = 0 filtered_variants: list[tuple[str, dict[str, Any]]] = [] errored_variants: list[tuple[str, dict[str, Any]]] = [] - for idx, variant in enumerate(batch_result.variants): + for idx, variant in enumerate(batch_result.queries): annotated_variant = batch_result.response[idx] vcf_record = batch_result.records[idx] if "filtered_out" in annotated_variant: @@ -331,8 +331,9 @@ async def _batch_worker( session: aiohttp.ClientSession, request_queue: asyncio.Queue, result_queue: asyncio.Queue, - url, - params, + url: str, + params: dict[str, Any] | None, + batch_key: str, ) -> None: """Consume batches of variants from the request queue and send them to the API.""" @@ -348,12 +349,12 @@ async def _batch_worker( path=url, method="POST", params=params, - json={"variants": variant_reprs}, + json={batch_key: variant_reprs}, headers={"Content-Type": "application/json"}, ) await result_queue.put( BatchResult( - variants=variant_reprs, records=records, response=response + queries=variant_reprs, records=records, response=response ) ) except VarSomeAPIException as e: From 6e4834bc9c3c8bd93ad9c261b0954b0d8e098ef5 Mon Sep 17 00:00:00 2001 From: Christos Kopanos Date: Tue, 7 Apr 2026 15:21:43 +0300 Subject: [PATCH 4/6] =?UTF-8?q?bump:=20version=201.0.0b0=20=E2=86=92=201.0?= =?UTF-8?q?.0b1?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .cz.toml | 2 +- CHANGELOG.md | 15 +++++++++++++++ pyproject.toml | 2 +- varsome_api/__init__.py | 2 +- 4 files changed, 18 insertions(+), 3 deletions(-) diff --git a/.cz.toml b/.cz.toml index 67ce01a..12a5985 100644 --- a/.cz.toml +++ b/.cz.toml @@ -1,7 +1,7 @@ [tool.commitizen] name = "cz_github_jira_conventional" tag_format = "v$major.$minor.$patch$prerelease" -version = "1.0.0b0" +version = "1.0.0b1" version_files = [ "varsome_api/__init__.py:__version__", "pyproject.toml:version", diff --git a/CHANGELOG.md b/CHANGELOG.md index 10a2a76..d460bf1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,4 +1,19 @@ +## v1.0.0b1 (2026-04-07) + +### BREAKING CHANGE + +- models/elements/* consolidated into models/annotation.py; +CLI moved from scripts/ to varsome_api/cli/ package; client and VCF +interfaces rewritten. [5daaa](https://github.com//saphetor/varsome-api-client-python/commit/5daaab4ed750b7fe11df892a58d99c23e914e618) + +### Refactor + +- **[DEV-1896](https://saphetor.atlassian.net/browse/DEV-1896)**: Update VarSomeAPIClient to support multiple query types [0f600](https://github.com//saphetor/varsome-api-client-python/commit/0f60016fc3f479c5c016387c763baa0d5220f28f) +- **[DEV-1896](https://saphetor.atlassian.net/browse/DEV-1896)**: complete rewrite of varsome-api-client-python v1 [5daaa](https://github.com//saphetor/varsome-api-client-python/commit/5daaab4ed750b7fe11df892a58d99c23e914e618) + +## v0.0.3 (2025-09-29) + ## v1.0.0b0 (2026-03-29) ### BREAKING CHANGE diff --git a/pyproject.toml b/pyproject.toml index be7dda6..8866469 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "varsome_api" -version = "1.0.0b0" +version = "1.0.0b1" description = "A basic python api client implementation for https://api.varsome.com" authors = ["Saphetor S.A. "] readme = "README.md" diff --git a/varsome_api/__init__.py b/varsome_api/__init__.py index c9bd737..5313823 100755 --- a/varsome_api/__init__.py +++ b/varsome_api/__init__.py @@ -1 +1 @@ -__version__ = "1.0.0b0" +__version__ = "1.0.0b1" From 90f8e2103d312bc0e9ed2ffe688c17ea927a8410 Mon Sep 17 00:00:00 2001 From: Christos Kopanos Date: Tue, 7 Apr 2026 17:06:51 +0300 Subject: [PATCH 5/6] refactor(DEV-1896): Clean up imports and improve code formatting --- .pre-commit-config.yaml | 3 +-- examples/parquet/annotate_to_parquet.py | 5 ++--- examples/parquet/models.py | 2 +- examples/parquet/writer.py | 6 ++---- tests/test_cli.py | 5 ----- tests/test_client.py | 20 ++++++++++++++++---- tests/test_sync.py | 3 ++- tests/test_vcf.py | 2 +- varsome_api/cli/varsome_api_run.py | 8 +++++--- varsome_api/client.py | 6 ++++-- varsome_api/vcf.py | 2 +- 11 files changed, 35 insertions(+), 27 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 5745743..fdf24a6 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -4,7 +4,6 @@ repos: rev: 26.3.0 hooks: - id: black - language_version: python3.11 - repo: https://github.com/PyCQA/isort rev: 8.0.1 hooks: @@ -15,7 +14,7 @@ repos: - id: flake8 fail_fast: true - repo: https://github.com/commitizen-tools/commitizen - rev: 4.13.9 + rev: v4.13.9 hooks: - id: commitizen stages: [commit-msg] diff --git a/examples/parquet/annotate_to_parquet.py b/examples/parquet/annotate_to_parquet.py index d0ebf51..55f9070 100644 --- a/examples/parquet/annotate_to_parquet.py +++ b/examples/parquet/annotate_to_parquet.py @@ -5,19 +5,18 @@ import time from pathlib import Path +from writer import ParquetWriter + from varsome_api.client import VarSomeAPIClient from varsome_api.constants import DEFAULT_REF_GENOME, REFERENCE_GENOMES, RefGenome from varsome_api.exceptions import VarSomeAPIException from varsome_api.log import logger from varsome_api.models.slim.annotation import AnnotatedVariant -from writer import ParquetWriter - DEFAULT_INPUT = Path(__file__).parent / "variants.csv" DEFAULT_OUTPUT = Path(__file__).parent / "annotated_variants.parquet" - def _build_arg_parser() -> argparse.ArgumentParser: parser = argparse.ArgumentParser( description="Annotate variants from a CSV file and write to Parquet.", diff --git a/examples/parquet/models.py b/examples/parquet/models.py index 7ed26bd..2903c79 100644 --- a/examples/parquet/models.py +++ b/examples/parquet/models.py @@ -4,7 +4,6 @@ from varsome_api.models.slim.annotation import AnnotatedVariant - PARQUET_SCHEMA: pa.Schema = pa.schema( [ pa.field("original_variant", pa.string(), nullable=True), @@ -32,6 +31,7 @@ def _coerce_float(value: float | str | None) -> float | None: except (TypeError, ValueError): return None + def to_parquet_row(variant: AnnotatedVariant) -> dict[str, Any]: clean_acmg_rules: list[str] = [ r for r in (variant.acmg_rules or []) if r is not None diff --git a/examples/parquet/writer.py b/examples/parquet/writer.py index 629d5a2..fb2bc53 100644 --- a/examples/parquet/writer.py +++ b/examples/parquet/writer.py @@ -2,8 +2,8 @@ import pyarrow as pa import pyarrow.parquet as pq - from models import PARQUET_SCHEMA, to_parquet_row + from varsome_api.models.slim.annotation import AnnotatedVariant @@ -38,7 +38,6 @@ def __exit__( if exc_type is None: self.write() - def _build_table(self) -> pa.Table: columns: dict[str, list] = {field.name: [] for field in self._schema} @@ -47,7 +46,6 @@ def _build_table(self) -> pa.Table: columns[field.name].append(row.get(field.name)) arrays: list[pa.Array] = [ - pa.array(columns[field.name], type=field.type) - for field in self._schema + pa.array(columns[field.name], type=field.type) for field in self._schema ] return pa.Table.from_arrays(arrays, schema=self._schema) diff --git a/tests/test_cli.py b/tests/test_cli.py index 6cfb179..4d7fd04 100644 --- a/tests/test_cli.py +++ b/tests/test_cli.py @@ -1,5 +1,3 @@ -import argparse -import logging from typing import Any from unittest.mock import MagicMock, patch @@ -7,10 +5,7 @@ from varsome_api.cli.utils import ( build_base_parser, - configure_logging, parse_request_parameters, - validate_batch_args, - validate_file_args, ) from varsome_api.cli.varsome_api_annotate_vcf import ( build_parser as build_annotate_parser, diff --git a/tests/test_client.py b/tests/test_client.py index e694e1e..f974d40 100644 --- a/tests/test_client.py +++ b/tests/test_client.py @@ -381,7 +381,12 @@ async def test_successful_batch_put_on_result_queue( await request_queue.put(None) with patch.object(type(client), "_make_request", side_effect=fake): await client._batch_worker( - session, request_queue, result_queue, "/lookup/batch/hg19", None, "variants" + session, + request_queue, + result_queue, + "/lookup/batch/hg19", + None, + "variants", ) result = result_queue.get_nowait() assert isinstance(result, BatchResult) @@ -402,7 +407,12 @@ async def failing_request(_session: Any, **kwargs: Any) -> Any: await request_queue.put(None) with patch.object(type(client), "_make_request", side_effect=failing_request): await client._batch_worker( - session, request_queue, result_queue, "/lookup/batch/hg19", None, "variants" + session, + request_queue, + result_queue, + "/lookup/batch/hg19", + None, + "variants", ) queued = result_queue.get_nowait() assert isinstance(queued, VarSomeAPIException) @@ -410,10 +420,12 @@ async def failing_request(_session: Any, **kwargs: Any) -> Any: class TestVarSomeAPIClientBatchLookup: - """Verify ``VarSomeAPIClient.abatch_lookup`` and its sync wrapper ``batch_lookup``.""" + """Verify ``VarSomeAPIClient.abatch_lookup`` + and its sync wrapper ``batch_lookup``.""" async def test_yields_batch_results(self, make_fake_request: Callable) -> None: - """Each yielded item must be a ``BatchResult`` covering at most *batch_size* variants.""" + """Each yielded item must be a ``BatchResult`` covering + at most *batch_size* variants.""" variants = ["v1", "v2", "v3", "v4", "v5"] mock_responses = { ("v1", "v2"): [{"id": "1"}, {"id": "2"}], diff --git a/tests/test_sync.py b/tests/test_sync.py index efb80c3..e72e4b4 100644 --- a/tests/test_sync.py +++ b/tests/test_sync.py @@ -40,7 +40,8 @@ async def pipeline() -> int: assert run_sync(pipeline()) == 6 async def test_fallback_when_loop_is_running(self) -> None: - """When called from within a running loop, must still work via thread fallback.""" + """When called from within a running loop, must still work + via thread fallback.""" async def inner() -> int: return 42 diff --git a/tests/test_vcf.py b/tests/test_vcf.py index e2f4cd2..4b32fe6 100644 --- a/tests/test_vcf.py +++ b/tests/test_vcf.py @@ -338,7 +338,7 @@ async def test_default_output_file_name(self, tmp_path: Path) -> None: header = pysam.VariantHeader() header.add_sample("S1") header.contigs.add("1") - with pysam.VariantFile(str(vcf_path), "w", header=header) as w: + with pysam.VariantFile(str(vcf_path), "w", header=header): pass annotator = VCFAnnotator( diff --git a/varsome_api/cli/varsome_api_run.py b/varsome_api/cli/varsome_api_run.py index b37e002..165e61a 100755 --- a/varsome_api/cli/varsome_api_run.py +++ b/varsome_api/cli/varsome_api_run.py @@ -1,5 +1,6 @@ #!/usr/bin/env python3 -"""CLI tool for performing single or batch lookups (variants, genes, or CNVs) via the VarSome API.""" +"""CLI tool for performing single or batch lookups (variants, genes, +or CNVs) via the VarSome API.""" import argparse import asyncio @@ -20,9 +21,9 @@ from varsome_api.constants import ( DEFAULT_QUERY_TYPE, DEFAULT_REF_GENOME, + QUERY_TYPES, QueryType, RefGenome, - QUERY_TYPES, ) from varsome_api.log import logger @@ -74,7 +75,8 @@ def build_parser() -> argparse.ArgumentParser: "-y", help=( "Query type: 'variants', 'genes', or 'cnvs'. " - "Note: CNV queries do not support batch mode, each CNV is looked up individually. " + "Note: CNV queries do not support batch mode, each " + "CNV is looked up individually. " "Check documentation for batch limits per environment" ), type=str, diff --git a/varsome_api/client.py b/varsome_api/client.py index 3be7176..fd24d12 100755 --- a/varsome_api/client.py +++ b/varsome_api/client.py @@ -257,7 +257,8 @@ async def post( class VarSomeAPIClient(VarSomeAPIClientBase): - """High-level client for single and batch lookups (variants, genes, or CNVs) via the VarSome API. + """High-level client for single and batch lookups (variants, genes, or CNVs) + via the VarSome API. Supports querying variants, genes, and CNVs with a unified interface. The query_type parameter controls endpoint selection and request/response handling. @@ -337,7 +338,8 @@ def _get_batch_key(query_type: QueryType) -> str | None: query_type: Type of query: 'variants', 'genes', or 'cnvs'. Returns: - The key name (e.g., 'variants' or 'genes'), or None if batch is not supported. + The key name (e.g., 'variants' or 'genes'), or None + if batch is not supported. """ return VarSomeAPIClient._ENDPOINTS[query_type]["batch_key"] diff --git a/varsome_api/vcf.py b/varsome_api/vcf.py index 6e70366..088e668 100755 --- a/varsome_api/vcf.py +++ b/varsome_api/vcf.py @@ -14,7 +14,7 @@ from varsome_api.constants import DEFAULT_REF_GENOME, RefGenome from varsome_api.exceptions import VarSomeAPIException from varsome_api.models.slim.annotation import AnnotatedVariant as SlimAnnotatedVariant -from varsome_api.models.variant import AnnotatedVariantPropertiesMixin, AnnotatedVariant +from varsome_api.models.variant import AnnotatedVariant try: import pysam From 960e38bb7343729efb924ef4f18575e1462bce46 Mon Sep 17 00:00:00 2001 From: Christos Kopanos Date: Tue, 7 Apr 2026 17:23:07 +0300 Subject: [PATCH 6/6] refactor(DEV-1896): Simplify error handling and clean up code in client.py Updated the error handling logic to check for response status codes greater than or equal to 400 --- .editorconfig | 3 --- varsome_api/client.py | 4 ++-- 2 files changed, 2 insertions(+), 5 deletions(-) diff --git a/.editorconfig b/.editorconfig index 30706b5..3ed8290 100644 --- a/.editorconfig +++ b/.editorconfig @@ -10,9 +10,6 @@ max_line_length = 120 tab_width = 4 trim_trailing_whitespace = true -[] -indent_size = 2 - [*.cjs] indent_size = 2 max_line_length = 80 diff --git a/varsome_api/client.py b/varsome_api/client.py index fd24d12..842b5d2 100755 --- a/varsome_api/client.py +++ b/varsome_api/client.py @@ -186,7 +186,7 @@ async def _make_request( request_kwargs["headers"] = headers try: async with session.request(method, **request_kwargs) as response: - if response.status in VarSomeAPIException.ERROR_CODES: + if response.status >= 400: error_message = await response.json() raise VarSomeAPIException(response.status, error_message) return await response.json() @@ -489,7 +489,7 @@ async def abatch_lookup( ] async def wrap_up(): - await producer_task + _ = await producer_task await request_queue.join() await response_queue.put(None)