COSMIC Somatic Cancer Mutations Database

COSMIC Somatic Cancer Mutations Database

Overview

COSMIC (Catalogue Of Somatic Mutations In Cancer) is the world's largest expert-curated database of somatic mutations in cancer, covering 6.7M+ coding mutations, 40,000+ cancer samples, 19,000+ genes across all cancer types. It includes the Cancer Gene Census (critical cancer genes), mutational signatures (SBS, DBS, ID), drug resistance variants, copy number data, gene expression, and methylation. The REST API v3.1 enables programmatic queries; most features are freely accessible after registration.

When to Use

• Checking whether a specific somatic variant in a cancer gene is annotated in COSMIC (frequency, cancer type distribution)
• Retrieving all somatic mutations in a gene of interest across COSMIC cancer samples
• Accessing COSMIC Cancer Gene Census classifications (Tier 1/2, role: oncogene/TSG/fusion)
• Looking up mutational signature attributions for samples or cancer types
• Identifying drug resistance variants (pharmacogenomic data) from COSMIC drug resistance database
• Building cancer driver gene lists for bioinformatic pipelines
• For germline/inherited variants use clinvar-database; for drug-target associations use opentargets-database

Prerequisites

• Python packages: requests, pandas
• Data requirements: gene symbols (HGNC), COSMIC mutation IDs (COSM), sample IDs, or genomic coordinates
• Environment: internet connection; free account registration at https://cancer.sanger.ac.uk/cosmic/register
• Rate limits: authenticated requests only; 10 requests/second max; API key required

pip install requests pandas
# Register at https://cancer.sanger.ac.uk/cosmic/register to obtain API credentials

Quick Start

import requests
import base64

# COSMIC API requires base64-encoded email:password authentication
EMAIL = "[email protected]"
PASSWORD = "your_password"
token = base64.b64encode(f"{EMAIL}:{PASSWORD}".encode()).decode()

BASE = "https://cancer.sanger.ac.uk/cosmic/api"