tools-only COSMIC Database Reference
Overview
COSMIC (Catalogue of Somatic Mutations in Cancer) is the world's largest and most comprehensive resource for exploring the impact of somatic mutations in human cancer. Maintained by the Wellcome Sanger Institute, it catalogs millions of mutations across thousands of cancer types.
Website: https://cancer.sanger.ac.uk/cosmic Release Schedule: Quarterly updates Current Version: v102 (May 2025), use "latest" in API calls for most recent
Data Access
Authentication
- Academic users: Free access (registration required)
- Commercial users: License required (contact QIAGEN)
- Registration: https://cancer.sanger.ac.uk/cosmic/register
Download Methods
- Web Browser: Interactive search at https://cancer.sanger.ac.uk/cosmic
- File Downloads: Programmatic access via download API
- Data Files: TSV, CSV, and VCF formats
Available Data Types
1. Core Mutation Data
Main Files:
CosmicMutantExport.tsv.gz- Complete coding mutationsCosmicCodingMuts.vcf.gz- Mutations in VCF formatCosmicNonCodingVariants.vcf.gz- Non-coding variantsCosmicMutantExportCensus.tsv.gz- Mutations in Cancer Gene Census genes only
Content:
- Point mutations (SNVs)
- Small insertions and deletions (indels)
- Genomic coordinates
- Variant annotations
- Sample information
- Tumor type associations
2. Cancer Gene Census
File: cancer_gene_census.csv
Content:
- Expert-curated list of cancer genes
- ~700+ genes with substantial evidence of involvement in cancer
- Gene roles (oncogene, tumor suppressor, fusion)
- Mutation types
- Tissue associations
- Molecular genetics information
3. Mutational Signatures
Files: Available in signatures/ directory
signatures.tsv- Signature definitions- Single Base Substitution (SBS) signatures
- Doublet Base Substitution (DBS) signatures
- Insertion/Deletion (ID) signatures
Current Version: v3.4 (released in COSMIC v98)
Content:
- Signature profiles (96-channel, 78-channel, 83-channel)
- Etiology annotations
- Reference signatures for signature analysis
4. Structural Variants
File: CosmicStructExport.tsv.gz
Content:
- Gene fusions
- Structural breakpoints
- Translocation events
- Large deletions/insertions
- Complex rearrangements
5. Copy Number Variations
File: CosmicCompleteCNA.tsv.gz
Content:
- Copy number gains and losses
- Amplifications and deletions
- Segment-level data
- Gene-level annotations
6. Gene Expression
File: CosmicCompleteGeneExpression.tsv.gz
Content:
- Over/under-expression data
- Gene expression Z-scores
- Tissue-specific expression patterns
7. Resistance Mutations
File: CosmicResistanceMutations.tsv.gz
Content:
- Drug resistance mutations
- Treatment associations
- Clinical relevance
8. Cell Lines Project
Files: Various cell line-specific files
Content:
- Mutations in cancer cell lines
- Copy number data for cell lines
- Fusion genes in cell lines
- Microsatellite instability status
9. Sample Information
File: CosmicSample.tsv.gz
Content:
- Sample metadata
- Tumor site/histology
- Sample sources
- Study references
Genome Assemblies
All genomic data is available for two reference genomes:
- GRCh37 (hg19) - Legacy assembly
- GRCh38 (hg38) - Current assembly (recommended)
File paths use the pattern: {assembly}/cosmic/{version}/{filename}
File Formats
TSV/CSV Format
- Tab or comma-separated values
- Column headers included
- Gzip compressed (.gz)
- Can be read with pandas, awk, or standard tools
VCF Format
- Standard Variant Call Format
- Version 4.x specification
- Includes INFO fields with COSMIC annotations
- Gzip compressed and indexed (.vcf.gz, .vcf.gz.tbi)
Common File Paths
Using latest for the most recent version:
# Coding mutations (TSV)
GRCh38/cosmic/latest/CosmicMutantExport.tsv.gz
# Coding mutations (VCF)
GRCh38/cosmic/latest/VCF/CosmicCodingMuts.vcf.gz
# Cancer Gene Census
GRCh38/cosmic/latest/cancer_gene_census.csv
# Structural variants
GRCh38/cosmic/latest/CosmicStructExport.tsv.gz
# Copy number alterations
GRCh38/cosmic/latest/CosmicCompleteCNA.tsv.gz
# Gene fusions
GRCh38/cosmic/latest/CosmicFusionExport.tsv.gz
# Gene expression
GRCh38/cosmic/latest/CosmicCompleteGeneExpression.tsv.gz
# Resistance mutations
GRCh38/cosmic/latest/CosmicResistanceMutations.tsv.gz
# Mutational signatures
signatures/signatures.tsv
# Sample information
GRCh38/cosmic/latest/CosmicSample.tsv.gz
Key Data Fields
Mutation Data Fields
- Gene name - HGNC gene symbol
- Accession Number - Transcript identifier
- COSMIC ID - Unique mutation identifier
- CDS mutation - Coding sequence change
- AA mutation - Amino acid change
- Primary site - Anatomical tumor location
- Primary histology - Tumor type classification
- Genomic coordinates - Chromosome, position, strand
- Mutation type - Substitution, insertion, deletion, etc.
- Zygosity - Heterozygous/homozygous status
- Pubmed ID - Literature references
Cancer Gene Census Fields
- Gene Symbol - Official gene name
- Entrez GeneId - NCBI gene identifier
- Role in Cancer - Oncogene, TSG, fusion
- Mutation Types - Types of alterations observed
- Translocation Partner - For fusion genes
- Tier - Evidence classification (1 or 2)
- Hallmark - Cancer hallmark associations
- Somatic - Whether somatic mutations are documented
- Germline - Whether germline mutations are documented
Data Updates
COSMIC is updated quarterly with new releases. Each release includes:
- New mutation data from literature and databases
- Updated Cancer Gene Census annotations
- Revised mutational signatures if applicable
- Enhanced sample annotations
Citation
When using COSMIC data, cite: Tate JG, Bamford S, Jubb HC, et al. COSMIC: the Catalogue Of Somatic Mutations In Cancer. Nucleic Acids Research. 2019;47(D1):D941-D947.
Additional Resources
- Documentation: https://cancer.sanger.ac.uk/cosmic/help
- Release Notes: https://cancer.sanger.ac.uk/cosmic/release_notes
- Contact: cosmic@sanger.ac.uk
- Licensing: cosmic-translation@sanger.ac.uk