Description

COSMIC, the "Catalogue Of Somatic Mutations In Cancer," is an online database of somatic mutations found in human cancer. Focused exclusively on non-inherited acquired mutations, COSMIC combines information from a range of sources, curating the described relationships between cancer phenotypes and gene (and genomic) mutations. These data are then made available in a number of ways including here in the UCSC genome browser, on the COSMIC website with custom analytical tools, or via the COSMIC sftp server. Publications using COSMIC as a data source may cite our reference below.

Methods

The data in COSMIC are curated from a number of high-quality sources and combined into a single resource. The sources include:

• Peer-reviewed journal articles
• CGP laboratories at the Sanger Institute, UK
• TCGA data portal
• The ICGC data portal
• IARC p53 database

Information on known cancer genes, selected from the Cancer Gene Census is curated manually to maximize its descriptive content.

UCSC was provided with the COSMIC annotations directly. The columns were reconfigured to match our BED format, and 35 mutations were removed as they had illegal coordinates (start>stop). The resulting file was converted to a bigBed for display using the bedToBigBed utility.

Display

• Dense - Indicate the positions where COSMIC mutations have been annotated in a single horizontal track.
• Squish - Indicate each mutation, in vertical pileups where appropriate, while minimizing screen space used.
• Pack - Indicate each mutation with Genomic Mutation ID (COSVnnnnn).
• Full - Show each mutation in detail, one per line, with Genomic Mutation ID (COSVnnnnn).

Clicking into any item also displays the reference allele, alternate allele, and the Cosmic legacy mutation identifier (COSNnnnnn). Outlinks can also be found directly to COSMIC for additional information.

Data Access

The limited data available to UCSC can be explored interactively with the Table Browser, or the Data Integrator. For automated analysis, the data may be queried from our REST API. Please refer to our mailing list archives for questions, or our Data Access FAQ for more information.

The complete data can be explored and downloaded via the COSMIC website.

Contacts

For further information on COSMIC, or for help with the information provided, please contact cosmic@sanger. ac. uk.

References

Forbes SA, Beare D, Boutselakis H, Bamford S, Bindal N, Tate J, Cole CG, Ward S, Dawson E, Ponting L et al. COSMIC: somatic cancer genetics at high-resolution. Nucleic Acids Res. 2017 Jan 4;45(D1):D777-D783. PMID: 27899578; PMC: PMC5210583