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.

The data was downloaded from the COSMIC sftp server. It was first converted to a bed file using the UCSC utility cosmicToBed, then converted into a bigBed file using the UCSC utility bedToBigBed. The bigBed file is used to generate the track.

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 COSMIC identifier (COSMnnnnn).
• Full - Show each mutation in detail, one per line, with COSM identifier (COSMnnnnn).

Data Access

Due to licensed material, we do not allow downloads or Table Browser access for the bigBed data. The raw data underlying this track can be explored and downloaded via the COSMIC website. The CosmicMutantExport.tsv.gz file was converted to a BED file using the cosmicToBed utility, and then converted into a bigBed file using the bedToBigBed utility. You can download these tools from the utilities directory.

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