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. This data is then made available in a number of ways including here in the UCSC genome browser, on the COSMIC website with custom analytical tools, via a federated Biomart, or offline via datasheets downloaded from the FTP site. Publications using COSMIC as a data source may cite any of our references below.

Methods

The data in COSMIC is 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 maximise its descriptive content. Data from large scale systematic screens are curated semi-automatically, using Vagrent software to reannotate mutant genomic positions (version 0.1 is described at VAGrENT: Variation Annotation Generator). The full curated dataset is exported from the COSMIC database in CSV format for uploading to UCSC for each bimonthly release; this file is also available on the COSMIC FTP site.

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, whilst minimizing screen space used.
• Pack - Indicate each mutation with COSMIC identifier (COSMnnnnn), mutation annotation, overall mutation frequency and tissues affected, with a link to further details.
• Full - Show each mutation in detail, one per line, with COSM identifier, mutation annotation, overall mutation frequency and tissues affected, with a link to even further details.

Contacts

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

References

Forbes SA, Bhamra G, Bamford S, Dawson E, Kok C, Clements J, Menzies A, Teague JW, Futreal PA, Stratton MR. The Catalogue of Somatic Mutations in Cancer (COSMIC). Curr Protoc Hum Genet. 2008 Apr 1;57:10.11.1-10.11.26.

Forbes SA, Bindal N, Bamford S, Cole C, Kok CY, Beare D, Jia M, Shepherd R, Leung K, Menzies A, et al. COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic Acids Res. 2011 Jan;39(Database issue):D945-50. Epub 2010 Oct 15.