COSMIC

COSMIC

COSMIC

Overview

COSMIC, the "Catalogue Of Somatic Mutations In Cancer" is an expert-curated database encompassing the wide variety of somatic mutation mechanisms causing human cancer (http://cancer.sanger.ac.uk). Growing in both content and scope, COSMIC holds details on millions of mutations across thousands of cancer types. Hand-curation of key cancer genes (selected from the Cancer Gene Census) provide in-depth detail on mutation distributions and effects, whilst semi-automated curation of cancer genomes provides broad somatic annotations toward target discovery and identification of patterns and signatures. This information is fully available via website or download, updated every three months.

Curation

Cancer Gene Census : This is a list of hundreds of genes with substantial published evidence in oncology. Necessarily conservative, this is a very high-confidence list based on good-quality publications. Selection of high-impact genes from this list for curation drives COSMIC.

COSMIC : Upon selection of a gene from the Census for full expert curation, all papers mentioning its mutation in human cancer are collected and exhaustively curated before it is released into a new version of COSMIC. Once this initial curation is released, the gene is updated as significant new information is published. Each curator is responsible for a defined set of 60 or more genes, developing substantial expertise. In parallel, cancer genomes are curated via a more bioinformatic approach. Genomic data is obtained in standard formats; roughly half is from published supplementary information tables, and the other half from genome consortia such as TCGA, ICGC. Standard pipelines (eg Ensembl VEP) annotate these genomic data in genic terms for COSMIC release. Such molecular profiling includes point mutations, gene fusions, copy number annotations, structural breakpoints, gene expression and CpG island methylation variants.

Cancer Cell Lines Project : The Cell lines Project in COSMIC is an effort to fully profile over 1000 cell lines regularly used in cancer research; annotations include exome sequencing, CNV and gene expression profiling, RNASeq and CpG methylation. This information is maintained in a separate, but parallel system alongside COSMIC and regularly updated to highlight the most valuable information across the cell line panel.

Download and Installation

The COSMIC group make this information available in many ways to suit a variety of scientific and informatic users. Most accessibly, it can be viewed and analysed in its custom website (http://cancer.sanger.ac.uk), where distributions across genes, genomes and diseases can be explored easily and in detail. A full genome browser provides even greater information, correlating COSMIC mutations with a range of genomic annotations including promoters, ncRNAs and polymorphisms. Full downloads are also provided, either in standardised text format (CSV) or as a full Oracle database.

Learn and Support

COSMIC is very intuitive and easy to use, we have provided substantial help pages explaining the various components and entry point into COSMIC. To further ease the navigation of the system, we also have Youtube Help tutorial videos.

License and Citation

COSMIC is now under license, with academic and non-profit access available freely and commercial access available for a license fee. These funds are being used to expand the COSMIC group, particularly our curation team. As we enhance the number of genes under curation, and the scope of data we aim to capture, an expansion of this team will ensure that COSMIC continues to succeed in supporting a wide range of oncology research and product development.

Contact

Interested in receiving COSMIC news and release information? Then sign up [here].

Please send all comments and suggestions to the cosmic@sanger.ac.uk

For licensing enquiries please contact cosmic-translation@sanger.ac.uk

Publications

  • COSMIC: exploring the world's knowledge of somatic mutations in human cancer.

    Forbes SA, Beare D, Gunasekaran P, Leung K, Bindal N et al.

    Nucleic acids research 2015;43;Database issue;D805-11

  • COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer.

    Forbes SA, Bindal N, Bamford S, Cole C, Kok CY et al.

    Nucleic acids research 2011;39;Database issue;D945-50

  • The Catalogue of Somatic Mutations in Cancer (COSMIC).

    Forbes SA, Bhamra G, Bamford S, Dawson E, Kok C et al.

    Current protocols in human genetics 2008;Chapter 10;Unit 10.11

  • Data mining using the Catalogue of Somatic Mutations in Cancer BioMart.

    Shepherd R, Forbes SA, Beare D, Bamford S, Cole CG et al.

    Database : the journal of biological databases and curation 2011;2011;bar018

  • COSMIC 2005.

    Forbes S, Clements J, Dawson E, Bamford S, Webb T et al.

    British journal of cancer 2006;94;2;318-22

  • The COSMIC (Catalogue of Somatic Mutations in Cancer) database and website.

    Bamford S, Dawson E, Forbes S, Clements J, Pettett R et al.

    British journal of cancer 2004;91;2;355-8