COSMIC (Catalogue Of Somatic Mutations In Cancer) | Cancer Genome Project

COSMIC (Catalogue Of Somatic Mutations In Cancer) | Cancer Genome Project

COSMIC (Catalogue Of Somatic Mutations In Cancer)

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Our Research and Approach

The COSMIC group are responsible for the "Catalogue Of Somatic Mutations In Cancer" (http://cancer.sanger.ac.uk). This is an expert-curated database encompassing the wide variety of somatic mutation mechanisms causing human cancer. This group is underpinned by a team of expert scientists who hand-curate somatic mutation data across all human cancers from the scientific literature, emphasising standardisation, descriptiveness and quality. Our bioinformaticians support curation, bringing context to this data, developing the website, and releasing new updated versions every three months.

Curation
Cancer Gene Census

Our expert curators, continuously immersed in the scientific literature, make regular additions to this Census, a list of hundreds of genes with substantial published evidence in oncology. Selection of high-impact genes from this list for curation drives the core of 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, with substantial post-doctoral or pharmaceutical experience, is responsible for a defined set of 60 or more genes, developing substantial expertise. In parallel, cancer genomes are curated by dedicated bioinformaticians who seek genomic data and adapt it to standard formats for genic and peptide annotation via standard pipelines (eg. Ensembl VEP). Roughly half this data is from published supplementary information tables, and the other half from genome consortia such as TCGA, ICGC. 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 developed and regularly extended by a scientist dedicated to this resource. A system to fully profile over 1000 cell lines regularly used in cancer research, annotations include variants from exome sequencing, CNV and gene expression profiling, RNASeq and CpG methylation. This information is maintained in a separate, but parallel system alongside COSMIC, regularly updated to highlight the most valuable information across the cell line panel.

We are always very interested to discuss the ways in which COSMIC is being used, and to explore how we can support these efforts. If you have any questions, or would like to discuss COSMIC further, please contact us at cosmic@sanger.ac.uk.

People

Dr Simon Forbes
Group Leader

Experienced as scientist and informatician, I designed and now lead the COSMIC project, collecting the world's knowledge of somatic mutations in human cancer.

Key Projects, Collaborations, Tools & Data

Research Programmes

Publications

  • COSMIC: somatic cancer genetics at high-resolution.

    Forbes SA, Beare D, Boutselakis H, Bamford S, Bindal N et al.

    Nucleic acids research 2017;45;D1;D777-D783

  • COSMIC: High-Resolution Cancer Genetics Using the Catalogue of Somatic Mutations in Cancer.

    Forbes SA, Beare D, Bindal N, Bamford S, Ward S et al.

    Current protocols in human genetics 2016;91;10.11.1-10.11.37

  • 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