COSMIC, curating the cancer variome

Simon A. Forbes, Gurpreet W. Tang, Jon W. Teague, P. Andrew Futreal, Michael R. Stratton
2008 European Conference on Computational Biology  
Background. COSMIC (http://www.sanger.ac.uk/cosmic) is a system designed to curate the world's literature on somatic mutations in known cancer genes. Initially conceived to capture the mutation spread in point-mutated genes, COSMIC has now grown to encompass gene fusion products of genome rearrangement events which generate completely novel transcripts, together with all the somatic mutation data from candidate gene screens at the Cancer Genome Project, UK (CGP), covering almost 5000 genes of
more » ... tential interest in cancer genetics. Results. The latest release of COSMIC (version 37; July 2008) now holds full and up-to-date curation of over 5,900 scientific papers, examining over 268,000 tumours, in which over 59,000 mutations are detailed through 60 pointmutated genes. Fusion gene products have been curated for 16 pairs of genes, described through over 4200 tumours. 2246 papers were rejected during manual curation, usually due to significant inconsistencies in the publication. A relational database holds the captured information, which is warehoused for each release. The information is presented on the internet with a series of graphical and tabulated views aiding navigation and interpretation. Conclusions. The current version of COSMIC is close to fulfilling its original intentions, with curation of most pointmutated genes in cancer complete. However, new challenges are emerging with the need to calculate the effect of high numbers of observed sequence changes to identify those driving tumour formation, and the need to meaningfully handle the increasing quantities of data from high-throughput screens and next-generation sequencing technologies.
dblp:conf/eccb/ForbesTTFS08 fatcat:l7kftokymnbqjfbmjdjomyxiim