COSMIC cancer database

The COSMIC (Catalogue of Somatic Mutations in Cancer) database was designed to collect and display information on somatic mutations in cancer. It was launched in 2004, with data from just four genes, HRAS, KRAS2, NRAS and BRAF.{{cite journal | vauthors = Bamford S, Dawson E, Forbes S, Clements J, Pettett R, Dogan A, Flanagan A, Teague J, Futreal PA, Stratton MR, Wooster R | display-authors = 6 | title = The COSMIC (Catalogue of Somatic Mutations in Cancer) database and website | journal = British Journal of Cancer | volume = 91 | issue = 2 | pages = 355–358 | date = July 2004 | pmid = 15188009 | pmc = 2409828 | doi = 10.1038/sj.bjc.6601894 }} These four genes are known to be somatically mutated in cancer. Since its creation, the database has expanded rapidly. By 2005 COSMIC contained 529 genes screened from 115,327 tumours, describing 20,981 mutations.{{cite book | vauthors = Hu H | title = Biomedical informatics in translational research | publisher = Artech House | year = 2008 | isbn = 978-1-59693-038-4 | display-authors = etal }} By August 2009 it contained information from 1.5 million experiments performed, encompassing 13,423 genes in almost 370,000 tumours and describing over 90,000 mutations.{{cite journal | vauthors = Forbes SA, Tang G, Bindal N, Bamford S, Dawson E, Cole C, Kok CY, Jia M, Ewing R, Menzies A, Teague JW, Stratton MR, Futreal PA | display-authors = 6 | title = COSMIC (the Catalogue of Somatic Mutations in Cancer): a resource to investigate acquired mutations in human cancer | journal = Nucleic Acids Research | volume = 38 | issue = Database issue | pages = D652–D657 | date = January 2010 | pmid = 19906727 | pmc = 2808858 | doi = 10.1093/nar/gkp995 }} COSMIC version 48, released in July 2010, incorporates mutation data from p53 in collaboration with the International Agency for Research on Cancer. In addition, it provided updated gene co-ordinates for the most recent human reference genome builds. This release includes data from over 2.76 million experiments on over half a million tumours. The number of mutations documented in this release totals 141,212.{{cite web |url=http://www.sanger.ac.uk/genetics/CGP/cosmic/News/ |title=COSMIC v48 Release |date=27 July 2010 |work=Catalogue Of Somatic Mutations In Cancer |publisher=Wellcome Trust Sanger Institute |access-date=1 September 2010}}

The website is focused on presenting complex phenotype-specific mutation data in a graphical manner. Data is taken from selected genes, initially in the Cancer Gene Census, as well as literature search from PubMed.

Data can be accessed via selection of a gene or cancer tissue type (phenotype), either using browse by features or the search box. Results show summary information with mutation counts and frequencies. The gene summary page provides a mutation spectrum map and external resources; the phenotype (tissue) summary page provides lists of mutated genes.

File:CDKN2A COSMIC histogram.png gene as produced by the COSMIC database.]]

The figure shows the CDKN2A gene, which is a tumor suppressor that leads to cancer when it is inactivated.

The COSMIC database contains thousands of somatic mutations that are implicated in the development of cancer. The database collects information from two major sources. Firstly, mutations in known cancer genes are collected from the literature. The list of genes that undergo manual curation are identified by their presence in the Cancer Gene Census.{{cite web|url=http://www.sanger.ac.uk/genetics/CGP/Census/|title=Cancer Gene Census|access-date=31 August 2010}}{{cite journal | vauthors = Futreal PA, Coin L, Marshall M, Down T, Hubbard T, Wooster R, Rahman N, Stratton MR | display-authors = 6 | title = A census of human cancer genes | journal = Nature Reviews. Cancer | volume = 4 | issue = 3 | pages = 177–183 | date = March 2004 | pmid = 14993899 | pmc = 2665285 | doi = 10.1038/nrc1299 }} Secondly, data for inclusion in the database is collected from whole genome resequencing studies of cancer samples undertaken by the Cancer Genome Project. For example, Campbell and colleagues used next generation sequencing to examine samples from two individuals with lung cancer which led to the identification of 103 somatic DNA rearrangements.{{cite journal | vauthors = Campbell PJ, Stephens PJ, Pleasance ED, O'Meara S, Li H, Santarius T, Stebbings LA, Leroy C, Edkins S, Hardy C, Teague JW, Menzies A, Goodhead I, Turner DJ, Clee CM, Quail MA, Cox A, Brown C, Durbin R, Hurles ME, Edwards PA, Bignell GR, Stratton MR, Futreal PA | display-authors = 6 | title = Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing | journal = Nature Genetics | volume = 40 | issue = 6 | pages = 722–729 | date = June 2008 | pmid = 18438408 | pmc = 2705838 | doi = 10.1038/ng.128 }} COSMIC also catalogues mutational signatures in human cancer through the COSMIC Signatures group, which represents a collaboration between COSMIC, the Wellcome Sanger Institute, and the University of California, San Diego. The COSMIC signatures database has been leveraged to catalogue the prevalence of specific mutational signatures in human cancer, such as the frequency of ultraviolet radiation-mediated mutagenesis in skin cancers.{{cite journal | vauthors = Mata DA, Williams EA, Sokol E, Oxnard GR, Fleischmann Z, Tse JY, Decker B | title = Prevalence of UV Mutational Signatures Among Cutaneous Primary Tumors | journal = JAMA Network Open | volume = 5 | issue = 3 | pages = e223833 | date = March 2022 | pmid = 35319765 | pmc = 8943639 | doi = 10.1001/jamanetworkopen.2022.3833 }}

• Wellcome Trust Sanger Institute
• Cancer Genome Project

{{reflist|2}}

• [http://www.sanger.ac.uk/genetics/CGP/cosmic/ Catalogue Of Somatic Mutations In Cancer] homepage
• [http://www.sanger.ac.uk/resources/databases/cosmic.html/ WTSI page describing COSMIC]
• [http://www-p53.iarc.fr/ IARC TP53 database]
• [http://cgap.nci.nih.gov/ Cancer genome anatomy project at the National Cancer Institute]
• [http://atlasgeneticsoncology.org/ Atlas of Genetics and Cytogenetics in Oncology and Haematology]
• [http://methycancer.psych.ac.cn/ MethyCancer, a database of human DNA methylation and cancer] {{Webarchive|url=https://web.archive.org/web/20100527041142/http://methycancer.psych.ac.cn/ |date=27 May 2010 }}
• [https://web.archive.org/web/20160304035947/http://bioinformatics.ca/links_directory/database/11912/cosmic COSMIC in the bioinformatics.ca Links Directory]

{{Wellcome Trust}}

Category:Cancer genome databases

Category:Cancer research

Category:Genetic engineering in the United Kingdom

Category:Medical databases in the United Kingdom

Category:Medical genetics in the United Kingdom

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