- COSMIC: somatic cancer genetics at high-resolution. [PMID: 27899578]
Simon A Forbes, David Beare, Harry Boutselakis, Sally Bamford, Nidhi Bindal, John Tate, Charlotte G Cole, Sari Ward, Elisabeth Dawson, Laura Ponting, Raymund Stefancsik, Bhavana Harsha, Chai Yin Kok, Mingming Jia, Harry Jubb, Zbyslaw Sondka, Sam Thompson, Tisham De, Peter J Campbell
Nucleic acids research 2017:45(D1)
1 Citations (Google Scholar as of 2017-02-17)
Abstract: COSMIC, the Catalogue of Somatic Mutations in Cancer (http://cancer.sanger.ac.uk) is a high-resolution resource for exploring targets and trends in the genetics of human cancer. Currently the broadest database of mutations in cancer, the information in COSMIC is curated by expert scientists, primarily by scrutinizing large numbers of scientific publications. Over 4 million coding mutations are described in v78 (September 2016), combining genome-wide sequencing results from 28 366 tumours with complete manual curation of 23 489 individual publications focused on 186 key genes and 286 key fusion pairs across all cancers. Molecular profiling of large tumour numbers has also allowed the annotation of more than 13 million non-coding mutations, 18 029 gene fusions, 187 429 genome rearrangements, 1 271 436 abnormal copy number segments, 9 175 462 abnormal expression variants and 7 879 142 differentially methylated CpG dinucleotides. COSMIC now details the genetics of drug resistance, novel somatic gene mutations which allow a tumour to evade therapeutic cancer drugs. Focusing initially on highly characterized drugs and genes, COSMIC v78 contains wide resistance mutation profiles across 20 drugs, detailing the recurrence of 301 unique resistance alleles across 1934 drug-resistant tumours. All information from the COSMIC database is available freely on the COSMIC website. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.
- COSMIC: High-Resolution Cancer Genetics Using the Catalogue of Somatic Mutations in Cancer. [PMID: 27727438]
S A Forbes, D Beare, N Bindal, S Bamford, S Ward, C G Cole, M Jia, C Kok, H Boutselakis, T De, Z Sondka, L Ponting, R Stefancsik, B Harsha, J Tate, E Dawson, S Thompson, H Jubb, P J Campbell
Current protocols in human genetics 2016:91
400 Citations (Google Scholar as of 2017-02-17)
Abstract: COSMIC (http://cancer.sanger.ac.uk) is an expert-curated database of somatic mutations in human cancer. Broad and comprehensive in scope, recent releases in 2016 describe over 4 million coding mutations across all human cancer disease types. Mutations are annotated across the entire genome, but expert curation is focused on over 400 key cancer genes. Now encompassing the majority of molecular mutation mechanisms in oncogenetics, COSMIC additionally describes 10 million non-coding mutations, 1 million copy-number aberrations, 9 million gene-expression variants, and almost 8 million differentially methylated CpGs. This information combines a consistent interpretation of the data from the major cancer genome consortia and cancer genome literature with exhaustive hand curation of over 22,000 gene-specific literature publications. This unit describes the graphical Web site in detail; alternative protocols overview other ways the entire database can be accessed, analyzed, and downloaded. © 2016 by John Wiley & Sons, Inc. Copyright © 2016 John Wiley & Sons, Inc.
- COSMIC: exploring the world's knowledge of somatic mutations in human cancer. [PMID: 25355519]
Simon A Forbes, David Beare, Prasad Gunasekaran, Kenric Leung, Nidhi Bindal, Harry Boutselakis, Minjie Ding, Sally Bamford, Charlotte Cole, Sari Ward, Chai Yin Kok, Mingming Jia, Tisham De, Jon W Teague, Michael R Stratton, Ultan McDermott, Peter J Campbell
Nucleic acids research 2015:43(Database issue)
731 Citations (Google Scholar as of 2017-02-17)
Abstract: COSMIC, the Catalogue Of Somatic Mutations In Cancer (http://cancer.sanger.ac.uk) is the world's largest and most comprehensive resource for exploring the impact of somatic mutations in human cancer. Our latest release (v70; Aug 2014) describes 2 002 811 coding point mutations in over one million tumor samples and across most human genes. To emphasize depth of knowledge on known cancer genes, mutation information is curated manually from the scientific literature, allowing very precise definitions of disease types and patient details. Combination of almost 20,000 published studies gives substantial resolution of how mutations and phenotypes relate in human cancer, providing insights into the stratification of mutations and biomarkers across cancer patient populations. Conversely, our curation of cancer genomes (over 12,000) emphasizes knowledge breadth, driving discovery of unrecognized cancer-driving hotspots and molecular targets. Our high-resolution curation approach is globally unique, giving substantial insight into molecular biomarkers in human oncology. In addition, COSMIC also details more than six million noncoding mutations, 10,534 gene fusions, 61,299 genome rearrangements, 695,504 abnormal copy number segments and 60,119,787 abnormal expression variants. All these types of somatic mutation are annotated to both the human genome and each affected coding gene, then correlated across disease and mutation types. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.
- COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. [PMID: 20952405]
Simon A Forbes, Nidhi Bindal, Sally Bamford, Charlotte Cole, Chai Yin Kok, David Beare, Mingming Jia, Rebecca Shepherd, Kenric Leung, Andrew Menzies, Jon W Teague, Peter J Campbell, Michael R Stratton, P Andrew Futreal
Nucleic acids research 2011:39(Database issue)
1515 Citations (Google Scholar as of 2017-02-17)
Abstract: COSMIC (http://www.sanger.ac.uk/cosmic) curates comprehensive information on somatic mutations in human cancer. Release v48 (July 2010) describes over 136,000 coding mutations in almost 542,000 tumour samples; of the 18,490 genes documented, 4803 (26%) have one or more mutations. Full scientific literature curations are available on 83 major cancer genes and 49 fusion gene pairs (19 new cancer genes and 30 new fusion pairs this year) and this number is continually increasing. Key amongst these is TP53, now available through a collaboration with the IARC p53 database. In addition to data from the Cancer Genome Project (CGP) at the Sanger Institute, UK, and The Cancer Genome Atlas project (TCGA), large systematic screens are also now curated. Major website upgrades now make these data much more mineable, with many new selection filters and graphics. A Biomart is now available allowing more automated data mining and integration with other biological databases. Annotation of genomic features has become a significant focus; COSMIC has begun curating full-genome resequencing experiments, developing new web pages, export formats and graphics styles. With all genomic information recently updated to GRCh37, COSMIC integrates many diverse types of mutation information and is making much closer links with Ensembl and other data resources.
- COSMIC (the Catalogue of Somatic Mutations in Cancer): a resource to investigate acquired mutations in human cancer. [PMID: 19906727]
Simon A Forbes, Gurpreet Tang, Nidhi Bindal, Sally Bamford, Elisabeth Dawson, Charlotte Cole, Chai Yin Kok, Mingming Jia, Rebecca Ewing, Andrew Menzies, Jon W Teague, Michael R Stratton, P Andrew Futreal
Nucleic acids research 2010:38(Database issue)
391 Citations (Google Scholar as of 2017-02-17)
Abstract: The catalogue of Somatic Mutations in Cancer (COSMIC) (http://www.sanger.ac.uk/cosmic/) is the largest public resource for information on somatically acquired mutations in human cancer and is available freely without restrictions. Currently (v43, August 2009), COSMIC contains details of 1.5-million experiments performed through 13,423 genes in almost 370,000 tumours, describing over 90,000 individual mutations. Data are gathered from two sources, publications in the scientific literature, (v43 contains 7797 curated articles) and the full output of the genome-wide screens from the Cancer Genome Project (CGP) at the Sanger Institute, UK. Most of the world's literature on point mutations in human cancer has now been curated into COSMIC and while this is continually updated, a greater emphasis on curating fusion gene mutations is driving the expansion of this information; over 2700 fusion gene mutations are now described. Whole-genome sequencing screens are now identifying large numbers of genomic rearrangements in cancer and COSMIC is now displaying details of these analyses also. Examination of COSMIC's data is primarily web-driven, focused on providing mutation range and frequency statistics based upon a choice of gene and/or cancer phenotype. Graphical views provide easily interpretable summaries of large quantities of data, and export functions can provide precise details of user-selected data.
- The Catalogue of Somatic Mutations in Cancer (COSMIC). [PMID: 18428421]
S A Forbes, G Bhamra, S Bamford, E Dawson, C Kok, J Clements, A Menzies, J W Teague, P A Futreal, M R Stratton
Current protocols in human genetics 2008:Chapter 10
4 Citations (Google Scholar as of 2017-02-17)
Abstract: COSMIC is currently the most comprehensive global resource for information on somatic mutations in human cancer, combining curation of the scientific literature with tumor resequencing data from the Cancer Genome Project at the Sanger Institute, U.K. Almost 4800 genes and 250000 tumors have been examined, resulting in over 50000 mutations available for investigation. This information can be accessed in a number of ways, the most convenient being the Web-based system which allows detailed data mining, presenting the results in easily interpretable formats. This unit describes the graphical system in detail, elaborating an example walkthrough and the many ways that the resulting information can be thoroughly investigated by combining data, respecializing the query, or viewing the results in different ways. Alternate protocols overview the available precompiled data files available for download. Copyright 2008 by John Wiley & Sons, Inc.
- COSMIC 2005. [PMID: 16421597]
S Forbes, J Clements, E Dawson, S Bamford, T Webb, A Dogan, A Flanagan, J Teague, R Wooster, P A Futreal, M R Stratton
British journal of cancer 2006:94(2)
315 Citations (Google Scholar as of 2017-02-17)
Abstract: The Catalogue Of Somatic Mutations In Cancer (COSMIC) database and web site was developed to preserve somatic mutation data and share it with the community. Over the past 25 years, approximately 350 cancer genes have been identified, of which 311 are somatically mutated. COSMIC has been expanded and now holds data previously reported in the scientific literature for 28 known cancer genes. In addition, there is data from the systematic sequencing of 518 protein kinase genes. The total gene count in COSMIC stands at 538; 25 have a mutation frequency above 5% in one or more tumour type, no mutations were found in 333 genes and 180 are rarely mutated with frequencies <5% in any tumour set. The COSMIC web site has been expanded to give more views and summaries of the data and provide faster query routes and downloads. In addition, there is a new section describing mutations found through a screen of known cancer genes in 728 cancer cell lines including the NCI-60 set of cancer cell lines.
- The COSMIC (Catalogue of Somatic Mutations in Cancer) database and website. [PMID: 15188009]
S Bamford, E Dawson, S Forbes, J Clements, R Pettett, A Dogan, A Flanagan, J Teague, P A Futreal, M R Stratton, R Wooster
British journal of cancer 2004:91(2)
661 Citations (Google Scholar as of 2017-02-17)
Abstract: The discovery of mutations in cancer genes has advanced our understanding of cancer. These results are dispersed across the scientific literature and with the availability of the human genome sequence will continue to accrue. The COSMIC (Catalogue of Somatic Mutations in Cancer) database and website have been developed to store somatic mutation data in a single location and display the data and other information related to human cancer. To populate this resource, data has currently been extracted from reports in the scientific literature for somatic mutations in four genes, BRAF, HRAS, KRAS2 and NRAS. At present, the database holds information on 66 634 samples and reports a total of 10 647 mutations. Through the web pages, these data can be queried, displayed as figures or tables and exported in a number of formats. COSMIC is an ongoing project that will continue to curate somatic mutation data and release it through the website.