COSMIC: exploring the world’s knowledge of somatic mutations in human cancer

COSMIC: exploring the world’s knowledge of somatic mutations in human cancer

2014 | 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 and Peter J. Campbell
COSMIC is the world's largest and most comprehensive resource for exploring the impact of somatic mutations in human cancer. The latest release (v70; Aug 2014) includes 2,002,811 coding point mutations in over one million tumor samples and across most human genes. Mutation information is manually curated from the scientific literature, allowing precise definitions of disease types and patient details. The database combines almost 20,000 published studies to provide insights into how mutations and phenotypes relate in human cancer, and emphasizes knowledge breadth through curation of over 12,000 cancer genomes, driving discovery of unrecognized cancer-driving hotspots and molecular targets. COSMIC also details over 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. COSMIC is a database system designed to bring together the world's information on somatic mutations in human cancer into one single system and make it easily explorable. Gene-focused manual curation delivers deep mutation profiles on known cancer genes selected from the Cancer Gene Census. These profiles, across more than 2500 human cancer diseases, allow deep stratification of which mutations are causing which cancers. Systematic curation of cancer genomes, both via publication and consortium data portals, generates huge breadth of knowledge across all somatic human genome annotations, providing substantial power to discover new cancer-causing events. COSMIC's database content includes manual curation of published cancer mutation data via two complementary approaches. Over 2500 cancer disease classifications are currently described in COSMIC, from 47 primary tissue types, and manual curation is the only way to capture the level of detail required to define these populations. Complementary to the manual curation effort, a semi-automated approach has been developed for curation of large cancer genome (and exome) data sets. Data sources are identified from the published literature and online data portals. Over 300 cancer genome publications have now been curated, and COSMIC includes substantial data sets from The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) projects. The data in COSMIC are available in a number of different ways, including a custom website, BioMart, and downloadable formats. The website provides a variety of tools for exploring mutation data, including a genome browser and various data visualizations. The database is also available for download in multiple formats, including CSV and VCF. COSMIC continues to grow, with the database size increasing significantly since its launch in 2004. The database is expected toCOSMIC is the world's largest and most comprehensive resource for exploring the impact of somatic mutations in human cancer. The latest release (v70; Aug 2014) includes 2,002,811 coding point mutations in over one million tumor samples and across most human genes. Mutation information is manually curated from the scientific literature, allowing precise definitions of disease types and patient details. The database combines almost 20,000 published studies to provide insights into how mutations and phenotypes relate in human cancer, and emphasizes knowledge breadth through curation of over 12,000 cancer genomes, driving discovery of unrecognized cancer-driving hotspots and molecular targets. COSMIC also details over 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. COSMIC is a database system designed to bring together the world's information on somatic mutations in human cancer into one single system and make it easily explorable. Gene-focused manual curation delivers deep mutation profiles on known cancer genes selected from the Cancer Gene Census. These profiles, across more than 2500 human cancer diseases, allow deep stratification of which mutations are causing which cancers. Systematic curation of cancer genomes, both via publication and consortium data portals, generates huge breadth of knowledge across all somatic human genome annotations, providing substantial power to discover new cancer-causing events. COSMIC's database content includes manual curation of published cancer mutation data via two complementary approaches. Over 2500 cancer disease classifications are currently described in COSMIC, from 47 primary tissue types, and manual curation is the only way to capture the level of detail required to define these populations. Complementary to the manual curation effort, a semi-automated approach has been developed for curation of large cancer genome (and exome) data sets. Data sources are identified from the published literature and online data portals. Over 300 cancer genome publications have now been curated, and COSMIC includes substantial data sets from The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) projects. The data in COSMIC are available in a number of different ways, including a custom website, BioMart, and downloadable formats. The website provides a variety of tools for exploring mutation data, including a genome browser and various data visualizations. The database is also available for download in multiple formats, including CSV and VCF. COSMIC continues to grow, with the database size increasing significantly since its launch in 2004. The database is expected to
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