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

By S. Forbes, D. Beare, P. Gunasekaran, Kenric Leung, Nidhi Bindal, Harry Boutselakis, Minjie Ding, S. Bamford, C. Cole, Sari Ward and 7 more. Nucleic Acids Res., 2014

2,319 citations recorded by the source corpus.

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.

Subfields: Cancer Research, Genetics

View Paper: https://www.semanticscholar.org/paper/c599f101a40d156d2bbd689c0dd08425e9a96194

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Citations in the corpus

Off-target toxicity is a common mechanism of action of cancer drugs undergoing clinical trials (2019, background): “S16C) and have not been previously observed in the Catalog of Somatic Mutations in Cancer database (41).”
The Human Gene Mutation Database: towards a comprehensive repository of inherited mutation data for medical research, genetic diagnosis and next-generation sequencing studies (2017, neutral): “HGMD has never sought to include either somatic or mitochondrial mutations, which are well covered by COSMIC (Forbes et al. 2015) and MitoMap (Lott et al.”
Integrated molecular analysis of tumor biopsies on sequential CTLA-4 and PD-1 blockade reveals markers of response and resistance (2017, methodology): “Tumor suppressor genes annotated in recurrent copy number loss plots were obtained as cancer genes present in both the COSMIC (v77) (68) and TSGene (69) databases.”
Universal Patterns of Selection in Cancer and Somatic Tissues (2018, positive): “Of these, 54% are canonical cancer genes present in the Cancer Gene Census (Forbes et al., 2015).”
COSMIC: somatic cancer genetics at high-resolution (2016, background): “As described previously (2,3), curation of somatic mutation data into COSMIC proceeds via two parallel pathways.”
Lnc2Cancer: a manually curated database of experimentally supported lncRNAs associated with various human cancers (2015, background): “For example, COSMIC (23) collects cancer genes and mutations, MethyCancer (24) and PubMeth (25) aim to investigate DNA methylation in cancer, and miRCancer (26) provides literature-supported microRNA and cancer associations; however, no resource is currently devoted to collecting the latest and expe”
Human Primary Liver Cancer -derived Organoid Cultures for disease modelling and drug screening (2017, positive): “A cancer related set of variants was defined by adding the following filtering 1261 steps: (v) SNVs which were included in dbSNP (v150) [77] were excluded, with the 1262 exception of those which were also included in COSMIC (v76) [78].”
A SPECTRAL APPROACH INTEGRATING FUNCTIONAL GENOMIC ANNOTATIONS FOR CODING AND NONCODING VARIANTS (2016, background): “non-recurrent somatic noncoding mutations in the COSMIC database [39] (the GWAVA scores are only available for a small number of the COSMIC variants, namely those that have been reported in dbSNP; therefore we omit the comparison with GWAVA for this dataset).”
Open Targets: a platform for therapeutic target identification and validation (2016, methodology): “For example, to compute the somatic mutation data type score for the association ‘BRCA2breast carcinoma’, the data source scores from Cancer Gene Census (31), the European Variation Archive (http://www.”