COSMIC: the Catalogue Of Somatic Mutations In Cancer.

John Tate ,Bhavana Harsha,Kate Noble,Shicai Wang,Celestino Creatore,Elisabeth Dawson,Laura Ponting,Harry Boutselakis,Nidhi Bindal,Sari Ward,Sally Bamford,Peter Fish,Charlie Hathaway,Chai Yin Kok,Helen E Speedy ,Peter J Campbell ,Charlotte G Cole ,Christopher Ramshaw ,Claire E Rye ,Sam Thompson ,David Beare ,Steve Jupe ,Raymund Stefancsik ,Zbysław Sońdka ,Harry Jubb ,Simon Forbes

doi:10.1093/nar/gky1015

John Tate , Bhavana Harsha + Show 24 more

Open Access

https://doi.org/10.1093/nar/gky1015

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Journal: Nucleic acids research	Publication Date: Oct 29, 2018
Citations: 3306	License type: CC BY 4.0

Affiliation: Wellcome Sanger Institute, Open Targets

Abstract

COSMIC, the Catalogue Of Somatic Mutations In Cancer (https://cancer.sanger.ac.uk) is the most detailed and comprehensive resource for exploring the effect of somatic mutations in human cancer. The latest release, COSMIC v86 (August 2018), includes almost 6 million coding mutations across 1.4 million tumour samples, curated from over 26 000 publications. In addition to coding mutations, COSMIC covers all the genetic mechanisms by which somatic mutations promote cancer, including non-coding mutations, gene fusions, copy-number variants and drug-resistance mutations. COSMIC is primarily hand-curated, ensuring quality, accuracy and descriptive data capture. Building on our manual curation processes, we are introducing new initiatives that allow us to prioritize key genes and diseases, and to react more quickly and comprehensively to new findings in the literature. Alongside improvements to the public website and data-download systems, new functionality in COSMIC-3D allows exploration of mutations within three-dimensional protein structures, their protein structural and functional impacts, and implications for druggability. In parallel with COSMIC’s deep and broad variant coverage, the Cancer Gene Census (CGC) describes a curated catalogue of genes driving every form of human cancer. Currently describing 719 genes, the CGC has recently introduced functional descriptions of how each gene drives disease, summarized into the 10 cancer Hallmarks.

Highlights

COSMIC, the Catalogue Of Somatic Mutations In Cancer, draws together the available information about the effects of somatic mutations across the range of human cancers
As described previously (1), the primary data in COSMIC are derived directly from the scientific literature by expert manual curators, who read and digest journal articles and extract the detailed mutation data within, along with any additional information such as environmental factors or patient pre-disposition that may be accessible. In parallel with this broad-ranging manual curation process, a second curation track brings into COSMIC a wealth of larger-scale but more narrowly-focussed data from systematic screens, via the major cancer data portals and from the supplementary tables and downloadable files associated with curated papers
A total of 223 key cancer genes are subject to deep, exhaustive curation by expert scientists, gathering information from 26 251 papers to date. This is merged with genome-wide annotations from 466 whole genome and large-scale systematic screens publications, as well as openaccess data from The Cancer Genome Atlas (TCGA) (3) and the International Cancer Genome Consortium (ICGC) (4)

Summary

Introduction

COSMIC, the Catalogue Of Somatic Mutations In Cancer, draws together the available information about the effects of somatic mutations across the range of human cancers. The CGC (https://cancer.sanger.ac.uk/census) is an ongoing, long-term project within COSMIC to catalogue all genes that are causally implicated in cancer through somatic and germline mutations. When a new cancer gene is added to the CGC at Tier 1, an exhaustive literature search is performed in PubMed to identity any publications reporting somatic mutations in cancer.

Results

Conclusion