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. 2019 Jan 8;47(D1):D941-D947.
doi: 10.1093/nar/gky1015.

COSMIC: the Catalogue Of Somatic Mutations In Cancer

John G Tate  1 , Sally Bamford  1 , Harry C Jubb  1   2 , Zbyslaw Sondka  1 , David M Beare  1 , Nidhi Bindal  1 , Harry Boutselakis  1 , Charlotte G Cole  1 , Celestino Creatore  1 , Elisabeth Dawson  1 , Peter Fish  1 , Bhavana Harsha  1 , Charlie Hathaway  1 , Steve C Jupe  1 , Chai Yin Kok  1 , Kate Noble  1 , Laura Ponting  1 , Christopher C Ramshaw  1 , Claire E Rye  1 , Helen E Speedy  1   3 , Ray Stefancsik  1 , Sam L Thompson  1 , Shicai Wang  1 , Sari Ward  1 , Peter J Campbell  1 , Simon A Forbes  1
Affiliations

COSMIC: the Catalogue Of Somatic Mutations In Cancer

John G Tate et al. Nucleic Acids Res. .

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.

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Figures

Figure 1.
Figure 1.
The gene histogram for the tumour suppressor gene TP53, showing the range of data available for TP53. When showing the amino acid sequence, as here, the top panel displays the single residue mutations across the gene. When zoomed in sufficiently, the amino acid sequence itself is shown beneath. If the gene has Pfam families associated with it, these are shown next, along with any Pfam annotations, such as the metal ion binding sites as here in TP53. Next, we show the presence of complex mutations and insertions/deletions, followed by copy number gain/loss, expression levels and methylation. A toggle in the filter panel in the gene page may be used to switch the view from amino acid to nucleic acid coordinate systems, and the switch is reflected in the exact data that is available in the histogram.
Figure 2.
Figure 2.
Cancer Gene Census Hallmark detail page. A gene page for DICER1 presents a spectrum of cancer-related functions of the protein coded by the gene. Involvement in each of the relevant hallmarks of cancer is concisely characterized with the indication whether the protein in its wild-type form promotes or suppresses each hallmark. All the information is referenced with links to the literature source via PubMed provided on the page.
Figure 3.
Figure 3.
Understanding the relevance of mutation peaks in protein structure. The repertoire of mutations across TP53 are represented on a protein structure in three dimensions (PDB id: 4HJE). High-frequency substitutions are highlighted in red to show their positions relative to protein features and each other. In this example, the most frequent two mutations observed across all cancers in TP53 (at codons R248 and R273) cluster at the DNA binding surface.
Figure 4.
Figure 4.
Pages showing data, such as the gene page, here shown for TP53, have been redesigned and restyled, with the page divided clearly into distinct sections.
See this image and copyright information in PMC

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