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. 2017 Jan 4;45(D1):D777-D783.
doi: 10.1093/nar/gkw1121. Epub 2016 Nov 28.

VSports - COSMIC: somatic cancer genetics at high-resolution

Simon A Forbes  1 , David Beare  2 , Harry Boutselakis  2 , Sally Bamford  2 , Nidhi Bindal  2 , John Tate  2 , Charlotte G Cole  2 , Sari Ward  2 , Elisabeth Dawson  2 , Laura Ponting  2 , Raymund Stefancsik  2 , Bhavana Harsha  2 , Chai Yin Kok  2 , Mingming Jia  2 , Harry Jubb  2 , Zbyslaw Sondka  2 , Sam Thompson  2 , Tisham De  2 , Peter J Campbell  2
Affiliations

COSMIC: somatic cancer genetics at high-resolution

Simon A Forbes et al. Nucleic Acids Res. .

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 VSports手机版. 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. .

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"V体育官网" Figures

Figure 1.
Figure 1.
The front page of COSMIC provides easy ways to search and navigate the database; various tools are available for different perspectives on similar data, and multiple descriptive pages detail data curation procedures and current contents.
Figure 2.
Figure 2.
The main Gene Analysis histogram summarises all mutation content across a single gene, in this case gene ABL1. From top-to-bottom, histograms represent mutation recurrence, at each nucleotide/amino acid position, divided into separate segments for single nucleotide substitutions, multinucleotide substitutions, insertions, deletions, copy number gain/loss, gene over/under-expression and CpG hyper/hypo-methylation. Mutation recurrence across the tyrosine kinase domain (highlighted in purple) indicates that this, when mutated, is the key region driving cancer.
Figure 3.
Figure 3.
Several named therapeutics have been described treating ABL1-driven cancers, and many studies have reported novel mutations causing resistance to these therapies. This histogram shows a long list of mutations associated with resistance to named therapeutics, with a histogram bar showing their recurrence.
Figure 4.
Figure 4.
COSMIC has grown rapidly in recent years, as larger numbers of genes are curated, and additional mutation mechanisms are encompassed. The graphic shows a simple representation of the size of the database supporting the COSMIC website from 2010 to 2016 (gzipped Oracle dmp file, in Mb).
See this image and copyright information in PMC

References

    1. Bamford S., Dawson E., Forbes S., Clements J., Pettett R., Dogan A., Flanagan A., Teague J., Futreal P.A., Stratton M.R., et al. The COSMIC (Catalogue of Somatic Mutations in Cancer) database and website. Br. J. Cancer. 2004;91:355–358. - PMC - PubMed
    1. Forbes S.A., Beare D., Gunasekaran P., Leung K., Bindal N., Boutselakis H., Ding M., Bamford S., Cole C., Ward S., et al. COSMIC: exploring the world's knowledge of somatic mutations in human cancer. Nucleic Acids Res. 2015;43:D805–D811. - PMC - PubMed
    1. Forbes S.A., Beare D., Bindal N., Bamford S., Ward S., Cole C.G., Jia M., Kok C., Boutselakis H., De T., et al. COSMIC: High-Resolution Cancer Genetics Using the Catalogue of Somatic Mutations in Cancer. Curr. Protoc. Hum. Genet. 2016;91:10.11.1–10.11.37. - PubMed
    1. Futreal P.A., Coin L., Marshall M., Down T., Hubbard T., Wooster R., Rahman N., Stratton M.R. A census of human cancer genes. Nat. Rev. Cancer. 2004;4:177–183. - PMC - PubMed
    1. Collins F.S., Barker A.D. Mapping the cancer genome. Pinpointing the genes involved in cancer will help chart a new course across the complex landscape of human malignancies. Sci. Am. 2007;296:50–57. - PubMed

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