COSMIC 2005

Abstract

The Catalogue Of Somatic Mutations In Cancer (COSMIC) database and web site was developed to preserve somatic mutation data and share it with the community. Over the past 25 years, approximately 350 cancer genes have been identified, of which 311 are somatically mutated. COSMIC has been expanded and now holds data previously reported in the scientific literature for 28 known cancer genes. In addition, there is data from the systematic sequencing of 518 protein kinase genes. The total gene count in COSMIC stands at 538; 25 have a mutation frequency above 5% in one or more tumour type, no mutations were found in 333 genes and 180 are rarely mutated with frequencies <5% in any tumour set. The COSMIC web site has been expanded to give more views and summaries of the data and provide faster query routes and downloads. In addition, there is a new section describing mutations found through a screen of known cancer genes in 728 cancer cell lines including the NCI-60 set of cancer cell lines.

Figure 1

Tissue overview. The mutation data for a selected tissue is presented in a summary format, in this case for prostate. The top 5 genes with data in COSMIC are selected as the genes with the highest rank score using the method; RankScore=number of mutations/number of samples – 1.6449 × squareroot((number of mutations/number of samples) × (1–(number of mutations/number of samples)/number of samples). The data is presented in both graphical and tabular formats. Further genes with and without mutations for the selected tissue are listed. All of the gene names can be followed to view the details of the mutations.

Figure 2

Gene summary. The initial output for a gene is a graphical view of the mutations distributed along the linear amino acid sequence of the gene. This is the data for RB1. The positions of the mutations are shown by tick marks with tracks showing the total number of mutations and mutations that are insertions, nonsense substitutions, missense substitutions, deletions and complex substitutions. In addition the summary presents the number of references curated, the number of samples for the gene and the number of samples with mutations. There are multiple links from this view leading to web pages describing more details of the mutations, the gene and the references that have been curated.