Somatic mutation data refers to mutations that may have clinical or treatment implications in cancer and possibly other diseases. This data type is obtained from the four data sources highlighted below.
Cancer Gene Census is a collection of genes for which mutations have been causally implicated in cancer. The Catalogue of Somatic Mutations in Cancer (COSMIC) at the Wellcome Sanger Institute provides us with the set of genes associated with specific cancers in the Cancer Gene Census, in addition to other cancers associated with that gene in the COSMIC database. The exhaustive curation of the Cancer Gene Census genes is merged with genome-wide annotations from whole genome and large-scale systematic screens publications as well as open-access data from The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC).
UniProt manually curates somatic mutations from the literature for the associations between genes and cancers.
The EMBL-EBI European Variation Archive (EVA) provides data on somatic mutations in both cancer and other diseases.
IntOGen provides somatic mutations, genes and pathways involved in tumorigenesis. We have imported the latest data from 6,792 samples across 28 cancer types described by Rubio-Perez et al (2015), including tumours of The Cancer Genome Atlas (TCGA) studies. In these new dataset, false mutation calls have been filtered out and additional expression data is available for a larger number of samples in certain tumour types. This analysis has now been updated but not yet released on the IntOGen website; so there can be discrepancies between the two resources.