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My lab has been using TCGA data (somatic mutations and clinical data) to develop panels of genes and of mutations we expect to see in certain cancer populations. We'd like to validate our panels by checking how they hold up against other cancer datasets.

I know that one resource we can use is the International Cancer Genome Consortium but I'm wondering if members of this forum can suggest a few other places we can get both clinical and somatic mutations data for cohorts of cancer patients.

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The cBioPortal is an extraordinarily useful centralized source of cancer datasets. As of this date, it contains data from 105 cancer genomics studies. Many of these are TCGA studies, but the list includes many others as well. Furthermore, the human interface to the data is among the best I've seen.

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    $\begingroup$ That's a really neat portal I was unaware of, and I'll certainly have to edit my answer now! But since the question needs a comparison dataset against TGCA, what is the use of more TGCA data? $\endgroup$
    – James
    Commented Dec 16, 2015 at 1:43
  • $\begingroup$ @James : many of the studies listed there are not TCGA. In my field of head and neck cancer, there are 2 (partially overlapping) TCGA data sets and 4 other data sets. The balance differs among cancer types. The TCGA data sets, of course, are typically the largest. $\endgroup$
    – EdM
    Commented Dec 16, 2015 at 1:50
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As I'm sure you're aware, there is no complete centralised database for cancer gene mutations. The most comprehensive database is the TGCA as you've already mentioned. That doesn't mean that other data isn't out there.

A broad option that might fit your needs is to query OMIM hosted by NCBI. You can search "cancer" or something more specific and then select the dbSNP tab and it will return a list of gene locations of mutations that match the query.

Screenshot of OMIM query of cancer.

For a more specific search, COSMIC hosted by SANGER allows downloads of the "cancer genes" in fasta format, and various other downloads with other information are available. It's manually curated which is always a bonus, however this does mean that it's limited to just a few genes. There is also BIC. This is specifically focussed on genes related to breast cancer and is hosted by NHGRI. Again, an account is required for the download and it is limited to genes affecting breast cancers.

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