Database for Somatic Copy Numbers

Question

[cookersjs]

Hello!

I am interested in, as the title implies, a relatively up-to-date database that contains information on copy number variation. I know COSMIC offers it, but I am not sure that they are somatic. I am inclined to think that they are, given they are the Catalogue of Somatic Mutations in Cancer, but I am not 100% sure.

I'd like to try and find out if other databases exist out there that I do not know about, or if someone could verify that these are in fact somatic copy number variation from COSMIC.

Thanks!

Answer 1

[Max Ivon]

If you want to focus on high confidence mutations you may want to have a look at results of the systemic studies like TCGA or ICGC rather than just mutation database. Try cbioportal.org to overview such projects for different tumor types and focus on the one you are interested in. If you dont need to focus on the certain tumor type have a look at pan-cancer studies which are also listed there (MSK-IMPACT for ex.). It has web-api which will help to grasp the data you need.

[cookersjs]

Thanks very much, I believe that COSMICs copy number data actually comes from both TCGA and ICGC, but I hadn't thought to try cbioportal -- definitely will!