SNP array genotyping data in cancer

Question

[imagineyd]

Hi all :)

I'm looking for SNP array genotyping data of cancer patients, especially germ line variants.

So, I downloaded lots of SNP data from controlled TCGA access, but I want to find independent TCGA data sets.

I think ICGC is one of the option, but I can't find SNP array genotyping data from ICGC (of course, I can access controlled data in ICGC). As you know, most cancer genome papers used SNP array for evaluating copy number alterations. So I'm sure there are these kinds of data set in ICGC or somewhere.

Does anybody know about this or could you give me some comments ?

Many thanks!

Answer 1

[5utr]

You can find a lot of SNP array data on GEO, some are on cancer types that are not present in TCGA. You can use the advanced search from GEO using "snp genotyping by snp array" in [DataSet Type] plus specific keyword for the type of cancer you are interested in.

[imagineyd]

Thanks Gian :) You're right, but I want to find "snp genotyping by snp array" with germline dataset.

I think GEO doesn't cover these kinds of datasets :(