Question: What's the difference between GWAS Catalog and COSMIC database ?
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gravatar for hsiaoyi0504
4 months ago by
hsiaoyi050440
Taiwan
hsiaoyi050440 wrote:

Hi there, I am new to analyze GWAS data. I see there are at least two major databases:

It looks like they have similar dataset. Can anyone tell me what's the difference between this two databases ?

snp gwas • 242 views
ADD COMMENTlink modified 4 months ago by Kevin Blighe41k • written 4 months ago by hsiaoyi050440
4
gravatar for Kevin Blighe
4 months ago by
Kevin Blighe41k
Guy's Hospital, London
Kevin Blighe41k wrote:

They are quite different, in fact.

I will not go into the finer details, but, as a quick summary:

COSMIC

Primary goal is to catalogue somatic mutations in cancer, so, mutations that are present in a tumour biopsy that are not present in the matched normal. In some cases, a variant that 'may' be somatic is included if it was identified in a tumour sample that came from a study where no matched normal was used (or a pool of normals was used).

GWAS Catalog

This catlogues statistically significant variants that were identified in GWAS. It catalogues these for cancer and other diseases / traits, too. So, these are likely germline variants that have been found to increase/decrease risk for the phenotype in question. It is obviously well documented that germline variants, even those with MAFs as high as 10%, can increase risk of cancer.

Trust this helps.

Kevin

ADD COMMENTlink written 4 months ago by Kevin Blighe41k
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