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 ?
They are quite different, in fact.
I will not go into the finer details, but, as a quick summary:
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).
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
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