Question: polygenic risk score
gravatar for maki.dur
2.7 years ago by
maki.dur0 wrote:

Hi, Recently, we got a project connected with genome genome wide association studies. We are trying to associate around 30 SNPs with aneurysm. We have in plan to calculate polygenic risk score using PRSice. The problem is that we cannot find any publicly available GWAS database as a reference.

Is there any recommendation for some possible GWAS databases or way to generate one?

I saw in PLINK resources there are some datasets(HapMap...). Does anybody have experience with that?

Thanks in advance, Marija

prs gwas • 1.8k views
ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by maki.dur0

So you are looking for a GWAS dataset of geographically matched individuals to your population without aneurysm? It would be better to chose a title reflecting that.

ADD REPLYlink written 2.7 years ago by WouterDeCoster38k

Yes, something like that. We have sample population, but we are missing GWAS databases for reference as it's required here.

ADD REPLYlink written 2.7 years ago by maki.dur0

Obviously you need a control population. Depending on the effect sizes (relative risk) you expect, you might need a few hundred up to tens of thousands of control individuals. How many cases/patients do you have? Which population are you studying?

ADD REPLYlink written 2.7 years ago by WouterDeCoster38k
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