HW 6 GRS

HW 6 GRS

by Teresa Kortz -

Hello,

I think we only spent one slide on GRS, so I am struggling to answer the last part of the GRS question. I also am not sure that I understand what it is asking. The question states:

"Suppose that you tested the GRS from your trait, and then you also tested the GRS with another trait, say, BMI for example. Say the GRS has p=10-4 for that trait – what does that mean? Was there any benefit to testing the GRS, versus the individual variants?"

Is the GRS p=10-4 referring to the p-value for BMI? I have no basis for reference for significant GRS p-values; is there a standard level of significance (like P<0.05) or is it affected by the number of SNPs in the GRS. Without knowing the p-values for the individual variants, how can we comment on whether there was a benefit to testing the GRS?


Thanks,
Teresa

Re: HW 6 GRS

by Thomas Hoffmann -

Hi Teresa,

A genetic risk score (GRS) is a sum of all of the SNPs that go into it. When you test the GRS, you are just testing the sum, not the individual SNPs that are added into it. So, when you are assessing significance of a GRS, that means you should be adjusting for doing just the one test, so the usual p<0.05 would be significant. If you were to be testing each individual variant, then you would have a higher multiple correction burden... what do you think that would do to the power?...

Best,

Tom