Question: Interpretation of Polygenic Risk Score
3
gravatar for Lb
19 months ago by
Lb40
Lb40 wrote:

Hi,

I am new to Bioinformatics and I would really appreciate some help with my new project. I am trying to calculate and interpret Polygenic Risk Score that I got with Model 4 described in this paper (page 9):

Image and video hosting by TinyPic

In Table 3 - Supplementary Data (at the end of the page) there is a list of all SNPs used in the model with the corresponding weights (betas). To observe the PRS distribution on a test set, I did the following:

I used R package: MafDb.gnomAD.r2.0.1.GRCh38 to get a MAF for each SNP listed in Sup. Table 3. Then I calculated the expected genotype frequencies under random mating using Hardy–Weinberg principle and used these frequencies to generate genotype data; more specifically, I generated the number of reference alleles for each pair (SNP, sample) which is either 0, 1 or 2 (g_it from the model mentioned above).

I plotted the distribution of PRS values and I got this: Image and video hosting by TinyPic

Now I am a bit confused about how to interpret these results. I would like to get the interpretation in the form of relative risk. Any tips on how to do that are welcome.

Thanks! :)

snp polygenic risk score maf • 1.0k views
ADD COMMENTlink modified 19 months ago • written 19 months ago by Lb40
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1998 users visited in the last hour
_