Combine the polygenic scores in the individuals

Question

[rse]

Hi,

I generated Polygenic scores (PGS) of several individuals using the plink software. Is there any way to combine all the polygenic scores in the individuals?

Thank you

[zx8754]

Why? Are we trying to compare populations?

[rse]

Yes, we are trying to compare populations

[zx8754]

Maybe compare distributions instead?

[rse]

Distributions means? I have SCORESUM (polygenic score values) and i have to test for phenotype enrichment against my phenotype file. How should i do it? Thanks in advance

[Kevin Blighe]

Perform a standard regression between the phenotype and the SCORESUM, and adjust for any covariates.

Keep in mind that 'polygenic risk score' is a general term and that there are so many ways to derive these. Most methods start from the beta coefficient from the regression fit, i.e., between phenotype ~ SNP

[rse]

Thank you everyone for your valuable responses. Will try it out on the data.

Answer 1

[Sam]

Maybe you can try out dedicated PRS softwares such as PRSice, lassosum or LDpred