Polygenic risk score percentile cutoff

Question

[endoplasmicreticulum12]

Dear everyone,

I working on PRS using information from PGS catalogue, however my data from illumina infinium GDA was not covered all SNP in each PGS catalogue just only 10-20%.

I would like to know that which percentile should I use as cutoff from Z score in PRS plot.

Edgar

Answer 1

[UnivStudent]

Hi Edgar, you need to use imputation to use the genotyped to get better coverage of the SNPs in the genome. Usually people use an imputation server like Michigan (https://imputationserver.sph.umich.edu) or TopMed (https://topmedimpute.readthedocs.io/en/latest/) for this.