Are the PRS (Polygenic Risk Scores) available for the SNP arrays from CommonMind and PsychENCODE? If not, what is the easiest way to calculate them?
Created by Assif Yitzhaky assify Hi @assify
I think that they don't share this information because the PRS can change depending on how you QC the genotype files, or if you subset the cohort differently, or if you use different base GWAS results to calculate your PRS (e.g. Ripke et al 2014 vs Pardiņas et al 2018), so it's not easy to share PRS values for the entire cohort. But you can generate your own PRSs using PRSice-2 (https://www.prsice.info/quick_start/). I am actually also doing this right now, and found some issues with the results, so I am going to create another thread to see if I can get any ideas on how to troubleshoot my analysis. Good luck!