A custom Java program, GeneticRiskScoreCalculator-v0.1.0c (https://github.com/molgenis/systemsgenetics/tree/master/GeneticRiskScoreCalculator), was used for calculating several PGSs in parallel. Independent effect SNPs for each summary statistics file were identified by double-clumping, first using a 250kb distance and subsequently a 5Mb distance with a linkage disequilibrium (LD) threshold R2=0.1. Weighted PGSs were calculated by summing the risk alleles for each independent SNP weighted by its GWAS effect size (beta or log(OR) from the GWAS study). Five GWAS P-value thresholds (P<5×10−8, 1×10−5, 1×10−4, 1×10−3 and 1×10−2) were used for constructing PGSs for each summary statistics file. HLA region (chr6:25,000,000–35,000,000) was omitted from calculations and PGSs were scaled to fall between 0 and 2, for compatibility with the QTL mapping pipeline.
