To create comparable polygenic risk scores across samples, we selected a set of SNPs that were available in all four samples with a minor allele frequency (MAF) > 5% and an imputation quality INFO/R2 score > .90 (n = 3,116,334). These SNPs were then used to create polygenic scores with the software package PRSice (Euesden et al., 2015), which automates the implementation of the score procedure in PLINK v. 1.9 (Chang et al., 2015) to optimize selection of the most informative pairwise polygenic score. Best-guess genotypes with a certainty above 0.9 were used in creating the polygenic scores for all samples.
