October 2014; build hg19) using SHAPEIT2 (Delaneau et al., 2012) and then Minimac3 (Das et al., 2016). Only non-palindromic variants, with missing rates < 5%, MAF > 3%, and HWE p values > 0.0001 were used for imputation. Imputed SNPs with information (INFO) scores < 0.30 or individual genotype probability scores < 0.90 were excluded. For the final dataset for PRS construction, palindromic SNPs (A/T or C/G), monomorphic SNPs, SNPs that did not pass Hardy-Weinberg equilibrium (HWE p < 1e-6), and SNPs with a minor allele frequency (MAF) less than 0.005 were excluded. In total, 6,881,872 SNPs passed quality control and data cleaning thresholds and were available for analysis. Genotypes that did not pass quality control prior to and upon imputation were excluded from PRS construction.
