Genotyping quality control was performed and SNPs with a minor allele frequency < 5 percent, significant deviation from Hardy‐Weinberg equilibrium (P < 0.001), or a call rate < 98 percent were removed from further analyses. Individuals with genotyping call rates lower than 95 percent were also removed. Any strand‐ambiguous SNPs were removed from the GS:SFHS dataset and genotypes were LD pruned using clump‐based pruning (r 2 = 0.25, 300 kb window) to create a set of SNPs in linkage equilibrium. GS:SFHS genetic data included only raw genotypes (unimputed data) and therefore only SNPs common to the Yale‐Penn/SAGE samples and GS:SFHS were used to create polygenic scores.
