We used the clump and score procedures separately by ancestry in PLINK to sum each individual’s total number of minor alleles from the score SNPs, with each SNP weighted by the negative log of the association p value and sign of the association (beta) statistic from the ancestry-specific results. Clumping was done with respect to the linkage disequilibrium (LD) pattern in the appropriate 1000 Genome Phase 3 ancestry sample (EUR and AFR) using a 500kb physical distance and an LD threshold of r2 >= 0.25. Thus, the polygenic scores were constructed from SNPs that captured independent genetic association signals from the discovery GWAS. We calculated a series of scores that included SNPs meeting increasingly stringent p-value thresholds (p < .0001, p < .001, p < .01, p < .05, p < .10, p < .20, p < .30, p < .40, and p < .50). All models included sex and the first 10 within-ancestry principal components as covariates.
