The odds ratio and effect allele coding were taken from the PGC results described earlier. First, we considered a polygenic risk score from the imputed PGC genome-wide-significant variants, corresponding to a p value threshold of 5 × 10−8. At this threshold, we included all the variants (and their surrogates) identified by the PGC. We then computed polygenic risk scores with increasing numbers of variants by relaxing the inclusion p value threshold at each order of magnitude below 5 × 10−8. For these scores, we only considered variants where the reference and alternate alleles matched between our imputed genotypes and the PGC-reported genotypes. Of the variants, 93.12% matched, and the majority of variants that did not match were indels or multi-allelic sites. We chose to exclude indels due to their allelic complexity and the multiple ways that indel alleles have been coded in sequence VCF files (Tan et al. 2015). It would be difficult if not impossible to ensure that we accurately coded effect alleles for indels and multi-allelic sites for all the variants. We also removed low-frequency SNPs (MAF <
