We used results from the Social Science Genetic Association Consortium (SSGAC) GWAS of educational attainment [20], to construct educational attainment genome-wide polygenic scores (EduYears-GPS) in the COGA sample. Although polygenic scores are often described as polygenic risk scores, we prefer the term genome-wide polygenic score for this study. This is because ‘risk’ connotes a negative outcome, whereas educational attainment is typically valued. After removing palindromic SNPs (which can be ambiguous with respect to the reference allele in different samples), we used the clump and score procedures in PLINK [42] to sum each individual’s total number of minor alleles from the score SNPs, with each SNP weighted by the negative log of the GWAS association p value and sign of the association (beta) statistic. Clumping was done with respect to the linkage disequilibrium (LD) pattern in the COGA EA sample (founders only) using a 500 kb physical distance and an LD threshold of r2≥0.25. Following conventions for polygenic scoring using the pruning-and-thresholding approach [18], we calculated a series of GPS in COGA that included SNPs meeting increasingly stringent p-value thresholds in the discovery GWAS (P<0.50, P<0.40, P<0.30, P<0.20, P<0.10, P<0.01, P<0.001, P<.0001).
