We calculated polygenic scores for each individual by summing the product of the genotypes (the number of minor alleles) and the regression coefficients from single SNP analyses for all SNPs that were to be included in the score. However, because markers within the same gene, or in proximal genes, may be in LD with each other, in order to ensure that markers contributing to the polygenic score reflected unique association signals, it was necessary to prune the results of single SNP analyses based on LD structure before calculating the GABA system polygenic score. We identified SNP pairs that were in substantial LD with each other, r2 > 0.5, when only the founders of each family were considered (1852 males, 2130 females; 3866 founders were parents, 116 founders were non-parent participants from families in which parental genotype data was not available). At each p-value threshold, for every pair of SNPs with LD r2 > 0.5 in which both SNPs in the pair were below the current p-value threshold, the effect of the SNP with the higher p-value was set to zero,
