For each of the eight GWAS disorders, LD Score regression was performed on the summary statistics of individual disease using LDSC to estimate SNP-based heritability in the liability scale and genetic correlation between pairs of disorders (Bulik-Sullivan et al., 2015b). LD scores and weights for European populations were downloaded from the LDSC website (http://www.broadinstitute.org/~bulik/eur_ldscores/). SNPs were removed if the minor allele frequency is smaller than 5% or an imputation quality score is less than 0.9; MHC region was excluded from the analysis. For single-trait LDSC, the slope of the regression estimates the SNP-based heritability, and the intercept greater than one captures the inflation in the summary statistics due to population stratification or other confounding factors. We confirmed that the heritability Z-scores (i.e., a measure of the polygenic signals) are greater than four, and the LDSC intercepts are approximately one and less than. suggesting that the increase in mean χ2 statistics is due to polygenicity and not due to stratification.
