Independent BP and SCZ datasets with no overlapping genotype data from controls were created by calculating relatedness across all pairs of individuals using an LD pruned set of SNPs directly genotyped in all studies. Controls found in more than one dataset were randomly allocated to balance the number of cases and controls accounting for population and genotyping platform effects. We grouped case-control samples by ancestry and genotyping array into 14 BP samples and 17 SCZ samples (Supplementary Table 1). We further grouped individuals by ancestry to perform a direct comparison of BP and SCZ (Supplementary Table 2).
