A total of 6,040 cases and 5,719 controls from CLOZUK were included in the recent PGC study5. We reanalyzed the PGC data after excluding all these cases and controls, obtaining a sample termed ‘INDEPENDENT PGC’ (29,415 cases and 40,101 controls). Adding the summary statistics from this independent sample to the CLOZUK GWAS results allowed for a combined analysis of 40,675 cases and 64,643 controls (without duplicates or related samples). This meta-analysis was performed using the fixed-effects procedure in METAL60 with weights derived from standard errors. For consistency with the PGC analysis, additional filters (INFO > 0.6 and MAF > 0.01) were applied to the CLOZUK and INDEPENDENT PGC summary statistics, leaving 8 million markers in the final meta-analysis results. Quantile–quantile and Manhattan plots are shown in Supplementary Fig. 3 and Fig. 2. The same procedure as above was used to report independent loci from this analysis (Supplementary Tables 3 and 4). As raw PGC genotypes were not available for the LD clumping procedure, phase 3 of the 1000 Genomes Project (1KGPp3) was used as a reference.
