Full details are given in the Supplementary File 1. All analysis sets were put through a common QC pipeline based on that used by the Psychiatric GWAS Consortium.25 SNPs were removed based on the following criteria: minor allele frequency (MAF) <0.01, Hardy–Weinberg equilibrium test P<1 × 10−6 in controls, missingness >0.01 or 0.02, missingness difference between cases and controls of 0.01 or 0.02, difference in frequency with HapMap of 0.07 or 0.15 (more stringent thresholds were applied when cases and controls were not genotyped concurrently, and were chosen to balance SNPs lost versus genomic control inflation factors). Samples were removed with missingness >0.02, if related to other samples or if identified as European ancestry outliers. Imputation was conducted in four analysis sets (I317, I370, I610, A6.0) in batches of ∼300 mixed cases and controls to a common set of SNPs present in HapMap3 CEU/TSI, consisting of 410 haplotypes, using Beagle 3.04.26, 27
