The Bipolar dataset was reported by the Wellcome Trust Case Control Consortium3 and consists of 1868 cases and 2938 controls typed with the GeneChip® 500K Mapping Array Set. The UK schizophrenia cases (n=479) were not part of that study but were typed contemporaneously with the WTCCC samples using the same pipeline20. The full details of the samples and methods for conduct of the GWAS studies are provided in the respective manuscripts. To make our analysis as conservative as possible, we only included autosomal SNPs which passed more stringent quality control criteria than used by the WTCCC, and, unlike that study, additionally corrected all p-values for inflation in the test statistics (see statistical section). Thus we excluded SNPs with Hardy-Weinberg equilibrium p< 0.001 in controls or p< 0.00001 in cases, with minor allele frequencies (MAF) < 0.01 in each of cases and controls, or with call rates<0.97.
