The GAIN and nonGAIN samples originated from the same Molecular Genetics of Schizophrenia study. These companion samples were genotyped separately, using the same platform (Affymetrix 6.0). Data from half of the Molecular Genetics of Schizophrenia study participants genotyped under the auspices of GAIN were obtained via dbGaP accession number phs000021.v3.p2, and data from the other half of the Molecular Genetics of Schizophrenia study participants (nonGAIN) were obtained via dbGaP accession number phs000167.v1.p1. We used only schizophrenia controls from GAIN (N=774) and nonGAIN (N=671), for which we applied our standard set of QC procedures (Supplementary Information).
