The ISC is described elsewhere (International Schizophrenia Consortium, 2008, Purcell et al., 2009). Briefly, we studied 3,322 European cases with DSM-IV or ICD-10 schizophrenia and 3,587 controls from seven sites. All work was approved by institutional review boards. After complete description of the study to the subjects, written informed consent was obtained. Genotyping was performed on DNA extracted from blood using Affymetrix 5.0 or 6.0 arrays. Genotypes were called using Birdsuite (Korn et al., 2008) and imputation conducted using Beagle (Browning and Browning, 2009, Browning and Browning, 2007) against the HapMap3 CEU data resulting in 1,948,385 autosomal SNPs with direct or imputed genotypes. The primary analysis was logistic regression of disease state on the imputed allele dosages with inclusion of covariates to adjust for population stratification effects. The GAIN study genotyped 1230 SCZ cases and 1136 controls of European ancestry on the Affymetrix 6.0 array (Shi et al., 2009).
