Samples were genotyped with the Affymetrix 6.0 genome-wide SNP array at the Broad Institute Center for Genotyping and Analysis (Cambridge, MA) in three batches: 863 controls, as part of the GAIN schizophrenia project (late 2007); GenRED cases (early 2008); and 773 controls, under MGS grant funding (mid-2008). Genotypes were called with Birdseed (version 2).22 QC analyses were carried out using PLINK23 supplemented by local software (see online Supplementary Methods for details). We excluded SNPs and control samples that failed either MGS or GenRED QC criteria, which were selected by determining thresholds that achieved a balance between a low genomic control λ value and inclusion of more data.
