Genotyping for CATIE genetic samples were done by Perlegen Sciences (Mountain View, CA, USA) using Affymetrix 500K ‘A’ and custom 164K chipsets. We obtained the genetic data set from the National Institutes of Mental Health (NIMH) Repository and Genomics Resource (https://www.nimhgenetics.org) after IRB and relevant data use approvals. Data received from the NIMH repository included information on 741 CATIE subjects and 751 controls. Information was available for a total of 495,172 single nucleotide polymorphisms (SNPs) in coordinates mapped in human genome build 17 (hg17, University of California, Santa Cruz). The data we received were pre-processed with some quality control filters applied by both Perlegen and CATIE investigators. SNPs were removed for low quality, minor allele frequency (maf) <0.01 and hardy-weinberg equilibrium (hwe) <1e-05. Subjects with >5% missing data were also removed. We did additional data processing by removing 21 subjects from the total sample (18 controls and 3 cases) with sex discrepancies in phenotypic and genotypic data and 12 subjects (8 cases and 4 controls) for relatedness. After extracting only cases from the sample and performing LiftOver (https://genome.ucsc.edu/cgi-bin/hgLiftOver) to update to a recent human genome build (hg19) we were left with 730 cases and 486,895 SNPs.
