All subjects were genotyped in two sample sets for the Affymetrix SNP Array 6.0. The initial sample of 321 Wave 5 subjects was genotyped at the Broad Institute as part of the Genetic Association Information Network (GAIN) and published previously as part of study of BD involving a larger sample of 1,001 BDI cases and 1,033 controls (32). Subsequent genotyping of the remaining 942 Wave 5 subjects was performed at the Translational Genomics Institute (TGEN) as part of a larger sample of 1,190 BDI cases and 401 controls. An extensive QC process (described elsewhere in detail, 32) was performed on each sample separately to eliminate individuals with >10% missing data and SNPs with poor allele clustering, >10% missing data, duplicate errors, minor allele frequencies (MAFs) <0.01, and Hardy-Weinberg Equilibrium p values <10−6. An additional round of QC performed on the merged GAIN and TGEN samples resulted in 703,012 passing SNPs.
