Genotyping was performed at Washington University School of Medicine in St. Louis on an OpenArray platform, and at Indiana University School of Medicine in Indianapolis on the Sequenom MassArray system on a larger group of COGA subjects of which the sample described here is a subset. OpenArray genotyping is a multiplex TaqMan assay platform. The OpenArray Genotyping Plate Configurator was used to design assays. Arrays were scanned on the OpenArray NT imager and genotypes were called using the OpenArray SNP Genotyping analysis software. Sequenom Assays (iPLEX Gold) were designed using MassArray Assay Design Software (Sequenom, San Diego, CA). Hardy-Weinberg equilibrium (HWE) was computed separately in European Americans and African Americans, and cluster data was re-evaluated if HWE p < 0.05. All SNPs were cleaned for Mendelian inheritance using PEDCHECK (O’Connell and Weeks, 1998). SNP allele frequencies and heterozygosities were computed in PLINK (http://pngu.mgh.harvard.edu/purcell/plink; Purcell et al. (2007)) using data on founders only included in the larger group. Ethnic stratification was assessed with SNPrelate (Zheng et al., 2012) using 64 ancestry-informative SNPs, as part of a larger 96 SNP panel developed
