For detailed descriptions of the genotyping and quality control procedures see Supplementary Materials. Briefly, in Stage I, the initial 300 subjects were genotyped using the Affymetrix GeneChip Mapping 500K Array Set and the remaining 2,776 samples were genotyped using the Affymetrix Genome-Wide Human SNP Array 6.0. In each of the 96-well plates genotyped using the Affymetrix SNP 6.0 array, three positive QC samples (NA15510, NA10851, and NA18505) purchased from Coriell Cell Repositories (http://ccr.coreill.org/), and a negative QC sample (water) were included. SNP data obtained from the positive QC samples showed a very high concordance rate of called genotypes based on 79,764,872 comparisons (mean, 99.87%; median, 100%). In addition, 742 SNPs were genotyped using the Affymetrix Target Genotyping System, TaqMan or Sequenom for a subset of subjects included in previous studies. A high concordance rate was also observed between genotypes determined using these platforms and Affymetrix SNP Array 6.0 based on 1,478,383 comparisons (mean, 99.1%; median, 99.8%). Samples with genotyping call rates less than 95% were excluded, and the remaining samples were recalled by using Birdseed v2. The gender of all
