Genomic DNA isolated from whole blood was genotyped with the Affymetrix GeneChip Human Mapping 500 K Array set (Affymetrix, Santa Clara, California). Total genomic DNA (250 ng) was digested with NspI or StyI enzymes and processed according to the Affymetrix protocol. The GeneChip genotyping analysis software (GTYPE version 4.0; Affymetrix) was used for automated genotype calling as part of the GeneChip operating software platform. The GTYPE-generated chip files were reanalyzed using the Bayesian robust linear model with Mahalanobis (BRLMM) genotype calling algorithm (free, downloadable software available at http://www.affymetrix.com/support/technical/whitepapers/brlmm_whitepaper.pdf) and a confidence threshold for call quality of 0.5. As an initial quality control measure, BRLMM-generated chip files with genotype call rates of less than 93% for both enzymes were excluded from further analysis. For this study, SNPs that were either monomorphic or that deviated from Hardy-Weinberg equilibrium using a cut point of P <.001 were excluded from analysis.
