Genotyping
DNA samples were isolated from the peripheral blood of participants and genotyped using Affymetrix Genomewide Human SNP Array 5.0 (Affymetrix Inc.) at DNA Link Inc. (Seoul, Korea). Internal quality control (QC) measures were employed to ensure accuracy of the data. The QC call rate (dynamic model algorithm) was ≥95%, and heterozygosity of X chromosome markers identified the gender for each sample. Genotype calling was performed by Birdseed (v2) algorithm. Chromosome Y was not analyzed. A total of 1,163 individuals were genotyped via this platform in the analysis. PLINK (v1.07) was used to estimate identity by state (IBS) over all SNPs [28]. A default set of 426,019 SNPs was used for further analysis, as recommended by Affymetrix. In the quality assurance screening, we flagged SNPs with genotype call rates < 95%, minor allele frequencies < 0.01, and SNPs showing deviation from Hardy-Weinberg equilibrium (HWE) at p < 0.0000001. The final set of acceptable markers included 312,506 autosomal SNPs. Accuracy of the genotyping was calculated by Bayesian robust linear modeling using the Mahalanobis distance (BRLMN) algorithm [29].