Genomic DNA was isolated from peripheral blood. All DNA samples from the 10,004 participants were genotyped with the Affymetrix Genome-Wide Human SNP Array 5.0. Genotypes were called by Bayesian Robust Linear Modeling using the Mahalanobis Distance (BRLMM) algorithm. After removing samples with low call rates (n = 401), contamination (n = 11), sex inconsistencies (n = 41), cryptic relatedness (n = 608), or serious concomitant illness (n = 101), 8,842 samples remained for use. Similarly, we removed those SNPs with Hardy–Weinberg equilibrium (HWE) p values <10− 6, minor allele frequencies >0.01, and genotype call rates >95%, leaving 352,228 SNPs. More detailed statistical analysis of the GWAS data can be found in a previous report (Cho et al. 2009). Considering the samples used for GWAS were recruited from different geographical locations of Korea, we used the magnitude of the genomic inflation factor and multidimensional scaling (MDS)/principal component analysis (PCA) plots to examining the presence of the population stratification, which revealed no evidence of this effect in the KARE samples (Cho et al. 2009).
