Genotyping
KARE samples were genotyped using Affymetrix Genome-Wide Human SNP array 5.0 (Affymetrix, Santa Clara, CA, USA) and processed by Bayesian Robust Linear Modeling using the Mahalanobis Distance (BRLMM) genotyping algorithm [16]. The HEXA shared sample was genotyped using Affymetrix Genome-Wide Human SNP array 6.0 and processed with the Birdseed Genotyping Algorithm [17]. The BioBank Japan study was genotyped using the Illumina Human610-Quad BeadChip (Illumina Inc., San Diego, CA, USA). A childhood obesity study was genotyped using the Illumina Omni1-Quad BeadChip. Individuals were excluded as follows: genotyping call rate, sex inconsistency, heterozygosity, identity-by-state value, and any kinds of tumor. For more information, the study has been reported [15].
For the replication study in Health2 (7,861), we performed a genotype assay using the TaqMan reaction for four single nucleotide polymorphisms (SNPs) (rs2074356, rs16940212, rs12708980, rs599839) and the GoldenGate assay (Illumina Inc.) for nine SNPs (rs780092, rs10503669, rs2001945, rs603446, rs12686004, rs11216126, rs12229654, rs519113, rs12654264, rs2738446). To analyze the quality control, we conducted duplicate genotyping using 1-2.5% of samples. For further association analyses, concordance rates were satisfied with duplicates of over 99% and a genotype success rate of over 98%.