Large-Scale Genotyping of Asian Cohorts

Genotyping of 3,072 and 1,952 samples in SiMES and SCES, respectively, was performed using Illumina Human610-Quad BeadChips (Illumina Inc.). A total of 620,901 SNPs were genotyped in each cohort. An additional 635 samples in SCES was genotyped using Illumina Human OmniExpress BeadChips with a total of 729,698 SNPs. Detailed quality control procedures for sample and SNPs were described elsewhere [20] (link), [21] (link). In brief, samples were excluded based on the following conditions: (1) sample call-rates of less than 95%; (2) excessive heterozygosity; (3) cryptic relatedness; (4) gender discrepancies; and (5) discordant ethnic memberships. We excluded SNPs with (1) high missingness (>5%); (2) gross departure from HWE (p value <10⁻⁶) and (3) MAF <1%. Detailed quality control procedures for SCES samples genotyped on OmniExpress chips were provided in the supplementary materials (Text S2). After quality control, we have the following samples and SNPs available for analysis: 2,542 samples and 557,824 SNPs in SiMES, 1,889 samples and 538,408 SNPs in SCES on Illumina Human610-Quad BeadChips, and 615 samples and 633,783 SNPs in SCES on Illumina Human OmniExpress BeadChips.