Infinium exome 24 v1.0 beadchip

Genomic DNA was extracted from peripheral blood leucocytes in whole blood samples. The DNA samples were genotyped using the Infinium Exome-24 v1.0 BeadChip (Illumina, Inc., San Diego, CA, USA), which included a total of 247,870 SNPs. Quality control (QC) was assessed at the individual and SNP levels. First, individuals with high levels of missingness, excess autosomal heterozygosity, high relatedness, ambiguous gender, and ancestry outliers estimated by using ancestry principal component analysis (PCA) were excluded. Next, criteria such as call rate < 98%, significant departures from Hardy–Weinberg equilibrium (P < 1 × 10⁻⁶), significant differences in allele frequency between case and control (P > 0.05), not on chromosomes 1–22, and minor allele frequency (MAF) < 1% were applied for excluding SNPs in further analysis. Finally, 32,387 SNPs and 297 individuals were selected for subsequent analysis. The detailed QC results are shown in Additional file 1: Tables S1 and S2; Figures S2, S3, S4 and S5.

Methods for sample collection and extraction of genomic DNA have been described previously [31 (link)]. EWASs for FPG concentration and blood HbA_1c content included 11,729 and 8635 subjects, respectively, whereas that for type 2 DM included 14,023 individuals (3573 subjects with type 2 DM, 10,450 controls). Data for FPG levels were obtained from subjects who had fasted overnight. Data for blood HbA_1c content were obtained from subjects with type 2 DM or impaired glucose tolerance or from those who had annual health checkup. The EWASs were performed with the use of a HumanExome-12 v1.1 or v1.2 DNA Analysis BeadChip or Infinium Exome-24 v1.0 BeadChip (Illumina, San Diego, CA, USA). Detailed information of the exome arrays and methods of quality control have been described previously [31 (link)]. Genotype data were examined for population stratification by principal components analysis [35 (link)] (Supplementary Figure 3). A total of 41,265 SNPs passed quality control and was subjected to analysis.

Methods for collection and extraction of genomic DNA samples were described previously [40 (link)]. EWASs for the serum concentrations of triglycerides (13,414 subjects), HDL-cholesterol (14,119 subjects), or LDL-cholesterol (13,577 subjects) or for hypertriglyceridemia (4742 cases, 8672 controls), hypo–HDL-cholesterolemia (2646 cases, 11,473 controls), or hyper-LDL-cholesterolemia (4489 cases, 9088 controls) were performed with HumanExome-12 v1.1 or v1.2 DNA Analysis BeadChip or Infinium Exome-24 v1.0 BeadChip arrays (Illumina, San Diego, CA). Detailed information of the exome arrays and methods of quality control were described previously [40 (link)]. Totals of 41,371, 41,225, and 41,347 SNPs passed quality control in the EWASs for hypertriglyceridemia, hypo–HDL-cholesterolemia, and hyper–LDL-cholesterolemia, respectively, and were included in the analysis.

Methods for collection and extraction of genomic DNA samples were described previously [53 (link)]. The EWASs were performed with the use of the HumanExome-12 v1.1 or v1.2 DNA Analysis BeadChip or Infinium Exome-24 v1.0 BeadChip (Illumina, San Diego, CA, USA). Detailed information of these exome arrays and methods of quality control were described previously [53 (link)]. Totals of 41,327 or 41,675 SNPs passed quality control for the BMI and obesity studies and for the MetS study, respectively, and were subjected to analysis.