Axiom taiwan biobank array plate twb chip

Genotyping with the Axiom-Taiwan Biobank Array Plate (TWB chip; Affymetrix Inc, Santa Clara, California) was performed at the National Center for Genome Medicine of Academia Sinica [21] . We use PLINK (version 1.07), an open-source whole-genome data analysis toolset, for quality control procedures [22] . For SNPs with batch effect, their genotypes were set as missing. SNPs were excluded if missing genotype rate was high (> 5%), minor allele frequency was low (< 1%) or deviated from Hardy-Weinberg equilibrium (P value < 10 - 5 ). Individuals with high missing genotyping rate (> 5%), extreme heterozygosity rate (more than 5 standard deviations away from the mean) or high identity-by-descent score (≥ 0.1875) implying close relatedness were excluded from subsequent analyses. We computed the principal components on a linkage disequilibrium (LD)-pruned (r 2 < 0.2) set of autosomal variants obtained by removing high-LD regions via PLINK. Genotype imputation was carried out with SHAPEIT [23] and IMPUTE2 [24] . We applied1000 Genomes Project Phase 3 East Asian Ancestry as the reference population. For gene annotation, Genome Reference Consortium Human Build 37 was used. Imputed SNPs with low quality score (info score [25] lower than 0.3) were excluded. Indels were removed by using VCFtools [26] .