Omni human 2.5m snp array

A subset of 13 genes was selected from whole-genome genotyping data generated from a cohort-wide GWAS utilizing the Omni Human 2.5M SNP Array (Illumina, San Diego CA). Genotypes for SNPs in genes involved in ADME pathways (e.g. CYP1A2, CYP2A6, CYP2B6, CYP2C9, CYP2C19, CYP2D6, CYP2E1, CYP3A4, CYP3A5, ADH1A, ABCB1, UGT1A1, and NR1I2) were extracted for participants eligible for this study. Genotype imputation was performed using IMPUTE2, with imputed genotypes generated by comparing our GWAS SNP data for each gene region with reference haplotype data from the 1000 Genomes Phase 1 variant set release (version 3). 90 Markov chain Monte Carlo iterations were used in the imputation process. Only genotypes with an imputation r² of 0.50 or higher are included in the analysis. Coverage for each of the gene regions was calculated in each racial group by calculating pairwise r² between our genotyped and imputed (imputation r² ≥ 0.5 or greater, MAF ≥ 0.05) SNPs and every 1000 Genomes SNP in the region (MAF ≥ 0.05) using the 1000 Genomes samples of each respective racial group. SNPs that had an r² of 0.95 or greater with our genotyped and imputed SNPs were considered "covered," and the proportion of SNPs covered in each region was calculated.