DNA samples were extracted from Oragene kits (DNA Genotek Inc., Ottawa, ON, Canada) at KPNC and genotyped at the Genomics Core Facility of the Institute for Human Genetics at the University of California, San Francisco (UCSF) on four race/ethnicity-specific Affymetrix Axiom arrays (Affymetrix, Santa Clara, CA, USA) optimized for individuals of European, African American, East Asian, and Latino race/ethnicity.32 Design details and genome-wide coverage of those arrays have been previously described.33, 34 Genotype quality control (QC) procedures for the GERA cohort were performed on an array-wise basis as described in detail elsewhere.32 Briefly, we included SNPs with initial genotyping call rate ≥ 97%, allele frequency difference (≤ 0.15) between males and females for autosomal markers, and genotype concordance rate (> 0.75) across duplicate samples. Around 94% of samples and more than 98% of genetic markers assayed passed QC procedures.32 Prior to imputation, we additionally excluded genetic markers with a minor allele frequency (MAF) < 1%, or a genotype call rate < 90%.
