All WIHS participants who consented were genotyped on the Illumina Omni2.5 BeadChip using blood as the DNA source. However, only the genotyped SNPs from the 8 selected genomic regions were provided to conduct imputation to the 692 follow-up SNPs and indels that were used for replication testing in the current study. The UHS QC and imputation procedures were repeated for the WIHS participants and their genotyped SNPs from the selected regions. The final analysis data set included 1,852 AAs (1,395 cases; 457 controls) and 681 EAs (513 cases; 168 controls). Imputed SNPs and indels were tested for association with HIV-1 acquisition in logistic regression models adjusted for age, sexual identity (heterosexual, bisexual, lesbian/gay, other), ever use of injected and non-injected drugs, ever had sex with HIV+ male, number of lifetime sexually transmitted diseases (other than HIV and chlamydia), ever had chlamydia, number of sex partners, collection site, wave of recruitment, and 10 principal components. The P value threshold for statistically significant replication was 3.21x10-4, corresponding to correction for 156 independent tests across the 692 selected SNPs and indels from 8 top gene regions (see S1 Methods).[31,32]
