Top GWAS meta-analysis results were tested for independent replication in AAs and EAs from the WIHS: the largest longitudinal cohort study of HIV+ and high-risk HIV- women.[26] Similarly to prior GWAS,[27]chromosomal regions from the discovery analysis were selected for replication beyond those with genome-wide significant SNPs. Promising regions / peaks for “deeper” replication testing were selected based imputed SNP/indel associations with P<1x10-6 or having the top genotyped SNP association (P = 1x10-5), following previously successful studies.[27,28] Each region was defined by 3MB spanning the top associated SNP, given that GWAS signals can reflect synthetic associations as far as 2.5MB away.[29,30] Thus, 692 SNPs and indels with P<1x10-3 across the selected regions were tested for replication in WIHS.[28]
