Imputed SNPs and indels were tested for association with HIV-1 case/control status using logistic regression models stratified by ancestry and adjusted for age, sex, behavioral risk class (based on latent class analysis), survey year, and the first 10 principal components to minimize bias due to population stratification (see S1 Methods). The final analysis included 2,004 AAs (628 cases; 1,376 controls) and 1,132 EAs (327 cases; 805 controls) who passed QC and had complete covariate data.
