All HIV+ cases in the UHS were genotyped. For every case, two HIV- controls were selected for genotyping based on frequency-matching with respect to five criteria: self-identified ancestry, self-identified sex, age group, survey year (pre/post antiretroviral therapy availability), and risk profile that included risky sexual and drug use behaviors (see S1 Methods and S1 Fig.). Genotyping was conducted on 3,732 samples using the Illumina Omni1-Quad BeadChip on restored genomic (not amplified) DNA samples from serum (see S1 Methods). Following quality control (QC), there remained 789,322 autosomal genotyped single nucleotide polymorphisms (SNPs) in 2,017 AAs and 792,340 autosomal genotyped SNPs in 1,142 EAs. Their ancestral proportions are shown in S2 Fig.
