Time from seroconversion to AIDS-diagnosis or AIDS-related death was normally distributed in the ACS (Figure 1). To find host genetic markers that associate with disease progression after HIV-1 infection, we genotyped 455 samples with Illumina's Infinium HumanHap300 BeadChip which assays 317,503 SNPs [29]. After quality control (see Methods) and population stratification, association analysis was performed for 309,494 SNPs and HIV-1 disease course in 404 HIV-1 infected MSM and DU from the ACS using Cox regression survival analyses with AIDS according to the CDC 1993 definition [30] or AIDS-related death, as endpoints. The calculated λ values of 1.0231 and 1.0197 for the P-values of SNP associations with either AIDS-free survival or time to AIDS-related death, respectively, indicate that the remaining population stratification effect, after correction by using the two first eigenvectors as covariates, is minimal.
