Cox regression survival analysis was used to analyze genome-wide associations for all SNP genotypes in a genotypic model and the course of HIV-1 infection, using AIDS and AIDS-related death as an endpoint. SNPs with less than 8 individuals homozygous for the minor allele were excluded from the analysis (n = 74,967). Cox proportional-hazards regressions and corresponding P-values were computed with ProbABEL v0.1-3 software [44] which is based on the R library ‘survival’ developed by Thomas Lumley (function coxfit2). The association of the SNP with viral load set-point was tested using one-way analysis of variance (ANOVA). All statistical analysis were performed using GraphPad Prism 5.0 software (GraphPad Software, San Diego, CA, USA), and the R package (http://www.r-project.org).
