Genome-wide SNP genotyping and whole-exome sequencing data for 84 samples were obtained from the International HIV Controllers Study14, of which 43 were genotyped on the Illumina HumanHap 650Y and 41 on the Human-1M-duo array. Of the 84 samples, 61 are HIV-1 controllers enrolled by the IHCS and 23 enrolled by the AIDS Clinical Trials Group. Only unrelated samples of European ancestry with high genotyping rates (>95%) were included, after filtering out SNPs with low minor allele frequency (MAF < 1%), >2% missing data, or departure from Hardy-Weinberg equilibrium (P < 10−6). The SNP sets were intersected to obtain 398,098 SNPs genotyped in all samples. Imputation was performed using all the 762 available 1000 Genomes phase 1 haplotypes as opposed to 381 for simulations using non-overlapping regions of size 2.5Mb with 250Kb flanking regions on either side.
