Figure 3

Variation differentiating MHC homozygotes from heterozygotes and SIV controllers from progressors. (A) Variants common to six M1/M1 animals, but absent from six M1/M3 animals (and the reciprocal), were identified. Using a Manhattan plot, genome-wide variation was plotted as variants per kilobase across 50 kb bins. Blue and red correspond to alternating chromosome numbers. The highest density of variation across the genome marked the MHC on macaque chromosome 4. Although their annotations do not adequately depict the dispersion of these multicopy loci throughout the MHC, Mamu-A, Mamu-B and Mamu-DQA are shown for reference. (B) Variants that strictly segregated between Group 1 (controllers) and Group 2 (progressors) were identified, and the density of this variation was plotted across 21 macaque chromosomes using 50 kb bins.