Our study included 1833 European Americans within the N haplogroup, which is ancestral to almost all European and many Eurasian haplogroups [48
]. The N subgroup frequencies (‘f’ in ) in our study were consistent with an independent population dataset (D.C.W. unpublished). Genetic association tests were performed on major haplogroups, and then on haplotypes from successively more definitive phylogenetic nodes (). Minor haplogroups with frequencies less than 0.01 were collapsed into more inclusive haplogroups to minimize type I errors. Statistical tests were non-independent for two reasons: 1) the phylogenetic overlap of haplogroups and subgroup haplotypes; and, 2) the non-independence of varying AIDS endpoint association tests. Since non-independence precludes Bonferoni corrections for multiple tests, we focused on signals that were a) repeated within successive nested haplogroups, b) replicated in cohorts tested separately in survivorship analyses, and/or c) had strong p-values in related hypotheses. We are also aware that the European American combined and MSM combined analyses had more power due to a larger sample size. This is important given the relative rarity of some of the haplogoups [49
]. presents a visual heat plot display of p-values for genetic association for each of the 34 mtDNA genotypes. Based on ARGARRAY visualization routine [37
], more intense color intensity represents increasing levels of statistical significance. MtDNA haplotypes related by a phylogenetic tree can be inspected individually or as a group for each AIDS progression test. presents the same ARGARRAY display for candidate SNP variants included within the mtDNA haplotypes that showed association signals in . The significant tests, p-values, RH, and CI values are tabulated in and . (Unabridged test results are provided in SOM: http://home.ncifcrf.gov/ccr/lgd/publications/index_n.asp
). The association tests revealed five mtDNA haplogroups that showed consistent, significant associations: IWX, U5a, Uk, J and H3 (; and ). Each haplogroup will be described separately.
Figure 1 A) An ARGARRAY display  of categorical and survival analyses for AIDS progression in 34 Caucasian mitochondrial haplogroups. A phylogenetic tree showing the relationship between haplogroups is shown on the left . Each major haplogroup was analyzed, (more ...)
Significant results in AIDS association tests for Cox Proportional Model
Significant results in AIDS association tests for Progression categorical analysis
The J haplogroup was associated with accelerated progression to AIDS’87 (RH=1.55, 95% CI=1.08–2.23, p=0.024) and AIDS-related death (RH=1.53, 95% CI=1.03–2.26, p=0.043) in all European Americans. This association appears to be primarily driven by the cohorts who were infected via sexual transmission (RH=1.84, 95% CI=1.22–2.76, p=0.006) (; , ), however the signal is observed in AIDS’87 and not in AIDS’93. Perhaps the J haplogroup specifically increases the risk of Kaposi’s sarcoma, an AIDS-defining condition seldom that occurred at high rates in MSM cohorts but that was seldom seen in injection drug use and hemophilia cohorts. Additional research will be needed to examine this hypothesis. When we consider the MSM cohorts individually, there is a significant acceleration of AIDS’87 with J haplotypes in the MACS cohort (RH=1.69, 95% CI=1.08–2.66, p=0.03), and a non-significant trend for acceleration in the SFCC (RH= 2.74, 95% CI=0.97–7.70, p= 0.08). Within haplogroup J, both sub-haplogroups J1and J2 are associated with accelerated disease progression. J1 is associated with accelerated AIDS’87 in European Americans (RH=1.57, 95% CI=1.03–2.38, p=0.046), and in MSM cohorts (RH=1.80, 95% CI=1.12–2.87, p=0.023). The J1 association signal for accelerated AIDS progression is driven largely by the J1c-14798* haplotype (f=0.057) which is consistently highly significant in Caucasian, MSM, and individual MSM cohorts (MACS and SFCC; ; ). J1c was significant for AIDS’87 (All RH=1.67, CI=1.07–2.61, p=0.034, MSM RH=1.94, 95% CI=1.18–3.17, p=0.016, MACS RH 2.25, 95% CI=1.27–3.98, p=0.012), AIDS’93 (MSM RH=1.64, 95% CI=1.05–2.55, p=0.041, MACS RH=1.82, 95% CI=1.08–3.09, p=0.038), and death (all RH=1.72, 95% CI=1.07–2.78, p=0.038). J2 shows an association with accelerated AIDS progress in the SFCC (CD4<200: RH=23.13, 95% CI=2.33–229.65, p=0.044; AIDS’87: RH=63.69, 95% CI=3.61–1124.28, p=0.019; AIDS’93: RH=44.26, 95% CI= 3.71–528.15, p=0.024). As this cohort is biased towards long-term survivors [35
], this signal may represent a moderate, late-term effect.
Figure 2 Representative Kaplan-Meier plots for significant results. a) J haplogroup and AIDS’87 progression in sexual transmission cohorts, b) SNP 13708 from the J haplogroups and AIDS’87 progression in sexual transmission cohorts, c) Haplogroup (more ...)
The U5a haplogroup is associated with accelerated AIDS progression to CD4<200 in European Americans (RH=1.78, 95% CI=1.11–2.85, p=0.028) and in MSM pooled cohorts (RH=2.06, 95% CI=1.17–3.63, p=0.024). The signal is largely driven by the U5a1-15218 haplotype, which comprises 79% of the U5a haplotype (; ).
The Uk haplotype was associated with a decrease in the rate of AIDS progression to CD4 <200 cells/μL in both dichotomous and multipoint categorical models (OR=0.47, 95% CI=0.24–0.85, p=0.008; Common OR=0.60, 95% CI=0.37–0.97, p=0.038 respectively) as shown in and . Uk was also protective against AIDS’93 () (OR=0.50, 95% CI=0.27–0.87, p=0.012; Common OR=0.61, 95% CI=0.40–0.95, p=0.022, dichotomous and multipoint models respectively). In survivorship analyses (, ), only one signal was observed indicating Uk is protective against AIDS’87 in the MSM cohorts (RH=0.53, 95% CI=0.29–1.00, p=0.031).
Frequencies of Uk in categorical analyses for Uk using dichotomous (a, c) and multipoint (b, d) models to CD4<200 cells/μL (a,b) and AIDS’93 (c,d). *Odds rations shown for multipoint models are Common Odds Ratios.
A strong association signal suggests H3 was protective for hemophiliacs against progression to AIDS’93 (RH= 0.21, 95% CI=0.06–0.72, p=0.003), AIDS’87 (RH=0.12, CI=0.02–0.94, p=0.006); and death (RH=undefined p=0.0004) (, ). However, this result is based on few individuals as only seven of the hemophiliacs analyzed in the survival model are in haplogroup H3, and of those, one patient developed AIDS and no patients died. Protection, albeit relatively weak and inconsistent, was also observed in H4, H5 and H6 (; ).
IWX haplogroup was associated with delayed progression to CD4<200 cells/μL in MSM cohorts, driven largely by the MACS cohort (RH=0.56, 95% CI=0.33–0.96, p=0.022, RH=0.52, 95% CI=0.29–0.94, p=0.017), however we do not see an association when we look at all European Americans combined. Within the IWX group, The W (W8994) haplotype showed the strongest protective association among MSM cohorts pooled or individually (; ).
Haplogroups U and J contain a number of functional variants that we analyzed separately (). Strong disease accelerating associations consistent with parent haplotypes were observed for SNP 3010 G>A (included in J1 and H1 haplotypes) and SNP 13708G>A found at the root of the J haplogroup. The 13708G>A SNP is a amino acid altering variant in the ND5 protein coding gene. Since both associated SNP variants, 3010G>A and 13708G>A are carried together on the J1 haplogroups, it was not possible to resolve their independent contributions to the J1 association with rapid AIDS progression among MSM. However, the 3010G>A association may explain the accelerating association seen in H1, which is counter to the protective associations observed for H3 and other H sub-haplogroups. The Uk haplotype protecting against AIDS progression was recapitulated by non-synonymous CYTB-14798T>C SNP. SNP 14798T>C is present on J1 and Uk haplotypes, but the protective influence was only apparent in Uk.