Background: Findings regarding associations of mitochondrial DNA (mtDNA) variants, haplogroups and heteroplasmy with Alzheimer disease (AD) have been inconsistent.

Methods: We investigated associations of mtDNA haplogroups, homoplasmy, and heteroplasmy with AD using whole genome sequence (WGS) data from the Alzheimer's Disease Sequencing Project (Release 4), including 9,720 genetically defined Non-Finnish Europeans (NFE), 5,660 Africans/African Americans (AFA), 3,578 Caribbean Hispanics (CH), 4,384 Native American Hispanics (NAH), and 954 Ashkenazi Jews (AJ). Haplogroups were collapsed into super-/macro-haplogroups and analyzed using logistic mixed-effects model and Cox models, with each haplogroup compared against all others. Gene-based association analyses, using both logistic and Cox frailty models, were conducted for rare homoplasmic (MAF < 0.01) across 13 coding genes, 2 rRNAs, a concatenated tRNA region, and the D-loop region. We calculated a modified mitochondrial local constraint score sum (mMSS) and number of heteroplasmic sites to quantify heteroplasmy burden and tested its association with AD in blood specimens. Mixed-effects cox proportional hazards models were used to assess whether heteroplasmy burden predicted conversion from cognitively normal (CN) to mild cognitive impairment (MCI) or from MCI to AD using Alzheimer’s Disease Neuroimaging Initiative data (ADNI). The association of AD biomarkers and cognitive functions with heteroplasmy burden in blood was evaluated using linear regression.

Results: Macro-haplogroup M was associated with lower AD risk in CH (OR = 0.74, P = 8.00 × 10^-3) but higher AD risk in NAH (OR = 1.25, P = 0.028). Super-haplogroup UK was found to be associated with higher AD risk in Cox model (HR = 1.09, P = 0.047). Gene-based analysis identified an association of MT-RNR2 with AD in NAH (SKAT-O P = 1.17 × 10^-3). Survival analysis of 354 ADNI baseline CN participants showed that higher blood mMSS predicted increased risk of conversion from CN to MCI (N_case=60, HR = 3.55, P = 0.033). We also identified significant associations of blood heteroplasmy count with total tau in cerebrospinal fluid (β = -0.06, P = 0.046).

Conclusions: Macro-haplogroup M and MT-RNR2 show ancestry-specific associations with AD. Increased blood mtDNA heteroplasmy burden is associated with elevated MCI incidence, rather than prevalent AD risk, supporting a role for mitochondrial dysfunction in AD pathogenesis.