A large-scale multi-ancestry mitochondrial variant association analysis for cardiometabolic traits

Studies linking mitochondrial DNA (mtDNA) with complex traits are often limited by small sample sizes or focused on specific phenotypes in clinically selected cohorts. Here, we use data from >600,000 participants in the Million Veteran Program (MVP) to perform a multi-ancestry analysis of mitochondrial DNA (mtDNA) variation and cardiometabolic phenotypes across European (EUR), African (AFR), Admixed American (AMR), and East Asian (EAS) populations. After validating 248 mtDNA loci, we identify 10 ancestry-stratified single-variant associations (8 EUR, 2 AFR) and 23 additional signals in sex- and type 2 diabetes (T2D)-stratified analyses. Four variants tagging haplogroup J, D-loop MT228G > A, MT-ND3 MT10398A > G (p.Thr114Ala), MT-ND5 MT13708G > A (p.Ala458Thr), and MT-CYB MT14798T > C (p.Phe18Leu), are associated with hypothyroidism in EUR and replicated in UK Biobank (UKBB) with concordant effects. In EUR females, MT-RNR1 MT1555A > G increases the risk of carditis and heart failure phenotypes, supporting prior reports of maternally inherited cardiomyopathy. Gene-based rare-variant tests (minor allele frequency ≤2%) yield 26 associations (12 EUR, 10 AFR, 2 AMR, 2 EAS), including mitochondrial tRNA burdens linked to primary cardiomyopathy (females) and exophthalmos (males). Twenty-three of the 33 single-variant signals map to the endocrine/metabolic category, indicating significant enrichment (Fisher's exact P = 0.003). These results define ancestry- and context-specific contributions of mtDNA to cardiometabolic disease, with a notable concentration in endocrine traits, and provide a framework for mtDNA analysis across diverse biobank cohorts.