The maternally transmitted mitochondria are the most abundant organelles in the human oocyte and early embryo, and serve as the primary generator of cellular energy and orchestrator of cellular metabolism via oxidative adenosine triphosphate production. Mitochondrial integrity is crucial to not only oxidative phosphorylation and generation of adenosine triphosphate, but plays a role in lipid and amino acid metabolism, cell proliferation, differentiation, and apoptosis. Mitochondria harbor their own 16.5-kilobase circular, double-stranded DNA genomes (mitochondrial DNA [mtDNA]), which contain a mere 37 genes encoding for 13 polypeptides for oxidative phosphorylation, as well as 22 transfer RNAs, and 2 rRNAs necessary for mitochondrial protein synthesis. Despite its diminutive size, mtDNA is of major evolutionary and functional importance as it is a legacy of the endosymbiosis from prokaryotes that likely created the eukaryotic cell >1.5 billion years ago. Although the vast majority of proteins involved in mitochondrial function are encoded by the nuclear genome, the 13 mtDNA encoded proteins are crucial for human life. Underscoring its role in human health, >200 mtDNA point mutations have been associated with a variety of human diseases ( http://www.mitomap.org ), including diabetes, cancer, and neurodegenerative disorders. With respect to perinatal disorders, there are initial studies suggesting a role for nonsynonymous (protein coding) mtDNA mutations in preeclampsia, oocyte wastage and early embryonic demise, and preterm birth. We have recently demonstrated that mtDNA variation of the human host significantly influences the structure and community members of the vaginal and gut human microbiome. Despite its evident importance in both cellular function and human disease, genomic variation studies of mtDNA have largely been relatively underrepresented when compared to nuclear DNA analyses.

The mitochondrial genome is inherited in a non-mendelian manner, vertically transmitted solely from the mitochondria of the oocyte. This so-called “maternal inheritance” pattern, whereby a mother carrying a mtDNA mutation will pass it on to all of her children regardless of sex, but only her daughters will transmit it to their progeny, has been the clinical hallmark of mitochondrial disorders. Since each cell contains varying numbers of mtDNA copies, some mtDNA genomes in any given cell or tissue are normal, while others contain mutations (defined as heteroplasmy, or intraindividual variation in mtDNA sequences). Homoplasmic mtDNA pathogenic mutations, when nearly 100% of mtDNA genomes in a given cell, tissue, or organism are severely variant, happens rarely, and are thought to result in fetal or neonatal lethality or organ-specific mitochondrial disease (eg, Leber hereditary optic neuropathy). Conversely, low level (1-10%) heteroplasmy is believed to be of little clinical significance and may actually represent a reservoir of genetic mtDNA variants that can increase the functional capacity in response to aging and environmental stressors. The degree of mtDNA mutation has been reported to vary between generations, although it remains unclear the degree to which bottlenecking during oogenesis and accumulated lifetime mutation rates contribute to generational differences in the mitochondrial genomic sequence. While a recent study by Rebolledo-Jaramillo et al estimated the rate of heteroplasmy in 39 maternal-child pairs with known mutations in 1 in 8 subjects, an accurate estimate of the mtDNA mutation rate at the time of birth from a healthy and nondiseased population is still lacking.

In this study, we investigated the maternally inheritable and de novo mutation frequency in fetal mtDNA from a relatively large population-based cohort composed of 90 maternal (blood)-fetal (placental) pairs as detected by NextGen sequencing technology (Illumina HiSeq platform; Illumina Inc., San Diego, CA). Because it was a formal possibility that neonatal cord blood and fetal (placental) detection of mutations may differ, we additionally sequenced 5 trios composed of maternal (blood), fetal (placental), and neonatal (cord blood) mitochondrial genomes. With derived high-fidelity and high-depth sequence data we determined: (1) 665 single nucleotide polymorphisms (SNP) and 82 insertions-deletions (indel) variants in the cohort at large; (2) the rate of haplogroup, SNP, and indel variation between maternal-fetal pairs; (3) the rate of mitochondrial SNP (mtSNP) discordance between maternal and fetal mitochondrial genomes; and (4) an estimate of the mtDNA de novo mutation rate at the time of birth. These findings have the potential to not only inform human developmental and perinatal genomics, but also underscore the rarity with which de novo mitochondrial disease would be anticipated in the newborn and thus provides subsequent insights into mtDNA disease pathogenesis.