This article questions the prevalence and reliability of human mitochondrial DNA heteroplasmy from massively parallel sequencing data.
In their analysis of massively parallel sequencing data (MPS) from the 1000 Genomes Project, Ye et al. (1) report a very high rate of human mitochondrial DNA (mtDNA) heteroplasmy (89.68 percent of individuals), including up to 71 point heteroplasmies within a single individual, when using an ∼1-percent minor allele frequency (MAF) threshold. Inspection of the heteroplasmy data detailed in dataset S1 of ref. 1 revealed that contamination, not intraindividual variation, is the source of at least some of the reported heteroplasmy. For example, among the 15 samples with 20 or more heteroplasmies, all appear to be a mixture of at least two distinct individuals, and a minimum of 80.7 percent of the 584 heteroplasmies occurred at positions diagnostic for the mtDNA haplogroups represented in each mixture. To cite specific examples: for sample HG00740, nearly all (90 percent) of the 71 heteroplasmies can be ascribed to one of two distinct mtDNA haplogroups (L1b1a7a, of sub-Saharan African ancestry, and B2b3a, a Native American lineage); and for sample HG01108, 50 and 12 of 69 total heteroplasmies are diagnostic for haplogroups L0a1a2 (sub-Saharan African) and M7c1b (East Asian), respectively [according to Build 16 of PhyloTree (2)] (Fig. 1). Even among the heteroplasmies reported for those samples that do not match an mtDNA haplogroup motif, some are likely a result of private mutations in either individual represented in each mixture, rather than true intra-individual variation. (publisher abstract modified)