mtDNA variant detection by exome sequencing

Next generation sequencing, especially exome sequencing, has revolutionised the diagnostics for mitochondrial disorders. However, the nuclear and mitochondrial DNA are investigated with separate tests, increasing costs and duration of diagnostics. However, the full potential of exome sequencing is often not exploited as the additional analysis of “off-target reads” deriving from the mitochondrial DNA can be used to analyse both genomes. Mitochondrial DNA analysis by exome sequencing of 2,111 cases (various, mostly neurological, referral indications) in a clinical setting identified 38 confirmed pathogenic mitochondrial DNA point mutations, increasing the diagnostic yield by nearly 2%. We show that analysis of mitochondrial DNA variants by exome sequencing has a high recall rate (96.2±5.6%) and an excellent precision (99.5±2.2%) when compared to the gold standard of targeted mitochondrial DNA next generation sequencing. Further, we demonstrate that exome sequencing estimates heteroplasmy levels with an average difference of 6.6±3.8% compared to targeted mitochondrial DNA next generation sequencing, sufficient for clinical decision making. Taken together, the mitochondrial DNA analysis from exome sequencing is of sufficient quality for clinical diagnostics, and should be included in the standard diagnostic exome analysis. Nonetheless, known pitfalls for mitochondrial DNA analysis like tissue specificity have to be taken into account.