Nanomito enables amplification-free full-length analysis of mitochondrial DNA variants and deletions
Abstract
Accurate analysis of mitochondrial DNA (mtDNA) requires reliable quantification of heteroplasmy and robust detection of large-scale deletions. However, routine PCR-based short-read workflows can introduce amplification bias and have limited structural resolution. Here, we developed Nanomito, an amplification-free long-read workflow for full-length sequencing of native mtDNA using Oxford Nanopore Technologies, and compared it with the routine long-range PCR-based Illumina approach in 15 retrospectively selected clinical samples previously characterized in mitochondrial diagnostics. The long-read workflow detected all clinically confirmed causal point variants and identified one low-level m.3243 A > G variant, present at 3.8% heteroplasmy by digital PCR, that was detected only among quality-filtered short-read calls. Relative to digital PCR, long-read heteroplasmy estimates showed a more stable quantitative relationship than the PCR-based short-read workflow. In deletion-positive samples, long-read sequencing confirmed the major deletions detected by routine testing with closely matching breakpoint coordinates and resolved a complex deletion spectrum in one sample. These findings support amplification-free full-length nanopore sequencing as a promising framework for integrated mtDNA variant and deletion analysis.
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BibTeX
@article{desquiretdumas2026nanomito,
title = {{Nanomito enables amplification-free full-length analysis of mitochondrial DNA variants and deletions}},
author = {Valérie Desquiret-Dumas and Solène Duverger and Patrizia Amati-Bonneau and Xavier Dieu and Delphine Mirebeau-Prunier and Pascal Reynier and Marc Ferré},
journal = {Scientific Reports},
year = {2026},
month = oct,
doi = {10.1038/s41598-026-74050-0},
url = {https://www.nature.com/articles/s41598-026-74050-0},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Nanomito enables amplification-free full-length analysis of mitochondrial DNA variants and deletions
AU - Valérie Desquiret-Dumas
AU - Solène Duverger
AU - Patrizia Amati-Bonneau
AU - Xavier Dieu
AU - Delphine Mirebeau-Prunier
AU - Pascal Reynier
AU - Marc Ferré
PY - 2026
DA - 2026/10/28
JO - Scientific Reports
DO - 10.1038/s41598-026-74050-0
UR - https://www.nature.com/articles/s41598-026-74050-0
AB - Accurate analysis of mitochondrial DNA (mtDNA) requires reliable quantification of heteroplasmy and robust detection of large-scale deletions. However, routine PCR-based short-read workflows can introduce amplification bias and have limited structural resolution. Here, we developed Nanomito, an amplification-free long-read workflow for full-length sequencing of native mtDNA using Oxford Nanopore Technologies, and compared it with the routine long-range PCR-based Illumina approach in 15 retrospectively selected clinical samples previously characterized in mitochondrial diagnostics. The long-read workflow detected all clinically confirmed causal point variants and identified one low-level m.3243 A > G variant, present at 3.8% heteroplasmy by digital PCR, that was detected only among quality-filtered short-read calls. Relative to digital PCR, long-read heteroplasmy estimates showed a more stable quantitative relationship than the PCR-based short-read workflow. In deletion-positive samples, long-read sequencing confirmed the major deletions detected by routine testing with closely matching breakpoint coordinates and resolved a complex deletion spectrum in one sample. These findings support amplification-free full-length nanopore sequencing as a promising framework for integrated mtDNA variant and deletion analysis.
SN - 2045-2322
ER -