ArticleNAR genomics and bioinformatics2022
A bioinformatics pipeline for estimating mitochondrial DNA copy number and heteroplasmy levels from whole genome sequencing data.
Article in NAR genomics and bioinformatics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
What it found
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The trial behind it
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Who cites it
37 citing papers in PubMed, 48 citations in OpenAlex.
- Variations in mitochondrial genome as potential prognostic markers in sickle cell disease.Haematologica · 2026Article
- Himito: a graph-based toolkit for mitochondrial genome analysis using long reads.Nature communications · 2026Article
- Genetic contributions to mitochondrial dysfunction in amyotrophic lateral sclerosis etiology.HGG advances · 2026Article
- Deleterious mitochondrial heteroplasmy drives high-risk clonal hematopoiesis and hematological malignancy.medRxiv : the preprint server for health sciences · 2026Article
- Mito_Plot: open-source pipeline for quantification and visualization of mitochondrial DNA heteroplasmy.BMC bioinformatics · 2026Article
- Comprehensive genome sequencing associates elevated mitochondrial DNA and homoplasmy with early stage I of pancreatic cancer.iScience · 2026Article
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- Association of mitochondrial genetic background with pS65-Ub in Lewy body disease.Acta neuropathologica · 2026Article
- Mitochondrial heteroplasmy is a risk factor for the development of chronic lymphocytic leukemia.Nature communications · 2026Article
- Mitochondrial DNA mutations and intercellular mitochondrial transfer in cancer: mechanisms, biological effects, and clinical potential.Biomarker research · 2026Review
- Associations of Blood Mitochondrial DNA Quality and Quantity with Risk of Kidney Function Decline.Clinical journal of the American Society of Nephrology : CJASN · 2026Article
- ASSOCIATION ANALYSIS OF MITOCHONDRIAL HETEROPLASMIC VARIANTS AND CARDIOMETABOLIC TRAITS.medRxiv : the preprint server for health sciences · 2026Article
- Epigenome-wide association study of nuclear DNA methylation in relation to mitochondrial heteroplasmy.Nature communications · 2025Article
- Association of Epigenetic Age Acceleration and Mitochondrial DNA-Based Aging Metrics Provides Insights Into Mechanisms of Aging-Related Diseases.Aging cell · 2025Article
- Reversible compromise of physiological resilience by accumulation of heteroplasmic mtDNA mutations.Science (New York, N.Y.) · 2025Article
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- Mitochondrial clonal mosaicism encodes a biphasic molecular clock of aging.Nature aging · 2025Article
- Deleterious mitochondrial heteroplasmies exhibit increased longitudinal change in variant allele fraction.iScience · 2025Article
- Mitochondrial DNA copy number variation in asthma risk, severity, and exacerbations.The Journal of allergy and clinical immunology · 2025Article
Corrections and comments
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Authors and funding
14 authors at 7 institutions in 2 countries.
Funding
Abstract
Mitochondrial diseases are a heterogeneous group of disorders that can be caused by mutations in the nuclear or mitochondrial genome. Mitochondrial DNA (mtDNA) variants may exist in a state of heteroplasmy, where a percentage of DNA molecules harbor a variant, or homoplasmy, where all DNA molecules have the same variant. The relative quantity of mtDNA in a cell, or copy number (mtDNA-CN), is associated with mitochondrial function, human disease, and mortality. To facilitate accurate identification of heteroplasmy and quantify mtDNA-CN, we built a bioinformatics pipeline that takes whole genome sequencing data and outputs mitochondrial variants, and mtDNA-CN. We incorporate variant annotations to facilitate determination of variant significance. Our pipeline yields uniform coverage by remapping to a circularized chrM and by recovering reads falsely mapped to nuclear-encoded mitochondrial sequences. Notably, we construct a consensus chrM sequence for each sample and recall heteroplasmy against the sample's unique mitochondrial genome. We observe an approximately 3-fold increased association with age for heteroplasmic variants in non-homopolymer regions and, are better able to capture genetic variation in the D-loop of chrM compared to existing software. Our bioinformatics pipeline more accurately captures features of mitochondrial genetics than existing pipelines that are important in understanding how mitochondrial dysfunction contributes to disease.
Identifiers
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.