ArticleBMC bioinformatics2017
Detection and quantification of mitochondrial DNA deletions from next-generation sequence data.
Article in BMC bioinformatics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- "NanoDel": identification of large-scale mitochondrial DNA deletions using long-read sequencing.Bioinformatics (Oxford, England) · 2026Article
- Common mitochondrial deletions in RNA-Seq: evaluation of bulk, single-cell, and spatial transcriptomic datasets.Communications biology · 2024Article
- Nanopore sequencing identifies a higher frequency and expanded spectrum of mitochondrial DNA deletion mutations in human aging.Aging cell · 2023Article
- A method for multiplexed full-length single-molecule sequencing of the human mitochondrial genome.Nature communications · 2022Article
- Another lesson from unmapped reads: in-depth analysis of RNA-Seq reads from various horse tissues.Journal of applied genetics · 2022Article
- Long read mitochondrial genome sequencing using Cas9-guided adaptor ligation.Mitochondrion · 2022Article
- Mitochondrial DNA Content Is Linked to Cardiovascular Disease Patient Phenotypes.Journal of the American Heart Association · 2021Article
- Accurate mapping of mitochondrial DNA deletions and duplications using deep sequencing.PLoS genetics · 2020Article
- Ultrasensitive deletion detection links mitochondrial DNA replication, disease, and aging.Genome biology · 2020Article
- Thinking outside the nucleus: Mitochondrial DNA copy number in health and disease.Mitochondrion · 2020Review
- Mitochondrial DNA alterations may influence the cisplatin responsiveness of oral squamous cell carcinoma.Scientific reports · 2020Article
- Enhanced Efflux Pump Expression inAntimicrobial agents and chemotherapy · 2020Article
- Splice-Break: exploiting an RNA-seq splice junction algorithm to discover mitochondrial DNA deletion breakpoints and analyses of psychiatric disorders.Nucleic acids research · 2019Article
- eKLIPse: a sensitive tool for the detection and quantification of mitochondrial DNA deletions from next-generation sequencing data.Genetics in medicine : official journal of the American College of Medical Genetics · 2019Article
- Detection and quantification of mitochondrial DNA deletions from next-generation sequence data.BMC bioinformatics · 2017Article
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Authors and funding
4 authors.
Funding
Abstract
backgroundChromosomal deletions represent an important class of human genetic variation. Various methods have been developed to mine "next-generation" sequencing (NGS) data to detect deletions and quantify their clonal abundances. These methods have focused almost exclusively on the nuclear genome, ignoring the mitochondrial chromosome (mtDNA). Detecting mtDNA deletions requires special care. First, the chromosome's relatively small size (16,569 bp) necessitates the ability to detect extremely focal events. Second, the chromosome can be present at thousands of copies in a single cell (in contrast to two copies of nuclear chromosomes), and mtDNA deletions may be present on only a very small percentage of chromosomes. Here we present a method, termed MitoDel, to detect mtDNA deletions from NGS data.
resultsWe validate the method on simulated and real data, and show that MitoDel can detect novel and previously-reported mtDNA deletions. We establish that MitoDel can find deletions such as the "common deletion" at heteroplasmy levels well below 1%.
conclusionsMitoDel is a tool for detecting large mitochondrial deletions at low heteroplasmy levels. The tool can be downloaded at http://mendel.gene.cwru.edu/laframboiselab/ .
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