ArticleGenetics in medicine : official journal of the American College of Medical Genetics2019
eKLIPse: a sensitive tool for the detection and quantification of mitochondrial DNA deletions from next-generation sequencing data.
Article in Genetics in medicine : official journal of the American College of Medical Genetics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers, 1 of them a synthesis that pooled it.
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35 citing papers in PubMed, 1 synthesis or guideline pooled it, 55 citations in OpenAlex.
- Comprehensive summary of mitochondrial DNA alterations in the postmortem human brain: A systematic review.EBioMedicine · 2022Pooled it
- Hypoxia and TTR dysregulation in astrocytes from Parkinson's disease with a specific mitochondrial haplogroup: A single-cell analysis.Neural regeneration research · 2026Article
- MitoClipSplice: a machine learning framework for resolving mitochondrial RNA cleavage sites from strand-specific RNA-seq soft-clips.Briefings in bioinformatics · 2026Article
- Clinical Heterogeneity and Candidate Biomarkers inNeurology. Genetics · 2026Article
- Enhancing the diagnostic yield of monogenic diabetes in unresolved cases with early-onset hyperglycemia.Communications medicine · 2025Article
- MitoDelta: identifying mitochondrial DNA deletions at cell-type resolution from single-cell RNA sequencing data.BMC genomics · 2025Article
- Identification of a novel truncated pathogenic variant in PUS1 gene in two siblings of consanguineous Tunisian family: intrafamilial phenotypic variability related to mtDNA copy number.Annals of hematology · 2025Article
- High frequency of mitochondrial DNA rearrangements in the peripheral blood of adults with intellectual disability.Journal of intellectual disability research : JIDR · 2025Article
- MtDNA copy number enrichment is associated with poor prognosis and eosinophilic morphology in clear cell renal cell carcinoma.Pathology oncology research : POR · 2025Article
- The Evolution and Role of Molecular Tools in Measuring Diversity and Genomic Selection in Livestock Populations (Traditional and Up-to-Date Insights): A Comprehensive Exploration.Veterinary sciences · 2024Review
- Best practices for germline variant and DNA methylation analysis of second- and third-generation sequencing data.Human genomics · 2024Review
- Common mitochondrial deletions in RNA-Seq: evaluation of bulk, single-cell, and spatial transcriptomic datasets.Communications biology · 2024Article
- The human OPA1Cellular and molecular life sciences : CMLS · 2024Article
- Cellular allostatic load is linked to increased energy expenditure and accelerated biological aging.Psychoneuroendocrinology · 2023Article
- Single-cell multi-omics of mitochondrial DNA disorders reveals dynamics of purifying selection across human immune cells.Nature genetics · 2023Article
- OxPhos defects cause hypermetabolism and reduce lifespan in cells and in patients with mitochondrial diseases.Communications biology · 2023Article
- Nanopore long-read next-generation sequencing for detection of mitochondrial DNA large-scale deletions.Frontiers in genetics · 2023Article
- A multi-omics longitudinal aging dataset in primary human fibroblasts with mitochondrial perturbations.Scientific data · 2022Article
- Next-generation sequencing of Tunisian Leigh syndrome patients reveals novel variations: impact for diagnosis and treatment.Bioscience reports · 2022Article
- Long-Term Persistence of Mitochondrial DNA Instability in HIV-Exposed Uninfected Children during and after Exposure to Antiretroviral Drugs and HIV.Biomedicines · 2022Article
Corrections and comments
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Authors and funding
15 authors at 6 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
purposeAccurate detection of mitochondrial DNA (mtDNA) alterations is essential for the diagnosis of mitochondrial diseases. The development of high-throughput sequencing technologies has enhanced the detection sensitivity of mtDNA pathogenic variants, but the detection of mtDNA rearrangements, especially multiple deletions, is still poorly processed. Here, we present eKLIPse, a sensitive and specific tool allowing the detection and quantification of large mtDNA rearrangements from single and paired-end sequencing data.
methodsThe methodology was first validated using a set of simulated data to assess the detection sensitivity and specificity, and second with a series of sequencing data from mitochondrial disease patients carrying either single or multiple deletions, related to pathogenic variants in nuclear genes involved in mtDNA maintenance.
resultseKLIPse provides the precise breakpoint positions and the cumulated percentage of mtDNA rearrangements at a given gene location with a detection sensitivity lower than 0.5% mutant. eKLIPse software is available either as a script to be integrated in a bioinformatics pipeline, or as user-friendly graphical interface to visualize the results through a Circos representation ( https://github.com/dooguypapua/eKLIPse ).
conclusionThus, eKLIPse represents a useful resource to study the causes and consequences of mtDNA rearrangements, for further genotype/phenotype correlations in mitochondrial disorders.
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