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. 2019 Jun;21(6):1407-1416.
doi: 10.1038/s41436-018-0350-8. Epub 2018 Nov 5.

eKLIPse: a sensitive tool for the detection and quantification of mitochondrial DNA deletions from next-generation sequencing data

David Goudenège  1   2 , Celine Bris  1   2 , Virginie Hoffmann  1 , Valerie Desquiret-Dumas  1   2 , Claude Jardel  3 , Benoit Rucheton  3 , Sylvie Bannwarth  4 , Veronique Paquis-Flucklinger  4 , Anne Sophie Lebre  5 , Estelle Colin  1   2 , Patrizia Amati-Bonneau  1   2 , Dominique Bonneau  1   2 , Pascal Reynier  1   2 , Guy Lenaers  1 , Vincent Procaccio  6   7
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Free article

eKLIPse: a sensitive tool for the detection and quantification of mitochondrial DNA deletions from next-generation sequencing data

David Goudenège et al. Genet Med. 2019 Jun.
Free article

Abstract

Purpose: Accurate 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.

Methods: The 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.

Results: eKLIPse 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 ).

Conclusion: Thus, eKLIPse represents a useful resource to study the causes and consequences of mtDNA rearrangements, for further genotype/phenotype correlations in mitochondrial disorders.

Keywords: mitochondrial diseases; mitochondrial genome; mtDNA deletions; next-generation sequencing; soft clipping.

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