Accurate mapping of mitochondrial DNA deletions and duplications using deep sequencing

Swaraj Basu,Stanka Matic,Olivier R Baris,Sammy Kimoloi,Dusanka Milenkovic,James B Stewart,Maria Falkenberg,Rudolf J Wiesner,Anders Oldfors,Erik Larsson,Carola Hedberg-Oldfors,Nils-Göran Larsson,Jay P Uhler,Xie Xie,Claes M Gustafsson

doi:10.1371/journal.pgen.1009242

Abstract

Deletions and duplications in mitochondrial DNA (mtDNA) cause mitochondrial disease and accumulate in conditions such as cancer and age-related disorders, but validated high-throughput methodology that can readily detect and discriminate between these two types of events is lacking. Here we establish a computational method, MitoSAlt, for accurate identification, quantification and visualization of mtDNA deletions and duplications from genomic sequencing data. Our method was tested on simulated sequencing reads and human patient samples with single deletions and duplications to verify its accuracy. Application to mouse models of mtDNA maintenance disease demonstrated the ability to detect deletions and duplications even at low levels of heteroplasmy.

Highlights

IntroductionMitochondria contain a separate genome which encodes essential subunits of the oxidative phosphorylation system and the RNA molecules (ribosomal and transfer RNA) needed for mitochondrial translation
Mitochondria contain a separate genome which encodes essential subunits of the oxidative phosphorylation system and the RNA molecules needed for mitochondrial translation
Deletions in the mitochondrial genome cause a wide variety of rare disorders, but are linked to more common conditions such as neurodegeneration, diabetes type 2, and the normal ageing process

Summary

Introduction

Mitochondria contain a separate genome which encodes essential subunits of the oxidative phosphorylation system and the RNA molecules (ribosomal and transfer RNA) needed for mitochondrial translation. Mitochondrial DNA (mtDNA) in humans is a small 16.6 kb circular molecule with only a few non-coding regions[1,2]. Large deletions and duplications in mtDNA almost invariably lead to disruption of mitochondrial gene function. These types of structural alterations can be spontaneous or attributed to mutations affecting the nuclearencoded mtDNA maintenance machinery, e.g. the mitochondrial DNA polymerase γ (POLγ) [3] or the replicative Twinkle helicase[4,5]. Deletions are a common cause of mitochondrial disorders[6,7,8,9] while being linked to cancer[10,11,12], diabetes[13,14], neurodegenerative disorders[15,16], and the ageing process[16,17]. Duplications are less commonly described, but have for instance been described in patients with disease-causing mutations in MGME1 [18,19] or in mice expressing a proof-reading-deficient version of Polγ[20]

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Discussion

Conclusion