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Accurate mitochondrial DNA sequencing using off-target reads provides a single test to identify pathogenic point mutations

Lookup NU author(s): Dr Helen GriffinORCiD, Dr Angela Pyle, Dr Charlotte Alston, Dr Jennifer Duff, Dr Gavin Hudson, Professor Rita HorvathORCiD, Dr Ian Wilson, Dr Mauro Santibanez Koref, Professor Robert Taylor, Professor Patrick Chinnery

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This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).


Abstract

Purpose: Mitochondrial disorders are a common cause of inherited metabolic disease and can be due to mutations affecting mitochondrial DNA or nuclear DNA. The current diagnostic approach involves the targeted resequencing of mitochondrial DNA and candidate nuclear genes, usually proceeds step by step, and is time consuming and costly. Recent evidence suggests that variations in mitochondrial DNA sequence can be obtained from whole-exome sequence data, raising the possibility of p. comprehensive single diagnostic test to detect pathogenic point mutations.Methods: We compared the mitochondrial DNA sequence derived from off-target exome reads with conventional mitochondrial DNA Sanger sequencing in 46 subjects.Results: Mitochondrial DNA sequences can be reliably obtained using three different whole-exome sequence capture kits. Coverage correlates with the relative amount of mitochondrial DNA in the original genomic DNA sample, heteroplasmy levels can be determined using variant and total read depths, and-providing there is a minimum read depth of 20-fold-rare sequencing errors occur at a rate similar to that observed with conventional Sanger sequencing.Conclusion: This offers the prospect of using whole-exome sequence in a diagnostic setting to screen not only all protein coding nuclear genes but also all mitochondrial DNA genes for pathogenic mutations. Off-target mitochondrial DNA reads can also be used to assess quality control and maternal ancestry, inform on ethnic origin, and allow genetic disease association studies not previously anticipated with existing whole-exome data sets.


Publication metadata

Author(s): Griffin HR, Pyle A, Blakely EL, Alston CL, Duff J, Hudson G, Horvath R, Wilson IJ, Santibanez-Koref M, Taylor RW, Chinnery PF

Publication type: Article

Publication status: Published

Journal: Genetics in Medicine

Year: 2014

Volume: 16

Issue: 12

Pages: 962-971

Print publication date: 01/12/2014

Online publication date: 05/06/2014

Acceptance date: 06/05/2014

Date deposited: 02/07/2015

ISSN (print): 1098-3600

ISSN (electronic): 1530-0366

Publisher: Nature Publishing Group

URL: http://dx.doi.org/10.1038/gim.2014.66

DOI: 10.1038/gim.2014.66


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Funding

Funder referenceFunder name
National Institute for Health Research (NIHR) Newcastle Biomedical Research Centre based at Newcastle upon Tyne Hospitals NHS Foundation Trust
UK NHS Highly Specialised "Rare Mitochondrial Disorders of Adults and Children" Service
EU FP7 TIRCON
Newcastle University
NIHR/CSO Healthcare Science Research Fellowship from the National Institute for Health Research
096919Z/11/ZWellcome Trust Centre for Mitochondrial Research
101876/Z/13/ZWellcome Trust Senior Fellow in Clinical Science
G0601943MRC Centre for Neuromuscular Diseases
G0601943Medical Research Council (UK) Neuromuscular Centre

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