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Mitochondrion. 2018 Aug 9. pii: S1567-7249(18)30087-4. doi: 10.1016/j.mito.2018.08.003. [Epub ahead of print]

Assessing mitochondrial heteroplasmy using next generation sequencing: A note of caution.

Author information

1
Institute of Genetic Medicine, International Centre for Life, Central Parkway, Newcastle upon Tyne NE1 3BZ, UK.
2
The Wellcome Centre for Mitochondrial Research, Newcastle University, Medical School, Framlington Place, Newcastle upon Tyne NE2 4HH, UK.
3
MRC Mitochondrial Biology Unit, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK.
4
The Wellcome Centre for Mitochondrial Research, Newcastle University, Medical School, Framlington Place, Newcastle upon Tyne NE2 4HH, UK; Newcastle Fertility Centre, International Centre for Life, Central Parkway, Newcastle upon Tyne NE1 3BZ, UK.
5
Institute of Genetic Medicine, International Centre for Life, Central Parkway, Newcastle upon Tyne NE1 3BZ, UK; The Wellcome Centre for Mitochondrial Research, Newcastle University, Medical School, Framlington Place, Newcastle upon Tyne NE2 4HH, UK. Electronic address: gavin.hudson@newcastle.ac.uk.

Abstract

The mitochondrial genome has recently become the focus of several high-impact next-generation sequencing studies investigating the effect of mutations in disease and assessing the efficacy of mitochondrial replacement therapies. However, these studies have failed to take into consideration the capture of recurring translocations of mitochondrial DNA to the nuclear genome, known as nuclear mitochondrial sequences (NUMTs), continuing to align sequence data to the revised Cambridge reference sequence alone. Here, using different mtDNA enrichment techniques and a variety of tissues, we demonstrate that NUMTs are present in sequence data and that, dependent upon downstream analysis, are at a level which affects variant calling.

KEYWORDS:

Bioinformatic analysis; Heteroplasmy; Mitochondrial DNA; Next-generation sequencing

PMID:
30098421
DOI:
10.1016/j.mito.2018.08.003
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