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Assessing mitochondrial heteroplasmy using next generation sequencing: A note of caution
Mauro Santibanez-Koref1, Helen Griffin1, Douglass M Turnbull2
1Institute of Genetic Medicine, International Centre for Life, Central Parkway, Newcastle upon Tyne NE1 3BZ, UK.
Mitochondrion
|August 12, 2018
Summary
Nuclear mitochondrial sequences (NUMTs) are often overlooked in next-generation sequencing studies. Our research shows NUMTs impact variant calling in mitochondrial DNA analysis.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Mitochondrial genome sequencing is crucial for disease research and therapies.
- Current studies often ignore nuclear mitochondrial sequences (NUMTs), which are mtDNA fragments in the nuclear genome.
- This oversight may affect the accuracy of variant calling in mitochondrial DNA analysis.
Purpose of the Study:
- To investigate the presence and impact of NUMTs in next-generation sequencing data.
- To highlight the necessity of accounting for NUMTs in mitochondrial DNA analysis.
Main Methods:
- Utilized various mtDNA enrichment techniques across diverse tissue types.
- Analyzed next-generation sequencing data to identify and quantify NUMTs.
- Assessed the influence of NUMTs on variant calling accuracy.
Main Results:
- Demonstrated the consistent presence of NUMTs in sequencing data.
- Showed that NUMTs, depending on downstream analysis, significantly affect variant calling outcomes.
- Highlighted the inadequacy of aligning sequence data solely to the revised Cambridge reference sequence.
Conclusions:
- NUMTs are a significant factor in mitochondrial DNA sequencing studies.
- Failure to account for NUMTs can lead to inaccurate variant calling.
- Future studies must incorporate NUMT detection and mitigation strategies for reliable mitochondrial genome analysis.
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