Investigation of length heteroplasmy in mitochondrial DNA control region by massively parallel sequencing

Lin, Chun-Yen; Tsai, Li-Chin; Hsieh, Hsing-Mei; Huang, Chia-Hung; Yu, Yu-Jen; Tseng, Bill; Linacre, Adrian; Lee, James Chun-I

doi:10.1016/j.fsigen.2017.07.003

Cited by 8 publications

(5 citation statements)

References 19 publications

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“…With the advent of MPS, analysis of only HV1, HV2 and the wider control region using these amplification strategies is still carried out (Holland et al, 2017; Lin et al, 2017; SWGDAM, 2019). The introduction of MPS has led to the commercialization of the mini‐primer amplification of the entire control region.…”

Section: Target Enrichmentmentioning

confidence: 99%

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Methods for the analysis of mitochondrial DNA

Forsythe

Melia

Harbison

2020

WIREs Forensic Science

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The use of mitochondrial DNA (mtDNA) profiling as a tool for forming a link between an individual and a crime sample is a well-established forensic biology technique. Though nuclear DNA typing is considered the gold standard method, certain evidence types have limited nuclear DNA available, such as telogen hairs and ancient or degraded remains, for which mtDNA analysis may be required. Traditionally mtDNA typing has been carried out using

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Section: Target Enrichmentmentioning

confidence: 99%

“…With the advent of MPS, analysis of only HV1, HV2 and the wider control region using these amplification strategies is still carried out Lin et al, 2017;SWGDAM, 2019)…”

Section: Control Region Amplificationmentioning

confidence: 99%

Methods for the analysis of mitochondrial DNA

Forsythe

Melia

Harbison

2020

WIREs Forensic Science

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“…We then isolated these fragments and used an ABI 3700 automated DNA sequencer and a BigDye Terminator Cycle sequencing reaction kit to determine their sequences, which were compared to the updated consensus Cambridge sequence (GenBank accession number: NC_012920) [14].…”

Section: Mitochondrial Genome Mutation Analysismentioning

confidence: 99%

Mutation at position 5628 in the mitochondrial tRNAAla gene in a Chinese pedigree with maternally diabetes mellitus

Li¹,

Wu²,

Lin³

et al. 2019

Preprint

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Background: To investigate the clinical, genetic and molecular characteristics of mitochondrial diabetes mellitus (MDM). Methods: Resultant variants were evaluated for evolutionary conservation, allelic frequencies, and structural and functional consequences. The mitochondrial function including mitochondrial tRNAAla levels, protein synthesis, membrane potential, adenosine triphosphate (ATP) production, and reactive oxygen species (ROS) generation were measured using lymphoblastoid cell lines carrying the m.5628T>C mutation and 2 controls .Results: We observed differences in the severity and age of onset in diabetes in affected maternally-related individuals, and through amolecular of the complete mitochondrial genome in this family, we identified a homoplasmic m.5628T>C mutation, located at conventional position 31 of tRNAAla, and we further detected distinct sets of mtDNA polymorphisms belonging to haplogroup L1. The identified mutation was further found be important for tRNA identity and stability. Using cellular models, we were able to determine that the respiratory deficiency caused arising as a consequence of the m.5628T>C mutation led to decreased efficiency of mitochondrial tRNAAla levels, protein synthesis, mitochondrial ATP synthesis and a reduced mitochondrial membrane potential.These mitochondrial dysfunctions caused an increase in the production of reactive oxygen species in the mutant cell lines. Conclusions: These data provide a direct evidence that novel m.5628T>C mutation may be associated with MDM, thus, offering novel insights into the understanding of pathophysiology of MDM.

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“…In addition, the MAF of PHP calls ranges from 1% to 10% [ 22 , 23 , 24 , 25 , 26 ], even dropping to as low as 0.15% [ 27 ]. Successful detection of C-stretches has also been realized [ 28 , 29 ]. Studies evaluating the germline bottleneck size [ 30 , 31 ] and mtDNA transmissions in pedigrees [ 32 , 33 ] and those distinguishing between the mother and offspring [ 24 ] have also been carried out with MPS detection of the mtGenome.…”

Section: Introductionmentioning

confidence: 99%

Whole Mitochondrial Genome Detection and Analysis of Two- to Four-Generation Maternal Pedigrees Using a New Massively Parallel Sequencing Panel

Peng

Geng

Yang

et al. 2023

Genes

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Mitochondrial DNA (mtDNA) is an effective genetic marker in forensic practice, especially for aged bones and hair shafts. Detection of the whole mitochondrial genome (mtGenome) using traditional Sanger-type sequencing is laborious and time-consuming. Additionally, its ability to distinguish point heteroplasmy (PHP) and length heteroplasmy (LHP) is limited. The application of massively parallel sequencing in mtDNA detection helps researchers to study the mtGenome in-depth. The ForenSeq mtDNA Whole Genome Kit, which contains a total of 245 short amplicons, is one of the multiplex library preparation kits for the mtGenome. We used this system to detect the mtGenome in the blood samples and hair shafts of thirty-three individuals from eight two-generation pedigrees, one three-generation pedigree, and one four-generation pedigree. High-quality sequencing results were obtained. Ten unique mtGenome haplotypes were observed in the mothers from the ten pedigrees. A total of 26 PHPs were observed using the interpretation threshold of 6%. Eleven types of LHPs in six regions were evaluated in detail. When considering homoplasmic variants only, consistent mtGenome haplotypes were observed between the twice-sequenced libraries and between the blood and hair shafts from the same individual and among maternal relatives in the pedigrees. Four inherited PHPs were observed, and the remainder were de novo/disappearing PHPs in the pedigrees. Our results demonstrate the effective capability of the ForenSeq mtDNA Whole Genome Kit to generate the complete mtGenome in blood and hair shafts, as well as the complexity of mtDNA haplotype comparisons between different types of maternal relatives when heteroplasmy is considered.

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Investigation of length heteroplasmy in mitochondrial DNA control region by massively parallel sequencing

Cited by 8 publications

References 19 publications

Methods for the analysis of mitochondrial DNA

Methods for the analysis of mitochondrial DNA

Mutation at position 5628 in the mitochondrial tRNAAla gene in a Chinese pedigree with maternally diabetes mellitus

Whole Mitochondrial Genome Detection and Analysis of Two- to Four-Generation Maternal Pedigrees Using a New Massively Parallel Sequencing Panel

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