Literature DB >> 29279961

Assessment of mitochondrial DNA heteroplasmy detected on commercial panel using MPS system with artificial mixture samples.

Sohee Cho1, Moon Young Kim2, Ji Hyun Lee2, Soong Deok Lee3,4.   

Abstract

Mitochondrial DNA (mtDNA) heteroplasmy is a potential genetic marker for forensic mtDNA analysis as well as phylogenic studies. Frequency of mtDNA heteroplasmy has been investigated in different populations through massively parallel sequencing (MPS) analysis, revealing various levels of frequency based on different MPS systems. For accurate heteroplasmy identification, it is essential to explore reliable detection threshold on various MPS systems. In addition, software solutions and pipelines need to be evaluated to analyze data effectively. In this study, heteroplasmy analysis was conducted on a commercially available mtDNA analysis system developed for forensic caseworks with artificially mixed DNA samples known for ratios and variant positions for assessment. mtDNA heteroplasmy > 10% was detectable with Torrent Variant Caller (TVC) while lower levels were identified using GeneMarker® HTS specialized software for minor variant detection. This study implies that analytical parameters and tools need to be optimized and evaluated for low-level heteroplasmy identification. Automated system with simple and efficient workflow is needed for forensic caseworks.

Entities:  

Keywords:  Low-level heteroplasmy; Massively parallel sequencing; Mitochondrial DNA; Mixture

Mesh：

Substances：

Year:  2017        PMID： 29279961     DOI： 10.1007/s00414-017-1755-7

Source DB:  PubMed          Journal:  Int J Legal Med        ISSN： 0937-9827            Impact factor:   2.686


  33 in total

1.  Heteroplasmy in mtDNA and the weight of evidence in forensic mtDNA analysis: a case report.

Authors:  A Salas; M V Lareu; A Carracedo
Journal:  Int J Legal Med       Date:  2001       Impact factor: 2.686

Review 2.  Mitochondrial DNA Sequence Analysis - Validation and Use for Forensic Casework.

Authors:  M M Holland; T J Parsons
Journal:  Forensic Sci Rev       Date:  1999-06

3.  Strategies for complete mitochondrial genome sequencing on Ion Torrent PGM™ platform in forensic sciences.

Authors:  Yishu Zhou; Fei Guo; Jiao Yu; Feng Liu; Jinling Zhao; Hongying Shen; Bin Zhao; Fei Jia; Zhu Sun; He Song; Xianhua Jiang
Journal:  Forensic Sci Int Genet       Date:  2016-01-15       Impact factor: 4.882

4.  Mitochondrial DNA sequence heteroplasmy in the Grand Duke of Russia Georgij Romanov establishes the authenticity of the remains of Tsar Nicholas II.

Authors:  P L Ivanov; M J Wadhams; R K Roby; M M Holland; V W Weedn; T J Parsons
Journal:  Nat Genet       Date:  1996-04       Impact factor: 38.330

5.  Evaluation of GeneMarker® HTS for improved alignment of mtDNA MPS data, haplotype determination, and heteroplasmy assessment.

Authors:  Mitchell M Holland; Erica D Pack; Jennifer A McElhoe
Journal:  Forensic Sci Int Genet       Date:  2017-02-06       Impact factor: 4.882

6.  Development and assessment of an optimized next-generation DNA sequencing approach for the mtgenome using the Illumina MiSeq.

Authors:  Jennifer A McElhoe; Mitchell M Holland; Kateryna D Makova; Marcia Shu-Wei Su; Ian M Paul; Christine H Baker; Seth A Faith; Brian Young
Journal:  Forensic Sci Int Genet       Date:  2014-05-20       Impact factor: 4.882

Review 7.  Number matters: control of mammalian mitochondrial DNA copy number.

Authors:  Laura L Clay Montier; Janice J Deng; Yidong Bai
Journal:  J Genet Genomics       Date:  2009-03       Impact factor: 4.275

8.  Second generation sequencing allows for mtDNA mixture deconvolution and high resolution detection of heteroplasmy.

Authors:  Mitchell M Holland; Megan R McQuillan; Katherine A O'Hanlon
Journal:  Croat Med J       Date:  2011-06       Impact factor: 1.351

9.  Entire Mitochondrial DNA Sequencing on Massively Parallel Sequencing for the Korean Population.

Authors:  Sohyung Park; Sohee Cho; Hee Jin Seo; Ji Hyun Lee; Moon Young Kim; Soong Deok Lee
Journal:  J Korean Med Sci       Date:  2017-04       Impact factor: 2.153

10.  Next-generation sequencing of human mitochondrial reference genomes uncovers high heteroplasmy frequency.

Authors:  Maria Ximena Sosa; I K Ashok Sivakumar; Samantha Maragh; Vamsi Veeramachaneni; Ramesh Hariharan; Minothi Parulekar; Karin M Fredrikson; Timothy T Harkins; Jeffrey Lin; Andrew B Feldman; Pramila Tata; Georg B Ehret; Aravinda Chakravarti
Journal:  PLoS Comput Biol       Date:  2012-10-25       Impact factor: 4.475
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  5 in total

1.  Massively parallel sequencing-enabled mixture analysis of mitochondrial DNA samples.

Authors:  Jennifer D Churchill; Monika Stoljarova; Jonathan L King; Bruce Budowle
Journal:  Int J Legal Med       Date:  2018-02-22       Impact factor: 2.686

2.  Estimating individual mtDNA haplotypes in mixed DNA samples by combining MinION and MiSeq.

Authors:  Hiroaki Nakanishi; Katsumi Yoneyama; Masaaki Hara; Aya Takada; Kentaro Sakai; Kazuyuki Saito
Journal:  Int J Legal Med       Date:  2022-01-10       Impact factor: 2.686

3.  Analyzing Low-Level mtDNA Heteroplasmy-Pitfalls and Challenges from Bench to Benchmarking.

Authors:  Federica Fazzini; Liane Fendt; Sebastian Schönherr; Lukas Forer; Bernd Schöpf; Gertraud Streiter; Jamie Lee Losso; Anita Kloss-Brandstätter; Florian Kronenberg; Hansi Weissensteiner
Journal:  Int J Mol Sci       Date:  2021-01-19       Impact factor: 5.923

4.  From Forensics to Clinical Research: Expanding the Variant Calling Pipeline for the Precision ID mtDNA Whole Genome Panel.

Authors:  Filipe Cortes-Figueiredo; Filipa S Carvalho; Ana Catarina Fonseca; Friedemann Paul; José M Ferro; Sebastian Schönherr; Hansi Weissensteiner; Vanessa A Morais
Journal:  Int J Mol Sci       Date:  2021-11-06       Impact factor: 5.923

5.  Developmental Validation of a MPS Workflow with a PCR-Based Short Amplicon Whole Mitochondrial Genome Panel.

Authors:  Jennifer Churchill Cihlar; Christina Amory; Robert Lagacé; Chantal Roth; Walther Parson; Bruce Budowle
Journal:  Genes (Basel)       Date:  2020-11-13       Impact factor: 4.096
  5 in total

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