4.5 Review

Interpreting NUMTs in forensic genetics: Seeing the forest for the trees

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Medicine, Legal

Damage patterns observed in mtDNA control region MPS data for a range of template concentrations and when using different amplification approaches

Charity A. Holland et al.

Summary: Massively parallel sequencing of mitochondrial DNA can help practitioners fully resolve heteroplasmic sites, especially in forensic DNA analysis. Damage and heteroplasmy can manifest similarly in DNA mixtures, highlighting the importance of differentiating between the two conditions. Controlled experiments involving DNA damage were conducted to evaluate the impact on samples with different template concentrations, aiming to improve mtDNA analysis for low template samples. Damage caused a decrease in mtDNA yield and lower quality sequencing results, especially in samples diluted prior to damage induction, indicating the susceptibility of low template samples to damage. This study's findings will aid forensic laboratories in distinguishing between damage and heteroplasmy, crucial for setting robust mtDNA interpretation guidelines.

INTERNATIONAL JOURNAL OF LEGAL MEDICINE (2021)

Article Biochemistry & Molecular Biology

Evidence for multi-copy Mega-NUMTs in the human genome

Sabine Lutz-Bonengel et al.

Summary: The study identified individuals in a family pedigree with maternal inheritance of mtDNA, where some tissues had repetitive complete mitochondrial genomes Mega-NUMTs, while hair shaft mtDNA sequencing was able to exclude the interference of NUMTs.

NUCLEIC ACIDS RESEARCH (2021)

Article Genetics & Heredity

A Continuous Statistical Phasing Framework for the Analysis of Forensic Mitochondrial DNA Mixtures

Utpal Smart et al.

Summary: Despite the challenges of resolving mitotypes from mixtures occurring in certain ratios, a bioinformatic mixture deconvolution method centered on population-based phasing was developed and validated in this study. By leveraging external reference panels and simulations, the accuracy of deconvolution was confirmed when haplotypes in the mixture were similar to those in the reference panel and the mixture ratios were appropriate. The proposed framework automates the reconstruction of complete individual mitotypes from mixtures, even in ratios that have traditionally been considered problematic.
Article Genetics & Heredity

Impact of the sequencing method on the detection and interpretation of mitochondrial DNA length heteroplasmy

Kimberly Sturk-Andreaggi et al.

FORENSIC SCIENCE INTERNATIONAL-GENETICS (2020)

Article Cell Biology

Sensitivity of mitochondrial DNA heteroplasmy detection using Next Generation Sequencing

Maria del Mar Gonzalez et al.

MITOCHONDRION (2020)

Review Medicine, Legal

Massive parallel sequencing in forensics: advantages, issues, technicalities, and prospects

David Ballard et al.

INTERNATIONAL JOURNAL OF LEGAL MEDICINE (2020)

Article Biochemical Research Methods

Numt identification and removal with RtN!

August E. Woerner et al.

BIOINFORMATICS (2020)

Article Genetics & Heredity

Platinum-Quality Mitogenome Haplotypes from United States Populations

Cassandra R. Taylor et al.

Article Cell Biology

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

Mauro Santibanez-Koref et al.

MITOCHONDRION (2019)

Letter Multidisciplinary Sciences

No further evidence for paternal leakage of mitochondrial DNA in humans yet

Sabine Lutz-Bonengel et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

Article Multidisciplinary Sciences

Germline selection shapes human mitochondrial DNA diversity

Wei Wei et al.

SCIENCE (2019)

Letter Multidisciplinary Sciences

Quasi-Mendelian paternal inheritance of mitochondrial DNA: A notorious artifact, or anticipated behavior?

Sofia Annis et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

Editorial Material Genetics & Heredity

A Nuclear mtDNA Concatemer (Mega-NUMT) Could Mimic Paternal Inheritance of Mitochondrial Genome

Jorune Balciuniene et al.

FRONTIERS IN GENETICS (2019)

Article Genetics & Heredity

SD quants-Sensitive detection tetraplex-system for nuclear and mitochondrial DNA quantification and degradation inference

Catarina Xavier et al.

FORENSIC SCIENCE INTERNATIONAL-GENETICS (2019)

Article Cell Biology

NUMT Confounding Biases Mitochondrial Heteroplasmy Calls in Favor of the Reference Allele

Hannah Maude et al.

FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY (2019)

Article Genetics & Heredity

A novel phylogenetic approach for de novo discovery of putative nuclear mitochondrial (pNumt) haplotypes

Utpal Smart et al.

FORENSIC SCIENCE INTERNATIONAL-GENETICS (2019)

Article Genetics & Heredity

Report from the STRAND Working Group on the 2019 STR sequence nomenclature meeting

Katherine Butler Gettings et al.

FORENSIC SCIENCE INTERNATIONAL-GENETICS (2019)

Article Genetics & Heredity

Assessing heteroplasmic variant drift in the mtDNA control region of human hairs using an MPS approach

Jamie M. Gallimore et al.

FORENSIC SCIENCE INTERNATIONAL-GENETICS (2018)

Article Genetics & Heredity

Developmental validation of a Nextera XT mitogenome Illumina MiSeq sequencing method for high-quality samples

Michelle A. Peck et al.

FORENSIC SCIENCE INTERNATIONAL-GENETICS (2018)

Article Genetics & Heredity

Repair of DNA damage caused by cytosine deamination in mitochondrial DNA of forensic case samples

Erin M. Gorden et al.

FORENSIC SCIENCE INTERNATIONAL-GENETICS (2018)

Article Genetics & Heredity

Evaluation of the precision ID mtDNA whole genome panel on two massively parallel sequencing systems

August E. Woerner et al.

FORENSIC SCIENCE INTERNATIONAL-GENETICS (2018)

Article Genetics & Heredity

Evaluation of the precision ID whole MtDNA genome panel for forensic analyses

Christina Strobl et al.

FORENSIC SCIENCE INTERNATIONAL-GENETICS (2018)

Article Medicine, Legal

Massively parallel sequencing-enabled mixture analysis of mitochondrial DNA samples

Jennifer D. Churchill et al.

INTERNATIONAL JOURNAL OF LEGAL MEDICINE (2018)

Article Multidisciplinary Sciences

Biparental Inheritance of Mitochondrial DNA in Humans

Shiyu Luo et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)

Article Genetics & Heredity

Fragmented Nuclear DNA Is the Predominant Genetic Material in Human Hair Shafts

Michael D. Brandhagen et al.

Article Genetics & Heredity

Considering DNA damage when interpreting mtDNA heteroplasmy in deep sequencing data

Molly M. Rathbun et al.

FORENSIC SCIENCE INTERNATIONAL-GENETICS (2017)

Article Genetics & Heredity

A phylogenetic approach for haplotype analysis of sequence data from complex mitochondrial mixtures

Samuel H. Vohr et al.

FORENSIC SCIENCE INTERNATIONAL-GENETICS (2017)

Article Medicine, Legal

MPS analysis of the mtDNA hypervariable regions on the MiSeq with improved enrichment

Mitchell M. Holland et al.

INTERNATIONAL JOURNAL OF LEGAL MEDICINE (2017)

Article Multidisciplinary Sciences

NumtS colonization in mammalian genomes

F. M. Calabrese et al.

SCIENTIFIC REPORTS (2017)

Article Genetics & Heredity

Age-Related and Heteroplasmy-Related Variation in Human mtDNA Copy Number

Manja Wachsmuth et al.

PLOS GENETICS (2016)

Article Medicine, General & Internal

Analysis of mixtures using next generation sequencing of mitochondrial DNA hypervariable regions

Hanna Kim et al.

CROATIAN MEDICAL JOURNAL (2015)

Article Genetics & Heredity

Mitochondrial DNA heteroplasmy in the emerging field of massively parallel sequencing

Rebecca S. Just et al.

FORENSIC SCIENCE INTERNATIONAL-GENETICS (2015)

Article Genetics & Heredity

Massively parallel sequencing of complete mitochondrial genomes from hair shaft samples

Walther Parson et al.

FORENSIC SCIENCE INTERNATIONAL-GENETICS (2015)

Article Genetics & Heredity

Next generation sequencing and its applications in forensic genetics

Claus Borsting et al.

FORENSIC SCIENCE INTERNATIONAL-GENETICS (2015)

Article Genetics & Heredity

PhyloTree Build 17: Growing the human mitochondrial DNA tree

Mannis van Oven

FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES (2015)

Article Genetics & Heredity

High-quality and high-throughput massively parallel sequencing of the human mitochondrial genome using the Illumina MiSeq

Jonathan L. King et al.

FORENSIC SCIENCE INTERNATIONAL-GENETICS (2014)

Article Genetics & Heredity

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

Jennifer A. McElhoe et al.

FORENSIC SCIENCE INTERNATIONAL-GENETICS (2014)

Review Cell Biology

High-throughput sequencing in mitochondrial DNA research

Fei Ye et al.

MITOCHONDRION (2014)

Article Biochemistry & Molecular Biology

The genomic landscape of polymorphic human nuclear mitochondrial insertions

Gargi Dayama et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Multidisciplinary Sciences

Maternal age effect and severe germ-line bottleneck in the inheritance of human mitochondrial DNA

Boris Rebolledo-Jaramillo et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)

Article Multidisciplinary Sciences

Identification of the remains of King Richard III

Turi E. King et al.

NATURE COMMUNICATIONS (2014)

Article Genetics & Heredity

Evaluation of next generation mtGenome sequencing using the Ion Torrent Personal Genome Machine (PGM)

Walther Parson et al.

FORENSIC SCIENCE INTERNATIONAL-GENETICS (2013)

Article Genetics & Heredity

Detecting Heteroplasmy from High-Throughput Sequencing of Complete Human Mitochondrial DNA Genomes

Mingkun Li et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2010)

Review Genetics & Heredity

Molecular Poltergeists: Mitochondrial DNA Copies (numts) in Sequenced Nuclear Genomes

Einat Hazkani-Covo et al.

PLOS GENETICS (2010)

Article Biochemistry & Molecular Biology

Postmortem Miscoding Lesions in Sequence Analysis of Human Ancient Mitochondrial DNA

Ryan Lamers et al.

JOURNAL OF MOLECULAR EVOLUTION (2009)

Article Biochemistry & Molecular Biology

A Comparative Approach Shows Differences in Patterns of Numt Insertion During Hominoid Evolution

M. I. Jensen-Seaman et al.

JOURNAL OF MOLECULAR EVOLUTION (2009)

Article Genetics & Heredity

Identifying NUMT contamination in mtDNA analyses

Ana Goios et al.

FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES (2009)

Article Genetics & Heredity

More evidence for non-maternal inheritance of mitochondrial DNA?

HJ Bandelt et al.

JOURNAL OF MEDICAL GENETICS (2005)

Article Biochemistry & Molecular Biology

Rates of DNA duplication and mitochondrial DNA insertion in the human genome

D Bensasson et al.

JOURNAL OF MOLECULAR EVOLUTION (2003)