Full mtDNA genome sequencing of Brazilian admixed populations: A forensic-focused evaluation of a MPS application as an alternative to Sanger sequencing methods

Avila, Eduardo; Graebin, Pietra; Chemale, Gustavo; Freitas, Jorge M.; Kahmann, Alessandro; Alho, Clarice Sampaio

doi:10.1016/j.fsigen.2019.07.004

Cited by 12 publications

(5 citation statements)

References 68 publications

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“…The effect of pathogenic variant filtering on haplotype frequency estimations was evaluated using forensic-quality mitogenome datasets ( Table S2 ). The datasets are described in [ 1 , 2 , 3 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 ] with the exception of two datasets that were recently submitted to and quality-controlled by EMPOP but are not published yet [ 25 ]. The datasets included 2488 haplotypes representing four global populations (West Eurasian n = 623, African n = 613, East Asian n = 630, and Hispanic/Native American n = 622).…”

Section: Methodsmentioning

confidence: 99%

Pathogenic Variant Filtering for Mitochondrial Genome Haplotype Reporting

Marshall

Sturk-Andreaggi

Ring³

et al. 2020

Genes

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Given the enhanced discriminatory power of the mitochondrial DNA (mtDNA) genome (mitogenome) over the commonly sequenced control region (CR) portion, the scientific merit of mitogenome sequencing is generally accepted. However, many laboratories remain beholden to CR sequencing due to privacy policies and legal requirements restricting the use of disease information or coding region (codR) information. In this report, we present an approach to obviate the reporting of sensitive codR data in forensic haplotypes. We consulted the MitoMap database to identify 92 mtDNA codR variants with confirmed pathogenicity. We determined the frequencies of these pathogenic variants in literature-quality and forensic-quality databases to be very low, at 1.2% and 0.36%, respectively. The observed effect of pathogenic variant filtering on random match statistics in 2488 forensic-quality mitogenome haplotypes from four populations was nil. We propose that pathogenic variant filtering should be incorporated into variant calling algorithms for mitogenome haplotype reporting to maximize the discriminatory power of the locus while minimizing the reveal of sensitive genetic information.

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Section: Methodsmentioning

confidence: 99%

Pathogenic Variant Filtering for Mitochondrial Genome Haplotype Reporting

Marshall

Sturk-Andreaggi

Ring³

et al. 2020

Genes

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“…Apart from the Illumina system, Ion Torrent sequencing was also reliable for mitogenome analysis [ 95 ]. Moreover, some commercial panels, kits and tools were developed for this purpose, such as the Precision ID mtDNA Whole Genome Panel [ 96 , 97 ].…”

Section: Mitochondrial Dna Analysis: the Basis Of Modern Human Popula...mentioning

confidence: 99%

Mitochondrial DNA in Human Diversity and Health: From the Golden Age to the Omics Era

Hernández

2023

Genes

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Mitochondrial DNA (mtDNA) is a small fraction of our hereditary material. However, this molecule has had an overwhelming presence in scientific research for decades until the arrival of high-throughput studies. Several appealing properties justify the application of mtDNA to understand how human populations are—from a genetic perspective—and how individuals exhibit phenotypes of biomedical importance. Here, I review the basics of mitochondrial studies with a focus on the dawn of the field, analysis methods and the connection between two sides of mitochondrial genetics: anthropological and biomedical. The particularities of mtDNA, with respect to inheritance pattern, evolutionary rate and dependence on the nuclear genome, explain the challenges of associating mtDNA composition and diseases. Finally, I consider the relevance of this single locus in the context of omics research. The present work may serve as a tribute to a tool that has provided important insights into the past and present of humankind.

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“…Since then, the forensic community has been testing the capabilities of mtMPS using both pristine (Brandhagen et al, 2020; Churchill et al, 2016; King, Larue, et al, 2014; Lee et al, 2016; Ma et al, 2018; Marshall et al, 2017; McElhoe et al, 2014; Parson et al, 2013; Peck et al, 2016; Strobl et al, 2019; Woerner et al, 2018; Zhou et al, 2016) and degraded mock casework type samples (van der Gaag et al, 2020; Ambers et al, 2020; Amorim et al, 2019; Brandhagen et al, 2020; Chaitanya et al, 2015; Gallimore et al, 2018; Holland et al, 2019; Holland, Wilson, et al, 2017; Kim et al, 2020; Marshall et al, 2017; Parson et al, 2015). For example, a population study to assess of the efficacy of an mtMPS approach in forensic laboratories (Avila et al, 2019), concluded that mtMPS analysis should be the method of choice. Other studies have illustrated that mtMPS is a powerful means of deconvoluting two or three‐person mixtures (Smart et al, 2021; Churchill et al, 2018; Vohr et al, 2017; Kim et al, 2015).…”

Section: Massively Parallel Sequencingmentioning

confidence: 99%

The time is now for ubiquitous forensicmtMPSanalysis

Canale

Parson

Holland

2021

WIREs Forensic Science

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Mitochondrial (mt) DNA sequence analysis is useful for assessing ancestral origin and migration, identifying human remains, and examining evidentiary material in forensic casework. Conventional Sanger‐type sequencing (STS) has been used for more than three decades to address these interests. This paper reviews the methodologies and merits of using a massively parallel sequencing (MPS) approach for mtDNA testing in forensic laboratories, as The Time is Now for Ubiquitous Forensic mtMPS Analysis. This article is categorized under: Forensic Biology > Haploid Markers Forensic Biology > Forensic DNA Technologies

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Full mtDNA genome sequencing of Brazilian admixed populations: A forensic-focused evaluation of a MPS application as an alternative to Sanger sequencing methods

Cited by 12 publications

References 68 publications

Pathogenic Variant Filtering for Mitochondrial Genome Haplotype Reporting

Pathogenic Variant Filtering for Mitochondrial Genome Haplotype Reporting

Mitochondrial DNA in Human Diversity and Health: From the Golden Age to the Omics Era

The time is now for ubiquitous forensicmtMPSanalysis

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