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Korolija M, Sukser V, Vlahoviček K. Mitochondrial point heteroplasmy: insights from deep-sequencing of human replicate samples. BMC Genomics 2024; 25:48. [PMID: 38200446 PMCID: PMC10782721 DOI: 10.1186/s12864-024-09963-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 01/03/2024] [Indexed: 01/12/2024] Open
Abstract
BACKGROUND Human mitochondrial heteroplasmy is an extensively investigated phenomenon in the context of medical diagnostics, forensic identification and molecular evolution. However, technical limitations of high-throughput sequencing hinder reliable determination of point heteroplasmies (PHPs) with minor allele frequencies (MAFs) within the noise threshold. RESULTS To investigate the PHP landscape at an MAF threshold down to 0.1%, we sequenced whole mitochondrial genomes at approximately 7.700x coverage, in multiple technical and biological replicates of longitudinal blood and buccal swab samples from 11 human donors (159 libraries in total). The results obtained by two independent sequencing platforms and bioinformatics pipelines indicate distinctive PHP patterns below and above the 1% MAF cut-off. We found a high inter-individual prevalence of low-level PHPs (MAF < 1%) at polymorphic positions of the mitochondrial DNA control region (CR), their tissue preference, and a tissue-specific minor allele linkage. We also established the position-dependent potential of minor allele expansion in PHPs, and short-term PHP instability in a mitotically active tissue. We demonstrate that the increase in sensitivity of PHP detection to minor allele frequencies below 1% within a robust experimental and analytical pipeline, provides new information with potential applicative value. CONCLUSIONS Our findings reliably show different mutational loads between tissues at sub-1% allele frequencies, which may serve as an informative medical biomarker of time-dependent, tissue-specific mutational burden, or help discriminate forensically relevant tissues in a single person, close maternal relatives or unrelated individuals of similar phylogenetic background.
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Affiliation(s)
- Marina Korolija
- Biology and Fibres Department, Forensic Science Centre "Ivan Vučetić", Ministry of the Interior of the Republic of Croatia, Ilica 335, HR-10000, Zagreb, Croatia.
| | - Viktorija Sukser
- Biology and Fibres Department, Forensic Science Centre "Ivan Vučetić", Ministry of the Interior of the Republic of Croatia, Ilica 335, HR-10000, Zagreb, Croatia
| | - Kristian Vlahoviček
- Bioinformatics group, Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, HR-10000, Zagreb, Croatia
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2
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Patterson EC, Lall GM, Neumann R, Ottolini B, Batini C, Sacchini F, Foster AP, Wetton JH, Jobling MA. Mitogenome sequences of domestic cats demonstrate lineage expansions and dynamic mutation processes in a mitochondrial minisatellite. BMC Genomics 2023; 24:690. [PMID: 37978434 PMCID: PMC10655372 DOI: 10.1186/s12864-023-09789-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND As a population genetic tool, mitochondrial DNA is commonly divided into the ~ 1-kb control region (CR), in which single nucleotide variant (SNV) diversity is relatively high, and the coding region, in which selective constraint is greater and diversity lower, but which provides an informative phylogeny. In some species, the CR contains variable tandemly repeated sequences that are understudied due to heteroplasmy. Domestic cats (Felis catus) have a recent origin and therefore traditional CR-based analysis of populations yields only a small number of haplotypes. RESULTS To increase resolution we used Nanopore sequencing to analyse 119 cat mitogenomes via a long-amplicon approach. This greatly improves discrimination (from 15 to 87 distinct haplotypes in our dataset) and defines a phylogeny showing similar starlike topologies within all major clades (haplogroups), likely reflecting post-domestication expansion. We sequenced RS2, a CR tandem array of 80-bp repeat units, placing RS2 array structures within the phylogeny and increasing overall haplotype diversity. Repeat number varies between 3 and 12 (median: 4) with over 30 different repeat unit types differing largely by SNVs. Five SNVs show evidence of independent recurrence within the phylogeny, and seven are involved in at least 11 instances of rapid spread along repeat arrays within haplogroups. CONCLUSIONS In defining mitogenome variation our study provides key information for the forensic genetic analysis of cat hair evidence, and for the first time a phylogenetically informed picture of tandem repeat variation that reveals remarkably dynamic mutation processes at work in the mitochondrion.
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Affiliation(s)
- Emily C Patterson
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Gurdeep Matharu Lall
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Rita Neumann
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Barbara Ottolini
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
- Present Address: Oxford Nanopore Technologies Plc., Oxford Science Park, Edmund Halley Rd, Oxford, OX4 4DQ, UK
| | - Chiara Batini
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
- Present Address: Department of Population Health Sciences, University of Leicester, Leicester, UK
- Biomedical Research Centre, Leicester National Institute for Health and Care Research, Glenfield Hospital, Leicester, UK
| | - Federico Sacchini
- IDEXX Laboratories Italia S.R.L., Via Guglielmo Silva, 36-20149, Milano, MI, Italy
| | - Aiden P Foster
- Bristol Veterinary School, University of Bristol, Langford House, Langford, BS40 5DU, North Somerset, UK
| | - Jon H Wetton
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK.
| | - Mark A Jobling
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK.
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3
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Childebayeva A, Zavala EI. Review: Computational analysis of human skeletal remains in ancient DNA and forensic genetics. iScience 2023; 26:108066. [PMID: 37927550 PMCID: PMC10622734 DOI: 10.1016/j.isci.2023.108066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023] Open
Abstract
Degraded DNA is used to answer questions in the fields of ancient DNA (aDNA) and forensic genetics. While aDNA studies typically center around human evolution and past history, and forensic genetics is often more concerned with identifying a specific individual, scientists in both fields face similar challenges. The overlap in source material has prompted periodic discussions and studies on the advantages of collaboration between fields toward mutually beneficial methodological advancements. However, most have been centered around wet laboratory methods (sampling, DNA extraction, library preparation, etc.). In this review, we focus on the computational side of the analytical workflow. We discuss limitations and considerations to consider when working with degraded DNA. We hope this review provides a framework to researchers new to computational workflows for how to think about analyzing highly degraded DNA and prompts an increase of collaboration between the forensic genetics and aDNA fields.
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Affiliation(s)
- Ainash Childebayeva
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Anthropology, University of Kansas, Lawrence, KS, USA
| | - Elena I. Zavala
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Department of Biology, University of Oregon, Eugene, OR, USA
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4
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Xavier C, Sutter C, Amory C, Niederstätter H, Parson W. NuMY-A qPCR Assay Simultaneously Targeting Human Autosomal, Y-Chromosomal, and Mitochondrial DNA. Genes (Basel) 2023; 14:1645. [PMID: 37628695 PMCID: PMC10454206 DOI: 10.3390/genes14081645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/13/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
The accurate quantification of DNA in forensic samples is of utmost importance. These samples are often present in limited amounts; therefore, it is indicated to use the appropriate analysis route with the optimum DNA amount (when possible). Also, DNA quantification can inform about the degradation stage and therefore support the decision on which downstream genotyping method to use. Consequently, DNA quantification aids in getting the best possible results from a forensic sample, considering both its DNA quantity and quality limitations. Here, we introduce NuMY, a new quantitative real-time PCR (qPCR) method for the parallel quantification of human nuclear (n) and mitochondrial (mt) DNA, assessing the male portion in mixtures of both sexes and testing for possible PCR inhibition. NuMY is based on previous work and follows the MIQE guidelines whenever applicable. Although quantification of nuclear (n)DNA by simultaneously analyzing autosomal and male-specific targets is available in commercial qPCR kits, tools that include the quantification of mtDNA are sparse. The quantification of mtDNA has proven relevant for samples with low nDNA content when conventional DNA fingerprinting techniques cannot be followed. Furthermore, the development and use of new massively parallel sequencing assays that combine multiple marker types, i.e., autosomal, Y-chromosomal, and mtDNA, can be optimized when precisely knowing the amount of each DNA component present in the input sample. For high-quality DNA extracts, NuMY provided nDNA results comparable to those of another quantification technique and has also proven to be a reliable tool for challenging, forensically relevant samples such as mixtures, inhibited, and naturally degraded samples.
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Affiliation(s)
- Catarina Xavier
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (C.S.); (C.A.); (H.N.)
- i3S—Institute for Research and Innovation in Health, University of Porto, 4099-002 Porto, Portugal
| | - Charlotte Sutter
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (C.S.); (C.A.); (H.N.)
| | - Christina Amory
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (C.S.); (C.A.); (H.N.)
| | - Harald Niederstätter
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (C.S.); (C.A.); (H.N.)
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (C.S.); (C.A.); (H.N.)
- Forensic Science Program, The Pennsylvania State University, University Park, PA 16801, USA
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5
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Korber JT, Canale LC, Holland MM. Massively Parallel Sequencing of the Mitogenome from Human Hair Shafts in Forensic Investigations. Curr Protoc 2023; 3:e865. [PMID: 37579069 DOI: 10.1002/cpz1.865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2023]
Abstract
This article highlights methods used to perform DNA extraction, mitochondrial DNA quantification, multiplex PCR amplification, amplicon-based massively parallel sequencing, and data analysis of the mitochondrial genome (mitogenome) from human hair shafts. The focus is on applications to forensic casework, but this set of protocols can be used for any purpose involving small cuttings (as small as 1 to 5 mm) of human hair shafts up to 40 years from the time of collection. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Extraction of mitochondrial DNA from human hair shafts Basic Protocol 2: Quantification of mitochondrial DNA (copies/μl) Basic Protocol 3: Multiplex amplification of the mitogenome Basic Protocol 4: Library preparation and sequencing of mitogenome amplicons Basic Protocol 5: Data analysis of mitogenome haplotypes.
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Affiliation(s)
- Jade T Korber
- Department of Biochemistry & Molecular Biology, Forensic Science Program, The Pennsylvania State University, University Park, Pennsylvania
| | - Lauren C Canale
- Department of Justice, Jan Bashinski DNA Laboratory, Richmond, California
| | - Mitchell M Holland
- Department of Biochemistry & Molecular Biology, Forensic Science Program, The Pennsylvania State University, University Park, Pennsylvania
- Mitotyping Technologies, State College, Pennsylvania
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6
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Heinrich J, Berger C, Berger B, Hecht W, Phillips C, Parson W. The LASSIE MPS panel: Predicting externally visible traits in dogs for forensic purposes. Forensic Sci Int Genet 2023; 66:102893. [PMID: 37290253 DOI: 10.1016/j.fsigen.2023.102893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 05/28/2023] [Accepted: 06/01/2023] [Indexed: 06/10/2023]
Abstract
Predicting the outward appearance of dogs via their DNA, also known as Canine DNA Phenotyping, is a young, emerging field of research in forensic genetics. The few previous studies published in this respect were restricted to the consecutive analysis of single DNA markers, a process that is time- and sample-consuming and therefore not a viable option for limited forensic specimens. Here, we report on the development and evaluation of a Massively Parallel Sequencing (MPS) based molecular genetic assay, the LASSIE MPS Panel. This panel aims to predict externally visible as well as skeletal traits, which include coat color, coat pattern, coat structure, tail morphology, skull shape, ear shape, eye color and body size from DNA using 44 genetic markers in a single molecular genetic assay. A biostatistical naïve Bayes classification approach was applied to identify the most informative marker combinations for predicting phenotypes. Overall, the predictive performance was characterized by a very high classification success for some of the trait categories, and high to moderate success for others. The performance of the developed predictive framework was further evaluated using blind samples from three randomly selected dog individuals, whose appearance was well predicted.
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Affiliation(s)
- Josephin Heinrich
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Cordula Berger
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Burkhard Berger
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Werner Hecht
- Institute of Veterinary Pathology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Christopher Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, University Park, PA, USA.
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7
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Peng D, Geng J, Yang J, Liu J, Wang N, Wu R, Sun H. Whole Mitochondrial Genome Detection and Analysis of Two- to Four-Generation Maternal Pedigrees Using a New Massively Parallel Sequencing Panel. Genes (Basel) 2023; 14:genes14040912. [PMID: 37107670 PMCID: PMC10137955 DOI: 10.3390/genes14040912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/08/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
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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Affiliation(s)
- Dan Peng
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Jiaojiao Geng
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Jingyi Yang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Jiajun Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Nana Wang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Riga Wu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Hongyu Sun
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
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8
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Liu Z, Simayijiang H, Wang Q, Yang J, Sun H, Wu R, Yan J. DNA and protein analyses of hair in forensic genetics. Int J Legal Med 2023; 137:613-633. [PMID: 36732435 DOI: 10.1007/s00414-023-02955-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 01/20/2023] [Indexed: 02/04/2023]
Abstract
Hair is one of the most common pieces of biological evidence found at a crime scene and plays an essential role in forensic investigation. Hairs, especially non-follicular hairs, are usually found at various crime scenes, either by natural shedding or by forcible shedding. However, the genetic material in hairs is usually highly degraded, which makes forensic analysis difficult. As a result, the value of hair has not been fully exploited in forensic investigations and trials. In recent years, with advances in molecular biology, forensic analysis of hair has achieved remarkable strides and provided crucial clues in numerous cases. This article reviews recent developments in DNA and protein analysis of hair and attempts to provide a comprehensive solution to improve forensic hair analysis.
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Affiliation(s)
- Zhiyong Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China
| | - Halimureti Simayijiang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030600, People's Republic of China
| | - Qiangwei Wang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China
| | - Jingyi Yang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China
| | - Hongyu Sun
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China.,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China
| | - Riga Wu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China. .,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China.
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030600, People's Republic of China.
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9
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Canale LC, McElhoe JA, Dimick G, DeHeer KM, Beckert J, Holland MM. Routine Mitogenome MPS Analysis from 1 and 5 mm of Rootless Human Hair. Genes (Basel) 2022; 13:2144. [PMID: 36421819 PMCID: PMC9690917 DOI: 10.3390/genes13112144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 11/14/2022] [Indexed: 08/16/2023] Open
Abstract
While hair shafts are a common evidence type in forensic cases, they are often excluded from DNA analysis due to their limited DNA quantity and quality. Mitochondrial (mt) DNA sequencing is the method of choice when working with rootless hair shaft fragments due to the elevated copy number of mtDNA and the highly degraded nature of nuclear (n) DNA. Using massively parallel sequencing (MPS) of the mitochondrial (mito) genome, we studied the impact of hair age (time since collection) and physical characteristics (hair diameter, medullary structure, and length of hair tested) on mtDNA recovery and MPS data quality. Hair shaft cuttings of 1 and 5 mm from hairs less than five years to 46 years of age from 60 donors were characterized microscopically. Mitogenome sequences were generated using the Promega PowerSeqTM Whole Mito System prototype kit and the Illumina MiSeq instrument. Reportable mitogenome sequences were obtained from all hairs up to 27 years of age (37 donors), with at least 98% of the mitogenome reported for more than 94% of the 74 hair samples analyzed; the minimum reported sequence was 88%. Furthermore, data from the 1 and 5 mm replicates gave concordant haplotypes. As expected, mtDNA yield decreased, mtDNA degradation increased, and mitogenome MPS data quality declined as the age of the hair increased. Hair diameter and medullary structure had minimal impact on yield and data quality. Our findings support that MPS is a robust and reliable method for routinely generating mitogenome sequences from 1 and 5 mm hair shaft samples up to 27 years of age, which is of interest to the forensic community, biological anthropologists, and medical geneticists.
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Affiliation(s)
- Lauren C. Canale
- Forensic Science Program, Department of Biochemistry & Molecular Biology, Eberly College of Science, Pennsylvania State University, University Park, PA 16802, USA
| | - Jennifer A. McElhoe
- Forensic Science Program, Department of Biochemistry & Molecular Biology, Eberly College of Science, Pennsylvania State University, University Park, PA 16802, USA
| | - Gloria Dimick
- Mitotyping Technologies, 2565 Park Center Blvd., Suite 200, State College, PA 16801, USA
| | | | - Jason Beckert
- Microtrace 790 Fletcher Drive, Suite 106, Elgin, IL 60123, USA
| | - Mitchell M. Holland
- Forensic Science Program, Department of Biochemistry & Molecular Biology, Eberly College of Science, Pennsylvania State University, University Park, PA 16802, USA
- Mitotyping Technologies, 2565 Park Center Blvd., Suite 200, State College, PA 16801, USA
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10
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Development and validation of a SYBR green-based mitochondrial DNA quantification method by following the MIQE and other guidelines. Leg Med (Tokyo) 2022; 58:102096. [PMID: 35689884 DOI: 10.1016/j.legalmed.2022.102096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 04/11/2022] [Accepted: 05/27/2022] [Indexed: 01/28/2023]
Abstract
In forensic mitochondrial DNA (mtDNA) analysis, quantitative PCR (qPCR) is usually performed to obtain high-quality sequence data for subsequent Sanger or massively parallel sequencing. Unlike methods for nuclear DNA quantification using qPCR, a calibrator is necessary to obtain mtDNA concentrations (i.e., copies/µL). Herein, we developed and validated a mtDNA quantification method based on a SYBR Green assay by following MIQE [Bustin et al., Clin. Chem. 55 (2009) 611-22] and other guidelines. Primers were designed to amplify nucleotide positions 16,190-16,420 in hypervariable region 1 for qPCR using PowerUp SYBR Green and QuantStudio 5. The optimized conditions were 0.3 µM each primer and an annealing temperature of 60 °C under a 2-step cycling protocol. K562 DNA at 100 pg/µL was converted into a mtDNA concentration of 16,400 copies/µL using linearized plasmid DNA. This mtDNA calibrator was obtained by cloning the synthesized DNA fragments of mtDNA (positions 16,140-16,470) containing a 100-bp inversion. The linear dynamic range of the K562 standard curve was 10,000-0.1 pg/µL (r2 ≥ 0.999). The accuracy was examined using NIST SRM 2372a, and its components A, B, and C were quantified with differences of -29.4%, -35.0%, and -22.0%, respectively, against the mtDNA concentrations calculated from published NIST data. We also examined the specificity of the primers, stability of the reaction mix, precision, tolerance against PCR inhibitors, and cross-reactivity against DNA from various animal taxa. Our newly developed mtDNA quantification method is expected to be useful for forensic mtDNA analysis.
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11
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Connell JR, Benton MC, Lea RA, Sutherland HG, Haupt LM, Wright KM, Griffiths LR. Evaluating the suitability of current mitochondrial DNA interpretation guidelines for multigenerational whole mitochondrial genome comparisons. J Forensic Sci 2022; 67:1766-1775. [PMID: 35855536 PMCID: PMC9543078 DOI: 10.1111/1556-4029.15097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/06/2022] [Accepted: 06/30/2022] [Indexed: 12/03/2022]
Abstract
Sanger sequencing of the mitochondrial DNA (mtDNA) control region was previously the only method available for forensic casework involving degraded samples from skeletal remains. The introduction of Next Generation Sequencing (NGS) has transformed genetic data generation and human identification using mtDNA. Whole mitochondrial genome (mtGenome) analysis is now being introduced into forensic laboratories around the world to analyze historical remains. Research into large pedigrees using the mtGenome is critical to evaluate currently available interpretation guidelines for mtDNA analysis, which were developed for comparisons using the control region. This study included mtGenomes from 225 individuals from the last four generations of the Norfolk Island (NI) genetic isolate pedigree consisting of 49 distinct maternal lineages. The data from these individuals were arranged into 2339 maternally related pairs separated by up to 18 meioses. Our results show that 97.3% of maternally related pairs were concordant at all nucleotide positions, resulting in the correct interpretation of “Cannot Exclude”; 2.7% of pairs produced an “Inconclusive” result, and there were no instances of false exclusion. While these results indicate that existing guidelines are suitable for multigenerational whole mtGenome analysis, we recommend caution be taken when classifying heteroplasmic changes as differences for human identification. Our data showed the classification of heteroplasmic changes as differences increases the prevalence of inconclusive identification by 6%, with false exclusions observed in 0.34% of pairs examined. Further studies of multigenerational pedigrees, however, are needed to validate mtGenome interpretation guidelines for historical case work to more fully utilize emerging advancements.
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Affiliation(s)
- Jasmine R Connell
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Kelvin Grove, Qld, Australia
| | - Miles C Benton
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Kelvin Grove, Qld, Australia.,Human Genomics, Kenepuru Science Centre, Institute of Environmental Science and Research, Wellington, New Zealand
| | - Rodney A Lea
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Kelvin Grove, Qld, Australia
| | - Heidi G Sutherland
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Kelvin Grove, Qld, Australia
| | - Larisa M Haupt
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Kelvin Grove, Qld, Australia
| | - Kirsty M Wright
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Kelvin Grove, Qld, Australia.,Unrecovered War Casualties-Army, Australian Defence Force, Russell Offices, Russell, ACT, Australia.,Royal Australian Air Force (RAAF), Headquarters History and Heritage, Unrecovered War Casualties-Air Force, Russell, ACT, Australia
| | - Lyn R Griffiths
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Kelvin Grove, Qld, Australia
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12
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Helena's Many Daughters: More Mitogenome Diversity behind the Most Common West Eurasian mtDNA Control Region Haplotype in an Extended Italian Population Sample. Int J Mol Sci 2022; 23:ijms23126725. [PMID: 35743173 PMCID: PMC9223851 DOI: 10.3390/ijms23126725] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/13/2022] [Accepted: 06/14/2022] [Indexed: 01/27/2023] Open
Abstract
The high number of matching haplotypes of the most common mitochondrial (mt)DNA lineages are considered to be the greatest limitation for forensic applications. This study investigates the potential to solve this constraint by massively parallel sequencing a large number of mitogenomes that share the most common West Eurasian mtDNA control region (CR) haplotype motif (263G 315.1C 16519C). We augmented a pilot study on 29 to a total of 216 Italian mitogenomes that represents the largest set of the most common CR haplotype compiled from a single country. The extended population sample confirmed and extended the huge coding region diversity behind the most common CR motif. Complete mitogenome sequencing allowed for the detection of 163 distinct haplotypes, raising the power of discrimination from 0 (CR) to 99.6% (mitogenome). The mtDNAs were clustered into 61 named clades of haplogroup H and did not reveal phylogeographic trends within Italy. Rapid individualization approaches for investigative purposes are limited to the most frequent H clades of the dataset, viz. H1, H3, and H7.
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13
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Fujii K, Mita Y, Watahiki H, Fukagawa T, Kitayama T, Mizuno N, Nakahara H, Sekiguchi K. Poly_NumtS_430 or HSA_NumtS_587 observed in massively parallel sequencing of the mitochondrial HV1 and HV2 regions. Forensic Sci Int Genet 2022; 59:102717. [DOI: 10.1016/j.fsigen.2022.102717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 03/12/2022] [Accepted: 05/01/2022] [Indexed: 11/04/2022]
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14
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Xin Y, Jia R, Zhang S, Guo F. Mitochondrial genome sequencing with short overlapping amplicons on MiSeq FGx system. Forensic Sci Res 2021; 7:142-153. [PMID: 35784421 PMCID: PMC9246037 DOI: 10.1080/20961790.2021.1963514] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/22/2021] [Accepted: 07/29/2021] [Indexed: 11/03/2022] Open
Abstract
With the development and maturation of massively parallel sequencing (MPS) technology, the mitochondrial genome (mitogenome) sequencing is increasingly applied in the forensic field. In this study, we employed the strategy of short overlapping amplicons for the whole mitogenome, library preparation with tagmentation using the Nextera® XT DNA Library Preparation Kit, sequencing on the MiSeq FGxTM Forensic Genomics System and analyzing data using the mitochondrial(mtDNA) MSR Plug-in and the mtDNA Variant Analyzer. A total of 27 libraries and 56 libraries were sequenced in a run using MiSeq Reagent Kit v2 and v3, respectively. Results showed more than 1800 × of averaged depth of coverage (DoC) at each position. Concordant haplotypes of 9947 A and 2800 M were obtained at 32 variants. Cross-reactivity was observed with 1 ng primate DNA and 10 ng non-primate DNA but could be easily distinguished. Full and accurate variants were obtained from at least 50 pg input DNA and from minor contributors between 19:1 and 1:19 mixed ratios with known reference profiles. More than 86% variants were detected from ≥200-bp degraded samples but its haplotype was assigned to more ancestral haplogroup. Further, a total of 3 962 variants were observed at 613 nucleotide positions from 103 Xibe mitogenomes with 25:1 ratio of transitions to transversions. Two new transversions (C13735A and A14755C) and two tri-alleles at nps 9824 and 16092 were identified. There were 103 unique mitogenome haplotypes from 103 Chinese Xibe that were assigned to 79 haplogroups. Haplogroup D was the preponderant top-level haplogroup in Xibe followed by F, B, M, A, N, G, C, Z, Y, HV and J. Random match probability (RMP) and haplotype diversity (HD) of the whole mitogenome was calculated as 0.0097 and 1.0000, respectively. Compared with HVS-I only, RMP decreased 33.56%, while the number of haplotypes and HD increased 15.73% and 0.49%, respectively. Principal component analysis (PCA) showed that Xibe was clustered to East and Southeast Asian. As a whole, this MPS strategy is suitable for the whole mitogenome sequencing especially for degraded samples and can facilitate generating mitogenome data to support the routine application in forensic sciences. EMP00726 is the first whole mitogenome dataset from Xibe contributed to the EMPOP. Supplemental data for this article are available online at.
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Affiliation(s)
- Yang Xin
- Forensic Science College, Criminal Investigation Police University of China, Shenyang, China
| | - Rulin Jia
- Forensic Science College, Criminal Investigation Police University of China, Shenyang, China
| | - Suhua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, China
| | - Fei Guo
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, China
- Forensic Science College, Criminal Investigation Police University of China, Shenyang, China
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Tie J, Uchigasaki S, Isobe E, Iwakami E, Okuda T. Detection of deletion/insertion polymorphism profiles from single human hair shafts. Mol Biol Rep 2021; 49:1017-1025. [PMID: 34739693 DOI: 10.1007/s11033-021-06921-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 10/30/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND Hair is a frequently encountered biological evidence in personal identification. The amount of nuclear DNA that can be extracted from a single strand of rootless hair is most limited, making the detection of short tandem repeat (STR) polymorphisms difficult. To overcome these limitations, deletion/insertion polymorphisms (DIP) as a new type of genetic marker have shown their benefits in detecting low-copy-number DNA. The Investigator DIPplex kit contains 30 biallelic autosomal DIP and amelogenin. The analysis of DIPs combines the advantages of both STR and single nucleotide polymorphism analyses. Thus, this study aimed to detect the DIP distribution of individual hair shafts from individuals. METHODS AND RESULTS DNA was extracted from the shaft of fresh, aged, and shed hair. After DNA was evaluated, the DIP profiles were detected by capillary electrophoresis. The results indicated that the amount of DNA extracted from hair roots was much higher than that from the hair shafts in the same individual for all samples. The degradation index values of DNA from the aged hair shafts were highest. It is classified to be "mildly degraded." Compared with their hair roots, the full DIP profiles were detected for fresh hair, 70% for aged hair, and 92% for shed hair. Contrarily, except for fresh hair shafts, only three STR loci of the aged and shed strands of hair could be genotyped using AmpFlSTR MiniFiler PCR Amplification Kit. CONCLUSIONS These results indicate that the detection of DIP profile is an effective tool for personal identification from hair shafts, including aged hair.
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Affiliation(s)
- Jian Tie
- Division of Legal Medicine, Department of Social Medicine, Nihon University School of Medicine, Tokyo, 1738610, Japan.
| | - Seisaku Uchigasaki
- Division of Legal Medicine, Department of Social Medicine, Nihon University School of Medicine, Tokyo, 1738610, Japan
| | - Eiji Isobe
- Division of Legal Medicine, Department of Social Medicine, Nihon University School of Medicine, Tokyo, 1738610, Japan
| | - Etsuko Iwakami
- Division of Legal Medicine, Department of Social Medicine, Nihon University School of Medicine, Tokyo, 1738610, Japan
| | - Takahisa Okuda
- Division of Legal Medicine, Department of Social Medicine, Nihon University School of Medicine, Tokyo, 1738610, Japan
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16
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Marshall C, Parson W. Interpreting NUMTs in forensic genetics: Seeing the forest for the trees. Forensic Sci Int Genet 2021; 53:102497. [PMID: 33740708 DOI: 10.1016/j.fsigen.2021.102497] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/10/2021] [Accepted: 03/11/2021] [Indexed: 01/29/2023]
Abstract
Nuclear mitochondrial DNA (mtDNA) segments (NUMTs) were discovered shortly after sequencing the first human mitochondrial genome. They have earlier been considered to represent archaic elements of ancient insertion events, but modern sequencing technologies and growing databases of mtDNA and NUMT sequences confirm that they are abundant and some of them phylogenetically young. Here, we build upon mtDNA/NUMT review articles published in the mid 2010 s and focus on the distinction of NUMTs and other artefacts that can be observed in aligned sequence reads, such as mixtures (contamination), point heteroplasmy, sequencing error and cytosine deamination. We show practical examples of the effect of the mtDNA enrichment method on the representation of NUMTs in the mapped sequence data and discuss methods to bioinformatically filter NUMTs from mtDNA reads.
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Affiliation(s)
- Charla Marshall
- Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, DE 19902, USA; SNA International, Contractor Supporting the AFMES-AFDIL, Alexandria, VA 22314, USA; Forensic Science Program, The Pennsylvania State University, University Park, PA 16802, USA
| | - Walther Parson
- Forensic Science Program, The Pennsylvania State University, University Park, PA 16802, USA; Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria.
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17
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Comparison of polymerases used for amplification of mitochondrial DNA from challenging hairs and hairs of various treatments. Forensic Sci Int Genet 2021; 52:102484. [PMID: 33662687 DOI: 10.1016/j.fsigen.2021.102484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 11/20/2022]
Abstract
Forensic DNA analysis of hair evidence typically involves the amplification and sequencing of the control region (CR) of the mitochondrial genome (mtgenome). In compromised hair samples, such as shed hairs, the number of mtgenome copies could be low; thus, it is imperative that the polymerase used in PCR is efficient to ensure maximum amplification. Considering this, the first phase of this study compared the yields obtained from 12 polymerases (sourced from a range of commercial companies) when amplifying the CR, hypervariable (HV) region II (HV2), and hypervariable subregion II-B (HV2B). This initial assessment was performed using mitochondrial DNA (mtDNA) extracted from 2 cm of hair adjacent to the root from three donors of different self-reported ancestries and hair color/texture. PrimeSTAR HS and KAPA HiFi HotStart consistently generated significantly higher amplicon yields (p < 0.05, ~5-fold increase) for most regions than AmpliTaq Gold DNA polymerase (the polymerase validated for use in most forensic laboratories). The second phase of this project was focused on assessing the broad utility of these top two performing polymerases for amplifying two regions of the mtgenome (CR and HV2B) from hair samples representing diverse self-reported ancestral origins (European, Latin American, African American, Asian, and Native American), characteristics/treatments (bleached, dyed, and chemically straightened), and anatomical origins (e.g., head and pubic region) (n = 41). These regions were chosen as they are the most challenging to amplify and sequence in compromised hair samples due to length (i.e., the CR is ~1.2 kb) and repeat structure (i.e., the polycytosine stretch within HV2B). The results indicated that regardless of sample type, PrimeSTAR HS and KAPA HiFi HotStart polymerases outperformed (p < 0.05) AmpliTaq Gold DNA polymerase (averaging 11- and 8-fold increased yields, respectively). The results from this study highlight that enhanced commercially available polymerases appear to significantly improve the amplification of mtDNA from challenging hair samples.
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18
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Assessment of Illumina® Human mtDNA Genome assay: workflow evaluation with development of analysis and interpretation guidelines. Int J Legal Med 2021; 135:1161-1178. [PMID: 33511452 DOI: 10.1007/s00414-021-02508-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 01/08/2021] [Indexed: 01/27/2023]
Abstract
Mitochondrial DNA (mtDNA) is a small but significant part of the human genome, whose applicability potential has gradually increased with the advent of massively parallel sequencing (MPS) technology. Knowledge of the particular workflow, equipment, and reagents used, along with extensive usage of negative controls to monitor all preparation steps constitute the prerequisites for confident reporting of results. In this study, we performed an assessment of Illumina® Human mtDNA Genome assay on MiSeq FGx™ instrument. Through analysis of several types of negative controls, as well as mtDNA positive controls, we established thresholds for data analysis and interpretation, consisting of several components: minimum read depth (220 reads), minimum quality score (41), percentage of minor allele sufficient for analysis (3.0%), percentage of minor allele sufficient for interpretation (6.0%), and percentage of major allele sufficient for homoplasmic variant call (97.0%). Based on these criteria, we defined internal guidelines for analysis and interpretation of mtDNA results obtained by MPS. Our study shows that the whole mtDNA assay on MiSeq FGx™ produces repeatable and reproducible results, independent of the analyst, which are also concordant with Sanger-type sequencing results for mtDNA control region, as well as with MPS results produced by NextSeq®. Overall, established thresholds and interpretation guidelines were successfully applied for the sequencing of complete mitochondrial genomes from high-quality samples. The underlying principles and proposed methodology on the definition of internal laboratory guidelines for analysis and interpretation of MPS results may be applicable to similar MPS workflows, e.g. targeting good-quality samples in forensic genetics and molecular diagnostics.
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19
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Developmental Validation of a MPS Workflow with a PCR-Based Short Amplicon Whole Mitochondrial Genome Panel. Genes (Basel) 2020; 11:genes11111345. [PMID: 33202822 PMCID: PMC7709034 DOI: 10.3390/genes11111345] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/21/2020] [Accepted: 11/10/2020] [Indexed: 01/10/2023] Open
Abstract
For the adoption of massively parallel sequencing (MPS) systems by forensic laboratories, validation studies on specific workflows are needed to support the feasibility of implementation and the reliability of the data they produce. As such, the whole mitochondrial genome sequencing methodology—Precision ID mtDNA Whole Genome Panel, Ion Chef, Ion S5, and Converge—has been subjected to a variety of developmental validation studies. These validation studies were completed in accordance with the Scientific Working Group on DNA Analysis Methods (SWGDAM) validation guidelines and assessed reproducibility, repeatability, accuracy, sensitivity, specificity to human DNA, and ability to analyze challenging (e.g., mixed, degraded, or low quantity) samples. Intra- and inter-run replicates produced an average maximum pairwise difference in variant frequency of 1.2%. Concordance with data generated with traditional Sanger sequencing and an orthogonal MPS platform methodology was used to assess accuracy, and generation of complete and concordant haplotypes at DNA input levels as low as 37.5 pg of nuclear DNA or 187.5 mitochondrial genome copies illustrated the sensitivity of the system. Overall, data presented herein demonstrate that highly accurate and reproducible results were generated for a variety of sample qualities and quantities, supporting the reliability of this specific whole genome mitochondrial DNA MPS system for analysis of forensic biological evidence.
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20
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Taylor CR, Kiesler KM, Sturk-Andreaggi K, Ring JD, Parson W, Schanfield M, Vallone PM, Marshall C. Platinum-Quality Mitogenome Haplotypes from United States Populations. Genes (Basel) 2020; 11:genes11111290. [PMID: 33138247 PMCID: PMC7716222 DOI: 10.3390/genes11111290] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 10/26/2020] [Accepted: 10/27/2020] [Indexed: 12/14/2022] Open
Abstract
A total of 1327 platinum-quality mitochondrial DNA haplotypes from United States (U.S.) populations were generated using a robust, semi-automated next-generation sequencing (NGS) workflow with rigorous quality control (QC). The laboratory workflow involved long-range PCR to minimize the co-amplification of nuclear mitochondrial DNA segments (NUMTs), PCR-free library preparation to reduce amplification bias, and high-coverage Illumina MiSeq sequencing to produce an average per-sample read depth of 1000 × for low-frequency (5%) variant detection. Point heteroplasmies below 10% frequency were confirmed through replicate amplification, and length heteroplasmy was quantitatively assessed using a custom read count analysis tool. Data analysis involved a redundant, dual-analyst review to minimize errors in haplotype reporting with additional QC checks performed by EMPOP. Applying these methods, eight sample sets were processed from five U.S. metapopulations (African American, Caucasian, Hispanic, Asian American, and Native American) corresponding to self-reported identity at the time of sample collection. Population analyses (e.g., haplotype frequencies, random match probabilities, and genetic distance estimates) were performed to evaluate the eight datasets, with over 95% of haplotypes unique per dataset. The platinum-quality mitogenome haplotypes presented in this study will enable forensic statistical calculations and thereby support the usage of mitogenome sequencing in forensic laboratories.
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Affiliation(s)
- Cassandra R. Taylor
- Armed Forces Medical Examiner System’s Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, DE 19002, USA; (C.R.T.); (K.S.-A.); (J.D.R.)
- SNA International, LLC; Alexandria, VA 22314, USA
| | - Kevin M. Kiesler
- National Institute of Standards and Technology (NIST), Gaithersburg, MD 20899, USA; (K.M.K.); (P.M.V.)
| | - Kimberly Sturk-Andreaggi
- Armed Forces Medical Examiner System’s Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, DE 19002, USA; (C.R.T.); (K.S.-A.); (J.D.R.)
- SNA International, LLC; Alexandria, VA 22314, USA
| | - Joseph D. Ring
- Armed Forces Medical Examiner System’s Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, DE 19002, USA; (C.R.T.); (K.S.-A.); (J.D.R.)
- SNA International, LLC; Alexandria, VA 22314, USA
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck 6020, Austria;
- Forensic Science Program, The Pennsylvania State University, State College, PA 16801, USA
| | - Moses Schanfield
- Department of Forensic Sciences, The George Washington University, Washington, DC 20007, USA;
| | - Peter M. Vallone
- National Institute of Standards and Technology (NIST), Gaithersburg, MD 20899, USA; (K.M.K.); (P.M.V.)
| | - Charla Marshall
- Armed Forces Medical Examiner System’s Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, DE 19002, USA; (C.R.T.); (K.S.-A.); (J.D.R.)
- SNA International, LLC; Alexandria, VA 22314, USA
- Forensic Science Program, The Pennsylvania State University, State College, PA 16801, USA
- Correspondence: ; Tel.: +1-302-346-8519
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21
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Melchionda F, Stanciu F, Buscemi L, Pesaresi M, Tagliabracci A, Turchi C. Searching the undetected mtDNA variants in forensic MPS data. Forensic Sci Int Genet 2020; 49:102399. [PMID: 33038616 DOI: 10.1016/j.fsigen.2020.102399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/27/2020] [Accepted: 09/21/2020] [Indexed: 10/23/2022]
Abstract
The efficiency of MPS in forensic mtDNA analysis has been thoroughly proven, although a reliable and well established data evaluation still remains a critical point. Numerous bioinformatics tools have been developed, but most of them require specific operating systems and high costs, while free open-source programs with user-friendly interfaces are few. In this study, 43 full mtGenomes were sequenced using the Ion Personal Genome Machine™ (PGM™) System and analyzed utilizing the plug-in Variant Caller (TVC) of the Ion Torrent Software Suite and the mtDNA-Server (mDS), a free web-based mitochondrial analysis tool for MPS data. The outcomes of these two different analysis tools were compared to variants noted after manual inspection of the aligned reads performed using Integrative Genomics Viewer (IGV). The comparison highlighted the presence of thirty-nine discordant variant calls, which were resolved by Sanger sequencing that confirmed the presence of all variants, except for 7 deletions. The combined adoption of IGV and Sanger type sequencing confirmatory steps, in addition of TVC and mDS analysis, resulted in a more accurate variants assignment with the detection of 32 additional true polymorphisms, which were noted in the final dataset. Regarding the heteroplasmy issue, out of a total of thirty heteroplasmic variants, twenty-eight were detected by the TVC, while the mDS detected twenty-two. Overall, none of the used bioinformatics tools were the perfect choice and a secondary analysis with an expert's opinion in complete mtGenome MPS data evaluation is still required in forensic genetic analysis.
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Affiliation(s)
- Filomena Melchionda
- Section of Legal Medicine, Department of Excellence of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy - Via Tronto, 60126 Torrette Ancona, Italy.
| | - Florin Stanciu
- Romanian National DNA Database, National Forensic Science Institute, General Inspectorate of Romanian Police, Bucharest, Romania.
| | - Loredana Buscemi
- Section of Legal Medicine, Department of Excellence of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy - Via Tronto, 60126 Torrette Ancona, Italy.
| | - Mauro Pesaresi
- Section of Legal Medicine, Department of Excellence of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy - Via Tronto, 60126 Torrette Ancona, Italy.
| | - Adriano Tagliabracci
- Section of Legal Medicine, Department of Excellence of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy - Via Tronto, 60126 Torrette Ancona, Italy.
| | - Chiara Turchi
- Section of Legal Medicine, Department of Excellence of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy - Via Tronto, 60126 Torrette Ancona, Italy.
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22
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Ballard D, Winkler-Galicki J, Wesoły J. Massive parallel sequencing in forensics: advantages, issues, technicalities, and prospects. Int J Legal Med 2020; 134:1291-1303. [PMID: 32451905 PMCID: PMC7295846 DOI: 10.1007/s00414-020-02294-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 04/03/2020] [Indexed: 12/13/2022]
Abstract
In the last decade, next-generation sequencing (NGS) technology, alternatively massive parallel sequencing (MPS), was applied to all fields of biological research. Its introduction to the field of forensics was slower, mainly due to lack of accredited sequencers, kits, and relatively higher sequencing error rates as compared with standardized Sanger sequencing. Currently, a majority of the problematic issues have been solved, which is proven by the body of reports in the literature. Here, we discuss the utility of NGS sequencing in forensics, emphasizing the advantages, issues, the technical aspects of the experiments, commercial solutions, and the potentially interesting applications of MPS.
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Affiliation(s)
- David Ballard
- King's Forensic Genetics, Faculty of Life Sciences and Medicine, King's College London, 150 Stamford Street, London, UK
| | - Jakub Winkler-Galicki
- Laboratory of High Throughput Technologies, Faculty of Biology, Adam Mickiewicz, University Poznan, 6 Uniwersytetu Poznanskiego Street, Poznan, Poland
| | - Joanna Wesoły
- Laboratory of High Throughput Technologies, Faculty of Biology, Adam Mickiewicz, University Poznan, 6 Uniwersytetu Poznanskiego Street, Poznan, Poland.
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23
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García Ó, Alonso S, Huber N, Bodner M, Parson W. Forensically relevant phylogeographic evaluation of mitogenome variation in the Basque Country. Forensic Sci Int Genet 2020; 46:102260. [PMID: 32062111 DOI: 10.1016/j.fsigen.2020.102260] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 11/26/2019] [Accepted: 02/01/2020] [Indexed: 11/19/2022]
Abstract
The Basque Country has been the focus of population (genetic) and evolutionary studies for decades, as it represents an interesting evolutionary feature: it is the only European country where a non-Indo-European language is still spoken today and, for which there are no known living or extinct relatives. Early studies that were based on anatomical and serological methods, along with subsequent molecular genetic investigations, contain controversial interpretations of their data. Additionally, the analysis of mitochondrial DNA, which is maternally inherited and thus suitable for the examination of the maternal phylogeny of the population, was the focus of some studies. Early mtDNA studies were however restricted to the information provided by the control region or its hypervariable segments only. These are known to harbour little phylogenetic information, particularly for haplogroup H that is dominant in Westeurasian populations including the Basques. Later studies analysed complete mitogenome sequences. Their information content is however limited, either because the number of samples was low, or because these studies only considered particular haplogroups. In this study we present the full mitogenome sequences of 178 autochthonous Basque individuals that were carefully selected based on their familial descent and discuss the observed phylogenetic signals in the light of earlier published findings. We confirm the presence of Basque-specific mtDNA lineages and extend the knowledge of these lineages by providing data on their distribution in comparison to other Basque and non-Basque populations. This dataset improves our understanding of the Basque mtDNA phylogeny and serves as a high-quality dataset that is provided via EMPOP for forensic genetic purposes.
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Affiliation(s)
- Óscar García
- Forensic Science Unit, Forensic Genetics Section, Basque Country Police, Erandio (Bizkaia), Spain.
| | - Santos Alonso
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, Spain.
| | - Nicole Huber
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria.
| | - Martin Bodner
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria.
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, University Park, Pennsylvania, USA.
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Sturk-Andreaggi K, Parson W, Allen M, Marshall C. Impact of the sequencing method on the detection and interpretation of mitochondrial DNA length heteroplasmy. Forensic Sci Int Genet 2020; 44:102205. [DOI: 10.1016/j.fsigen.2019.102205] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 11/09/2019] [Accepted: 11/09/2019] [Indexed: 02/04/2023]
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25
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Yao Y, Nishimura M, Murayama K, Kuranobu N, Tojo S, Beppu M, Ishige T, Itoga S, Tsuchida S, Mori M, Takayanagi M, Yokoyama M, Yamagata K, Kishita Y, Okazaki Y, Nomura F, Matsushita K, Tanaka T. A simple method for sequencing the whole human mitochondrial genome directly from samples and its application to genetic testing. Sci Rep 2019; 9:17411. [PMID: 31757988 PMCID: PMC6874554 DOI: 10.1038/s41598-019-53449-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 10/31/2019] [Indexed: 12/23/2022] Open
Abstract
Next-generation sequencing (NGS) is a revolutionary sequencing technology for analyzing genomes. However, preprocessing methods for mitochondrial DNA (mtDNA) sequencing remain complex, and it is required to develop an authenticated preprocessing method. Here, we developed a simple and easy preprocessing method based on isothermal rolling circle mtDNA amplification using commercially available reagents. Isothermal amplification of mtDNA was successfully performed using both nanoliter quantities of plasma directly and 25 ng of total DNA extracted from blood or tissue samples. Prior to mtDNA amplification, it was necessary to treat the extracted total DNA with Exonuclease V, but it was not required to treat plasma. The NGS libraries generated from the amplified mtDNA provided sequencing coverage of the entire human mitochondrial genome. Furthermore, the sequencing results successfully detected heteroplasmy in patient samples, with called mutations and variants matching those from previous, independent, Sanger sequencing analysis. Additionally, a novel single nucleotide variant was detected in a healthy volunteer. The successful analysis of mtDNA using very small samples from patients is likely to be valuable in clinical medicine, as it could reduce patient discomfort by reducing sampling-associated damage to tissues. Overall, the simple and convenient preprocessing method described herein may facilitate the future development of NGS-based clinical and forensic mtDNA tests.
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Affiliation(s)
- Yue Yao
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
| | - Motoi Nishimura
- Division of Laboratory Medicine, Clinical Genetics and Proteomics, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
| | - Kei Murayama
- Division of Metabolism, Chiba Children's Hospital, Chiba, 266-0007, Japan
| | - Naomi Kuranobu
- Division of Metabolism, Chiba Children's Hospital, Chiba, 266-0007, Japan
| | - Satomi Tojo
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
| | - Minako Beppu
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
- Division of Laboratory Medicine, Clinical Genetics and Proteomics, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
| | - Takayuki Ishige
- Division of Laboratory Medicine, Clinical Genetics and Proteomics, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
| | - Sakae Itoga
- Division of Laboratory Medicine, Clinical Genetics and Proteomics, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
| | - Sachio Tsuchida
- Division of Clinical Mass Spectrometry, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
| | - Masato Mori
- Department of Pediatrics, Matsudo City Hospital, Matsudo, 270-2296, Japan
| | - Masaki Takayanagi
- Division of Metabolism, Chiba Children's Hospital, Chiba, 266-0007, Japan
| | - Masataka Yokoyama
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
| | - Kazuyuki Yamagata
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
| | - Yoshihito Kishita
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Hongo 2-1-1, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Yasushi Okazaki
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Hongo 2-1-1, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Fumio Nomura
- Division of Clinical Mass Spectrometry, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
| | - Kazuyuki Matsushita
- Division of Laboratory Medicine, Clinical Genetics and Proteomics, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
| | - Tomoaki Tanaka
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan.
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Young JM, Higgins D, Austin JJ. Hybridization Enrichment to Improve Forensic Mitochondrial DNA Analysis of Highly Degraded Human Remains. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00450] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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27
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Kim BM, Hong SR, Chun H, Kim S, Shin KJ. Comparison of whole mitochondrial genome variants between hair shafts and reference samples using massively parallel sequencing. Int J Legal Med 2019; 134:853-861. [PMID: 31734723 DOI: 10.1007/s00414-019-02205-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 11/07/2019] [Indexed: 10/25/2022]
Abstract
Hair shafts are one of the most common types of evidence at crime scenes, and mitochondrial DNA (mtDNA) has been analyzed as a valuable genetic marker for hair shafts in forensic casework. However, the mtDNA analysis strategy may vary according to the quantity and quality of DNA extracted from a forensic sample and the available massively parallel sequencing (MPS) platform in laboratories. Forensic practitioners often have to interpret mtDNA sequences exhibiting point heteroplasmy (PHP) that are analyzed using different analytical methods. In the present study, the whole mitochondrial genome (mtGenome) variants of hair shaft samples obtained from 20 donors, which were sampled in duplicate and stored at room temperature for > 1 year, were analyzed using the Precision ID mtDNA Whole Genome Panel and Ion S5 system. The whole mtGenome variants of 20 blood and 20 buccal swab samples (reference samples) from the hair shaft donors were analyzed using the Nextera XT DNA Library Prep Kit and MiSeq System. A total of 20 unique mtGenome haplotypes were observed, and 56 PHP variants were identified across the 4 sets of tissue. When the major nucleotide of PHP was considered, 16 of 20 haplotypes of the hair shaft samples matched those of the corresponding blood and buccal swab samples. In four donors, the major nucleotide of PHP was inverted at one nucleotide position between the hair shaft and reference samples. However, the data obtained on MPS, showing high PHP resolution, provided substantial information to avoid false exclusion when comparing two haplotypes containing PHP with inverted major nucleotides. In conclusion, the present study demonstrates the utility of MPS in forensic casework in the comparative analysis of mtGenome variants containing PHP.
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Affiliation(s)
- Bo Min Kim
- Department of Forensic Medicine, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.,Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Sae Rom Hong
- Department of Forensic Medicine, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.,Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Hein Chun
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.,Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Sangwoo Kim
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.,Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Kyoung-Jin Shin
- Department of Forensic Medicine, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea. .,Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.
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28
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Catlin LA, Chou RM, Goecker ZC, Mullins LA, Silva DSBSS, Spurbeck RR, Parker GJ, Bartling CM. Demonstration of a mitochondrial DNA-compatible workflow for genetically variant peptide identification from human hair samples. Forensic Sci Int Genet 2019; 43:102148. [DOI: 10.1016/j.fsigen.2019.102148] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 07/29/2019] [Accepted: 08/14/2019] [Indexed: 12/01/2022]
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29
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Yuan L, Chen X, Liu Z, Liu Q, Song A, Bao G, Wei G, Zhang S, Lu J, Wu Y. Identification of the perpetrator among identical twins using next-generation sequencing technology: A case report. Forensic Sci Int Genet 2019; 44:102167. [PMID: 31605960 DOI: 10.1016/j.fsigen.2019.102167] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 09/12/2019] [Accepted: 09/26/2019] [Indexed: 11/20/2022]
Abstract
BACKGROUND Monozygotic (MZ) twins, considered genetically identical, cannot be distinguished using regular short tandem repeats (STR) typing, thus presenting a challenge for forensic geneticists. In paternity testing, single nucleotide polymorphisms (SNPs) in nuclear DNA can help distinguish MZ twins. However, the unique features of the mitochondrial genome, such as high copy number, small genome size, and high substitution rate, make it a promising source for applications in forensic science. METHODS Whole-genome sequencing (WGS) was performed on blood samples, and bioinformatic analysis was used to distinguish between MZ twins. Amplification refractory mutation system polymerase chain reaction (ARMS-PCR) was used to confirm the WGS results. This methodology was further applied to forensic samples from criminal cases. Amplicon sequencing was also performed to further exclude the innocent twin. RESULTS The monozygosity of the twins was confirmed using STR typing. Only one potential somatic mutation, m.6903 T > C (2.6%), in the mitochondrial genome of one of the twins was verified when the sequence depth was set to 2000-fold, while no other distinguishing locus in the nuclear genome was identified. By dividing the number of C-reads by total reads, WGS data confirmed the amount of the minor component C to be 2.6%, which was further confirmed by ARMS-PCR. In addition, the heterogeneous locus was used to identify samples obtained from four criminal cases for forensic testing. Two heterogeneous loci in the sperm DNA of the other twin were identified by amplicon sequencing, and the amount of minor component T in m.6935C > T and m.6938C > T was estimated to be 17.91% and 18.79%, respectively. CONCLUSION The biological samples taken from the MZ twins were distinguished using a combination of WGS, allele-specific PCR, and deep-amplicon sequencing. Compared with nuclear DNA, mitochondrial DNA exhibited a higher potential for distinguishing between the MZ twins. The distinguishing feature of the mitochondrial DNA was the heterogeneous SNPs that occurred in only one twin. One SNP was further verified in the samples from the criminal cases and helped identify the perpetrator in case 1 and case 2. Furthermore, two heterogeneous SNPs found by amplicon sequencing helped to exclude the innocent twin in all four cases. Our findings demonstrated that a combination of deep sequencing and molecular analysis can be an effective way to distinguish between identical twins and can be used to analyze samples from criminal cases.
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Affiliation(s)
- Lijuan Yuan
- Department of Biochemistry and Molecular Biology, Center for DNA Typing, Air Force Medical University, 169 Changle West Road, Xi'an, Shaanxi 710032, PR China; Department of General Surgery, Tangdu Hospital, Air Force Medical University, 569 Xinsi Road, Xi'an, Shaanxi 710038, PR China
| | - Xihui Chen
- Department of Biochemistry and Molecular Biology, Center for DNA Typing, Air Force Medical University, 169 Changle West Road, Xi'an, Shaanxi 710032, PR China
| | - Ziyu Liu
- Department of Microbiology, Air Force Medical University, 169 Changle West Road, Xi'an, Shaanxi 710032, PR China
| | - Qingbo Liu
- Department of Biochemistry and Molecular Biology, Center for DNA Typing, Air Force Medical University, 169 Changle West Road, Xi'an, Shaanxi 710032, PR China
| | - An Song
- Department of Biochemistry and Molecular Biology, Center for DNA Typing, Air Force Medical University, 169 Changle West Road, Xi'an, Shaanxi 710032, PR China
| | - Guoqiang Bao
- Department of General Surgery, Tangdu Hospital, Air Force Medical University, 569 Xinsi Road, Xi'an, Shaanxi 710038, PR China
| | - Gang Wei
- Department of General Surgery, Tangdu Hospital, Air Force Medical University, 569 Xinsi Road, Xi'an, Shaanxi 710038, PR China
| | - Sijia Zhang
- Department of Biochemistry and Molecular Biology, Center for DNA Typing, Air Force Medical University, 169 Changle West Road, Xi'an, Shaanxi 710032, PR China
| | - Jianguo Lu
- Department of General Surgery, Tangdu Hospital, Air Force Medical University, 569 Xinsi Road, Xi'an, Shaanxi 710038, PR China.
| | - Yuanming Wu
- Department of Biochemistry and Molecular Biology, Center for DNA Typing, Air Force Medical University, 169 Changle West Road, Xi'an, Shaanxi 710032, PR China.
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30
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Brandhagen MD, Just RS, Irwin JA. Validation of NGS for mitochondrial DNA casework at the FBI Laboratory. Forensic Sci Int Genet 2019; 44:102151. [PMID: 31629185 DOI: 10.1016/j.fsigen.2019.102151] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 08/21/2019] [Accepted: 08/22/2019] [Indexed: 01/09/2023]
Abstract
As a first step towards integrating next generation sequencing (NGS) technology into the FBI Laboratory's operational casework, the PowerSeq™ CRM Nested System, an NGS-based mitochondrial DNA (mtDNA) control region assay, was developmentally and internally validated. The validation studies were conducted in accordance with the Scientific Working Group on DNA Analysis Methods (SWGDAM) Validation Guidelines for Forensic DNA Analysis Methods, and the FBI's Quality Assurance Standards (QAS) for Forensic DNA Testing Laboratories. The assay was shown to be highly reproducible, with variant frequencies across intra and inter-run replicates of the same sample differing, on average, by just 0.3% for substitutions and point heteroplasmies and 1.5% for insertions and deletions. The assay was also shown to be extremely sensitive, yielding complete control region sequence data from as few as 2000 copies of mtDNA. This is a more than 20-fold increase in sensitivity when compared to the FBI Laboratory's current Sanger sequencing-based protocols and, based on mtDNA quantitation values of samples routinely encountered in mtDNA casework, suggests that the percentage of questioned samples from which full control region data can be recovered will increase from our current 20% to approximately 90% success with NGS technology. In addition, the assay requires on average only 30% of the extract volume typically required to develop control region profiles from degraded samples via Sanger sequencing. Overall, these studies establish the reliability of the PowerSeq™ CRM Nested System for accurate mtDNA control region typing and can serve as a model for laboratories seeking to validate NGS protocols for forensic mtDNA analysis.
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Affiliation(s)
| | - Rebecca S Just
- FBI Laboratory, 2501 Investigation Parkway, Quantico, VA 22135, USA.
| | - Jodi A Irwin
- FBI Laboratory, 2501 Investigation Parkway, Quantico, VA 22135, USA.
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31
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Lan Q, Xie T, Jin X, Fang Y, Mei S, Yang G, Zhu B. MtDNA polymorphism analyses in the Chinese Mongolian group: Efficiency evaluation and further matrilineal genetic structure exploration. Mol Genet Genomic Med 2019; 7:e00934. [PMID: 31478599 PMCID: PMC6785450 DOI: 10.1002/mgg3.934] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 05/26/2019] [Accepted: 07/07/2019] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Profiling of mitochondrial DNA is surely to provide valuable investigative clues for forensic cases involving highly degraded specimens or complex maternal lineage kinship determination. But traditionally used hypervariable region sequencing of mitochondrial DNA is less frequently suggested by the forensic community for insufficient informativeness. Genome-wide sequencing of mitochondrial DNA can provide considerable amount of variant information but can be high cost at the same time. METHODS Efficiency of the 60 mitochondrial DNA polymorphic sites dispersing across the control region and coding region of mitochondrial DNA genome was evaluated with 106 Mongolians recruited from the Xinjiang Uyghur Autonomous Region, China, and allele-specific PCR technique was employed for mitochondrial DNA typing. RESULTS Altogether 58 haplotypes were observed and the haplotypic diversity, discrimination power and random match probability were calculated to be 0.981, 0.972, and 0.028, respectively. Mitochondrial DNA haplogroup affiliation exhibited an exceeding percentage (12.26%) of west Eurasian lineage (H haplogroup) in the studied Mongolian group, which needed to be further verified with more samples. Furthermore, the genetic relationships between the Xinjiang Mongolian group and the comparison populations were also investigated and the genetic affinity was discovered between the Xinjiang Mongolian group and the Xinjiang Kazak group in this study. CONCLUSION It was indicated that the panel was potentially enough to be used as a supplementary tool for forensic applications. And the matrilineal genetic structure analyses based on mitochondrial DNA variants in the Xinjiang Mongolian group could be helpful for subsequent anthropological studies.
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Affiliation(s)
- Qiong Lan
- Department of Forensic Genetics, School of Forensic MedicineSouthern Medical UniversityGuangzhouChina
| | - Tong Xie
- Department of Forensic Genetics, School of Forensic MedicineSouthern Medical UniversityGuangzhouChina
| | - Xiaoye Jin
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of StomatologyXi'an Jiaotong UniversityXi'anChina
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of StomatologyXi'an Jiaotong UniversityXi'anChina
| | - Yating Fang
- Department of Forensic Genetics, School of Forensic MedicineSouthern Medical UniversityGuangzhouChina
| | - Shuyan Mei
- Department of Forensic Genetics, School of Forensic MedicineSouthern Medical UniversityGuangzhouChina
| | - Guang Yang
- Department of Laboratory Medicine and PathologyMayo ClinicRochesterMNUSA
| | - Bofeng Zhu
- Department of Forensic Genetics, School of Forensic MedicineSouthern Medical UniversityGuangzhouChina
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of StomatologyXi'an Jiaotong UniversityXi'anChina
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of StomatologyXi'an Jiaotong UniversityXi'anChina
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32
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Strobl C, Churchill Cihlar J, Lagacé R, Wootton S, Roth C, Huber N, Schnaller L, Zimmermann B, Huber G, Lay Hong S, Moura-Neto R, Silva R, Alshamali F, Souto L, Anslinger K, Egyed B, Jankova-Ajanovska R, Casas-Vargas A, Usaquén W, Silva D, Barletta-Carrillo C, Tineo DH, Vullo C, Würzner R, Xavier C, Gusmão L, Niederstätter H, Bodner M, Budowle B, Parson W. Evaluation of mitogenome sequence concordance, heteroplasmy detection, and haplogrouping in a worldwide lineage study using the Precision ID mtDNA Whole Genome Panel. Forensic Sci Int Genet 2019; 42:244-251. [PMID: 31382159 DOI: 10.1016/j.fsigen.2019.07.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 07/09/2019] [Accepted: 07/21/2019] [Indexed: 12/24/2022]
Abstract
The emergence of Massively Parallel Sequencing technologies enabled the analysis of full mitochondrial (mt)DNA sequences from forensically relevant samples that have, so far, only been typed in the control region or its hypervariable segments. In this study, we evaluated the performance of a commercially available multiplex-PCR-based assay, the Precision ID mtDNA Whole Genome Panel (Thermo Fisher Scientific), for the amplification and sequencing of the entire mitochondrial genome (mitogenome) from even degraded forensic specimens. For this purpose, more than 500 samples from 24 different populations were selected to cover the vast majority of established superhaplogroups. These are known to harbor different signature sequence motifs corresponding to their phylogenetic background that could have an effect on primer binding and, thus, could limit a broad application of this molecular genetic tool. The selected samples derived from various forensically relevant tissue sources and were DNA extracted using different methods. We evaluated sequence concordance and heteroplasmy detection and compared the findings to conventional Sanger sequencing as well as an orthogonal MPS platform. We discuss advantages and limitations of this approach with respect to forensic genetic workflow and analytical requirements.
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Affiliation(s)
- Christina Strobl
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Robert Lagacé
- Human Identification Group, ThermoFisher Scientific, San Francisco, CA, USA
| | - Sharon Wootton
- Human Identification Group, ThermoFisher Scientific, San Francisco, CA, USA
| | - Chantal Roth
- Human Identification Group, ThermoFisher Scientific, San Francisco, CA, USA
| | - Nicole Huber
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Lisa Schnaller
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Bettina Zimmermann
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Gabriela Huber
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Seah Lay Hong
- School of Health Sciences, Universiti Sains Malaysia, Kubang Kerian, Kelantan, Malaysia
| | - Rodrigo Moura-Neto
- Laboratório de Biologia Molecular Forense, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Rosane Silva
- Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Farida Alshamali
- Dubai Police, Gen. Dept. Forensic Science & Criminology, Dubai, United Arab Emirates
| | - Luis Souto
- Laboratorio de Genética Aplicada, Departamento de Biologia, Universidade de Aveiro, Portugal
| | | | - Balazs Egyed
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Renata Jankova-Ajanovska
- Institute of Forensic Medicine, Criminalistic and Medical Deontology, Medical Faculty, University "St. Cyril and Methodius", Skopje, Macedonia
| | - Andrea Casas-Vargas
- Group of Population Genetics and Identification, Genetics Institute, National University of Colombia, Bogotá, Colombia
| | - Wiliam Usaquén
- Group of Population Genetics and Identification, Genetics Institute, National University of Colombia, Bogotá, Colombia
| | - Dayse Silva
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | | | - Dean Herman Tineo
- Universidad Nacional Mayor de San Marcos, Instituto de Medicina Legal del Perú, Lima, Peru
| | - Carlos Vullo
- DNA Forensic Laboratory, Argentinean Forensic Anthropology team (EAAF), Córdoba, Argentina
| | - Reinhard Würzner
- Division of Hygiene & Med. Microbiology, Medical University of Innsbruck, Austria
| | - Catarina Xavier
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Leonor Gusmão
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Harald Niederstätter
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Martin Bodner
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, TX, USA
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, University Park, PA, USA.
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Avila E, Graebin P, Chemale G, Freitas J, Kahmann A, Alho CS. Full mtDNA genome sequencing of Brazilian admixed populations: A forensic-focused evaluation of a MPS application as an alternative to Sanger sequencing methods. Forensic Sci Int Genet 2019; 42:154-164. [PMID: 31325893 DOI: 10.1016/j.fsigen.2019.07.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 07/03/2019] [Accepted: 07/08/2019] [Indexed: 12/13/2022]
Abstract
The use of Massive Parallel Sequencing (MPS) techniques have been proposed by the forensic community as an alternative to Sanger sequencing methods in routine forensic casework analysis regarding mitochondrial DNA (mtDNA). Interesting features of MPS include high throughput, ability to simultaneously genotype a significant number of samples by barcoding techniques, processing automation, reduced time and costs, among others. Advantages include the capability of generating full mtDNA genome sequences versus usual techniques, usually limited to hypervariable or control regions exclusively. In this work, 96 reference single-source samples from three different Brazilian cities were subjected to full mtDNA genome sequencing by MPS techniques using an early-access version of Precision ID mtDNA Whole Genome Panel on an Ion Torrent PGM platform (Thermo Fisher Scientific, Waltham, MA, USA). Complete, high-quality sequences were obtained and sequencing performance was evaluated via four different metrics. As a subset of evaluated samples have been previously submitted for Sanger sequencing of the control region, a comparative analysis of both methods' results was conducted in order to compare technique adequacy within a forensic context. Even though this study is one of the first to report full mtDNA genome sequences for Brazilian admixed populations, the observed haplotypes exhibit a predominance of Native American and African maternal lineages in the studied sample set, reproducing results described in the literature for control regions only. Interpopulation analysis among Brazilian and 26 worldwide populations was also carried out. The results indicate that MPS-generated full mtDNA genome sequences may have great utility in forensic real casework applications, with a pronounced gain of genetic information and discrimination power provided by coding region evaluation and the enhanced capacity of heteroplasmies determination. Database construction and other relevant factors concerning implementation of such techniques in Brazilian forensic laboratories are also discussed.
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Affiliation(s)
- E Avila
- Setor Técnico-Científico, Superintendência Regional do Rio Grande do Sul, Polícia Federal, Porto Alegre, Brazil; Escola de Ciências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil; Instituto Nacional de Ciência e Tecnologia INCT Ciências Forenses, Porto Alegre, Brazil.
| | - P Graebin
- Escola de Ciências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - G Chemale
- Setor Técnico-Científico, Superintendência Regional do Rio Grande do Sul, Polícia Federal, Porto Alegre, Brazil
| | - J Freitas
- Instituto Nacional de Criminalística, Polícia Federal, Brasília, DF, Brazil
| | - A Kahmann
- Instituto de Matemática, Estatística e Física, Universidade Federal de Rio Grande, Rio Grande, Brazil
| | - C S Alho
- Escola de Ciências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil; Instituto Nacional de Ciência e Tecnologia INCT Ciências Forenses, Porto Alegre, Brazil
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34
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Zavala EI, Rajagopal S, Perry GH, Kruzic I, Bašić Ž, Parsons TJ, Holland MM. Impact of DNA degradation on massively parallel sequencing-based autosomal STR, iiSNP, and mitochondrial DNA typing systems. Int J Legal Med 2019; 133:1369-1380. [PMID: 31267160 DOI: 10.1007/s00414-019-02110-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 06/19/2019] [Indexed: 10/26/2022]
Abstract
Biological samples, including skeletal remains exposed to environmental insults for extended periods of time, exhibit increasing levels of DNA damage and fragmentation. Human forensic identification methods typically use a combination of mitochondrial (mt) DNA sequencing and short tandem repeat (STR) analysis, which target segments of DNA ranging from 80 to 500 base pairs (bps). Larger templates are often unavailable as skeletal samples age and the associated DNA degrades. Single-nucleotide polymorphism (SNP) loci target shorter templates and may serve as a solution to the problem. Recently developed assays for STR and SNP analysis using a massively parallel sequencing approach, such as the ForenSeq kit (Verogen, San Diego, CA), offer a means for generating results from degraded samples as they target templates down to 60 to 170 bps. We performed a modeling study that demonstrates that SNPs can increase the significance of an identification when analyzing DNA down to an average size of 100 bps for input amounts between 0.375 and 1 ng of nuclear DNA. Observations from this study were then compared with human skeletal material results (n = 14, ninth to eighteenth centuries), which further demonstrated the utility of the ForenSeq kit for degraded samples. The robustness of the Promega PowerSeq™ Mito System was also tested with human skeletal remains (n = 70, ninth to eighteenth centuries), resulting in successful coverage of 99.29% of the mtDNA control region at 50× coverage or more. This was accompanied by modifications to a mainstream DNA extraction technique for skeletal remains that improved recovery of shorter templates.
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Affiliation(s)
- Elena I Zavala
- Department of Biochemistry and Molecular Biology, Forensic Science Program, Pennsylvania State University, State College, PA, USA.
| | - Swetha Rajagopal
- Department of Biochemistry and Molecular Biology, Forensic Science Program, Pennsylvania State University, State College, PA, USA.,Department of Forensic Science, John Jay College of Criminal Justice, New York, NY, USA
| | - George H Perry
- Departments of Anthropology and Biology, Pennsylvania State University, State College, PA, USA
| | - Ivana Kruzic
- University Department of Forensic Sciences, University of Split, Split, Croatia
| | - Željana Bašić
- University Department of Forensic Sciences, University of Split, Split, Croatia
| | - Thomas J Parsons
- International Commission on Missing Persons, The Hague, Netherlands
| | - Mitchell M Holland
- Department of Biochemistry and Molecular Biology, Forensic Science Program, Pennsylvania State University, State College, PA, USA
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35
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Xavier C, Eduardoff M, Strobl C, Parson W. SD quants-Sensitive detection tetraplex-system for nuclear and mitochondrial DNA quantification and degradation inference. Forensic Sci Int Genet 2019; 42:39-44. [PMID: 31216503 DOI: 10.1016/j.fsigen.2019.06.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/06/2019] [Accepted: 06/07/2019] [Indexed: 01/05/2023]
Abstract
Measuring the quantity of DNA present in a forensic sample is relevant in a number of ways. First, it informs the analyst about the general DNA content to adjust the volume of DNA extract used for the genotyping assay to the optimal conditions (when possible). Second, quantification values can serve as plausibility checks for the performance of the DNA extraction method used as extraction positive and negative controls demand expected values. Third and relevant to highly compromised specimens, DNA quantification can inform about the degradation state of the DNA extracted from the unknown biological sample and aid the choice of downstream genotyping assays. While there are different, commercial products for the quantification of nuclear DNA available, commercial mitochondrial DNA (mtDNA) quantification systems are rare. Even more so, the simultaneous quantification of nuclear and mtDNA that is of relevance in highly degraded forensic specimens has rarely been described. We present here a novel real-time qPCR based tetraplex system termed SD quants that targets two different-sized mtDNA and a nuclear DNA region and includes an internal positive control to monitor potential inhibition. SD quants was compared to other existing quantification systems and subjected to analysis of severely degraded DNA present in ancient DNA and aged forensic specimens. This study complies with the MIQE (Bustin et al., 2009) guidelines (when applicable).
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Affiliation(s)
- Catarina Xavier
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria.
| | - Mayra Eduardoff
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Christina Strobl
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, University Park, PA, USA
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36
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Jiang E, Zhang S, Pang H. Genotyping genetic markers from LCN and degraded DNA by HRM and their application in hair shaft. Int J Legal Med 2019; 134:31-37. [PMID: 31062081 DOI: 10.1007/s00414-019-02045-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 03/18/2019] [Indexed: 01/13/2023]
Abstract
Degraded and low copy number (LCN) DNA samples are common challenging materials in forensic casework because they increase the difficulty of sample processing and reduce the possibility of obtaining genetic information from DNA. High-resolution melting (HRM) curve analysis is promising for genotyping genetic markers and has been applied to the detection of LCN and degraded DNA in the field of forensic science. However, the exact assessment based on HRM at multiple genetic markers from both degraded and LCN DNA materials has not been optimized. To explore the ability of HRM to genotype LCN and degraded DNA samples, we selected three genetic markers to genotype in experimental LCN and degraded DNA and practical hair shaft materials, which are often encountered as degraded and LCN DNA in forensic medicine. The results show that DNA samples of as low as 100 pg and as short as 60 bp were successfully genotyped by the HRM assay at all three genetic markers, whereas in hair shaft DNA, two loci were accurately genotyped. The HRM assay established in this study can be applied to LCN and degraded DNA analysis in forensic casework and can act as a reference point before genotyping short tandem repeat markers. Developing the HRM strategy for genotyping DNA genetic markers enriches detectable targets in hair shaft samples and provides valuable data for further exploration.
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Affiliation(s)
- Enzhu Jiang
- Department of Forensic Genetics and Biology, School of Forensic Medicine, China Medical University, No.77 Puhe Road, Shenyang North New Area, Shenyang, 110122, People's Republic of China
| | - Siyi Zhang
- Department of Forensic Genetics and Biology, School of Forensic Medicine, China Medical University, No.77 Puhe Road, Shenyang North New Area, Shenyang, 110122, People's Republic of China
| | - Hao Pang
- Department of Forensic Genetics and Biology, School of Forensic Medicine, China Medical University, No.77 Puhe Road, Shenyang North New Area, Shenyang, 110122, People's Republic of China.
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37
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Young JM, Martin B, Linacre A. Evaluation of the QIAGEN 140-SNP forensic identification multiplex from latent DNA using massively parallel sequencing. AUST J FORENSIC SCI 2019. [DOI: 10.1080/00450618.2019.1573923] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- J. M. Young
- College of Science & Engineering, Flinders University, Adelaide, Australia
| | - B. Martin
- College of Science & Engineering, Flinders University, Adelaide, Australia
| | - A. Linacre
- College of Science & Engineering, Flinders University, Adelaide, Australia
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38
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Holland MM, Bonds RM, Holland CA, McElhoe JA. Recovery of mtDNA from unfired metallic ammunition components with an assessment of sequence profile quality and DNA damage through MPS analysis. Forensic Sci Int Genet 2018; 39:86-96. [PMID: 30611826 DOI: 10.1016/j.fsigen.2018.12.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 11/27/2018] [Accepted: 12/19/2018] [Indexed: 12/14/2022]
Abstract
Recovery of suitable amounts of quality DNA from copper and brass surfaces, like those encountered in ammunition, has been a challenge for the forensic community. The ability of copper ions to rapidly facilitate oxidative damage leading to fragmentation of DNA significantly reduces the pool of templates for PCR amplification. We compared two methods for recovering mitochondrial (mt) DNA from the surface of unfired copper projectiles, brass casings, and aluminum casings, and found that using a cotton swab moistened with 0.5M EDTA was the favored approach, especially when the metallic surface was etched. Degradation was significantly higher for DNA samples recovered from copper and brass surfaces, when compared to aluminum. Massively parallel sequencing (MPS) of the control region, using the PowerSeq™ CRM Nested System kit and the Illumina MiSeq instrument, produced full haplotypes for aluminum samples regardless of the method used to deposit or collect DNA, while less than 60% of the copper and brass samples produced partial or full profile information. Touch DNA collected from copper and brass samples produced higher rates of partial or full MPS profile information (∼88-96%), while collection with 0.5M EDTA produced better results than when collection was performed with water; average of ∼70% versus ∼47%. While MPS data was not impacted by noise in the sequencing process, a higher than expected rate of noise was observed, potentially due to an increase in low-level damage lesions. Noise patterns were strikingly different when compared to control data, suggesting that noisy sites may be predictable when testing samples with high levels of oxidative damage. Library preparation was a poor predictor of MPS data quality, as a large percentage of reads did not align with the reference genome. This may impact the number of samples that can be run when a deep-coverage MPS approach is being considered for analysis of mtDNA heteroplasmy. Overall, when applying an MPS approach to the analysis of mtDNA recovered from ammunition, results are expected from touch DNA, will be limited for copper and brass components when the DNA is exposed to an aqueous environment, and DNA degradation will be accelerated when DNA comes in contact with copper or brass surfaces. Practitioners should consider collecting DNA from metallic surfaces with 0.5M EDTA, as this will maximize yield and mitigate degradation. The results of this study directly impact MPS analysis of minor mtDNA sequence variants from metallic surfaces, and are particularly relevant to forensic investigations.
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Affiliation(s)
- Mitchell M Holland
- Forensic Science Program, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, 014 Thomas Building, University Park, PA, 16802, United States.
| | - Rachel M Bonds
- Forensic Science Program, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, 014 Thomas Building, University Park, PA, 16802, United States
| | - Charity A Holland
- Forensic Science Program, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, 014 Thomas Building, University Park, PA, 16802, United States
| | - Jennifer A McElhoe
- Forensic Science Program, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, 014 Thomas Building, University Park, PA, 16802, United States
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39
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Brandhagen MD, Loreille O, Irwin JA. Fragmented Nuclear DNA is the Predominant Genetic Material in Human Hair Shafts. Genes (Basel) 2018; 9:genes9120640. [PMID: 30567392 PMCID: PMC6316335 DOI: 10.3390/genes9120640] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 12/03/2018] [Accepted: 12/10/2018] [Indexed: 01/18/2023] Open
Abstract
While shed hairs are one of the most commonly encountered evidence types, they are among the most limited in terms of DNA quantity and quality. As a result, nuclear DNA short tandem repeat (STR) profiling is generally unsuccessful and DNA testing of shed hair is instead performed by targeting the mitochondrial DNA control region. Although the high copy number of mitochondrial DNA relative to nuclear DNA routinely permits the recovery of mitochondrial DNA (mtDNA) data in these cases, mtDNA profiles do not offer the discriminatory power of nuclear DNA profiles. In order to better understand the total content and degradation state of DNA in single shed hairs and assess the feasibility of recovering highly discriminatory nuclear DNA data from this common evidence type, high throughput shotgun sequencing was performed on both recently collected and aged (approximately 50-year-old) hair samples. The data reflect trends that have been demonstrated previously with other technologies, namely that mtDNA quantity and quality decrease along the length of the hair shaft. In addition, the shotgun data reveal that nuclear DNA is present in shed hair and surprisingly abundant relative to mitochondrial DNA, even in the most distal fragments. Nuclear DNA comprised, at minimum, 88% of the total human reads in any given sample, and generally more than 95%. Here, we characterize both the nuclear and mitochondrial DNA content of shed hairs and discuss the implications of these data for forensic investigations.
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Affiliation(s)
- Michael D Brandhagen
- DNA Support Unit, FBI Laboratory, 2501 Investigation Parkway, Quantico, VA 22135, USA.
| | - Odile Loreille
- DNA Support Unit, FBI Laboratory, 2501 Investigation Parkway, Quantico, VA 22135, USA.
| | - Jodi A Irwin
- DNA Support Unit, FBI Laboratory, 2501 Investigation Parkway, Quantico, VA 22135, USA.
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40
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Current and emerging tools for the recovery of genetic information from post mortem samples: New directions for disaster victim identification. Forensic Sci Int Genet 2018; 37:270-282. [DOI: 10.1016/j.fsigen.2018.08.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 08/27/2018] [Accepted: 08/27/2018] [Indexed: 01/14/2023]
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41
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Ring JD, Sturk-Andreaggi K, Alyse Peck M, Marshall C. Bioinformatic removal of NUMT-associated variants in mitotiling next-generation sequencing data from whole blood samples. Electrophoresis 2018; 39:2785-2797. [DOI: 10.1002/elps.201800135] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 07/16/2018] [Accepted: 08/16/2018] [Indexed: 11/05/2022]
Affiliation(s)
- Joseph David Ring
- Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL); DE United States
- ARP Sciences, LLC; Rockville MD United States
| | - Kimberly Sturk-Andreaggi
- Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL); DE United States
- ARP Sciences, LLC; Rockville MD United States
| | - Michelle Alyse Peck
- Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL); DE United States
- ARP Sciences, LLC; Rockville MD United States
| | - Charla Marshall
- Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL); DE United States
- ARP Sciences, LLC; Rockville MD United States
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42
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Kavlick MF. Development of a triplex mtDNA qPCR assay to assess quantification, degradation, inhibition, and amplification target copy numbers. Mitochondrion 2018; 46:41-50. [PMID: 30261278 DOI: 10.1016/j.mito.2018.09.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 05/11/2018] [Accepted: 09/18/2018] [Indexed: 01/11/2023]
Abstract
A hybrid absolute/relative qPCR assay which provides information regarding the condition of mitochondrial DNA (mtDNA) in a DNA sample is described. MtDNA concentration (copy number/μL) is determined via absolute quantification using a standard curve of a synthetic duplex DNA previously described (Kavlick et al., 2011). The state of mtDNA degradation is determined via the relative quantification of a mtDNA target found within the 16 s rRNA gene which is 3× longer than that of the short target in the former duplex assay, using the delta, delta Ct (ΔΔCt) method. The presence or absence of PCR inhibitors in the sample is qualitatively determined using a custom internal positive control (IPC) system which targets a unique and non-naturally occurring duplex DNA sequence. This IPC effectively detected inhibition by humic acid, tannic acid, melanin, and EDTA. All three assay components utilize sensitive and specific hydrolysis probes. The utility of ΔΔCt method was demonstrated in a series of experiments involving laboratory-fragmented DNA. Also described is a method for estimating copy number of any mtDNA target longer than the two targets amplified. The described triplex assay works well for intact and for fragmented or degraded mtDNA and therefore may be useful in forensic and ancient DNA disciplines as well as in biomedical research or practice.
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Affiliation(s)
- Mark F Kavlick
- Counterterrorism and Forensic Science Research Unit, Laboratory Division, Federal Bureau of Investigation, 2501 Investigation Parkway, Quantico, VA 22135, United States.
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43
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King JL, Churchill JD, Novroski NM, Zeng X, Warshauer DH, Seah LH, Budowle B. Increasing the discrimination power of ancestry- and identity-informative SNP loci within the ForenSeq™ DNA Signature Prep Kit. Forensic Sci Int Genet 2018; 36:60-76. [DOI: 10.1016/j.fsigen.2018.06.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 05/03/2018] [Accepted: 06/05/2018] [Indexed: 11/26/2022]
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44
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Recovery of whole mitochondrial genome from compromised samples via multiplex PCR and massively parallel sequencing. Future Sci OA 2018; 4:FSO336. [PMID: 30416745 PMCID: PMC6222269 DOI: 10.4155/fsoa-2018-0059] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 07/16/2018] [Indexed: 01/26/2023] Open
Abstract
In forensic casework, compromised samples often possess limited or degraded nuclear DNA, rendering mitochondrial DNA a more feasible option for forensic DNA analyses. The emergence of massively parallel sequencing (MPS) has enabled the recovery of extensive sequence information from very low quantities of DNA. We have developed a multiplex PCR method that amplifies the complete mitochondrial genome in a range of forensically relevant samples including single cells, cremated remains, bone, maggot and hairs isolated from dust bunnies. Following library preparation, MPS yields complete or nearly complete mitochondrial genome coverage for all samples. To confirm concordance between sample types and between sequencing platforms, we compared sequencing results from hair and buccal swabs from two references. Low initial DNA input into the multiplex PCR allows for conservation of precious DNA while MPS maximizes recovery of genetic information. Compromised samples are routine in forensic casework, and evidence DNA is often limited and/or degraded. Mitochondrial DNA is often a suitable option for forensic analysis as it is available in multiple copies per cell. We have established a method that amplifies the complete mitochondrial genome in a range of compromised samples and utilizes new high-throughput sequencing technologies to recover maximal genetic information from a small amount of sample. Combination of the aforementioned amplification method and high-throughput sequencing allows the analyst to conserve DNA in forensic cases where DNA is often limited.
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45
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Bulbul O, Filoglu G. Development of a SNP panel for predicting biogeographical ancestry and phenotype using massively parallel sequencing. Electrophoresis 2018; 39:2743-2751. [DOI: 10.1002/elps.201800243] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 07/18/2018] [Accepted: 07/23/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Ozlem Bulbul
- Institute of Forensic Science; Istanbul University; Istanbul Turkey
| | - Gonul Filoglu
- Institute of Forensic Science; Istanbul University; Istanbul Turkey
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46
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Pereira V, Longobardi A, Børsting C. Sequencing of mitochondrial genomes using the Precision ID mtDNA Whole Genome Panel. Electrophoresis 2018; 39:2766-2775. [DOI: 10.1002/elps.201800088] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 06/26/2018] [Accepted: 07/19/2018] [Indexed: 02/06/2023]
Affiliation(s)
- Vania Pereira
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences; University of Copenhagen; Copenhagen Denmark
| | - Antonio Longobardi
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences; University of Copenhagen; Copenhagen Denmark
| | - Claus Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences; University of Copenhagen; Copenhagen Denmark
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47
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Zhang QX, Yang M, Pan YJ, Zhao J, Qu BW, Cheng F, Yang YR, Jiao ZP, Liu L, Yan JW. Development of a massively parallel sequencing assay for investigating sequence polymorphisms of 15 short tandem repeats in a Chinese Northern Han population. Electrophoresis 2018; 39:2725-2731. [DOI: 10.1002/elps.201800071] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 04/11/2018] [Accepted: 05/07/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Qing-Xia Zhang
- Forensic Science Service; Beijing Public Security Bureau; Beijing P. R. China
| | - Meng Yang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics; Chinese Academy of Sciences; Beijing P. R. China
| | | | - Jing Zhao
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics; Chinese Academy of Sciences; Beijing P. R. China
- University of Chinese Academy of Sciences; Beijing P. R. China
| | | | - Feng Cheng
- College of forensic medicine; Shanxi Medical University; Taiyuan P. R. China
| | - Ya-Ran Yang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics; Chinese Academy of Sciences; Beijing P. R. China
| | - Zhang-Ping Jiao
- Forensic Science Service; Beijing Public Security Bureau; Beijing P. R. China
| | - Li Liu
- Forensic Science Service; Beijing Public Security Bureau; Beijing P. R. China
- College of forensic medicine; Shanxi Medical University; Taiyuan P. R. China
| | - Jiang-Wei Yan
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics; Chinese Academy of Sciences; Beijing P. R. China
- University of Chinese Academy of Sciences; Beijing P. R. China
- College of forensic medicine; Shanxi Medical University; Taiyuan P. R. China
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48
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Gorden EM, Sturk-Andreaggi K, Marshall C. Repair of DNA damage caused by cytosine deamination in mitochondrial DNA of forensic case samples. Forensic Sci Int Genet 2018; 34:257-264. [DOI: 10.1016/j.fsigen.2018.02.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 02/01/2018] [Accepted: 02/17/2018] [Indexed: 01/14/2023]
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49
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Evaluation of the precision ID whole MtDNA genome panel for forensic analyses. Forensic Sci Int Genet 2018; 35:21-25. [PMID: 29626805 DOI: 10.1016/j.fsigen.2018.03.013] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Revised: 02/20/2018] [Accepted: 03/28/2018] [Indexed: 12/18/2022]
Abstract
Mitochondrial DNA (mtDNA) amplification and Massively Parallel Sequencing (MPS) using an early access version of the Precision ID Whole MtDNA Genome Panel (Thermo Fisher Scientific) and the Ion Personal Genome Machine (PGM) were evaluated using 15 forensically relevant samples. Samples were selected to represent typical forensic specimens for mtDNA analysis including hairs, hair shafts, swabs and ancient solid tissue samples (bones and teeth) that were stored in the freezer for up to several years after having been typed with conventional Sanger-type Sequencing and Capillary Electrophoresis. The MPS haplotypes confirmed the earlier results in all samples and provided additional sequence information that improved discrimination power and haplogroup estimation. The results raised the appetite for further experiments to validate and apply the new technology in forensic practice.
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50
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Yao L, Xu Z, Zhao H, Tu Z, Liu Z, Li W, Hu L, Wan L. Concordance of mitochondrial DNA sequencing methods on bloodstains using Ion PGM™. Leg Med (Tokyo) 2018; 32:27-30. [PMID: 29499472 DOI: 10.1016/j.legalmed.2018.02.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 12/03/2017] [Accepted: 02/23/2018] [Indexed: 11/28/2022]
Abstract
In this study, the complete mitochondrial genome (mtGenome) of six samples from three forensic cases was sequenced using the Ion Torrent Personal Genome Machine (PGM). The analyzed samples from forensic cases included bloodstains from several materials, such as gauze, Flinder's Technology Associates (FTA) cards and swabs. The age of the samples ranged from two months to twelve years. The complete mtGenomes were amplified using the tiling sequencing strategy which divided the whole mtGenome into 162 amplicons. All amplicons were successfully recovered. A phylogenetic analysis was performed to determine the accuracy of the PGM data, and which were compared to partial Sanger-based sequencing data. The average coverage of the PGM data were above 4000× in all case samples, and 99.86% concordance was observed using both sequencing methods. In conclusion, we demonstrate the ability to recover the complete mtGenome from bloodstains with relatively poor DNA quality by PGM. Moreover, the results are concordant with Sanger sequencing data. This new method has potential use in forensic practice.
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Affiliation(s)
- Lan Yao
- College of Basic Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Zhen Xu
- Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing 100038, PR China
| | - Hemiao Zhao
- Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing 100038, PR China
| | - Zheng Tu
- Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing 100038, PR China
| | - Zhifang Liu
- Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing 100038, PR China
| | - Wanshui Li
- Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing 100038, PR China
| | - Lan Hu
- Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing 100038, PR China
| | - Lihua Wan
- College of Basic Medicine, Chongqing Medical University, Chongqing 400016, PR China.
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