1
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Chiao A, Ge J. Determining lineages between individuals with high-density mitochondrial and Y-chromosomal single-nucleotide polymorphisms. Electrophoresis 2024; 45:843-851. [PMID: 38010138 DOI: 10.1002/elps.202300142] [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: 06/29/2023] [Revised: 10/19/2023] [Accepted: 11/12/2023] [Indexed: 11/29/2023]
Abstract
Genetic genealogy has been more frequently used in forensic investigations in identifying criminals. However, the current genetic genealogy applications usually do not consider lineage markers (including both Y and mitochondrial deoxyribonucleic acid (DNA)), which is probably because not all distant relatives share the same lineage markers. In addition, there is no study to show how to use lineage markers and what methods or thresholds should be applied in genetic genealogy. In this study, we developed a method to quickly determine if two single-nucleotide polymorphism (SNP) profiles are from the same paternal or material lineages by using a mismatch frequency of the SNPs in Y-chromosomal or mitochondrial DNA. For both Y and mitochondrial SNPs, profile pairs from the same or different lineages can be decided with high accuracies (i.e., 0.380% or 0.157% error rates with Y and mitochondrial DNA, respectively). With kinship coefficient filtering based on autosomal SNPs, the accuracies of determining maternal and paternal lineage can be further improved (i.e., 0.120% or 0.057% error rates with Y and mitochondrial DNA, respectively, using a threshold of kinship coefficient >0). This study shows that lineage markers can be very powerful tools with high accuracies to determine lineages, which could help solve cases and reduce costs for genetic genealogy investigations.
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Affiliation(s)
- Austin Chiao
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, Texas, USA
- Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Jianye Ge
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, Texas, USA
- Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, Texas, USA
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2
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McDonald C, Taylor D, Linacre A. PCR in Forensic Science: A Critical Review. Genes (Basel) 2024; 15:438. [PMID: 38674373 PMCID: PMC11049589 DOI: 10.3390/genes15040438] [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: 03/07/2024] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
The polymerase chain reaction (PCR) has played a fundamental role in our understanding of the world, and has applications across a broad range of disciplines. The introduction of PCR into forensic science marked the beginning of a new era of DNA profiling. This era has pushed PCR to its limits and allowed genetic data to be generated from trace DNA. Trace samples contain very small amounts of degraded DNA associated with inhibitory compounds and ions. Despite significant development in the PCR process since it was first introduced, the challenges of profiling inhibited and degraded samples remain. This review examines the evolution of the PCR from its inception in the 1980s, through to its current application in forensic science. The driving factors behind PCR evolution for DNA profiling are discussed along with a critical comparison of cycling conditions used in commercial PCR kits. Newer PCR methods that are currently used in forensic practice and beyond are examined, and possible future directions of PCR for DNA profiling are evaluated.
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Affiliation(s)
- Caitlin McDonald
- College of Science & Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia; (C.M.); (A.L.)
| | - Duncan Taylor
- College of Science & Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia; (C.M.); (A.L.)
- Forensic Science SA, GPO Box 2790, Adelaide, SA 5001, Australia
| | - Adrian Linacre
- College of Science & Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia; (C.M.); (A.L.)
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3
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Naue J, Xavier C, Hörer S, Parson W, Lutz-Bonengel S. Assessment of mitochondrial DNA copy number variation relative to nuclear DNA quantity between different tissues. Mitochondrion 2024; 74:101823. [PMID: 38040171 DOI: 10.1016/j.mito.2023.11.006] [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: 08/17/2023] [Revised: 10/23/2023] [Accepted: 11/26/2023] [Indexed: 12/03/2023]
Abstract
Mitochondrial DNA is a widely tested genetic marker in various fields of research and diagnostics. Nonetheless, there is still little understanding on its abundance and quality within different tissues. Aiming to obtain deeper knowledge about the content and quality of mtDNA, we investigated nine tissues including blood, bone, brain, hair (root and shaft), cardiac muscle, liver, lung, skeletal muscle, and buccal mucosa of 32 deceased individuals using two real-time quantitative PCR-based assays with differently sized mtDNA and nDNA targets. The results revealed that the quantity of nDNA is a weak surrogate to estimate mtDNA quantities among tissues of an individual, as well as tissues across individuals. Especially hair showed extreme variation, depicting a range of multiple magnitudes of mtDNA molecules per hair fragment. Furthermore, degradation can lead to fewer fragments being available for PCR. The results call for parallel determination of the quantity and quality of mtDNA prior to downstream genotyping assays.
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Affiliation(s)
- Jana Naue
- Institute of Forensic Medicine, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Albertstrasse 9, Freiburg 79104, Germany
| | - Catarina Xavier
- Institute of Legal Medicine, Medical University of Innsbruck, Muellerstrasse 44, Innsbruck 6020, Austria; i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal
| | - Steffen Hörer
- Institute of Forensic Medicine, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Albertstrasse 9, Freiburg 79104, Germany
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Muellerstrasse 44, Innsbruck 6020, Austria; Forensic Science Program, The Pennsylvania State University, USA.
| | - Sabine Lutz-Bonengel
- Institute of Forensic Medicine, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Albertstrasse 9, Freiburg 79104, Germany
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4
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Panneerchelvam S, Norazmi MN. DNA Profiling in Human Identification: From Past to Present. Malays J Med Sci 2023; 30:5-21. [PMID: 38239252 PMCID: PMC10793127 DOI: 10.21315/mjms2023.30.6.2] [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] [Received: 04/27/2022] [Accepted: 12/02/2022] [Indexed: 01/22/2024] Open
Abstract
Forensic DNA typing has been widely accepted in the courts all over the world. This is because DNA profiling is a very powerful tool to identify individuals on the basis of their unique genetic makeup. DNA evidence is capable of not only identifying the presence of specific biospecimens in a crime scene, but it is also used to exonerate suspects who are innocent of a crime. Technological advancements in DNA profiling, including the development of validated kits and statistical methods have made this tool to be more precise in forensic investigations. Therefore, validated combined DNA index system (CODIS) short tandem repeats (STRs) kits which require very small amount of DNA, coupled with real-time polymerase chain reaction (PCR) and the statistical strengths are used routinely to identify human remains, establish paternity or to match suspected crime scene biospecimens. The road to modern DNA profiling has been long, and it has taken scientists decades of work and fine tuning to develop highly accurate testing and analyses that are used today. This review will discuss the various DNA polymorphisms and their utility in human identity testing.
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Affiliation(s)
| | - Mohd Nor Norazmi
- School of Health Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
- Malaysia Genome and Vaccine Institute, National Institutes of Biotechnology Malaysia, Selangor, Malaysia
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Liu G, Zheng Y, Wu Q, Feng T, Xia Y, Chen D, Ren L, Bai X, Li Q, Chen D, Lv M, Liao M, Liang W, Zhang L, Qu S. Assessment of ForenSeq mtDNA Whole Genome Kit for forensic application. Int J Legal Med 2023; 137:1693-1703. [PMID: 37731065 DOI: 10.1007/s00414-023-03084-0] [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: 07/14/2023] [Accepted: 09/07/2023] [Indexed: 09/22/2023]
Abstract
Mitochondrial DNA (mtDNA) is an indispensable genetic marker in forensic genetics. The emergence and development of massively parallel sequencing (MPS) makes it possible to obtain complete mitochondrial genome sequences more quickly and accurately. The study evaluated the advantages and limitations of the ForenSeq mtDNA Whole Genome Kit in the practical application of forensic genetics by detecting human genomic DNA standards and thirty-three case samples. We used control DNA with different amount to determine sensitivity of the assay. Even when the input DNA is as low as 2.5 pg, most of the mitochondrial genome sequences could still be covered. For the detection of buccal swabs and aged case samples (bloodstains, bones, teeth), most samples could achieve complete coverage of mitochondrial genome. However, when ancient samples and hair samples without hair follicles were sequenced by the kit, it failed to obtain sequence information. In general, the ForenSeq mtDNA Whole Genome Kit has certain applicability to forensic low template and degradation samples, and these results provide the data basis for subsequent forensic applications of the assay. The overall detection process and subsequent analysis are easy to standardize, and it has certain application potential in forensic cases.
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Affiliation(s)
- Guihong Liu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Yazi Zheng
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Qiushuo Wu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Tao Feng
- Criminal Investigation Bureau, Chengdu Public Security Bureau, Criminal Science and Technology Division, Chengdu, 610000, Sichuan, China
| | - Yu Xia
- Criminal Investigation Bureau, Chengdu Public Security Bureau, Criminal Science and Technology Division, Chengdu, 610000, Sichuan, China
| | - Dan Chen
- Criminal Investigation Bureau, Chengdu Public Security Bureau, Criminal Science and Technology Division, Chengdu, 610000, Sichuan, China
| | - Li Ren
- Criminal Investigation Bureau, Chengdu Public Security Bureau, Criminal Science and Technology Division, Chengdu, 610000, Sichuan, China
| | - Xiaogang Bai
- Criminal Investigation Bureau, Chengdu Public Security Bureau, Criminal Science and Technology Division, Chengdu, 610000, Sichuan, China
| | - Qingqing Li
- Criminal Investigation Bureau, Chengdu Public Security Bureau, Criminal Science and Technology Division, Chengdu, 610000, Sichuan, China
| | - Dezhi Chen
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Meili Lv
- Department of Immunology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Miao Liao
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Weibo Liang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Lin Zhang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China.
| | - Shengqiu Qu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China.
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Patterson EC, Lall GM, Neumann R, Ottolini B, Sacchini F, Foster AP, Jobling MA, Wetton JH. Defining cat mitogenome variation and accounting for numts via multiplex amplification and Nanopore sequencing. Forensic Sci Int Genet 2023; 67:102944. [PMID: 37820546 DOI: 10.1016/j.fsigen.2023.102944] [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: 06/24/2023] [Revised: 09/14/2023] [Accepted: 10/04/2023] [Indexed: 10/13/2023]
Abstract
Hair shed by domestic cats is a potentially useful source of forensic evidence. Analysable hair DNA is predominantly mitochondrial, but the recent domestication history of cats means that mtDNA diversity is low. A 402-bp control region segment is usually sequenced, defining only a small number of distinct haplotypes in populations. Previously, we used a long-amplicon approach to sequence whole mitogenomes in a sample of blood DNAs from 119 UK cats, greatly increasing observed diversity and reducing random match probabilities. To exploit this variation for forensic analysis, we here describe a multiplex system that amplifies the cat mitogenome in 60 overlapping amplicons of mean length 360 bp, followed by Nanopore sequencing. Variants detected in multiplex sequence data from unrooted hair completely mirror those from long-amplicon data from blood from the same individuals. However, applying the multiplex to matched blood DNA reveals additional sequence variants which derive from the major feline nuclear mitochondrial insertion sequence (numt), which covers 7.9 kb of the 17-kb mitogenome and exists in multiple tandem copies. We use long-amplicon Nanopore sequencing to investigate numt variation in a set of cats, together with an analysis of published genome sequences, and show that numt arrays are variable in both structure and sequence, thus providing a potential source of uncertainty when nuclear DNA predominates in a sample. Forensic application of the multiplex was demonstrated by matching hairs from a cat with skeletal remains from its putative mother, both of which shared a globally common haplotype at the control region. The random match probability in this case with the CR 402-bp segment was 0.21 and this decreased to 0.03 when considering the whole mitogenome. The developed multiplex and sequencing approach, when applied to cat hair where nuclear DNA is scarce, can provide a reliable and highly discriminating source of forensic genetic evidence from a single hair. The confounding effect of numt co-amplification in degraded samples where mixed sequences are observed can be mitigated by variant phasing, and by comparison with numt sequence diversity data, such as those presented here.
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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
| | - 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, North Somerset BS40 5DU, UK
| | - Mark A Jobling
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester LE1 7RH UK.
| | - Jon H Wetton
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester LE1 7RH UK.
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Mahar NS, Satyam R, Sundar D, Gupta I. A systematic comparison of human mitochondrial genome assembly tools. BMC Bioinformatics 2023; 24:341. [PMID: 37704952 PMCID: PMC10498642 DOI: 10.1186/s12859-023-05445-3] [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: 01/25/2023] [Accepted: 08/14/2023] [Indexed: 09/15/2023] Open
Abstract
BACKGROUND Mitochondria are the cell organelles that produce most of the chemical energy required to power the cell's biochemical reactions. Despite being a part of a eukaryotic host cell, the mitochondria contain a separate genome whose origin is linked with the endosymbiosis of a prokaryotic cell by the host cell and encode independent genomic information throughout their genomes. Mitochondrial genomes accommodate essential genes and are regularly utilized in biotechnology and phylogenetics. Various assemblers capable of generating complete mitochondrial genomes are being continuously developed. These tools often use whole-genome sequencing data as an input containing reads from the mitochondrial genome. Till now, no published work has explored the systematic comparison of all the available tools for assembling human mitochondrial genomes using short-read sequencing data. This evaluation is required to identify the best tool that can be well-optimized for small-scale projects or even national-level research. RESULTS In this study, we have tested the mitochondrial genome assemblers for both simulated datasets and whole genome sequencing (WGS) datasets of humans. For the highest computational setting of 16 computational threads with the simulated dataset having 1000X read depth, MitoFlex took the least execution time of 69 s, and IOGA took the longest execution time of 1278 s. NOVOPlasty utilized the least computational memory of approximately 0.098 GB for the same setting, whereas IOGA utilized the highest computational memory of 11.858 GB. In the case of WGS datasets for humans, GetOrganelle and MitoFlex performed the best in capturing the SNPs information with a mean F1-score of 0.919 at the sequencing depth of 10X. MToolBox and NOVOPlasty performed consistently across all sequencing depths with a mean F1 score of 0.897 and 0.890, respectively. CONCLUSIONS Based on the overall performance metrics and consistency in assembly quality for all sequencing data, MToolBox performed the best. However, NOVOPlasty was the second fastest tool in execution time despite being single-threaded, and it utilized the least computational resources among all the assemblers when tested on simulated datasets. Therefore, NOVOPlasty may be more practical when there is a significant sample size and a lack of computational resources. Besides, as long-read sequencing gains popularity, mitochondrial genome assemblers must be developed to use long-read sequencing data.
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Affiliation(s)
- Nirmal Singh Mahar
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi, 110016, India
| | - Rohit Satyam
- Jamia Millia Islamia, Jamia Nagar, Okhla, New Delhi, 110025, India
| | - Durai Sundar
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi, 110016, India
| | - Ishaan Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi, 110016, India.
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8
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Hernández CL. Mitochondrial DNA in Human Diversity and Health: From the Golden Age to the Omics Era. Genes (Basel) 2023; 14:1534. [PMID: 37628587 PMCID: PMC10453943 DOI: 10.3390/genes14081534] [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: 06/19/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
Mitochondrial DNA (mtDNA) is a small fraction of our hereditary material. However, this molecule has had an overwhelming presence in scientific research for decades until the arrival of high-throughput studies. Several appealing properties justify the application of mtDNA to understand how human populations are-from a genetic perspective-and how individuals exhibit phenotypes of biomedical importance. Here, I review the basics of mitochondrial studies with a focus on the dawn of the field, analysis methods and the connection between two sides of mitochondrial genetics: anthropological and biomedical. The particularities of mtDNA, with respect to inheritance pattern, evolutionary rate and dependence on the nuclear genome, explain the challenges of associating mtDNA composition and diseases. Finally, I consider the relevance of this single locus in the context of omics research. The present work may serve as a tribute to a tool that has provided important insights into the past and present of humankind.
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Affiliation(s)
- Candela L Hernández
- Department of Biodiversity, Ecology and Evolution, Faculty of Biological Sciences, Complutense University of Madrid, 28040 Madrid, Spain
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Rubin JD, Vogel NA, Gopalakrishnan S, Sackett PW, Renaud G. HaploCart: Human mtDNA haplogroup classification using a pangenomic reference graph human mtDNA haplogroup inference. PLoS Comput Biol 2023; 19:e1011148. [PMID: 37285390 DOI: 10.1371/journal.pcbi.1011148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 05/02/2023] [Indexed: 06/09/2023] Open
Abstract
Current mitochondrial DNA (mtDNA) haplogroup classification tools map reads to a single reference genome and perform inference based on the detected mutations to this reference. This approach biases haplogroup assignments towards the reference and prohibits accurate calculations of the uncertainty in assignment. We present HaploCart, a probabilistic mtDNA haplogroup classifier which uses a pangenomic reference graph framework together with principles of Bayesian inference. We demonstrate that our approach significantly outperforms available tools by being more robust to lower coverage or incomplete consensus sequences and producing phylogenetically-aware confidence scores that are unbiased towards any haplogroup. HaploCart is available both as a command-line tool and through a user-friendly web interface. The C++ program accepts as input consensus FASTA, FASTQ, or GAM files, and outputs a text file with the haplogroup assignments of the samples along with the level of confidence in the assignments. Our work considerably reduces the amount of data required to obtain a confident mitochondrial haplogroup assignment.
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Affiliation(s)
- Joshua Daniel Rubin
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Nicola Alexandra Vogel
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Peter Wad Sackett
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Gabriel Renaud
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
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Implications of Vascularized Composite Allotransplantation in Plastic Surgery on Legal Medicine. J Clin Med 2023; 12:jcm12062308. [PMID: 36983310 PMCID: PMC10054408 DOI: 10.3390/jcm12062308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/08/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023] Open
Abstract
Background: When a patient receives a transplant—be it classically an organ or bone marrow or, more recently, composite allotransplantations of the limb or face—it can result in artificial chimerism. Such chimerism raises considerations in forensic medicine, a field that relies on the collection and identification of biological samples from crime scenes. Beyond this chimerism, composite allotransplantations create further challenges. Methods: After screening the literature and press releases, we provide a brief history and summary of some of the technologies used in forensic identification, explaining their advantages and pitfalls in the light of transplantation and cautioning against misidentifying those who evade justice by taking advantage of such considerations. Results: With face transplantation, patients can receive the skin, hair, salivary glands, teeth, and oral and nasal mucosa of their donors, components which hold great importance in forensic science. Modern technologies such as computer-assisted facial recognition, although gradually becoming more accurate over time, also face new challenges in this post-transplantation era as facial recognition software can be misled by surgical alterations of the face or face transplantation. With limb transplantation, there is an impact on fingerprint identification. Conclusions: Both surgical transplantation techniques and forensic technologies have seen incomprehensibly great innovation in the past century. Given the growing rate of successful composite transplantation in the USA and worldwide, it is now important for law enforcement agents to be aware of the new possibility of having two sets of genetic material, hair, saliva, fingerprints, or even facial recognition data for the same individual.
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Vanichanukulyakit J, Khacha-ananda S, Monum T, Mahawong P, Moophayak K, Penkhrue W, Khumpook T, Thongsahuan S. The Analysis of Genetic Polymorphism on Mitochondrial Hypervariable Region III in Thai Population. Genes (Basel) 2023; 14:genes14030682. [PMID: 36980954 PMCID: PMC10048634 DOI: 10.3390/genes14030682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 03/03/2023] [Accepted: 03/07/2023] [Indexed: 03/12/2023] Open
Abstract
Mitochondrial DNA (mtDNA) analysis is a genetic marker for human identification, especially matrilineal inheritance. Hypervariable regions (HVR) I and II of mtDNA have been currently performed for human identification worldwide. Further examination of HVRIII has been conducted with the aim of enhancing the power of discrimination. The aim of this research is to provide informative data on the polymorphisms of HVRIII in the Thai population in order to establish a national database for human identification. Thai people who were unrelated through the maternal lineage were recruited for blood collections. The mtDNA was extracted by Chelex extraction, amplified by polymerase chain reaction, and analyzed using Sequencing Analysis Software. The most common mutation in HVRIII was base substitution, followed by deletion and insertion. We discovered 40 unique haplotypes, with haplotype 489C being the most frequent. The haplotype diversity, power of discrimination, and random match probability were 0.8014, 0.7987, and 0.2013, respectively. Five-CA repeats were the most frequently observed in nucleotide positions 514–523. Our database can be employed as supplementary markers in addition to nuclear deoxyribonucleic acid (DNA) markers in forensic investigations. Moreover, the data could potentially enhance genetic identification and anthropological genetics research in Thailand.
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Affiliation(s)
- Jirat Vanichanukulyakit
- Department of Forensic Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (J.V.); (T.M.); (P.M.)
| | - Supakit Khacha-ananda
- Department of Forensic Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (J.V.); (T.M.); (P.M.)
- Research Center in Bioresources for Agriculture, Industry and Medicine, Chiang Mai University, 239, Huay Kaew Road, Muang, Chiang Mai 50200, Thailand
- Correspondence:
| | - Tawachai Monum
- Department of Forensic Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (J.V.); (T.M.); (P.M.)
| | - Phatcharin Mahawong
- Department of Forensic Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (J.V.); (T.M.); (P.M.)
| | | | - Watsana Penkhrue
- School of Preclinic, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand;
| | - Taddaow Khumpook
- Faculty of Science at Sriracha, Kasetsart University, Sriracha Campus, Chonburi 20230, Thailand;
| | - Sorawat Thongsahuan
- Faculty of Veterinary Science, Prince of Songkla University, Songkhla 90110, Thailand;
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12
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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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Cooley AM. Mitochondrial DNA Analysis. Methods Mol Biol 2023; 2685:331-349. [PMID: 37439991 DOI: 10.1007/978-1-0716-3295-6_20] [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: 07/14/2023]
Abstract
Mitochondrial DNA (mtDNA) is a 16,569 base pair (bp) circular genome that is passed from generation to generation through the maternal line. mtDNA analysis in the context of the forensic science field usually involves unidentified human remains or missing persons. These cases tend to have more challenging sample types (e.g., rootless hairs, bone, blood, and saliva), and mtDNA analysis can be an additional method to assist in identification efforts. Due to the multifaceted protection of mtDNA within cells, mtDNA is able to be extracted even in cases of extreme degradation. mtDNA analysis for forensic science has been both peer-reviewed in academic journals and has been testified to in criminal court procedures since the late 1990s, allowing for consistent and reliable usage in casework. This chapter describes the general methodology of extracting, amplifying, quantifying, and analyzing an mtDNA sequence for use in forensic casework, specifically for these common items of evidence.
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Alqaisi MHM, Ekka MM, Patel BC. Forensic evaluation of mitochondrial DNA heteroplasmy in Gujarat population, India. Ann Hum Biol 2022; 49:332-341. [PMID: 36343161 DOI: 10.1080/03014460.2022.2144447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
BACKGROUND Owing to its high copy number and its small size, mtDNA analysis is the most reliable choice when biological materials from crime scenes are degraded or have mixed STR profiles. AIM To examine the occurrence of heteroplasmy along with its frequency and pattern in both HV1 and HV2 regions of the mtDNA among unrelated individuals from India. SUBJECTS AND METHODS Mitochondrial DNA control region [hypervariable region one (HV1) and hypervariable region two (HV2)] were analysed in blood and buccal tissues of 104 unrelated individuals from the Indian state of Gujarat. RESULTS A high frequency of point heteroplasmy (PH) and length heteroplasmy (LH) was revealed. PH was detected in 7.69% of the population, with a higher frequency observed in blood than in buccal samples. However, there were no statistically significant differences in PH between the two tissues (Chi-square = 0.552, p ≥ 0.05). A total of six PH positions were detected: three at HV1, and another three at HV2. The studied population showed 46.15% LH in the HV1 and HV2 regions of both tissues. The LH positions observed in the Gujarat population were the same as those previously reported at HV1 np16184-16193 and HV2 np303-315. CONCLUSIONS Our findings suggest that differences in the pattern of heteroplasmy found in different tissues can complicate the forensic analysis, on the other hand, the probability of a match between the questioned and reference samples increases when the heteroplasmy is identical in both tissues. Variability of PH among persons and even within tissues recommends analysing multiple tissue samples before drawing a conclusion in forensic mtDNA analyses.
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Affiliation(s)
- Mohammed H M Alqaisi
- Laboratory of Forensic Biology and Biotechnology, National Forensic Sciences University (NFSU), Gandhinagar, Gujarat, India
| | - Molina Madhulika Ekka
- Laboratory of Forensic Biology and Biotechnology, National Forensic Sciences University (NFSU), Gandhinagar, Gujarat, India
| | - Bhargav C Patel
- Laboratory of Forensic Biology and Biotechnology, National Forensic Sciences University (NFSU), Gandhinagar, Gujarat, India
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Ren Z, Feng Y, Zhang H, Wang Q, Yang M, Liu Y, Le C, Wang J, Huang J. Genetic analysis of the mitochondrial DNA control region in Tai-Kadai-speaking Dong population in southwest China. Ann Hum Biol 2022; 49:354-360. [PMID: 36190920 DOI: 10.1080/03014460.2022.2131334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
BACKGROUND Dong people in Southwest China are officially recognised as an ethnic group, but there has been a lack of population genetic research on this group, especially based on mitochondrial DNA data. AIM To study the sequences and haplogroups of the mitochondrial DNA control region in a typical Dong population, and to provide help for the construction of a forensic mitochondrial DNA analysis reference database in East Asia. SUBJECTS AND METHODS The sequences of the mitochondrial DNA control region were analysed in 200 individuals of Dong in Guizhou. The haplotype frequencies, haplogroup distribution and paired Fst values of Guizhou Dong and 51 other populations in the world were calculated and explained to explore the genetic polymorphism and population relationships. RESULTS A total of 180 haplotypes were detected, with frequencies of 0.005-0.02. All haplotypes were assigned to 97 different haplogroups. The haplotype diversity and random matching probability were 0.998643 and 0.00635, respectively. The paired Fst values and correlation p values of 52 populations showed that the Guizhou Dong had the closest genetic relationship with the Henan Han and the Guizhou Miao in China, and were closest to the Punjab population in Pakistan and the Kashmiri population when compared with the world populations. CONCLUSIONS Our study was based on the matrilineal genetic structure of Guizhou Dong to study mitochondrial DNA, which was helpful to promote the establishment of the forensic DNA reference database in East Asia and provide reference for anthropological research.
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Affiliation(s)
- Zheng Ren
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, P. R. China
| | - Yuhang Feng
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, P. R. China
| | - Hongling Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, P. R. China
| | - Qiyan Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, P. R. China
| | - Meiqing Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, P. R. China
| | - Yubo Liu
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, P. R. China
| | - Cuiyun Le
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, P. R. China
| | - Jie Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, P. R. China
| | - Jiang Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, P. R. China
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Kakkar S, Sarma P, Panigrahi I, Mandal SP, Shrivastava P, Kumawat RK. Development of a new screening method for faster kinship analyses in mass disasters: a proof of concept study. Sci Rep 2022; 12:20372. [PMID: 36437267 PMCID: PMC9701697 DOI: 10.1038/s41598-022-22805-w] [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] [Received: 05/14/2021] [Accepted: 10/19/2022] [Indexed: 11/29/2022] Open
Abstract
Kinship analysis in forensics is based on the calculation of the respective kinship indices. However, this calculation is only possible when the subject under identification has been associated with a particular population, whose allele frequency data is available for the particular set of STR markers used in the forensic practices. In the case of mass disasters, where a large number of individuals are to be identified, gathering the population frequency data and calculating the kinship indices can be an intricate process which requires a lot of time and huge resources. The new method of allele matching cut off score (AMCOS) developed in this study is based on the allele sharing approach. This approach simply refers to the number of shared alleles (1 or 2) between the two individuals; also known as identical by state (IBS) alleles which might have been inherited from a recent common ancestor in which the alleles are identical by descendent (IBD). In case of mass disasters, this method can be used to narrow down the number of pairs (dead and alive) to be matched for kinship without using the allele frequency data. The results obtained from this method could further be confirmed by LR based method, which uses the allele frequency data of the respective population of the pairs being tested for kinship. AMCOS method has been tested for its sensitivity, specificity and various other statistical parameters and has shown promising values for the same in various types of kinship analyses. This ascertains the authenticity and potential use of this method in forensic practice but only after its validation in a larger sample size. AMCOS method has been tested on siblings and grandparent-grandchildren by using autosomal and X-STR markers both, as the reference samples from the parents cannot always be available for the identification. The present study also compared the results shown by the autosomal and X-STR markers in siblings and grandparent-grandchildren identification, thereby suggesting the use of better set of markers on the basis of obtained values of various statistical parameters.
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Affiliation(s)
- Sonia Kakkar
- grid.415131.30000 0004 1767 2903Department of Forensic Medicine, PGIMER, Chandigarh, 160012 India
| | - Phulen Sarma
- Department of Pharmacology, AIIMS, Guwahati, 781101 India
| | - Inusha Panigrahi
- grid.415131.30000 0004 1767 2903Advanced Pediatrics Centre, PGIMER, Chandigarh, 160012 India
| | - S. P. Mandal
- grid.415131.30000 0004 1767 2903Department of Forensic Medicine, PGIMER, Chandigarh, 160012 India
| | - Pankaj Shrivastava
- Biology and Serology Division, Department of Home (Police), Govt. of MP, Regional Forensic Science Laboratory, Bhopal, 462003 India
| | - R. K. Kumawat
- grid.513284.9DNA Division, State Forensic Science Laboratory, Jaipur, Rajasthan 302016 India
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17
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Targeted next generation sequencing of Cyclospora cayetanensis mitochondrial genomes from seeded fresh produce and other seeded food samples. Heliyon 2022; 8:e11575. [DOI: 10.1016/j.heliyon.2022.e11575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 08/17/2022] [Accepted: 11/08/2022] [Indexed: 11/14/2022] Open
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Andreeva T, Manakhov A, Kunizheva S, Rogaev E. Genetic Evidence of Authenticity of a Hair Shaft Relic from the Portrait of Tsesarevich Alexei, Son of the Last Russian Emperor. BIOCHEMISTRY. BIOKHIMIIA 2021; 86:1572-1578. [PMID: 34937536 DOI: 10.1134/s0006297921120063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 11/11/2021] [Accepted: 11/12/2021] [Indexed: 06/14/2023]
Abstract
To determine the value of an art piece, authenticity of the artwork must be verified. We demonstrate here a genetic approach to determine origin of a historic relic in the museum piece. We tested two hair shafts of unknown origin framed into a watercolor portrait of Tsesarevich Alexei Romanov, son of the last Russian Tzar Nicholas II, which is a unique item kept in the State Historical Museum. Genetic identification of the hair shafts was performed by analysis of mitochondrial DNA (mtDNA) markers using both massive parallel genomic sequencing and multiplex targeted PCR, followed by Sanger sequencing. In previous works, we reconstructed the complete mtDNA sequence inherited to Alexei Romanov through the Queen Victoria lineage [Rogaev et al. (2009) Proc. Natl. Acad. Sci. USA, 106, 5258-5263]. DNA extracts were obtained from the two thin hair shafts and used for comparative genetic analysis. Despite the very low quantity and quality of the DNA templates retrieved from the historical single hair shaft specimen, informative mtDNA sequences were determined. The mtDNA haplotype in the hair shafts corresponds to the mtDNA haplotype of Tsarevich Alexei, his sisters, and his mother, Empress Alexandra Feodorovna. This haplotype remains unique in the currently available mtDNA databases. Our results reveal that the hair relic from the portrait is associated with the family of the last Russian Emperor Nicholas II. The study is an example of first application of the genetic methodology for verification of the value of museum artwork items.
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Affiliation(s)
- Tatiana Andreeva
- Centre for Genetics and Genetic Technologies, Department of Genetics, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119192, Russia.
- Department of Genomics and Human Genetics, Laboratory of Evolutionary Genomics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia
| | - Andrey Manakhov
- Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, 354340, Russia.
| | - Svetlana Kunizheva
- Centre for Genetics and Genetic Technologies, Department of Genetics, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119192, Russia.
| | - Evgeny Rogaev
- Centre for Genetics and Genetic Technologies, Department of Genetics, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119192, Russia.
- Department of Genomics and Human Genetics, Laboratory of Evolutionary Genomics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia
- Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, 354340, Russia
- Department of Psychiatry, UMass Chan Medical School, Shrewsbury, MA 01545, USA
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Laurent FX, Fischer A, Oldt RF, Kanthaswamy S, Buckleton JS, Hitchin S. Streamlining the decision-making process for international DNA kinship matching using Worldwide allele frequencies and tailored cutoff log 10LR thresholds. Forensic Sci Int Genet 2021; 57:102634. [PMID: 34871915 DOI: 10.1016/j.fsigen.2021.102634] [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: 02/16/2021] [Revised: 10/13/2021] [Accepted: 11/15/2021] [Indexed: 11/30/2022]
Abstract
The identification of human remains belonging to missing persons is one of the main challenges for forensic genetics. Although other means of identification can be applied to missing person investigations, DNA is often extremely valuable to further support or refute potential associations. When reference DNA samples cannot be collected from personal items belonging to a missing person, a direct DNA identification cannot be carried out. However, identifications can be made indirectly using DNA from the missing person's relatives. The ranking of likelihood ratio (LR) values, which measure the fit of a missing person for any given pedigree, is often the first step in selecting candidates in a DNA database. Although implementing DNA kinship matching in a national environment is feasible, many challenges need to be resolved before applying this method to an international configuration. In this study, we present an innovative and intuitive method to perform international DNA kinship matching and facilitate the comparison of DNA profiles when the ancestry is unknown or unsure and/or when different marker sets are used. This straightforward method, which is based on calculations performed with the DNA matching software BONAPARTE, Worldwide allele frequencies and tailored cutoff log10LR thresholds, allows for the classification of potential candidates according to the strength of the DNA evidence and the predicted proportion of adventitious matches. This is a powerful method for streamlining the decision-making process in missing person investigations and DVI processes, especially when there are low numbers of overlapping typed STRs. Intuitive interpretation tables and a decision tree will help strengthen international data comparison for the identification of reported missing individuals discovered outside their national borders.
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Affiliation(s)
- François-Xavier Laurent
- International Criminal Police Organization - INTERPOL, DNA Unit, 200 quai Charles de Gaulle, 69006 Lyon, France.
| | - Andrea Fischer
- International Criminal Police Organization - INTERPOL, DNA Unit, 200 quai Charles de Gaulle, 69006 Lyon, France; Landeskriminalamt Baden-Württemberg, Taubenheimstr. 85, 70372 Stuttgart, Germany
| | - Robert F Oldt
- School of Mathematical and Natural Sciences, Arizona State University, Phoenix, AZ 85004, USA
| | - Sree Kanthaswamy
- School of Mathematical and Natural Sciences, Arizona State University, Phoenix, AZ 85004, USA
| | - John S Buckleton
- University of Auckland, Department of Statistics, Private Bag, 92019 Auckland, New Zealand
| | - Susan Hitchin
- International Criminal Police Organization - INTERPOL, DNA Unit, 200 quai Charles de Gaulle, 69006 Lyon, France.
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Mandape SN, Smart U, King JL, Muenzler M, Kapema KB, Budowle B, Woerner AE. MMDIT: A tool for the deconvolution and interpretation of mitochondrial DNA mixtures. Forensic Sci Int Genet 2021; 55:102568. [PMID: 34416654 DOI: 10.1016/j.fsigen.2021.102568] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 06/22/2021] [Accepted: 08/03/2021] [Indexed: 01/01/2023]
Abstract
Short tandem repeats of the nuclear genome have been the preferred markers for analyzing forensic DNA mixtures. However, when nuclear DNA in a sample is degraded or limited, mitochondrial DNA (mtDNA) markers provide a powerful alternative. Though historically considered challenging, the interpretation and analysis of mtDNA mixtures have recently seen renewed interest with the advent of massively parallel sequencing. However, there are only a few software tools available for mtDNA mixture interpretation. To address this gap, the Mitochondrial Mixture Deconvolution and Interpretation Tool (MMDIT) was developed. MMDIT is an interactive application complete with a graphical user interface that allows users to deconvolve mtDNA (whole or partial genomes) mixtures into constituent donor haplotypes and estimate random match probabilities on these resultant haplotypes. In cases where deconvolution might not be feasible, the software allows mixture analysis directly within a binary framework (i.e. qualitatively, only using data on allele presence/absence). This paper explains the functionality of MMDIT, using an example of an in vitro two-person mtDNA mixture with a ratio of 1:4. The uniqueness of MMDIT lies in its ability to resolve mixtures into complete donor haplotypes using a statistical phasing framework before mixture analysis and evaluating statistical weights employing a novel graph algorithm approach. MMDIT is the first available open-source software that can automate mtDNA mixture deconvolution and analysis. The MMDIT web application can be accessed online at https://www.unthsc.edu/mmdit/. The source code is available at https://github.com/SammedMandape/MMDIT_UI and archived on zenodo (https://doi.org/10.5281/zenodo.4770184).
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Affiliation(s)
- Sammed N Mandape
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA
| | - Utpal Smart
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA
| | - Jonathan L King
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA
| | - Melissa Muenzler
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA
| | - Kapema Bupe Kapema
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA; Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
| | - August E Woerner
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA; Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA.
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21
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Singh G, Yellapu S, Sandhu HS, Sharma I, Sharma V, Bhanwer AJS. Genetic characterisation of the North-West Indian populations: analysis of mitochondrial DNA control region variations. Ann Hum Biol 2021; 48:166-172. [PMID: 33494619 DOI: 10.1080/03014460.2021.1879933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
BACKGROUND Human mitochondrial DNA presents several interesting characteristics, making it a favourable tool in the field of molecular anthropology, medical genetics, population history, and forensic science. AIM The present study investigated the mitochondrial DNA (mtDNA) control region variations in diverse ethnic groups of North-West India for which population data is insufficient. SUBJECTS AND METHODS The complete mtDNA control regions of 197 unrelated (for up to three generations) healthy individuals belonging to different ethnic groups of North-West India were sequenced. The haplotype frequencies, haplogroup distribution, and pairwise FST values between the studied and other worldwide populations were generated to study patterns of variation in human mtDNA. RESULTS The results ascertained high gene diversity (0.998) in the studied maternal lineages, identifying 166 distinct haplotypes, of which 158 were unique and characterised by 117 variable sites. Three haplogroups: M3, M30, and U7 were observed to be the most prevalent, and phylogeographically a total of 55.86% of sequences were characterised into South Asian, followed by West Eurasian (40.18%) and East Asian (3.96%), ancestry haplogroups. Pairwise genetic differentiation comparisons revealed maternal homogeneity in the studied groups. No population substructure was detected within the North-West Indian populations. CONCLUSION The results of this preliminary study will contribute to an existing database of mtDNA variations of the Indian population and facilitate prospective studies investigating population genetics and human diseases.
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Affiliation(s)
- Gagandeep Singh
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, India.,Department of Anthropology, Panjab University, Chandigarh, India
| | | | | | - Indu Sharma
- Ancient DNA Laboratory, Birbal Sahni Institute of Palaeosciences, Lucknow, India
| | - Varun Sharma
- Ancient DNA Laboratory, Birbal Sahni Institute of Palaeosciences, Lucknow, India
| | - A J S Bhanwer
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, India
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Yang FC, Tseng B, Lin CY, Yu YJ, Linacre A, Lee JCI. Population inference based on mitochondrial DNA control region data by the nearest neighbors algorithm. Int J Legal Med 2021; 135:1191-1199. [PMID: 33586030 DOI: 10.1007/s00414-021-02520-3] [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: 11/30/2020] [Accepted: 01/27/2021] [Indexed: 11/24/2022]
Abstract
Population and geographic assignment are frequently undertaken using DNA sequences on the mitochondrial genome. Assignment to broad continental populations is common, although finer resolution to subpopulations can be less accurate due to shared genetic ancestry at a local level and members of different ancestral subpopulations cohabiting the same geographic area. This study reports on the accuracy of population and subpopulation assignment by using the sequence data obtained from the 3070 mitochondrial genomes and applying the K-nearest neighbors (KNN) algorithm. These data also included training samples used for continental and population assignment comprised of 1105 Europeans (including Austria, France, Germany, Spain, and England and Caucasian countries), 374 Africans (including North and East Africa and non-specific area (Pan-Africa)), and 1591 Asians (including Japan, Philippines, and Taiwan). Subpopulations included in this study were 1153 mitochondrial DNA (mtDNA) control region sequences from 12 subpopulations in Taiwan (including Han, Hakka, Ami, Atayal, Bunun, Paiwan, Puyuma, Rukai, Saisiyat, Tsou, Tao, and Pingpu). Additionally, control region sequence data from a further 50 samples, obtained from the Sigma Company, were included after they were amplified and sequenced. These additional 50 samples acted as the "testing samples" to verify the accuracy of the population. In this study, based on genetic distances as genetic metric, we used the KNN algorithm and the K-weighted-nearest neighbors (KWNN) algorithm weighted by genetic distance to classify individuals into continental populations, and subpopulations within the same continent. Accuracy results of ethnic inferences at the level of continental populations and of subpopulations among KNN and KWNN algorithms were obtained. The training sample set achieved an overall accuracy of 99 to 82% for assignment to their continental populations with K values from 1 to 101. Population assignment for subpopulations with K assignments from 1 to 5 reached an accuracy of 77 to 54%. Four out of 12 Taiwanese populations returned an accuracy of assignment of over 60%, Ami (66%), Atayal (67%), Saisiyat (66%), and Tao (80%). For the testing sample set, results of ethnic prediction for continental populations with recommended K values as 5, 10, and 35, based on results of the training sample set, achieved overall an accuracy of 100 to 94%. This study provided an accurate method in population assignment for not only continental populations but also subpopulations, which can be useful in forensic and anthropological studies.
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Affiliation(s)
- Fu-Chi Yang
- Department of Forensic Medicine, College of Medicine, National Taiwan University, No.1 Jen-Ai Road Section 1, Taipei, 10051, Taiwan
| | - Bill Tseng
- Department of Forensic Medicine, College of Medicine, National Taiwan University, No.1 Jen-Ai Road Section 1, Taipei, 10051, Taiwan
| | - Chun-Yen Lin
- Institute of Forensic Medicine, Ministry of Justice, New Taipei City, 23016, Taiwan
| | - Yu-Jen Yu
- Department of Forensic Medicine, College of Medicine, National Taiwan University, No.1 Jen-Ai Road Section 1, Taipei, 10051, Taiwan
| | - Adrian Linacre
- College of Science & Engineering, Flinders University, Adelaide, 5001, Australia
| | - James Chun-I Lee
- Department of Forensic Medicine, College of Medicine, National Taiwan University, No.1 Jen-Ai Road Section 1, Taipei, 10051, Taiwan.
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Smart U, Cihlar JC, Mandape SN, Muenzler M, King JL, Budowle B, Woerner AE. A Continuous Statistical Phasing Framework for the Analysis of Forensic Mitochondrial DNA Mixtures. Genes (Basel) 2021; 12:128. [PMID: 33498312 PMCID: PMC7909279 DOI: 10.3390/genes12020128] [Citation(s) in RCA: 9] [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: 12/21/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 11/16/2022] Open
Abstract
Despite the benefits of quantitative data generated by massively parallel sequencing, resolving mitotypes from mixtures occurring in certain ratios remains challenging. In this study, a bioinformatic mixture deconvolution method centered on population-based phasing was developed and validated. The method was first tested on 270 in silico two-person mixtures varying in mixture proportions. An assortment of external reference panels containing information on haplotypic variation (from similar and different haplogroups) was leveraged to assess the effect of panel composition on phasing accuracy. Building on these simulations, mitochondrial genomes from the Human Mitochondrial DataBase were sourced to populate the panels and key parameter values were identified by deconvolving an additional 7290 in silico two-person mixtures. Finally, employing an optimized reference panel and phasing parameters, the approach was validated with in vitro two-person mixtures with differing proportions. Deconvolution was most accurate when the haplotypes in the mixture were similar to haplotypes present in the reference panel and when the mixture ratios were neither highly imbalanced nor subequal (e.g., 4:1). Overall, errors in haplotype estimation were largely bounded by the accuracy of the mixture's genotype results. The proposed framework is the first available approach that automates the reconstruction of complete individual mitotypes from mixtures, even in ratios that have traditionally been considered problematic.
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Affiliation(s)
- Utpal Smart
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA; (U.S.); (J.C.C.); (S.N.M.); (M.M.); (J.L.K.); (B.B.)
| | - Jennifer Churchill Cihlar
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA; (U.S.); (J.C.C.); (S.N.M.); (M.M.); (J.L.K.); (B.B.)
- Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
| | - Sammed N. Mandape
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA; (U.S.); (J.C.C.); (S.N.M.); (M.M.); (J.L.K.); (B.B.)
| | - Melissa Muenzler
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA; (U.S.); (J.C.C.); (S.N.M.); (M.M.); (J.L.K.); (B.B.)
| | - Jonathan L. King
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA; (U.S.); (J.C.C.); (S.N.M.); (M.M.); (J.L.K.); (B.B.)
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA; (U.S.); (J.C.C.); (S.N.M.); (M.M.); (J.L.K.); (B.B.)
- Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
| | - August E. Woerner
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA; (U.S.); (J.C.C.); (S.N.M.); (M.M.); (J.L.K.); (B.B.)
- Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
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Cihlar JC, Amory C, Lagacé R, Roth C, Parson W, Budowle B. Developmental Validation of a MPS Workflow with a PCR-Based Short Amplicon Whole Mitochondrial Genome Panel. Genes (Basel) 2020; 11:E1345. [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] [MESH Headings] [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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Affiliation(s)
- Jennifer Churchill Cihlar
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Boulevard, Fort Worth, TX 76107, USA;
- Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Boulevard, Fort Worth, TX 76107, USA
| | - Christina Amory
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (C.A.); (W.P.)
| | - Robert Lagacé
- Human Identification Group, Thermo Fisher Scientific, South San Francisco, CA 94080, USA; (R.L.); (C.R.)
| | - Chantal Roth
- Human Identification Group, Thermo Fisher Scientific, South San Francisco, CA 94080, USA; (R.L.); (C.R.)
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (C.A.); (W.P.)
- Forensic Science Program, The Pennsylvania State University, University Park, PA 16802, USA
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Boulevard, Fort Worth, TX 76107, USA;
- Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Boulevard, Fort Worth, TX 76107, USA
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25
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Jabbar SM, Al-Rashedi NAM. Mitochondrial DNA control region variation in an Iraqi population sample. Int J Legal Med 2020; 135:421-425. [PMID: 33150489 DOI: 10.1007/s00414-020-02452-4] [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: 04/06/2020] [Accepted: 10/30/2020] [Indexed: 11/30/2022]
Abstract
BACKGROUND Although Iraq has one of the world's oldest cultural histories and an important geographic location, forensic reference data on mitochondrial DNA (mtDNA) control region in Iraqi populations are scarce, particularly for populations residing in the southern part of Iraq. Mitochondrial DNA typing is an excellent tool for forensic investigations and in missing-person cases because of its unique qualities, such as mtDNA non-coding control region with specific genetic markers, high copy numbers in cells, maternal inheritance, and lack of recombination. METHODS Forensic analysis was performed on the entire mtDNA control region in 203 unrelated Iraqi individuals residing in Samawah City of Iraq. Polymorphisms in the mtDNA were detected using polymerase chain reaction and Sanger-type sequencing, and the sequences were aligned to compare with revised Cambridge Reference Sequence (rCRS). RESULTS The sequencing results revealed 111 haplotypes characterized by 143 polymorphic positions. Of these haplotypes, 63 were unique and 48 were shared by more than one person. The haplotype data generated in this study will be available on EMPOP via accession number EMP00814.
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Affiliation(s)
- Suhair M Jabbar
- Department of Biology, College of Science, Al Muthanna University, Samawah, Iraq
| | - Nihad A M Al-Rashedi
- Department of Biology, College of Science, Al Muthanna University, Samawah, Iraq.
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26
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Bañó M, Morén C, Barroso S, Juárez DL, Guitart-Mampel M, González-Casacuberta I, Canto-Santos J, Lozano E, León A, Pedrol E, Miró Ò, Tobías E, Mallolas J, Rojas JF, Cardellach F, Martínez E, Garrabou G. Mitochondrial Toxicogenomics for Antiretroviral Management: HIV Post-exposure Prophylaxis in Uninfected Patients. Front Genet 2020; 11:497. [PMID: 32528527 PMCID: PMC7264262 DOI: 10.3389/fgene.2020.00497] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 04/21/2020] [Indexed: 01/09/2023] Open
Abstract
Background: Mitochondrial genome has been used across multiple fields in research, diagnosis, and toxicogenomics. Several compounds damage mitochondrial DNA (mtDNA), including biological and therapeutic agents like the human immunodeficiency virus (HIV) but also its antiretroviral treatment, leading to adverse clinical manifestations. HIV-infected and treated patients may show impaired mitochondrial and metabolic profile, but specific contribution of viral or treatment toxicity remains elusive. The evaluation of HIV consequences without treatment interference has been performed in naïve (non-treated) patients, but assessment of treatment toxicity without viral interference is usually restricted to in vitro assays. Objective: The objective of the present study is to determine whether antiretroviral treatment without HIV interference can lead to mtDNA disturbances. We studied clinical, mitochondrial, and metabolic toxicity in non-infected healthy patients who received HIV post-exposure prophylaxis (PEP) to prevent further infection. We assessed two different PEP regimens according to their composition to ascertain if they were the cause of tolerability issues and derived toxicity. Methods: We analyzed reasons for PEP discontinuation and main secondary effects of treatment withdrawal, mtDNA content from peripheral blood mononuclear cells and metabolic profile, before and after 28 days of PEP, in 23 patients classified depending on PEP composition: one protease inhibitor (PI) plus Zidovudine/Lamivudine (PI plus AZT + 3TC; n = 9) or PI plus Tenofovir/Emtricitabine (PI plus TDF + FTC; n = 14). Results: Zidovudine-containing-regimens showed an increased risk for drug discontinuation (RR = 9.33; 95% CI = 1.34–65.23) due to adverse effects of medication related to gastrointestinal complications. In the absence of metabolic disturbances, 4-week PEP containing PI plus AZT + 3TC led to higher mitochondrial toxicity (−17.9 ± 25.8 decrease in mtDNA/nDNA levels) than PI plus TDF + FTC (which increased by 43.2 ± 24.3 units mtDNA/nDNA; p < 0.05 between groups). MtDNA changes showed a significant and negative correlation with baseline alanine transaminase levels (p < 0.05), suggesting that a proper hepatic function may protect from antiretroviral toxicity. Conclusions: In absence of HIV infection, preventive short antiretroviral treatment can cause secondary effects responsible for treatment discontinuation and subclinical mitochondrial damage, especially pyrimidine analogs such as AZT, which still rank as the alternative option and first choice in certain cohorts for PEP. Forthcoming efforts should be focused on launching new strategies with safer clinical and mitotoxic profile.
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Affiliation(s)
- Maria Bañó
- Muscle Research and Mitochondrial Function Laboratory, Cellex-August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Faculty of Medicine and Health Science-University of Barcelona, Internal Medicine Department, Hospital Clínic of Barcelona, Barcelona, Spain.,U722 CIBERER, Barcelona, Spain
| | - Constanza Morén
- Muscle Research and Mitochondrial Function Laboratory, Cellex-August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Faculty of Medicine and Health Science-University of Barcelona, Internal Medicine Department, Hospital Clínic of Barcelona, Barcelona, Spain.,U722 CIBERER, Barcelona, Spain
| | - Sergio Barroso
- Muscle Research and Mitochondrial Function Laboratory, Cellex-August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Faculty of Medicine and Health Science-University of Barcelona, Internal Medicine Department, Hospital Clínic of Barcelona, Barcelona, Spain.,U722 CIBERER, Barcelona, Spain
| | - Diana Luz Juárez
- Muscle Research and Mitochondrial Function Laboratory, Cellex-August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Faculty of Medicine and Health Science-University of Barcelona, Internal Medicine Department, Hospital Clínic of Barcelona, Barcelona, Spain.,U722 CIBERER, Barcelona, Spain
| | - Mariona Guitart-Mampel
- Muscle Research and Mitochondrial Function Laboratory, Cellex-August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Faculty of Medicine and Health Science-University of Barcelona, Internal Medicine Department, Hospital Clínic of Barcelona, Barcelona, Spain.,U722 CIBERER, Barcelona, Spain
| | - Ingrid González-Casacuberta
- Muscle Research and Mitochondrial Function Laboratory, Cellex-August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Faculty of Medicine and Health Science-University of Barcelona, Internal Medicine Department, Hospital Clínic of Barcelona, Barcelona, Spain.,U722 CIBERER, Barcelona, Spain
| | - Judith Canto-Santos
- Muscle Research and Mitochondrial Function Laboratory, Cellex-August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Faculty of Medicine and Health Science-University of Barcelona, Internal Medicine Department, Hospital Clínic of Barcelona, Barcelona, Spain.,U722 CIBERER, Barcelona, Spain
| | - Ester Lozano
- Muscle Research and Mitochondrial Function Laboratory, Cellex-August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Faculty of Medicine and Health Science-University of Barcelona, Internal Medicine Department, Hospital Clínic of Barcelona, Barcelona, Spain.,U722 CIBERER, Barcelona, Spain
| | - Agathe León
- Infectious Disease Department, Hospital Clinic of Barcelona, Barcelona, Spain
| | - Enric Pedrol
- Internal Medicine Department, Hospital de Viladecans, Barcelona, Spain
| | - Òscar Miró
- Emergency Department, Hospital Clinic of Barcelona, Barcelona, Spain
| | - Ester Tobías
- Muscle Research and Mitochondrial Function Laboratory, Cellex-August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Faculty of Medicine and Health Science-University of Barcelona, Internal Medicine Department, Hospital Clínic of Barcelona, Barcelona, Spain.,U722 CIBERER, Barcelona, Spain
| | - Josep Mallolas
- Infectious Disease Department, Hospital Clinic of Barcelona, Barcelona, Spain
| | - Jhon F Rojas
- Infectious Disease Department, Hospital Clinic of Barcelona, Barcelona, Spain
| | - Francesc Cardellach
- Muscle Research and Mitochondrial Function Laboratory, Cellex-August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Faculty of Medicine and Health Science-University of Barcelona, Internal Medicine Department, Hospital Clínic of Barcelona, Barcelona, Spain.,U722 CIBERER, Barcelona, Spain
| | - Esteban Martínez
- Infectious Disease Department, Hospital Clinic of Barcelona, Barcelona, Spain
| | - Gloria Garrabou
- Muscle Research and Mitochondrial Function Laboratory, Cellex-August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Faculty of Medicine and Health Science-University of Barcelona, Internal Medicine Department, Hospital Clínic of Barcelona, Barcelona, Spain.,U722 CIBERER, Barcelona, Spain
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27
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Cinar HN, Gopinath G, Murphy HR, Almeria S, Durigan M, Choi D, Jang A, Kim E, Kim R, Choi S, Lee J, Shin Y, Lee J, Qvarnstrom Y, Benedict TK, Bishop HS, da Silva A. Molecular typing of Cyclospora cayetanensis in produce and clinical samples using targeted enrichment of complete mitochondrial genomes and next-generation sequencing. Parasit Vectors 2020; 13:122. [PMID: 32143704 PMCID: PMC7060604 DOI: 10.1186/s13071-020-3997-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 02/26/2020] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Outbreaks of cyclosporiasis, a diarrheal illness caused by Cyclospora cayetanensis, have been a public health issue in the USA since the mid 1990's. In 2018, 2299 domestically acquired cases of cyclosporiasis were reported in the USA as a result of multiple large outbreaks linked to different fresh produce commodities. Outbreak investigations are hindered by the absence of standardized molecular epidemiological tools for C. cayetanensis. For other apicomplexan coccidian parasites, multicopy organellar DNA such as mitochondrial genomes have been used for detection and molecular typing. METHODS We developed a workflow to obtain complete mitochondrial genome sequences from cilantro samples and clinical samples for typing of C. cayetanensis isolates. The 6.3 kb long C. cayetanensis mitochondrial genome was amplified by PCR in four overlapping amplicons from genomic DNA extracted from cilantro, seeded with oocysts, and from stool samples positive for C. cayetanensis by diagnostic methods. DNA sequence libraries of pooled amplicons were prepared and sequenced via next-generation sequencing (NGS). Sequence reads were assembled using a custom bioinformatics pipeline. RESULTS This approach allowed us to sequence complete mitochondrial genomes from the samples studied. Sequence alterations, such as single nucleotide polymorphism (SNP) profiles and insertion and deletions (InDels), in mitochondrial genomes of 24 stool samples from patients with cyclosporiasis diagnosed in 2014, exhibited discriminatory power. The cluster dendrogram that was created based on distance matrices of the complete mitochondrial genome sequences, indicated distinct strain-level diversity among the 2014 C. cayetanensis outbreak isolates analyzed in this study. CONCLUSIONS Our results suggest that genomic analyses of mitochondrial genome sequences may help to link outbreak cases to the source.
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Affiliation(s)
- Hediye Nese Cinar
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD USA
| | - Gopal Gopinath
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD USA
| | - Helen R. Murphy
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD USA
| | - Sonia Almeria
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD USA
| | - Mauricio Durigan
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD USA
| | - Dajung Choi
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD USA
| | - AhYoung Jang
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD USA
| | - Eunje Kim
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD USA
| | - RaeYoung Kim
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD USA
| | - Seonju Choi
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD USA
| | - Jeongu Lee
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD USA
| | - Yurim Shin
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD USA
| | - Jieon Lee
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD USA
| | - Yvonne Qvarnstrom
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA USA
| | - Theresa K. Benedict
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA USA
| | - Henry S. Bishop
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA USA
| | - Alexandre da Silva
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD USA
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28
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Mitochondrial DNA screening by melting curve analysis using peptide nucleic acid probes. Forensic Sci Int Genet 2019; 45:102228. [PMID: 31911363 DOI: 10.1016/j.fsigen.2019.102228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 12/18/2019] [Accepted: 12/18/2019] [Indexed: 11/22/2022]
Abstract
Analysis of single nucleotide polymorphisms (SNPs) in mitochondrial (mt)DNA hypervariable regions (HV) 1/2 is valuable in forensic investigations. We developed a method for mtDNA screening of the HV1 and HV2 regions by melting curve analysis, using peptide nucleic acid (PNA) probes. This method focuses on melting peak patterns obtained by thermal dissociation of PNA/DNA duplexes in amplified mtDNA products. Five PNA probe sets were designed to detect 25 SNPs in the two HV regions. We also detected non-target SNPs based on unexpected melting temperature (Tm) shifts. In fact, 62 SNPs (42 SNPs in HV1 and 20 in HV2) were identified, including the 25 target SNPs. Using this method, 46 melting peak patterns, including 8 pattern groups, were obtained in 60 unrelated individuals. The peak patterns were compared to 55 haplotypes identified by Sanger sequencing. The results obtained from analysis of target mtDNA SNPs were entirely consistent with those obtained by Sanger sequencing. Screening the HV1 and HV2 regions of mtDNA by this method may help minimize unnecessary recourse to full sequence analysis, allows to rapidly exclude samples that do not match evidence and reference samples, and may reduce turnaround times and analysis costs. Overall, this method may be effective and helpful in forensic investigations.
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29
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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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30
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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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31
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Ishar SM, Parameswaran K, Masduki NS, Rus Din RD. Variations in mitochondrial DNA control region among Malay and Chinese subpopulations (sequence 16000-16200). Mitochondrial DNA A DNA Mapp Seq Anal 2019; 30:843-847. [PMID: 31709874 DOI: 10.1080/24701394.2019.1687693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
DNA variations are alterations found in DNA sequence, occurring in both nuclear DNA and mitochondrial DNA. Variations might differ in individual following population, respectively. The aim of this study was to find variations in target sequence of mtDNA (16000-16200) to be used as marker in Malay and Chinese population. A total of 30 buccal swab samples from 20 Malay and 10 Chinese subjects were collected and preserved on FTA card. The FTA card that contained DNA sample was punched to be included into polymerase chain reaction mixture. Amplification was carried out and the products were sequenced. Sequence variations were found in both Malay and Chinese populations. A total of nine variations (16129, 16108, 16162, 16172, 16148, 16127, 16173, 16099 and 16100) were found in Malay population while a total of seven variations (16129, 16104, 16111, 16109, 16164, 16170 and 16136) were found in Chinese population. Nucleotide position 16129 was found as variation in both Malay and Chinese populations. This study implies that np 16129 can be used as a marker for Malaysian population. For further investigation, the length of the target sequence may be increased to obtain more variations that can be used as markers. This will increase the discrimination power of Malaysian population.
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Affiliation(s)
| | | | | | - Rus Dina Rus Din
- Faculty of Health Sciences, Universiti Kebangsaan Malaysia, Bangi, Malaysia
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32
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Rajpoot A, Bahuguna A, Kumar VP. Molecular study of globally threatened turtle species (families Trionychidae and Geoemydidae) of Uttarakhand and their relationship with other Indian populations: A wildlife forensic and conservation genetic approach. FORENSIC SCIENCE INTERNATIONAL: REPORTS 2019. [DOI: 10.1016/j.fsir.2019.100039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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33
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Desmyter S, Dognaux S, Noel F, Prieto L. Base specific variation rates at mtDNA positions 16093 and 16183 in human hairs. Forensic Sci Int Genet 2019; 43:102142. [PMID: 31437782 DOI: 10.1016/j.fsigen.2019.102142] [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: 04/23/2019] [Revised: 07/25/2019] [Accepted: 08/11/2019] [Indexed: 10/26/2022]
Abstract
Small variations between haplotypes detected in different tissues from the same individual have been previously described. These differences complicate the interpretation of mtDNA results in real forensic casework. mtDNA haplotypes detected in hair strands collected at the crime scene have to be frequently compared with haplotypes of reference samples (buccal swabs) from victims or suspects. Nucleotide position 16093 is a well-known hot spot where differences can accumulate between different tissues of the same individual. Intra individual variation was also detected at positions 16182 and 16183 in haplotypes showing an uninterrupted HV1 poly-C stretch (with 16189C). In order to better characterize the type of variation in these positions between buccal cells and hair strands from the same individual, we have performed Sanger sequencing in 25-28 hair strands (411 in total) from 15 individuals showing either an uninterrupted HV1 polyC-stretch (16189C) or 16093C/Y in their buccal cells. The results have been evaluated by also taking into account our previous results published in [19]. We have found that no variation among hair strands was detected in individuals showing T16093 in buccal cells, while variation in hair strands (T16093, 16093C and 16093Y) were detected in individuals showing 16093C or 16093Y in buccal cells. Regarding nucleotide positions 16182 and 16183 in combination with an uninterrupted polyC-stretch, no variation was detected in hairs from individuals showing A16182 16183C in their buccal cells. In contrast, individuals A16182 A16183 showed hair strands with A16182 16183 M and A16182 16183C. And finally, individuals with 16182C 16183C showed some variation in a small amount of their hair strands (some hairs with 16182 M 16183C). These results can be relevant for forensic practitioners when comparing reference samples with hair strands, which is the type of sample most tested by using mtDNA analysis in forensic casework.
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Affiliation(s)
- Stijn Desmyter
- NICC - Belgian Institute for Forensic Science and Criminology, Vilvoordsesteenweg 100, B-1120, Brussels, Belgium.
| | - Sophie Dognaux
- NICC - Belgian Institute for Forensic Science and Criminology, Vilvoordsesteenweg 100, B-1120, Brussels, Belgium
| | - Fabrice Noel
- NICC - Belgian Institute for Forensic Science and Criminology, Vilvoordsesteenweg 100, B-1120, Brussels, Belgium
| | - Lourdes Prieto
- Instituto de Ciencias Forenses. Grupo de Medicina Xenómica. Universidade de Santiago de Compostela, Spain; Laboratorio ADN. Comisaría General de Policía Científica, Madrid, Spain
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Amorim A, Fernandes T, Taveira N. Mitochondrial DNA in human identification: a review. PeerJ 2019; 7:e7314. [PMID: 31428537 PMCID: PMC6697116 DOI: 10.7717/peerj.7314] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 06/18/2019] [Indexed: 11/21/2022] Open
Abstract
Mitochondrial DNA (mtDNA) presents several characteristics useful for forensic studies, especially related to the lack of recombination, to a high copy number, and to matrilineal inheritance. mtDNA typing based on sequences of the control region or full genomic sequences analysis is used to analyze a variety of forensic samples such as old bones, teeth and hair, as well as other biological samples where the DNA content is low. Evaluation and reporting of the results requires careful consideration of biological issues as well as other issues such as nomenclature and reference population databases. In this work we review mitochondrial DNA profiling methods used for human identification and present their use in the main cases of humanidentification focusing on the most relevant issues for forensics.
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Affiliation(s)
- António Amorim
- Instituto Nacional de Medicina Legal e Ciências Forenses, Lisboa, Portugal
- Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Teresa Fernandes
- Escola de Ciências e Tecnologias, Universidade de Évora, Évora, Portugal
- Research Center for Anthropology and Health (CIAS), Universidade de Coimbra, Coimbra, Portugal
| | - Nuno Taveira
- Instituto Universitário Egas Moniz (IUEM), Almada, Portugal
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
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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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Mitochondrial DNA, a Powerful Tool to Decipher Ancient Human Civilization from Domestication to Music, and to Uncover Historical Murder Cases. Cells 2019; 8:cells8050433. [PMID: 31075917 PMCID: PMC6562384 DOI: 10.3390/cells8050433] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 04/17/2019] [Accepted: 05/07/2019] [Indexed: 11/28/2022] Open
Abstract
Mitochondria are unique organelles carrying their own genetic material, independent from that in the nucleus. This review will discuss the nature of mitochondrial DNA (mtDNA) and its levels in the cell, which are the key elements to consider when trying to achieve molecular identification in ancient and degraded samples. mtDNA sequence analysis has been appropriately validated and is a consistent molecular target for the examination of biological evidence encountered in forensic cases—and profiling, in certain conditions—especially for burnt bodies and degraded samples of all types. Exceptional cases and samples will be discussed in this review, such as mtDNA from leather in Beethoven’s grand piano, mtDNA in mummies, and solving famous historical criminal cases. In addition, this review will be discussing the use of ancient mtDNA to understand past human diet, to trace historical civilizations and ancient trade routes, and to uncover geographical domestication origins and lineage relationships. In each topic, we will present the power of mtDNA and how, in many cases, no nuclear DNA was left, leaving mitochondrial DNA analysis as a powerful alternative. Exploring this powerful tool further will be extremely useful to modern science and researchers, due to its capabilities in providing us with previously unattainable knowledge.
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Eom YB. Microbial Forensics: Human Identification. BIOMEDICAL SCIENCE LETTERS 2018; 24:292-304. [DOI: 10.15616/bsl.2018.24.4.292] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 12/11/2018] [Accepted: 12/12/2018] [Indexed: 09/01/2023]
Affiliation(s)
- Yong-Bin Eom
- Department of Biomedical Laboratory Science, College of Medical Sciences, Soonchunhyang University, Asan, Chungnam 31538, Korea
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38
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Khatoon F. USE OF DNA IN HUMAN IDENTIFICATION: FROM SKIN TO GENES. GOMAL JOURNAL OF MEDICAL SCIENCES 2018. [DOI: 10.46903/gjms/16.04.1783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
This article is based on ‘use of Deoxyribonucleic Acid (DNA) in human identification, from skin to genes’. DNA has been used as a vital element in the identification of the individuals on the basis of the human genes. The study is based on secondary data analysis. The sources were analyzed critically, and information relevant to the research was extracted. Many different kinds of libraries, journals and articles were reviewed in order to gain extensive insight about the proposed study. Some of the databases include Google scholar, sage publications and other relevant websites. Today, the accuracy of DNA tests requires a commitment to quality scientific excellence, since the results may be crucial for resolving cases of child custody, inheritance, assaults, identification of biological remains or finding the missing link in searching the lineage of an adopted.
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Zhao W, Wang L, Yu Y. Gene module analysis of juvenile myelomonocytic leukemia and screening of anticancer drugs. Oncol Rep 2018; 40:3155-3170. [PMID: 30272300 PMCID: PMC6196601 DOI: 10.3892/or.2018.6709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Accepted: 07/19/2018] [Indexed: 11/05/2022] Open
Abstract
Juvenile myelomonocytic leukemia (JMML) is a rare but severe primary hemopoietic system tumor of childhood, most frequent in children 4 years and younger. There are currently no specific anticancer therapies targeting JMML, and the underlying gene expression changes have not been revealed. To define molecular targets and possible biomarkers for early diagnosis, optimal treatment, and prognosis, we conducted microarray data analysis using the Gene Expression Omnibus, and constructed protein‑protein interaction networks of all differentially expressed genes. Modular bioinformatics analysis revealed four core functional modules for JMML. We analyzed the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway functions associated with these modules. Using the CMap database, nine potential anticancer drugs were identified that modulate expression levels of many JMML‑associated genes. In addition, we identified possible miRNAs and transcription factors regulating these differentially expressed genes. This study defines a new research strategy for developing JMML‑targeted chemotherapies.
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Affiliation(s)
- Wencheng Zhao
- Department of Paediatrics, The First Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Lin Wang
- Key Laborarory, The First Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Yongbin Yu
- Key Laborarory, The First Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
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40
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Zander J, Otremba P, Nagy M. Validation of haplotype-specific extraction for separating a mitochondrial DNA model mixture and application to simulated casework. Forensic Sci Int Genet 2018; 35:57-64. [PMID: 29665468 DOI: 10.1016/j.fsigen.2018.04.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 04/04/2018] [Accepted: 04/07/2018] [Indexed: 01/14/2023]
Abstract
Haplotype-specific extraction (HSE) is a new field of application for the separation of mitochondrial DNA (mtDNA) mixtures and is developed to identify the mtDNA haplotypes of the contributors subsequently by sequencing. Here we show the validation of HSE with an exemplary mitochondrial DNA mixture into its individual haplotypes according to our laboratory standards. These specify several critical areas of assay performance to be tested, such as sensitivity, robustness and mixture studies comprising varying proportions of their components,degraded samples and samples of different qualities and material. Wereport the successful and unambiguous analysis of the exemplary separated mitochondrial DNA mixture under various conditions as well as simulated casework samples, which manifest as mixed nucleotide calls at single base positions previously. Here we demonstrate that the HSE assay is high sensitive, stable against degradation and applicable in a wide range of sample qualities. Based on our findings from the validation study, we believe that this assay has great potential power and may be useful for distinguishing among the mtDNA of individuals and their geographical origin in mixed DNA samples.
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Affiliation(s)
- Judith Zander
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité - Universitätsmedizin, Augustenburger Platz 1, 13353, Berlin, Forum 4/Westring 3, Germany.
| | - Petra Otremba
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité - Universitätsmedizin, Augustenburger Platz 1, 13353, Berlin, Forum 4/Westring 3, Germany.
| | - Marion Nagy
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité - Universitätsmedizin, Augustenburger Platz 1, 13353, Berlin, Forum 4/Westring 3, Germany.
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41
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Kumar VP, Shukla M, Rajpoot A, Thakur M, Nigam P, Kumar D, Mehta AK, Goyal SP. DNA barcoding as a tool for robust identification of cervids of India and its utility in wildlife forensics. MITOCHONDRIAL DNA PART B-RESOURCES 2018; 3:250-255. [PMID: 33474133 PMCID: PMC7800678 DOI: 10.1080/23802359.2018.1438858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA barcoding has become a popular method of choice for identification of specimen based on molecular techniques. Here, we present preliminary findings on generating robust DNA barcode library of Cervids of India. The dataset comprising the DNA barcode library of seven deer species included in the genus Cervus, Axis and Muntiacus classified under family Cervidae. Mitochondrial Cytochrome C Oxidase subunit I gene of ca. 710 bp accepted widely as DNA barcode region, was used for generating species specific signature from 31 known samples of seven Indian deer species. Expectedly, the NJ tree clustered three genera i.e. Cervus, Axis and Muntiacus of Cervids of India into three clades. Further, the intra- and interspecies distances based on Kimura 2 parameter model also supported the results. The average intra- and interspecies sequence divergence were 0.011 (±0.09) and 0.65 (±0.14), respectively. The present study has exhibited that DNA barcoding has discriminating power to delineate boundaries among the closely related species. The data generated are of high importance to the law enforcement agencies in effective identification of species in wildlife offence cases. The similar approach can be utilized for generating DNA barcodes for other Indian mammals for making effective management and conservation action decisions.
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Affiliation(s)
- Ved P Kumar
- Wildlife Forensic Cell, Wildlife Institute of India, Dehradun, Uttarakhand, India.,Department of Zoology, Veer Kunwar Singh University, Arrah, Bihar, India
| | - Malay Shukla
- Wildlife Forensic Cell, Wildlife Institute of India, Dehradun, Uttarakhand, India.,Institute of Forensic Science, Gujarat Forensic Sciences University, Gandhinagar, Gujarat, India
| | - Ankita Rajpoot
- Molecular Systematics Laboratory, Zoological Survey of India, Northern Regional Centre, Dehradun, Uttarakhand, India
| | - Mukesh Thakur
- Molecular Systematics Division,Centre for DNA Taxonomy, Zoological Survey of India, Kolkata, India
| | - Parag Nigam
- Wildlife Forensic Cell, Wildlife Institute of India, Dehradun, Uttarakhand, India
| | - Dhyanendra Kumar
- Department of Zoology, Veer Kunwar Singh University, Arrah, Bihar, India
| | - Anil Kumar Mehta
- Institute of Forensic Science, Gujarat Forensic Sciences University, Gandhinagar, Gujarat, India
| | - Surendra P Goyal
- Department of Zoology, Veer Kunwar Singh University, Arrah, Bihar, India
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42
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Massive parallel sequencing of mitochondrial DNA genomes from mother-child pairs using the ion torrent personal genome machine (PGM). Forensic Sci Int Genet 2018; 32:88-93. [DOI: 10.1016/j.fsigen.2017.11.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 09/26/2017] [Accepted: 11/05/2017] [Indexed: 11/15/2022]
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43
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Cho S, Kim MY, Lee JH, Lee SD. Assessment of mitochondrial DNA heteroplasmy detected on commercial panel using MPS system with artificial mixture samples. Int J Legal Med 2017; 132:1049-1056. [PMID: 29279961 DOI: 10.1007/s00414-017-1755-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 11/30/2017] [Indexed: 01/05/2023]
Abstract
Mitochondrial DNA (mtDNA) heteroplasmy is a potential genetic marker for forensic mtDNA analysis as well as phylogenic studies. Frequency of mtDNA heteroplasmy has been investigated in different populations through massively parallel sequencing (MPS) analysis, revealing various levels of frequency based on different MPS systems. For accurate heteroplasmy identification, it is essential to explore reliable detection threshold on various MPS systems. In addition, software solutions and pipelines need to be evaluated to analyze data effectively. In this study, heteroplasmy analysis was conducted on a commercially available mtDNA analysis system developed for forensic caseworks with artificially mixed DNA samples known for ratios and variant positions for assessment. mtDNA heteroplasmy > 10% was detectable with Torrent Variant Caller (TVC) while lower levels were identified using GeneMarker® HTS specialized software for minor variant detection. This study implies that analytical parameters and tools need to be optimized and evaluated for low-level heteroplasmy identification. Automated system with simple and efficient workflow is needed for forensic caseworks.
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Affiliation(s)
- Sohee Cho
- Institute of Forensic Science, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul, 03080, South Korea
| | - Moon Young Kim
- Department of Forensic Medicine, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul, 03080, South Korea
| | - Ji Hyun Lee
- Department of Forensic Medicine, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul, 03080, South Korea
| | - Soong Deok Lee
- Institute of Forensic Science, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul, 03080, South Korea. .,Department of Forensic Medicine, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul, 03080, South Korea.
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Pan Z, Usui H, Sato A, Shozu M. Complete hydatidiform moles are composed of paternal chromosomes and maternal mitochondria. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:943-950. [PMID: 29037102 DOI: 10.1080/24701394.2017.1389916] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Mitochondrial DNA (mtDNA) and genomic DNA are produced in separate subcellular compartments. Human mtDNA is transmitted via maternal transmission in general. Complete hydatidiform moles (CHMs) represent major trophoblastic diseases that are cytogenetically exceptional because the chromosomal genomic DNA is derived only from sperm cells, making them strikingly different from normal concepti. However, few reports have described the mtDNA-transmission pattern in hydatidiform moles. To evaluate mtDNA transmission in androgenetic CHMs, we compared the sequences of hypervariable regions in 16 trios sets of mtDNAs from maternal, paternal, and villous samples of androgenetic CHMs diagnosed by short tandem repeat-polymorphism analysis. All mtDNAs in androgenetic CHMs were maternally derived, in line with the general human inheritance pattern. Three maternal mtDNAs were heteroplasmic. The heterozygous status of maternal mtDNA was reflected in villous tissue, in which variants status was also heterozygous. CHMs are composed of paternal chromosomes and maternal mitochondria.
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Affiliation(s)
- Zijun Pan
- a Department of Reproductive Medicine , Graduate School of Medicine, Chiba University , Chiba , Japan
| | - Hirokazu Usui
- a Department of Reproductive Medicine , Graduate School of Medicine, Chiba University , Chiba , Japan
| | - Asuka Sato
- a Department of Reproductive Medicine , Graduate School of Medicine, Chiba University , Chiba , Japan
| | - Makio Shozu
- a Department of Reproductive Medicine , Graduate School of Medicine, Chiba University , Chiba , Japan
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Wesselink M, Desmyter S, Kuiper I. Local populations and inaccuracies: Determining the relevant mitochondrial haplotype distributions for North West European cats. Forensic Sci Int Genet 2017. [DOI: 10.1016/j.fsigen.2017.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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46
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Arenas M, Pereira F, Oliveira M, Pinto N, Lopes AM, Gomes V, Carracedo A, Amorim A. Forensic genetics and genomics: Much more than just a human affair. PLoS Genet 2017; 13:e1006960. [PMID: 28934201 PMCID: PMC5608170 DOI: 10.1371/journal.pgen.1006960] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
While traditional forensic genetics has been oriented towards using human DNA in criminal investigation and civil court cases, it currently presents a much wider application range, including not only legal situations sensu stricto but also and, increasingly often, to preemptively avoid judicial processes. Despite some difficulties, current forensic genetics is progressively incorporating the analysis of nonhuman genetic material to a greater extent. The analysis of this material-including other animal species, plants, or microorganisms-is now broadly used, providing ancillary evidence in criminalistics in cases such as animal attacks, trafficking of species, bioterrorism and biocrimes, and identification of fraudulent food composition, among many others. Here, we explore how nonhuman forensic genetics is being revolutionized by the increasing variety of genetic markers, the establishment of faster, less error-burdened and cheaper sequencing technologies, and the emergence and improvement of models, methods, and bioinformatics facilities.
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Affiliation(s)
- Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Filipe Pereira
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Porto, Portugal
| | - Manuela Oliveira
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- Faculty of Sciences, University of Porto, Porto, Portugal
| | - Nadia Pinto
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- Centre of Mathematics of the University of Porto, Porto, Portugal
| | - Alexandra M. Lopes
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Veronica Gomes
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Angel Carracedo
- Institute of Forensic Sciences Luis Concheiro, University of Santiago de Compostela, Santiago de Compostela, Spain
- Genomics Medicine Group, CIBERER, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Antonio Amorim
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- Faculty of Sciences, University of Porto, Porto, Portugal
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47
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Riman S, Kiesler KM, Borsuk LA, Vallone PM. Characterization of NIST human mitochondrial DNA SRM-2392 and SRM-2392-I standard reference materials by next generation sequencing. Forensic Sci Int Genet 2017; 29:181-192. [DOI: 10.1016/j.fsigen.2017.04.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 03/17/2017] [Accepted: 04/04/2017] [Indexed: 12/12/2022]
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48
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Bhatti S, Aslam Khan M, Abbas S, Attimonelli M, Gonzalez GR, Aydin HH, de Souza EMS. Problems in Mitochondrial DNA forensics: while interpreting length heteroplasmy conundrum of various Sindhi and Baluchi ethnic groups of Pakistan. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:501-510. [DOI: 10.1080/24701394.2017.1310853] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Shahzad Bhatti
- Human genetics and Molecular Biology, University of Health Sciences, Lahore, Pakistan
- IMBB, The University of Lahore, Lahore, Pakistan
| | - Muhammad Aslam Khan
- Human Genetics and Molecular Biology, University of Health Sciences Lahore, Lahore, Pakistan
| | - Sana Abbas
- Institute of Molecular Biology and Biotechnology, University of Lahore, Lahore, Pakistan
| | - Marcella Attimonelli
- Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy
| | | | | | - Erica Martinha Silva de Souza
- Nacional de Pesquisa, Manaus Programa de Pós Graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia Av. André Araújo, Manaus, Aleixo, Brazil
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Park S, Cho S, Seo HJ, Lee JH, Kim MY, Lee SD. Entire Mitochondrial DNA Sequencing on Massively Parallel Sequencing for the Korean Population. J Korean Med Sci 2017; 32:587-592. [PMID: 28244283 PMCID: PMC5334155 DOI: 10.3346/jkms.2017.32.4.587] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 01/15/2017] [Indexed: 12/02/2022] Open
Abstract
Mitochondrial DNA (mtDNA) genome analysis has been a potent tool in forensic practice as well as in the understanding of human phylogeny in the maternal lineage. The traditional mtDNA analysis is focused on the control region, but the introduction of massive parallel sequencing (MPS) has made the typing of the entire mtDNA genome (mtGenome) more accessible for routine analysis. The complete mtDNA information can provide large amounts of novel genetic data for diverse populations as well as improved discrimination power for identification. The genetic diversity of the mtDNA sequence in different ethnic populations has been revealed through MPS analysis, but the Korean population not only has limited MPS data for the entire mtGenome, the existing data is mainly focused on the control region. In this study, the complete mtGenome data for 186 Koreans, obtained using Ion Torrent Personal Genome Machine (PGM) technology and retrieved from rather common mtDNA haplogroups based on the control region sequence, are described. The results showed that 24 haplogroups, determined with hypervariable regions only, branched into 47 subhaplogroups, and point heteroplasmy was more frequent in the coding regions. In addition, sequence variations in the coding regions observed in this study were compared with those presented in other reports on different populations, and there were similar features observed in the sequence variants for the predominant haplogroups among East Asian populations, such as Haplogroup D and macrohaplogroups M9, G, and D. This study is expected to be the trigger for the development of Korean specific mtGenome data followed by numerous future studies.
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Affiliation(s)
- Sohyung Park
- Medical Examiner's Office, National Forensic Service, Wonju, Korea
| | - Sohee Cho
- Institute of Forensic Science, Seoul National University College of Medicine, Seoul, Korea
| | - Hee Jin Seo
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Ji Hyun Lee
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Moon Young Kim
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Soong Deok Lee
- Institute of Forensic Science, Seoul National University College of Medicine, Seoul, Korea
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, Korea.
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Williams DW, Gibson G. Individualization of pubic hair bacterial communities and the effects of storage time and temperature. Forensic Sci Int Genet 2017; 26:12-20. [DOI: 10.1016/j.fsigen.2016.09.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 09/12/2016] [Accepted: 09/26/2016] [Indexed: 12/30/2022]
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