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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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2
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Mitchell MR, Chaseling J, Jones L, White T, Bernie A, Haupt LM, Griffiths LR, Wright KM. Improving the strategy to identify historical military remains: a literature review and Y-STR meta-analysis. Forensic Sci Res 2024; 9:owad050. [PMID: 38562552 PMCID: PMC10982847 DOI: 10.1093/fsr/owad050] [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: 09/08/2022] [Accepted: 09/26/2023] [Indexed: 04/04/2024] Open
Abstract
The identification of historical military remains by Unrecovered War Casualties-Army (UWC-A) currently relies on Y-chromosome Short Tandem Repeat (Y-STR) testing when maternal relatives are not available, or when a mitochondrial DNA match does not provide sufficient certainty of identification. However, common Y-STR profiles (using Yfiler™) between sets of remains or families often prevent identification. To resolve these cases, an investigation of additional Y-DNA markers is needed for their potential inclusion into the DNA identification strategy. The number of genetic transmissions between missing soldiers and their living relatives needs to be considered to avoid false exclusions between paternal relatives. Analysis of 236 World War I/II (WWI/II) era pairs of relatives identified up to seven genetic transmissions between WWII soldiers and their living relatives, and nine for WWI. Previous Y-STR meta-analyses were published approximately 10 years ago when rapidly mutating markers were relatively new. This paper reports a contemporary literature review and meta-analysis of 35 studies (which includes 23 studies not previously used in meta-analysis) and 23 commonly used Y-STR's mutation rates to inform the inclusion of additional loci to UWC-A's DNA identification strategy. Meta-analysis found mutation data for a given Y-STR locus could be pooled between studies and that the mutation rates were significantly different between some loci (at P < 0.05). Based on this meta-analysis, we have identified two additional markers from PowerPlex® Y23 for potential inclusion in UWC-A's identification strategy. Further avenues for potential experimental exploration are discussed. Key points From 236 UWC-A pairs of relatives, we observed up to nine genetic transmissions between WWI soldiers and their living relatives, and seven for WWII.MedCalc® software for meta-analysis utilizing the Freeman-Tukey transformation was run, which analysed 35 published studies and 23 commonly used loci. Previous Y-STR mutation rate meta-analyses are now 10 years old; this paper includes 23 studies that were not included in previous meta-analyses.Through meta-analysis, we identify two markers from PowerPlex® Y23 for potential inclusion in UWC-A's historical remains identification strategy (alongside Yfiler™). We discuss potential next steps for experimental exploration of additional Y-DNA markers.
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Affiliation(s)
- Melinda R Mitchell
- Queensland University of Technology (QUT), Genomics Research Centre, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Kelvin Grove, Queensland, Australia
| | - Janet Chaseling
- Queensland University of Technology (QUT), Genomics Research Centre, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Kelvin Grove, Queensland, Australia
| | - Lee Jones
- Queensland University of Technology (QUT), Research Methods Group, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Kelvin Grove, Queensland, Australia
| | - Toni White
- Queensland University of Technology (QUT), Defence Innovation Hub, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Kelvin Grove, Queensland, Australia
| | - Andrew Bernie
- Unrecovered War Casualties-Army, Australian Defence Force, Russell Offices, Russell, Australian Capital Territory, Australia
| | - Larisa M Haupt
- Queensland University of Technology (QUT), Genomics Research Centre, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Kelvin Grove, Queensland, Australia
| | - Lyn R Griffiths
- Queensland University of Technology (QUT), Genomics Research Centre, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Kelvin Grove, Queensland, Australia
| | - Kirsty M Wright
- Queensland University of Technology (QUT), Genomics Research Centre, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Kelvin Grove, Queensland, Australia
- Unrecovered War Casualties-Army, Australian Defence Force, Russell Offices, Russell, Australian Capital Territory, Australia
- Royal Australian Air Force (RAAF), No 2 Expeditionary Health Squadron, RAAF Base Williamtown, Williamtown, New South Wales, Australia
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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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Zupanič Pajnič I, Mlinšek T, Počivavšek T, Leskovar T. Genetic sexing of subadult skeletal remains. Sci Rep 2023; 13:20463. [PMID: 37993531 PMCID: PMC10665466 DOI: 10.1038/s41598-023-47836-9] [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: 07/20/2023] [Accepted: 11/19/2023] [Indexed: 11/24/2023] Open
Abstract
When subadult skeletons need to be identified, biological sex diagnosis is one of the first steps in the identification process. Sex assessment of subadults using morphological features is unreliable, and molecular genetic methods were applied in this study. Eighty-three ancient skeletons were used as models for poorly preserved DNA. Three sex-informative markers on the Y and X chromosome were used for sex identification: a qPCR test using the PowerQuant Y target included in PowerQuant System (Promega), the amelogenin test included in ESI 17 Fast STR kit (Promega), and a Y-STR amplification test using the PowerPlex Y-23 kit (Promega). Sex was successfully determined in all but five skeletons. Successful PowerQuant Y-target, Y-amelogenin, and Y-chromosomal STR amplifications proved the presence of male DNA in 35 skeletons, and in 43 subadults female sex was established. No match was found between the genetic profiles of subadult skeletons, and the elimination database and negative control samples produced no profiles, indicating no contamination issue. Our study shows that genetic sex identification is a very successful approach for biological sexing of subadult skeletons whose sex cannot be assessed by anthropological methods. The results of this study are applicable for badly preserved subadult skeletons from routine forensic casework.
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Affiliation(s)
- Irena Zupanič Pajnič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia.
| | - Teo Mlinšek
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia
| | - Tadej Počivavšek
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia
| | - Tamara Leskovar
- Centre for Interdisciplinary Research in Archaeology, Department of Archaeology, Faculty of Arts, University of Ljubljana, Ljubljana, Slovenia
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Jiang L, Liu J, Li S, Wen Y, Zheng X, Qin L, Hou Y, Wang Z. CmVCall: An automated and adjustable nanopore analysis pipeline for heteroplasmy detection of the control region in human mitochondrial genome. Forensic Sci Int Genet 2023; 67:102930. [PMID: 37595417 DOI: 10.1016/j.fsigen.2023.102930] [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: 04/13/2023] [Revised: 08/09/2023] [Accepted: 08/10/2023] [Indexed: 08/20/2023]
Abstract
Genetic associations between human mitochondrial DNA (mtDNA) heteroplasmy and mitochondrial diseases, aging, and cancer have been elaborated, contributing a lot to the further understanding of mtDNA polymorphic spectrum in anthropology, population, and forensic genetics. In the past decade, heteroplasmy detection using Sanger sequencing and next generation sequencing (NGS) was hampered by the former's inefficiency and the latter's inherent bias due to amplification and mapping of short reads, respectively. Nanopore sequencing stands out for its ability to yield long contiguous segments of DNA, providing a new insight into heterogeneity authentication. In addition to MinION from Oxford Nanopore Technologies, an alternative nanopore sequencer QNome (Qitan Technology) has also been applied to various biological research and the forensic applicability of this platform has been proved recently. In this study, we evaluated the performance of four commonly used variant callers in the heterogeneity authentication of the control region of human mtDNA based on simulations of different ratios generated by mixing QNome nanopore sequencing reads of two synthetic sequences. Then, an open-source and python-based nanopore analytics pipeline, CmVCall was developed and incorporated multiple programs including reads filtering, removal of nuclear mitochondrial sequences (NUMTs), alignment, optional 'Correction' mode, and heterogeneity identification. CmVCall can achieve high precision, accuracy, and recall of 100%, 99.9%, and 92.3% with a 5% heteroplasmy level in 'Correction' mode. Moreover, blood, saliva, and hair shaft samples from monozygotic (MZ) twins were used for heterogeneity evaluation and comparison with the NGS data. Results of MZ twin samples showed that CmVCall could identify more point heteroplasmy sites, revealing significant levels of inter- and intra-individual mtDNA polymorphism. In conclusion, we believe that this analysis pipeline will lay a solid foundation for the development of a comprehensive nanopore analysis pipeline targeting the whole mitochondrial genome.
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Affiliation(s)
- Lirong Jiang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Jing Liu
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Suyu Li
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Yufeng Wen
- School of Life Sciences, Jilin University, Changchun 130012, China
| | - Xinyue Zheng
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Liu Qin
- Qitan Technology Ltd., Chengdu, Chengdu 610044, China.
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China.
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China.
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Ibrahim AH, Rahman NNA, Saifuddeen SM. Mitochondrial Replacement Therapy: An Islamic Perspective. JOURNAL OF BIOETHICAL INQUIRY 2023; 20:485-495. [PMID: 37440155 DOI: 10.1007/s11673-023-10279-y] [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: 09/06/2021] [Accepted: 01/19/2023] [Indexed: 07/14/2023]
Abstract
Mitochondrial replacement technology (MRT) is an emerging and complex bioethical issue. This treatment aims to eliminate maternal inherited mitochondrial DNA (mtDNA) disorders. For Muslims, its introduction affects every aspect of human life, especially the five essential interests of human beings-namely, religion, life, lineage, intellect, and property. Thus, this technology must be assessed using a comprehensive and holistic approach addressing these human essential interests. Consequently, this article analyses and assesses tri-parent baby technology from the perspective of Maqasidic bioethics-that is, Islamic bioethics based on the framework of Maqasid al-Shariah. Using this analysis, this article suggests that tri-parent baby technology should not be permitted for Muslims due to the existence of third-party cell gametes which lead to lineage mixing and due to the uncertain safety of the therapy itself and because the major aim of the technology is to fulfil the affected couples interest to conceive their own genetically healthy child, not to treat and cure mtDNA disorders sufferers.
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Affiliation(s)
- Abdul Halim Ibrahim
- Programme of Applied Science with Islamic Studies, Academy of Islamic Studies, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Noor Naemah Abdul Rahman
- Department of Fiqh and Usul, Academy of Islamic Studies, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Shaikh Mohd Saifuddeen
- Centre for Science and Environment Studies, Institute of Islamic Understanding Malaysia, 2 Langgak Tunku Off Jalan Tuanku Abdul Halim, 50480, Kuala Lumpur, Malaysia
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Leskovar T, Mlinšek T, Počivavšek T, Zupanič Pajnič I. Comparison of Morphological Sex Assessment and Genetic Sex Determination on Adult and Sub-Adult 17th-19th Century Skeletal Remains. Genes (Basel) 2023; 14:1561. [PMID: 37628613 PMCID: PMC10454762 DOI: 10.3390/genes14081561] [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: 06/14/2023] [Revised: 07/22/2023] [Accepted: 07/25/2023] [Indexed: 08/27/2023] Open
Abstract
The first step in the analysis of human skeletal remains is the establishment of the biological profile of an individual. This includes sex assessment, which depends highly on the age of the individual and on the completeness and preservation state of the remains. Macroscopic methods only provide the assessment of sex, while for sex determination, molecular methods need to be included. However, poor preservation of the remains can make molecular methods impossible and only assessment can be performed. Presented research compares DNA-determined and morphologically assessed sex of adult and non-adult individuals buried in a modern-age cemetery (17th to late 19th century) in Ljubljana, Slovenia. The aim of the study was to assess the accuracy of commonly used macroscopic methods for sex assessment on a Slovenian post-medieval population. Results demonstrate that for adults, macroscopic methods employed are highly reliable and pelvic morphology, even the sciatic notch alone, is more reliable than skull. In non-adults, macroscopic methods are not as reliable as in adults, which agrees with previous research. This study shows how morphological and molecular methods can go hand in hand when building a biological profile of an individual. On their own, each methodology presented some individuals with undetermined sex, while together, sex of all the individuals was provided. Results confirm suitability of sex assessment based on skull and especially pelvic morphology in Slovenian post-medieval adults, while in the non-adult population molecular methods are advised.
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Affiliation(s)
- Tamara Leskovar
- Centre for Interdisciplinary Research in Archaeology, Department of Archaeology, Faculty of Arts, University of Ljubljana, 1000 Ljubljana, Slovenia;
| | - Teo Mlinšek
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia; (T.M.); (T.P.)
| | - Tadej Počivavšek
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia; (T.M.); (T.P.)
| | - Irena Zupanič Pajnič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia; (T.M.); (T.P.)
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8
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Zupanič Pajnič I, Geršak ŽM, Leskovar T, Črešnar M. Kinship analysis of 5th- to 6th-century skeletons of Romanized indigenous people from the Bled-Pristava archaeological site. Forensic Sci Int Genet 2023; 65:102886. [PMID: 37137206 DOI: 10.1016/j.fsigen.2023.102886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 03/31/2023] [Accepted: 04/27/2023] [Indexed: 05/05/2023]
Abstract
The familial relationship between skeletons buried together in a shared grave is important for understanding the burial practices of past human populations. Four skeletons were excavated from the Late Antiquity part of the Bled-Pristava burial site in Slovenia, dated to the 5th to 6th century. They were anthropologically characterized as two adults (a middle-aged man and a young woman) and two non-adults (of unknown sex). Based on stratigraphy, the skeletons were considered to be buried simultaneously in one grave. Our aim was to determine whether the skeletons were related. Petrous bones and teeth were used for genetic analysis. Specific precautions were followed to prevent contamination of ancient DNA with contemporary DNA, and an elimination database was established. Bone powder was obtained using a MillMix tissue homogenizer. Prior to extracting the DNA using Biorobot EZ1, 0.5 g of powder was decalcified. The PowerQuant System was used for quantification, various autosomal kits for autosomal short tandem repeat (STR) typing, and the PowerPlex Y23 kit for Y-STR typing. All analyses were performed in duplicate. Up to 28 ng DNA/g of powder was extracted from the samples analyzed. Almost full autosomal STR profiles obtained from all four skeletons and almost full Y-STR haplotypes obtained from two male skeletons were compared, and the possibility of a familial relationship was evaluated. No amplification was obtained in the negative controls, and no match was found in the elimination database. Autosomal STR statistical calculations confirmed that the adult male was the father of two non-adult individuals and one young adult individual from the grave. The relationship between the males (father and son) was additionally confirmed by an identical Y-STR haplotype that belonged to the E1b1b haplogroup, and a combined likelihood ratio for autosomal and Y-STRs was calculated. Kinship analysis confirmed with high confidence (kinship probability greater than 99.9% was calculated for all three children) that all four skeletons belonged to the same family (a father, two daughters, and a son). Through genetic analysis, the burial of members of the same family in a shared grave was confirmed as a burial practice of the population living in the Bled area in Late Antiquity.
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Affiliation(s)
- Irena Zupanič Pajnič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia.
| | - Živa Miriam Geršak
- Institute of Radiology, University Medical Centre Ljubljana, Zaloška 7, Ljubljana, Slovenia
| | - Tamara Leskovar
- Centre for Interdisciplinary Research in Archaeology, Department of Archaeology, Faculty of Arts, University of Ljubljana, Ljubljana, Slovenia
| | - Matija Črešnar
- Centre for Interdisciplinary Research in Archaeology, Department of Archaeology, Faculty of Arts, University of Ljubljana, Ljubljana, Slovenia
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Peng D, Geng J, Yang J, Liu J, Wang N, Wu R, Sun H. Whole Mitochondrial Genome Detection and Analysis of Two- to Four-Generation Maternal Pedigrees Using a New Massively Parallel Sequencing Panel. Genes (Basel) 2023; 14:genes14040912. [PMID: 37107670 PMCID: PMC10137955 DOI: 10.3390/genes14040912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/08/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Mitochondrial DNA (mtDNA) is an effective genetic marker in forensic practice, especially for aged bones and hair shafts. Detection of the whole mitochondrial genome (mtGenome) using traditional Sanger-type sequencing is laborious and time-consuming. Additionally, its ability to distinguish point heteroplasmy (PHP) and length heteroplasmy (LHP) is limited. The application of massively parallel sequencing in mtDNA detection helps researchers to study the mtGenome in-depth. The ForenSeq mtDNA Whole Genome Kit, which contains a total of 245 short amplicons, is one of the multiplex library preparation kits for the mtGenome. We used this system to detect the mtGenome in the blood samples and hair shafts of thirty-three individuals from eight two-generation pedigrees, one three-generation pedigree, and one four-generation pedigree. High-quality sequencing results were obtained. Ten unique mtGenome haplotypes were observed in the mothers from the ten pedigrees. A total of 26 PHPs were observed using the interpretation threshold of 6%. Eleven types of LHPs in six regions were evaluated in detail. When considering homoplasmic variants only, consistent mtGenome haplotypes were observed between the twice-sequenced libraries and between the blood and hair shafts from the same individual and among maternal relatives in the pedigrees. Four inherited PHPs were observed, and the remainder were de novo/disappearing PHPs in the pedigrees. Our results demonstrate the effective capability of the ForenSeq mtDNA Whole Genome Kit to generate the complete mtGenome in blood and hair shafts, as well as the complexity of mtDNA haplotype comparisons between different types of maternal relatives when heteroplasmy is considered.
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Affiliation(s)
- Dan Peng
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Jiaojiao Geng
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Jingyi Yang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Jiajun Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Nana Wang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Riga Wu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Hongyu Sun
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
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Wagner JK, Yu JH, Fullwiley D, Moore C, Wilson JF, Bamshad MJ, Royal CD. Guidelines for genetic ancestry inference created through roundtable discussions. HGG ADVANCES 2023; 4:100178. [PMID: 36798092 PMCID: PMC9926022 DOI: 10.1016/j.xhgg.2023.100178] [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: 09/02/2022] [Accepted: 01/03/2023] [Indexed: 01/15/2023] Open
Abstract
The use of genetic and genomic technology to infer ancestry is commonplace in a variety of contexts, particularly in biomedical research and for direct-to-consumer genetic testing. In 2013 and 2015, two roundtables engaged a diverse group of stakeholders toward the development of guidelines for inferring genetic ancestry in academia and industry. This report shares the stakeholder groups' work and provides an analysis of, commentary on, and views from the groundbreaking and sustained dialogue. We describe the engagement processes and the stakeholder groups' resulting statements and proposed guidelines. The guidelines focus on five key areas: application of genetic ancestry inference, assumptions and confidence/laboratory and statistical methods, terminology and population identifiers, impact on individuals and groups, and communication or translation of genetic ancestry inferences. We delineate the terms and limitations of the guidelines and discuss their critical role in advancing the development and implementation of best practices for inferring genetic ancestry and reporting the results. These efforts should inform both governmental regulation and self-regulation.
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Affiliation(s)
- Jennifer K. Wagner
- School of Engineering Design and Innovation, Pennsylvania State University, University Park, PA 16802, USA
- Institute for Computational and Data Science, Pennsylvania State University, University Park, PA 16802, USA
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
- Rock Ethics Institute, Pennsylvania State University, University Park, PA 16802, USA
- Penn State Law, University Park, PA 16802, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Joon-Ho Yu
- Department of Pediatrics and Institute for Public Health Genetics, University of Washington, Seattle, WA 98195, USA
- Treuman Katz Center for Pediatric Bioethics, Seattle Children’s Hospital and Research Institute, Seattle, WA 98101, USA
| | - Duana Fullwiley
- Department of Anthropology, Stanford University, Stanford, CA 94305, USA
| | | | - James F. Wilson
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh EH8 9AG, Scotland
| | - Michael J. Bamshad
- Department of Pediatrics and Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Division of Genetic Medicine, Seattle Children’s Hospital, Seattle, WA 98101, USA
| | - Charmaine D. Royal
- Departments of African and African American Studies, Biology, Global Health, and Family Medicine and Community Health, Duke University, Durham, NC 27708, USA
| | - Genetic Ancestry Inference Roundtable Participants
- School of Engineering Design and Innovation, Pennsylvania State University, University Park, PA 16802, USA
- Institute for Computational and Data Science, Pennsylvania State University, University Park, PA 16802, USA
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
- Rock Ethics Institute, Pennsylvania State University, University Park, PA 16802, USA
- Penn State Law, University Park, PA 16802, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
- Department of Pediatrics and Institute for Public Health Genetics, University of Washington, Seattle, WA 98195, USA
- Treuman Katz Center for Pediatric Bioethics, Seattle Children’s Hospital and Research Institute, Seattle, WA 98101, USA
- Department of Anthropology, Stanford University, Stanford, CA 94305, USA
- The DNA Detectives, Dana Point, CA, USA
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh EH8 9AG, Scotland
- Department of Pediatrics and Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Division of Genetic Medicine, Seattle Children’s Hospital, Seattle, WA 98101, USA
- Departments of African and African American Studies, Biology, Global Health, and Family Medicine and Community Health, Duke University, Durham, NC 27708, USA
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Dzehverovic M, Jusic B, Pilav A, Lukic T, Cakar J. Kinship analysis of skeletal remains from the Middle Ages. Forensic Sci Int Genet 2023; 63:102829. [PMID: 36669262 DOI: 10.1016/j.fsigen.2023.102829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 01/13/2023] [Accepted: 01/15/2023] [Indexed: 01/17/2023]
Abstract
Medieval cemeteries Klisa-Guca Gora, Alihodze and Glavica-Han Bila located in the Travnik area (Travnik, Bosnia and Herzegovina) were archaeologically examined in the period 2011-2014, revealing human skeletal remains of 11 individuals in total. Archaeological skeletal samples, previously deposited in Travnik Homeland Museum (Travnik, Bosnia and Herzegovina) were subjected to genetic analysis. The aim of this research was to test familiar relationship of 11 individuals excavated from three medieval cemeteries and to predict Y-haplogroup for male individuals. In order to perform molecular-genetic characterisation of collected human skeletal remains, two systems of genetic markers were analysed: autosomal and Y-STR loci. Complete or partial data obtained by autosomal STR typing of 11 individuals were subjected to kinship analysis. Male sex was determined in eight samples out of 11. Direct relatives of the "brother-brother" type were detected in one case with high kinship probability (KP) value of 99.99996 %. Complete or nearly complete and usable Y-STR profiles were obtained for six out of eight male individuals. The presence of identical haplotypes at Y-STR loci and results of Y-haplogroup prediction suggest that all male individuals share the same paternal lineage and belong to J2a haplogroup. Overall, this study emphasises the usefulness, efficiency and sensitivity of STR markers in the molecular-genetic characterisation of old skeletal remains as well as the importance of employing additional markers like Y-STRs in archaeogenetic studies, besides traditionally used autosomal STR markers, in order to get a comprehensive information about close and distant relatives, and ancestry.
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Affiliation(s)
- Mirela Dzehverovic
- University of Sarajevo-Institute for Genetic Engineering and Biotechnology, Zmaja od Bosne 8, Sarajevo, Bosnia and Herzegovina
| | - Belma Jusic
- University of Sarajevo-Institute for Genetic Engineering and Biotechnology, Zmaja od Bosne 8, Sarajevo, Bosnia and Herzegovina.
| | - Amela Pilav
- University of Sarajevo-Institute for Genetic Engineering and Biotechnology, Zmaja od Bosne 8, Sarajevo, Bosnia and Herzegovina
| | - Tamara Lukic
- Faculty of Science, University of Sarajevo, Zmaja od Bosne 33-35, Sarajevo, Bosnia and Herzegovina
| | - Jasmina Cakar
- University of Sarajevo-Institute for Genetic Engineering and Biotechnology, Zmaja od Bosne 8, Sarajevo, Bosnia and Herzegovina
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12
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An Accurate and Rapid Way for Identifying Food Geographical Origin and Authenticity: Editable DNA-Traceable Barcode. Foods 2022; 12:foods12010017. [PMID: 36613233 PMCID: PMC9818171 DOI: 10.3390/foods12010017] [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: 11/15/2022] [Revised: 12/08/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022] Open
Abstract
DNA offers significant advantages in information density, durability, and replication efficiency compared with information labeling solutions using electronic, magnetic, or optical devices. Synthetic DNA containing specific information via gene editing techniques is a promising identifying approach. We developed a new traceability approach to convert traditional digitized information into DNA sequence information. We used encapsulation to make it stable for storage and to enable reading and detection by DNA sequencing and PCR-capillary electrophoresis (PCR-CE). The synthesized fragment consisted of a short fragment of the mitochondrial cytochrome oxidase subunit I (COI) gene from the Holothuria fuscogilva (ID: LC593268.1), inserted geographical origin information (18 bp), and authenticity information from Citrus sinensis (20 bp). The obtained DNA-traceable barcodes were cloned into vector PMD19-T. Sanger sequencing of the DNA-traceable barcode vector was 100% accurate and provided a complete readout of the traceability information. Using selected recognition primers CAI-B, DNA-traceable barcodes were identified rapidly by PCR amplification. We encapsulated the DNA-traceable barcodes into amorphous silica spheres and improved the encapsulation procedure to ensure the durability of the DNA-traceable barcodes. To demonstrate the applicability of DNA-traceable barcodes as product labels, we selected Citrus sinensis as an example. We found that the recovered and purified DNA-traceable barcode can be analyzed by standard techniques (PCR-CE for DNA-traceable barcode identification and DNA sequencing for readout). This study provides an accurate and rapid approach to identifying and certifying products' authenticity and traceability.
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13
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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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14
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Loreille O, Tillmar A, Brandhagen MD, Otterstatter L, Irwin JA. Improved DNA Extraction and Illumina Sequencing of DNA Recovered from Aged Rootless Hair Shafts Found in Relics Associated with the Romanov Family. Genes (Basel) 2022; 13:genes13020202. [PMID: 35205247 PMCID: PMC8872530 DOI: 10.3390/genes13020202] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/18/2022] [Accepted: 01/20/2022] [Indexed: 12/04/2022] Open
Abstract
This study describes an optimized DNA extraction protocol targeting ultrashort DNA molecules from single rootless hairs. It was applied to the oldest samples available to us: locks of hairs that were found in relics associated with the Romanov family. Published mitochondrial DNA genome sequences of Tsar Nicholas II and his wife, Tsarina Alexandra, made these samples ideal to assess this DNA extraction protocol and evaluate the types of genetic information that can be recovered by sequencing ultrashort fragments. Using this method, the mtGenome of the Tsarina’s lineage was identified in hairs that were concealed in a pendant made by Karl Fabergé for Alexandra Feodorovna Romanov. In addition, to determine if the lock originated from more than one individual, two hairs from the lock were extracted independently and converted into Illumina libraries for shotgun sequencing on a NextSeq 500 platform. From these data, autosomal SNPs were analyzed to assess relatedness. The results indicated that the two hairs came from a single individual. Genetic testing of hairs that were found in the second artifact, a framed photograph of Louise of Hesse-Kassel, Queen of Denmark and maternal grandmother of Tsar Nicholas II, revealed that the hair belonged to a woman who shared Tsar Nicholas’ maternal lineage, including the well-known point heteroplasmy at position 16169.
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Affiliation(s)
- Odile Loreille
- Federal Bureau of Investigation Laboratory, DNA Support Unit, Quantico, VA 22135, USA; (M.D.B.); (J.A.I.)
- Correspondence:
| | - Andreas Tillmar
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, SE-587 58 Linkoping, Sweden;
- Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University, SE-582 25 Linkoping, Sweden
| | - Michael D. Brandhagen
- Federal Bureau of Investigation Laboratory, DNA Support Unit, Quantico, VA 22135, USA; (M.D.B.); (J.A.I.)
| | - Linda Otterstatter
- Federal Bureau of Investigation Laboratory, Trace Evidence Unit, Quantico, VA 22135, USA;
| | - Jodi A. Irwin
- Federal Bureau of Investigation Laboratory, DNA Support Unit, Quantico, VA 22135, USA; (M.D.B.); (J.A.I.)
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15
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Xin Y, Jia R, Zhang S, Guo F. Mitochondrial genome sequencing with short overlapping amplicons on MiSeq FGx system. Forensic Sci Res 2021; 7:142-153. [PMID: 35784421 PMCID: PMC9246037 DOI: 10.1080/20961790.2021.1963514] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/22/2021] [Accepted: 07/29/2021] [Indexed: 11/03/2022] Open
Abstract
With the development and maturation of massively parallel sequencing (MPS) technology, the mitochondrial genome (mitogenome) sequencing is increasingly applied in the forensic field. In this study, we employed the strategy of short overlapping amplicons for the whole mitogenome, library preparation with tagmentation using the Nextera® XT DNA Library Preparation Kit, sequencing on the MiSeq FGxTM Forensic Genomics System and analyzing data using the mitochondrial(mtDNA) MSR Plug-in and the mtDNA Variant Analyzer. A total of 27 libraries and 56 libraries were sequenced in a run using MiSeq Reagent Kit v2 and v3, respectively. Results showed more than 1800 × of averaged depth of coverage (DoC) at each position. Concordant haplotypes of 9947 A and 2800 M were obtained at 32 variants. Cross-reactivity was observed with 1 ng primate DNA and 10 ng non-primate DNA but could be easily distinguished. Full and accurate variants were obtained from at least 50 pg input DNA and from minor contributors between 19:1 and 1:19 mixed ratios with known reference profiles. More than 86% variants were detected from ≥200-bp degraded samples but its haplotype was assigned to more ancestral haplogroup. Further, a total of 3 962 variants were observed at 613 nucleotide positions from 103 Xibe mitogenomes with 25:1 ratio of transitions to transversions. Two new transversions (C13735A and A14755C) and two tri-alleles at nps 9824 and 16092 were identified. There were 103 unique mitogenome haplotypes from 103 Chinese Xibe that were assigned to 79 haplogroups. Haplogroup D was the preponderant top-level haplogroup in Xibe followed by F, B, M, A, N, G, C, Z, Y, HV and J. Random match probability (RMP) and haplotype diversity (HD) of the whole mitogenome was calculated as 0.0097 and 1.0000, respectively. Compared with HVS-I only, RMP decreased 33.56%, while the number of haplotypes and HD increased 15.73% and 0.49%, respectively. Principal component analysis (PCA) showed that Xibe was clustered to East and Southeast Asian. As a whole, this MPS strategy is suitable for the whole mitogenome sequencing especially for degraded samples and can facilitate generating mitogenome data to support the routine application in forensic sciences. EMP00726 is the first whole mitogenome dataset from Xibe contributed to the EMPOP. Supplemental data for this article are available online at.
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Affiliation(s)
- Yang Xin
- Forensic Science College, Criminal Investigation Police University of China, Shenyang, China
| | - Rulin Jia
- Forensic Science College, Criminal Investigation Police University of China, Shenyang, China
| | - Suhua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, China
| | - Fei Guo
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, China
- Forensic Science College, Criminal Investigation Police University of China, Shenyang, China
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16
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Genealogy: The Tree Where History Meets Genetics. GENEALOGY 2021. [DOI: 10.3390/genealogy5040098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Although biological relationships are a universal reality for all human beings, the concepts of “family” and “family bond” depend on both the geographic region and the historical moment to which they refer. However, the concept of “family” can be determinant in a large variety of societies, since it can influence the lines of succession, inheritances and social relationships, as well as where and with whom an individual is buried. The relation between a deceased person and other members of a community, other individuals of the same necropolis, or even with those who are buried in the same tomb can be analysed from the genetic point of view, considering different perspectives: archaeological, historical, and forensic. In the present work, the concepts of “family” and “kinship” are discussed, explaining the relevance of genetic analysis, such as nuclear and lineage markers, and their contribution to genealogical research, for example in the heritage of surnames and Y-chromosome, as well as those cases where some discrepancies with historical record are detected, such as cases of adoption. Finally, we explain how genetic genealogical analyses can help to solve some cold cases, through the analysis of biologically related relatives.
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17
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Moltke I, Korneliussen TS, Seguin-Orlando A, Moreno-Mayar JV, LaPointe E, Billeck W, Willerslev E. Identifying a living great-grandson of the Lakota Sioux leader Tatanka Iyotake (Sitting Bull). SCIENCE ADVANCES 2021; 7:eabh2013. [PMID: 34705496 PMCID: PMC8550246 DOI: 10.1126/sciadv.abh2013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
A great-grandson of the legendary Lakota Sioux leader Sitting Bull (Tatanka Iyotake), Ernie LaPointe, wished to have their familial relationship confirmed via genetic analysis, in part, to help settle concerns over Sitting Bull’s final resting place. To address Ernie LaPointe’s claim of family relationship, we obtained minor amounts of genomic data from a small piece of hair from Sitting Bull’s scalp lock, which was repatriated in 2007. We then compared these data to genome-wide data from LaPointe and other Lakota Sioux using a new probabilistic approach and concluded that Ernie LaPointe is Sitting Bull’s great-grandson. To our knowledge, this is the first published example of a familial relationship between contemporary and a historical individual that has been confirmed using such limited amounts of ancient DNA across such distant relatives. Hence, this study opens the possibility for broadening genealogical research, even when only minor amounts of ancient genetic material are accessible.
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Affiliation(s)
- Ida Moltke
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Thorfinn Sand Korneliussen
- Lundbeck Foundation GeoGenetics Centre, University of Copenhagen, Copenhagen, Denmark
- National Research University Higher School of Economics, Moscow, Russian Federation
| | - Andaine Seguin-Orlando
- Lundbeck Foundation GeoGenetics Centre, University of Copenhagen, Copenhagen, Denmark
- Centre for Anthropobiology and Genomics of Toulouse UMR 5288, CNRS, University of Toulouse III Paul Sabatier, Toulouse, France
- Institute for Advanced Study in Toulouse, University of Toulouse I Capitole, Toulouse, France
| | | | | | - William Billeck
- Department of Anthropology, Smithsonian Institution, National Museum of Natural History, Washington, DC 20560, USA
| | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Centre, University of Copenhagen, Copenhagen, Denmark
- Department of Zoology, University of Cambridge, Cambridge, UK
- Wellcome Trust Sanger Institute, Cambridge, UK
- Danish Institute for Advanced Study, University of Southern Denmark, Odense, Denmark
- Corresponding author.
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18
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Wurst C, Maixner F, Castella V, Cipollini G, Hotz G, Zink A. The Lady from Basel's Barfüsserkirche - Molecular confirmation of the Mummy's identity through mitochondrial DNA of living relatives spanning 22 generations. Forensic Sci Int Genet 2021; 56:102604. [PMID: 34656830 DOI: 10.1016/j.fsigen.2021.102604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/04/2021] [Accepted: 10/06/2021] [Indexed: 11/26/2022]
Abstract
The identity of the mummified Lady from the Barfüsser Church in Basel, Switzerland has been unsolved for decades, despite the prominent location of the burial place in front of the choir screen. A recent multidisciplinary research approach came up with a possible candidate, Anna Catharina Bischoff who died in Basel in 1787 with an age of 69 years (1719-1787). To verify the identity of the mummy, genealogists of the Citizen Science Basel discovered three living individuals of the maternal lineage of two different family branches, separated from Anna Catharina Bischoff by up to 22 generations. In this study we compare the ancient mitochondrial DNA of the mummy recovered from a premolar to the mitochondrial DNA of these three candidates. Initially the mitochondrial hypervariable regions I and II of the living individuals were screened using the Sanger sequencing method. This was followed by a mitochondrial capture approach and next generation sequencing to enrich for the whole mitochondrial genome of the mummy and one living person. A full mitochondrial genome has been recovered of both individuals sharing an identical haplotype. The sequence was assigned to the mitochondrial haplogroup U5a1+!16192 including two private mutations 10006G and 16293C. Only by using an interdisciplinary approach combining ancient DNA analysis and genealogy a maternal lineage of a non-noble family spanning 22 generations could be confirmed.
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Affiliation(s)
- Christina Wurst
- Institute for Mummy Studies, Eurac Research, Drususallee/Viale Druso 1, 39100 Bozen, Bolzano, Italy; Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg-University Mainz, Saarstraße 21, 55122 Mainz, Germany.
| | - Frank Maixner
- Institute for Mummy Studies, Eurac Research, Drususallee/Viale Druso 1, 39100 Bozen, Bolzano, Italy
| | - Vincent Castella
- Forensic Genetics Unit, University Center of Legal Medicine, Lausanne - Geneva, Lausanne University Hospital and University of Lausanne, Ch. de la Vulliette 4, 1000 Lausanne 25, Switzerland
| | - Giovanna Cipollini
- Institute for Mummy Studies, Eurac Research, Drususallee/Viale Druso 1, 39100 Bozen, Bolzano, Italy
| | - Gerhard Hotz
- Natural History Museum Basel, Augustinergasse 2, 4051 Basel, Switzerland; Integrative Prehistory and Archaeological Science, University of Basel, Bernoullistrasse 32, 4056 Basel, Switzerland
| | - Albert Zink
- Institute for Mummy Studies, Eurac Research, Drususallee/Viale Druso 1, 39100 Bozen, Bolzano, Italy
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19
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St John JC. Epigenetic Regulation of the Nuclear and Mitochondrial Genomes: Involvement in Metabolism, Development, and Disease. Annu Rev Anim Biosci 2021; 9:203-224. [PMID: 33592161 DOI: 10.1146/annurev-animal-080520-083353] [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] [Indexed: 11/09/2022]
Abstract
Our understanding of the interactions between the nuclear and mitochondrial genomes is becoming increasingly important as they are extensively involved in establishing early development and developmental progression. Evidence from various biological systems indicates the interdependency between the genomes, which requires a high degree of compatibility and synchrony to ensure effective cellular function throughout development and in the resultant offspring. During development, waves of DNA demethylation, de novo methylation, and maintenance methylation act on the nuclear genome and typify oogenesis and pre- and postimplantation development. At the same time, significant changes in mitochondrial DNA copy number influence the metabolic status of the developing organism in a typically cell-type-specific manner. Collectively, at any given stage in development, these actions establish genomic balance that ensures each developmental milestone is met and that the organism's program for life is established.
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Affiliation(s)
- Justin C St John
- Mitochondrial Genetics Group, Robinson Research Institute and School of Medicine, University of Adelaide, Adelaide, South Australia 5005, Australia;
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20
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Mitochondrial DNA in forensic use. Emerg Top Life Sci 2021; 5:415-426. [PMID: 34374411 PMCID: PMC8457767 DOI: 10.1042/etls20210204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 06/27/2021] [Accepted: 07/22/2021] [Indexed: 01/02/2023]
Abstract
Genetic analysis of mitochondrial DNA (mtDNA) has always been a useful tool for forensic geneticists, mainly because of its ubiquitous presence in biological material, even in the absence of nuclear DNA. Sequencing, however, is not a skill that is part of the routine forensic analysis because of the relative rarity of requests, and the need for retention of necessary skill sets and associated accreditation issues. While standard Sanger sequencing may be relatively simple, many requests are made in the face of compromised biological samples. Newer technologies, provided through massively parallel sequencing (MPS), will increase the opportunity for scientists to include this tool in their routine, particularly for missing person investigations. MPS has also enabled a different approach to sequencing that can increase sensitivity in a more targeted approach. In these circumstances it is likely that only a laboratory that specialises in undertaking forensic mtDNA analysis will be able to take these difficult cases forward, more so because reviews of the literature have revealed significantly high levels of typing errors in publications reporting mtDNA sequences. The forensic community has set out important guidelines, not only in the practical aspects of analysis, but also in the interpretation of that sequence to ensure that accurate comparisons can be made. Analysis of low-level, compromised and ancient DNA is not easy, however, as contamination is extremely difficult to eliminate and circumstances leading to sequencing errors are all too easily introduced. These problems, and solutions, are discussed in the article in relation to several historic cases.
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21
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Bae JH, Zhang DY. Predicting stability of DNA bulge at mononucleotide microsatellite. Nucleic Acids Res 2021; 49:7901-7908. [PMID: 34308470 PMCID: PMC8373066 DOI: 10.1093/nar/gkab616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 06/28/2021] [Accepted: 07/07/2021] [Indexed: 11/14/2022] Open
Abstract
Mononucleotide microsatellites are clinically and forensically crucial DNA sequences due to their high mutability and abundance in the human genome. As a mutagenic intermediate of an indel in a microsatellite and a consequence of probe hybridization after such mutagenesis, a bulge with structural degeneracy sliding within a microsatellite is formed. Stability of such dynamic bulges, however, is still poorly understood despite their critical role in cancer genomics and neurological disease studies. In this paper, we have built a model that predicts the thermodynamics of a sliding bulge at a microsatellite. We first identified 40 common bulge states that can be assembled into any sliding bulges, and then characterized them with toehold exchange energy measurement and the partition function. Our model, which is the first to predict the free energy of sliding bulges with more than three repeats, can infer the stability penalty of a sliding bulge of any sequence and length with a median prediction error of 0.22 kcal/mol. Patterns from the prediction clearly explain landscapes of microsatellites observed in the literature, such as higher mutation rates of longer microsatellites and C/G microsatellites.
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Affiliation(s)
- Jin H Bae
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
| | - David Yu Zhang
- Department of Bioengineering, Rice University, Houston, TX 77005, USA.,Systems, Synthetic, and Physical Biology, Rice University, Houston, TX 77005, USA
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22
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Hofreiter M, Sneberger J, Pospisek M, Vanek D. Progress in forensic bone DNA analysis: Lessons learned from ancient DNA. Forensic Sci Int Genet 2021; 54:102538. [PMID: 34265517 DOI: 10.1016/j.fsigen.2021.102538] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 03/07/2021] [Accepted: 05/25/2021] [Indexed: 01/18/2023]
Abstract
Research on ancient and forensic DNA is related in many ways, and the two fields must deal with similar obstacles. Therefore, communication between these two communities has the potential to improve results in both research fields. Here, we present the insights gained in the ancient DNA community with regard to analyzing DNA from aged skeletal material and the potential use of the developed protocols in forensic work. We discuss the various steps, from choosing samples for DNA extraction to deciding between classical PCR amplification and massively parallel sequencing approaches. Based on the progress made in ancient DNA analyses combined with the requirements of forensic work, we suggest that there is substantial potential for incorporating ancient DNA approaches into forensic protocols, a process that has already begun to a considerable extent. However, taking full advantage of the experiences gained from ancient DNA work will require comparative studies by the forensic DNA community to tailor the methods developed for ancient samples to the specific needs of forensic studies and case work. If successful, in our view, the benefits for both communities would be considerable.
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Affiliation(s)
- Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany.
| | - Jiri Sneberger
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Vinicna 5, Prague 2 12843, Czech Republic; Department of the History of the Middle Ages of Museum of West Bohemia, Kopeckeho sady 2, Pilsen 30100, Czech Republic; Nuclear Physics Institute of the CAS, Na Truhlarce 39/64, Prague 18086, Czech Republic
| | - Martin Pospisek
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Vinicna 5, Prague 2 12843, Czech Republic; Biologicals s.r.o., Sramkova 315, Ricany 25101, Czech Republic
| | - Daniel Vanek
- Forensic DNA Service, Janovskeho 18, Prague 7 17000, Czech Republic; Institute of Legal Medicine, Bulovka Hospital, Prague, Czech Republic; Charles University in Prague, 2nd Faculty of Medicine, Prague, Czech Republic.
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23
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Torres JB. A history of you, me, and humanity: mitochondrial DNA in anthropological research. AIMS GENETICS 2021. [DOI: 10.3934/genet.2016.2.146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
AbstractWithin genetic anthropology, mitochondrial DNA (mtDNA) has garnered a prominent if not enduring place within the anthropological toolkit. MtDNA has provided new and innovative perspectives on the emergence and dispersal of our species, interactions with extinct human species, and illuminated relationships between human groups. In this paper, I provide a brief overview of the major findings ascertained from mtDNA about human origins, human dispersal across the globe, interactions with other hominin species, and the more recent uses of mtDNA in direct to consumer ancestry tests. Relative to nuclear DNA, mtDNA is a small section of the genome and due to its inheritance pattern provides a limited resolution of population history and an individual's genetic ancestry. Consequently, some scholars dismiss mtDNA as insignificant due to the limited inferences that may be made using the locus. Regardless, mtDNA provides some useful insights to understanding how social, cultural, and environmental factors have shaped patterns of genetic variability. Furthermore, with regard to the experiences of historically marginalized groups, in particular those of African descent throughout the Americas, mtDNA has the potential to fill gaps in knowledge that would otherwise remain unknown. Within anthropological sciences, the value of this locus for understanding human experience is maximized when contextualized with complementary lines of evidence.
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Affiliation(s)
- Jada Benn Torres
- Laboratory of Genetic Anthropology, Department of Anthropology, Vanderbilt University, Nashville, TN 37325, USA
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24
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Holt CL, Stephens KM, Walichiewicz P, Fleming KD, Forouzmand E, Wu SF. Human Mitochondrial Control Region and mtGenome: Design and Forensic Validation of NGS Multiplexes, Sequencing and Analytical Software. Genes (Basel) 2021; 12:genes12040599. [PMID: 33921728 PMCID: PMC8073089 DOI: 10.3390/genes12040599] [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: 12/24/2020] [Revised: 03/11/2021] [Accepted: 03/11/2021] [Indexed: 02/07/2023] Open
Abstract
Forensic mitochondrial DNA (mtDNA) analysis conducted using next-generation sequencing (NGS), also known as massively parallel sequencing (MPS), as compared to Sanger-type sequencing brings modern advantages, such as deep coverage per base (herein referred to as read depth per base pair (bp)), simultaneous sequencing of multiple samples (libraries) and increased operational efficiencies. This report describes the design and developmental validation, according to forensic quality assurance standards, of end-to-end workflows for two multiplexes, comprised of ForenSeq mtDNA control region and mtDNA whole-genome kits the MiSeq FGxTM instrument and ForenSeq universal analysis software (UAS) 2.0/2.1. Polymerase chain reaction (PCR) enrichment and a tiled amplicon approach target small, overlapping amplicons (60–150 bp and 60–209 bp for the control region and mtGenome, respectively). The system provides convenient access to data files that can be used outside of the UAS if desired. Studies assessed a range of environmental and situational variables, including but not limited to buccal samples, rootless hairs, dental and skeletal remains, concordance of control region typing between the two multiplexes and as compared to orthogonal data, assorted sensitivity studies, two-person DNA mixtures and PCR-based performance testing. Limitations of the system and implementation considerations are discussed. Data indicated that the two mtDNA multiplexes, MiSeq FGx and ForenSeq software, meet or exceed forensic DNA quality assurance (QA) guidelines with robust, reproducible performance on samples of various quantities and qualities.
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Alterauge A, Lösch S, Sulzer A, Gysi M, Haas C. Beyond simple kinship and identification: aDNA analyses from a 17th-19th century crypt in Germany. Forensic Sci Int Genet 2021; 53:102498. [PMID: 33872864 DOI: 10.1016/j.fsigen.2021.102498] [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: 10/05/2020] [Revised: 02/24/2021] [Accepted: 03/15/2021] [Indexed: 11/26/2022]
Abstract
Ancient DNA (aDNA) analysis is a powerful tool in multidisciplinary research on human remains, potentially leading to kinship scenarios and historical identifications. In this study, we present a genetic investigation of three noble families from the 17th to 19th centuries AD entombed in burial crypts at the cloister church of Riesa (Germany). Tests were aimed at identifying anticipated and incidental genetic relationships in our sample and the implications thereof for the assumed identity of the deceased. A total of 17 individuals were investigated via morphological, radiographic and aDNA analysis, yielding complete and partial autosomal and Y-STR profiles and reliable mtDNA sequences. Biostatistics and lineage markers revealed the presence of first to third degree relationships within the cohort. The pedigrees of the families Hanisch/von Odeleben and von Welck were thereby successfully reproduced, while four previously unknown individuals could be linked to the von Felgenhauer family. However, limitations of biostatistical kinship analysis became evident when the kinship scenario went beyond simple relationships. A combined analysis with archaeological data and historical records resulted in (almost) unambiguous identification of 14 of the 17 individuals.
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Affiliation(s)
- Amelie Alterauge
- Department of Prehistoric Archaeology, Institute of Archaeological Sciences, University of Bern, Mittelstrasse 43, 3012 Bern, Switzerland; Department of Physical Anthropology, Institute of Forensic Medicine, University of Bern, Sulgenauweg 40, 3007 Bern, Switzerland
| | - Sandra Lösch
- Department of Physical Anthropology, Institute of Forensic Medicine, University of Bern, Sulgenauweg 40, 3007 Bern, Switzerland
| | - Andrea Sulzer
- Department of Forensic Genetics, Zurich Institute of Forensic Medicine, University of Zurich, Winterthurerstrasse 190/52, 8057 Zürich, Switzerland
| | - Mario Gysi
- Department of Forensic Genetics, Zurich Institute of Forensic Medicine, University of Zurich, Winterthurerstrasse 190/52, 8057 Zürich, Switzerland
| | - Cordula Haas
- Department of Forensic Genetics, Zurich Institute of Forensic Medicine, University of Zurich, Winterthurerstrasse 190/52, 8057 Zürich, Switzerland.
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The genetic legacy of legendary and historical Siberian chieftains. Commun Biol 2020; 3:581. [PMID: 33067556 PMCID: PMC7567834 DOI: 10.1038/s42003-020-01307-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 09/15/2020] [Indexed: 02/02/2023] Open
Abstract
Seventeen years of archaeological and anthropological expeditions in North-Eastern Siberia (in the Sakha Republic, Yakutia) have permitted the genetic analysis of 150 ancient (15th-19th century) and 510 modern individuals. Almost all males were successfully analysed (Y-STR) and this allowed us to identify paternal lineages and their geographical expansion through time. This genetic data was confronted with mythological, historical and material evidence to establish the sequence of events that built the modern Yakut genetic diversity. We show that the ancient Yakuts recovered from this large collection of graves are not representative of an ancient population. Uncommonly, we were also able to demonstrate that the funerary preference observed here involved three specific male lineages, especially in the 18th century. Moreover, this dominance was likely caused by the Russian conquest of Siberia which allowed some male clans to rise to new levels of power. Finally, we give indications that some mythical and historical figures might have been the actors of those genetic changes. These results help us reconsider the genetic dynamics of colonization in some regions, question the distinction between fact and myth in national histories and provide a rare insight into a funerary ensemble by revealing the biased process of its composition.
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Katsanis SH. Pedigrees and Perpetrators: Uses of DNA and Genealogy in Forensic Investigations. Annu Rev Genomics Hum Genet 2020; 21:535-564. [DOI: 10.1146/annurev-genom-111819-084213] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the past few years, cases with DNA evidence that could not be solved with direct matches in DNA databases have benefited from comparing single-nucleotide polymorphism data with private and public genomic databases. Using a combination of genome comparisons and traditional genealogical research, investigators can triangulate distant relatives to the contributor of DNA data from a crime scene, ultimately identifying perpetrators of violent crimes. This approach has also been successful in identifying unknown deceased persons and perpetrators of lesser crimes. Such advances are bringing into focus ethical questions on how much access to DNA databases should be granted to law enforcement and how best to empower public genome contributors with control over their data. The necessary policies will take time to develop but can be informed by reflection on the familial searching policies developed for searches of the federal DNA database and considerations of the anonymity and privacy interests of civilians.
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Affiliation(s)
- Sara H. Katsanis
- Mary Ann & J. Milburn Smith Child Health Research, Outreach, and Advocacy Center, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois 60611, USA
- Department of Pediatrics, Northwestern University, Chicago, Illinois 60611, USA
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28
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Bouakaze C, Delehelle F, Saenz-Oyhéréguy N, Moreira A, Schiavinato S, Croze M, Delon S, Fortes-Lima C, Gibert M, Bujan L, Huyghe E, Bellis G, Calderon R, Hernández CL, Avendaño-Tamayo E, Bedoya G, Salas A, Mazières S, Charioni J, Migot-Nabias F, Ruiz-Linares A, Dugoujon JM, Thèves C, Mollereau-Manaute C, Noûs C, Poulet N, King T, D'Amato ME, Balaresque P. Predicting haplogroups using a versatile machine learning program (PredYMaLe) on a new mutationally balanced 32 Y-STR multiplex (CombYplex): Unlocking the full potential of the human STR mutation rate spectrum to estimate forensic parameters. Forensic Sci Int Genet 2020; 48:102342. [PMID: 32818722 DOI: 10.1016/j.fsigen.2020.102342] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 06/10/2020] [Accepted: 06/11/2020] [Indexed: 12/24/2022]
Abstract
We developed a new mutationally well-balanced 32 Y-STR multiplex (CombYplex) together with a machine learning (ML) program PredYMaLe to assess the impact of STR mutability on haplogourp prediction, while respecting forensic community criteria (high DC/HD). We designed CombYplex around two sub-panels M1 and M2 characterized by average and high-mutation STR panels. Using these two sub-panels, we tested how our program PredYmale reacts to mutability when considering basal branches and, moving down, terminal branches. We tested first the discrimination capacity of CombYplex on 996 human samples using various forensic and statistical parameters and showed that its resolution is sufficient to separate haplogroup classes. In parallel, PredYMaLe was designed and used to test whether a ML approach can predict haplogroup classes from Y-STR profiles. Applied to our kit, SVM and Random Forest classifiers perform very well (average 97 %), better than Neural Network (average 91 %) and Bayesian methods (< 90 %). We observe heterogeneity in haplogroup assignation accuracy among classes, with most haplogroups having high prediction scores (99-100 %) and two (E1b1b and G) having lower scores (67 %). The small sample sizes of these classes explain the high tendency to misclassify the Y-profiles of these haplogroups; results were measurably improved as soon as more training data were added. We provide evidence that our ML approach is a robust method to accurately predict haplogroups when it is combined with a sufficient number of markers, well-balanced mutation rate Y-STR panels, and large ML training sets. Further research on confounding factors (such as CNV-STR or gene conversion) and ideal STR panels in regard to the branches analysed can be developed to help classifiers further optimize prediction scores.
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Affiliation(s)
- Caroline Bouakaze
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Franklin Delehelle
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France; REVA Unit, UMR 5505 - CNRS & Université de Toulouse, Institut de Recherche en Informatique de Toulouse, 31400 Toulouse, France
| | - Nancy Saenz-Oyhéréguy
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Andreia Moreira
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Stéphanie Schiavinato
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Myriam Croze
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Solène Delon
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Cesar Fortes-Lima
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Morgane Gibert
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Louis Bujan
- Equipe d'acceuil EA3694, Hôpital Paule de Viguier, 330 Avenue de Grande Bretagne, TSA 70034, 31059 Toulouse Cedex 9, France
| | - Eric Huyghe
- Equipe d'acceuil EA3694, Hôpital Paule de Viguier, 330 Avenue de Grande Bretagne, TSA 70034, 31059 Toulouse Cedex 9, France
| | - Gil Bellis
- INED Institut National d'Etudes Démographiques, 133 Boulevard Davout, 75980 Paris cedex 20, France
| | - Rosario Calderon
- Department of Biodiversity, Ecology and Evolution, Faculty of Biology, Complutense University. 28040 Madrid, Spain
| | - Candela Lucia Hernández
- Department of Biodiversity, Ecology and Evolution, Faculty of Biology, Complutense University. 28040 Madrid, Spain
| | - Efren Avendaño-Tamayo
- Grupo de Ciencias Básicas Aplicadas del Tecnológico de Antioquia, Tecnológico de Antioquia, Institución Universitaria, Medellín 050034, Colombia
| | - Gabriel Bedoya
- GENMOL (Genética Molecular), Instituto de Biología, Universidad de Antioquia Medellín Colombia, Colombia
| | - Antonio Salas
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, GenPoB Research Group, Instituto de Investigaciones, Sanitarias (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain
| | | | - Jacques Charioni
- Aix Marseille Univ, CNRS, EFS, ADES, Marseille, France; Etablissement Français du Sang PACA Corse, Marseille, France
| | | | - Andres Ruiz-Linares
- Aix Marseille Univ, CNRS, EFS, ADES, Marseille, France; Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Jean-Michel Dugoujon
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Catherine Thèves
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Catherine Mollereau-Manaute
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Camille Noûs
- Laboratoire Cogitamous, CNRS & Université Toulouse III, 31000 Toulouse, France
| | - Nicolas Poulet
- Pôle écohydraulique AFB-IMT, allée du Pr Camille Soula, 31400 Toulouse, France
| | - Turi King
- Department of Genetics, University of Leicester, Leicester, United Kingdom
| | - Maria Eugenia D'Amato
- Forensic DNA Laboratory, Department of Biotechnology, Faculty of Natural Sciences, University of Western Cape, Cape Town, South Africa
| | - Patricia Balaresque
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France.
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Abstract
The brutal execution of Tsar Nicholas II, his wife and five children at Yekaterinberg in July 1918 was followed by apparently inept attempts to conceal the bodies. Despite this, the skeletons remained undiscovered until 1979. Even after anthropological and DNA analyses, the absence of two of the children in the grave raised doubts as to the identity of the remains. The discovery of the skeletal fragments of a young woman aged between 18 to 25 years and a boy aged between 10 to 14 years in a shallow grave near the primary burial site in 2007 enabled full DNA investigations of the remains to be undertaken in association with analyses of living Romanov descendants. Autosomal short tandem repeat (STR) testing revealed the sex and familial relationships within the group, and mitochondrial DNA (mtDNA) testing of the two hypervariable regions (HVI and HVII) showed links between the Tsar and Tsarina and living maternal relatives. The same point heteroplasmy in both the Tsar and his brother, Georgii provided further supportive evidence. There appears little doubt that the skeletal remains in the two graves outside Yekaterinburg are those of Tsar Nicholas, his wife and their five children. The genetic analyses and the features of the fragmented remains are all very consistent with the tragic story of the last days of the Romanov family and with the subsequent desecration and destruction of their bodies.
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Affiliation(s)
- Roger W Byard
- Discipline of Anatomy and Pathology, The University of Adelaide, Level 2 Helen Mayo Building North, Frome Road, Adelaide, South Australia, 5005, Australia.
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30
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Harding T, Milot E, Moreau C, Lefebvre JF, Bournival JS, Vézina H, Laprise C, Lalueza-Fox C, Anglada R, Loewen B, Casals F, Ribot I, Labuda D. Historical human remains identification through maternal and paternal genetic signatures in a founder population with extensive genealogical record. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 171:645-658. [PMID: 32064591 DOI: 10.1002/ajpa.24024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 01/13/2020] [Accepted: 02/04/2020] [Indexed: 11/12/2022]
Abstract
OBJECTIVES We describe a method to identify human remains excavated from unmarked graves in historical Québec cemeteries by combining parental-lineage genetic markers with the whole-population genealogy of Québec contained in the BALSAC database. MATERIALS AND METHODS The remains of six men were exhumed from four historical cemeteries in the province of Québec, Canada. DNA was extracted from the remains and genotyped to reveal their mitochondrial and Y-chromosome haplotypes, which were compared to a collection of haplotypes of genealogically-anchored modern volunteers. Maternal and paternal genealogies were searched in the BALSAC genealogical record for parental couples matching the mitochondrial and the Y-chromosome haplotypic signatures, to identify candidate sons from whom the remains could have originated. RESULTS Analysis of the matching genealogies identified the parents of one man inhumed in the cemetery of the investigated parish during its operating time. The candidate individual died in 1833 at the age of 58, a plausible age at death in light of osteological analysis of the remains. DISCUSSION This study demonstrates the promising potential of coupling genetic information from living individuals to genealogical data in BALSAC to identify historical human remains. If genetic coverage is increased, the genealogical information in BALSAC could enable the identification of 87% of the men (n = 178,435) married in Québec before 1850, with high discriminatory power in most cases since >75% of the parental couples have unique biparental signatures in most regions. Genotyping and identifying Québec's historical human remains are a key to reconstructing the genomes of the founders of Québec and reinhuming archeological remains with a marked grave.
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Affiliation(s)
- Tommy Harding
- Centre de recherche du CHU Sainte-Justine, Université de Montréal, Montréal, Canada.,Laboratoire de recherche en criminalistique, Département de chimie, biochimie et sciences de l'énergie, Université du Québec à Trois-Rivières, Trois-Rivières, Canada
| | - Emmanuel Milot
- Laboratoire de recherche en criminalistique, Département de chimie, biochimie et sciences de l'énergie, Université du Québec à Trois-Rivières, Trois-Rivières, Canada.,Centre international de criminologie comparée and Centre interuniversitaire d'études québécoises, Université du Québec à Trois-Rivières, Trois-Rivières, Canada
| | - Claudia Moreau
- Centre de recherche du CHU Sainte-Justine, Université de Montréal, Montréal, Canada.,Centre intersectoriel en santé durable, Université du Québec à Chicoutimi, Chicoutimi, Canada
| | | | | | - Hélène Vézina
- Centre intersectoriel en santé durable, Université du Québec à Chicoutimi, Chicoutimi, Canada.,Projet BALSAC, Université du Québec à Chicoutimi, Chicoutimi, Canada.,Département des sciences humaines et sociales, Université du Québec à Chicoutimi, Chicoutimi, Canada
| | - Catherine Laprise
- Centre intersectoriel en santé durable, Université du Québec à Chicoutimi, Chicoutimi, Canada.,Département des sciences fondamentales, Université du Québec à Chicoutimi, Chicoutimi, Canada
| | - Carles Lalueza-Fox
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Roger Anglada
- Genomics Core Facility, Universitat Pompeu Fabra, Barcelona, Spain
| | - Brad Loewen
- Département d'anthropologie, Université de Montréal, Montréal, Canada
| | - Ferran Casals
- Genomics Core Facility, Universitat Pompeu Fabra, Barcelona, Spain
| | - Isabelle Ribot
- Département d'anthropologie, Université de Montréal, Montréal, Canada
| | - Damian Labuda
- Centre de recherche du CHU Sainte-Justine, Université de Montréal, Montréal, Canada.,Département de pédiatrie, Université de Montréal, Montréal, Canada
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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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Importance of DNA analysis for identification and confirmation of human remains, following a forensic autopsy. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.09.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Zgonjanin D, Nedić D, Alghafri R, Petković S, Vuković R. DNA typing from skeletal remains using GlobalFiler™ PCR amplification and Investigator® 24plex QS kits. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.09.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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34
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Young JM, Higgins D, Austin JJ. Hybridization Enrichment to Improve Forensic Mitochondrial DNA Analysis of Highly Degraded Human Remains. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00450] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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35
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Perego UA, Bodner M, Raveane A, Woodward SR, Montinaro F, Parson W, Achilli A. Resolving a 150-year-old paternity case in Mormon history using DTC autosomal DNA testing of distant relatives. Forensic Sci Int Genet 2019; 42:1-7. [DOI: 10.1016/j.fsigen.2019.05.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 05/31/2019] [Accepted: 05/31/2019] [Indexed: 01/01/2023]
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DNA Testing Reveals the Putative Identity of JB55, a 19th Century Vampire Buried in Griswold, Connecticut. Genes (Basel) 2019; 10:genes10090636. [PMID: 31443502 PMCID: PMC6769528 DOI: 10.3390/genes10090636] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 07/22/2019] [Accepted: 08/20/2019] [Indexed: 11/25/2022] Open
Abstract
In 1990 in Griswold, Connecticut, archaeologists excavated a burial found in a “skull and crossbones” orientation. The lid of the 19th century coffin had brass tacks that spelled “JB55”, the initials of the person lying there and age at death. JB55 had evidence of chronic pulmonary infection, perhaps tuberculosis. It is possible that JB55 was deemed a vampire due to his disease, and therefore had to be “killed” by mutilating his corpse. In an attempt to reveal the identity of JB55, DNA testing was performed. Ancestry informative single nucleotide polymorphism (SNP) analysis using the Precision ID Ancestry Panel indicated European ancestry. A full Y-chromosomal short tandem repeat (Y-STR) profile was obtained, belonging to haplogroup R1b. When the Y-STR profile was searched in the publicly accessible FamilyTreeDNA R1b Project website, the two closest matches had the surname “Barber”. A search of historical records led to a death notice mentioning John Barber, whose son Nathan Barber was buried in Griswold in 1826. The description of Nathan Barber closely fits the burial of “NB13,” found near JB55. By applying modern forensic DNA tools to a historical mystery, the identity of JB55 as John Barber, the 19th century Connecticut vampire, has been revealed.
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37
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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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Vitoševic K, Todorovic D, Slovic Z, Zivkovic-Zaric R, Todorovic M. Forensic Genetics and Genotyping. SERBIAN JOURNAL OF EXPERIMENTAL AND CLINICAL RESEARCH 2019. [DOI: 10.1515/sjecr-2016-0074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
AbstractForensic genetics represents a combination of molecular and population genetics. Personal identification and kinship analysis (e.g. paternity testing) are the two main subjects of forensic DNA analysis. Biological specimens from which DNA is isolated are blood, semen, saliva, tissues, bones, teeth, hairs. Genotyping has become a basis in the characterization of forensic biological evidence. It is performed using a variety of genetic markers, which are divided into two large groups: bi-allelic (single-nucleotide polymorphisms, SNP) and multi-allelic polymorphisms (variable number of tandem repeats, VNTR and short tandem repeats, STR). This review describes the purpose of genetic markers in forensic investigation and their limitations. The STR loci are currently the most informative genetic markers for identity testing, but in cases without a suspect SNP can predict offender’s ancestry and phenotype traits such as skin, eyes and hair color. Nowadays, many countries worldwide have established forensic DNA databases based on autosomal short tandem repeats and other markers. In order for DNA profile database to be useful at a national or international level, it is essential to standardize genetic markers used in laboratories.
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Affiliation(s)
- Katarina Vitoševic
- Department of Anatomy and Forensic Medicine, Faculty of Medical Sciences , University of Kragujevac , Kragujevac , Serbia
| | - Danijela Todorovic
- Department of Human Genetics, Faculty of Medical Sciences , University of Kragujevac , Kragujevac , Serbia
| | - Zivana Slovic
- Department of Anatomy and Forensic Medicine, Faculty of Medical Sciences , University of Kragujevac , Kragujevac , Serbia
| | - Radica Zivkovic-Zaric
- Department of Anatomy and Forensic Medicine, Faculty of Medical Sciences , University of Kragujevac , Kragujevac , Serbia
| | - Milos Todorovic
- Department of Anatomy and Forensic Medicine, Faculty of Medical Sciences , University of Kragujevac , Kragujevac , Serbia
- Department of Forensic Medicine and Toxicology , Clinical Centre Kragujevac , Kragujevac , Serbia
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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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Ibrahim AH, Rahman NNA, Saifuddeen SM, Baharuddin M. Tri-parent Baby Technology and Preservation of Lineage: An Analysis from the Perspective of Maqasid al-Shari'ah Based Islamic Bioethics. SCIENCE AND ENGINEERING ETHICS 2019; 25:129-142. [PMID: 29071572 DOI: 10.1007/s11948-017-9980-5] [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: 06/21/2017] [Accepted: 09/19/2017] [Indexed: 06/07/2023]
Abstract
Tri-parent baby technology is an assisted reproductive treatment which aims to minimize or eliminate maternal inheritance of mutated mitochondrial DNA (mtDNA). The technology became popular following the move by the United Kingdom in granting license to a group of researchers from the Newcastle Fertility Centre, Newcastle University to conduct research on the symptoms of defective mtDNA. This technology differs from other assisted reproductive technology because it involves the use of gamete components retrieved from three different individuals. Indirectly, it affects the preservation of lineage which is important from an Islamic point of view. This paper aims to analyze and discuss the implications of the tri-parent technology on preservation of lineage from the perspective of Maqasid al-Shari'ah based the Islamic bioethics. The analysis shows that there are a few violations of the preservation of lineage, hence the tri-parent baby technology should not be permitted.
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Affiliation(s)
- Abdul Halim Ibrahim
- Programme of Applied Science with Islamic Studies, Academy of Islamic Studies, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Noor Naemah Abdul Rahman
- Department of Fiqh and Usul, Academy of Islamic Studies, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Shaikh Mohd Saifuddeen
- Programme of Applied Science with Islamic Studies, Academy of Islamic Studies, University of Malaya, 50603, Kuala Lumpur, Malaysia
- Centre for Science and Environment Studies, Institute of Islamic Understanding Malaysia, 2 Langgak Tunku Off Jalan Tuanku Abdul Halim, 50480, Kuala Lumpur, Malaysia
| | - Madiha Baharuddin
- Programme of Applied Science with Islamic Studies, Academy of Islamic Studies, University of Malaya, 50603, Kuala Lumpur, Malaysia
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McCall S, Kreindl G, Kastinger T, Müller E, Zahrer W, Grießner I, Dunkelmann B, Tutsch-Bauer E, Neuhuber F, Pittman PR, Wahl R, Lowry M, Cemper-Kiesslich J. Rudolf Hess - The Doppelgänger conspiracy theory disproved. Forensic Sci Int Genet 2019; 40:18-22. [PMID: 30685710 DOI: 10.1016/j.fsigen.2019.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 05/28/2018] [Accepted: 01/09/2019] [Indexed: 10/27/2022]
Abstract
The Deputy Führer of the Third Reich Rudolf Hess was captured after a controversial flight to Scotland in 1941. Hess was sentenced to life imprisonment during the Nuremberg War Crimes Trials. He was detained in Berlin's Spandau Prison under the official security designation 'Spandau #7.' Early doubts arose about the true identity of prisoner 'Spandau #7.' This evolved to a frequently espoused conspiracy theory that prisoner 'Spandau #7' was an imposter and not Rudolf Hess. After Hess's reputed 1987 suicide, the family grave became a Neo-Nazi pilgrimage site. In 2011, the grave was abandoned and the family remains cremated. Here we report the forensic DNA analysis of the only known extant DNA sample from prisoner 'Spandau #7' and a match to the Hess male line, thereby refuting the Doppelgänger Theory.
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Affiliation(s)
- Sherman McCall
- Medical Corps, United States Army Retired, United States
| | - Gabriele Kreindl
- Interfaculty Department of Legal Medicine, University of Salzburg, Ignaz Harrer-strasse 79, 5020 Salzburg, Austria
| | - Tamara Kastinger
- Interfaculty Department of Legal Medicine, University of Salzburg, Ignaz Harrer-strasse 79, 5020 Salzburg, Austria
| | - Eva Müller
- Interfaculty Department of Legal Medicine, University of Salzburg, Ignaz Harrer-strasse 79, 5020 Salzburg, Austria
| | - Waltraud Zahrer
- Interfaculty Department of Legal Medicine, University of Salzburg, Ignaz Harrer-strasse 79, 5020 Salzburg, Austria
| | - Ines Grießner
- Interfaculty Department of Legal Medicine, University of Salzburg, Ignaz Harrer-strasse 79, 5020 Salzburg, Austria
| | - Bettina Dunkelmann
- Interfaculty Department of Legal Medicine, University of Salzburg, Ignaz Harrer-strasse 79, 5020 Salzburg, Austria
| | - Edith Tutsch-Bauer
- Interfaculty Department of Legal Medicine, University of Salzburg, Ignaz Harrer-strasse 79, 5020 Salzburg, Austria; CAMAS - Center of Archaeometry and Applied Molecular Archaeology Salzburg, c/o University of Salzburg, Austria
| | - Franz Neuhuber
- Interfaculty Department of Legal Medicine, University of Salzburg, Ignaz Harrer-strasse 79, 5020 Salzburg, Austria
| | - Phillip R Pittman
- Medical Corps, United States Army Retired, United States; United States Army Medical Research Institute for Infectious Diseases (USAMRIID), 1425 Porter Street, USAMRIID/MED, Fort Detrick, MD, 21702-5011, United States
| | - Rick Wahl
- Medical Corps, United States Army Retired, United States
| | - Mark Lowry
- Medical Corps, United States Army Reserve, United States
| | - Jan Cemper-Kiesslich
- Interfaculty Department of Legal Medicine, University of Salzburg, Ignaz Harrer-strasse 79, 5020 Salzburg, Austria; CAMAS - Center of Archaeometry and Applied Molecular Archaeology Salzburg, c/o University of Salzburg, Austria.
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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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Large scale DNA identification: The ICMP experience. Forensic Sci Int Genet 2018; 38:236-244. [PMID: 30469017 DOI: 10.1016/j.fsigen.2018.11.008] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 11/07/2018] [Accepted: 11/07/2018] [Indexed: 01/11/2023]
Abstract
The International Commission on Missing Persons (ICMP) is a treaty-based international organization with a global mandate to address the issue of missing persons. It works with governments, civil society organizations, and others, and utilizes data systems and technical assistance in forensic science. ICMP's initial work focused on the ∼40,000 people missing in the Western Balkans from the conflicts of the 1990s. A "DNA-led" approach to large-scale DNA identification of the missing was developed, based on high-throughput autosomal STR testing of skeletal remains from mass graves and other sites, and the establishment of a regional database of DNA profiles from family members of the missing. Database pairwise and pedigree kinship searching is conducted using in-house DNA matching software, the Identification Data Management System (iDMS), providing high-certainty DNA matches that are integrated in a multi-disciplinary identification process. Anthropological guidelines for sampling skeletal remains for DNA testing are based on tens of thousands of tests from a wide range of skeletal elements, allowing for prioritization based on DNA preservation. Large-scale collection of family reference samples has been conducted, resulting in a database of more than 100,000 family reference DNA profiles across all projects and delivering family DNA match reports for more than 20,000 individuals. From the 1995 Srebrenica event, ICMP provided DNA matches for 6887 of the ∼8000 missing from that event. In assistance to justice, ICMP has provided extensive evidence and expert testimony in multiple war crimes trials, including those conducted at the ICTY. This article provides an overview of ICMP's technical involvement over the last 17 years in areas of DNA testing and database matching, and training and capacity building projects with partners. It also touches on the development of massively parallel sequencing (MPS) strategies specifically tailored to missing persons applications.
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Current and emerging tools for the recovery of genetic information from post mortem samples: New directions for disaster victim identification. Forensic Sci Int Genet 2018; 37:270-282. [DOI: 10.1016/j.fsigen.2018.08.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 08/27/2018] [Accepted: 08/27/2018] [Indexed: 01/14/2023]
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Woerner AE, Ambers A, Wendt FR, King JL, Moura-Neto RS, Silva R, Budowle B. Evaluation of the precision ID mtDNA whole genome panel on two massively parallel sequencing systems. Forensic Sci Int Genet 2018; 36:213-224. [DOI: 10.1016/j.fsigen.2018.07.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 07/13/2018] [Accepted: 07/16/2018] [Indexed: 10/28/2022]
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Karmacharya D, Sherchan AM, Dulal S, Manandhar P, Manandhar S, Joshi J, Bhattarai S, Bhatta TR, Awasthi N, Sharma AN, Bista M, Silwal NR, Pokharel P, Lamichhane RR, Sharma N, Llewellyn B, Wultsch C, Kelly MJ, Gour D, Waits L, Hero JM, Hughes J. Species, sex and geo-location identification of seized tiger (Panthera tigris tigris) parts in Nepal-A molecular forensic approach. PLoS One 2018; 13:e0201639. [PMID: 30138352 PMCID: PMC6107122 DOI: 10.1371/journal.pone.0201639] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 07/19/2018] [Indexed: 11/19/2022] Open
Abstract
Tiger (Panthera tigris) populations are in danger across their entire range due to habitat loss, poaching and the demand for tiger parts. The Bengal tiger (Panthera tigris tigris) is an endangered apex predator with a population size estimated to be less than 200 in Nepal. In spite of strict wildlife protection laws, illegal trade of tiger parts is increasing; and Nepal has become one of the major sources and transit routes for poached wildlife parts. Identification of wildlife parts is often challenging for law enforcement officials due to inadequate training and lack of available tools. Here, we describe a molecular forensic approach to gain insight into illegally trafficked tiger parts seized across Nepal. We created Nepal's first comprehensive reference genetic database of wild tigers through the Nepal Tiger Genome Project (2011-2013). This database has nuclear DNA microsatellite genotype and sex profiles, including geo-spatial information, of over 60% (n = 120) of the wild tigers of Nepal. We analyzed 15 putative cases of confiscated poached tiger parts and all were confirmed to be of tiger. Ten samples were identified as male and five were female. We determined probable geo-source location for 9 of the 14 samples with 6-8 nuclear DNA microsatellite loci using inferences from four different statistical assignment methods. Six samples were assigned to Bardia National Park and one of these was an exact match to a female tiger previously profiled in our fecal DNA reference database. Two tiger samples were assigned to Shuklaphanta Wildlife Reserve and one to Chitwan National Park. We are unable to definitively assign five tiger samples which could be offspring dispersers or might have come from tiger population outside of Nepal. Our study revealed that the western region, particularly Bardia National Park, is a poaching hotspot for illegal tiger trade in Nepal. We present feasibility of using molecular forensic based evidence to incriminate criminals in a court of law in the fight against wildlife crime.
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Affiliation(s)
- Dibesh Karmacharya
- Center for Molecular Dynamics Nepal, Thapathali-11, Kathmandu, Nepal
- School of Environment, Griffith University, Gold Coast, Queensland, Australia
| | | | - Santosh Dulal
- Center for Molecular Dynamics Nepal, Thapathali-11, Kathmandu, Nepal
| | - Prajwol Manandhar
- Center for Molecular Dynamics Nepal, Thapathali-11, Kathmandu, Nepal
| | | | - Jyoti Joshi
- Center for Molecular Dynamics Nepal, Thapathali-11, Kathmandu, Nepal
| | - Susmita Bhattarai
- Center for Molecular Dynamics Nepal, Thapathali-11, Kathmandu, Nepal
| | - Tarka R. Bhatta
- Center for Molecular Dynamics Nepal, Thapathali-11, Kathmandu, Nepal
| | - Nagendra Awasthi
- Center for Molecular Dynamics Nepal, Thapathali-11, Kathmandu, Nepal
| | - Ajay N. Sharma
- Center for Molecular Dynamics Nepal, Thapathali-11, Kathmandu, Nepal
| | - Manisha Bista
- Center for Molecular Dynamics Nepal, Thapathali-11, Kathmandu, Nepal
| | - Nawa R. Silwal
- Central Investigation Bureau (CIB), Pillar 4, Nepal Police, Kathmandu, Nepal
| | - Pravin Pokharel
- Central Investigation Bureau (CIB), Pillar 4, Nepal Police, Kathmandu, Nepal
| | - Rom R. Lamichhane
- Bio-Diversity Section, Ministry of Forest and Soil Conservation, Kathmandu, Nepal
| | - Netra Sharma
- Environment Team, U.S. Agency for International Development (USAID), Kathmandu, Nepal
| | - Bronwyn Llewellyn
- Environment Team, U.S. Agency for International Development (USAID), Kathmandu, Nepal
| | - Claudia Wultsch
- Sackler Institute for Comparative Genomics, American Natural History Museum, New York, New York, United States of America
| | - Marcella J. Kelly
- Department of Fish and Wildlife Conservation, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Digpal Gour
- Laboratory for Ecological, Evolutionary and Conservation Genetics, University of Idaho, Moscow, Idaho, United States of America
| | - Lisette Waits
- Laboratory for Ecological, Evolutionary and Conservation Genetics, University of Idaho, Moscow, Idaho, United States of America
| | - Jean-Marc Hero
- School of Science and Engineering, University of the Sunshine Coast, Sunshine Coast, Queensland, Australia
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Canterbury, United Kingdom
| | - Jane Hughes
- School of Environment, Griffith University, Gold Coast, Queensland, Australia
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The biological relevance of a medieval king's DNA. Biochem Soc Trans 2018; 46:1013-1020. [DOI: 10.1042/bst20170173] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Revised: 03/27/2018] [Accepted: 04/04/2018] [Indexed: 11/17/2022]
Abstract
The discovery of the presumably lost grave of the controversial English king Richard III in Leicester (U.K.) was one of the most important archaeological achievements of the last decennium. The skeleton was identified beyond reasonable doubt, mainly by the match of mitochondrial DNA to that of living maternal relatives, along with the specific archaeological context. Since the genetic genealogical analysis only involved the DNA sequences of a single 15th century individual and a few reference persons, biologists might consider this investigation a mere curiosity. This mini-review shows that the unique context of a historical king's DNA also has relevance for biological research per se — in addition to the more obvious historical, societal and educational value. In the first place, the historical identification appeared to be a renewed forensic case realising a conservative statement with statistical power based on genetic and non-genetic data, including discordant elements. Secondly, the observation of historical non-paternity events within Richard III's patrilineage has given rise to new research questions about potential factors influencing the extra-pair paternity rate in humans and the importance of biological relatedness for the legal recognition of a child in the past. Thirdly, the identification of a named and dated skeleton with the known historical context serves as a reference for bioarchaeological investigations and studies on the spatio-temporal distribution of particular genetic variance. Finally, the Richard III case revealed privacy issues for living relatives which appear to be inherent to any publication of genetic genealogical data.
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Shi CM, Li C, Ma L, Chi L, Zhao J, Yuan W, Zhou Z, Yan JW, Chen H. Inferring Chinese surnames with Y-STR profiles. Forensic Sci Int Genet 2018; 33:66-71. [DOI: 10.1016/j.fsigen.2017.11.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Revised: 11/21/2017] [Accepted: 11/23/2017] [Indexed: 10/18/2022]
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Deep-Coverage MPS Analysis of Heteroplasmic Variants within the mtGenome Allows for Frequent Differentiation of Maternal Relatives. Genes (Basel) 2018; 9:genes9030124. [PMID: 29495418 PMCID: PMC5867845 DOI: 10.3390/genes9030124] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Revised: 02/15/2018] [Accepted: 02/20/2018] [Indexed: 12/11/2022] Open
Abstract
Distinguishing between maternal relatives through mitochondrial (mt) DNA sequence analysis has been a longstanding desire of the forensic community. Using a deep-coverage, massively parallel sequencing (DCMPS) approach, we studied the pattern of mtDNA heteroplasmy across the mtgenomes of 39 mother-child pairs of European decent; haplogroups H, J, K, R, T, U, and X. Both shared and differentiating heteroplasmy were observed on a frequent basis in these closely related maternal relatives, with the minor variant often presented as 2–10% of the sequencing reads. A total of 17 pairs exhibited differentiating heteroplasmy (44%), with the majority of sites (76%, 16 of 21) occurring in the coding region, further illustrating the value of conducting sequence analysis on the entire mtgenome. A number of the sites of differentiating heteroplasmy resulted in non-synonymous changes in protein sequence (5 of 21), and to changes in transfer or ribosomal RNA sequences (5 of 21), highlighting the potentially deleterious nature of these heteroplasmic states. Shared heteroplasmy was observed in 12 of the 39 mother-child pairs (31%), with no duplicate sites of either differentiating or shared heteroplasmy observed; a single nucleotide position (16093) was duplicated between the data sets. Finally, rates of heteroplasmy in blood and buccal cells were compared, as it is known that rates can vary across tissue types, with similar observations in the current study. Our data support the view that differentiating heteroplasmy across the mtgenome can be used to frequently distinguish maternal relatives, and could be of interest to both the medical genetics and forensic communities.
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Improved Y-STR typing for disaster victim identification, missing persons investigations, and historical human skeletal remains. Int J Legal Med 2018; 132:1545-1553. [DOI: 10.1007/s00414-018-1794-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 02/09/2018] [Indexed: 10/18/2022]
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