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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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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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3
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Zupanič Pajnič I, Leskovar T, Črešnar M. Eye and hair color prediction of an early medieval adult and subadult skeleton using massive parallel sequencing technology. Int J Legal Med 2023; 137:1629-1638. [PMID: 37284851 PMCID: PMC10421759 DOI: 10.1007/s00414-023-03032-y] [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: 01/13/2023] [Accepted: 05/24/2023] [Indexed: 06/08/2023]
Abstract
Phenotypic trait prediction in ancient DNA analysis can provide information about the external appearance of individuals from past human populations. Some studies predicting eye and hair color in ancient adult skeletons have been published, but not for ancient subadult skeletons, which are more prone to decay. In this study, eye and hair color were predicted for an early medieval adult skeleton and a subadult skeleton that was anthropologically characterized as a middle-aged man and a subadult of unknown sex about 6 years old. When processing the petrous bones, precautions were taken to prevent contamination with modern DNA. The MillMix tissue homogenizer was used for grinding, 0.5 g of bone powder was decalcified, and DNA was purified in Biorobot EZ1. The PowerQuant System was used for quantification and a customized version of the HIrisPlex panel for massive parallel sequencing (MPS) analysis. Library preparation and templating were performed on the HID Ion Chef Instrument and sequencing on the Ion GeneStudio S5 System. Up to 21 ng DNA/g of powder was obtained from ancient petrous bones. Clean negative controls and no matches with elimination database profiles confirmed no contamination issue. Brown eyes and dark brown or black hair were predicted for the adult skeleton and blue eyes and brown or dark brown hair for the subadult skeleton. The MPS analysis results obtained proved that it is possible to predict hair and eye color not only for an adult from the Early Middle Ages, but also for a subadult skeleton dating to this period.
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Affiliation(s)
- Irena Zupanič Pajnič
- 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
| | - Matija Črešnar
- Centre for Interdisciplinary Research in Archaeology, Department of Archaeology, Faculty of Arts, University of Ljubljana, Ljubljana, Slovenia
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4
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Jacobs HT. A century of mitochondrial research, 1922-2022. Enzymes 2023; 54:37-70. [PMID: 37945177 DOI: 10.1016/bs.enz.2023.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Although recognized earlier as subcellular entities by microscopists, mitochondria have been the subject of functional studies since 1922, when their biochemical similarities with bacteria were first noted. In this overview I trace the history of research on mitochondria from that time up to the present day, focussing on the major milestones of the overlapping eras of mitochondrial biochemistry, genetics, pathology and cell biology, and its explosion into new areas in the past 25 years. Nowadays, mitochondria are considered to be fully integrated into cell physiology, rather than serving specific functions in isolation.
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Affiliation(s)
- Howard T Jacobs
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland; Department of Environment and Genetics, La Trobe University, Melbourne, VIC, Australia.
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5
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Inkret J, Zupanc T, Zupanič Pajnič I. A Multisample Approach in Forensic Phenotyping of Chronological Old Skeletal Remains Using Massive Parallel Sequencing (MPS) Technology. Genes (Basel) 2023; 14:1449. [PMID: 37510353 PMCID: PMC10379588 DOI: 10.3390/genes14071449] [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: 06/08/2023] [Revised: 07/05/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
It is very important to generate phenotypic results that are reliable when processing chronological old skeletal remains for cases involving the identification of missing persons. To improve the success of pigmentation prediction in Second World War victims, three bones from each of the eight skeletons analyzed were included in the study, which makes it possible to generate a consensus profile. The PowerQuant System was used for quantification, the ESI 17 Fast System was used for STR typing, and a customized version of the HIrisPlex panel was used for PCR-MPS. The HID Ion Chef Instrument was used for library preparation and templating. Sequencing was performed with the Ion GeneStudio S5 System. Identical full profiles and identical hair and eye color predictions were achieved from three bones analyzed per skeleton. Blue eye color was predicted in five skeletons and brown in three skeletons. Blond hair color was predicted in one skeleton, blond to dark blond in three skeletons, brown to dark brown in two skeletons, and dark brown to black in two skeletons. The reproducibility and reliability of the results proved the multisample analysis method to be beneficial for phenotyping chronological old skeletons because differences in DNA yields in different bone types provide a greater possibility of obtaining a better-quality consensus profile.
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Affiliation(s)
- Jezerka Inkret
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia
| | - Tomaž Zupanc
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia
| | - Irena Zupanič Pajnič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia
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6
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Marsico FL, Caridi I. Incorporating non-genetic evidence in large scale missing person searches: A general approach beyond filtering. Forensic Sci Int Genet 2023; 66:102891. [PMID: 37523799 DOI: 10.1016/j.fsigen.2023.102891] [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: 12/30/2022] [Revised: 04/12/2023] [Accepted: 05/22/2023] [Indexed: 08/02/2023]
Abstract
The search for missing persons implies several steps, from the preliminary investigation that involves collecting background data related to the case to the genetic kinship testing. Despite its crucial importance in identifications, only some approaches mathematically formalize the possibility of using preliminary investigation data. In some cases, a filtering strategy is applied, which implies selecting a subset of possible victims where some non-genetic variables perfectly match those of the missing. Through a Bayesian approach, we propose a mathematical model for computing the prior odds based on non-genetic variables usually collected during the preliminary investigation, such as biological sex, hair colour, and age. We use computational simulations to show how to incorporate these prior odds in DNA-database searches. Importantly, our results suggest that applying the proposed model leads to better search performance in underpowered cases from the genetic point of view, where few or distant relatives of the missing person are available for genotyping. Furthermore, the results are also helpful when using non-genetic data for prior odds in well-powered cases, where genetic data are enough to reach a reliable conclusion. It performs better than other approaches, such as using non-genetic data for filtering. The software mispitools, freely available on CRAN, implements all described methods (https://CRAN.R-project.org/package=mispitools).
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Affiliation(s)
- Franco L Marsico
- Calculus Institute, University of Buenos Aires, Argentina; IDEPI, National University of Jose Clemente Paz, Argentina.
| | - Inés Caridi
- Calculus Institute, University of Buenos Aires, Argentina.
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7
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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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8
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Kayser M, Sajantila A, Butler JM, Parson W, Salas A, Gill P, Parsons T, Phillips C, Egeland T, Marshall C. Special issue: Forensic Genetics: Unde venisti et quo vadis? Forensic Sci Int Genet 2023:102881. [PMID: 37173159 DOI: 10.1016/j.fsigen.2023.102881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023]
Affiliation(s)
- Manfred Kayser
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, the Netherland.
| | - Antti Sajantila
- Department of Forensic Medicine, University of Helsinki and Finnish Institute for Health and Welfare, Helsinki, Finland
| | - John M Butler
- National Institute of Standards and Technology, Special Programs Office, Gaithersburg, MD, USA
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Austria and Forensic Science Program, The Pennsylvania State University, University Park, PA, USA
| | - Antonio Salas
- Forensic Genetics Unit, Institute of Forensic Sciences and GenPoB Research Group, Institute of Health Research, Clinic Hospital, University of Santiago de Compostela, Spain
| | - Peter Gill
- Forensic Genetics Research Group, Oslo University Hospital and Department of Clinical Medicine, University of Oslo, Norway
| | - Thomas Parsons
- International Commission on Missing Persons, Den Haag, the Netherlands
| | - Chris Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - Thore Egeland
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Aas, Norway
| | - Charla Marshall
- Emerging Technologies Section, Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, DE, USA
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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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Chen Y, Hysi P, Maj C, Heilmann-Heimbach S, Spector TD, Liu F, Kayser M. Genetic prediction of male pattern baldness based on large independent datasets. Eur J Hum Genet 2023; 31:321-328. [PMID: 36336714 PMCID: PMC9995341 DOI: 10.1038/s41431-022-01201-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 09/15/2022] [Accepted: 09/20/2022] [Indexed: 11/09/2022] Open
Abstract
Genetic prediction of male pattern baldness (MPB) is important in science and society. Previous genetic MPB prediction models were limited by sparse marker coverage, small sample size, and/or data dependency in the different analytical steps. Here, we present novel models for genetic prediction of MPB based on a large set of markers and large independent subsample sets drawn among 187,435 European subjects. We selected 117 SNP predictors within 85 distinct loci from a list of 270 previously MPB-associated SNPs in 55,573 males of the UK Biobank Study (UKBB). Based on these 117 SNPs with and without age as additional predictor, we trained, by use of different methods, prediction models in a non-overlapping subset of 104,694 UKBB males and tested them in a non-overlapping subset of 26,177 UKBB males. Estimates of prediction accuracy were similar between methods with AUC ranges of 0.725-0.728 for severe, 0.631-0.635 for moderate, 0.598-0.602 for slight, and 0.708-0.711 for no hair loss with age, and slightly lower without, while prediction of any versus no hair loss gave 0.690-0.711 with age and slightly lower without. External validation in an early-onset enriched MPB dataset from the Bonn Study (N = 991) showed improved prediction accuracy without considering age such as AUC of 0.830 for no vs. any hair loss. Because of the large number of markers and the large independent datasets used for the different analytical steps, the newly presented genetic prediction models are the most reliable ones currently available for MPB or any other human appearance trait.
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Affiliation(s)
- Yan Chen
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Pirro Hysi
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Carlo Maj
- Institute for Genomic Statistics and Bioinformatics (IGSB), University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Stefanie Heilmann-Heimbach
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Timothy D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Fan Liu
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.
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11
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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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Application of Forensic DNA Phenotyping for Prediction of Eye, Hair and Skin Colour in Highly Decomposed Bodies. Healthcare (Basel) 2023; 11:healthcare11050647. [PMID: 36900653 PMCID: PMC10000573 DOI: 10.3390/healthcare11050647] [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: 01/31/2023] [Revised: 02/18/2023] [Accepted: 02/21/2023] [Indexed: 02/25/2023] Open
Abstract
In the last few years, predicting externally visible characteristics (EVCs) by adopting informative DNA molecular markers has become a method in forensic genetics that has increased its value, giving rise to an interesting field called "Forensic DNA Phenotyping" (FDP). The most meaningful forensic applications of EVCs prediction are those in which, having only a DNA sample isolated from highly decomposed remains, it is essential to reconstruct the physical appearance of a person. Through this approach, we set out to evaluate 20 skeletal remains of Italian provenance in order to associate them with as many cases of missing persons as possible. To achieve the intended goal, in this work we applied the HIrisPlex-S multiplex system through the conventional short tandem repeats (STR) method to confirm the expected identity of subjects by evaluating phenotypic features. To investigate the reliability and accuracy of the DNA-based EVCs prediction, pictures of the cases were compared as they were available to researchers. Results showed an overall prediction accuracy greater than 90% for all three phenotypic features-iris, hair, and skin colour-at a probability threshold of 0.7. The experimental analysis showed inconclusive results in only two cases; this is probably due to the characteristics of subjects who had an intermediate eye and hair colour, for which the DNA-based system needs to improve the prediction accuracy.
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13
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Danielewski M, Żuraszek J, Zielińska A, Herzig KH, Słomski R, Walkowiak J, Wielgus K. Methodological Changes in the Field of Paleogenetics. Genes (Basel) 2023; 14:genes14010234. [PMID: 36672975 PMCID: PMC9859346 DOI: 10.3390/genes14010234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/07/2023] [Accepted: 01/11/2023] [Indexed: 01/17/2023] Open
Abstract
Paleogenetics has significantly changed since its inception almost forty years ago. Initially, molecular techniques available to the researchers offered minimal possibilities for ancient DNA analysis. The subsequent expansion of the scientific tool cabinet allowed for more remarkable achievements, combined has with the newfound popularity of this budding field of science. Finally, a breakthrough was made with the development of next-generation sequencing (NGS) technologies and the update of DNA isolation protocols, through which even very fragmented aDNA samples could be used to sequence whole genomes. In this paper, we review the achievements made thus far and compare the methodologies utilized in this field of science, discussing their benefits and challenges.
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Affiliation(s)
- Mikołaj Danielewski
- Department of Pediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Szpitalna 27/33, 60-572 Poznan, Poland
| | - Joanna Żuraszek
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, 60-479 Poznan, Poland
| | - Aleksandra Zielińska
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, 60-479 Poznan, Poland
| | - Karl-Heinz Herzig
- Department of Pediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Szpitalna 27/33, 60-572 Poznan, Poland
- Research Unit of Biomedicine, Faculty of Medicine, University of Oulu, Medical Research Center, Oulu University Hospital, P.O. Box 5000, FIN-90014 Oulu, Finland
- Correspondence: (K.-H.H.); (K.W.)
| | - Ryszard Słomski
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, 60-479 Poznan, Poland
| | - Jarosław Walkowiak
- Department of Pediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Szpitalna 27/33, 60-572 Poznan, Poland
| | - Karolina Wielgus
- Department of Pediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Szpitalna 27/33, 60-572 Poznan, Poland
- Correspondence: (K.-H.H.); (K.W.)
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14
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Advancement in Human Face Prediction Using DNA. Genes (Basel) 2023; 14:genes14010136. [PMID: 36672878 PMCID: PMC9858985 DOI: 10.3390/genes14010136] [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: 10/26/2022] [Revised: 12/15/2022] [Accepted: 12/21/2022] [Indexed: 01/05/2023] Open
Abstract
The rapid improvements in identifying the genetic factors contributing to facial morphology have enabled the early identification of craniofacial syndromes. Similarly, this technology can be vital in forensic cases involving human identification from biological traces or human remains, especially when reference samples are not available in the deoxyribose nucleic acid (DNA) database. This review summarizes the currently used methods for predicting human phenotypes such as age, ancestry, pigmentation, and facial features based on genetic variations. To identify the facial features affected by DNA, various two-dimensional (2D)- and three-dimensional (3D)-scanning techniques and analysis tools are reviewed. A comparison between the scanning technologies is also presented in this review. Face-landmarking techniques and face-phenotyping algorithms are discussed in chronological order. Then, the latest approaches in genetic to 3D face shape analysis are emphasized. A systematic review of the current markers that passed the threshold of a genome-wide association (GWAS) of single nucleotide polymorphism (SNP)-face traits from the GWAS Catalog is also provided using the preferred reporting items for systematic reviews and meta-analyses (PRISMA), approach. Finally, the current challenges in forensic DNA phenotyping are analyzed and discussed.
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15
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The genetic legacy of the Hunyadi descendants. Heliyon 2022; 8:e11731. [DOI: 10.1016/j.heliyon.2022.e11731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 10/11/2022] [Accepted: 11/11/2022] [Indexed: 11/18/2022] Open
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16
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A concerted effort combating hepatitis. Biomed J 2022; 45:727-732. [DOI: 10.1016/j.bj.2022.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 10/03/2022] [Indexed: 11/24/2022] Open
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17
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Zupanič Pajnič I, Zupanc T, Leskovar T, Črešnar M, Fattorini P. Eye and Hair Color Prediction of Ancient and Second World War Skeletal Remains Using a Forensic PCR-MPS Approach. Genes (Basel) 2022; 13:genes13081432. [PMID: 36011343 PMCID: PMC9407562 DOI: 10.3390/genes13081432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/01/2022] [Accepted: 08/08/2022] [Indexed: 11/16/2022] Open
Abstract
To test the usefulness of the forensic PCR-MPS approach to eye and hair color prediction for aged skeletons, a customized version of the PCR-MPS HIrisPlex panel was used on two sets of samples. The first set contained 11 skeletons dated from the 3rd to the 18th centuries AD, and for each of them at least four bone types were analyzed (for a total of 47 samples). In the second set, 24 skeletons from the Second World War were analyzed, and only petrous bones from the skulls were tested. Good-quality libraries were achieved in 83.3% of the cases for the ancient skeletons and in all Second World War petrous bones, with 94.7% and 100% of the markers, respectively, suitable for SNP typing. Consensus typing was achieved for about 91.7% of the markers in 10 out of 11 ancient skeletons, and the HIrisPlex-S webtool was then used to generate phenotypic predictions. Full predictions were achieved for 3 (27.3%) ancient skeletons and 12 (50%) Second World War petrous bones. In the remaining cases, different levels of AUC (area under the receiver operating curve) loss were computed because of no available data (NA) for 8.3% of markers in ancient skeletons and 4.2% of markers in Second World War petrous bones. Although the PCR-based approach has been replaced with new techniques in ancient DNA studies, the results show that customized forensic technologies can be successfully applied to aged bone remains, highlighting the role of the template in the success of PCR-MPS analysis. However, because several typical errors of ancient DNA sequencing were scored, replicate tests and accurate evaluation by an expert remain indispensable tools.
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Affiliation(s)
- Irena Zupanič Pajnič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia
| | - Tomaž Zupanc
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia
| | - Tamara Leskovar
- Department of Archaeology, Faculty of Arts, University of Ljubljana, Zavetiška 5, 1000 Ljubljana, Slovenia
| | - Matija Črešnar
- Department of Archaeology, Faculty of Arts, University of Ljubljana, Zavetiška 5, 1000 Ljubljana, Slovenia
| | - Paolo Fattorini
- Department of Medicine, Surgery and Health, University of Trieste, Strada per Fiume 447, 34149 Trieste, Italy
- Correspondence: ; Tel.: +39-040-399-3265
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18
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Dabas P, Jain S, Khajuria H, Nayak BP. Forensic DNA phenotyping: Inferring phenotypic traits from crime scene DNA. J Forensic Leg Med 2022; 88:102351. [DOI: 10.1016/j.jflm.2022.102351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 03/01/2022] [Accepted: 04/04/2022] [Indexed: 10/18/2022]
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19
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McElhoe JA, Wilton PR, Parson W, Holland MM. Exploring statistical weight estimates for mitochondrial DNA matches involving heteroplasmy. Int J Legal Med 2022; 136:671-685. [PMID: 35243529 DOI: 10.1007/s00414-022-02774-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 01/12/2022] [Indexed: 11/26/2022]
Abstract
Massively parallel sequencing (MPS) of mitochondrial (mt) DNA allows forensic laboratories to report heteroplasmy on a routine basis. Statistical approaches will be needed to determine the relative frequency of observing an mtDNA haplotype when including the presence of a heteroplasmic site. Here, we examined 1301 control region (CR) sequences, collected from individuals in four major population groups (European, African, Asian, and Latino), and covering 24 geographically distributed haplogroups, to assess the rates of point heteroplasmy (PHP) on an individual and nucleotide position (np) basis. With a minor allele frequency (MAF) threshold of 2%, the data was similar across population groups, with an overall PHP rate of 37.7%, and the majority of heteroplasmic individuals (77.3%) having only one site of heteroplasmy. The majority (75.2%) of identified PHPs had an MAF of 2-10%, and were observed at 12.6% of the nps across the CR. Both the broad and phylogenetic testing suggested that in many cases the low number of observations of heteroplasmy at any one np results in a lack of statistical association. The posterior frequency estimates, which skew conservative to a degree depending on the sample size in a given haplogroup, had a mean of 0.152 (SD 0.134) and ranged from 0.031 to 0.83. As expected, posterior frequency estimates decreased in accordance with 1/n as the sample size (n) increased. This provides a proposed conservative statistical framework for assessing haplotype/heteroplasmy matches when applying an MPS technique in forensic cases and will allow for continual refinement as more data is generated, both within the CR and across the mitochondrial genome.
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Affiliation(s)
- Jennifer A McElhoe
- Department of Biochemistry & Molecular Biology, Forensic Science Program, The Pennsylvania State University, University Park, 014 Thomas Building, State College, PA, 16802, USA.
| | - Peter R Wilton
- Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
- 23andMe Inc, Sunnyvale, CA, 94086, USA
| | - Walther Parson
- Department of Biochemistry & Molecular Biology, Forensic Science Program, The Pennsylvania State University, University Park, 014 Thomas Building, State College, PA, 16802, USA
- Institute of Legal Medicine, Medical University of Innsbruck, Müllerstraße 44, 6020, Innsbruck, Austria
| | - Mitchell M Holland
- Department of Biochemistry & Molecular Biology, Forensic Science Program, The Pennsylvania State University, University Park, 014 Thomas Building, State College, PA, 16802, USA
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20
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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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21
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Pilli E, Tarallo R, Riccia PL, Berti A, Novelletto A. Kinship assignment with the ForenSeq™ DNA Signature Prep Kit: Sources of error in simulated and real cases. Sci Justice 2022; 62:1-9. [PMID: 35033321 DOI: 10.1016/j.scijus.2021.10.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 08/31/2021] [Accepted: 10/21/2021] [Indexed: 11/30/2022]
Abstract
Kinship recognition between anonymous DNA samples is becoming a relevant issue in forensics, more so with the increasing number of DNA profiles in databanks. Also, NGS-based genotyping is being increasingly used in routine personal identification, to simultaneously type large numbers of markers of different kind. In the present work, we explored computationally and experimentally the performance of the ForenSeq™ DNA Signature Prep Kit in identifying the true relationship between two anonymous samples, distinguishing it from other possible relationships. We analyzed with Familias R series of 10,000 pairs with 9 different simulated relationships, corresponding to different degrees of autosomal sharing. For each pair we obtained likelihood ratios for five kinship hypotheses vs. unrelatedness, and used their ranking to identify the preferred relationship. We also typed 21 subjects from two pedigrees, representing from parent-child to 4th cousins relationships. As expected, the power for identifying the true relationship decays in the order of autosomal sharing. Parent-child and full siblings can be robustly identified against other relationships. For half-siblings the chance of reaching a significant conclusion is already small. For more distant relationships the proportion of cases correctly and significantly identified is 10% or less. Bidirectional errors in kinship attribution include the suggestion of relatedness when this does not exist (10-50%), and the suggestion of independence in pairs of individuals more than 4 generations apart (25-60%). The real cases revealed a relevant effect of genotype miscalling at some loci, which could only be partly avoided by modulating the analysis parameters. In conclusion, with the exception of first degree relatives, the kit can be useful to inform additional investigations, but does not usually provide probatory results.
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Affiliation(s)
- Elena Pilli
- Department of Biology, University of Florence, Florence, Italy.
| | - Roberta Tarallo
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - Pietro La Riccia
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - Andrea Berti
- Reparto Carabinieri Investigazioni Scientifiche, Sezione di Biologia, Roma, Italy
| | - Andrea Novelletto
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
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22
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Pośpiech E, Teisseyre P, Mielniczuk J, Branicki W. Predicting Physical Appearance from DNA Data-Towards Genomic Solutions. Genes (Basel) 2022; 13:genes13010121. [PMID: 35052461 PMCID: PMC8774670 DOI: 10.3390/genes13010121] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/03/2022] [Accepted: 01/04/2022] [Indexed: 02/04/2023] Open
Abstract
The idea of forensic DNA intelligence is to extract from genomic data any information that can help guide the investigation. The clues to the externally visible phenotype are of particular practical importance. The high heritability of the physical phenotype suggests that genetic data can be easily predicted, but this has only become possible with less polygenic traits. The forensic community has developed DNA-based predictive tools by employing a limited number of the most important markers analysed with targeted massive parallel sequencing. The complexity of the genetics of many other appearance phenotypes requires big data coupled with sophisticated machine learning methods to develop accurate genomic predictors. A significant challenge in developing universal genomic predictive methods will be the collection of sufficiently large data sets. These should be created using whole-genome sequencing technology to enable the identification of rare DNA variants implicated in phenotype determination. It is worth noting that the correctness of the forensic sketch generated from the DNA data depends on the inclusion of an age factor. This, however, can be predicted by analysing epigenetic data. An important limitation preventing whole-genome approaches from being commonly used in forensics is the slow progress in the development and implementation of high-throughput, low DNA input sequencing technologies. The example of palaeoanthropology suggests that such methods may possibly be developed in forensics.
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Affiliation(s)
- Ewelina Pośpiech
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland;
| | - Paweł Teisseyre
- Institute of Computer Science, Polish Academy of Sciences, 01-248 Warsaw, Poland; (P.T.); (J.M.)
- Faculty of Mathematics and Information Science, Warsaw University of Technology, 00-662 Warsaw, Poland
| | - Jan Mielniczuk
- Institute of Computer Science, Polish Academy of Sciences, 01-248 Warsaw, Poland; (P.T.); (J.M.)
- Faculty of Mathematics and Information Science, Warsaw University of Technology, 00-662 Warsaw, Poland
| | - Wojciech Branicki
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland;
- Central Forensic Laboratory of the Police, 00-583 Warsaw, Poland
- Correspondence: ; Tel.: +48-126-645-024
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23
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Warne DJ, Baker RE, Simpson MJ. Rapid Bayesian Inference for Expensive Stochastic Models. J Comput Graph Stat 2021. [DOI: 10.1080/10618600.2021.2000419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- David J. Warne
- School of Mathematical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Ruth E. Baker
- Mathematical Institute, University of Oxford, Oxford, UK
| | - Matthew J. Simpson
- School of Mathematical Sciences, Queensland University of Technology, Brisbane, Australia
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24
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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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25
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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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26
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Complete mitogenome in a population sample from Cameroon. Forensic Sci Int Genet 2021; 55:102597. [PMID: 34560341 DOI: 10.1016/j.fsigen.2021.102597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 08/30/2021] [Accepted: 09/05/2021] [Indexed: 11/23/2022]
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27
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Zupanič Pajnič I. Identification of a Slovenian prewar elite couple killed in the Second World War. Forensic Sci Int 2021; 327:110994. [PMID: 34536754 DOI: 10.1016/j.forsciint.2021.110994] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/30/2021] [Accepted: 09/03/2021] [Indexed: 11/28/2022]
Abstract
Genetic identification of a Slovenian prewar elite couple killed in 1944 was performed by typing autosomal and Y-chromosomal STRs, and phenotypic HIrisPlex SNPs for hair and eye color prediction were analyzed for the female skeleton using next-generation sequencing (NGS) technology. The clandestine grave containing the couple's skeletal remains was found in 2015 and only the partial remains were found. Living distant relatives could be found only for the male victim. Because of a lack of comparative reference samples, it was not possible to identify the female victim through autosomal and mitochondrial DNA typing. However, the possibility of comparison of eye and hair color with a painting exhibited in the City Museum of Ljubljana by the prominent Slovenian painter Ivana Kobilca existed. Nuclear DNA obtained from the samples was quantified using the PowerQuant System, and then STR typing was carried out with different autosomal and Y-STR kits. From 0.09-9.36 ng DNA/g of powder was obtained from teeth and bones analyzed. Complete autosomal and Y-STR profiles made it possible to identify the male skeleton via comparison with two nephews. For the female victim, predicted eye and hair color was compared to colors on the painting. Kobilca's painting confirms the genetically predicted eye and hair color. After more than seventy years, the skeletal remains of the couple were handed over to their relatives, who buried the victims with dignity in a family grave.
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Affiliation(s)
- Irena Zupanič Pajnič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia.
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de la Puente M, Ruiz-Ramírez J, Ambroa-Conde A, Xavier C, Pardo-Seco J, Álvarez-Dios J, Freire-Aradas A, Mosquera-Miguel A, Gross TE, Cheung EYY, Branicki W, Nothnagel M, Parson W, Schneider PM, Kayser M, Carracedo Á, Lareu MV, Phillips C. Development and Evaluation of the Ancestry Informative Marker Panel of the VISAGE Basic Tool. Genes (Basel) 2021; 12:1284. [PMID: 34440458 PMCID: PMC8391248 DOI: 10.3390/genes12081284] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/18/2021] [Accepted: 08/18/2021] [Indexed: 11/29/2022] Open
Abstract
We detail the development of the ancestry informative single nucleotide polymorphisms (SNPs) panel forming part of the VISAGE Basic Tool (BT), which combines 41 appearance predictive SNPs and 112 ancestry predictive SNPs (three SNPs shared between sets) in one massively parallel sequencing (MPS) multiplex, whereas blood-based age analysis using methylation markers is run in a parallel MPS analysis pipeline. The selection of SNPs for the BT ancestry panel focused on established forensic markers that already have a proven track record of good sequencing performance in MPS, and the overall SNP multiplex scale closely matched that of existing forensic MPS assays. SNPs were chosen to differentiate individuals from the five main continental population groups of Africa, Europe, East Asia, America, and Oceania, extended to include differentiation of individuals from South Asia. From analysis of 1000 Genomes and HGDP-CEPH samples from these six population groups, the BT ancestry panel was shown to have no classification error using the Bayes likelihood calculators of the Snipper online analysis portal. The differentiation power of the component ancestry SNPs of BT was balanced as far as possible to avoid bias in the estimation of co-ancestry proportions in individuals with admixed backgrounds. The balancing process led to very similar cumulative population-specific divergence values for Africa, Europe, America, and Oceania, with East Asia being slightly below average, and South Asia an outlier from the other groups. Comparisons were made of the African, European, and Native American estimated co-ancestry proportions in the six admixed 1000 Genomes populations, using the BT ancestry panel SNPs and 572,000 Affymetrix Human Origins array SNPs. Very similar co-ancestry proportions were observed down to a minimum value of 10%, below which, low-level co-ancestry was not always reliably detected by BT SNPs. The Snipper analysis portal provides a comprehensive population dataset for the BT ancestry panel SNPs, comprising a 520-sample standardised reference dataset; 3445 additional samples from 1000 Genomes, HGDP-CEPH, Simons Foundation and Estonian Biocentre genome diversity projects; and 167 samples of six populations from in-house genotyping of individuals from Middle East, North and East African regions complementing those of the sampling regimes of the other diversity projects.
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Affiliation(s)
- María de la Puente
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain; (M.d.l.P.); (J.R.-R.); (A.A.-C.); (A.F.-A.); (A.M.-M.); (Á.C.); (M.V.L.)
| | - Jorge Ruiz-Ramírez
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain; (M.d.l.P.); (J.R.-R.); (A.A.-C.); (A.F.-A.); (A.M.-M.); (Á.C.); (M.V.L.)
| | - Adrián Ambroa-Conde
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain; (M.d.l.P.); (J.R.-R.); (A.A.-C.); (A.F.-A.); (A.M.-M.); (Á.C.); (M.V.L.)
| | - Catarina Xavier
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (C.X.); (W.P.)
| | - Jacobo Pardo-Seco
- Genetics, Vaccines, Infectious Diseases and Pediatrics Research Group (GENVIP Group), Instituto de Investigación Sanitaria de Santiago de Compostela, 15706 Santiago de Compostela, Spain;
| | - Jose Álvarez-Dios
- Faculty of Mathematics, University of Santiago de Compostela, 15705 Santiago de Compostela, Spain;
| | - Ana Freire-Aradas
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain; (M.d.l.P.); (J.R.-R.); (A.A.-C.); (A.F.-A.); (A.M.-M.); (Á.C.); (M.V.L.)
| | - Ana Mosquera-Miguel
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain; (M.d.l.P.); (J.R.-R.); (A.A.-C.); (A.F.-A.); (A.M.-M.); (Á.C.); (M.V.L.)
| | - Theresa E. Gross
- Institute of Legal Medicine, Faculty of Medicine and University Clinic, University of Cologne, 50823 Cologne, Germany; (T.E.G.); (E.Y.Y.C.); (P.M.S.)
- Hessisches Landeskriminalamt, 65187 Wiesbaden, Germany
| | - Elaine Y. Y. Cheung
- Institute of Legal Medicine, Faculty of Medicine and University Clinic, University of Cologne, 50823 Cologne, Germany; (T.E.G.); (E.Y.Y.C.); (P.M.S.)
| | - Wojciech Branicki
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland;
| | - Michael Nothnagel
- Cologne Center for Genomics, University of Cologne, 50823 Cologne, Germany;
- University Hospital Cologne, 50937 Cologne, Germany
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (C.X.); (W.P.)
- Forensic Science Program, The Pennsylvania State University, University Park, State College, PA 16802, USA
| | - Peter M. Schneider
- Institute of Legal Medicine, Faculty of Medicine and University Clinic, University of Cologne, 50823 Cologne, Germany; (T.E.G.); (E.Y.Y.C.); (P.M.S.)
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, 3015 CN Rotterdam, South Holland, The Netherlands;
| | - Ángel Carracedo
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain; (M.d.l.P.); (J.R.-R.); (A.A.-C.); (A.F.-A.); (A.M.-M.); (Á.C.); (M.V.L.)
- Fundación Pública Galega de Medicina Xenómica (FPGMX), 15706 Santiago de Compostela, Spain
| | - Maria Victoria Lareu
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain; (M.d.l.P.); (J.R.-R.); (A.A.-C.); (A.F.-A.); (A.M.-M.); (Á.C.); (M.V.L.)
| | - Christopher Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain; (M.d.l.P.); (J.R.-R.); (A.A.-C.); (A.F.-A.); (A.M.-M.); (Á.C.); (M.V.L.)
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Kukla-Bartoszek M, Teisseyre P, Pośpiech E, Karłowska-Pik J, Zieliński P, Woźniak A, Boroń M, Dąbrowski M, Zubańska M, Jarosz A, Płoski R, Grzybowski T, Spólnicka M, Mielniczuk J, Branicki W. Searching for improvements in predicting human eye colour from DNA. Int J Legal Med 2021; 135:2175-2187. [PMID: 34259936 PMCID: PMC8523394 DOI: 10.1007/s00414-021-02645-5] [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: 03/31/2021] [Accepted: 06/17/2021] [Indexed: 01/29/2023]
Abstract
Increasing understanding of human genome variability allows for better use of the predictive potential of DNA. An obvious direct application is the prediction of the physical phenotypes. Significant success has been achieved, especially in predicting pigmentation characteristics, but the inference of some phenotypes is still challenging. In search of further improvements in predicting human eye colour, we conducted whole-exome (enriched in regulome) sequencing of 150 Polish samples to discover new markers. For this, we adopted quantitative characterization of eye colour phenotypes using high-resolution photographic images of the iris in combination with DIAT software analysis. An independent set of 849 samples was used for subsequent predictive modelling. Newly identified candidates and 114 additional literature-based selected SNPs, previously associated with pigmentation, and advanced machine learning algorithms were used. Whole-exome sequencing analysis found 27 previously unreported candidate SNP markers for eye colour. The highest overall prediction accuracies were achieved with LASSO-regularized and BIC-based selected regression models. A new candidate variant, rs2253104, located in the ARFIP2 gene and identified with the HyperLasso method, revealed predictive potential and was included in the best-performing regression models. Advanced machine learning approaches showed a significant increase in sensitivity of intermediate eye colour prediction (up to 39%) compared to 0% obtained for the original IrisPlex model. We identified a new potential predictor of eye colour and evaluated several widely used advanced machine learning algorithms in predictive analysis of this trait. Our results provide useful hints for developing future predictive models for eye colour in forensic and anthropological studies.
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Affiliation(s)
- Magdalena Kukla-Bartoszek
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland. .,Malopolska Centre of Biotechnology of the Jagiellonian University, Kraków, Poland.
| | - Paweł Teisseyre
- Institute of Computer Science, Polish Academy of Sciences, Warsaw, Poland.,Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | - Ewelina Pośpiech
- Malopolska Centre of Biotechnology of the Jagiellonian University, Kraków, Poland
| | - Joanna Karłowska-Pik
- Faculty of Mathematics and Computer Science, Nicolaus Copernicus University in Toruń, Toruń, Poland
| | - Piotr Zieliński
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Anna Woźniak
- Central Forensic Laboratory of the Police, Warsaw, Poland
| | - Michał Boroń
- Central Forensic Laboratory of the Police, Warsaw, Poland
| | - Michał Dąbrowski
- Laboratory of Bioinformatics, Neurobiology Centre, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Magdalena Zubańska
- Faculty of Law and Administration, Department of Criminology and Forensic Sciences, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland.,Unit of Forensic Sciences, Faculty of Internal Security, Police Academy, Szczytno, Poland
| | - Agata Jarosz
- Malopolska Centre of Biotechnology of the Jagiellonian University, Kraków, Poland
| | - Rafał Płoski
- Department of Medical Genetics, Warsaw Medical University, Warsaw, Poland
| | - Tomasz Grzybowski
- Division of Molecular and Forensic Genetics, Department of Forensic Medicine, Nicolaus Copernicus University in Toruń, Collegium Medicum in Bydgoszcz, Bydgoszcz, Poland
| | | | - Jan Mielniczuk
- Institute of Computer Science, Polish Academy of Sciences, Warsaw, Poland.,Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | - Wojciech Branicki
- Malopolska Centre of Biotechnology of the Jagiellonian University, Kraków, Poland. .,Central Forensic Laboratory of the Police, Warsaw, Poland.
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Ta MTA, Nguyen NN, Tran DM, Nguyen TH, Vu TA, Le DT, Le PT, Do TTH, Hoang H, Chu HH. Massively parallel sequencing of human skeletal remains in Vietnam using the precision ID mtDNA control region panel on the Ion S5™ system. Int J Legal Med 2021; 135:2285-2294. [PMID: 34196785 DOI: 10.1007/s00414-021-02649-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/21/2021] [Indexed: 11/30/2022]
Abstract
Mitochondrial DNA (mtDNA) analysis using Sanger sequencing has been a routine practice for the identification of human skeletal remains. However, this process is usually challenging since DNA from the remains is highly degraded and at low concentration. Recently, the advent and implementation of massively parallel sequencing (MPS) have been offered the ability to improve mtDNA sequence data for forensic analysis. To assess the utility of the Ion S5™ system - an MPS platform for mtDNA analysis in challenging samples, we sequenced the mitochondrial control region of 52 age-old skeletal remains. Using the Precision ID mtDNA Control Region Panel, 50 full and two partial control region haplotypes at relatively high mean coverage of 2494 × were achieved for variant calling. Further variant analysis at 10% threshold for point heteroplasmy showed high degradation degree in terms of DNA damage in our bone samples. A higher point heteroplasmy threshold of 20% was required to diminish most of background noise caused by the damage. The results from this study indicated the potential application of the Ion S5™ system in sequencing degraded samples in Vietnam and provided valuable data sources for forensic analyses in the future.
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Affiliation(s)
- May Thi Anh Ta
- Centre for DNA Identification, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Nam Ngoc Nguyen
- Centre for DNA Identification, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Duc Minh Tran
- Centre for DNA Identification, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Trang Hong Nguyen
- National Key Laboratory of Gene Technology, Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Hanoi, 100000, Vietnam
| | - Tuan Anh Vu
- Centre for DNA Identification, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Dung Thi Le
- Centre for DNA Identification, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Phuong Thi Le
- Centre for DNA Identification, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Thu Thi Hong Do
- Centre for DNA Identification, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Ha Hoang
- Centre for DNA Identification, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam.,National Key Laboratory of Gene Technology, Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Hanoi, 100000, Vietnam
| | - Hoang Ha Chu
- National Key Laboratory of Gene Technology, Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Hanoi, 100000, Vietnam. .,Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam.
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31
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Gurkan C, Bulbul O, Kidd KK. Editorial: Current and Emerging Trends in Human Identification and Molecular Anthropology. Front Genet 2021; 12:708222. [PMID: 34249111 PMCID: PMC8262838 DOI: 10.3389/fgene.2021.708222] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 05/24/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Cemal Gurkan
- Turkish Cypriot DNA Laboratory, Committee on Missing Persons in Cyprus Turkish Cypriot Member's Office, Nicosia, Turkey.,Dr. Fazil Küçük Faculty of Medicine, Eastern Mediterranean University, Famagusta, Turkey
| | - Ozlem Bulbul
- Institute of Forensic Science, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Kenneth K Kidd
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States
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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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Palmal S, Adhikari K, Mendoza-Revilla J, Fuentes-Guajardo M, Silva de Cerqueira CC, Bonfante B, Chacón-Duque JC, Sohail A, Hurtado M, Villegas V, Granja V, Jaramillo C, Arias W, Lozano RB, Everardo-Martínez P, Gómez-Valdés J, Villamil-Ramírez H, Hünemeier T, Ramallo V, Parolin ML, Gonzalez-José R, Schüler-Faccini L, Bortolini MC, Acuña-Alonzo V, Canizales-Quinteros S, Gallo C, Poletti G, Bedoya G, Rothhammer F, Balding D, Faux P, Ruiz-Linares A. Prediction of eye, hair and skin colour in Latin Americans. Forensic Sci Int Genet 2021; 53:102517. [PMID: 33865096 DOI: 10.1016/j.fsigen.2021.102517] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 03/19/2021] [Accepted: 03/30/2021] [Indexed: 10/21/2022]
Abstract
Here we evaluate the accuracy of prediction for eye, hair and skin pigmentation in a dataset of > 6500 individuals from Mexico, Colombia, Peru, Chile and Brazil (including genome-wide SNP data and quantitative/categorical pigmentation phenotypes - the CANDELA dataset CAN). We evaluated accuracy in relation to different analytical methods and various phenotypic predictors. As expected from statistical principles, we observe that quantitative traits are more sensitive to changes in the prediction models than categorical traits. We find that Random Forest or Linear Regression are generally the best performing methods. We also compare the prediction accuracy of SNP sets defined in the CAN dataset (including 56, 101 and 120 SNPs for eye, hair and skin colour prediction, respectively) to the well-established HIrisPlex-S SNP set (including 6, 22 and 36 SNPs for eye, hair and skin colour prediction respectively). When training prediction models on the CAN data, we observe remarkably similar performances for HIrisPlex-S and the larger CAN SNP sets for the prediction of hair (categorical) and eye (both categorical and quantitative), while the CAN sets outperform HIrisPlex-S for quantitative, but not for categorical skin pigmentation prediction. The performance of HIrisPlex-S, when models are trained in a world-wide sample (although consisting of 80% Europeans, https://hirisplex.erasmusmc.nl), is lower relative to training in the CAN data (particularly for hair and skin colour). Altogether, our observations are consistent with common variation of eye and hair colour having a relatively simple genetic architecture, which is well captured by HIrisPlex-S, even in admixed Latin Americans (with partial European ancestry). By contrast, since skin pigmentation is a more polygenic trait, accuracy is more sensitive to prediction SNP set size, although here this effect was only apparent for a quantitative measure of skin pigmentation. Our results support the use of HIrisPlex-S in the prediction of categorical pigmentation traits for forensic purposes in Latin America, while illustrating the impact of training datasets on its accuracy.
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Affiliation(s)
- Sagnik Palmal
- UMR 7268 ADES, CNRS, Aix-Marseille Université, EFS, Faculté de Médecine Timone, Marseille 13005, France
| | - Kaustubh Adhikari
- School of Mathematics and Statistics, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes MK7 6AA, UK; Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Javier Mendoza-Revilla
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Perú; Unit of Human Evolutionary Genetics, Institut Pasteur, Paris 75015, France
| | - Macarena Fuentes-Guajardo
- Departamento de Tecnología Médica, Facultad de Ciencias de la Salud, Universidad de Tarapacá, Arica 1000000, Chile
| | | | - Betty Bonfante
- UMR 7268 ADES, CNRS, Aix-Marseille Université, EFS, Faculté de Médecine Timone, Marseille 13005, France
| | - Juan Camilo Chacón-Duque
- Division of Vertebrates and Anthropology, Department of Earth Sciences, Natural History Museum, London SW7 5BD, UK
| | - Anood Sohail
- Department of Biotechnology, Kinnaird College for Women, 93 - Jail Road, Lahore 54000, Pakistan
| | - Malena Hurtado
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Perú
| | - Valeria Villegas
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Perú
| | - Vanessa Granja
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Perú
| | - Claudia Jaramillo
- Department of Biotechnology, Kinnaird College for Women, 93 - Jail Road, Lahore 54000, Pakistan; GENMOL (Genética Molecular), Universidad de Antioquia, Medellín 5001000, Colombia
| | - William Arias
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín 5001000, Colombia
| | - Rodrigo Barquera Lozano
- National Institute of Anthropology and History, Mexico City 6600, Mexico; Department of Archaeogenetics, Max Planck Institute for the Science of Human History (MPI-SHH), Jena 07745, Germany
| | | | - Jorge Gómez-Valdés
- National Institute of Anthropology and History, Mexico City 6600, Mexico
| | - Hugo Villamil-Ramírez
- Unidad de Genomica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, Mexico City 4510, Mexico
| | - Tábita Hünemeier
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP 05508-090, Brazil
| | - Virginia Ramallo
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 90040-060, Brazil; Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, CONICET, Puerto Madryn U9129ACD, Argentina
| | - Maria-Laura Parolin
- Instituto de Diversidad y Evolución Austral (IDEAus), Centro Nacional Patagónico, CONICET, Puerto Madryn, Argentina
| | - Rolando Gonzalez-José
- Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, CONICET, Puerto Madryn U9129ACD, Argentina
| | - Lavinia Schüler-Faccini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 90040-060, Brazil
| | - Maria-Cátira Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 90040-060, Brazil
| | | | - Samuel Canizales-Quinteros
- Unidad de Genomica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, Mexico City 4510, Mexico
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Perú
| | - Giovanni Poletti
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Perú
| | - Gabriel Bedoya
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín 5001000, Colombia
| | - Francisco Rothhammer
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica 1000000, Chile; Programa de Genetica Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Arica 1000000, Chile
| | - David Balding
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London WC1E 6BT, UK; Melbourne Integrative Genomics, Schools of BioSciences and Mathematics & Statistics, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Pierre Faux
- UMR 7268 ADES, CNRS, Aix-Marseille Université, EFS, Faculté de Médecine Timone, Marseille 13005, France.
| | - Andrés Ruiz-Linares
- UMR 7268 ADES, CNRS, Aix-Marseille Université, EFS, Faculté de Médecine Timone, Marseille 13005, France; Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London WC1E 6BT, UK; Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Yangpu District, Shanghai, China.
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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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35
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Marshall C, Parson W. Interpreting NUMTs in forensic genetics: Seeing the forest for the trees. Forensic Sci Int Genet 2021; 53:102497. [PMID: 33740708 DOI: 10.1016/j.fsigen.2021.102497] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/10/2021] [Accepted: 03/11/2021] [Indexed: 01/29/2023]
Abstract
Nuclear mitochondrial DNA (mtDNA) segments (NUMTs) were discovered shortly after sequencing the first human mitochondrial genome. They have earlier been considered to represent archaic elements of ancient insertion events, but modern sequencing technologies and growing databases of mtDNA and NUMT sequences confirm that they are abundant and some of them phylogenetically young. Here, we build upon mtDNA/NUMT review articles published in the mid 2010 s and focus on the distinction of NUMTs and other artefacts that can be observed in aligned sequence reads, such as mixtures (contamination), point heteroplasmy, sequencing error and cytosine deamination. We show practical examples of the effect of the mtDNA enrichment method on the representation of NUMTs in the mapped sequence data and discuss methods to bioinformatically filter NUMTs from mtDNA reads.
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Affiliation(s)
- Charla Marshall
- Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, DE 19902, USA; SNA International, Contractor Supporting the AFMES-AFDIL, Alexandria, VA 22314, USA; Forensic Science Program, The Pennsylvania State University, University Park, PA 16802, USA
| | - Walther Parson
- Forensic Science Program, The Pennsylvania State University, University Park, PA 16802, USA; Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria.
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36
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Simcoe M, Valdes A, Liu F, Furlotte NA, Evans DM, Hemani G, Ring SM, Smith GD, Duffy DL, Zhu G, Gordon SD, Medland SE, Vuckovic D, Girotto G, Sala C, Catamo E, Concas MP, Brumat M, Gasparini P, Toniolo D, Cocca M, Robino A, Yazar S, Hewitt A, Wu W, Kraft P, Hammond CJ, Shi Y, Chen Y, Zeng C, Klaver CCW, Uitterlinden AG, Ikram MA, Hamer MA, van Duijn CM, Nijsten T, Han J, Mackey DA, Martin NG, Cheng CY, Hinds DA, Spector TD, Kayser M, Hysi PG. Genome-wide association study in almost 195,000 individuals identifies 50 previously unidentified genetic loci for eye color. SCIENCE ADVANCES 2021; 7:7/11/eabd1239. [PMID: 33692100 PMCID: PMC7946369 DOI: 10.1126/sciadv.abd1239] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 01/25/2021] [Indexed: 05/03/2023]
Abstract
Human eye color is highly heritable, but its genetic architecture is not yet fully understood. We report the results of the largest genome-wide association study for eye color to date, involving up to 192,986 European participants from 10 populations. We identify 124 independent associations arising from 61 discrete genomic regions, including 50 previously unidentified. We find evidence for genes involved in melanin pigmentation, but we also find associations with genes involved in iris morphology and structure. Further analyses in 1636 Asian participants from two populations suggest that iris pigmentation variation in Asians is genetically similar to Europeans, albeit with smaller effect sizes. Our findings collectively explain 53.2% (95% confidence interval, 45.4 to 61.0%) of eye color variation using common single-nucleotide polymorphisms. Overall, our study outcomes demonstrate that the genetic complexity of human eye color considerably exceeds previous knowledge and expectations, highlighting eye color as a genetically highly complex human trait.
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Affiliation(s)
- Mark Simcoe
- Department of Twins Research and Genetic Epidemiology, King's College London, London, UK
- Department of Ophthalmology, King's College London, London, UK
| | - Ana Valdes
- Department of Twins Research and Genetic Epidemiology, King's College London, London, UK
- Division of Rheumatology, Orthopaedics and Dermatology, School of Medicine, University of Nottingham, Nottingham, UK
| | - Fan Liu
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | | | - David M Evans
- University of Queensland Diamantina Institute, University of Queensland, Brisbane, Queensland, Australia
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Gibran Hemani
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences Bristol Medical School University of Bristol, Bristol, UK
| | - Susan M Ring
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences Bristol Medical School University of Bristol, Bristol, UK
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences Bristol Medical School University of Bristol, Bristol, UK
| | - David L Duffy
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Gu Zhu
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Scott D Gordon
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Sarah E Medland
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Dragana Vuckovic
- Department of Medical Sciences, University of Trieste, Trieste, Italy
- Institute for Maternal and Child Health IRCCS "Burlo Garofolo", Trieste, Italy
- Epidemiology and Biostatistics Department, Faculty of Medicine, School of Public Health, Imperial College London, London, UK
| | - Giorgia Girotto
- Department of Medical Sciences, University of Trieste, Trieste, Italy
- Institute for Maternal and Child Health IRCCS "Burlo Garofolo", Trieste, Italy
| | - Cinzia Sala
- Division of Genetics of Common Disorders, S. Raffaele Scientific Institute, Milan, Italy
| | - Eulalia Catamo
- Department of Medical Sciences, University of Trieste, Trieste, Italy
| | - Maria Pina Concas
- Institute for Maternal and Child Health IRCCS "Burlo Garofolo", Trieste, Italy
| | - Marco Brumat
- Department of Medical Sciences, University of Trieste, Trieste, Italy
| | - Paolo Gasparini
- Department of Medical Sciences, University of Trieste, Trieste, Italy
- Institute for Maternal and Child Health IRCCS "Burlo Garofolo", Trieste, Italy
| | - Daniela Toniolo
- Division of Genetics of Common Disorders, S. Raffaele Scientific Institute, Milan, Italy
| | - Massimiliano Cocca
- Institute for Maternal and Child Health IRCCS "Burlo Garofolo", Trieste, Italy
| | - Antonietta Robino
- Institute for Maternal and Child Health IRCCS "Burlo Garofolo", Trieste, Italy
| | - Seyhan Yazar
- Centre for Ophthalmology and Visual Science, University of Western Australia, Lions Eye Institute, Perth, Australia
| | - Alex Hewitt
- Centre for Ophthalmology and Visual Science, University of Western Australia, Lions Eye Institute, Perth, Australia
- Centre for Eye Research Australia, University of Melbourne, Department of Ophthalmology, Royal Victorian Eye and Ear Hospital, Melbourne, Australia
- School of Medicine, Menzies Research Institute Tasmania, University of Tasmania, Hobart, Australia
| | - Wenting Wu
- Department of Epidemiology, Fairbanks School of Public Health, Indiana University, and Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN, USA
| | - Peter Kraft
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Christopher J Hammond
- Department of Twins Research and Genetic Epidemiology, King's College London, London, UK
- Department of Ophthalmology, King's College London, London, UK
| | - Yuan Shi
- Singapore Eye Research Institute, Singapore National Eye Center, Singapore
| | - Yan Chen
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Changqing Zeng
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Caroline C W Klaver
- Department of Ophthalmology, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Andre G Uitterlinden
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
- Department of Internal Medicine, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Merel A Hamer
- Department of Dermatology, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Tamar Nijsten
- Department of Dermatology, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Jiali Han
- Department of Epidemiology, Fairbanks School of Public Health, Indiana University, and Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN, USA
| | - David A Mackey
- Centre for Ophthalmology and Visual Science, University of Western Australia, Lions Eye Institute, Perth, Australia
| | - Nicholas G Martin
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Ching-Yu Cheng
- Singapore Eye Research Institute, Singapore National Eye Center, Singapore
- Duke-NUS Medical School, Singapore
| | | | - Timothy D Spector
- Department of Twins Research and Genetic Epidemiology, King's College London, London, UK
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands.
| | - Pirro G Hysi
- Department of Twins Research and Genetic Epidemiology, King's College London, London, UK.
- Department of Ophthalmology, King's College London, London, UK
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37
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Melchionda F, Stanciu F, Buscemi L, Pesaresi M, Tagliabracci A, Turchi C. Searching the undetected mtDNA variants in forensic MPS data. Forensic Sci Int Genet 2020; 49:102399. [PMID: 33038616 DOI: 10.1016/j.fsigen.2020.102399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/27/2020] [Accepted: 09/21/2020] [Indexed: 10/23/2022]
Abstract
The efficiency of MPS in forensic mtDNA analysis has been thoroughly proven, although a reliable and well established data evaluation still remains a critical point. Numerous bioinformatics tools have been developed, but most of them require specific operating systems and high costs, while free open-source programs with user-friendly interfaces are few. In this study, 43 full mtGenomes were sequenced using the Ion Personal Genome Machine™ (PGM™) System and analyzed utilizing the plug-in Variant Caller (TVC) of the Ion Torrent Software Suite and the mtDNA-Server (mDS), a free web-based mitochondrial analysis tool for MPS data. The outcomes of these two different analysis tools were compared to variants noted after manual inspection of the aligned reads performed using Integrative Genomics Viewer (IGV). The comparison highlighted the presence of thirty-nine discordant variant calls, which were resolved by Sanger sequencing that confirmed the presence of all variants, except for 7 deletions. The combined adoption of IGV and Sanger type sequencing confirmatory steps, in addition of TVC and mDS analysis, resulted in a more accurate variants assignment with the detection of 32 additional true polymorphisms, which were noted in the final dataset. Regarding the heteroplasmy issue, out of a total of thirty heteroplasmic variants, twenty-eight were detected by the TVC, while the mDS detected twenty-two. Overall, none of the used bioinformatics tools were the perfect choice and a secondary analysis with an expert's opinion in complete mtGenome MPS data evaluation is still required in forensic genetic analysis.
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Affiliation(s)
- Filomena Melchionda
- Section of Legal Medicine, Department of Excellence of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy - Via Tronto, 60126 Torrette Ancona, Italy.
| | - Florin Stanciu
- Romanian National DNA Database, National Forensic Science Institute, General Inspectorate of Romanian Police, Bucharest, Romania.
| | - Loredana Buscemi
- Section of Legal Medicine, Department of Excellence of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy - Via Tronto, 60126 Torrette Ancona, Italy.
| | - Mauro Pesaresi
- Section of Legal Medicine, Department of Excellence of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy - Via Tronto, 60126 Torrette Ancona, Italy.
| | - Adriano Tagliabracci
- Section of Legal Medicine, Department of Excellence of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy - Via Tronto, 60126 Torrette Ancona, Italy.
| | - Chiara Turchi
- Section of Legal Medicine, Department of Excellence of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy - Via Tronto, 60126 Torrette Ancona, Italy.
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38
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Chen Y, Branicki W, Walsh S, Nothnagel M, Kayser M, Liu F. The impact of correlations between pigmentation phenotypes and underlying genotypes on genetic prediction of pigmentation traits. Forensic Sci Int Genet 2020; 50:102395. [PMID: 33070049 DOI: 10.1016/j.fsigen.2020.102395] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/25/2020] [Accepted: 09/15/2020] [Indexed: 12/31/2022]
Abstract
Predicting appearance phenotypes from genotypes is relevant for various areas of human genetic research and applications such as genetic epidemiology, human history, anthropology, and particularly in forensics. Many appearance phenotypes, and thus their underlying genotypes, are highly correlated, with pigmentation traits serving as primary examples. However, all available genetic prediction models, including those for pigmentation traits currently used in forensic DNA phenotyping, ignore phenotype correlations. Here, we investigated the impact of appearance phenotype correlations on genetic appearance prediction in the exemplary case of three pigmentation traits. We used data for categorical eye, hair and skin colour as well as 41 DNA markers utilized in the recently established HIrisPlex-S system from 762 individuals with complete phenotype and genotype information. Based on these data, we performed genetic prediction modelling of eye, hair and skin colour via three different strategies, namely the established approach of predicting phenotypes solely based on genotypes while not considering phenotype correlations, and two novel approaches that considered phenotype correlations, either incorporating truly observed correlated phenotypes or DNA-predicted correlated phenotypes in addition to the DNA predictors. We found that using truly observed correlated pigmentation phenotypes as additional predictors increased the DNA-based prediction accuracies for almost all eye, hair and skin colour categories, with the largest increase for intermediate eye colour, brown hair colour, dark to black skin colour, and particularly for dark skin colour. Outcomes of dedicated computer simulations suggest that this prediction accuracy increase is due to the additional genetic information that is implicitly provided by the truly observed correlated pigmentation phenotypes used, yet not covered by the DNA predictors applied. In contrast, considering DNA-predicted correlated pigmentation phenotypes as additional predictors did not improve the performance of the genetic prediction of eye, hair and skin colour, which was in line with the results from our computer simulations. Hence, in practical applications of DNA-based appearance prediction where no phenotype knowledge is available, such as in forensic DNA phenotyping, it is not advised to use DNA-predicted correlated phenotypes as predictors in addition to the DNA predictors. In the very least, this is not recommended for the pigmentation traits and the established pigmentation DNA predictors tested here.
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Affiliation(s)
- Yan Chen
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands; Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Wojciech Branicki
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Susan Walsh
- Department of Biology, Indiana University Purdue University Indianapolis (IUPUI), Indianapolis, IN, USA
| | - Michael Nothnagel
- Cologne Center for Genomics, University of Cologne, Cologne, Germany; University Hospital Cologne, Cologne, Germany
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Fan Liu
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands; Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China.
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39
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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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40
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Wagner JK, Colwell C, Claw KG, Stone AC, Bolnick DA, Hawks J, Brothers KB, Garrison NA. Fostering Responsible Research on Ancient DNA. Am J Hum Genet 2020; 107:183-195. [PMID: 32763189 PMCID: PMC7413888 DOI: 10.1016/j.ajhg.2020.06.017] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Anticipating and addressing the social implications of scientific work is a fundamental responsibility of all scientists. However, expectations for ethically sound practices can evolve over time as the implications of science come to be better understood. Contemporary researchers who work with ancient human remains, including those who conduct ancient DNA research, face precisely this challenge as it becomes clear that practices such as community engagement are needed to address the important social implications of this work. To foster and promote ethical engagement between researchers and communities, we offer five practical recommendations for ancient DNA researchers: (1) formally consult with communities; (2) address cultural and ethical considerations; (3) engage communities and support capacity building; (4) develop plans to report results and manage data; and (5) develop plans for long-term responsibility and stewardship. Ultimately, every member of a research team has an important role in fostering ethical research on ancient DNA.
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Affiliation(s)
- Jennifer K Wagner
- Professional Practice and Social Implications Committee (formerly the Social Issues Committee), American Society of Human Genetics, Bethesda, MD 20814, USA; Responsible Ancient DNA Research Working Group, American Society of Human Genetics, Bethesda, MD 20814, USA; Center for Translational Bioethics and Health Care Policy, Geisinger, Danville, PA 17822, USA.
| | - Chip Colwell
- Responsible Ancient DNA Research Working Group, American Society of Human Genetics, Bethesda, MD 20814, USA; Department of Anthropology, Denver Museum of Nature and Science, Denver, CO 80205, USA
| | - Katrina G Claw
- Responsible Ancient DNA Research Working Group, American Society of Human Genetics, Bethesda, MD 20814, USA; Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Anne C Stone
- Responsible Ancient DNA Research Working Group, American Society of Human Genetics, Bethesda, MD 20814, USA; School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85287, USA
| | - Deborah A Bolnick
- Responsible Ancient DNA Research Working Group, American Society of Human Genetics, Bethesda, MD 20814, USA; Department of Anthropology, University of Connecticut, Storrs, CT 06269, USA; Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
| | - John Hawks
- Responsible Ancient DNA Research Working Group, American Society of Human Genetics, Bethesda, MD 20814, USA; Department of Anthropology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Kyle B Brothers
- Professional Practice and Social Implications Committee (formerly the Social Issues Committee), American Society of Human Genetics, Bethesda, MD 20814, USA; Responsible Ancient DNA Research Working Group, American Society of Human Genetics, Bethesda, MD 20814, USA; Department of Pediatrics, University of Louisville, Louisville, KY 40202, USA
| | - Nanibaa' A Garrison
- Professional Practice and Social Implications Committee (formerly the Social Issues Committee), American Society of Human Genetics, Bethesda, MD 20814, USA; Responsible Ancient DNA Research Working Group, American Society of Human Genetics, Bethesda, MD 20814, USA; Institute for Society and Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Institute for Precision Health, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Division of General Internal Medicine and Health Services Research, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
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41
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Carratto TMT, Marcorin L, Debortoli G, Hünemeier T, Norton H, Parra EJ, Castelli EC, Mendes-Junior CT. Insights on hair, skin and eye color of ancient and contemporary Native Americans. Forensic Sci Int Genet 2020; 48:102335. [PMID: 32593164 DOI: 10.1016/j.fsigen.2020.102335] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/20/2020] [Accepted: 06/08/2020] [Indexed: 12/28/2022]
Abstract
Over the past few years, tools capable of predicting pigmentation phenotypes have been developed aiming to contribute for criminal and anthropological investigations. In this study, we used eight genetic systems to infer eye, hair, and skin color of ancient and contemporary Native Americans. To achieve this goal, we retrieved 61 SNPs from 42 samples available in free online repositories of DNA sequences. We performed pigmentation predictions using two freely available tools, HIrisPlex-S and Snipper, in addition to two other published models. This workflow made possible to predict all three phenotypes with at least one tool for 29 out of the 42 samples. Considering these 29 individuals, predictions for eye, hair, and skin color were obtained with HIrisPlex-S for 27, 28 and 27 individuals, respectively, while 24, 25 and 25 individuals had such predictions with Snipper. In general, ancient and contemporary Native Americans were predicted to have intermediate/brown eyes, black hair, and intermediate/darker skin pigmentation.
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Affiliation(s)
- Thássia Mayra Telles Carratto
- Departamento de Química, Laboratório de Pesquisas Forenses e Genômicas, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, 14040-901, Ribeirão Preto, SP, Brazil
| | - Letícia Marcorin
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, 14049-900, Ribeirão Preto, SP, Brazil
| | - Guilherme Debortoli
- Department of Anthropology, University of Toronto at Mississauga, L5L 1C6, Mississauga, ON, Canada
| | - Tábita Hünemeier
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, 05508-090, São Paulo, SP, Brazil
| | - Heather Norton
- Department of Anthropology, University of Cincinnati, 45221, Cincinnati, OH, United States
| | - Esteban Juan Parra
- Department of Anthropology, University of Toronto at Mississauga, L5L 1C6, Mississauga, ON, Canada
| | - Erick C Castelli
- São Paulo State University (UNESP), Department of Pathology, School of Medicine, Botucatu, SP, Brazil
| | - Celso Teixeira Mendes-Junior
- Departamento de Química, Laboratório de Pesquisas Forenses e Genômicas, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, 14040-901, Ribeirão Preto, SP, Brazil.
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42
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Davidovic S, Malyarchuk B, Grzybowski T, Aleksic JM, Derenko M, Litvinov A, Rogalla-Ładniak U, Stevanovic M, Kovacevic-Grujicic N. Complete mitogenome data for the Serbian population: the contribution to high-quality forensic databases. Int J Legal Med 2020; 134:1581-1590. [PMID: 32504149 DOI: 10.1007/s00414-020-02324-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 05/28/2020] [Indexed: 11/24/2022]
Abstract
Mitochondrial genome (mtDNA) is a valuable resource in resolving various human forensic casework. The usage of variability of complete mtDNA genomes increases their discriminatory power to the maximum and enables ultimate resolution of distinct maternal lineages. However, their wider employment in forensic casework is nowadays limited by the lack of appropriate reference database. In order to fill in the gap in the reference data, which, considering Slavic-speaking populations, currently comprises only mitogenomes of East and West Slavs, we present mitogenome data for 226 Serbians, representatives of South Slavs from the Balkan Peninsula. We found 143 (sub)haplogroups among which West Eurasian ones were dominant. The percentage of unique haplotypes was 85%, and the random match probability was as low as 0.53%. We support previous findings on both high levels of genetic diversity in the Serbian population and patterns of genetic differentiation among this and ten studied European populations. However, our high-resolution data supported more pronounced genetic differentiation among Serbians and two Slavic populations (Russians and Poles) as well as expansion of the Serbian population after the Last Glacial Maximum and during the Migration period (fourth to ninth century A.D.), as inferred from the Bayesian skyline analysis. Phylogenetic analysis of haplotypes found in Serbians contributed towards the improvement of the worldwide mtDNA phylogeny, which is essential for the interpretation of the mtDNA casework.
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Affiliation(s)
- Slobodan Davidovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, PO Box 23, Vojvode Stepe 444a, Belgrade, 11010, Serbia.,Department of Genetics of Populations and Ecogenotoxicology, Institute for Biological Research "Siniša Stanković", National Institute of Republic of Serbia, University of Belgrade, Bulevar despota Stefana 142, Belgrade, 11060, Serbia
| | - Boris Malyarchuk
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya 18, Magadan, 685000, Russia
| | - Tomasz Grzybowski
- Department of Forensic Medicine, Division of Molecular and Forensic Genetics, Ludwik Rydygier Collegium Medicum, Faculty of Medicine, Nicolaus Copernicus University, Marii-Sklodowskiej-Curie Str. 9, 85-094, Bydgoszcz, Poland
| | - Jelena M Aleksic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, PO Box 23, Vojvode Stepe 444a, Belgrade, 11010, Serbia
| | - Miroslava Derenko
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya 18, Magadan, 685000, Russia
| | - Andrey Litvinov
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya 18, Magadan, 685000, Russia
| | - Urszula Rogalla-Ładniak
- Department of Forensic Medicine, Division of Molecular and Forensic Genetics, Ludwik Rydygier Collegium Medicum, Faculty of Medicine, Nicolaus Copernicus University, Marii-Sklodowskiej-Curie Str. 9, 85-094, Bydgoszcz, Poland
| | - Milena Stevanovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, PO Box 23, Vojvode Stepe 444a, Belgrade, 11010, Serbia.,Faculty of Biology, University of Belgrade, Studentski Trg 16, Belgrade, 11000, Serbia.,Serbian Academy of Sciences and Arts, Kneza Mihaila 35, Belgrade, 11000, Serbia
| | - Natasa Kovacevic-Grujicic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, PO Box 23, Vojvode Stepe 444a, Belgrade, 11010, Serbia.
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de-Dios T, van Dorp L, Charlier P, Morfopoulou S, Lizano E, Bon C, Le Bitouzé C, Alvarez-Estape M, Marquès-Bonet T, Balloux F, Lalueza-Fox C. Metagenomic analysis of a blood stain from the French revolutionary Jean-Paul Marat (1743-1793). INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2020; 80:104209. [PMID: 32004756 PMCID: PMC7615110 DOI: 10.1016/j.meegid.2020.104209] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 01/24/2020] [Accepted: 01/26/2020] [Indexed: 12/31/2022]
Abstract
The French revolutionary Jean-Paul Marat (1743-1793) was assassinated in 1793 in his bathtub, where he was trying to find relief from the debilitating skin disease he was suffering from. At the time of his death, Marat was annotating newspapers, which got stained with his blood and were subsequently preserved by his sister. We extracted and sequenced DNA from the blood stain and also from another section of the newspaper, which we used for comparison. Results from the human DNA sequence analyses were compatible with a heterogeneous ancestry of Marat, with his mother being of French origin and his father born in Sardinia. Metagenomic analyses of the non-human reads uncovered the presence of fungal, bacterial and low levels of viral DNA. Relying on the presence/absence of microbial species in the samples, we could cast doubt on several putative infectious agents that have been previously hypothesised as the cause of his condition but for which we detect not a single sequencing read. Conversely, some of the species we detect are uncommon as environmental contaminants and may represent plausible infective agents. Based on all the available evidence, we hypothesize that Marat may have suffered from a fungal infection (seborrheic dermatitis), possibly superinfected with bacterial opportunistic pathogens.
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Affiliation(s)
- Toni de-Dios
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003 Barcelona, Spain
| | - Lucy van Dorp
- UCL Genetics Institute, University College London, London WC1E 6BT, UK.
| | - Philippe Charlier
- Département de la Recherche et de l'Enseignement, Musée du Quai Branly - Jacques Chirac, 75007 Paris, France; Université Paris-Saclay (UVSQ), Laboratory Anthropology, Archaeology, Biology (LAAB), 78180 Montigny-le-bretonneux, France
| | - Sofia Morfopoulou
- UCL Genetics Institute, University College London, London WC1E 6BT, UK; Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Esther Lizano
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003 Barcelona, Spain
| | - Celine Bon
- Département Hommes, Natures, Sociétés, Muséum National d'Histoire Naturelle, 75116 Paris, France
| | | | - Marina Alvarez-Estape
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003 Barcelona, Spain
| | - Tomas Marquès-Bonet
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003 Barcelona, Spain; Catalan Institution of Research and Advanced Studies (ICREA), 08010 Barcelona, Spain; CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), 08036 Barcelona, Spain; Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - François Balloux
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003 Barcelona, Spain
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44
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Joint Genetic Analyses of Mitochondrial and Y-Chromosome Molecular Markers for a Population from Northwest China. Genes (Basel) 2020; 11:genes11050564. [PMID: 32443545 PMCID: PMC7290686 DOI: 10.3390/genes11050564] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/09/2020] [Accepted: 05/11/2020] [Indexed: 12/27/2022] Open
Abstract
The genetic markers on mitochondria DNA (mtDNA) and Y-chromosome can be applied as a powerful tool in population genetics. We present a study to reveal the genetic background of Kyrgyz group, a Chinese ethnic group living in northwest China, and genetic polymorphisms of 60 loci on maternal inherited mtDNA and 24 loci on paternal inherited Y-chromosome short tandem repeats (Y-STRs) were investigated. The relationship between the two systems was tested, and the result indicated that they were statistically independent from each other. The genetic distances between Kyrgyz group and 11 reference populations for mtDNA, and 13 reference populations for Y-STRs were also calculated, respectively. The present results demonstrated that the Kyrgyz group was genetically closer to East Asian populations than European populations based on the mtDNA loci but the other way around for the Y-STRs. The genetic analyses could largely strengthen the understanding for the genetic background of the Kyrgyz group.
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45
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Kukla-Bartoszek M, Szargut M, Pośpiech E, Diepenbroek M, Zielińska G, Jarosz A, Piniewska-Róg D, Arciszewska J, Cytacka S, Spólnicka M, Branicki W, Ossowski A. The challenge of predicting human pigmentation traits in degraded bone samples with the MPS-based HIrisPlex-S system. Forensic Sci Int Genet 2020; 47:102301. [PMID: 32387914 DOI: 10.1016/j.fsigen.2020.102301] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 03/02/2020] [Accepted: 04/10/2020] [Indexed: 10/24/2022]
Abstract
Identification of human remains is an important part of human DNA analysis studies. STR and mitochondrial DNA markers are well suited for the analysis of degraded biological samples including bone material. However, these DNA markers may be useless when reference material is not available. In these cases, predictive DNA analysis can support the process of human identification by providing investigative leads. Forensic DNA phenotyping has progressed significantly by offering new methods based on massively parallel sequencing technology, but the frequent degradation processes observed in skeletal remains can make analysis of such samples challenging. In this study, we demonstrate the usefulness of a recently established Ion AmpliSeqTM HIrisPlex-S panel using Ion Torrent technology for analyzing bone samples that show different levels of DNA degradation. In total, 63 bone samples at post-mortem intervals up to almost 80 years were genotyped and eye, hair and skin colour predictions were performed using the HIrisPlex-S models. Following the recommended coverage thresholds, it was possible to establish full DNA profiles comprising of 41 DNA variants for 35 samples (55.6%). For 5 samples (7.9%) no DNA profiles were generated. The remaining 23 samples (36.5%) produced partial profiles and showed a clear underperformance of 3 HIrisPlex-S SNPs - rs1545397 (OCA2), rs1470608 (OCA2) and rs10756819 (BNC2), all used for skin colour prediction only. None of the 23 samples gave complete genotypes needed for skin colour prediction was obtained, and in 7 of them (25.9%) the 3 underperformed SNPs were the cause. At the same time, the prediction of eye and hair colour using complete IrisPlex and HIrisPlex profiles could be made for these 23 samples in 20 (87.0%) and 12 cases (52.2%), respectively. Complete HIrisPlex-S profiles were generated from as little as 49 pg of template DNA. Five samples for which the HIrisPlex-S analysis failed, consistently failed in standard STR analysis. Importantly, the 3 underperforming SNPs produced significantly lower number of reads in good quality samples. Nonetheless, the AUC loss resulting from missing data for these 3 SNPs is not considered large (≤0.004) and the prediction of pigmentation from partial profiles is also available in the current HPS tool. The study shows that DNA degradation and the resulting loss of data are the most serious challenge to DNA phenotyping of skeletal remains. Although the newly developed HIrisPlex-S panel has been successfully validated in the current research, primer redesign for the 3 underperforming SNPs in the MPS design should be considered in the future.
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Affiliation(s)
- Magdalena Kukla-Bartoszek
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa St. 7, 30-387, Kraków, Poland; Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa St. 7A, 30-387, Kraków, Poland
| | - Maria Szargut
- Department of Forensic Genetics, Pomeranian Medical University in Szczecin, Powstancow Wlkp. St. 72, 70-111, Szczecin, Poland; The Polish Genetic Database of Totalitarianism Victims, Powstancow Wlkp. St. 72, 70-111, Szczecin, Poland
| | - Ewelina Pośpiech
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa St. 7A, 30-387, Kraków, Poland
| | - Marta Diepenbroek
- Department of Forensic Genetics, Pomeranian Medical University in Szczecin, Powstancow Wlkp. St. 72, 70-111, Szczecin, Poland; The Polish Genetic Database of Totalitarianism Victims, Powstancow Wlkp. St. 72, 70-111, Szczecin, Poland; Institut für Rechtsmedizin der Universität München, Nußbaumstr. 26, 80336, München, Germany
| | - Grażyna Zielińska
- Department of Forensic Genetics, Pomeranian Medical University in Szczecin, Powstancow Wlkp. St. 72, 70-111, Szczecin, Poland; The Polish Genetic Database of Totalitarianism Victims, Powstancow Wlkp. St. 72, 70-111, Szczecin, Poland
| | - Agata Jarosz
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa St. 7A, 30-387, Kraków, Poland
| | - Danuta Piniewska-Róg
- Department of Forensic Medicine, Jagiellonian University Medical College, Grzegórzecka St. 16, 31-531, Kraków, Poland
| | - Joanna Arciszewska
- Department of Forensic Genetics, Pomeranian Medical University in Szczecin, Powstancow Wlkp. St. 72, 70-111, Szczecin, Poland; The Polish Genetic Database of Totalitarianism Victims, Powstancow Wlkp. St. 72, 70-111, Szczecin, Poland
| | - Sandra Cytacka
- Department of Forensic Genetics, Pomeranian Medical University in Szczecin, Powstancow Wlkp. St. 72, 70-111, Szczecin, Poland; The Polish Genetic Database of Totalitarianism Victims, Powstancow Wlkp. St. 72, 70-111, Szczecin, Poland
| | - Magdalena Spólnicka
- Biology Department, Central Forensic Laboratory of the Police, Aleje Ujazdowskie 7, 00-583, Warszawa, Poland
| | - Wojciech Branicki
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa St. 7A, 30-387, Kraków, Poland; Department of Forensic Medicine, Jagiellonian University Medical College, Grzegórzecka St. 16, 31-531, Kraków, Poland
| | - Andrzej Ossowski
- Department of Forensic Genetics, Pomeranian Medical University in Szczecin, Powstancow Wlkp. St. 72, 70-111, Szczecin, Poland; The Polish Genetic Database of Totalitarianism Victims, Powstancow Wlkp. St. 72, 70-111, Szczecin, Poland
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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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47
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Byard RW. King Richard III revisited. Forensic Sci Med Pathol 2020; 16:548-551. [PMID: 31900841 DOI: 10.1007/s12024-019-00215-1] [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] [Accepted: 12/03/2019] [Indexed: 11/25/2022]
Abstract
Forensic examination of skeletal remains exhumed in 2012 from the site of the former Church of the Greyfriars in Leicester, United Kingdom, revealed a gracile adult male of around 30 to 34 years of age with 11 perimortem injuries. These were consistent with descriptions of injuries sustained by King Richard III, the last Plantagenet King of England, at the Battle of Bosworth Field in 1485. Combining these features with DNA analyses proved that the remains were those of Richard. The finding of a severe thoracic scoliosis with a raised right shoulder confirmed that the king did have a" hunchback" which was not a later invention of Tudor and subsequent chroniclers. This investigation provides an excellent demonstration of how contemporary forensic techniques can answer historical questions. The remains of the last Plantagenet king have been identified, his vertebral disease confirmed, and the nature of his last moments verified.
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Affiliation(s)
- Roger W Byard
- Discipline of Anatomy and Pathology, The University of Adelaide, Frome Road, Level 2 Helen Mayo Building North, Adelaide, South Australia, 5005, Australia.
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48
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Mitochondrial DNA variation in Sub-Saharan Africa: Forensic data from a mixed West African sample, Côte d'Ivoire (Ivory Coast), and Rwanda. Forensic Sci Int Genet 2019; 44:102202. [PMID: 31775077 DOI: 10.1016/j.fsigen.2019.102202] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 11/04/2019] [Accepted: 11/06/2019] [Indexed: 11/23/2022]
Abstract
This study provides 398 novel complete mitochondrial control region sequences that augment the still underrepresented data from Africa by three datasets: a mixed West African sample set deriving from 12 countries (n = 145) and datasets from Côte d'Ivoire (Ivory Coast) (n = 100) as well as Rwanda (n = 153). The analysis of mtDNA variation and genetic comparisons with published data revealed low random match probabilities in all three datasets and typical West African and East African diversity, respectively. Genetic parameters indicate that the presented mixed West African dataset may serve as first forensic mtDNA control region database for West Africa in general. In addition, a strategy for responsible forensic application of precious mtDNA population samples potentially containing close maternal relatives is outlined. The datasets will be uploaded to the forensic mtDNA database EMPOP (https://empop.online) upon publication.
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HIrisPlex-S system for eye, hair, and skin color prediction from DNA: Massively parallel sequencing solutions for two common forensically used platforms. Forensic Sci Int Genet 2019; 43:102152. [DOI: 10.1016/j.fsigen.2019.102152] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/26/2019] [Accepted: 08/22/2019] [Indexed: 11/22/2022]
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50
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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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