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Claerhout S, Verstraete P, Warnez L, Vanpaemel S, Larmuseau M, Decorte R. CSYseq: The first Y-chromosome sequencing tool typing a large number of Y-SNPs and Y-STRs to unravel worldwide human population genetics. PLoS Genet 2021; 17:e1009758. [PMID: 34491993 PMCID: PMC8423258 DOI: 10.1371/journal.pgen.1009758] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 08/05/2021] [Indexed: 11/26/2022] Open
Abstract
Male-specific Y-chromosome (chrY) polymorphisms are interesting components of the DNA for population genetics. While single nucleotide polymorphisms (Y-SNPs) indicate distant evolutionary ancestry, short tandem repeats (Y-STRs) are able to identify close familial kinships. Detailed chrY analysis provides thus both biogeographical background information as paternal lineage identification. The rapid advancement of high-throughput massive parallel sequencing (MPS) technology in the past decade has revolutionized genetic research. Using MPS, single-base information of both Y-SNPs as Y-STRs can be analyzed in a single assay typing multiple samples at once. In this study, we present the first extensive chrY-specific targeted resequencing panel, the ‘CSYseq’, which simultaneously identifies slow mutating Y-SNPs as evolution markers and rapid mutating Y-STRs as patrilineage markers. The panel was validated by paired-end sequencing of 130 males, distributed over 65 deep-rooted pedigrees covering 1,279 generations. The CSYseq successfully targets 15,611 Y-SNPs including 9,014 phylogenetic informative Y-SNPs to identify 1,443 human evolutionary Y-subhaplogroup lineages worldwide. In addition, the CSYseq properly targets 202 Y-STRs, including 81 slow, 68 moderate, 27 fast and 26 rapid mutating Y-STRs to individualize close paternal relatives. The targeted chrY markers cover a high average number of reads (Y-SNP = 717, Y-STR = 150), easy interpretation, powerful discrimination capacity and chrY specificity. The CSYseq is interesting for research on different time scales: to identify evolutionary ancestry, to find distant family and to discriminate closely related males. Therefore, this panel serves as a unique tool valuable for a wide range of genetic-genealogical applications in interdisciplinary research within evolutionary, population, molecular, medical and forensic genetics. Around 95% of the male-specific Y-chromosome (chrY) is non-recombining and therefore inherited in a conserved manner from father to son. It can therefore serve as a powerful marker for interdisciplinary genetic-genealogical research as it provides a strong link between genetic information and a family tree or pedigree. While Y-chromosomal short tandem repeats (Y-STRs) discriminate close paternal kinships, single nucleotide polymorphisms (Y-SNPs) enables the identification of far evolutionary ancestry. Unfortunately, an extensive chrY-specific sequencing panel combining a large number of familial Y-STRs and evolutionary Y-SNPs was not yet available. Therefore, chrY is rarely included in research projects and not often linked to a genealogical, history-demographical or life science database. In this way, the importance of chrY still remains not yet fully understood. Massive parallel sequencing (MPS) allows the simultaneous analysis at sequence level of Y-SNPs and Y-STRs with variable mutation rates in a large number of males. However, up until today, no commercial kit is exploiting the full potential that MPS offers on chrY. Therefore, we developed the ‘CSYseq’, which is the first extensive chrY-specific sequencing panel. The CSYseq simultaneously identifies 9,014 slow mutating Y-SNPs to identify evolutionary ancestry, and 202 rapid mutating Y-STRs to investigate paternal relationships. We validated and optimized the panel through the analysis of 130 males distributed over 65 families. This novel MPS panel is useful for biogeographical identity and ancestry analysis, together with Y-chromosome profiling for the identification of patrilineages and discrimination of closely related males. As the CSYseq includes a very diverse set of markers that can be easily interpreted, it is interesting for different interdisciplinary applications within evolutionary, population, molecular, medical and forensic genetics.
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Affiliation(s)
- Sofie Claerhout
- Forensic Biomedical Sciences, Department of Imaging & Pathology, KU Leuven, Leuven, Belgium
- * E-mail:
| | - Paulien Verstraete
- Forensic Biomedical Sciences, Department of Imaging & Pathology, KU Leuven, Leuven, Belgium
| | - Liesbeth Warnez
- Forensic Biomedical Sciences, Department of Imaging & Pathology, KU Leuven, Leuven, Belgium
| | - Simon Vanpaemel
- KU Leuven, Department of Mechanical Engineering, Noise and Vibration Engineering, Leuven, Belgium
- DMMS Lab, Flanders Make, Heverlee, Belgium
| | - Maarten Larmuseau
- Histories vzw, Mechelen, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Ronny Decorte
- Forensic Biomedical Sciences, Department of Imaging & Pathology, KU Leuven, Leuven, Belgium
- Laboratory of Forensic genetics and Molecular Archaeology, UZ Leuven, Leuven, Belgium
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Antiga LG, Sibbens L, Abakkouy Y, Decorte R, Van Den Bogaert W, Van de Voorde W, Bekaert B. Cell survival and DNA damage repair are promoted in the human blood thanatotranscriptome shortly after death. Sci Rep 2021; 11:16585. [PMID: 34400689 PMCID: PMC8368024 DOI: 10.1038/s41598-021-96095-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 07/30/2021] [Indexed: 11/09/2022] Open
Abstract
RNA analysis of post-mortem tissues, or thanatotranscriptomics, has become a topic of interest in forensic science due to the essential information it can provide in forensic investigations. Several studies have previously investigated the effect of death on gene transcription, but it has never been conducted with samples of the same individual. For the first time, a longitudinal mRNA expression analysis study was performed with post-mortem human blood samples from individuals with a known time of death. The results reveal that, after death, two clearly differentiated groups of up- and down-regulated genes can be detected. Pathway analysis suggests active processes that promote cell survival and DNA damage repair, rather than passive degradation, are the source of early post-mortem changes of gene expression in blood. In addition, a generalized linear model with an elastic net restriction predicted post-mortem interval with a root mean square error of 4.75 h. In conclusion, we demonstrate that post-mortem gene expression data can be used as biomarkers to estimate the post-mortem interval though further validation using independent sample sets is required before use in forensic casework.
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Affiliation(s)
- Laura G Antiga
- Forensic Biomedical Sciences, Department of Imaging and Pathology, KU Leuven, Herestraat 49, Box 7003 71, 3000, Leuven, Belgium
- Department of Experimental and Health Sciences (CEXS), University Pompeu Fabra (UPF), Barcelona, Spain
| | - Lode Sibbens
- Forensic Biomedical Sciences, Department of Imaging and Pathology, KU Leuven, Herestraat 49, Box 7003 71, 3000, Leuven, Belgium
| | - Yasmina Abakkouy
- Forensic Biomedical Sciences, Department of Imaging and Pathology, KU Leuven, Herestraat 49, Box 7003 71, 3000, Leuven, Belgium
| | - Ronny Decorte
- Forensic Biomedical Sciences, Department of Imaging and Pathology, KU Leuven, Herestraat 49, Box 7003 71, 3000, Leuven, Belgium
- Laboratory of Forensic Genetics, UZ Leuven, 3000, Leuven, Belgium
| | - Wouter Van Den Bogaert
- Forensic Biomedical Sciences, Department of Imaging and Pathology, KU Leuven, Herestraat 49, Box 7003 71, 3000, Leuven, Belgium
- Laboratory of Forensic Genetics, UZ Leuven, 3000, Leuven, Belgium
| | - Wim Van de Voorde
- Forensic Biomedical Sciences, Department of Imaging and Pathology, KU Leuven, Herestraat 49, Box 7003 71, 3000, Leuven, Belgium
- Laboratory of Forensic Genetics, UZ Leuven, 3000, Leuven, Belgium
| | - Bram Bekaert
- Forensic Biomedical Sciences, Department of Imaging and Pathology, KU Leuven, Herestraat 49, Box 7003 71, 3000, Leuven, Belgium.
- Laboratory of Forensic Genetics, UZ Leuven, 3000, Leuven, Belgium.
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Ahannach S, Spacova I, Decorte R, Jehaes E, Lebeer S. At the Interface of Life and Death: Post-mortem and Other Applications of Vaginal, Skin, and Salivary Microbiome Analysis in Forensics. Front Microbiol 2021; 12:694447. [PMID: 34394033 PMCID: PMC8355522 DOI: 10.3389/fmicb.2021.694447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/14/2021] [Indexed: 12/13/2022] Open
Abstract
Microbial forensics represents a promising tool to strengthen traditional forensic investigative methods and fill related knowledge gaps. Large-scale microbiome studies indicate that microbial fingerprinting can assist forensics in areas such as trace evidence, source tracking, geolocation, and circumstances of death. Nevertheless, the majority of forensic microbiome studies focus on soil and internal organ samples, whereas the microbiome of skin, mouth, and especially vaginal samples that are routinely collected in sexual assault and femicide cases remain underexplored. This review discusses the current and emerging insights into vaginal, skin, and salivary microbiome-modulating factors during life (e.g., lifestyle and health status) and after death (e.g., environmental influences and post-mortem interval) based on next-generation sequencing. We specifically highlight the key aspects of female reproductive tract, skin, and mouth microbiome samples relevant in forensics. To fill the current knowledge gaps, future research should focus on the degree to which the post-mortem succession rate and profiles of vaginal, skin, and saliva microbiota are sensitive to abiotic and biotic factors, presence or absence of oxygen and other gases, and the nutrient richness of the environment. Application of this microbiome-related knowledge could provide valuable complementary data to strengthen forensic cases, for example, to shed light on the circumstances surrounding death with (post-mortem) microbial fingerprinting. Overall, this review synthesizes the present knowledge and aims to provide a framework to adequately comprehend the hurdles and potential application of vaginal, skin, and salivary post-mortem microbiomes in forensic investigations.
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Affiliation(s)
- Sarah Ahannach
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
| | - Irina Spacova
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
| | - Ronny Decorte
- Laboratory of Forensic Genetics, Department of Forensic Medicine, University Hospitals Leuven, Leuven, Belgium.,Department of Imaging and Pathology, Forensic Biomedical Sciences, KU Leuven, Leuven, Belgium
| | - Els Jehaes
- Forensic DNA Laboratory, Department of Forensic Medicine, Antwerp University Hospital, Edegem, Belgium
| | - Sarah Lebeer
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
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Claerhout S, Vanpaemel S, Gill MS, Antiga LG, Baele G, Decorte R. YMrCA: Improving Y-chromosomal ancestor time estimation for DNA kinship research. Hum Mutat 2021; 42:1307-1320. [PMID: 34265144 DOI: 10.1002/humu.24259] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 06/21/2021] [Accepted: 07/12/2021] [Indexed: 11/09/2022]
Abstract
The Y-chromosome is a valuable kinship indicator in family history and forensic research. To reconstruct genealogies, the time to the most recent common ancestor (tMRCA) between paternal relatives can be estimated through Y-STR analysis. Existing models are the stepwise mutation model (SMM, only one-step Y-STR changes) and the infinite allele model (IAM, new allele per Y-STR change). In this study, these mutation models and all existing tMRCA calculators were validated through a genetic-genealogy database containing 1,120 biologically related genealogical pairs confirmed by 46 Y-STRs with known tMRCA (18,109 generations). Consistent under- and overestimation and broad confidence intervals were observed, leading to dubious tMRCA estimates. This is because they do not include individual mutation rates or multi-step changes and ignore hidden multiple, back, or parallel modifications. To improve tMRCA estimation, we developed a user-friendly calculator, the "YMrCA", including all previously mentioned mutation characteristics. After extensive validation, we observed that the YMrCA calculator demonstrated a promising performance. The YMrCA yields a significantly higher tMRCA success rate (96%; +20%) and a lower tMRCA error (7; -3) compared to the mutation models and all online tMRCA calculators. Therefore, YMrCA offers the next step towards more objective tMRCA estimation for DNA kinship research.
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Affiliation(s)
- Sofie Claerhout
- Department of Imaging & Pathology, KU Leuven, Forensic Biomedical Sciences, Leuven, Belgium
| | - Simon Vanpaemel
- Department of Mechanical Engineering, KU Leuven, Noise and Vibration Engineering, Heverlee, Belgium.,DMMS Lab, Flanders Make, Heverlee, Belgium
| | - Mandev S Gill
- Department of Microbiology, KU Leuven, Immunology and Transplantation, Rega Institute, Laboratory of Evolutionary and Computational Virology, Leuven, Belgium
| | - Laura G Antiga
- Department of Imaging & Pathology, KU Leuven, Forensic Biomedical Sciences, Leuven, Belgium.,Bioinformatics for Health Science, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Guy Baele
- Department of Microbiology, KU Leuven, Immunology and Transplantation, Rega Institute, Laboratory of Evolutionary and Computational Virology, Leuven, Belgium
| | - Ronny Decorte
- Department of Imaging & Pathology, KU Leuven, Forensic Biomedical Sciences, Leuven, Belgium.,Laboratory of Forensic Genetics, Department of Forensic Medicine, UZ Leuven, Leuven, Belgium
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Larmuseau MH, van den Berg P, Claerhout S, Calafell F, Boattini A, Gruyters L, Vandenbosch M, Nivelle K, Decorte R, Wenseleers T. A Historical-Genetic Reconstruction of Human Extra-Pair Paternity. Curr Biol 2019; 29:4102-4107.e7. [DOI: 10.1016/j.cub.2019.09.075] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 08/12/2019] [Accepted: 09/30/2019] [Indexed: 11/25/2022]
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Claerhout S, Roelens J, Van der Haegen M, Verstraete P, Larmuseau MHD, Decorte R. Ysurnames? The patrilineal Y-chromosome and surname correlation for DNA kinship research. Forensic Sci Int Genet 2019; 44:102204. [PMID: 31760354 DOI: 10.1016/j.fsigen.2019.102204] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 11/08/2019] [Accepted: 11/09/2019] [Indexed: 11/30/2022]
Abstract
The Y-chromosome is a widely studied and useful small part of the genome providing different applications for interdisciplinary research. In many (Western) societies, the Y-chromosome and surnames are paternally co-inherited, suggesting a corresponding Y-haplotype for every namesake. While it has already been observed that this correlation may be disrupted by a false-paternity event, adoption, anonymous sperm donor or the co-founding of surnames, extensive information on the strength of the surname match frequency (SMF) with the Y-chromosome remains rather unknown. For the first time in Belgium and the Netherlands, we were able to study this correlation using 2,401 males genotyped for 46 Y-STRs and 183 Y-SNPs. The SMF was observed to be dependent on the number of Y-STRs analyzed, their mutation rates and the number of Y-STR differences allowed for a kinship. For a perfect match, the Yfiler® Plus and our in-house YForGen kit gave a similar high SMF of 98%, but for non-perfect matches, the latter could overall be identified as the best kit. The SMF generally increased due to less mismatches when encountering [1] deep Y-subhaplogroups, [2] less frequently occurring surnames, and [3] small geographical distances between relatives. This novel information enabled the design of a surname prediction model based on genetic and geographical distances of a kinship. The prediction model has an area under the curve (AUC) of 0.9 and is therefore useable for DNA kinship priority listing in estimation applications like forensic familial searching.
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Affiliation(s)
- Sofie Claerhout
- Forensic Biomedical Sciences, Department of Imaging & Pathology, KU Leuven, Leuven 3000, Belgium.
| | - Jennifer Roelens
- Department of Earth and Environmental Sciences, KU Leuven, Leuven 3000, Belgium
| | - Michiel Van der Haegen
- Forensic Biomedical Sciences, Department of Imaging & Pathology, KU Leuven, Leuven 3000, Belgium
| | - Paulien Verstraete
- Forensic Biomedical Sciences, Department of Imaging & Pathology, KU Leuven, Leuven 3000, Belgium
| | - Maarten H D Larmuseau
- Laboratory of Socioecology and Social Evolution, Department of Biology, KU Leuven, Leuven 3000, Belgium; Histories vzw, Mechelen 2800, Belgium; Department of Human Genetics, KU Leuven, Leuven 3000, Belgium
| | - Ronny Decorte
- Forensic Biomedical Sciences, Department of Imaging & Pathology, KU Leuven, Leuven 3000, Belgium; Laboratory of Forensic genetics and Molecular Archaeology, UZ Leuven, Leuven 3000, Belgium
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Altena E, Smeding R, van der Gaag KJ, Larmuseau MHD, Decorte R, Lao O, Kayser M, Kraaijenbrink T, de Knijff P. Correction to: The Dutch Y-chromosomal landscape. Eur J Hum Genet 2019; 28:399. [PMID: 31645767 PMCID: PMC7028942 DOI: 10.1038/s41431-019-0528-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Eveline Altena
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Risha Smeding
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Kristiaan J van der Gaag
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.,Department of Human Biological Traces, Netherlands Forensic Institute, The Hague, The Netherlands
| | - Maarten H D Larmuseau
- Forensic Biomedical Sciences, Department of Imaging & Pathology, KU Leuven, Leuven, Belgium.,Laboratory of Socioecology and Social Evolution, Department of Biology, KU Leuven, Leuven, Belgium.,Histories vzw, Mechelen, Belgium
| | - Ronny Decorte
- Forensic Biomedical Sciences, Department of Imaging & Pathology, KU Leuven, Leuven, Belgium.,Laboratory of Forensic Genetics and Molecular Archaeology, UZ Leuven, Leuven, Belgium
| | - Oscar Lao
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands.,Universitat Pompeu Fabra, Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Thirsa Kraaijenbrink
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter de Knijff
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
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Decorte R, Polet C, Boudin M, Tilquin F, Matroule JY, Dieu M, Charles C, Carlier A, Lebecque F, Deparis O. An interdisciplinary study around the reliquary of the late cardinal Jacques de Vitry. PLoS One 2019; 14:e0201424. [PMID: 30794540 PMCID: PMC6386372 DOI: 10.1371/journal.pone.0201424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 01/18/2019] [Indexed: 11/24/2022] Open
Abstract
The reliquary of Jacques de Vitry, a prominent clergyman and theologian in the early 13th century, has experienced several transfers over the last centuries, which seriously question the attribution of the remains to the late Cardinal. Uncertainty about the year of his birth poses an additional question regarding his age at death in 1240. The reliquary, located in the Saint Marie d'Oigines church, Belgium, was reopened in 2015 for an interdisciplinary study around his relics as well as the Treasure of Oignies, a remarkable cultural heritage notably built from Jacques de Vitry's donation. Anthropological, isotopic and genetic analyses were performed independently on the remains found in the reliquary. Results of the analyses provided evidence that the likelihood that these remains are those of Jacques de Vitry is very high: the remains belong to the same human male individual and the historical tradition about his age is confirmed. In addition, a separate relic (left tibia) was analysed and found to match with the remains of the reliquary (right tibia). The unique Jacques de Vitry's mitre, made of parchment, was sampled non-destructively and the extracted parchment collagen was analysed by a proteomic method in order to determine the animal species. The results showed that, surprisingly, not all parts of the mitre were made from the same species. All together, these findings are expected to fertilize knowledge carried by historical tradition around the relics of Jacques de Vitry and his related cultural heritage.
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Affiliation(s)
- Ronny Decorte
- Forensic Biomedical Sciences, Department of Imaging & Pathology, KU Leuven (KUL), Leuven, Belgium
- Laboratory of Forensic Genetics and Molecular Archaeology, Department of Forensic Medicine, UZ Leuven (UZL), Leuven, Belgium
| | - Caroline Polet
- Department of Palaeontology, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Mathieu Boudin
- Radiocarbon Dating Laboratory, Royal Institute for Cultural Heritage (KIK-IRPA), Brussels, Belgium
| | - Françoise Tilquin
- Research Unit in Microorganisms Biology (URBM), Narilis Institute, ILEE Institute, University of Namur, Namur, Belgium
| | - Jean-Yves Matroule
- Research Unit in Microorganisms Biology (URBM), Narilis Institute, ILEE Institute, University of Namur, Namur, Belgium
| | - Marc Dieu
- Mass Spectrometry Facility (MaSUN), University of Namur, Namur, Belgium
| | - Catherine Charles
- Moretus Plantin University Library, University of Namur, Namur, Belgium
| | | | | | - Olivier Deparis
- Heritages, Transmissions, Inheritances (PaTHs) Institute & Department of Physics, University of Namur, Namur, Belgium
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Claerhout S, Vandenbosch M, Nivelle K, Gruyters L, Peeters A, Larmuseau MH, Decorte R. Determining Y-STR mutation rates in deep-routing genealogies: Identification of haplogroup differences. Forensic Sci Int Genet 2018; 34:1-10. [DOI: 10.1016/j.fsigen.2018.01.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 01/10/2018] [Accepted: 01/14/2018] [Indexed: 10/18/2022]
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Smeers I, Decorte R, Van de Voorde W, Bekaert B. Evaluation of three statistical prediction models for forensic age prediction based on DNA methylation. Forensic Sci Int Genet 2018; 34:128-133. [DOI: 10.1016/j.fsigen.2018.02.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 12/27/2017] [Accepted: 02/05/2018] [Indexed: 11/15/2022]
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Larmuseau MHD, Calafell F, Princen SA, Decorte R, Soen V. The black legend on the Spanish presence in the low countries: Verifying shared beliefs on genetic ancestry. Am J Phys Anthropol 2018; 166:219-227. [PMID: 29327450 DOI: 10.1002/ajpa.23409] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 11/28/2017] [Accepted: 01/01/2018] [Indexed: 11/08/2022]
Abstract
OBJECTIVES War atrocities committed by the Spanish army in the Low Countries during the 16th century are so ingrained in the collective memory of Belgian and Dutch societies that they generally assume a signature of this history to be present in their genetic ancestry. Historians claim this assumption is a consequence of the so-called "Black Legend" and negative propaganda portraying and remembering Spanish soldiers as extreme sexual aggressors. The impact of the presence of Spaniards during the Dutch Revolt on the genetic variation in the Low Countries has been verified in this study. MATERIALS AND METHODS A recent population genetic analysis of Iberian-associated Y-chromosomal variation among Europe is enlarged with representative samples of Dutch (N = 250) and Flemish (N = 1,087) males. Frequencies of these variants are also compared between donors whose oldest reported paternal ancestors lived in-nowadays Flemish-cities affected by so-called Spanish Furies (N = 116) versus other patrilineages in current Flemish territory (N = 971). RESULTS The frequencies of Y-chromosomal markers Z195 and SRY2627 decline steeply going north from Spain and the data for the Flemish and Dutch populations fits within this pattern. No trend of higher frequencies of these variants has been found within the well-ascertained samples associated with Spanish Fury cities. DISCUSSION Although sexual aggression did occur in the 16th century, these activities did not leave a traceable "Spanish" genetic signature in the autochthonous genome of the Low Countries. Our results support the view that the 'Black Legend' and historical propaganda on sexual aggression have nurtured today's incorrect assumptions regarding genetic ancestry.
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Affiliation(s)
- Maarten H D Larmuseau
- Department of Forensic Biomedical Sciences, Laboratory of Forensic Genetics and Molecular Archaeology, KU Leuven, Leuven, Belgium.,Department of Biology, Laboratory of Socioecology and Social Evolution, KU Leuven, Leuven, Belgium
| | - Francesc Calafell
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | - Sarah A Princen
- Department of Biology, Laboratory of Socioecology and Social Evolution, KU Leuven, Leuven, Belgium
| | - Ronny Decorte
- Department of Forensic Biomedical Sciences, Laboratory of Forensic Genetics and Molecular Archaeology, KU Leuven, Leuven, Belgium
| | - Violet Soen
- Early Modern History (15th-18th Centuries), Faculty of Arts, KU Leuven, Leuven, Belgium
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Sibbens L, Van de Voorde W, Decorte R, Bekaert B. The development of a forensic clock to determine time of death. Forensic Science International: Genetics Supplement Series 2017. [DOI: 10.1016/j.fsigss.2017.09.059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Larmuseau MHD, Claerhout S, Gruyters L, Nivelle K, Vandenbosch M, Peeters A, van den Berg P, Wenseleers T, Decorte R. Genetic-genealogy approach reveals low rate of extrapair paternity in historical Dutch populations. Am J Hum Biol 2017; 29. [PMID: 28742271 DOI: 10.1002/ajhb.23046] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 05/01/2017] [Accepted: 07/07/2017] [Indexed: 11/09/2022] Open
Abstract
OBJECTIVE Evolutionary theory has shown that seeking out extrapair paternity (EPP) can be a viable reproductive strategy for both sexes in pair-bonded species, also in humans. As yet, estimates of the contemporary or historical EPP rate in human population are still rare. In the present study, we estimated the historical EPP rate in the Dutch population over the last 400 years and compared the rate with those obtained for other human populations to determine the evolutionary, cultural, and socio-demographic factors that influence human cuckoldry behavior. METHODS We estimated the historical EPP rate for the Dutch population via the "genealogical pair method", in which the EPP rate is derived from Y-chromosome mismatches between pairs of individuals that, based on genealogical evidence, share a common paternal ancestor. RESULTS Based on the analysis of 68 representative genealogical pairs, separated by a total of 1013 fertilization events, we estimated that the historical EPP rate for the Dutch population over the last 400 years was 0.96% per generation (95% confidence interval 0.46%-1.76%). CONCLUSION The Dutch EPP rate fits perfectly within the range reported for other contemporary and historical populations in Western Europe and was highly congruent with that estimated for neighboring Flanders, despite the socio-economic and religious differences between both populations. The estimated low EPP rate challenges the "dual mating strategy hypothesis" that states that women could obtain fitness benefits by securing investment from one man while cuckolding him to obtain good genes from an affair partner.
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Affiliation(s)
- Maarten H D Larmuseau
- Laboratory of Socioecology and Social Evolution, Department of Biology, KU Leuven, Leuven, Belgium.,Department of Imaging & Pathology, KU Leuven, Forensic Biomedical Sciences, Leuven, Belgium
| | - Sofie Claerhout
- Department of Imaging & Pathology, KU Leuven, Forensic Biomedical Sciences, Leuven, Belgium
| | - Leen Gruyters
- Laboratory of Socioecology and Social Evolution, Department of Biology, KU Leuven, Leuven, Belgium
| | - Kelly Nivelle
- Department of Imaging & Pathology, KU Leuven, Forensic Biomedical Sciences, Leuven, Belgium
| | - Michiel Vandenbosch
- Department of Imaging & Pathology, KU Leuven, Forensic Biomedical Sciences, Leuven, Belgium
| | - Anke Peeters
- Department of Imaging & Pathology, KU Leuven, Forensic Biomedical Sciences, Leuven, Belgium
| | - Pieter van den Berg
- Laboratory of Socioecology and Social Evolution, Department of Biology, KU Leuven, Leuven, Belgium
| | - Tom Wenseleers
- Laboratory of Socioecology and Social Evolution, Department of Biology, KU Leuven, Leuven, Belgium
| | - Ronny Decorte
- Department of Imaging & Pathology, KU Leuven, Forensic Biomedical Sciences, Leuven, Belgium.,Laboratory of Forensic genetics and Molecular Archaeology, UZ Leuven, Leuven, Belgium
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14
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Ottoni C, Van Neer W, De Cupere B, Daligault J, Guimaraes S, Peters J, Spassov N, Prendergast ME, Boivin N, Morales-Muñiz A, Bălăşescu A, Becker C, Benecke N, Boroneant A, Buitenhuis H, Chahoud J, Crowther A, Llorente L, Manaseryan N, Monchot H, Onar V, Osypińska M, Putelat O, Quintana Morales EM, Studer J, Wierer U, Decorte R, Grange T, Geigl EM. The palaeogenetics of cat dispersal in the ancient world. Nat Ecol Evol 2017. [DOI: 10.1038/s41559-017-0139] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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15
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Primativo G, Ottoni C, Biondi G, Serafino S, Martínez-Labarga C, Larmuseau MHD, Scardi M, Decorte R, Rickards O. Bight of Benin: a Maternal Perspective of Four Beninese Populations and their Genetic Implications on the American Populations of African Ancestry. Ann Hum Genet 2017; 81:78-90. [PMID: 28205221 DOI: 10.1111/ahg.12186] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 01/03/2017] [Indexed: 12/01/2022]
Abstract
The understanding of the first movements of the ancestral populations within the African continent is still unclear, particularly in West Africa, due to several factors that have shaped the African genetic pool across time. To improve the genetic representativeness of the Beninese population and to better understand the patterns of human settlement inside West Africa and the dynamics of peopling of the Democratic Republic of Benin, we analyzed the maternal genetic variation of 193 Beninese individuals belonging to Bariba, Berba, Dendi, and Fon populations. Results support the oral traditions indicating that the western neighbouring populations have been the ancestors of the first Beninese populations, and the extant genetic structure of the Beninese populations is most likely the result of admixture between populations from neighbouring countries and native people. The present findings highlight how the Beninese populations contributed to the gene pool of the extant populations of some American populations of African ancestry. This strengthens the hypothesis that the Bight of Benin was not only an assembly point for the slave trade during the Trans-Atlantic Slave Trade but also an important slave trapping area.
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Affiliation(s)
| | - Claudio Ottoni
- Department of Imaging and Pathology, Center for Archaeological Sciences, KU Leuven - University of Leuven, Leuven, Belgium.,Laboratory of Forensic Genetics and Molecular Archaeology, University Hospitals Leuven, Leuven, Belgium
| | - Gianfranco Biondi
- Department of Clinical Medicine, Public Health, Life and Environment, University of L'Aquila, L'Aquila, Italy
| | - Sara Serafino
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy.,Department of Public Health and Infectious Diseases, University of Rome Sapienza, Rome, Italy
| | | | - Maarten H D Larmuseau
- Department of Imaging and Pathology, Center for Archaeological Sciences, KU Leuven - University of Leuven, Leuven, Belgium.,Department of Biology, Laboratory of Socioecology and Social Evolution, KU Leuven - University of Leuven, Leuven, Belgium
| | - Michele Scardi
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - Ronny Decorte
- Department of Imaging and Pathology, Center for Archaeological Sciences, KU Leuven - University of Leuven, Leuven, Belgium.,Laboratory of Forensic Genetics and Molecular Archaeology, University Hospitals Leuven, Leuven, Belgium
| | - Olga Rickards
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
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16
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Ottoni C, Rasteiro R, Willet R, Claeys J, Talloen P, Van de Vijver K, Chikhi L, Poblome J, Decorte R. Comparing maternal genetic variation across two millennia reveals the demographic history of an ancient human population in southwest Turkey. R Soc Open Sci 2016; 3:150250. [PMID: 26998313 PMCID: PMC4785964 DOI: 10.1098/rsos.150250] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 01/20/2016] [Indexed: 06/05/2023]
Abstract
More than two decades of archaeological research at the site of Sagalassos, in southwest Turkey, resulted in the study of the former urban settlement in all its features. Originally settled in late Classical/early Hellenistic times, possibly from the later fifth century BCE onwards, the city of Sagalassos and its surrounding territory saw empires come and go. The Plague of Justinian in the sixth century CE, which is considered to have caused the death of up to a third of the population in Anatolia, and an earthquake in the seventh century CE, which is attested to have devastated many monuments in the city, may have severely affected the contemporary Sagalassos community. Human occupation continued, however, and Byzantine Sagalassos was eventually abandoned around 1200 CE. In order to investigate whether these historical events resulted in demographic changes across time, we compared the mitochondrial DNA variation of two population samples from Sagalassos (Roman and Middle Byzantine) and a modern sample from the nearby town of Ağlasun. Our analyses revealed no genetic discontinuity across two millennia in the region and Bayesian coalescence-based simulations indicated that a major population decline in the area coincided with the final abandonment of Sagalassos, rather than with the Plague of Justinian or the mentioned earthquake.
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Affiliation(s)
- Claudio Ottoni
- Center for Archaeological Sciences, University of Leuven, Leuven, Belgium
- Department of Imaging & Pathology, University of Leuven, Leuven, Belgium
- Laboratory of Forensic Genetics and Molecular Archaeology, UZ Leuven, Belgium
| | - Rita Rasteiro
- Department of Genetics, School of History, University of Leicester, Leicester, UK
| | - Rinse Willet
- Depatment of Humanities, Institute of History, Leiden University, Leiden, The Netherlands
| | - Johan Claeys
- Sagalassos Archaeological Research Project, University of Leuven, Leuven, Belgium
| | - Peter Talloen
- Sagalassos Archaeological Research Project, University of Leuven, Leuven, Belgium
| | | | - Lounès Chikhi
- CNRS, Université Paul Sabatier, ENFA; UMR5174 EDB (Laboratoire Évolution & Diversité Biologique), Toulouse, France
- Université Toulouse 3 Paul Sabatier, CNRS; UMR5174 EDB, Toulouse, France
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Jeroen Poblome
- Sagalassos Archaeological Research Project, University of Leuven, Leuven, Belgium
| | - Ronny Decorte
- Department of Imaging & Pathology, University of Leuven, Leuven, Belgium
- Laboratory of Forensic Genetics and Molecular Archaeology, UZ Leuven, Belgium
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17
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Bekaert B, Kamalandua A, Zapico S, Van de Voorde W, Decorte R. A selective set of DNA-methylation markers for age determination of blood, teeth and buccal samples. Forensic Science International: Genetics Supplement Series 2015. [DOI: 10.1016/j.fsigss.2015.09.058] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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18
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Bekaert B, Kamalandua A, Zapico SC, Van de Voorde W, Decorte R. Improved age determination of blood and teeth samples using a selected set of DNA methylation markers. Epigenetics 2015; 10:922-30. [PMID: 26280308 DOI: 10.1080/15592294.2015.1080413] [Citation(s) in RCA: 143] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Age estimation from DNA methylation markers has seen an exponential growth of interest, not in the least from forensic scientists. The current published assays, however, can still be improved by lowering the number of markers in the assay and by providing more accurate models to predict chronological age. From the published literature we selected 4 age-associated genes (ASPA, PDE4C, ELOVL2, and EDARADD) and determined CpG methylation levels from 206 blood samples of both deceased and living individuals (age range: 0-91 years). This data was subsequently used to compare prediction accuracy with both linear and non-linear regression models. A quadratic regression model in which the methylation levels of ELOVL2 were squared showed the highest accuracy with a Mean Absolute Deviation (MAD) between chronological age and predicted age of 3.75 years and an adjusted R(2) of 0.95. No difference in accuracy was observed for samples obtained either from living and deceased individuals or between the 2 genders. In addition, 29 teeth from different individuals (age range: 19-70 years) were analyzed using the same set of markers resulting in a MAD of 4.86 years and an adjusted R(2) of 0.74. Cross validation of the results obtained from blood samples demonstrated the robustness and reproducibility of the assay. In conclusion, the set of 4 CpG DNA methylation markers is capable of producing highly accurate age predictions for blood samples from deceased and living individuals.
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Affiliation(s)
- Bram Bekaert
- a KU Leuven - University of Leuven ; Department of Imaging & Pathology ; Leuven , Belgium.,b KU-Leuven - University of Leuven; University Hospitals Leuven; Department of Forensic Medicine; Laboratory of Forensic Genetics and Molecular Archeology ; Leuven , Belgium
| | - Aubeline Kamalandua
- a KU Leuven - University of Leuven ; Department of Imaging & Pathology ; Leuven , Belgium
| | - Sara C Zapico
- c Smithsonian Institution; NMNH; MRC112 ; Anthropology Department ; Washington, DC USA
| | - Wim Van de Voorde
- a KU Leuven - University of Leuven ; Department of Imaging & Pathology ; Leuven , Belgium.,b KU-Leuven - University of Leuven; University Hospitals Leuven; Department of Forensic Medicine; Laboratory of Forensic Genetics and Molecular Archeology ; Leuven , Belgium
| | - Ronny Decorte
- a KU Leuven - University of Leuven ; Department of Imaging & Pathology ; Leuven , Belgium.,b KU-Leuven - University of Leuven; University Hospitals Leuven; Department of Forensic Medicine; Laboratory of Forensic Genetics and Molecular Archeology ; Leuven , Belgium
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19
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Larmuseau MHD, Boon N, Vanderheyden N, Van Geystelen A, Larmuseau HFM, Matthys K, De Clercq W, Decorte R. High Y-chromosomal diversity and low relatedness between paternal lineages on a communal scale in the Western European Low Countries during the surname establishment. Heredity (Edinb) 2015; 115:3-12. [PMID: 25873146 DOI: 10.1038/hdy.2015.5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 11/20/2014] [Accepted: 12/23/2014] [Indexed: 01/02/2023] Open
Abstract
There is limited knowledge on the biological relatedness between citizens and on the demographical dynamics within villages, towns and cities in pre-17th century Western Europe. By combining Y-chromosomal genotypes, in-depth genealogies and surname data in a strict genetic genealogical approach, it is possible to provide insights into the genetic diversity and the relatedness between indigenous paternal lineages within a particular community at the time of the surname adoption. To obtain these insights, six Flemish communities were selected in this study based on the differences in geography and historical development. After rigorous selection of appropriate DNA donors, low relatedness between Y chromosomes of different surnames was found within each community, although there is co-occurrence of these surnames in each community since the start of the surname adoption between the 14th and 15th century. Next, the high communal diversity in Y-chromosomal lineages was comparable with the regional diversity across Flanders at that time. Moreover, clinal distributions of particular Y-chromosomal lineages between the communities were observed according to the clinal distributions earlier observed across the Flemish regions and Western Europe. No significant indication for genetic differences between communities with distinct historical development was found in the analysis. These genetic results provide relevant information for studies in historical sciences, archaeology, forensic genetics and genealogy.
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Affiliation(s)
- M H D Larmuseau
- 1] Laboratory of Forensic Genetics and Molecular Archaeology, UZ Leuven, Leuven, Belgium [2] Department of Imaging and Pathology, Forensic Biomedical Sciences, KU Leuven, Leuven, Belgium [3] Laboratory of Socioecology and Social Evolution, Department of Biology, KU Leuven, Leuven, Belgium
| | - N Boon
- 1] Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, KU Leuven, Leuven, Belgium [2] Institute of Tropical Medicine, Antwerp, Belgium
| | - N Vanderheyden
- Laboratory of Forensic Genetics and Molecular Archaeology, UZ Leuven, Leuven, Belgium
| | - A Van Geystelen
- Laboratory of Socioecology and Social Evolution, Department of Biology, KU Leuven, Leuven, Belgium
| | - H F M Larmuseau
- Faculty of Social Sciences, Department of Social Sciences,Centre of Sociological Research (CESO), KU Leuven, Leuven, Belgium
| | - K Matthys
- Faculty of Social Sciences, Department of Social Sciences,Centre of Sociological Research (CESO), KU Leuven, Leuven, Belgium
| | - W De Clercq
- Faculty of Arts and Philosophy, Department of Archaeology, Ghent University, Ghent, Belgium
| | - R Decorte
- 1] Laboratory of Forensic Genetics and Molecular Archaeology, UZ Leuven, Leuven, Belgium [2] Department of Imaging and Pathology, Forensic Biomedical Sciences, KU Leuven, Leuven, Belgium
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20
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Larmuseau MHD, Van Geystelen A, Kayser M, van Oven M, Decorte R. Towards a consensus Y-chromosomal phylogeny and Y-SNP set in forensics in the next-generation sequencing era. Forensic Sci Int Genet 2014; 15:39-42. [PMID: 25488610 DOI: 10.1016/j.fsigen.2014.11.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 11/07/2014] [Accepted: 11/09/2014] [Indexed: 11/19/2022]
Abstract
Currently, several different Y-chromosomal phylogenies and haplogroup nomenclatures are presented in scientific literature and at conferences demonstrating the present diversity in Y-chromosomal phylogenetic trees and Y-SNP sets used within forensic and anthropological research. This situation can be ascribed to the exponential growth of the number of Y-SNPs discovered due to mostly next-generation sequencing (NGS) studies. As Y-SNPs and their respective phylogenetic positions are important in forensics, such as for male lineage characterization and paternal bio-geographic ancestry inference, there is a need for forensic geneticists to know how to deal with these newly identified Y-SNPs and phylogenies, especially since these phylogenies are often created with other aims than to carry out forensic genetic research. Therefore, we give here an overview of four categories of currently used Y-chromosomal phylogenies and the associated Y-SNP sets in scientific research in the current NGS era. We compare these categories based on the construction method, their advantages and disadvantages, the disciplines wherein the phylogenetic tree can be used, and their specific relevance for forensic geneticists. Based on this overview, it is clear that an up-to-date reduced tree with a consensus Y-SNP set and a stable nomenclature will be the most appropriate reference resource for forensic research. Initiatives to reach such an international consensus are therefore highly recommended.
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Affiliation(s)
- Maarten H D Larmuseau
- UZ Leuven, Laboratory of Forensic Genetics and Molecular Archaeology, Leuven, Belgium; KU Leuven, Forensic Biomedical Sciences, Department of Imaging & Pathology, Leuven, Belgium; KU Leuven, Laboratory of Socioecology and Social Evolution, Department of Biology, Leuven, Belgium.
| | - Anneleen Van Geystelen
- KU Leuven, Laboratory of Socioecology and Social Evolution, Department of Biology, Leuven, Belgium
| | - Manfred Kayser
- Department of Forensic Molecular Biology, Erasmus MC - University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Mannis van Oven
- Department of Forensic Molecular Biology, Erasmus MC - University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Ronny Decorte
- UZ Leuven, Laboratory of Forensic Genetics and Molecular Archaeology, Leuven, Belgium; KU Leuven, Forensic Biomedical Sciences, Department of Imaging & Pathology, Leuven, Belgium
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21
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Purps J, Siegert S, Willuweit S, Nagy M, Alves C, Salazar R, Angustia SMT, Santos LH, Anslinger K, Bayer B, Ayub Q, Wei W, Xue Y, Tyler-Smith C, Bafalluy MB, Martínez-Jarreta B, Egyed B, Balitzki B, Tschumi S, Ballard D, Court DS, Barrantes X, Bäßler G, Wiest T, Berger B, Niederstätter H, Parson W, Davis C, Budowle B, Burri H, Borer U, Koller C, Carvalho EF, Domingues PM, Chamoun WT, Coble MD, Hill CR, Corach D, Caputo M, D'Amato ME, Davison S, Decorte R, Larmuseau MHD, Ottoni C, Rickards O, Lu D, Jiang C, Dobosz T, Jonkisz A, Frank WE, Furac I, Gehrig C, Castella V, Grskovic B, Haas C, Wobst J, Hadzic G, Drobnic K, Honda K, Hou Y, Zhou D, Li Y, Hu S, Chen S, Immel UD, Lessig R, Jakovski Z, Ilievska T, Klann AE, García CC, de Knijff P, Kraaijenbrink T, Kondili A, Miniati P, Vouropoulou M, Kovacevic L, Marjanovic D, Lindner I, Mansour I, Al-Azem M, Andari AE, Marino M, Furfuro S, Locarno L, Martín P, Luque GM, Alonso A, Miranda LS, Moreira H, Mizuno N, Iwashima Y, Neto RSM, Nogueira TLS, Silva R, Nastainczyk-Wulf M, Edelmann J, Kohl M, Nie S, Wang X, Cheng B, Núñez C, Pancorbo MMD, Olofsson JK, Morling N, Onofri V, Tagliabracci A, Pamjav H, Volgyi A, Barany G, Pawlowski R, Maciejewska A, Pelotti S, Pepinski W, Abreu-Glowacka M, Phillips C, Cárdenas J, Rey-Gonzalez D, Salas A, Brisighelli F, Capelli C, Toscanini U, Piccinini A, Piglionica M, Baldassarra SL, Ploski R, Konarzewska M, Jastrzebska E, Robino C, Sajantila A, Palo JU, Guevara E, Salvador J, Ungria MCD, Rodriguez JJR, Schmidt U, Schlauderer N, Saukko P, Schneider PM, Sirker M, Shin KJ, Oh YN, Skitsa I, Ampati A, Smith TG, Calvit LSD, Stenzl V, Capal T, Tillmar A, Nilsson H, Turrina S, De Leo D, Verzeletti A, Cortellini V, Wetton JH, Gwynne GM, Jobling MA, Whittle MR, Sumita DR, Wolańska-Nowak P, Yong RYY, Krawczak M, Nothnagel M, Roewer L. A global analysis of Y-chromosomal haplotype diversity for 23 STR loci. Forensic Sci Int Genet 2014; 12:12-23. [PMID: 24854874 PMCID: PMC4127773 DOI: 10.1016/j.fsigen.2014.04.008] [Citation(s) in RCA: 189] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 04/19/2014] [Indexed: 02/05/2023]
Abstract
In a worldwide collaborative effort, 19,630 Y-chromosomes were sampled from 129 different populations in 51 countries. These chromosomes were typed for 23 short-tandem repeat (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, GATAH4, DYS481, DYS533, DYS549, DYS570, DYS576, and DYS643) and using the PowerPlex Y23 System (PPY23, Promega Corporation, Madison, WI). Locus-specific allelic spectra of these markers were determined and a consistently high level of allelic diversity was observed. A considerable number of null, duplicate and off-ladder alleles were revealed. Standard single-locus and haplotype-based parameters were calculated and compared between subsets of Y-STR markers established for forensic casework. The PPY23 marker set provides substantially stronger discriminatory power than other available kits but at the same time reveals the same general patterns of population structure as other marker sets. A strong correlation was observed between the number of Y-STRs included in a marker set and some of the forensic parameters under study. Interestingly a weak but consistent trend toward smaller genetic distances resulting from larger numbers of markers became apparent.
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Affiliation(s)
- Josephine Purps
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin, Berlin, Germany
| | - Sabine Siegert
- Department of Statistical Genetics and Bioinformatics, Cologne Center for Genomics, University of Cologne, Germany
| | - Sascha Willuweit
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin, Berlin, Germany
| | - Marion Nagy
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin, Berlin, Germany
| | - Cíntia Alves
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Renato Salazar
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Portugal
| | | | - Lorna H Santos
- Philippine National Police Crime Laboratory, Quezon City, Philippines
| | - Katja Anslinger
- Institut für Rechtsmedizin, Ludwig-Maximilians-Universität, München, Germany
| | - Birgit Bayer
- Institut für Rechtsmedizin, Ludwig-Maximilians-Universität, München, Germany
| | - Qasim Ayub
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Wei Wei
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Yali Xue
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Chris Tyler-Smith
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | | | | | - Balazs Egyed
- GenoID Forensic DNA Laboratory, Department of Genetics, Eötvös Loránd University, Budapest, Hungary
| | - Beate Balitzki
- Institut für Rechtsmedizin, Universität Basel, Switzerland
| | | | - David Ballard
- Department of Forensic and Analytical Science, King's College London, London, UK
| | | | - Xinia Barrantes
- Forensic Sciences Department, Poder Judicial, Heredia, Costa Rica
| | | | - Tina Wiest
- Landeskriminalamt Baden-Württemberg, Germany
| | - Burkhard Berger
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria
| | | | - Walther Parson
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria; Penn State Eberly College of Science, University Park, PA, USA
| | - Carey Davis
- Institute of Applied Genetics and Department of Molecular and Medical Genetics, Ft. Worth, USA
| | - Bruce Budowle
- Institute of Applied Genetics and Department of Molecular and Medical Genetics, Ft. Worth, USA; Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia
| | - Helen Burri
- Forensische Genetik, Kantonsspital Aarau AG, Switzerland
| | - Urs Borer
- Forensische Genetik, Kantonsspital Aarau AG, Switzerland
| | | | - Elizeu F Carvalho
- Laboratorio de Diagnósticos por DNA, Instituto de Biologia, Universidade do Estado do Rio de Janeiro, Brazil
| | - Patricia M Domingues
- Laboratorio de Diagnósticos por DNA, Instituto de Biologia, Universidade do Estado do Rio de Janeiro, Brazil
| | | | - Michael D Coble
- National Institute of Standards and Technology, Gaithersburg, USA
| | - Carolyn R Hill
- National Institute of Standards and Technology, Gaithersburg, USA
| | - Daniel Corach
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquimica, Servicio de Huellas Digitales Genetica and CONICET (National Scientific and Technical Research Council), Buenos Aires, Argentina
| | - Mariela Caputo
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquimica, Servicio de Huellas Digitales Genetica and CONICET (National Scientific and Technical Research Council), Buenos Aires, Argentina
| | - Maria E D'Amato
- University of the Western Cape, Biotechnology Department, Forensic DNA Laboratory, Cape Town, South Africa
| | - Sean Davison
- University of the Western Cape, Biotechnology Department, Forensic DNA Laboratory, Cape Town, South Africa
| | - Ronny Decorte
- KU Leuven, Department of Imaging & Pathology, Laboratory of Forensic Genetics and Molecular Archaeology, Leuven, Belgium
| | - Maarten H D Larmuseau
- KU Leuven, Department of Imaging & Pathology, Laboratory of Forensic Genetics and Molecular Archaeology, Leuven, Belgium
| | - Claudio Ottoni
- KU Leuven, Department of Imaging & Pathology, Laboratory of Forensic Genetics and Molecular Archaeology, Leuven, Belgium
| | - Olga Rickards
- Centre of Molecular Antropology For Ancient DNA Studies, Department of Biology, University of Rome Tor Vergata, Italy
| | - Di Lu
- Collaborative Innovation Center of Judicial Civilization, Institute of Evidence Law and Forensic Science, China University of Political Science and Law, Beijing, China
| | - Chengtao Jiang
- Collaborative Innovation Center of Judicial Civilization, Institute of Evidence Law and Forensic Science, China University of Political Science and Law, Beijing, China
| | - Tadeusz Dobosz
- Institute of Forensic Medicine, Medical University, Wroclaw, Poland
| | - Anna Jonkisz
- Institute of Forensic Medicine, Medical University, Wroclaw, Poland
| | - William E Frank
- Illinois State Police, Research & Development Laboratory, Springfield, USA
| | - Ivana Furac
- Department of Forensic Medicine and Criminology, University of Zagreb, Croatia
| | - Christian Gehrig
- University Center of Legal Medicine, Lausanne-Geneva, Lausanne, Switzerland
| | - Vincent Castella
- University Center of Legal Medicine, Lausanne-Geneva, Lausanne, Switzerland
| | - Branka Grskovic
- Forensic Science Centre "Ivan Vucetic", General Police Directorate, Ministry of Interior, Zagreb, Croatia
| | - Cordula Haas
- Institut für Rechtsmedizin, Universität Zürich, Switzerland
| | - Jana Wobst
- Institut für Rechtsmedizin, Universität Zürich, Switzerland
| | | | | | - Katsuya Honda
- Department of Legal Medicine, Faculty of Medicine, University of Tsukuba, Japan
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine Sichuan University, Chengdu, China
| | - Di Zhou
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine Sichuan University, Chengdu, China
| | - Yan Li
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine Sichuan University, Chengdu, China
| | - Shengping Hu
- Molecular Biology and Forensic Genetics Laboratory, Shantou University Medical College, Shantou, China
| | - Shenglan Chen
- Molecular Biology and Forensic Genetics Laboratory, Shantou University Medical College, Shantou, China
| | | | | | - Zlatko Jakovski
- Institute for Forensic Medicine and Criminalistics, Medical Faculty, University "Ss. Cyril and Methodius", Skopje, Macedonia
| | - Tanja Ilievska
- Institute for Forensic Medicine and Criminalistics, Medical Faculty, University "Ss. Cyril and Methodius", Skopje, Macedonia
| | - Anja E Klann
- Institut für Rechtsmedizin, Universitätsmedizin Greifswald, Germany
| | | | - Peter de Knijff
- Forensic Laboratory for DNA Research, Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Thirsa Kraaijenbrink
- Forensic Laboratory for DNA Research, Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Aikaterini Kondili
- Subdivision of Biological and Biochemical Examinations and Analyses F.S.D. - Hellenic Police, Athens, Greece
| | - Penelope Miniati
- Subdivision of Biological and Biochemical Examinations and Analyses F.S.D. - Hellenic Police, Athens, Greece
| | - Maria Vouropoulou
- Subdivision of Biological and Biochemical Examinations and Analyses F.S.D. - Hellenic Police, Athens, Greece
| | - Lejla Kovacevic
- Institute for Genetic Engineering and Biotechnology, Sarajevo, Bosnia and Herzegovina
| | - Damir Marjanovic
- Institute for Genetic Engineering and Biotechnology, Sarajevo, Bosnia and Herzegovina
| | - Iris Lindner
- Institut für Rechtsmedizin, Universität Rostock, Germany
| | - Issam Mansour
- Molecular Biology Laboratory, American University of Science and Technology Beirut, Lebanon and School of Criminal Justice, University of Lausanne, Switzerland
| | - Mouayyad Al-Azem
- Molecular Biology Laboratory, American University of Science and Technology Beirut, Lebanon and School of Criminal Justice, University of Lausanne, Switzerland
| | - Ansar El Andari
- Molecular Biology Laboratory, American University of Science and Technology Beirut, Lebanon and School of Criminal Justice, University of Lausanne, Switzerland
| | - Miguel Marino
- Laboratorio de Análisis de ADN, FCM - National University of Cuyo, Mendoza, Argentina
| | - Sandra Furfuro
- Laboratorio de Análisis de ADN, FCM - National University of Cuyo, Mendoza, Argentina
| | - Laura Locarno
- Laboratorio de Análisis de ADN, FCM - National University of Cuyo, Mendoza, Argentina
| | - Pablo Martín
- Instituto Nacional de Toxicología y Ciencias Forenses, Madrid, Spain
| | - Gracia M Luque
- Instituto Nacional de Toxicología y Ciencias Forenses, Madrid, Spain
| | - Antonio Alonso
- Instituto Nacional de Toxicología y Ciencias Forenses, Madrid, Spain
| | | | - Helena Moreira
- Departamento de Biologia, Universidade de Aveiro, Portugal
| | - Natsuko Mizuno
- National Research Institute of Police Science, Chiba, Japan
| | | | - Rodrigo S Moura Neto
- Instituto de Biologia, Universidade Federal do Rio de Janeiro and DIMAV/INMETRO, Brazil
| | | | - Rosane Silva
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Brazil
| | | | | | - Michael Kohl
- Institut für Rechtsmedizin, Universität Leipzig, Germany
| | - Shengjie Nie
- School of Forensic Medicine, Kunming Medical University, Kunming, China
| | - Xianping Wang
- Department of Criminal Investigation, Xuanwei Public Security Bureau, Xuanwei, China
| | - Baowen Cheng
- Department of Criminal Investigation, Yunnan Provincial Public Security Bureau, Kunming, China
| | - Carolina Núñez
- BIOMICs Research Group, Universidad del País Vasco, Vitoria, Spain
| | | | - Jill K Olofsson
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Valerio Onofri
- Section of Legal Medicine, Università Politecnica delle Marche, Ancona, Italy
| | | | - Horolma Pamjav
- DNA Laboratory, Institute for Forensic Medicine, Network of Forensic Science Institutes, Ministry of Public Administration and Justice, Budapest, Hungary
| | - Antonia Volgyi
- DNA Laboratory, Institute for Forensic Medicine, Network of Forensic Science Institutes, Ministry of Public Administration and Justice, Budapest, Hungary
| | - Gusztav Barany
- DNA Laboratory, Institute for Forensic Medicine, Network of Forensic Science Institutes, Ministry of Public Administration and Justice, Budapest, Hungary
| | - Ryszard Pawlowski
- Forensic Genetics Laboratory, Institute of Forensic Medicine, Medical University of Gdansk, Poland
| | - Agnieszka Maciejewska
- Forensic Genetics Laboratory, Institute of Forensic Medicine, Medical University of Gdansk, Poland
| | - Susi Pelotti
- Department of Medical and Surgical Sciences (DIMEC), Institute of Legal Medicine, School of Medicine, University of Bologna, Italy
| | - Witold Pepinski
- Department of Forensic Medicine, Medical University of Bialystok, Poland
| | | | - Christopher Phillips
- Unidade de Xenética Forense, Instituto de Ciencias Forenses, Grupo de Medicina Xenómica, Facultade de Medicina, Universidade de Santiago de Compostela, Spain
| | - Jorge Cárdenas
- Unidade de Xenética Forense, Instituto de Ciencias Forenses, Grupo de Medicina Xenómica, Facultade de Medicina, Universidade de Santiago de Compostela, Spain
| | - Danel Rey-Gonzalez
- Unidade de Xenética Forense, Instituto de Ciencias Forenses, Grupo de Medicina Xenómica, Facultade de Medicina, Universidade de Santiago de Compostela, Spain
| | - Antonio Salas
- Unidade de Xenética Forense, Instituto de Ciencias Forenses, Grupo de Medicina Xenómica, Facultade de Medicina, Universidade de Santiago de Compostela, Spain
| | - Francesca Brisighelli
- Unidade de Xenética Forense, Instituto de Ciencias Forenses, Grupo de Medicina Xenómica, Facultade de Medicina, Universidade de Santiago de Compostela, Spain; Forensic Genetics Laboratory, Institute of Legal Medicine, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Cristian Capelli
- Unidade de Xenética Forense, Instituto de Ciencias Forenses, Grupo de Medicina Xenómica, Facultade de Medicina, Universidade de Santiago de Compostela, Spain; Department of Zoology, University of Oxford, Oxford, UK
| | - Ulises Toscanini
- Unidade de Xenética Forense, Instituto de Ciencias Forenses, Grupo de Medicina Xenómica, Facultade de Medicina, Universidade de Santiago de Compostela, Spain; PRICAI-Fundación Favaloro, Buenos Aires, Argentina
| | - Andrea Piccinini
- Forensic Genetics Laboratory, Department of Human Morphology and Biomedical Sciences, Università degli Studi di Milano, Italy
| | - Marilidia Piglionica
- Interdisciplinary Department of Medicine, Section of Legal Medicine, University of Bari, Italy
| | - Stefania L Baldassarra
- Interdisciplinary Department of Medicine, Section of Legal Medicine, University of Bari, Italy
| | - Rafal Ploski
- Department of Medical Genetics, Warsaw Medical University, Poland
| | | | | | - Carlo Robino
- Department of Public Health Sciences and Pediatrics, University of Turin, Italy
| | - Antti Sajantila
- Institute of Applied Genetics and Department of Molecular and Medical Genetics, Ft. Worth, USA; Department of Forensic Medicine, University of Helsinki, Finland
| | - Jukka U Palo
- Department of Forensic Medicine, University of Helsinki, Finland
| | - Evelyn Guevara
- Department of Forensic Medicine, University of Helsinki, Finland
| | - Jazelyn Salvador
- DNA Analysis Laboratory, Natural Sciences Research Institute, University of the Philippines Diliman, Philippines
| | - Maria Corazon De Ungria
- DNA Analysis Laboratory, Natural Sciences Research Institute, University of the Philippines Diliman, Philippines
| | - Jae Joseph Russell Rodriguez
- DNA Analysis Laboratory, Natural Sciences Research Institute, University of the Philippines Diliman, Philippines; Institute of Biological Sciences, University of the Philippines Los Baños, Laguna, Philippines
| | - Ulrike Schmidt
- Institut für Rechtsmedizin, Universitätsklinikum Freiburg, Germany
| | | | - Pekka Saukko
- Department of Forensic Medicine, University of Turku, Finland
| | - Peter M Schneider
- Institute of Legal Medicine, Faculty of Medicine, University of Cologne, Germany
| | - Miriam Sirker
- Institute of Legal Medicine, Faculty of Medicine, University of Cologne, Germany
| | - Kyoung-Jin Shin
- Department of Forensic Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Yu Na Oh
- Department of Forensic Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Iulia Skitsa
- Athens Dept. of Legal Medicine, DNA Analysis Laboratory, Athens, Greece
| | - Alexandra Ampati
- Athens Dept. of Legal Medicine, DNA Analysis Laboratory, Athens, Greece
| | - Tobi-Gail Smith
- Department of Basic Medical Sciences, University of the West Indies, Kingston, Jamaica
| | | | - Vlastimil Stenzl
- Laboratory of Forensic Genetics, Institute of Criminalistics, Prague, Czech Republic
| | - Thomas Capal
- Laboratory of Forensic Genetics, Institute of Criminalistics, Prague, Czech Republic
| | - Andreas Tillmar
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden
| | - Helena Nilsson
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden
| | - Stefania Turrina
- Sezione di Medicina Legale, Dipartimento di Medicina e Sanità Pubblica, Università degli Studi di Verona, Italy
| | - Domenico De Leo
- Sezione di Medicina Legale, Dipartimento di Medicina e Sanità Pubblica, Università degli Studi di Verona, Italy
| | - Andrea Verzeletti
- Istituto di Medicina Legale, Universitá degli Studi di Brescia, Italy
| | | | - Jon H Wetton
- Department of Genetics, University of Leicester, UK
| | | | | | | | | | | | - Rita Y Y Yong
- Defence Medical & Environmental Research Institute, DSO National Laboratories, Singapore
| | - Michael Krawczak
- Institute of Medical Informatics and Statistics, Christian-Albrechts University Kiel, Germany
| | - Michael Nothnagel
- Department of Statistical Genetics and Bioinformatics, Cologne Center for Genomics, University of Cologne, Germany
| | - Lutz Roewer
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin, Berlin, Germany.
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Ballantyne KN, Ralf A, Aboukhalid R, Achakzai NM, Anjos MJ, Ayub Q, Balažic J, Ballantyne J, Ballard DJ, Berger B, Bobillo C, Bouabdellah M, Burri H, Capal T, Caratti S, Cárdenas J, Cartault F, Carvalho EF, Carvalho M, Cheng B, Coble MD, Comas D, Corach D, D'Amato ME, Davison S, de Knijff P, De Ungria MCA, Decorte R, Dobosz T, Dupuy BM, Elmrghni S, Gliwiński M, Gomes SC, Grol L, Haas C, Hanson E, Henke J, Henke L, Herrera-Rodríguez F, Hill CR, Holmlund G, Honda K, Immel UD, Inokuchi S, Jobling MA, Kaddura M, Kim JS, Kim SH, Kim W, King TE, Klausriegler E, Kling D, Kovačević L, Kovatsi L, Krajewski P, Kravchenko S, Larmuseau MHD, Lee EY, Lessig R, Livshits LA, Marjanović D, Minarik M, Mizuno N, Moreira H, Morling N, Mukherjee M, Munier P, Nagaraju J, Neuhuber F, Nie S, Nilasitsataporn P, Nishi T, Oh HH, Olofsson J, Onofri V, Palo JU, Pamjav H, Parson W, Petlach M, Phillips C, Ploski R, Prasad SPR, Primorac D, Purnomo GA, Purps J, Rangel-Villalobos H, Rębała K, Rerkamnuaychoke B, Gonzalez DR, Robino C, Roewer L, Rosa A, Sajantila A, Sala A, Salvador JM, Sanz P, Schmitt C, Sharma AK, Silva DA, Shin KJ, Sijen T, Sirker M, Siváková D, Skaro V, Solano-Matamoros C, Souto L, Stenzl V, Sudoyo H, Syndercombe-Court D, Tagliabracci A, Taylor D, Tillmar A, Tsybovsky IS, Tyler-Smith C, van der Gaag KJ, Vanek D, Völgyi A, Ward D, Willemse P, Yap EPH, Yong RYY, Pajnič IZ, Kayser M. Toward male individualization with rapidly mutating y-chromosomal short tandem repeats. Hum Mutat 2014; 35:1021-32. [PMID: 24917567 PMCID: PMC4145662 DOI: 10.1002/humu.22599] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 05/26/2014] [Indexed: 11/30/2022]
Abstract
Relevant for various areas of human genetics, Y-chromosomal short tandem repeats (Y-STRs) are commonly used for testing close paternal relationships among individuals and populations, and for male lineage identification. However, even the widely used 17-loci Yfiler set cannot resolve individuals and populations completely. Here, 52 centers generated quality-controlled data of 13 rapidly mutating (RM) Y-STRs in 14,644 related and unrelated males from 111 worldwide populations. Strikingly, >99% of the 12,272 unrelated males were completely individualized. Haplotype diversity was extremely high (global: 0.9999985, regional: 0.99836–0.9999988). Haplotype sharing between populations was almost absent except for six (0.05%) of the 12,156 haplotypes. Haplotype sharing within populations was generally rare (0.8% nonunique haplotypes), significantly lower in urban (0.9%) than rural (2.1%) and highest in endogamous groups (14.3%). Analysis of molecular variance revealed 99.98% of variation within populations, 0.018% among populations within groups, and 0.002% among groups. Of the 2,372 newly and 156 previously typed male relative pairs, 29% were differentiated including 27% of the 2,378 father–son pairs. Relative to Yfiler, haplotype diversity was increased in 86% of the populations tested and overall male relative differentiation was raised by 23.5%. Our study demonstrates the value of RM Y-STRs in identifying and separating unrelated and related males and provides a reference database.
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Affiliation(s)
- Kaye N Ballantyne
- Department of Forensic Molecular Biology, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands; Office of the Chief Forensic Scientist, Victoria Police Forensic Services Department, Macleod, Victoria, Australia
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23
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Larmuseau MH, Vanderheyden N, Van Geystelen A, Decorte R. A substantially lower frequency of uninformative matches between 23 versus 17 Y-STR haplotypes in north Western Europe. Forensic Sci Int Genet 2014; 11:214-9. [DOI: 10.1016/j.fsigen.2014.04.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 04/03/2014] [Accepted: 04/05/2014] [Indexed: 01/31/2023]
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Van Geystelen A, Wenseleers T, Decorte R, Caspers MJL, Larmuseau MHD. In silico detection of phylogenetic informative Y-chromosomal single nucleotide polymorphisms from whole genome sequencing data. Electrophoresis 2014; 35:3102-10. [DOI: 10.1002/elps.201300459] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 12/03/2013] [Accepted: 01/07/2014] [Indexed: 12/25/2022]
Affiliation(s)
- Anneleen Van Geystelen
- Laboratory of Forensic Genetics and Molecular Archaeology; UZ Leuven Leuven Belgium
- Laboratory of Socioecology and Social Evolution; Department of Biology; KU Leuven Leuven Belgium
| | - Tom Wenseleers
- Laboratory of Socioecology and Social Evolution; Department of Biology; KU Leuven Leuven Belgium
| | - Ronny Decorte
- Laboratory of Forensic Genetics and Molecular Archaeology; UZ Leuven Leuven Belgium
- Biomedical Forensic Sciences; Department of Imaging & Pathology; KU Leuven Leuven Belgium
| | - Maarten J. L. Caspers
- Laboratory of Forensic Genetics and Molecular Archaeology; UZ Leuven Leuven Belgium
- Laboratory of Biodiversity and Evolutionary Genomics; Department of Biology; KU Leuven Leuven Belgium
| | - Maarten H. D. Larmuseau
- Laboratory of Forensic Genetics and Molecular Archaeology; UZ Leuven Leuven Belgium
- Biomedical Forensic Sciences; Department of Imaging & Pathology; KU Leuven Leuven Belgium
- Laboratory of Biodiversity and Evolutionary Genomics; Department of Biology; KU Leuven Leuven Belgium
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25
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Larmuseau MHD, Vanderheyden N, Van Geystelen A, Oven M, Knijff P, Decorte R. Recent Radiation within Y‐chromosomal Haplogroup R‐M269 Resulted in High Y‐STR Haplotype Resemblance. Ann Hum Genet 2014; 78:92-103. [DOI: 10.1111/ahg.12050] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 11/07/2013] [Indexed: 01/18/2023]
Affiliation(s)
- Maarten H. D. Larmuseau
- Laboratory of Forensic Genetics and Molecular ArchaeologyUZ Leuven Leuven Belgium
- Department of Imaging & PathologyBiomedical Forensic SciencesKU Leuven Leuven Belgium
- Laboratory of Biodiversity and Evolutionary GenomicsDepartment of BiologyKU Leuven Leuven Belgium
| | - Nancy Vanderheyden
- Laboratory of Forensic Genetics and Molecular ArchaeologyUZ Leuven Leuven Belgium
| | - Anneleen Van Geystelen
- Laboratory of Socioecology and Social EvolutionDepartment of BiologyKU Leuven Leuven Belgium
| | - Mannis Oven
- Department of Forensic Molecular BiologyErasmus MC – University Medical Center Rotterdam Rotterdam The Netherlands
| | - Peter Knijff
- Department of Human GeneticsLeiden University Medical Center Leiden The Netherlands
| | - Ronny Decorte
- Laboratory of Forensic Genetics and Molecular ArchaeologyUZ Leuven Leuven Belgium
- Department of Imaging & PathologyBiomedical Forensic SciencesKU Leuven Leuven Belgium
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26
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Larmuseau MHD, Vanoverbeke J, Van Geystelen A, Defraene G, Vanderheyden N, Matthys K, Wenseleers T, Decorte R. Low historical rates of cuckoldry in a Western European human population traced by Y-chromosome and genealogical data. Proc Biol Sci 2013; 280:20132400. [PMID: 24266034 PMCID: PMC3813347 DOI: 10.1098/rspb.2013.2400] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 09/30/2013] [Indexed: 11/12/2022] Open
Abstract
Recent evidence suggests that seeking out extra-pair paternity (EPP) can be a viable alternative reproductive strategy for both males and females in many pair-bonded species, including humans. Accurate data on EPP rates in humans, however, are scant and mostly restricted to extant populations. Here, we provide the first large-scale, unbiased genetic study of historical EPP rates in a Western European human population based on combining Y-chromosomal data to infer genetic patrilineages with genealogical and surname data, which reflect known historical presumed paternity. Using two independent methods, we estimate that over the last few centuries, EPP rates in Flanders (Belgium) were only around 1–2% per generation. This figure is substantially lower than the 8–30% per generation reported in some behavioural studies on historical EPP rates, but comparable with the rates reported by other genetic studies of contemporary Western European populations. These results suggest that human EPP rates have not changed substantially during the last 400 years in Flanders and imply that legal genealogies rarely differ from the biological ones. This result has significant implications for a diverse set of fields, including human population genetics, historical demography, forensic science and human sociobiology.
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Affiliation(s)
- M. H. D. Larmuseau
- Laboratory of Forensic Genetics and Molecular Archaeology, UZ Leuven, Leuven, Belgium
- Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, KU Leuven, Leuven, Belgium
- Laboratory of Socioecology and Social Evolution, Department of Biology, KU Leuven, Leuven, Belgium
| | - J. Vanoverbeke
- Laboratory of Aquatic Ecology and Evolutionary Biology, Department of Biology, KU Leuven, Leuven, Belgium
| | - A. Van Geystelen
- Laboratory of Socioecology and Social Evolution, Department of Biology, KU Leuven, Leuven, Belgium
| | - G. Defraene
- Department of Radiation Oncology, UZ Leuven, Leuven, Belgium
| | - N. Vanderheyden
- Laboratory of Forensic Genetics and Molecular Archaeology, UZ Leuven, Leuven, Belgium
| | - K. Matthys
- Centre for Sociological Research (CESO), Family and Population Studies, KU Leuven, Leuven, Belgium
| | - T. Wenseleers
- Laboratory of Socioecology and Social Evolution, Department of Biology, KU Leuven, Leuven, Belgium
| | - R. Decorte
- Laboratory of Forensic Genetics and Molecular Archaeology, UZ Leuven, Leuven, Belgium
- Biomedical Forensic Sciences, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
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27
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Larmuseau MHD, Cassiman JJ, Decorte R. Controversial identification in a historical case is illustrative of the complexity of DNA typing in forensic research. Response to Charlier et al. Forensic Sci Int Genet 2013; 9:e18-9. [PMID: 24275144 DOI: 10.1016/j.fsigen.2013.10.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 10/31/2013] [Indexed: 10/26/2022]
Abstract
The previously published genetic identification of presumptive samples attributed to two French kings, Henri IV and Louis XVI, by Charlier et al., was recently refuted by a genetic genealogic approach. This (provisional) refutation illustrates the difficulties in confirming the identification of historical DNA samples using limited genetic data. Therefore, we want to stress the necessity of including the genetic genealogic approach--which relies on DNA typing of living relatives of the presumptive donor as a confirmed reference--to validate genetic results in historical cases. Moreover, the popularity and broad media coverage of such studies are useful in bringing awareness to the general public, non-DNA forensic experts and lawyers about the complexity of DNA typing in forensic cases.
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Affiliation(s)
- Maarten H D Larmuseau
- UZ Leuven, Laboratory of Forensic Genetics and Molecular Archaeology, Leuven, Belgium; KU Leuven, Forensic Biomedical Sciences, Department of Imaging & Pathology, Leuven, Belgium; KU Leuven, Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, Leuven, Belgium.
| | - Jean-Jacques Cassiman
- UZ Leuven, Laboratory of Forensic Genetics and Molecular Archaeology, Leuven, Belgium; KU Leuven, Forensic Biomedical Sciences, Department of Imaging & Pathology, Leuven, Belgium
| | - Ronny Decorte
- UZ Leuven, Laboratory of Forensic Genetics and Molecular Archaeology, Leuven, Belgium; KU Leuven, Forensic Biomedical Sciences, Department of Imaging & Pathology, Leuven, Belgium
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28
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van Oven M, Van Geystelen A, Kayser M, Decorte R, Larmuseau MHD. Seeing the wood for the trees: a minimal reference phylogeny for the human Y chromosome. Hum Mutat 2013; 35:187-91. [PMID: 24166809 DOI: 10.1002/humu.22468] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 10/11/2013] [Indexed: 11/11/2022]
Abstract
During the last few decades, a wealth of studies dedicated to the human Y chromosome and its DNA variation, in particular Y-chromosome single-nucleotide polymorphisms (Y-SNPs), has led to the construction of a well-established Y-chromosome phylogeny. Since the recent advent of new sequencing technologies, the discovery of additional Y-SNPs is exploding and their continuous incorporation in the phylogenetic tree is leading to an ever higher resolution. However, the large and increasing amount of information included in the "complete" Y-chromosome phylogeny, which now already includes many thousands of identified Y-SNPs, can be overwhelming and complicates its understanding as well as the task of selecting suitable markers for genotyping purposes in evolutionary, demographic, anthropological, genealogical, medical, and forensic studies. As a solution, we introduce a concise reference phylogeny whereby we do not aim to provide an exhaustive tree that includes all known Y-SNPs but, rather, a quite stable reference tree aiming for optimal global discrimination capacity based on a strongly reduced set that includes only the most resolving Y-SNPs. Furthermore, with this reference tree, we wish to propose a common standard for Y-marker as well as Y-haplogroup nomenclature. The current version of our tree is based on a core set of 417 branch-defining Y-SNPs and is available online at http://www.phylotree.org/Y.
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Affiliation(s)
- Mannis van Oven
- Department of Forensic Molecular Biology, Erasmus MC - University Medical Center Rotterdam, Rotterdam, The Netherlands
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Larmuseau MHD, Delorme P, Germain P, Vanderheyden N, Gilissen A, Van Geystelen A, Cassiman JJ, Decorte R. Genetic genealogy reveals true Y haplogroup of House of Bourbon contradicting recent identification of the presumed remains of two French Kings. Eur J Hum Genet 2013; 22:681-7. [PMID: 24105374 DOI: 10.1038/ejhg.2013.211] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 08/12/2013] [Accepted: 08/15/2013] [Indexed: 11/09/2022] Open
Abstract
Genetic analysis strongly increases the opportunity to identify skeletal remains or other biological samples from historical figures. However, validation of this identification is essential and should be done by DNA typing of living relatives. Based on the similarity of a limited set of Y-STRs, a blood sample and a head were recently identified as those belonging respectively to King Louis XVI and his paternal ancestor King Henry IV. Here, we collected DNA samples from three living males of the House of Bourbon to validate the since then controversial identification of these remains. The three living relatives revealed the Bourbon's Y-chromosomal variant on a high phylogenetic resolution for several members of the lineage between Henry IV and Louis XVI. This 'true' Bourbon's variant is different from the published Y-STR profiles of the blood as well as of the head. The earlier identifications of these samples can therefore not be validated. Moreover, matrilineal genealogical data revealed that the published mtDNA sequence of the head was also different from the one of a series of relatives. This therefore leads to the conclusion that the analyzed samples were not from the French kings. Our study once again demonstrated that in order to realize an accurate genetic identification of historical remains DNA typing of living persons, who are paternally or maternally related with the presumed donor of the samples, is required.
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Affiliation(s)
- Maarten H D Larmuseau
- 1] Laboratory of Forensic Genetics and Molecular Archaeology, UZ Leuven, Leuven, Belgium [2] Forensic Biomedical Sciences, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium [3] Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, KU Leuven, Leuven, Belgium
| | | | | | - Nancy Vanderheyden
- Laboratory of Forensic Genetics and Molecular Archaeology, UZ Leuven, Leuven, Belgium
| | - Anja Gilissen
- Laboratory of Forensic Genetics and Molecular Archaeology, UZ Leuven, Leuven, Belgium
| | - Anneleen Van Geystelen
- 1] Laboratory of Forensic Genetics and Molecular Archaeology, UZ Leuven, Leuven, Belgium [2] Laboratory of Socioecology and Social Evolution, Department of Biology, KU Leuven, Leuven, Belgium
| | - Jean-Jacques Cassiman
- Laboratory of Forensic Genetics and Molecular Archaeology, UZ Leuven, Leuven, Belgium
| | - Ronny Decorte
- 1] Laboratory of Forensic Genetics and Molecular Archaeology, UZ Leuven, Leuven, Belgium [2] Forensic Biomedical Sciences, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
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Larmuseau MHD, Vanderheyden N, Van Geystelen A, van Oven M, Kayser M, Decorte R. Increasing phylogenetic resolution still informative for Y chromosomal studies on West-European populations. Forensic Sci Int Genet 2013; 9:179-85. [PMID: 23683810 DOI: 10.1016/j.fsigen.2013.04.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 03/22/2013] [Accepted: 04/07/2013] [Indexed: 01/28/2023]
Abstract
Many Y-chromosomal lineages which are defined in the latest phylogenetic tree of the human Y chromosome by the Y Chromosome Consortium (YCC) in 2008 are distributed in (Western) Europe due to the fact that a large number of phylogeographic studies focus on this area. Therefore, the question arises whether newly discovered polymorphisms on the Y chromosome will still be interesting to study Western Europeans on a population genetic level. To address this question, the West-European region of Flanders (Belgium) was selected as study area since more than 1000 Y chromosomes from this area have previously been genotyped at the highest resolution of the 2008 YCC-tree and coupled to in-depth genealogical data. Based on these data the temporal changes of the population genetic pattern over the last centuries within Flanders were studied and the effects of several past gene flow events were identified. In the present study a set of recently reported novel Y-SNPs were genotyped to further characterize all those Flemish Y chromosomes that belong to haplogroups G, R-M269 and T. Based on this extended Y-SNP set the discrimination power increased drastically as previous large (sub-)haplogroups are now subdivided in several non-marginal groups. Next, the previously observed population structure within Flanders appeared to be the result of different gradients of independent sub-haplogroups. Moreover, for the first time within Flanders a significant East-West gradient was observed in the frequency of two R-M269 lineages, and this gradient is still present when considering the current residence of the DNA donors. Our results thus suggest that an update of the Y-chromosomal tree based on new polymorphisms is still useful to increase the discrimination power based on Y-SNPs and to study population genetic patterns in more detail, even in an already well-studied region such as Western Europe.
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Affiliation(s)
- M H D Larmuseau
- UZ Leuven, Laboratory of Forensic Genetics and Molecular Archaeology, Leuven, Belgium; KU Leuven, Forensic Medicine, Department of Imaging & Pathology, Leuven, Belgium; KU Leuven, Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, Leuven, Belgium.
| | - N Vanderheyden
- UZ Leuven, Laboratory of Forensic Genetics and Molecular Archaeology, Leuven, Belgium
| | - A Van Geystelen
- UZ Leuven, Laboratory of Forensic Genetics and Molecular Archaeology, Leuven, Belgium; KU Leuven, Laboratory of Socioecology and Social Evolution, Department of Biology, Leuven, Belgium
| | - M van Oven
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - M Kayser
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - R Decorte
- UZ Leuven, Laboratory of Forensic Genetics and Molecular Archaeology, Leuven, Belgium; KU Leuven, Forensic Medicine, Department of Imaging & Pathology, Leuven, Belgium
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Van Geystelen A, Decorte R, Larmuseau MHD. Updating the Y-chromosomal phylogenetic tree for forensic applications based on whole genome SNPs. Forensic Sci Int Genet 2013; 7:573-580. [PMID: 23597787 DOI: 10.1016/j.fsigen.2013.03.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Accepted: 03/19/2013] [Indexed: 01/17/2023]
Abstract
The Y-chromosomal phylogenetic tree has a wide variety of important forensic applications and therefore it needs to be state-of-the-art. Nevertheless, since the last 'official' published tree many publications reported additional Y-chromosomal lineages and other phylogenetic topologies. Therefore, it is difficult for forensic scientists to interpret those reports and use an up-to-date tree and corresponding nomenclature in their daily work. Whole genome sequencing (WGS) data is useful to verify and optimise the current phylogenetic tree for haploid markers. The AMY-tree software is the first open access program which analyses WGS data for Y-chromosomal phylogenetic applications. Here, all published information is collected in a phylogenetic tree and the correctness of this tree is checked based on the first large analysis of 747 WGS samples with AMY-tree. The obtained result is one phylogenetic tree with all peer-reviewed reported Y-SNPs without the observed recurrent and ambiguous mutations. Nevertheless, the results showed that currently only the genomes of a limited set of Y-chromosomal (sub-)haplogroups is available and that many newly reported Y-SNPs based on WGS projects are false positives, even with high sequencing coverage methods. This study demonstrates the usefulness of AMY-tree in the process of checking the quality of the present Y-chromosomal tree and it accentuates the difficulties to enlarge this tree based on only WGS methods.
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Affiliation(s)
- A Van Geystelen
- UZ Leuven, Laboratory of Forensic Genetics and Molecular Archaeology, Leuven, Belgium; KU Leuven, Department of Biology, Laboratory of Socioecology and Social Evolution, Leuven, Belgium
| | - R Decorte
- UZ Leuven, Laboratory of Forensic Genetics and Molecular Archaeology, Leuven, Belgium; KU Leuven, Department of Imaging & Pathology, Forensic Medicine, Leuven, Belgium
| | - M H D Larmuseau
- UZ Leuven, Laboratory of Forensic Genetics and Molecular Archaeology, Leuven, Belgium; KU Leuven, Department of Imaging & Pathology, Forensic Medicine, Leuven, Belgium; KU Leuven, Department of Biology, Laboratory of Biodiversity and Evolutionary Genomics, Leuven, Belgium.
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Larmuseau MHD, Van Geystelen A, van Oven M, Decorte R. Genetic genealogy comes of age: perspectives on the use of deep-rooted pedigrees in human population genetics. Am J Phys Anthropol 2013; 150:505-11. [PMID: 23440589 DOI: 10.1002/ajpa.22233] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Revised: 12/21/2012] [Accepted: 01/03/2013] [Indexed: 11/06/2022]
Abstract
In this article, we promote the implementation of extensive genealogical data in population genetic studies. Genealogical records can provide valuable information on the origin of DNA donors in a population genetic study, going beyond the commonly collected data such as residence, birthplace, language, and self-reported ethnicity. Recent studies demonstrated that extended genealogical data added to surname analysis can be crucial to detect signals of (past) population stratification and to interpret the population structure in a more objective manner. Moreover, when in-depth pedigree data are combined with haploid markers, it is even possible to disentangle signals of temporal differentiation within a population genetic structure during the last centuries. Obtaining genealogical data for all DNA donors in a population genetic study is a labor-intensive task but the vastly growing (genetic) genealogical databases, due to the broad interest of the public, are making this job more time-efficient if there is a guarantee for sufficient data quality. At the end, we discuss the advantages and pitfalls of using genealogy within sampling campaigns and we provide guidelines for future population genetic studies.
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Affiliation(s)
- M H D Larmuseau
- UZ Leuven, Laboratory of Forensic Genetics and Molecular Archaeology, Leuven, Belgium.
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Bekaert B, Massoli C, Anandarajah A, Van de Voorde W, Decorte R. Multiplex DNA amplification and barcoding in a single reaction for 454 Roche sequencing: A comprehensive study on the control region of the mitochondrial genome. Forensic Science International: Genetics Supplement Series 2013. [DOI: 10.1016/j.fsigss.2013.10.057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Ottoni C, Flink LG, Evin A, Geörg C, De Cupere B, Van Neer W, Bartosiewicz L, Linderholm A, Barnett R, Peters J, Decorte R, Waelkens M, Vanderheyden N, Ricaut FX, Cakirlar C, Cevik O, Hoelzel AR, Mashkour M, Karimlu AFM, Seno SS, Daujat J, Brock F, Pinhasi R, Hongo H, Perez-Enciso M, Rasmussen M, Frantz L, Megens HJ, Crooijmans R, Groenen M, Arbuckle B, Benecke N, Vidarsdottir US, Burger J, Cucchi T, Dobney K, Larson G. Pig domestication and human-mediated dispersal in western Eurasia revealed through ancient DNA and geometric morphometrics. Mol Biol Evol 2012. [PMID: 23180578 PMCID: PMC3603306 DOI: 10.1093/molbev/mss261] [Citation(s) in RCA: 164] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Zooarcheological evidence suggests that pigs were domesticated in Southwest Asia ∼8,500 BC. They then spread across the Middle and Near East and westward into Europe alongside early agriculturalists. European pigs were either domesticated independently or more likely appeared so as a result of admixture between introduced pigs and European wild boar. As a result, European wild boar mtDNA lineages replaced Near Eastern/Anatolian mtDNA signatures in Europe and subsequently replaced indigenous domestic pig lineages in Anatolia. The specific details of these processes, however, remain unknown. To address questions related to early pig domestication, dispersal, and turnover in the Near East, we analyzed ancient mitochondrial DNA and dental geometric morphometric variation in 393 ancient pig specimens representing 48 archeological sites (from the Pre-Pottery Neolithic to the Medieval period) from Armenia, Cyprus, Georgia, Iran, Syria, and Turkey. Our results reveal the first genetic signatures of early domestic pigs in the Near Eastern Neolithic core zone. We also demonstrate that these early pigs differed genetically from those in western Anatolia that were introduced to Europe during the Neolithic expansion. In addition, we present a significantly more refined chronology for the introduction of European domestic pigs into Asia Minor that took place during the Bronze Age, at least 900 years earlier than previously detected. By the 5th century AD, European signatures completely replaced the endemic lineages possibly coinciding with the widespread demographic and societal changes that occurred during the Anatolian Bronze and Iron Ages.
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Affiliation(s)
- Claudio Ottoni
- Center for Archaeological Sciences, Department of Earth and Environmental Sciences, University of Leuven, Leuven, Belgium
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Larmuseau MHD, Vanoverbeke J, Gielis G, Vanderheyden N, Larmuseau HFM, Decorte R. In the name of the migrant father--analysis of surname origins identifies genetic admixture events undetectable from genealogical records. Heredity (Edinb) 2012; 109:90-5. [PMID: 22511074 PMCID: PMC3400745 DOI: 10.1038/hdy.2012.17] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Revised: 03/01/2012] [Accepted: 03/09/2012] [Indexed: 11/08/2022] Open
Abstract
Patrilineal heritable surnames are widely used to select autochthonous participants for studies on small-scale population genetic patterns owing to the unique link between the surname and a genetic marker, the Y-chromosome (Y-chr). Today, the question arises as to whether the surname origin will be informative on top of in-depth genealogical pedigrees. Admixture events that happened in the period after giving heritable surnames but before the start of genealogical records may be informative about the additional value of the surname origin. In this context, an interesting historical event is the demic migration from French-speaking regions in Northern France to the depopulated and Dutch-speaking region Flanders at the end of the sixteenth century. Y-chr subhaplogroups of individuals with a French/Roman surname that could be associated with this migration event were compared with those of a group with autochthonous Flemish surnames. Although these groups could not be differentiated based on in-depth genealogical data, they were significantly genetically different from each other. Moreover, the observed genetic divergence was related to the differences in the distributions of main Y-subhaplogroups between contemporary populations from Northern France and Flanders. Therefore, these results indicate that the surname origin can be an important feature on top of in-depth genealogical results to select autochthonous participants for a regional population genetic study based on Y-chromosomes.
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Affiliation(s)
- M H D Larmuseau
- UZ Leuven, Department of Forensic Medicine, Laboratory of Forensic Genetics and Molecular Archaeology, Leuven, Belgium.
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Bekaert B, Wens J, Decorte R. Optimization and validation of the SNPforID 34-SNPplex for POP7™. Forensic Science International: Genetics Supplement Series 2011. [DOI: 10.1016/j.fsigss.2011.08.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Bekaert B, Larmuseau MHD, Vanhove MPM, Opdekamp A, Decorte R. Automated DNA extraction of single dog hairs without roots for mitochondrial DNA analysis. Forensic Sci Int Genet 2011; 6:277-81. [PMID: 21531187 DOI: 10.1016/j.fsigen.2011.04.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Revised: 04/04/2011] [Accepted: 04/05/2011] [Indexed: 11/29/2022]
Abstract
Dogs are intensely integrated in human social life and their shed hairs can play a major role in forensic investigations. The overall aim of this study was to validate a semi-automated extraction method for mitochondrial DNA analysis of telogenic dog hairs. Extracted DNA was amplified with a 95% success rate from 43 samples using two new experimental designs in which the mitochondrial control region was amplified as a single large (± 1260 bp) amplicon or as two individual amplicons (HV1 and HV2; ± 650 and 350 bp) with tailed-primers. The results prove that the extraction of dog hair mitochondrial DNA can easily be automated to provide sufficient DNA yield for the amplification of a forensically useful long mitochondrial DNA fragment or alternatively two short fragments with minimal loss of sequence in case of degraded samples.
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Affiliation(s)
- Bram Bekaert
- Laboratory of Forensic Genetics and Molecular Archaeology, UZ Leuven, Kapucijnenvoer 33, B-3000 Leuven, Belgium.
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Ottoni C, Larmuseau MHD, Vanderheyden N, Martínez-Labarga C, Primativo G, Biondi G, Decorte R, Rickards O. Deep into the roots of the Libyan Tuareg: a genetic survey of their paternal heritage. Am J Phys Anthropol 2011; 145:118-24. [PMID: 21312181 DOI: 10.1002/ajpa.21473] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Accepted: 11/23/2010] [Indexed: 11/05/2022]
Abstract
Recent genetic studies of the Tuareg have begun to uncover the origin of this semi-nomadic northwest African people and their relationship with African populations. For centuries they were caravan traders plying the trade routes between the Mediterranean coast and south-Saharan Africa. Their origin most likely coincides with the fall of the Garamantes who inhabited the Fezzan (Libya) between the 1st millennium BC and the 5th century AD. In this study we report novel data on the Y-chromosome variation in the Libyan Tuareg from Al Awaynat and Tahala, two villages in Fezzan, whose maternal genetic pool was previously characterized. High-resolution investigation of 37 Y-chromosome STR loci and analysis of 35 bi-allelic markers in 47 individuals revealed a predominant northwest African component (E-M81, haplogroup E1b1b1b) which likely originated in the second half of the Holocene in the same ancestral population that contributed to the maternal pool of the Libyan Tuareg. A significant paternal contribution from south-Saharan Africa (E-U175, haplogroup E1b1a8) was also detected, which may likely be due to recent secondary introduction, possibly through slavery practices or fusion between different tribal groups. The difference in haplogroup composition between the villages of Al Awaynat and Tahala suggests that founder effects and drift played a significant role in shaping the genetic pool of the Libyan Tuareg.
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Affiliation(s)
- Claudio Ottoni
- Laboratory of Forensic Genetics and Molecular Archaeology, Universitaire Ziekenhuizen, Leuven, Belgium.
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Ottoni C, Ricaut FX, Vanderheyden N, Brucato N, Waelkens M, Decorte R. Mitochondrial analysis of a Byzantine population reveals the differential impact of multiple historical events in South Anatolia. Eur J Hum Genet 2011; 19:571-6. [PMID: 21224890 DOI: 10.1038/ejhg.2010.230] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The archaeological site of Sagalassos is located in Southwest Turkey, in the western part of the Taurus mountain range. Human occupation of its territory is attested from the late 12th millennium BP up to the 13th century AD. By analysing the mtDNA variation in 85 skeletons from Sagalassos dated to the 11th-13th century AD, this study attempts to reconstruct the genetic signature potentially left in this region of Anatolia by the many civilizations, which succeeded one another over the centuries until the mid-Byzantine period (13th century BC). Authentic ancient DNA data were determined from the control region and some SNPs in the coding region of the mtDNA in 53 individuals. Comparative analyses with up to 157 modern populations allowed us to reconstruct the origin of the mid-Byzantine people still dwelling in dispersed hamlets in Sagalassos, and to detect the maternal contribution of their potential ancestors. By integrating the genetic data with historical and archaeological information, we were able to attest in Sagalassos a significant maternal genetic signature of Balkan/Greek populations, as well as ancient Persians and populations from the Italian peninsula. Some contribution from the Levant has been also detected, whereas no contribution from Central Asian population could be ascertained.
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Affiliation(s)
- Claudio Ottoni
- Laboratory of Forensic Genetics and Molecular Archaeology, Universitaire Ziekenhuizen, Leuven, Belgium.
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Larmuseau MHD, Vanderheyden N, Jacobs M, Coomans M, Larno L, Decorte R. Micro-geographic distribution of Y-chromosomal variation in the central-western European region Brabant. Forensic Sci Int Genet 2010; 5:95-9. [PMID: 21036685 DOI: 10.1016/j.fsigen.2010.08.020] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Revised: 08/12/2010] [Accepted: 08/25/2010] [Indexed: 11/16/2022]
Abstract
One of the future issues in the forensic application of the haploid Y-chromosome (Y-chr) is surveying the distribution of the Y-chr variation on a micro-geographical scale. Studies on such a scale require observing Y-chr variation on a high resolution, high sampling efforts and reliable genealogical data of all DNA-donors. In the current study we optimised this framework by surveying the micro-geographical distribution of the Y-chr variation in the central-western European region named Brabant. The Duchy of Brabant was a historical region in the Low Countries containing three contemporary Belgian provinces and one Dutch province (Noord-Brabant). 477 males from five a priori defined regions within Brabant were selected based on their genealogical ancestry (known pedigree at least before 1800). The Y-haplotypes were determined based on 37 Y-STR loci and the finest possible level of substructuring was defined according to the latest published Y-chr phylogenetic tree. In total, eight Y-haplogroups and 32 different subhaplogroups were observed, whereby 70% of all participants belonged to only four subhaplogroups: R1b1b2a1 (R-U106), R1b1b2a2* (R-P312*), R1b1b2a2g (R-U152) and I1* (I-M253*). Significant micro-geographical differentiation within Brabant was detected between the Dutch (Noord-Brabant) vs. the Flemish regions based on the differences in (sub)haplogroup frequencies but not based on Y-STR variation within the main subhaplogroups. A clear gradient was found with higher frequencies of R1b1b2 (R-M269) chromosomes in the northern vs. southern regions, mainly related to a trend in the frequency of R1b1b2a1 (R-U106).
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Affiliation(s)
- Maarten H D Larmuseau
- UZ Leuven, Department of Forensic Medicine, Laboratory of Forensic Genetics and Molecular Archaeology, Kapucijnenvoer 33, B-3000 Leuven, Belgium.
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Ballantyne KN, Goedbloed M, Fang R, Schaap O, Lao O, Wollstein A, Choi Y, van Duijn K, Vermeulen M, Brauer S, Decorte R, Poetsch M, von Wurmb-Schwark N, de Knijff P, Labuda D, Vézina H, Knoblauch H, Lessig R, Roewer L, Ploski R, Dobosz T, Henke L, Henke J, Furtado MR, Kayser M. Mutability of Y-chromosomal microsatellites: rates, characteristics, molecular bases, and forensic implications. Am J Hum Genet 2010; 87:341-53. [PMID: 20817138 DOI: 10.1016/j.ajhg.2010.08.006] [Citation(s) in RCA: 271] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Revised: 08/02/2010] [Accepted: 08/13/2010] [Indexed: 11/24/2022] Open
Abstract
Nonrecombining Y-chromosomal microsatellites (Y-STRs) are widely used to infer population histories, discover genealogical relationships, and identify males for criminal justice purposes. Although a key requirement for their application is reliable mutability knowledge, empirical data are only available for a small number of Y-STRs thus far. To rectify this, we analyzed a large number of 186 Y-STR markers in nearly 2000 DNA-confirmed father-son pairs, covering an overall number of 352,999 meiotic transfers. Following confirmation by DNA sequence analysis, the retrieved mutation data were modeled via a Bayesian approach, resulting in mutation rates from 3.78 × 10(-4) (95% credible interval [CI], 1.38 × 10(-5) - 2.02 × 10(-3)) to 7.44 × 10(-2) (95% CI, 6.51 × 10(-2) - 9.09 × 10(-2)) per marker per generation. With the 924 mutations at 120 Y-STR markers, a nonsignificant excess of repeat losses versus gains (1.16:1), as well as a strong and significant excess of single-repeat versus multirepeat changes (25.23:1), was observed. Although the total repeat number influenced Y-STR locus mutability most strongly, repeat complexity, the length in base pairs of the repeated motif, and the father's age also contributed to Y-STR mutability. To exemplify how to practically utilize this knowledge, we analyzed the 13 most mutable Y-STRs in an independent sample set and empirically proved their suitability for distinguishing close and distantly related males. This finding is expected to revolutionize Y-chromosomal applications in forensic biology, from previous male lineage differentiation toward future male individual identification.
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Decorte R. Genetic identification in the 21st century—Current status and future developments. Forensic Sci Int 2010; 201:160-4. [DOI: 10.1016/j.forsciint.2010.02.029] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2010] [Accepted: 02/23/2010] [Indexed: 11/25/2022]
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Bekaert B, Coomans M, Knaepen K, Larno L, Thijs N, Vanhoutte E, Van de Voorde W, Decorte R. Validation of a microchip electrophoresis system as a DNA amplification control. Forensic Science International: Genetics Supplement Series 2009. [DOI: 10.1016/j.fsigss.2009.08.092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Janssen L, Jacobs M, Vanderheyden N, Bekaert B, Van de Voorde W, Decorte R. Increased sensitivity for amplified STR alleles on capillary sequencers with BigDye® XTerminator™. Forensic Science International: Genetics Supplement Series 2009. [DOI: 10.1016/j.fsigss.2009.08.118] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Vanderheyden N, Mai A, Gilissen A, Cassiman JJ, Decorte R. Identification and sequence analysis of discordant phenotypes between AmpFlSTR SGM Plus and PowerPlex 16. Int J Legal Med 2007; 121:297-301. [PMID: 17406881 DOI: 10.1007/s00414-007-0167-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2006] [Accepted: 03/15/2007] [Indexed: 10/23/2022]
Abstract
During duplicate analysis of buccal swabs from 1,377 individuals with 2 commercial short tandem repeat (STR) kits, we observed 8 discordant phenotypes with SGM Plus (SGM, second generation multiplex) for the STRs THO1 (2), vWA (4) and D18S51 (2), and 1 discrepancy with PowerPlex 16 for D18S51. One individual even showed two discrepancies (vWA and THO1) for SGM Plus. In each case, the difference observed was due to the non-amplification or allele dropout of the second allele in a heterozygous genotype. Sequence analysis revealed each time the presence of a mutation that probably coincided with the primer-binding site. Primer-binding site mutations for vWA and D18S51 have been reported previously, while the mutation for THO1 (C-to-T substitution at position 1286 of GenBank sequence D00269) is reported here for the first time. While the frequency of these silent alleles remains low (0.58% in our study), it is suggested that appropriate measures should be taken for database comparisons and that allelic dropout should be further investigated by sequence analysis and be reported to the forensic community.
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Affiliation(s)
- Nancy Vanderheyden
- Laboratory of Forensic Genetics and Molecular Archaeology, K.U. Leuven, Campus Gasthuisberg O&N, Herestraat 49-bus 602, 3000 Leuven, Belgium
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Decorte R, Verhoeven E, Vanhoutte E, Knaepen K, Cassiman JJ. Allele frequency data for 19 short tandem repeats (PowerPlex 16 and FFFl) in a Belgian population sample. J Forensic Sci 2006; 51:436-7. [PMID: 16566792 DOI: 10.1111/j.1556-4029.2006.00089.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Ronny Decorte
- Laboratory for Forensic Genetics and Molecular Archaeology, K.U. Leuven, Campus Gasthuisberg O&N, Herestraat 49-bus 602, B-3000 Leuven, Belgium.
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Leemans P, Vandeput A, Vanderheyden N, Cassiman JJ, Decorte R. Evaluation of methodology for the isolation and analysis of LCN-DNA before and after dactyloscopic enhancement of fingerprints. ACTA ACUST UNITED AC 2006. [DOI: 10.1016/j.ics.2005.09.079] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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De Maesschalck K, Vanhoutte E, Knaepen K, Vanderheyden N, Cassiman JJ, Decorte R. Y-chromosomal STR haplotypes in a Belgian population sample and identification of a micro-variant with a flanking site mutation at DYS19. Forensic Sci Int 2005; 152:89-94. [PMID: 15939180 DOI: 10.1016/j.forsciint.2005.02.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2005] [Revised: 02/13/2005] [Accepted: 02/13/2005] [Indexed: 11/19/2022]
Abstract
Allele frequencies and haplotypes for 12 Y-chromosomal STR loci included in the Powerplex System (Promega, Madison, USA) were determined in a sample of 113 unrelated males of Belgian origin. Ninety-nine different haplotypes were observed with an overall haplotype diversity of 0.997.
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Affiliation(s)
- Kris De Maesschalck
- Laboratory for Forensic Genetics and Molecular Archaeology, K.U. Leuven, Campus Gasthuisberg O&N, Herestraat 49--bus 602, B-3000 Leuven, Belgium
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Decorte R, Engelen M, Larno L, Nelissen K, Gilissen A, Cassiman JJ. Belgian population data for 15 STR loci (AmpFlSTR SGM Plus and AmpFlSTR profiler PCR amplification kit). Forensic Sci Int 2004; 139:211-3. [PMID: 15040919 DOI: 10.1016/j.forsciint.2003.11.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2003] [Revised: 11/03/2003] [Accepted: 11/07/2003] [Indexed: 11/27/2022]
Abstract
The allele and genotype distributions for 15 STR loci included in the AmpFlSTR SGM Plus and AmpFlSTR Profiler kits (Applied Biosystems, Foster City, USA) were determined in a sample of 222 unrelated individuals of Belgian origin.
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Affiliation(s)
- Ronny Decorte
- Laboratory for Forensic Genetics and Molecular Archaeology, K.U. Leuven, Campus Gasthuisberg O and N, Herestraat 49, B-3000 Leuven, Belgium.
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Schneider PM, Bender K, Mayr WR, Parson W, Hoste B, Decorte R, Cordonnier J, Vanek D, Morling N, Karjalainen M, Marie-Paule Carlotti C, Sabatier M, Hohoff C, Schmitter H, Pflug W, Wenzel R, Patzelt D, Lessig R, Dobrowolski P, O'Donnell G, Garafano L, Dobosz M, De Knijff P, Mevag B, Pawlowski R, Gusmão L, Conceicao Vide M, Alonso Alonso A, García Fernández O, Sanz Nicolás P, Kihlgreen A, Bär W, Meier V, Teyssier A, Coquoz R, Brandt C, Germann U, Gill P, Hallett J, Greenhalgh M. STR analysis of artificially degraded DNA—results of a collaborative European exercise. Forensic Sci Int 2004; 139:123-34. [PMID: 15040905 DOI: 10.1016/j.forsciint.2003.10.002] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2003] [Revised: 10/02/2003] [Accepted: 10/03/2003] [Indexed: 11/21/2022]
Abstract
Degradation of human DNA extracted from forensic stains is, in most cases, the result of a natural process due to the exposure of the stain samples to the environment. Experiences with degraded DNA from casework samples show that every sample may exhibit different properties in this respect, and that it is difficult to systematically assess the performance of routinely used typing systems for the analysis of degraded DNA samples. Using a batch of artificially degraded DNA with an average fragment size of approx. 200 bp a collaborative exercise was carried out among 38 forensic laboratories from 17 European countries. The results were assessed according to correct allele detection, peak height and balance as well as the occurrence of artefacts. A number of common problems were identified based on these results such as strong peak imbalance in heterozygous genotypes for the larger short tandem repeat (STR) fragments after increased PCR cycle numbers, artefact signals and allelic drop-out. Based on the observations, strategies are discussed to overcome these problems. The strategies include careful balancing of the amount of template DNA and the PCR cycle numbers, the reaction volume and the amount of Taq polymerase. Furthermore, a careful evaluation of the results of the fragment analysis and of automated allele calling is necessary to identify the correct alleles and avoid artefacts.
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