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Wang Z, Wang M, Hu L, He G, Nie S. Evolutionary profiles and complex admixture landscape in East Asia: New insights from modern and ancient Y chromosome variation perspectives. Heliyon 2024; 10:e30067. [PMID: 38756579 PMCID: PMC11096704 DOI: 10.1016/j.heliyon.2024.e30067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 04/08/2024] [Accepted: 04/18/2024] [Indexed: 05/18/2024] Open
Abstract
Human Y-chromosomes are characterized by nonrecombination and uniparental inheritance, carrying traces of human history evolution and admixture. Large-scale population-specific genomic sources based on advanced sequencing technologies have revolutionized our understanding of human Y chromosome diversity and its anthropological and forensic applications. Here, we reviewed and meta-analyzed the Y chromosome genetic diversity of modern and ancient people from China and summarized the patterns of founding lineages of spatiotemporally different populations associated with their origin, expansion, and admixture. We emphasized the strong association between our identified founding lineages and language-related human dispersal events correlated with the Sino-Tibetan, Altaic, and southern Chinese multiple-language families related to the Hmong-Mien, Tai-Kadai, Austronesian, and Austro-Asiatic languages. We subsequently summarize the recent advances in translational applications in forensic and anthropological science, including paternal biogeographical ancestry inference (PBGAI), surname investigation, and paternal history reconstruction. Whole-Y sequencing or high-resolution panels with high coverage of terminal Y chromosome lineages are essential for capturing the genomic diversity of ethnolinguistically diverse East Asians. Generally, we emphasized the importance of including more ethnolinguistically diverse, underrepresented modern and spatiotemporally different ancient East Asians in human genetic research for a comprehensive understanding of the paternal genetic landscape of East Asians with a detailed time series and for the reconstruction of a reference database in the PBGAI, even including new technology innovations of Telomere-to-Telomere (T2T) for new genetic variation discovery.
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Affiliation(s)
- Zhiyong Wang
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China
| | - Mengge Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510275, China
| | - Liping Hu
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Guanglin He
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China
| | - Shengjie Nie
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
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2
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Chiao A, Ge J. Determining lineages between individuals with high-density mitochondrial and Y-chromosomal single-nucleotide polymorphisms. Electrophoresis 2024; 45:843-851. [PMID: 38010138 DOI: 10.1002/elps.202300142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 10/19/2023] [Accepted: 11/12/2023] [Indexed: 11/29/2023]
Abstract
Genetic genealogy has been more frequently used in forensic investigations in identifying criminals. However, the current genetic genealogy applications usually do not consider lineage markers (including both Y and mitochondrial deoxyribonucleic acid (DNA)), which is probably because not all distant relatives share the same lineage markers. In addition, there is no study to show how to use lineage markers and what methods or thresholds should be applied in genetic genealogy. In this study, we developed a method to quickly determine if two single-nucleotide polymorphism (SNP) profiles are from the same paternal or material lineages by using a mismatch frequency of the SNPs in Y-chromosomal or mitochondrial DNA. For both Y and mitochondrial SNPs, profile pairs from the same or different lineages can be decided with high accuracies (i.e., 0.380% or 0.157% error rates with Y and mitochondrial DNA, respectively). With kinship coefficient filtering based on autosomal SNPs, the accuracies of determining maternal and paternal lineage can be further improved (i.e., 0.120% or 0.057% error rates with Y and mitochondrial DNA, respectively, using a threshold of kinship coefficient >0). This study shows that lineage markers can be very powerful tools with high accuracies to determine lineages, which could help solve cases and reduce costs for genetic genealogy investigations.
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Affiliation(s)
- Austin Chiao
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, Texas, USA
- Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Jianye Ge
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, Texas, USA
- Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, Texas, USA
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3
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Cusick MF, Clark L, Tu T, Goforth J, Zhang X, LaRue B, Gutierrez R, Jindra PT. Performance characteristics of chimerism testing by next generation sequencing. Hum Immunol 2021; 83:61-69. [PMID: 34728094 DOI: 10.1016/j.humimm.2021.10.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/23/2021] [Accepted: 10/20/2021] [Indexed: 11/27/2022]
Abstract
Chimerism testing provides informative clinical data regarding the status of a biological sample mixture. For years, this testing was achieved by measuring the peaks of informative short tandem repeat (STR) loci using capillary electrophoresis (CE). With the advent of next generation sequencing (NGS) technology, the quantification of the percentage of donor/recipient mixtures is more easily done using sequence reads in large batches of samples run on a single flow cell. In this study, we present data on using a FORENSIC NGS chimerism platform to accurately measure the percentage of donor/recipient mixtures. We were able to detect chimerism to a limit threshold of 1% using both STR and single nucleotide polymorphism (SNP) informative loci. Importantly, a significant correlation was observed between NGS and CE chimerism methods when compared at donor detection ranges from 1% to 10%. Furthermore, 100% accuracy was achieved through proficiency testing over six surveys. Its usefulness was expanded beyond this to help identify suitable donors for solid organ transplant patients using ancestry SNP profiles. In summary, the NGS method provides a sensitive and reliable alternative to traditional CE for chimerism testing of clinical samples.
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Affiliation(s)
- Matthew F Cusick
- Department of Pathology, University of Michigan Medicine, 2800 Plymouth Rd., Building 36, Ann Arbor, MI 48109, USA.
| | - Lauren Clark
- Department of Surgery, Baylor College of Medicine, One Baylor Plaza, MS:BCM 504, Houston, TX 77030, USA
| | - Thuydung Tu
- Department of Surgery, Baylor College of Medicine, One Baylor Plaza, MS:BCM 504, Houston, TX 77030, USA
| | - John Goforth
- Department of Surgery, Baylor College of Medicine, One Baylor Plaza, MS:BCM 504, Houston, TX 77030, USA
| | - Xiaohai Zhang
- HLA and Immunogenetics, Laboratory, Cedars-Sinai Medical Center, Lab-SSB 197, 8723 Alden D, Los Angeles, CA 90048, USA
| | - Bobby LaRue
- Department of Forensic Science, 1003 Bowers Blvd, Sam Houston, State University Huntsville, TX 77340, USA
| | - Ryan Gutierrez
- Department of Forensic Science, 1003 Bowers Blvd, Sam Houston, State University Huntsville, TX 77340, USA
| | - Peter T Jindra
- Department of Surgery, Baylor College of Medicine, One Baylor Plaza, MS:BCM 504, Houston, TX 77030, USA.
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4
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Yin C, Ren Y, Adnan A, Tian J, Guo K, Xia M, He Z, Zhai D, Chen X, Wang L, Li X, Qin X, Li S, Jin L. Title: Developmental validation of Y-SNP pedigree tagging system: A panel via quick ARMS PCR. Forensic Sci Int Genet 2020; 46:102271. [DOI: 10.1016/j.fsigen.2020.102271] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 03/01/2020] [Accepted: 03/02/2020] [Indexed: 11/26/2022]
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5
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Wang CZ, Wei LH, Wang LX, Wen SQ, Yu XE, Shi MS, Li H. Relating Clans Ao and Aisin Gioro from northeast China by whole Y-chromosome sequencing. J Hum Genet 2019; 64:775-780. [PMID: 31148597 DOI: 10.1038/s10038-019-0622-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 05/14/2019] [Accepted: 05/14/2019] [Indexed: 11/09/2022]
Abstract
The Y-chromosome haplogroup C2b1a3a2-F8951 is the paternal lineage of the Aisin Gioro clan, the most important brother branch of the famous Mongolic-speaking population characteristic haplogroup C2*-Star Cluster (C2b1a3a1-F3796). However, investigations on its internal phylogeny are still limited. In this study, we used whole Y-chromosome sequencing to update its phylogenetic tree. In the revised tree, C2b1a3a2-F8951 and C2*-Star Cluster differentiated 3852 years ago (95% CI = 3295-4497). Approximately 3558 years ago (95% CI = 3013-4144), C2b1a3a2-F8951 was divided into two main subclades, C2b1a3a2a-F14753 and C2b1a3a2b-F5483. Currently, samples of C2b1a3a2-F8951 were mainly from the House of Aisin Gioro clan, the Ao family from Daur and some individuals mainly from northeast China. Although other haplogroups are also found in the Ao family, including C2b1a2-M48, C2b1a3a1-F3796, C2a1b-F845, and N1c-M178, the haplogroup C2b1a3a2-F8951 is still the most distinct genetic component. For haplogroup C2b1a3a2-F8951, the time of the most recent common ancestor of the House of Aisin Gioro clan and the Ao family were both very late, just a few hundred years ago. Some family-specific Y-SNPs of the House of Aisin Gioro and the Ao family were also discovered. This revision evidently improved the resolving power of Y-chromosome phylogeny in northeast Asia, deepening our understanding of the origin of these two families, even the Mongolic-speaking population.
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Affiliation(s)
- Chi-Zao Wang
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, 200438, Shanghai, China
| | - Lan-Hai Wei
- Department of Anthropology and Ethnology, Xiamen University, 361005, Xiamen, China
| | - Ling-Xiang Wang
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, 200438, Shanghai, China
| | - Shao-Qing Wen
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, 200438, Shanghai, China
| | - Xue-Er Yu
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, 200438, Shanghai, China
| | - Mei-Sen Shi
- Institute of the Investigation, School of Criminal Justice, China University of Political Science and Law, 100088, Beijing, China.
| | - Hui Li
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, 200438, Shanghai, China. .,Shanxi Academy of Advanced Research and Innovation, Fudan-Datong Institute of Chinese Origin, 037006, Datong, China.
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6
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Ralf A, van Oven M, Montiel González D, de Knijff P, van der Beek K, Wootton S, Lagacé R, Kayser M. Forensic Y-SNP analysis beyond SNaPshot: High-resolution Y-chromosomal haplogrouping from low quality and quantity DNA using Ion AmpliSeq and targeted massively parallel sequencing. Forensic Sci Int Genet 2019; 41:93-106. [PMID: 31063905 DOI: 10.1016/j.fsigen.2019.04.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 04/08/2019] [Accepted: 04/08/2019] [Indexed: 02/07/2023]
Abstract
Y-chromosomal haplogroups assigned from male-specific Y-chromosomal single nucleotide polymorphisms (Y-SNPs) allow paternal lineage identification and paternal bio-geographic ancestry inference, both being relevant in forensic genetics. However, most previously developed forensic Y-SNP tools did not provide Y haplogroup resolution on the high level needed in forensic applications, because the limited multiplex capacity of the DNA technologies used only allowed the inclusion of a relatively small number of Y-SNPs. In a proof-of-principle study, we recently demonstrated that high-resolution Y haplogrouping is feasible via two AmpliSeq PCR analyses and simultaneous massively parallel sequencing (MPS) of 530 Y-SNPs allowing the inference of 432 Y-haplogroups. With the current study, we present a largely improved Y-SNP MPS lab tool that we specifically designed for the analysis of low quality and quantity DNA often confronted with in forensic DNA analysis. Improvements include i) Y-SNP marker selection based on the "minimal reference phylogeny for the human Y chromosome" (PhyloTree Y), ii) strong increase of the number of targeted Y-SNPs allowing many more Y haplogroups to be inferred, iii) focus on short amplicon length enabling successful analysis of degraded DNA, and iv) combination of all amplicons in a single AmpliSeq PCR and simultaneous sequencing allowing single DNA aliquot use. This new MPS tool simultaneously analyses 859 Y-SNPs and allows inferring 640 Y haplogroups. Preliminary forensic developmental validation testing revealed that this tool performs highly accurate, is sensitive and robust. We also provide a revised software tool for analysing the sequencing data produced by the new MPS lab tool including final Y haplogroup assignment. We envision the tools introduced here for high-resolution Y-chromosomal haplogrouping to determine a man's paternal lineage and/or paternal bio-geographic ancestry to become widely used in forensic Y-chromosome DNA analysis and other applications were Y haplogroup information from low quality / quantity DNA samples is required.
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Affiliation(s)
- Arwin Ralf
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Wytemaweg 80, 3000 CA, Rotterdam, the Netherlands
| | - Mannis van Oven
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Wytemaweg 80, 3000 CA, Rotterdam, the Netherlands
| | - Diego Montiel González
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Wytemaweg 80, 3000 CA, Rotterdam, the Netherlands
| | - Peter de Knijff
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, the Netherlands
| | - Kees van der Beek
- Netherlands Forensic Institute, Laan van Ypenburg 6, 2497 GB, The Hague, the Netherlands
| | - Sharon Wootton
- Human Identification Group, Thermo Fisher Scientific, 180 Oyster Point Blvd, South San Francisco, CA, 94080, USA
| | - Robert Lagacé
- Human Identification Group, Thermo Fisher Scientific, 180 Oyster Point Blvd, South San Francisco, CA, 94080, USA
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Wytemaweg 80, 3000 CA, Rotterdam, the Netherlands.
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7
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Roewer L. Y‐chromosome short tandem repeats in forensics—Sexing, profiling, and matching male DNA. ACTA ACUST UNITED AC 2019. [DOI: 10.1002/wfs2.1336] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Lutz Roewer
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences Corporate Member of Freie Universität Berlin, Humboldt‐Universität zu Berlin and Berlin Institute of Health, Charité‐Universitätsmedizin Berlin 13353 Berlin Germany
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8
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Felkel S, Vogl C, Rigler D, Dobretsberger V, Chowdhary BP, Distl O, Fries R, Jagannathan V, Janečka JE, Leeb T, Lindgren G, McCue M, Metzger J, Neuditschko M, Rattei T, Raudsepp T, Rieder S, Rubin CJ, Schaefer R, Schlötterer C, Thaller G, Tetens J, Velie B, Brem G, Wallner B. The horse Y chromosome as an informative marker for tracing sire lines. Sci Rep 2019; 9:6095. [PMID: 30988347 PMCID: PMC6465346 DOI: 10.1038/s41598-019-42640-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 04/04/2019] [Indexed: 12/31/2022] Open
Abstract
Analysis of the Y chromosome is the best-established way to reconstruct paternal family history in humans. Here, we applied fine-scaled Y-chromosomal haplotyping in horses with biallelic markers and demonstrate the potential of our approach to address the ancestry of sire lines. We de novo assembled a draft reference of the male-specific region of the Y chromosome from Illumina short reads and then screened 5.8 million basepairs for variants in 130 specimens from intensively selected and rural breeds and nine Przewalski's horses. Among domestic horses we confirmed the predominance of a young'crown haplogroup' in Central European and North American breeds. Within the crown, we distinguished 58 haplotypes based on 211 variants, forming three major haplogroups. In addition to two previously characterised haplogroups, one observed in Arabian/Coldblooded and the other in Turkoman/Thoroughbred horses, we uncovered a third haplogroup containing Iberian lines and a North African Barb Horse. In a genealogical showcase, we distinguished the patrilines of the three English Thoroughbred founder stallions and resolved a historic controversy over the parentage of the horse 'Galopin', born in 1872. We observed two nearly instantaneous radiations in the history of Central and Northern European Y-chromosomal lineages that both occurred after domestication 5,500 years ago.
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Affiliation(s)
- Sabine Felkel
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, 1210, Austria
- Vienna Graduate School of Population Genetics, Vienna, Austria
| | - Claus Vogl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, 1210, Austria
| | - Doris Rigler
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, 1210, Austria
| | - Viktoria Dobretsberger
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, 1210, Austria
| | | | - Ottmar Distl
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, 30559, Germany
| | - Ruedi Fries
- Lehrstuhl fuer Tierzucht, Technische Universitaet Muenchen, Freising, 85354, Germany
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
| | - Jan E Janečka
- Department of Biological Sciences, Duquesne University, Pittsburgh, 15282, USA
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
| | - Gabriella Lindgren
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, 75007, Sweden
- Department of Biosystems, KU Leuven, Leuven, 3001, Belgium
| | - Molly McCue
- Veterinary Population Medicine Department, University of Minnesota, St. Paul, MN, 55108, USA
| | - Julia Metzger
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, 30559, Germany
| | | | - Thomas Rattei
- Department of Microbiology and Ecosystem Science, Division of Computational Systems Biology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Terje Raudsepp
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843-4458, USA
| | - Stefan Rieder
- Agroscope, Swiss National Stud Farm, Avenches, 1580, Switzerland
| | - Carl-Johan Rubin
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, 75123, Sweden
| | - Robert Schaefer
- Agroscope, Swiss National Stud Farm, Avenches, 1580, Switzerland
| | - Christian Schlötterer
- Institut fuer Populationsgenetik, University of Veterinary Medicine Vienna, Vienna, 1210, Austria
| | - Georg Thaller
- Institute of Animal Breeding and Husbandry, University of Kiel, Kiel, 24098, Germany
| | - Jens Tetens
- Institute of Animal Breeding and Husbandry, University of Kiel, Kiel, 24098, Germany
- Functional Breeding Group, Department of Animal Sciences, Georg-August-University Göttingen, Göttingen, 37077, Germany
| | - Brandon Velie
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, 75007, Sweden
- School of Life and Environmental Sciences, University of Sydney, Sydney, 2006, Australia
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, 1210, Austria
| | - Barbara Wallner
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, 1210, Austria.
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Kowalczyk M, Zawadzka E, Szewczuk D, Gryzińska M, Jakubczak A. Molecular markers used in forensic genetics. MEDICINE, SCIENCE, AND THE LAW 2018; 58:201-209. [PMID: 30269675 DOI: 10.1177/0025802418803852] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Forensic genetics is a field that has become subject to increasing interest in recent years. Both the technology and the markers used for forensic purposes have changed since the 1980s. The minisatellite sequences used in the famous Pitchfork case introduced genetics to the forensic sciences. Minisatellite sequences have now been replaced by more sensitive microsatellite markers, which have become the basis for the creation of genetic profile databases. Modern molecular methods also exploit single nucleotide polymorphisms, which are often the only way to identify degraded DNA samples. The same type of variation is taken into consideration in attempting to establish the ethnicity of a perpetrator and to determine phenotypic traits such as the eye or hair colour of the individual who is the source of the genetic material. This paper contains a review of the techniques and molecular markers used in human and animal forensic genetics, and also presents the potential trends in forensic genetics such as phenotyping.
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Affiliation(s)
- Marek Kowalczyk
- 1 Department of Biological Basis of Animal Production, Faculty of Biology, Animal Sciences and Bioeconomy, University of Life Sciences in Lublin, Poland
| | - Ewelina Zawadzka
- 1 Department of Biological Basis of Animal Production, Faculty of Biology, Animal Sciences and Bioeconomy, University of Life Sciences in Lublin, Poland
| | | | - Magdalena Gryzińska
- 1 Department of Biological Basis of Animal Production, Faculty of Biology, Animal Sciences and Bioeconomy, University of Life Sciences in Lublin, Poland
| | - Andrzej Jakubczak
- 1 Department of Biological Basis of Animal Production, Faculty of Biology, Animal Sciences and Bioeconomy, University of Life Sciences in Lublin, Poland
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Larmuseau MHD, Ottoni C. Mediterranean Y-chromosome 2.0-why the Y in the Mediterranean is still relevant in the postgenomic era. Ann Hum Biol 2018; 45:20-33. [PMID: 29382278 DOI: 10.1080/03014460.2017.1402956] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
CONTEXT Due to its unique paternal inheritance, the Y-chromosome has been a highly popular marker among population geneticists for over two decades. Recently, the advent of cost-effective genome-wide methods has unlocked information-rich autosomal genomic data, paving the way to the postgenomic era. This seems to have announced the decreasing popularity of investigating Y-chromosome variation, which provides only the paternal perspective of human ancestries and is strongly influenced by genetic drift and social behaviour. OBJECTIVE For this special issue on population genetics of the Mediterranean, the aim was to demonstrate that the Y-chromosome still provides important insights in the postgenomic era and in a time when ancient genomes are becoming exponentially available. METHODS A systematic literature search on Y-chromosomal studies in the Mediterranean was performed. RESULTS Several applications of Y-chromosomal analysis with future opportunities are formulated and illustrated with studies on Mediterranean populations. CONCLUSIONS There will be no reduced interest in Y-chromosomal studies going from reconstruction of male-specific demographic events to ancient DNA applications, surname history and population-wide estimations of extra-pair paternity rates. Moreover, more initiatives are required to collect population genetic data of Y-chromosomal markers for forensic research, and to include Y-chromosomal data in GWAS investigations and studies on male infertility.
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Affiliation(s)
- Maarten H D Larmuseau
- a KU Leuven, Forensic Biomedical Sciences , Department of Imaging & Pathology , Leuven , Belgium.,b KU Leuven, Laboratory of Socioecology and Social Evolution , Department of Biology , Leuven , Belgium
| | - Claudio Ottoni
- c Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences , University of Oslo , Oslo , Norway
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11
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Methodology for Y Chromosome Capture: A complete genome sequence of Y chromosome using flow cytometry, laser microdissection and magnetic streptavidin-beads. Sci Rep 2018; 8:9436. [PMID: 29930304 PMCID: PMC6013464 DOI: 10.1038/s41598-018-27819-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 06/01/2018] [Indexed: 12/13/2022] Open
Abstract
This study is a comparison of the efficiency of three technologies used for Y chromosome capture and the next-generation sequencing (NGS) technologies applied for determining its whole sequence. Our main findings disclose that streptavidin-biotin magnetic particle-based capture methodology offers better and a deeper sequence coverage for Y chromosome capture, compared to chromosome sorting and microdissection procedures. Moreover, this methodology is less time consuming and the most selective for capturing only Y chromosomal material, in contrast with other methodologies that result in considerable background material from other, non-targeted chromosomes. NGS results compared between two platforms, NextSeq 500 and SOLID 5500xl, produce the same coverage results. This is the first study to explore a methodological comparison of Y chromosome capture and genetic analysis. Our results indicate an improved strategy for Y chromosome research with applications in several scientific fields where this chromosome plays an important role, such as forensics, medical sciences, molecular anthropology and cancer sciences.
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12
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Defining Y-SNP variation among the Flemish population (Western Europe) by full genome sequencing. Forensic Sci Int Genet 2017; 31:e12-e16. [PMID: 29089250 DOI: 10.1016/j.fsigen.2017.10.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 10/10/2017] [Accepted: 10/24/2017] [Indexed: 12/27/2022]
Abstract
Y-chromosomal single nucleotide polymorphisms (Y-SNPs) represent a powerful tool in forensic research and casework, especially for inferring paternal ancestry of unknown perpetrators and unidentified bodies. However, the wealth of recently discovered Y-SNPs, the 'jungle' of different evolutionary lineage trees and nomenclatures, and the lack of population-wide data of many phylogenetically mapped Y-SNPs, limits the use of Y-SNPs in routine forensic approaches. Recently, a concise reference phylogeny of the human Y chromosome, the 'Minimal Reference Y-tree', was introduced aiming to provide a stable phylogeny with optimal global discrimination capacity by including the most resolving Y-SNPs. Here, we obtained a representative sample of 270 whole-genome sequences (WGS) to grasp the Y-SNP variation within the autochthonous Flemish population (Belgium, Western Europe) according to this reference Y-tree. The high quality of the Y-SNP calling was guaranteed for the WGS sample as well as its representativeness for the Flemish population based on the comparison of the main haplogroup frequencies with those from earlier studies on Flanders and the Netherlands. The 270 Flemish Y chromosomes were assigned to 98 different sub-haplogroups of the Minimal Reference Y-tree, showing its high potential of discrimination and confirming the spectrum of evolutionary lineages within Western Europe in general and within Flanders in particular. The full database with all Y-SNP calls of the Flemish sample is public available for future updates including forensic and population genetic studies. New initiatives to categorise Y-SNP variation in other populations according to the reference phylogeny of the Y chromosome are highly encouraged for forensic applications. Recommendations to realise such future population sample sets are discussed based on this study.
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Alvarez-Cubero MJ, Saiz M, Martínez-García B, Sayalero SM, Entrala C, Lorente JA, Martinez-Gonzalez LJ. Next generation sequencing: an application in forensic sciences? Ann Hum Biol 2017; 44:581-592. [PMID: 28948844 DOI: 10.1080/03014460.2017.1375155] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
CONTEXT Over the last few decades, advances in sequencing have improved greatly. One of the most important achievements of Next Generation Sequencing (NGS) is to produce millions of sequence reads in a short period of time, and to produce large sequences of DNA in fragments of any size. Libraries can be generated from whole genomes or any DNA or RNA region of interest without the need to know its sequence beforehand. This allows for looking for variations and facilitating genetic identification. OBJECTIVES A deep analysis of current NGS technologies and their application, especially in forensics, including a discussion about the pros and cons of these technologies in genetic identification. METHODS A systematic literature search in PubMed, Science Direct and Scopus electronic databases was performed for the period of December 2012 to June 2015. RESULTS In the forensic field, one of the main problems is the limited amount of sample available, as well as its degraded state. If the amount of DNA input required for preparing NGS libraries continues to decrease, nearly any sample could be sequenced; therefore, the maximum information from any biological remains could be obtained. Additionally, microbiome typification could be an interesting application to study for crime scene characterisation. CONCLUSIONS NGS technologies are going to be crucial for DNA human typing in cases like mass disasters or other events where forensic specimens and samples are compromised and degraded. With the use of NGS it will be possible to achieve the simultaneous analysis of the standard autosomal DNA (STRs and SNPs), mitochondrial DNA, and X and Y chromosomal markers.
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Affiliation(s)
- Maria Jesus Alvarez-Cubero
- a GENYO , Centro Pfizer-Universidad de Granada-Junta de Andalucía de Genómica e Investigación Oncológica, Parque Tecnológico de Ciencias de la Salud (PTS) , Granada , España
| | - Maria Saiz
- b Laboratorio de Identificación Genética, Departamento de Medicina Legal, Toxicología y Antropología Física, Facultad de Medicina , Universidad de Granada , Granada , España
| | - Belén Martínez-García
- a GENYO , Centro Pfizer-Universidad de Granada-Junta de Andalucía de Genómica e Investigación Oncológica, Parque Tecnológico de Ciencias de la Salud (PTS) , Granada , España
| | - Sara M Sayalero
- c CRAG - Centre de Recerca en Agrigenòmica - CSIC IRTA UAB UB , Barcelona , España
| | - Carmen Entrala
- d LORGEN G.P. , PT, Ciencias de la Salud - BIC , Granada , España
| | - Jose Antonio Lorente
- a GENYO , Centro Pfizer-Universidad de Granada-Junta de Andalucía de Genómica e Investigación Oncológica, Parque Tecnológico de Ciencias de la Salud (PTS) , Granada , España.,b Laboratorio de Identificación Genética, Departamento de Medicina Legal, Toxicología y Antropología Física, Facultad de Medicina , Universidad de Granada , Granada , España
| | - Luis Javier Martinez-Gonzalez
- a GENYO , Centro Pfizer-Universidad de Granada-Junta de Andalucía de Genómica e Investigación Oncológica, Parque Tecnológico de Ciencias de la Salud (PTS) , Granada , España
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Ullah I, Olofsson JK, Margaryan A, Ilardo M, Ahmad H, Sikora M, Hansen AJ, Shahid Nadeem M, Fazal N, Ali M, Buchard A, Hemphill BE, Willerslev E, Allentoft ME. High Y-chromosomal Differentiation Among Ethnic Groups of Dir and Swat Districts, Pakistan. Ann Hum Genet 2017; 81:234-248. [PMID: 28771684 DOI: 10.1111/ahg.12204] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 04/26/2017] [Accepted: 06/02/2017] [Indexed: 10/19/2022]
Abstract
The ethnic groups that inhabit the mountainous Dir and Swat districts of northern Pakistan are marked by high levels of cultural and phenotypic diversity. To obtain knowledge of the extent of genetic diversity in this region, we investigated Y-chromosomal diversity in five population samples representing the three main ethnic groups residing within these districts, including Gujars, Pashtuns and Kohistanis. A total of 27 Y-chromosomal short tandem repeats (Y-STRs) and 331 Y-chromosomal single nucleotide polymorphisms (Y-SNPs) were investigated. In the Y-STRs, we observed very high and significant levels of genetic differentiation in nine of the 10 pairwise between-group comparisons (RST 0.179-0.746), and the differences were mirrored in the Y-SNP haplogroup frequency distribution. No genetic differences were found between the two Pashtun subethnic groups Tarklanis and Yusafzais (RST = 0.000). Utmankhels, also considered Pashtuns culturally, were not closely related to any of the other population samples (RST 0.451-0.746). Thus, our findings provide examples of both associations and dissociations between cultural and genetic legacies. When analyzed within a larger continental-scale context, these five ethnic groups fall mostly outside the previously characterized Y-chromosomal gene pools of the Indo-Pakistani subcontinent. Male founder effects, coupled with culturally and topographically based constraints upon marriage and movement, are likely responsible for the high degree of genetic structure in this region.
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Affiliation(s)
- Inam Ullah
- Department of Genetics, Hazara University, Garden Campus, Mansehra, Pakistan.,Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark
| | - Jill K Olofsson
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, United Kingdom
| | - Ashot Margaryan
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark
| | - Melissa Ilardo
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark
| | - Habib Ahmad
- Department of Genetics, Hazara University, Garden Campus, Mansehra, Pakistan.,Islamia University, Peshawar, Pakistan
| | - Martin Sikora
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark
| | - Anders J Hansen
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark
| | - Muhammad Shahid Nadeem
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Numan Fazal
- Department of Genetics, Hazara University, Garden Campus, Mansehra, Pakistan
| | - Murad Ali
- Department of Genetics, Hazara University, Garden Campus, Mansehra, Pakistan
| | - Anders Buchard
- Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Brian E Hemphill
- Department of Anthropology, University of Alaska, Fairbanks, AK, USA
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark
| | - Morten E Allentoft
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark
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15
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Wallner B, Palmieri N, Vogl C, Rigler D, Bozlak E, Druml T, Jagannathan V, Leeb T, Fries R, Tetens J, Thaller G, Metzger J, Distl O, Lindgren G, Rubin CJ, Andersson L, Schaefer R, McCue M, Neuditschko M, Rieder S, Schlötterer C, Brem G. Y Chromosome Uncovers the Recent Oriental Origin of Modern Stallions. Curr Biol 2017; 27:2029-2035.e5. [PMID: 28669755 DOI: 10.1016/j.cub.2017.05.086] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 04/19/2017] [Accepted: 05/26/2017] [Indexed: 11/25/2022]
Abstract
The Y chromosome directly reflects male genealogies, but the extremely low Y chromosome sequence diversity in horses has prevented the reconstruction of stallion genealogies [1, 2]. Here, we resolve the first Y chromosome genealogy of modern horses by screening 1.46 Mb of the male-specific region of the Y chromosome (MSY) in 52 horses from 21 breeds. Based on highly accurate pedigree data, we estimated the de novo mutation rate of the horse MSY and showed that various modern horse Y chromosome lineages split much later than the domestication of the species. Apart from few private northern European haplotypes, all modern horse breeds clustered together in a roughly 700-year-old haplogroup that was transmitted to Europe by the import of Oriental stallions. The Oriental horse group consisted of two major subclades: the Original Arabian lineage and the Turkoman horse lineage. We show that the English Thoroughbred MSY was derived from the Turkoman lineage and that English Thoroughbred sires are largely responsible for the predominance of this haplotype in modern horses.
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Affiliation(s)
- Barbara Wallner
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria.
| | - Nicola Palmieri
- Institut für Populationsgenetik, University of Veterinary Medicine Vienna, Vienna 1210, Austria; Institute of Parasitology, University of Veterinary Medicine Vienna, Vienna 1210, Austria
| | - Claus Vogl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria
| | - Doris Rigler
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria
| | - Elif Bozlak
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria
| | - Thomas Druml
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern 3001, Switzerland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern 3001, Switzerland
| | - Ruedi Fries
- Lehrstuhl für Tierzucht, Technische Universität München, Freising 85354, Germany
| | - Jens Tetens
- Institute of Animal Breeding and Husbandry, University of Kiel, Kiel 24098, Germany; Functional Breeding Group, Department of Animal Sciences, Georg-August-University Göttingen, Göttingen 37077, Germany
| | - Georg Thaller
- Institute of Animal Breeding and Husbandry, University of Kiel, Kiel 24098, Germany
| | - Julia Metzger
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover 30559, Germany
| | - Ottmar Distl
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover 30559, Germany
| | - Gabriella Lindgren
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala 75007, Sweden
| | - Carl-Johan Rubin
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala 75123, Sweden
| | - Leif Andersson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala 75007, Sweden; Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala 75123, Sweden; Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843-4461, USA
| | - Robert Schaefer
- Veterinary Population Medicine Department, University of Minnesota, St. Paul, MN 55108, USA
| | - Molly McCue
- Veterinary Population Medicine Department, University of Minnesota, St. Paul, MN 55108, USA
| | | | - Stefan Rieder
- Agroscope, Swiss National Stud Farm, Avenches 1580, Switzerland
| | - Christian Schlötterer
- Institut für Populationsgenetik, University of Veterinary Medicine Vienna, Vienna 1210, Austria
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria
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16
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Li L, Wang Y, Yang S, Xia M, Yang Y, Wang J, Lu D, Pan X, Ma T, Jiang P, Yu G, Zhao Z, Ping Y, Zhou H, Zhao X, Sun H, Liu B, Jia D, Li C, Hu R, Lu H, Liu X, Chen W, Mi Q, Xue F, Su Y, Jin L, Li S. Genome-wide screening for highly discriminative SNPs for personal identification and their assessment in world populations. Forensic Sci Int Genet 2017; 28:118-127. [PMID: 28249201 DOI: 10.1016/j.fsigen.2017.02.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 02/07/2017] [Accepted: 02/10/2017] [Indexed: 10/20/2022]
Abstract
The applications of DNA profiling aim to identify perpetrators, missing family members and disaster victims in forensic investigations. Single nucleotide polymorphisms (SNPs) based forensic applications are emerging rapidly with a potential to replace short tandem repeats (STRs) based panels which are now being used widely, and there is a need for a well-designed SNP panel to meet such challenge for this transition. Here we present a panel of 175 SNP markers (referred to as Fudan ID Panel or FID), selected from ∼3.6 million SNPs, for the application of personal identification. We optimized and validated FID panel using 729 Chinese individuals using a next generation sequencing (NGS) technology. We showed that the SNPs in the panel possess very high heterozygosity as well as low within- and among-continent differentiations, enabling FID panel exhibit discrimination power in both regional and worldwide populations, with the average match probabilities ranging from 4.77×10-71 to 1.06×10-64 across 54 world populations. With the advent of biomedical research, the SNPs connecting physical anthropological, physiological, behavioral and phenotypic traits will be eventually added to the forensic panels that will revolutionize criminal investigation.
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Affiliation(s)
- Liming Li
- MOE Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Developmental Biology and School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yi Wang
- MOE Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Developmental Biology and School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Shuping Yang
- MOE Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Developmental Biology and School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Mingying Xia
- MOE Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Developmental Biology and School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yajun Yang
- MOE Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Developmental Biology and School of Life Sciences, Fudan University, Shanghai, 200438, China; Fudan-Taizhou Institute of Health Sciences, Jiangsu, 225300, China
| | - Jiucun Wang
- MOE Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Developmental Biology and School of Life Sciences, Fudan University, Shanghai, 200438, China; Fudan-Taizhou Institute of Health Sciences, Jiangsu, 225300, China
| | - Daru Lu
- MOE Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Developmental Biology and School of Life Sciences, Fudan University, Shanghai, 200438, China; Fudan-Taizhou Institute of Health Sciences, Jiangsu, 225300, China
| | - Xingwei Pan
- MOE Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Developmental Biology and School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Teng Ma
- MOE Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Developmental Biology and School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Pei Jiang
- MOE Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Developmental Biology and School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Ge Yu
- MOE Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Developmental Biology and School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Ziqin Zhao
- Department of Forensic Medicine, Shanghai Medicine College, Fudan University, Shanghai, 200000, China
| | - Yuan Ping
- Shanghai Public Security Bureau-Fudan University Joint Laboratory of Human Biology and Forensic Techniques for Crime Scenes, Shanghai Research Institute of Criminal Science and Technology, Shanghai Key Laboratory of Crime Scene Evidence, Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Shanghai, 200000, China
| | - Huaigu Zhou
- Shanghai Public Security Bureau-Fudan University Joint Laboratory of Human Biology and Forensic Techniques for Crime Scenes, Shanghai Research Institute of Criminal Science and Technology, Shanghai Key Laboratory of Crime Scene Evidence, Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Shanghai, 200000, China
| | - Xueying Zhao
- Shanghai Public Security Bureau-Fudan University Joint Laboratory of Human Biology and Forensic Techniques for Crime Scenes, Shanghai Research Institute of Criminal Science and Technology, Shanghai Key Laboratory of Crime Scene Evidence, Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Shanghai, 200000, China
| | - Hui Sun
- MOE Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Developmental Biology and School of Life Sciences, Fudan University, Shanghai, 200438, China; Beijing Engineering Research Center of Crime Scene Evidence Examination, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Bing Liu
- Beijing Engineering Research Center of Crime Scene Evidence Examination, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Dongtao Jia
- Nantong Bureau of Public Safety, Jiangsu, 226000, China
| | - Chengtao Li
- National Institute of Forensics, Ministry of Justice, Shanghai, 200000, China
| | - Rile Hu
- MOE Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Developmental Biology and School of Life Sciences, Fudan University, Shanghai, 200438, China; Medical College of Inner Mongolia, Ulaanbaatar, Autonomous Region of Inner Mongolia, 010000, China
| | - Hongzhou Lu
- Department of Infectious Diseases, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 200000, China
| | - Xiaoyang Liu
- China-Japan Friendship Hospital, Jilin University, Changchun, Jilin, 130000, China
| | - Wenqing Chen
- Cancer Hospital, Changchun, Jilin, 130000, China
| | - Qin Mi
- Department of Biology and Geography, Qinghai Normal University, Xining, Qinghai, 810000, China
| | - Fuzhong Xue
- School of Public Health, Shandong University, Jinan, Shandong, 250000, China
| | - Yongdong Su
- Bureau of Public Safety, Lhasa, Autonomous Region of Tibet, 850000, China
| | - Li Jin
- MOE Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Developmental Biology and School of Life Sciences, Fudan University, Shanghai, 200438, China; Fudan-Taizhou Institute of Health Sciences, Jiangsu, 225300, China.
| | - Shilin Li
- MOE Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Developmental Biology and School of Life Sciences, Fudan University, Shanghai, 200438, China; Fudan-Taizhou Institute of Health Sciences, Jiangsu, 225300, China.
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Biohistorical materials and contemporary privacy concerns-the forensic case of King Albert I. Forensic Sci Int Genet 2016; 24:202-210. [PMID: 27470949 DOI: 10.1016/j.fsigen.2016.07.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 06/21/2016] [Accepted: 07/14/2016] [Indexed: 12/31/2022]
Abstract
The rapid advancement of technology in genomic analysis increasingly allows researchers to study human biohistorical materials. Nevertheless, little attention has been paid to the privacy of the donor's living relatives and the negative impact they might experience from the (public) availability of genetic results, even in cases of scientific, forensic or historical relevance. This issue has become clear during a cold case investigation of a relic attributed to Belgian King and World War I-hero Albert I who died, according to the official version, in a solo climbing accident in 1934. Authentication of the relic with blood stains assigned to the King and collected on the place where his body was discovered is recognised as one of the final opportunities to test the plausibility of various conspiracy theories on the King's demise. While the historical value and current technological developments allow the genomic analysis of this relic, publication of genetic data would immediately lead to privacy concerns for living descendants and relatives of the King, including the Belgian and British royal families, even after more than 80 years. Therefore, the authentication study of the relic of King Albert I has been a difficult exercise towards balancing public research interests and privacy interests. The identification of the relic was realised by using a strict genetic genealogical approach including Y-chromosome and mitochondrial genome comparison with living relatives, thereby limiting the analysis to genomic regions relevant for identification. The genetic results combined with all available historical elements concerning the relic, provide strong evidence that King Albert I was indeed the donor of the blood stains, which is in line with the official climbing accident hypothesis and contradicts widespread 'mise-en-scène' scenarios. Since publication of the haploid data of the blood stains has the potential to violate the privacy of living relatives, we opted for external and independent reviewing of (the quality of) our data and statistical interpretation by external forensic experts in haploid markers to guarantee the objectivity and scientific accuracy of the identification data analysis as well as the privacy of living descendants and relatives. Although the cold case investigation provided relevant insights into the circumstances surrounding the death of King Albert I, it also revealed the insufficient ethical guidance for current genomic studies of biohistorical material.
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Churchill JD, Chang J, Ge J, Rajagopalan N, Wootton SC, Chang CW, Lagacé R, Liao W, King JL, Budowle B. Blind study evaluation illustrates utility of the Ion PGM™ system for use in human identity DNA typing. Croat Med J 2016; 56:218-29. [PMID: 26088846 PMCID: PMC4500968 DOI: 10.3325/cmj.2015.56.218] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Aim To perform a blind study to assess the capability of the Ion Personal Genome Machine™ (PGM) system to sequence forensically relevant genetic marker panels and to characterize unknown individuals for ancestry and possible relatedness. Methods Twelve genomic samples were provided by a third party for blinded genetic analysis. For these 12 samples, the mitochondrial genome and three PGM™ panels containing human identity single nucleotide polymorphisms (SNPs), ancestry informative SNPs, and short tandem repeats (STRs) were sequenced on the PGM™ system and analyzed. Results All four genetic systems were run and analyzed on the PGM™ system in a reasonably quick time frame. Completeness of genetic profiles, depth of coverage, strand balance, and allele balance were informative metrics that illustrated the quality and reliability of the data produced. SNP genotypes allowed for identification of sex, paternal lineage, and population ancestry. STR genotypes were shown to be in complete concordance with genotypes generated by standard capillary electrophoresis-based technologies. Variants in the mitochondrial genome data provided information on population background and maternal relationships. Conclusion All results from analysis of the 12 genomic samples were consistent with sample information provided by the sample providers at the end of the blinded study. The relatively easy identification of intra-STR allele SNPs offered the potential for increased discrimination power. The promising nature of these results warrants full validation studies of this massively parallel sequencing technology and its further development for forensic data analysis.
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Affiliation(s)
- Jennifer D Churchill
- Jennifer D. Churchill, 3500 Camp Bowie Blvd, CBH-250, Fort Worth, TX 76107, USA,
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He W, Mao J, Feng T, Wang L, Li Z, Zu W, Liang W, Zhang L. A novel system for forensic SNP analysis through PCR–ligase detection reaction. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2015. [DOI: 10.1016/j.fsigss.2015.09.092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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20
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The Paternal Landscape along the Bight of Benin - Testing Regional Representativeness of West-African Population Samples Using Y-Chromosomal Markers. PLoS One 2015; 10:e0141510. [PMID: 26544036 PMCID: PMC4636292 DOI: 10.1371/journal.pone.0141510] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 10/08/2015] [Indexed: 11/19/2022] Open
Abstract
Patterns of genetic variation in human populations across the African continent are still not well studied in comparison with Eurasia and America, despite the high genetic and cultural diversity among African populations. In population and forensic genetic studies a single sample is often used to represent a complete African region. In such a scenario, inappropriate sampling strategies and/or the use of local, isolated populations may bias interpretations and pose questions of representativeness at a macrogeographic-scale. The non-recombining region of the Y-chromosome (NRY) has great potential to reveal the regional representation of a sample due to its powerful phylogeographic information content. An area poorly characterized for Y-chromosomal data is the West-African region along the Bight of Benin, despite its important history in the trans-Atlantic slave trade and its large number of ethnic groups, languages and lifestyles. In this study, Y-chromosomal haplotypes from four Beninese populations were determined and a global meta-analysis with available Y-SNP and Y-STR data from populations along the Bight of Benin and surrounding areas was performed. A thorough methodology was developed allowing comparison of population samples using Y-chromosomal lineage data based on different Y-SNP panels and phylogenies. Geographic proximity turned out to be the best predictor of genetic affinity between populations along the Bight of Benin. Nevertheless, based on Y-chromosomal data from the literature two population samples differed strongly from others from the same or neighbouring areas and are not regionally representative within large-scale studies. Furthermore, the analysis of the HapMap sample YRI of a Yoruban population from South-western Nigeria based on Y-SNPs and Y-STR data showed for the first time its regional representativeness, a result which is important for standard population and forensic genetic applications using the YRI sample. Therefore, the uniquely and powerful geographical information carried by the Y-chromosome makes it an important locus to test the representativeness of a certain sample even in the genomic era, especially in poorly investigated areas like Africa.
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Churchill JD, Schmedes SE, King JL, Budowle B. Evaluation of the Illumina(®) Beta Version ForenSeq™ DNA Signature Prep Kit for use in genetic profiling. Forensic Sci Int Genet 2015; 20:20-29. [PMID: 26433485 DOI: 10.1016/j.fsigen.2015.09.009] [Citation(s) in RCA: 157] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 09/01/2015] [Accepted: 09/17/2015] [Indexed: 10/23/2022]
Abstract
While capillary electrophoresis-based technologies have been the mainstay for human identity typing applications, there are limitations with this methodology's resolution, scalability, and throughput. Massively parallel sequencing (MPS) offers the capability to multiplex multiple types of forensically-relevant markers and multiple samples together in one run all at an overall lower cost per nucleotide than traditional capillary electrophoresis-based methods; thus, addressing some of these limitations. MPS also is poised to expand forensic typing capabilities by providing new strategies for mixture deconvolution with the identification of intra-STR allele sequence variants and the potential to generate new types of investigative leads with an increase in the overall number and types of genetic markers being analyzed. The beta version of the Illumina ForenSeq DNA Signature Prep Kit is a MPS library preparation method with a streamlined workflow that allows for targeted amplification and sequencing of 63 STRs and 95 identity SNPs, with the option to include an additional 56 ancestry SNPs and 22 phenotypic SNPs depending on the primer mix chosen for amplification, on the MiSeq desktop sequencer (Illumina). This study was divided into a series of experiments that evaluated reliability, sensitivity of detection, mixture analysis, concordance, and the ability to analyze challenged samples. Genotype accuracy, depth of coverage, and allele balance were used as informative metrics for the quality of the data produced. The ForenSeq DNA Signature Prep Kit produced reliable, reproducible results and obtained full profiles with DNA input amounts of 1ng. Data were found to be concordant with current capillary electrophoresis methods, and mixtures at a 1:19 ratio were resolved accurately. Data from the challenged samples showed concordant results with current DNA typing methods with markers in common and minimal allele drop out from the large number of markers typed on these samples. This set of experiments indicates the beta version of the ForenSeq DNA Signature Prep Kit is a valid tool for forensic DNA typing and warrants full validation studies of this MPS technology.
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Affiliation(s)
- Jennifer D Churchill
- Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA.
| | - Sarah E Schmedes
- Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
| | - Jonathan L King
- Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
| | - Bruce Budowle
- Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA; Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia
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Rothe J, Nagy M. Separation of Y-chromosomal haplotypes from male DNA mixtures via multiplex haplotype-specific extraction. Forensic Sci Int Genet 2015; 19:223-231. [PMID: 26275613 DOI: 10.1016/j.fsigen.2015.07.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 06/05/2015] [Accepted: 07/06/2015] [Indexed: 11/26/2022]
Abstract
In forensic analysis, the interpretation of DNA mixtures is the subject of ongoing debate and requires expertise knowledge. Haplotype-specific extraction (HSE) is an alternative method that enables the separation of large chromosome fragments or haplotypes by using magnetic beads in conjunction with allele-specific probes. HSE thus allows physical separation of the components of a DNA mixture. Here, we present the first multiplex HSE separation of a Y-chromosomal haplotype consisting of six Yfiler short tandem repeat markers from a mixture of male DNA.
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Affiliation(s)
- Jessica Rothe
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité- Campus Virchow-Klinikum, Augustenburger Platz 1, Forum 4, 13353 Berlin, Germany.
| | - Marion Nagy
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité- Campus Virchow-Klinikum, Augustenburger Platz 1, Forum 4, 13353 Berlin, Germany
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