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Zhabagin M, Bukayev A, Dyussenova Z, Zhuraliyeva A, Tashkarayeva A, Zhunussova A, Aidarov B, Darmenov A, Akilzhanova A, Schamiloglu U, Sabitov Z. Y-Chromosomal insights into the paternal genealogy of the Kerey tribe have called into question their descent from the Stepfather of Genghis Khan. PLoS One 2024; 19:e0309080. [PMID: 39231100 PMCID: PMC11373838 DOI: 10.1371/journal.pone.0309080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Accepted: 08/05/2024] [Indexed: 09/06/2024] Open
Abstract
The Kerey is one of the prominent Kazakh tribes and has long been a subject of ethnographic scrutiny, with a lack of consensus on its origin and traditional genealogy. Their historical significance, intertwined with the emergence of the empire established by Genghis Khan, necessitates a comprehensive understanding of their genetic history. This study focuses on unraveling the genetic heritage of the Kerey tribe. We conducted a comprehensive analysis of Y-chromosome data from genetic genealogy as citizen science and genetic screening of 23 Y-STRs and 37 Y-SNPs on 207 males from the Kerey tribe within academic science. Our results reveal two prevalent phylogenetic lineages within the C2a1a3a-F3796 haplogroup, also known as the C2*-Star Cluster (C2*-ST), which is one of the founding paternal lineages of the ancient Niru'un clan of the Mongols: C2-FT411734 and C2-FT224144, corresponding to the Abak and Ashamaily clans. While indicating a common male ancestry for them, our findings challenge the notion that they are full siblings. Additionally, genetic diversity analysis of the Y-chromosomes in the Kerey tribe and Kazakhs confirms their kinship with the Uissun tribe but refutes the claim of the Abak clan's progenitor originating from this tribe. Furthermore, genetic evidence fails to support popular historical and ethnographic hypotheses regarding the Kerey tribe's kinship with the Uak, Sirgeli, Adai, Törtkara, Karakerey, and Kereyit Kazakh tribes. The absence of a genetic paternal connection with the Kereyt tribe raises doubts about the genealogical link between the Kerey tribe and the stepfather of Genghis Khan.
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Affiliation(s)
- Maxat Zhabagin
- National Center for Biotechnology, Astana, Kazakhstan
- Nazarbayev University, Astana, Kazakhstan
- International Science Complex “Astana”, Astana, Kazakhstan
| | - Alizhan Bukayev
- National Center for Biotechnology, Astana, Kazakhstan
- Nazarbayev University, Astana, Kazakhstan
| | | | | | - Assel Tashkarayeva
- Research Institute for Jochi Ulus Studies, Astana, Kazakhstan
- Astana International University, Astana, Kazakhstan
| | | | | | - Akynkali Darmenov
- Karaganda Academy of the Ministry of Internal Affairs of the Republic of Kazakhstan named after Barimbek Beisenov, Karaganda, Kazakhstan
| | | | | | - Zhaxylyk Sabitov
- International Science Complex “Astana”, Astana, Kazakhstan
- L.N. Gumilyov Eurasian National University, Astana, Kazakhstan
- Kazak Historical Society, Astana, Kazakhstan
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2
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Sun C, Wang X, Wang S, Zhou Y, Jiang L, Wang Z, Yao H, Zhang Z, Zha L, Luo H, Song F. Developmental validation of the AGCU YNFS Y Kit: A new 6-dye multiplex system with 44 Y-STRs and 5 Y-InDels for forensic application. PLoS One 2024; 19:e0308535. [PMID: 39121067 PMCID: PMC11315348 DOI: 10.1371/journal.pone.0308535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Accepted: 07/24/2024] [Indexed: 08/11/2024] Open
Abstract
With the widespread use of the Y chromosome in genetics, a lot of commercially available Y chromosome kits were developed, validated, and applied to forensic science practice. The AGCU YNFS Y Kit is a new Y chromosome system containing forty-four preferred Y short tandem repeats (Y-STRs) and five common Y-InDels. In this study, the AGCU YNFS Y system was validated to verify its performance by following the guidelines of the Scientific Working Group on DNA Analysis Methods (SWGDAM). A series of validation experiments included the following parameters: PCR-based studies, sensitivity studies, species specificity studies, stability studies, mixture studies, precision studies, stutter calculation, mutation and statistical analysis, population study, and case samples and degradation studies. The results suggested that appropriately changing PCR amplification conditions did not affect genotyping; the kit had good sensitivity for trace amounts of DNA (0.0625 ng), mixtures of multiple male individuals (minor: major = 1: 9), and three PCR inhibitors (more than 250 μM hematin, 250 ng/μL humic acid and 50 ng/μL tannic acid). The maximum standard deviation of allele size did not exceed 0.1552 reflecting the high accuracy of the system. By this, 87 DNA-confirmed pairs of father-son pairs were also analyzed for mutations. A total of 18 loci were mutated, with mutation rates ranging from 11.5×10-3 to 34.5×10-3 (95% CI 7.2×10-3-97.5×10-3, DYS627 and DYF404S1). In the population study, the haplotype diversity of 87 unrelated individuals was 0.9997, and discrimination capacity was 0.9885. Degradation studies have demonstrated that UV-C light exposure for up to 120 hours has no effect on male blood and semen-vaginal secretion mixtures. However, complete typing could no longer be obtained after 48 hours of UV exposure in single male saliva and in male saliva and female blood mixed samples. Collectively, the AGCU YNFS Y Kit is sensitive and accurate and can play its application value in forensic science practice.
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Affiliation(s)
- Chaoran Sun
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan Province, China
| | - Xindi Wang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan Province, China
| | - Shuangshuang Wang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan Province, China
| | - Yuxiang Zhou
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan Province, China
| | - Lanrui Jiang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan Province, China
| | - Zefei Wang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan Province, China
| | - Hewen Yao
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan Province, China
| | - Zhirui Zhang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan Province, China
| | - Lagabaiyila Zha
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan Province, China
| | - Haibo Luo
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan Province, China
| | - Feng Song
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan Province, China
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Fan H, Xu Y, Zhao Y, Feng K, Hong L, Zhao Q, Lu X, Shi M, Li H, Wang L, Wen S. Development and validation of YARN: A novel SE-400 MPS kit for East Asian paternal lineage analysis. Forensic Sci Int Genet 2024; 71:103029. [PMID: 38518712 DOI: 10.1016/j.fsigen.2024.103029] [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: 07/29/2023] [Revised: 02/12/2024] [Accepted: 03/03/2024] [Indexed: 03/24/2024]
Abstract
Y-chromosomal short tandem repeat polymorphisms (Y-STRs) and Y-chromosomal single nucleotide polymorphisms (Y-SNPs) are valuable genetic markers used in paternal lineage identification and population genetics. Currently, there is a lack of an effective panel that integrates Y-STRs and Y-SNPs for studying paternal lineages, particularly in East Asian populations. Hence, we developed a novel Y-chromosomal targeted panel called YARN (Y-chromosome Ancestry and Region Network) based on multiplex PCR and a single-end 400 massive parallel sequencing (MPS) strategy, consisting of 44 patrilineage Y-STRs and 260 evolutionary Y-SNPs. A total of 386 reactions were validated for the effectiveness and applicability of YARN according to SWGDAM validation guidelines, including sensitivity (with a minimum input gDNA of 0.125 ng), mixture identification (ranging from 1:1-1:10), PCR inhibitor testing (using substances such as 50 μM hematin, 100 μM hemoglobin, 100 μM humic acid, and 2.5 mM indigo dye), species specificity (successfully distinguishing humans from other animals), repeatability study (achieved 100% accuracy), and concordance study (with 99.91% accuracy for 1121 Y-STR alleles). Furthermore, we conducted a pilot study using YARN in a cohort of 484 Han Chinese males from Huaiji County, Zhaoqing City, Guangdong, China (GDZQHJ cohort). In this cohort, we identified 52 different Y-haplogroups and 73 different surnames. We found weak to moderate correlations between the Y-haplogroups, Chinese surnames, and geographical locations of the GDZQHJ cohort (with λ values ranging from 0.050 to 0.340). However, when we combined two different categories into a new independent variable, we observed stronger correlations (with λ values ranging from 0.617 to 0.754). Overall, the YARN panel, which combines Y-STR and Y-SNP genetic markers, meets forensic DNA quality assurance guidelines and holds potential for East Asian geographical origin inference and paternal lineage analysis.
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Affiliation(s)
- Haoliang Fan
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China; School of Forensic Medicine, Shanxi Medical University, Taiyuan 030001, China.
| | - Yiran Xu
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China.
| | - Yutao Zhao
- Public Security Bureau of Zhaoqing Municipality, Zhaoqing 526000, China.
| | - Kai Feng
- Duanzhou Branch of Zhaoqing Public Security Bureau, Zhaoqing 526060, China.
| | - Liuxi Hong
- Sihui Public Security Bureau of Guangdong Province, Zhaoqing 526299, China.
| | - Qiancheng Zhao
- Public Security Bureau of Zhaoqing Municipality, Zhaoqing 526000, China.
| | - Xiaoyu Lu
- Deepreads Biotech Company Limited, Guangzhou 510663, China.
| | - Meisen Shi
- Criminal Justice College of China University of Political Science and Law, Beijing 100088, China.
| | - Haiyan Li
- Criminal Technology Center of Guangdong Provincial Public Security Department, Guangzhou 510050, China.
| | - Lingxiang Wang
- MOE Laboratory for National Development and Intelligent Governance, Fudan University, Shanghai 200433, China.
| | - Shaoqing Wen
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China; Institute of Archaeological Science, Fudan University, Shanghai 200433, China; MOE Laboratory for National Development and Intelligent Governance, Fudan University, Shanghai 200433, China.
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Hodișan R, Zaha DC, Jurca CM, Petchesi CD, Bembea M. Genetic Diversity Based on Human Y Chromosome Analysis: A Bibliometric Review Between 2014 and 2023. Cureus 2024; 16:e58542. [PMID: 38887511 PMCID: PMC11182565 DOI: 10.7759/cureus.58542] [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] [Accepted: 04/18/2024] [Indexed: 06/20/2024] Open
Abstract
The Y chromosome has gained significant importance in the examination of genetic studies of populations because of its non-recombinant character and its form of uniparental inheritance. This work seeks to offer a comprehensive review of the specialty literature in the field of population genetics, focusing specifically on the analysis of the human Y chromosome using a bibliometric approach and knowledge mapping. This involves establishing worldwide structural networks by identifying the primary research themes, authors, and papers that have had a significant impact on the academic community. The objective is to examine global publications by analyzing citations at both the document and country level. This will involve conducting co-citation analysis for references with a high number of citations, examining bibliographic coupling through journal analysis, analyzing the co-occurrence of keywords, and investigating collaboration between authors from a country perspective. The research papers have been extracted from the Web of Science database. The bibliometric analysis was performed using the Bibliometrix and VOSviewer software tools. The purpose of this article is to serve as a starting point for future research dedicated to the analysis of the diversity of human Y chromosome haplotypes. The objectives of the study were to identify and present the most cited publications and references with the highest number of citations, and to highlight current publications at the national level.
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Affiliation(s)
- Ramona Hodișan
- Doctoral School of Biomedical Sciences, University of Oradea, Oradea, ROU
- Department of Preclinical Disciplines, University of Oradea, Faculty of Medicine and Pharmacy, Oradea, ROU
| | - Dana C Zaha
- Department of Preclinical Disciplines, University of Oradea, Faculty of Medicine and Pharmacy, Oradea, ROU
| | - Claudia M Jurca
- Department of Preclinical Disciplines, University of Oradea, Faculty of Medicine and Pharmacy, Oradea, ROU
| | - Codruta D Petchesi
- Department of Preclinical Disciplines, University of Oradea, Faculty of Medicine and Pharmacy, Oradea, ROU
| | - Marius Bembea
- Doctoral School of Biomedical Sciences, University of Oradea, Oradea, ROU
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5
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Antão-Sousa S, Gusmão L, Modesti NM, Feliziani S, Faustino M, Marcucci V, Sarapura C, Ribeiro J, Carvalho E, Pereira V, Tomas C, de Pancorbo MM, Baeta M, Alghafri R, Almheiri R, Builes JJ, Gouveia N, Burgos G, Pontes MDL, Ibarra A, da Silva CV, Parveen R, Benitez M, Amorim A, Pinto N. Microsatellites' mutation modeling through the analysis of the Y-chromosomal transmission: Results of a GHEP-ISFG collaborative study. Forensic Sci Int Genet 2024; 69:102999. [PMID: 38181588 DOI: 10.1016/j.fsigen.2023.102999] [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: 05/08/2023] [Revised: 10/25/2023] [Accepted: 12/10/2023] [Indexed: 01/07/2024]
Abstract
The Spanish and Portuguese Speaking Working Group of the International Society for Forensic Genetics (GHEP-ISFG) organized a collaborative study on mutations of Y-chromosomal short tandem repeats (Y-STRs). New data from 2225 father-son duos and data from 44 previously published reports, corresponding to 25,729 duos, were collected and analyzed. Marker-specific mutation rates were estimated for 33 Y-STRs. Although highly dependent on the analyzed marker, mutations compatible with the gain or loss of a single repeat were 23.2 times more likely than those involving a greater number of repeats. Longer alleles (relatively to the modal one) showed to be nearly twice more mutable than the shorter ones. Within the subset of longer alleles, the loss of repeats showed to be nearly twice more likely than the gain. Conversely, shorter alleles showed a symmetrical trend, with repeat gains being twofold more frequent than reductions. A positive correlation between the paternal age and the mutation rate was observed, strengthening previous findings. The results of a machine learning approach, via logistic regression analyses, allowed the establishment of algebraic formulas for estimating the probability of mutation depending on paternal age and allele length for DYS389I, DYS393 and DYS627. Algebraic formulas could also be established considering only the allele length as predictor for DYS19, DYS389I, DYS389II-I, DYS390, DYS391, DYS393, DYS437, DYS439, DYS449, DYS456, DYS458, DYS460, DYS481, DYS518, DYS533, DYS576, DYS626 and DYS627 loci. For the remaining Y-STRs, a lack of statistical significance was observed, probably as a consequence of the small effective size of the subsets available, a common difficulty in the modeling of rare events as is the case of mutations. The amount of data used in the different analyses varied widely, depending on how the data were reported in the publications analyzed. This shows a regrettable waste of produced data, due to inadequate communication of the results, supporting an urgent need of publication guidelines for mutation studies.
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Affiliation(s)
- Sofia Antão-Sousa
- Instituto de Investigação e Inovação em Saúde (i3S), Porto, Portugal; Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP), Porto, Portugal; Faculty of Sciences of the University of Porto (FCUP), Porto, Portugal; DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Leonor Gusmão
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Nidia M Modesti
- Centro de Genética Forense, Poder Judicial de Córdoba, Argentina
| | - Sofía Feliziani
- Centro de Genética Forense, Poder Judicial de Córdoba, Argentina
| | - Marisa Faustino
- Instituto de Investigação e Inovação em Saúde (i3S), Porto, Portugal; Faculty of Sciences of the University of Porto (FCUP), Porto, Portugal
| | - Valeria Marcucci
- Laboratorio Regional de Investigación Forense, Tribunal Superior de Justicia de Santa Cruz, Argentina
| | - Claudia Sarapura
- Laboratorio Regional de Investigación Forense, Tribunal Superior de Justicia de Santa Cruz, Argentina
| | - Julyana Ribeiro
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Elizeu Carvalho
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Vania Pereira
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Carmen Tomas
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Marian M de Pancorbo
- BIOMICs Research Group, Lascaray Research Center, Department of Zoology and Animal Cell Biology, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Miriam Baeta
- BIOMICs Research Group, Lascaray Research Center, Department of Zoology and Animal Cell Biology, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Rashed Alghafri
- International Center for Forensic Sciences, Dubai Police G.H.Q., Dubai, United Arab Emirates
| | - Reem Almheiri
- International Center for Forensic Sciences, Dubai Police G.H.Q., Dubai, United Arab Emirates
| | - Juan José Builes
- GENES SAS Laboratory, Medellín, Colombia; Institute of Biology, University of Antioquia, Medellín, Colombia
| | - Nair Gouveia
- Instituto Nacional de Medicina Legal e Ciências Forenses, I.P. / Serviço de Genética e Biologia Forenses, Delegação do Centro, Portugal
| | - German Burgos
- One Health Global Research Group, Facultad de Medicina, Universidad de Las Américas (UDLA), Quito, Ecuador; Grupo de Medicina Xenómica, Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - Maria de Lurdes Pontes
- Instituto Nacional de Medicina Legal e Ciências Forenses, I.P. / Serviço de Genética e Biologia Forenses, Delegação do Norte, Portugal
| | - Adriana Ibarra
- Laboratorio IDENTIGEN, Universidad de Antioquia, Colombia
| | - Claudia Vieira da Silva
- Instituto Nacional de Medicina Legal e Ciências Forenses, I.P. / Serviço de Genética e Biologia Forenses, Delegação do Sul, Portugal
| | - Rukhsana Parveen
- Forensic Services Laboratory, Centre for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Marc Benitez
- Policia de la Generalitat de Catalunya - Mossos d'Esquadra. Unitat Central del Laboratori Biològic, Barcelona, Spain
| | - António Amorim
- Instituto de Investigação e Inovação em Saúde (i3S), Porto, Portugal; Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP), Porto, Portugal; Faculty of Sciences of the University of Porto (FCUP), Porto, Portugal
| | - Nadia Pinto
- Instituto de Investigação e Inovação em Saúde (i3S), Porto, Portugal; Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP), Porto, Portugal; Centre of Mathematics of the University of Porto, Porto, Portugal.
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6
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Puch-Solis R, Pope S, Tully G. Considerations on the application of a mutation model for Y-STR interpretation. Sci Justice 2024; 64:180-192. [PMID: 38431375 DOI: 10.1016/j.scijus.2024.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/08/2024] [Accepted: 01/14/2024] [Indexed: 03/05/2024]
Abstract
If Y-STR profiling is to be more effective in criminal casework, the methods used to evaluate evidential weight require improvement. Many forensic scientists assign an evidential weight by estimating the number of times a Y-STR profile obtained from a questioned sample has been observed in YHRD datasets. More sophisticated models have been suggested but not yet implemented into routine casework, e.g. Andersen & Balding [1]. Mutation is inherent to STR meiosis (or inheritance) and is encountered in practice. We evaluated a mutation model that can be incorporated into a method for assigning evidential weight to Y-STR profiles, an essential part of bringing any method into practice. Since an important part of implementation to casework is communication, the article is written in an accessible format for practitioners as well as statisticians. The mutation component within the MUTEA model by Willems et al. [2] incorporates the potential for multistep mutations and a tendency for alleles to revert towards a central length, reflecting observed mutation data, e.g. [3]. We have estimated the parameters in this model and in a simplified symmetric version of this model, using sequence data from father/son pairs [4] and deep-rooted pedigrees [5]. Both datasets contain multistep mutations, which may have an effect on models based on simulations [1]. We introduce Beta-Binomial and Beta-Geometric conjugate analyses for estimating rate and step parameters for the mutation models presented here, which require only summations and multiplications. We proved mathematically that the parameters can be estimated independently. We show the importance of reporting the variability of the parameters and not only a point estimate. The parameters can be easily incorporated into statistical models, and updated sequentially as more data becomes available. We recommend fuller publication of data to enable the development and evaluation of a wider range of mutation models.
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Affiliation(s)
- Roberto Puch-Solis
- Leverhulme Research Centre for Forensic Science, University of Dundee, Dundee DD1 4HN, United Kingdom.
| | - Susan Pope
- Principal Forensic Services, 34 Southborough Road, Bromley, Kent BR1 2EB, United Kingdom
| | - Gillian Tully
- King's Forensics, King's College London, Franklin-Wilkins Building, London, SE1 9NH, United Kingdom
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Mitchell MR, Chaseling J, Jones L, White T, Bernie A, Haupt LM, Griffiths LR, Wright KM. Improving the strategy to identify historical military remains: a literature review and Y-STR meta-analysis. Forensic Sci Res 2024; 9:owad050. [PMID: 38562552 PMCID: PMC10982847 DOI: 10.1093/fsr/owad050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 09/26/2023] [Indexed: 04/04/2024] Open
Abstract
The identification of historical military remains by Unrecovered War Casualties-Army (UWC-A) currently relies on Y-chromosome Short Tandem Repeat (Y-STR) testing when maternal relatives are not available, or when a mitochondrial DNA match does not provide sufficient certainty of identification. However, common Y-STR profiles (using Yfiler™) between sets of remains or families often prevent identification. To resolve these cases, an investigation of additional Y-DNA markers is needed for their potential inclusion into the DNA identification strategy. The number of genetic transmissions between missing soldiers and their living relatives needs to be considered to avoid false exclusions between paternal relatives. Analysis of 236 World War I/II (WWI/II) era pairs of relatives identified up to seven genetic transmissions between WWII soldiers and their living relatives, and nine for WWI. Previous Y-STR meta-analyses were published approximately 10 years ago when rapidly mutating markers were relatively new. This paper reports a contemporary literature review and meta-analysis of 35 studies (which includes 23 studies not previously used in meta-analysis) and 23 commonly used Y-STR's mutation rates to inform the inclusion of additional loci to UWC-A's DNA identification strategy. Meta-analysis found mutation data for a given Y-STR locus could be pooled between studies and that the mutation rates were significantly different between some loci (at P < 0.05). Based on this meta-analysis, we have identified two additional markers from PowerPlex® Y23 for potential inclusion in UWC-A's identification strategy. Further avenues for potential experimental exploration are discussed. Key points From 236 UWC-A pairs of relatives, we observed up to nine genetic transmissions between WWI soldiers and their living relatives, and seven for WWII.MedCalc® software for meta-analysis utilizing the Freeman-Tukey transformation was run, which analysed 35 published studies and 23 commonly used loci. Previous Y-STR mutation rate meta-analyses are now 10 years old; this paper includes 23 studies that were not included in previous meta-analyses.Through meta-analysis, we identify two markers from PowerPlex® Y23 for potential inclusion in UWC-A's historical remains identification strategy (alongside Yfiler™). We discuss potential next steps for experimental exploration of additional Y-DNA markers.
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Affiliation(s)
- Melinda R Mitchell
- Queensland University of Technology (QUT), Genomics Research Centre, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Kelvin Grove, Queensland, Australia
| | - Janet Chaseling
- Queensland University of Technology (QUT), Genomics Research Centre, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Kelvin Grove, Queensland, Australia
| | - Lee Jones
- Queensland University of Technology (QUT), Research Methods Group, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Kelvin Grove, Queensland, Australia
| | - Toni White
- Queensland University of Technology (QUT), Defence Innovation Hub, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Kelvin Grove, Queensland, Australia
| | - Andrew Bernie
- Unrecovered War Casualties-Army, Australian Defence Force, Russell Offices, Russell, Australian Capital Territory, Australia
| | - Larisa M Haupt
- Queensland University of Technology (QUT), Genomics Research Centre, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Kelvin Grove, Queensland, Australia
| | - Lyn R Griffiths
- Queensland University of Technology (QUT), Genomics Research Centre, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Kelvin Grove, Queensland, Australia
| | - Kirsty M Wright
- Queensland University of Technology (QUT), Genomics Research Centre, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Kelvin Grove, Queensland, Australia
- Unrecovered War Casualties-Army, Australian Defence Force, Russell Offices, Russell, Australian Capital Territory, Australia
- Royal Australian Air Force (RAAF), No 2 Expeditionary Health Squadron, RAAF Base Williamtown, Williamtown, New South Wales, Australia
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8
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Ralf A, van Wersch B, Montiel González D, Kayser M. Male Pedigree Toolbox: A Versatile Software for Y-STR Data Analyses. Genes (Basel) 2024; 15:227. [PMID: 38397216 PMCID: PMC10887500 DOI: 10.3390/genes15020227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/06/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
Y-chromosomal short tandem repeats (Y-STRs) are widely used in forensic, genealogical, and population genetics. With the recent increase in the number of rapidly mutating (RM) Y-STRs, an unprecedented level of male differentiation can be achieved, widening and improving the applications of Y-STRs in various fields, including forensics. The growing complexity of Y-STR data increases the need for automated data analyses, but dedicated software tools are scarce. To address this, we present the Male Pedigree Toolbox (MPT), a software tool for the automated analysis of Y-STR data in the context of patrilineal genealogical relationships. The MPT can estimate mutation rates and male relative differentiation rates from input Y-STR pedigree data. It can aid in determining ancestral haplotypes within a pedigree and visualize the genetic variation within pedigrees in all branches of family trees. Additionally, it can provide probabilistic classifications using machine learning, helping to establish or prove the structure of the pedigree and the level of relatedness between males, even for closely related individuals with highly similar haplotypes. The tool is flexible and easy to use and can be adjusted to any set of Y-STR markers by modifying the intuitive input file formats. We introduce the MPT software tool v1.0 and make it publicly available with the goal of encouraging and supporting forensic, genealogical, and other geneticists in utilizing the full potential of Y-STRs for both research purposes and practical applications, including criminal casework.
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Affiliation(s)
- Arwin Ralf
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, 3015 CN Rotterdam, The Netherlands
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Malyarchuk BA, Derenko MV. Genetic history of the Koryaks and Evens of the Magadan region based on Y chromosome polymorphism data. Vavilovskii Zhurnal Genet Selektsii 2024; 28:90-97. [PMID: 38465253 PMCID: PMC10917666 DOI: 10.18699/vjgb-24-11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 11/29/2023] [Accepted: 11/29/2023] [Indexed: 03/12/2024] Open
Abstract
In order to clarify the history of gene pool formation of the indigenous populations of the Northern Priokhotye (the northern coast of the Sea of Okhotsk), Y-chromosome polymorphisms were studied in the Koryaks and Evens living in the Magadan region. The results of the study showed that the male gene pool of the Koryaks is represented by haplogroups C-B90-B91, N-B202, and Q-B143, which are also widespread in other peoples of Northeastern Siberia, mainly of Paleo-Asiatic origin. High frequency of haplogroup C-B80, typical of other Tungus-Manchurian peoples, is characteristic of the Evens of the Magadan region. The shared components of the gene pools of the Koryaks and Evens are haplogroups R-M17 and I-P37.2 inherited as a result of admixture with Eastern Europeans (mainly Russians). The high frequency of such Y chromosome haplogroups in the Koryaks (16.7 %) and Evens (37.8 %) is indicative of close interethnic contacts during the last centuries, and most probably especially during the Soviet period. The genetic contribution of the European males' Y chromosome significantly prevails over that of maternally inherited mitochondrial DNA. The study of the Y chromosome haplogroup diversity has shown that only relatively young phylogenetic branches have been preserved in the Koryak gene pool. The age of the oldest component of the Koryak gene pool (haplogroup C-B90-B91) is estimated to be about 3.8 thousand years, the age of the younger haplogroups Q-B143 and N-B202 is about 2.8 and 2.4 thousand years, respectively. Haplogroups C-B90-B91 and N-B202 are Siberian in origin, and haplogroup Q-B143 was apparently inherited by the ancestors of the Koryaks and other Paleo-Asiatic peoples from the Paleo-Eskimos as a result of their migrations to Northeast Asia from the Americas. The analysis of microsatellite loci for haplogroup Q-B143 in the Eskimos of Greenland, Canada and Alaska as well as in the indigenous peoples of Northeastern Siberia showed a decrease in genetic diversity from east to west, pointing to the direction of distribution of the Paleo-Eskimo genetic component in the circumpolar region of America and Asia. At the same time, the Evens appeared in the Northern Priokhotye much later (in the XVII century) as a result of the expansion of the Tungusic tribes, which is confirmed by the results of the analysis of haplogroup C-B80 polymorphisms.
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Affiliation(s)
- B A Malyarchuk
- Institute of Biological Problems of the North of the Far-Eastern Branch of the Russian Academy of Sciences, Magadan, Russia
| | - M V Derenko
- Institute of Biological Problems of the North of the Far-Eastern Branch of the Russian Academy of Sciences, Magadan, Russia
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Zhang H, Huang X, Jin X, Ren Z, Wang Q, Yang M, Xu R, Yuan X, Yang D, Liu H, Shen W, Zhang H, Que Y, Huang J. Comprehensive analyses of genetic diversities and population structure of the Guizhou Dong group based on 44 Y-markers. PeerJ 2023; 11:e16183. [PMID: 37780380 PMCID: PMC10538297 DOI: 10.7717/peerj.16183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 09/05/2023] [Indexed: 10/03/2023] Open
Abstract
Background The non-recombining region of the human Y chromosome (NRY) is a strictly paternally inherited genetic marker and the best material to trace the paternal lineages of populations. Y chromosomal short tandem repeat (Y-STR) is characterized by high polymorphism and paternal inheritance pattern, so it has been widely used in forensic medicine and population genetic research. This study aims to understand the genetic distribution of Y-STRs in the Guizhou Dong population, provide reference data for forensic application, and explore the phylogenetic relationships between the Guizhou Dong population and other comparison populations. Methods Based on the allele profile of 44 Y-markers in the Guizhou Dong group, we estimate their allele frequencies and haplotype frequencies. In addition, we also compare the forensic application efficiency of different Y-STR sets in the Guizhou Dong group. Finally, genetic relationships among Guizhou Dong and other reference populations are dissected by the multi-dimensional scaling and the phylogenetic tree. Results A total of 393 alleles are observed in 312 Guizhou Dong individuals for these Y-markers, with allele frequencies ranging from 0.0032 to 0.9679. The haplotype diversity and discriminatory capacity for these Y-markers in the Guizhou Dong population are 0.99984 and 0.97440, respectively. The population genetic analyses of the Guizhou Dong group and other reference populations show that the Guizhou Dong group has the closest genetic relationship with the Hunan Dong population, and followed by the Guizhou Tujia population. Conclusions In conclusion, these 44 Y-markers can be used as an effective tool for male differentiation in the Guizhou Dong group. The haplotype data in this study not only enrich the Y-STR data of different ethnic groups in China, but also have important significance for population genetics and forensic research.
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Affiliation(s)
- Hongling Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Xiaolan Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Xiaoye Jin
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Zheng Ren
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Qiyan Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Meiqing Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Ronglan Xu
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Xiang Yuan
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Daiquan Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Hongyan Liu
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Wanyi Shen
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Huiying Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Yangjie Que
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Jiang Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
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Almohammed EK, Hadi A, Al-Asmakh M, Lazim H. The Qatari population's genetic structure and gene flow as revealed by the Y chromosome. PLoS One 2023; 18:e0290844. [PMID: 37656680 PMCID: PMC10473524 DOI: 10.1371/journal.pone.0290844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 08/16/2023] [Indexed: 09/03/2023] Open
Abstract
The Y-chromosome has been widely used in forensic genetic applications and human population genetic studies due to its uniparental origins. A large database on the Qatari population was created for comparison with other databases from the Arabian Peninsula, the Middle East, and Africa. We provide a study of 23 Y-STR loci included in PowerPlex Y23 (Promega, USA) that were genotyped to produce haplotypes in 379 unrelated males from Qatar, a country at the crossroads of migration patterns. Overall, the most polymorphic locus provided by the Promega kit was DYS458, with a genetic diversity value of 0.85 and a haplotype diversity of 0.998924. Athey's Haplogroup Predictor tool was used to predict haplogroups from Y-STR haplotypes in the Qatari population. In a median-joining network, the haplogroup J1 predominance (49%) in Qatar generated a star-like expansion cluster. The graph of population Q-matrix was developed using Y-STR data from 38 Middle Eastern and 97 African populations (11,305 individuals), and it demonstrated a stronger sub-grouping of countries within each ethnic group and showed the effect of Arabs on the indigenous Berbers of North Africa. The estimated migration rate between the Qatari and other Arabian populations was inferred using Bayesian coalescence theory in the Migrate-n program. According to the Gene Flow study, the main migration route was from Yemen to Kuwait through Qatar. Our research, using the PowerPlex Y23 database, shows the importance of gene diversity, as well as regional and social structuring, in determining the utility of demographic and forensic databases.
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Affiliation(s)
- Eida Khalaf Almohammed
- Ministry of Interior of Qatar, Doha, Qatar
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha, Qatar
| | - Abdullah Hadi
- University of Central Lancashire Medical School, Preston, United Kingdom
| | - Maha Al-Asmakh
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha, Qatar
| | - Hayder Lazim
- School of Medicine, Faculty of Health, Social Care and Medicine (FHSCM), Edge Hill University, Ormskirk, United Kingdom
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Sala A, Caputo M, Corach D. Three mutations at a Y-STR haplotype defy a paternal half-brothers kinship case analysis. Int J Legal Med 2023; 137:1017-1022. [PMID: 37209137 DOI: 10.1007/s00414-023-03027-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/16/2023] [Indexed: 05/22/2023]
Abstract
This work presents the results of a DNA test aimed to determine a possible biological link of paternal half brotherhood of two males. The combined use of biparentally inherited markers (autosomal STRs) and a panel of 27 Y-STRs allowed us to determine the existence of a biological relationship of kinship, even after detecting three mutations at their Y-STR haplotypes along the analyses, constituting an infrequent multiple mutation situation. This case is an example illustrating the importance of having different analytical markers sets and strategies for clarifying complex kinship cases where mutations occur.
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Affiliation(s)
- A Sala
- Facultad de Farmacia y Bioquímica- Departamento de Microbiología, Inmunología, Biotecnología y Genética. Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas, Universidad de Buenos Aires, Junín 956, 1113, Ciudad Autónoma de Buenos Aires, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas-CONICET, Godoy Cruz 2290, C1425FQB, Ciudad Autónoma de Buenos Aires, Argentina.
| | - M Caputo
- Facultad de Farmacia y Bioquímica- Departamento de Microbiología, Inmunología, Biotecnología y Genética. Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas, Universidad de Buenos Aires, Junín 956, 1113, Ciudad Autónoma de Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas-CONICET, Godoy Cruz 2290, C1425FQB, Ciudad Autónoma de Buenos Aires, Argentina
| | - D Corach
- Facultad de Farmacia y Bioquímica- Departamento de Microbiología, Inmunología, Biotecnología y Genética. Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas, Universidad de Buenos Aires, Junín 956, 1113, Ciudad Autónoma de Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas-CONICET, Godoy Cruz 2290, C1425FQB, Ciudad Autónoma de Buenos Aires, Argentina
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13
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Antão-Sousa S, Pinto N, Rende P, Amorim A, Gusmão L. The sequence of the repetitive motif influences the frequency of multistep mutations in Short Tandem Repeats. Sci Rep 2023; 13:10251. [PMID: 37355683 PMCID: PMC10290632 DOI: 10.1038/s41598-023-32137-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 03/23/2023] [Indexed: 06/26/2023] Open
Abstract
Microsatellites, or Short Tandem Repeats (STRs), are subject to frequent length mutations that involve the loss or gain of an integer number of repeats. This work aimed to investigate the correlation between STRs' specific repetitive motif composition and mutational dynamics, specifically the occurrence of single- or multistep mutations. Allelic transmission data, comprising 323,818 allele transfers and 1,297 mutations, were gathered for 35 Y-chromosomal STRs with simple structure. Six structure groups were established: ATT, CTT, TCTA/GATA, GAAA/CTTT, CTTTT, and AGAGAT, according to the repetitive motif present in the DNA leading strand of the markers. Results show that the occurrence of multistep mutations varies significantly among groups of markers defined by the repetitive motif. The group of markers with the highest frequency of multistep mutations was the one with repetitive motif CTTTT (25% of the detected mutations) and the lowest frequency corresponding to the group with repetitive motifs TCTA/GATA (0.93%). Statistically significant differences (α = 0.05) were found between groups with repetitive motifs with different lengths, as is the case of TCTA/GATA and ATT (p = 0.0168), CTT (p < 0.0001) and CTTTT (p < 0.0001), as well as between GAAA/CTTT and CTTTT (p = 0.0102). The same occurred between the two tetrameric groups GAAA/CTTT and TCTA/GATA (p < 0.0001) - the first showing 5.7 times more multistep mutations than the second. When considering the number of repeats of the mutated paternal alleles, statistically significant differences were found for alleles with 10 or 12 repeats, between GATA and ATT structure groups. These results, which demonstrate the heterogeneity of mutational dynamics across repeat motifs, have implications in the fields of population genetics, epidemiology, or phylogeography, and whenever STR mutation models are used in evolutionary studies in general.
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Affiliation(s)
- Sofia Antão-Sousa
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal.
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.
- Department of Biology, Faculty of Sciences of University of Porto (FCUP), Porto, Portugal.
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil.
| | - Nádia Pinto
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- Center of Mathematics of University of Porto (CMUP), Porto, Portugal
| | - Pablo Rende
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Department of Biology, Faculty of Sciences of University of Porto (FCUP), Porto, Portugal
| | - António Amorim
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- Department of Biology, Faculty of Sciences of University of Porto (FCUP), Porto, Portugal
| | - Leonor Gusmão
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
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14
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Liu Z, Long G, Lang Y, Liu D, Zhang B, Yu S, Guo F. Sequence-based mutation patterns at 41 Y chromosomal STRs in 2 548 father-son pairs. Forensic Sci Res 2023; 8:152-162. [PMID: 37621447 PMCID: PMC10445670 DOI: 10.1093/fsr/owad016] [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: 03/25/2022] [Accepted: 06/16/2023] [Indexed: 08/26/2023] Open
Abstract
A total of 2 548 unrelated healthy father-son pairs from a Northern Han Chinese population were genotyped at 41 Y chromosomal short tandem repeat (Y-STRs) including DYS19, DYS388, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS444, DYS447, DYS448, DYS449, DYS456, DYS458, DYS460, DYS481, DYS518, DYS522, DYS549, DYS533, DYS557, DYS570, DYS576, DYS593, DYS596, DYS627, DYS635, DYS643, DYS645, Y-GATA-H4, DYF387S1a/b, DYF404S1a/b, DYS385a/b, and DYS527a/b. In 2 548 father samples, 2 387 unique haplotypes were detected with the haplotype diversity and discrimination capacity values of 0.999 956 608 and 0.96 741 007. The average gene diversity (GD) value was 0.6934 with a range from 0.1051 at DYS645 to 0.9657 at DYS385a/b. When comparing alleles at 24 overlapped Y-STRs between the ForenSeq™ deoxyribonucleic acid (DNA) Signature Prep Kit on the MiSeq FGx® Forensic Genomics System and the Goldeneye® DNA ID Y Plus Kit on the Applied Biosystems™ 3730 DNA Analyzer from 308 father samples in mutational pairs, 258 alleles were detected by massively parallel sequencing (MPS) typing including 156 length-based alleles that could be obtained by capillary electrophoresis (CE) typing, 95 repeat region (RR) variant alleles and seven flanking region variant alleles. Hereof, we found 16 novel RR variant alleles and firstly identified two SNPs (rs2016239814 at DYS19 and rs2089968964 at DYS448) and one 4-bp deletion (rs2053269960 at DYS439) that had been validated by the Database of Short Genetic Variation. Sanger sequencing or MPS was employed to confirm 356 mutations from 104 468 allele transfers generated from CE, where 96.63% resulted in one-step mutations, 2.25% in two-step, and 1.12% in multi-step, and the overall ratio of repeat gains versus losses was balanced (173 gains vs. 183 losses). In 308 father-son pairs, 268 pairs occurred mutations at a single locus, 33 pairs at two loci, six pairs at three loci, and one pair at four loci. The average Y-STR mutation rate at 41 Y-STRs was ⁓3.4 × 10-3 (95% confidence intervals: 3.1 × 10-3-3.8 × 10-3). The mutation rates at DYS576 and DYS627 were higher than 1 × 10-2 in Northern Han Chinese, whilst the mutation rates at DYF387S1a/b, DYF404S1a/b, DYS449, DYS518, and DYS570 were lower than initially defined. In this study, the classical molecular factors (the longer STR region, the more complex motif and the order father) were confirmed to drive Y-STR mutation rates increased, but the length of repeat unit did not conform to the convention. Lastly, the interactive graphical and installable StatsY was developed to facilitate forensic scientists to automatically calculate allele and haplotype frequencies, forensic parameters, and mutation rates at Y-STRs. Key points 308 of 2 548 father-son pairs from Northern Han Chinese occurred at least one mutation(s) across 41 Y-STRs.Sanger sequencing or MPS was employed to confirm those mutations generated from CE.The longer STR region, the more complex motif and the order father drove Y-STR mutation rates increased.StatsY was developed to calculate allele and haplotype frequencies, forensic parameters and mutation rates at Y-STRs.
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Affiliation(s)
- Ze Liu
- DNA Laboratory of Forensic Science Center, Shenyang Public Security Bureau, Shenyang, China
| | - Guannan Long
- DNA Laboratory of Forensic Science Center, Shenyang Public Security Bureau, Shenyang, China
| | - Yubo Lang
- School of Public Security Information Technology and Intelligence, Criminal Investigation Police University of China, Shenyang, China
| | - Dahua Liu
- Department of Forensic Medicine, Jinzhou Medical University, Jinzhou, China
| | - Biao Zhang
- DNA Laboratory of Forensic Science Center, Shenyang Public Security Bureau, Shenyang, China
| | - Shaobo Yu
- DNA Laboratory of Forensic Science Center, Shenyang Public Security Bureau, Shenyang, China
| | - Fei Guo
- School of Forensic Science and Technology, Criminal Investigation Police University of China, Shenyang, China
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15
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Chai S, Li M, Tao R, Xia R, Kong Q, Qu Y, Chen L, Liu S, Li C, Chen P, Zhang S. Internal validation of an improved system for forensic application: a 41-plex Y-STR panel. Forensic Sci Res 2023; 8:70-78. [PMID: 37415794 PMCID: PMC10265952 DOI: 10.1093/fsr/owad012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 03/22/2023] [Indexed: 07/08/2023] Open
Abstract
Y-chromosome short tandem repeats (Y-STRs) have a unique role in forensic investigation. However, low-medium mutating Y-STRs cannot meet the requirements for male lineage differentiation in inbred populations, whereas rapidly mutating (RM) high-resolution Y-STRs might cause unexpected exclusion of paternal lineages. Thus, combining Y-STRs with low and high mutation rates helps to distinguish male individuals and lineages in family screening and analysis of genetic relationships. In this study, a novel 6-dye, 41-plex Y-STR panel was developed and validated, which included 17 loci from the Yfiler kit, nine RM Y-STR loci, 15 low-medium mutating Y-STR loci, and three Y-InDels. Developmental validation was performed for this panel, including size precision testing, stutter analysis, species specificity analysis, male specificity testing, sensitivity testing, concordance evaluation, polymerase chain reaction inhibitors analysis, and DNA mixture examination. The results demonstrated that the novel 41-plex Y-STR panel, developed in-house, was time efficient, accurate, and reliable. It showed good adaptability to directly amplify a variety of case-type samples. Furthermore, adding multiple Y-STR loci significantly improved the system's ability to distinguish related males, making it highly informative for forensic applications. In addition, the data obtained were compatible with the widely used Y-STR kits, facilitating the search and construction of population databases. Moreover, the addition of Y-Indels with short amplicons improves the analyses of degraded samples. Key Points A novel multiplex comprising 41 Y-STR and 3 Y-InDel was developed for forensic application.The multiplex included rapidly mutating Y-STRs and low-medium mutating Y-STRs, which is compatible with many commonly used Y-STR kits.The multiplex is a powerful tool for distinguishing related males, familial searching, and constructing DNA databases.
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Affiliation(s)
| | | | - Ruiyang Tao
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, China, Shanghai, China
| | - Ruocheng Xia
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, China, Shanghai, China
| | - Qianqian Kong
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, China, Shanghai, China
- Department of Forensic Medicine, Inner Mongolia Medical University, Hohhot, China
| | - Yiling Qu
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, China, Shanghai, China
- Department of Forensic Science, Medical School of Soochow University, Suzhou, China
| | - Liqin Chen
- Department of Forensic Medicine, Inner Mongolia Medical University, Hohhot, China
| | - Shiquan Liu
- Institute of Evidence Law and Forensic Science, China University of Political Science and Law, Beijing, China
| | - Chengtao Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, China, Shanghai, China
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张 世, 蹇 慧, 王 倩, 王 威, 丁 艳, 张 宵, 徐 冬, 杜 冰, 金 波. [Polymorphism and Mutation Rate of 20 Rapidly Mutating Y-Chromosomal Short Tandem Repeats in Chinese Han Population of Sichuan Province]. SICHUAN DA XUE XUE BAO. YI XUE BAN = JOURNAL OF SICHUAN UNIVERSITY. MEDICAL SCIENCE EDITION 2023; 54:367-373. [PMID: 36949700 PMCID: PMC10409182 DOI: 10.12182/20230260308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Indexed: 03/24/2023]
Abstract
Objective To explore the applicability of 20 rapidly mutating Y-chromosomal short tandem repeats (RM Y-STRs) in Chinese Han population of Sichuan province. Methods Two RM Y-STR multiple amplification systems (RM1, including DYF404S1, DYF399S1, DYS547, DYS526a/b, DYS626, DYF403S1a/b, and DYS612, and RM2, including DYS1003, DYS1007, DYR88, DYS712, DYS711, DYS724, and DYF1002, with 14 RM Y-STR loci in total) and Y41SE-V1.2 (including 6 RM Y-STR loci of DYS627, DYS576, DYF387S1, DYS518, DYS570, and DYS449, 30 ordinary Y-chromosomal short tandem repeats [Y-STR] loci, and 1 Indel locus) were used for the amplification and typing of 200 unrelated males and 260 father-son pairs. The polymorphisms and mutation rates of 20 RM Y-STRs and 30 ordinary Y-STRs in Chinese Han population of Sichuan province were investigated and compared. Results In the 200 unrelated males, the gene diversity (GD) of 20 RM Y-STR loci ranged from 0.7910 to 0.9975, and there were 200 haplotypes. Haplotype diversity (HD) was 1 and the discriminative capacity (DC) was 1. A total of 198 haplotypes were found in Y41se-v1.2 (the 30 Y-STRs), with 4 cases sharing two haplotypes, the haplotype diversity being 0.9999, and the discriminative capacity being 0.99. A total of 68 mutations were found at the 20 RM Y-STRs loci in the 260 father-son pairs, and there was slightly more increase than decrease of allele repeats (1.19∶1), with the mutation rate ranging from <3.85×10 -3 (95% C I: 0.00-1.41×10 -2) to 2.69×10 -2 (95% CI: 1.09×10 -2-5.47×10 -2), and the average mutation rate being 1.19×10 -2 (95% CI: 9.20×10 -3-1.51×10 -2). The 20 RM Y-STRs and the Y41SE-V1.2 (the 30 Y-STRs) could be used to distinguish 22.3% and 13.8% father-son pairs, respectively. Conclusion The 20 RM Y-STRs have high gene and haplotype diversity and paternal lineage differentiation rate in Chinese Han population of Sichuan province, showing great potential for application in Chinese Han population of Sichuan province.
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Affiliation(s)
- 世林 张
- 川北医学院基础医学与法医学研究所 (南充 637000)Institute of Basic Medicine Sciences and Forensic Medicine, North Sichuan Medical College, Nanchong 637000, China
| | - 慧 蹇
- 川北医学院基础医学与法医学研究所 (南充 637000)Institute of Basic Medicine Sciences and Forensic Medicine, North Sichuan Medical College, Nanchong 637000, China
| | - 倩 王
- 川北医学院基础医学与法医学研究所 (南充 637000)Institute of Basic Medicine Sciences and Forensic Medicine, North Sichuan Medical College, Nanchong 637000, China
| | - 威 王
- 川北医学院基础医学与法医学研究所 (南充 637000)Institute of Basic Medicine Sciences and Forensic Medicine, North Sichuan Medical College, Nanchong 637000, China
| | - 艳杰 丁
- 川北医学院基础医学与法医学研究所 (南充 637000)Institute of Basic Medicine Sciences and Forensic Medicine, North Sichuan Medical College, Nanchong 637000, China
| | - 宵 张
- 川北医学院基础医学与法医学研究所 (南充 637000)Institute of Basic Medicine Sciences and Forensic Medicine, North Sichuan Medical College, Nanchong 637000, China
| | - 冬冬 徐
- 川北医学院基础医学与法医学研究所 (南充 637000)Institute of Basic Medicine Sciences and Forensic Medicine, North Sichuan Medical College, Nanchong 637000, China
| | - 冰 杜
- 川北医学院基础医学与法医学研究所 (南充 637000)Institute of Basic Medicine Sciences and Forensic Medicine, North Sichuan Medical College, Nanchong 637000, China
| | - 波 金
- 川北医学院基础医学与法医学研究所 (南充 637000)Institute of Basic Medicine Sciences and Forensic Medicine, North Sichuan Medical College, Nanchong 637000, China
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17
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Ashirbekov Y, Nogay A, Abaildayev A, Zhunussova A, Sabitov Z, Zhabagin M. Genetic polymorphism of 27 Y-STR loci in Kazakh populations from Eastern Kazakhstan. Ann Hum Biol 2023; 50:48-51. [PMID: 36650935 DOI: 10.1080/03014460.2023.2170465] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
BACKGROUND The establishment of a national haplotype database is important for forensic and genetic applications and requires studying genetic polymorphisms at Y-STR sites. However, the genetic structure of the Eastern Kazakhstan population is poorly characterised. AIM To investigate the genetic polymorphisms of 27 Y-STR loci in the Kazakh population from Eastern Kazakhstan and analyse the population genetic relationships of the Eastern Kazakhs with other populations. SUBJECTS AND METHODS The Yfiler Plus kit was utilised to genotype 246 healthy, unrelated males from Eastern Kazakhstan. Based on the raw data, haplotype and allele frequencies along with forensic parameters were calculated, and an MDS plot was constructed. RESULTS A total of 207 haplotypes were detected, of which 186 were unique. The haplotype diversity and discrimination capacity were 0.997 and 0.841, respectively. Population comparisons showed that Eastern Kazakhs have close genetic relationships with Kazakhs from Xinjiang, China. At the same time, a difference was found between the studied population and the previous one in the same part of Kazakhstan. CONCLUSIONS The obtained haplotypes will help to expand the Kazakhstan Y-chromosome reference database and will be useful for future genetic research and forensic applications.
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Affiliation(s)
- Yeldar Ashirbekov
- M. Aitkhozhin Institute of Molecular Biology and Biochemistry, Almaty, Republic of Kazakhstan
| | - Anastassiya Nogay
- National Center for Biotechnology, Astana, Republic of Kazakhstan.,School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan
| | - Arman Abaildayev
- M. Aitkhozhin Institute of Molecular Biology and Biochemistry, Almaty, Republic of Kazakhstan
| | - Aigul Zhunussova
- National Center for Biotechnology, Astana, Republic of Kazakhstan
| | - Zhaxylyk Sabitov
- National Center for Biotechnology, Astana, Republic of Kazakhstan.,L.N. Gumilyov Eurasian National University, Astana, Republic of Kazakhstan.,Research Institute for Jochi Ulus Studies, Astana, Republic of Kazakhstan
| | - Maxat Zhabagin
- National Center for Biotechnology, Astana, Republic of Kazakhstan
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18
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Xu C, Wei W, Zuo M, Zuo W, Li K, Lian X, Wang S, Zhou X, Zhang X, Zhong S. Genetic polymorphisms and phylogenetic characteristics of Tibeto-Burman-speaking Lahu population from southwest China based on 41 Y-STR loci. Ann Hum Biol 2023; 50:75-81. [PMID: 36688851 DOI: 10.1080/03014460.2023.2171123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
BACKGROUND Male sex-linked Y-chromosome short tandem repeats (Y-STRs) have been widely used in forensic cases and population genetics research. At present, the forensic-related Y-STR data in the Chinese Lahu population are still poorly understood. AIM To enrich the available Y-STR data of this Chinese minority population and investigate its phylogenetic relationships with other reported populations. SUBJECTS AND METHODS The genetic polymorphisms of 41 Y-STR loci were analysed in 299 unrelated healthy Lahu male individuals from Southwest China. Phylogenetic analyses were performed by multidimensional scaling analysis and neighbor-joining phylogenetic tree construction. RESULTS A total of 379 alleles were observed at the 41 Y-STR loci. The allele frequencies ranged from 0.0033 to 0.9666. The genetic diversity values ranged from 0.0653 to 0.9072. A total of 254 different haplotypes of the 41 Y-STR loci were observed in 299 individuals. The values of haplotype diversity, haplotype match probability, and discrimination capacity were 0.9987, 0.0047, and 0.8495, respectively. The phylogenetic analysis indicated that the Tibeto-Burman-speaking Lahu population showed a close genetic relationship with the Yunnan Yi population. CONCLUSIONS The haplotype data of the present study can enrich the forensic databases of this Chinese minority population and will be useful for population genetics and forensic DNA application.
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Affiliation(s)
- Chongchong Xu
- School of Forensic Medicine, Kunming Medical University, Kunming, China
| | - Wei Wei
- School of Forensic Medicine, Kunming Medical University, Kunming, China
| | - Mingxin Zuo
- School of Forensic Medicine, Kunming Medical University, Kunming, China
| | - Wu Zuo
- Institute of Criminal Science and Technology, Yuxi Municipal Public Security Bureau, Yuxi, China
| | - Kuan Li
- School of Forensic Medicine, Kunming Medical University, Kunming, China
| | - Xinqing Lian
- School of Forensic Medicine, Kunming Medical University, Kunming, China
| | - Shixu Wang
- School of Forensic Medicine, Kunming Medical University, Kunming, China
| | - Xuemei Zhou
- School of Forensic Medicine, Kunming Medical University, Kunming, China
| | - Xiufeng Zhang
- School of Forensic Medicine, Kunming Medical University, Kunming, China.,Judicial Expertise Center of Kunming Medical University, Kunming, China
| | - Shurong Zhong
- School of Forensic Medicine, Kunming Medical University, Kunming, China.,Judicial Expertise Center of Kunming Medical University, Kunming, China
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19
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Zhang X, Zheng H, Liu C. Genetic diversity of 23 Y-STR loci of the Lisu ethnic minority residing in Chuxiong Yi Autonomous Prefecture, Yunnan province, Southwest China. Ann Hum Biol 2023; 50:356-359. [PMID: 37523197 DOI: 10.1080/03014460.2023.2224972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/17/2023] [Accepted: 05/30/2023] [Indexed: 08/01/2023]
Abstract
BACKGROUND The Lisu group is a unique minority in Yunnan province. However, there is a lack of Y-STR population data for Chinese Lisu and the genetic structure of the Lisu group and other populations is unclear. AIM To provide genetic data for 23 Y-STRs in the Chinese Lisu population from Chuxiong Yi Autonomous Prefecture, as well as to analyse population genetic relationships between Chinese Lisu ethnic minority and other reference groups. SUBJECTS AND METHODS 423 unrelated healthy Lisu males were genotyped using the PowerPlex® Y23 system. Forensic parameters were calculated according to the previously published studies. Genetic structure analysis among Chinese Lisu and other populations was conducted using the YHRD's AMOVA tools. RESULTS Gene diversity (GD) ranged from 0.2,466 (DYS438) to 0.8,945 (DYS385a/b) among the 23 Y-STR loci. According to haplotype analysis, 323 different haplotypes were obtained, out of which 271 were unique. The haplotype diversity (HD) and discrimination capacity (DC) were 0.9,977 and 0.7,636, respectively. MDS plot indicated that the Chuxiong Lisu group is genetically related to the Yunnan Yi group. CONCLUSIONS This is the first report on Y-STR population data for the Chinese Lisu population. These data would be valuable for forensic applications.
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Affiliation(s)
- Xiufeng Zhang
- School of Forensic Medicine, Kunming Medical University, Kunming, Yunnan Province, China
- Judicial Expertise Center, Kunming Medical University, Kunming, Yunnan Province, China
| | - Hecheng Zheng
- Chuxiong Public Security Bureau, Chuxiong, Yunnan Province, China
| | - Chengjing Liu
- Chuxiong Public Security Bureau, Chuxiong, Yunnan Province, China
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20
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Tao R, Li M, Chai S, Xia R, Qu Y, Yuan C, Yang G, Dong X, Bian Y, Zhang S, Li C. Developmental validation of a 381 Y-chromosome SNP panel for haplogroup analysis in the Chinese populations. Forensic Sci Int Genet 2023; 62:102803. [PMID: 36368220 DOI: 10.1016/j.fsigen.2022.102803] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 09/19/2022] [Accepted: 10/26/2022] [Indexed: 01/15/2023]
Abstract
Y-chromosome single nucleotide polymorphism (Y-SNP) shows great variation in geographical distribution and population heterogeneity and can be used to map population genetics around the world. Massive parallel sequencing (MPS) methodology enables high-resolution Y-SNP haplogrouping for a certain male and is widely used in forensic genetics and evolutionary studies. In this present study, we used MPS to develop a customized 381 Y-SNP panel (SifaMPS 381 Y-SNP panel) to investigate the basic structure and subbranches of the haplogroup tree of the Chinese populations. The SifaMPS 381 Y-SNP panel covers all the Y-SNPs from our previously designed 183 Y-SNP panel and additional SNPs under the predominant haplogroups in the Chinese populations based on certain criteria. We also evaluated the sequencing matrix, concordance, sensitivity, repeatability of this panel and the ability to analyze mixed and case-type samples based on the Illumina MiSeq System. The results demonstrated that the novel MPS Y-SNP panel possessed good sequencing performance and generated accurate Y-SNP genotyping results. Although the recommended DNA input was greater than 1.25 ng, we observed that a lower DNA amount could still be used to analyze haplogroups correctly. In addition, this panel could handle mixed samples and common case-type samples and had higher resolution among Chinese Han males than previously reported. In conclusion, the SifaMPS 381 Y-SNP panel showed an overall good performance and offers a better choice for Y-SNP haplogrouping of the Chinese population, thereby facilitating paternal lineage classification, familial searching and other forensic applications.
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Affiliation(s)
- Ruiyang Tao
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, P.R. China, Shanghai 200063, China
| | - Min Li
- School of Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250117, Shandong, China
| | - Siyu Chai
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, P.R. China, Shanghai 200063, China; Department of Forensic Medicine, Zunyi Medical University, Zunyi 563099, Guizhou, China
| | - Ruocheng Xia
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, P.R. China, Shanghai 200063, China
| | - Yiling Qu
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, P.R. China, Shanghai 200063, China; Department of Forensic Science, Medical School of Soochow University, Suzhou 215123, China
| | - Chunyan Yuan
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, P.R. China, Shanghai 200063, China; Department of Forensic Medicine, Inner Mongolia Medical University, Hohhot 010110, China
| | - Guangyuan Yang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, P.R. China, Shanghai 200063, China; Department of Forensic Medicine, Inner Mongolia Medical University, Hohhot 010110, China
| | - Xinyu Dong
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, P.R. China, Shanghai 200063, China; School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Yingnan Bian
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, P.R. China, Shanghai 200063, China
| | - Suhua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, P.R. China, Shanghai 200063, China.
| | - Chengtao Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, P.R. China, Shanghai 200063, China.
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21
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Grosjean F, Favre M, Castella V. Comparison between MACSprep™ forensic sperm microbead kit and Erase Sperm Isolation kit for the enrichment of sperm fractions recovered from sexual assault samples. Int J Legal Med 2023; 137:267-278. [PMID: 35773355 PMCID: PMC9816209 DOI: 10.1007/s00414-022-02861-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 06/21/2022] [Indexed: 01/11/2023]
Abstract
Sexual assault samples often contain mixtures of cells coming from at least two donors. Ideally, one would need to separate the cells into two cellular fractions: one consisting of the alleged aggressor's spermatozoa (the sperm fraction) and the other containing the victim's epithelial cells (the non-sperm fraction). This separation increases the probability of obtaining the alleged offender's autosomal DNA profile. However, spermatozoa are often collected along with an excess of biological material originating from the victim, and with unfavorable male:female biological material ratios, the absence of separation could result in the PCR amplification of the victim's DNA profile only. Several approaches are available to enrich/purify the spermatozoa present on sexual assault samples. In this paper, we compare a new method, the MACSprep™ Forensic Sperm MicroBead Kit (MACSprep, based on microbeads conjugated with antibodies bound to spermatozoa and their retention within a magnetic column) with the Erase Sperm Isolation Kit (Erase, a standard differential lysis separation procedure combined with a specific removal of free DNA) routinely used in our lab. The performance of both kits was tested using sets of vaginal and buccal swabs loaded with different dilutions of sperm, or azoospermic semen, representing a total of 120 independent samples. For the samples containing undiluted sperm, an average recovery of 58% was observed for the MACSprep's sperm fractions and 43% for Erase's. Significantly better recovery of azoospermic semen was observed in MACSprep's non-sperm fractions (~ 85%) compared to Erase (~ 28%). Erase performed significantly better than MACSprep in terms of recovery for diluted sperm samples (1:10 to 1:800 sperm dilutions) in the presence of vaginal cells, while the purities of the achieved sperm fractions were in favor of MACSprep for the highest sperm dilutions tested. Similar trends were observed with buccal swabs loaded with 1:200 sperm dilutions. Increased sperm dilutions on vaginal swabs resulted in higher variability in the male material recovered, whatever the separation method used. Both methods were easy to perform and resulted in male DNA extracts ready to use in less than 2 h. Both kits showed their specificities in terms of recovery efficiency and purity of the sperm fractions. Ideally, additional experiments should be performed in different laboratories, using workflow and chemistries different than ours, to better define the peculiarities observed with MACSprep for high dilutions. Improving the recovery of MACSprep for diluted samples, in addition to its better purity observed in the experiments performed, could make it a method of choice for laboratory workflow, despite MACSprep's current price per sample being about twice the price of Erase's.
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Affiliation(s)
- Frederic Grosjean
- grid.411686.c0000 0004 0511 8059Forensic Genetics Unit, University Center of Legal Medicine, Lausanne – Geneva, Lausanne University Hospital and University of Lausanne, Chemin de la Vulliette 4, 1000 Lausanne 25, Switzerland
| | - Marylou Favre
- grid.411686.c0000 0004 0511 8059Forensic Genetics Unit, University Center of Legal Medicine, Lausanne – Geneva, Lausanne University Hospital and University of Lausanne, Chemin de la Vulliette 4, 1000 Lausanne 25, Switzerland
| | - Vincent Castella
- grid.411686.c0000 0004 0511 8059Forensic Genetics Unit, University Center of Legal Medicine, Lausanne – Geneva, Lausanne University Hospital and University of Lausanne, Chemin de la Vulliette 4, 1000 Lausanne 25, Switzerland
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22
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Steely CJ, Watkins WS, Baird L, Jorde LB. The mutational dynamics of short tandem repeats in large, multigenerational families. Genome Biol 2022; 23:253. [PMID: 36510265 PMCID: PMC9743774 DOI: 10.1186/s13059-022-02818-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 11/17/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Short tandem repeats (STRs) compose approximately 3% of the genome, and mutations at STR loci have been linked to dozens of human diseases including amyotrophic lateral sclerosis, Friedreich ataxia, Huntington disease, and fragile X syndrome. Improving our understanding of these mutations would increase our knowledge of the mutational dynamics of the genome and may uncover additional loci that contribute to disease. To estimate the genome-wide pattern of mutations at STR loci, we analyze blood-derived whole-genome sequencing data for 544 individuals from 29 three-generation CEPH pedigrees. These pedigrees contain both sets of grandparents, the parents, and an average of 9 grandchildren per family. RESULTS We use HipSTR to identify de novo STR mutations in the 2nd generation of these pedigrees and require transmission to the third generation for validation. Analyzing approximately 1.6 million STR loci, we estimate the empirical de novo STR mutation rate to be 5.24 × 10-5 mutations per locus per generation. Perfect repeats mutate about 2 × more often than imperfect repeats. De novo STRs are significantly enriched in Alu elements. CONCLUSIONS Approximately 30% of new STR mutations occur within Alu elements, which compose only 11% of the genome, but only 10% are found in LINE-1 insertions, which compose 17% of the genome. Phasing these mutations to the parent of origin shows that parental transmission biases vary among families. We estimate the average number of de novo genome-wide STR mutations per individual to be approximately 85, which is similar to the average number of observed de novo single nucleotide variants.
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Affiliation(s)
- Cody J. Steely
- grid.223827.e0000 0001 2193 0096Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112 USA
| | - W. Scott Watkins
- grid.223827.e0000 0001 2193 0096Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112 USA
| | - Lisa Baird
- grid.223827.e0000 0001 2193 0096Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112 USA
| | - Lynn B. Jorde
- grid.223827.e0000 0001 2193 0096Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112 USA
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23
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He G, Adnan A, Al-Qahtani WS, Safhi FA, Yeh HY, Hadi S, Wang CC, Wang M, Liu C, Yao J. Genetic admixture history and forensic characteristics of Tibeto-Burman-speaking Qiang people explored via the newly developed Y-STR panel and genome-wide SNP data. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.939659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Fine-scale patterns of population genetic structure and diversity of ethnolinguistically diverse populations are important for biogeographical ancestry inference, kinship testing, and development and validation of new kits focused on forensic personal identification. Analyses focused on forensic markers and genome-wide single nucleotide polymorphism (SNP) data can provide new insights into the origin, admixture processes, and forensic characteristics of targeted populations. Qiang people had a large sample size among Tibeto-Burmanspeaking populations, which widely resided in the middle latitude of the Tibetan Plateau. However, their genetic structure and forensic features have remained uncharacterized because of the paucity of comprehensive genetic analyses. Here, we first developed and validated the forensic performance of the AGCU-Y30 Y-short tandem repeats (STR) panel, which contains slowly and moderately mutating Y-STRs, and then we conducted comprehensive population genetic analyses based on Y-STRs and genome-wide SNPs to explore the admixture history of Qiang people and their neighbors. The validated results of this panel showed that the new Y-STR kit was sensitive and robust enough for forensic applications. Haplotype diversity (HD) ranging from 0.9932 to 0.9996 and allelic frequencies ranging from 0.001946 to 0.8326 in 514 Qiang people demonstrated that all included markers were highly polymorphic in Tibeto-Burman people. Population genetic analyses based on Y-STRs [RST, FST, multidimensional scaling (MDS) analysis, neighboring-joining (NJ) tree, principal component analysis (PCA), and median-joining network (MJN)] revealed that the Qiang people harbored a paternally close relationship with lowland Tibetan-Yi corridor populations. Furthermore, we conducted a comprehensive population admixture analysis among modern and ancient Eurasian populations based on genome-wide shared SNPs. We found that the Qiang people were a genetically admixed population and showed closest relationship with Tibetan and Neolithic Yellow River farmers. Admixture modeling showed that Qiang people shared the primary ancestry related to Tibetan, supporting the hypothesis of common origin between Tibetan and Qiang people from North China.
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24
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Zhou Y, Cui W, Wu B, Zhu B. Development and validation of a new multiplex Y-STR panel designed to increase the power of discrimination. Electrophoresis 2022; 43:1899-1910. [PMID: 35856743 DOI: 10.1002/elps.202100313] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 03/28/2022] [Accepted: 07/08/2022] [Indexed: 12/14/2022]
Abstract
In an attempt to increase the discrimination capacity (DC) and reduce the adventitious match probability, a 6-dye multiplex Y-chromosomal short tandem repeat (Y-STR) panel named Y34plex was constructed that combined 25 Y-chromosomal markers (DYS456, DYS627, DYS390, DYS570, DYS635, DYS385a/b, DYS448, DYS437, DYS533, DYS449, DYS481, DYS392, DYS391, DYS389I, DYS460, YGATAH4, DYS438, DYS389II, DYS19, DYS458, DYF387S1a/b, DYS439, DYS393, DYS576, and DYS518) in widely used commercial kits, with nine highly polymorphic Y-STR loci (DYS557, DYS527a/b, DYS593, DYS444, DYS596, DYS643, DYS447, DYS549, and DYS645). The Y34plex is a promising type system to distinguish both unrelated and related male individuals due to the incorporation of rapidly mutated Y-STR loci. A validation study of the Y34plex was performed and followed the guidelines of the Scientific Working Group on DNA analysis methods. Results show that full Y-STR profiles were obtained from male/female DNA mixtures with 125 pg of male DNA in the presence of 50 ng of female DNA. The ability to tolerate polymerase chain reaction inhibitors commonly contained in forensic casework samples demonstrated the applicability and robustness of the Y34plex. Compared with the Yfiler Plus kit, the novel panel showed an increased power of discrimination in Chinese Wuxi Han population (n = 434). The overall haplotype diversity of the Y34plex was 0.999606, whereas DC value was 0.956221, which is suitable for use on forensic paternal investigation.
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Affiliation(s)
- Yongsong Zhou
- Shenzhen Stomatology Hospital (Pingshan), Southern Medical University, Shenzhen, P. R. China.,Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Wei Cui
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Buling Wu
- Shenzhen Stomatology Hospital (Pingshan), Southern Medical University, Shenzhen, P. R. China
| | - Bofeng Zhu
- Shenzhen Stomatology Hospital (Pingshan), Southern Medical University, Shenzhen, P. R. China.,Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China.,Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, P. R. China
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25
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Albastaki A, Naji M, Lootah R, Almheiri R, Almulla H, Alreyami A, Almarri I, Yu Z, Zhang Y, Shu C, Alghafri R. Design and development of novel single multiplex system incorporating 26 rapidly mutating Y-STRs; 26 RM Yplex. Electrophoresis 2022; 43:1911-1919. [PMID: 35899438 DOI: 10.1002/elps.202200099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 07/09/2022] [Accepted: 07/14/2022] [Indexed: 01/07/2023]
Abstract
This article details the development of a single multiplex system amplifying 26 rapidly mutating Y-STR markers. A sequenced allelic ladder, constructed for calling alleles of all loci, is introduced. The multiplex system shows the ability to address the limitations of Y-STRs commercial kits in differentiating closely related males. The multiplex performed well in the prevalidation tests and showed great potential to be used in forensic casework.
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Affiliation(s)
- Abdulla Albastaki
- International Center for Forensic Sciences, Dubai Police G.H.Q., Dubai, United Arab Emirates
| | - Mohammed Naji
- International Center for Forensic Sciences, Dubai Police G.H.Q., Dubai, United Arab Emirates
| | - Reem Lootah
- International Center for Forensic Sciences, Dubai Police G.H.Q., Dubai, United Arab Emirates
| | - Reem Almheiri
- International Center for Forensic Sciences, Dubai Police G.H.Q., Dubai, United Arab Emirates
| | - Hanan Almulla
- International Center for Forensic Sciences, Dubai Police G.H.Q., Dubai, United Arab Emirates
| | - Afra Alreyami
- International Center for Forensic Sciences, Dubai Police G.H.Q., Dubai, United Arab Emirates
| | - Iman Almarri
- International Center for Forensic Sciences, Dubai Police G.H.Q., Dubai, United Arab Emirates
| | - Zailiang Yu
- Suzhou Microread Genetics Co., Ltd, Suzhou, P. R. China
| | - Yueke Zhang
- Suzhou Microread Genetics Co., Ltd, Suzhou, P. R. China
| | - Chang Shu
- Beijing Microread Genetics Co., Ltd, Beijing, P. R. China
| | - Rashed Alghafri
- International Center for Forensic Sciences, Dubai Police G.H.Q., Dubai, United Arab Emirates
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26
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Mutation analysis for newly suggested 30 Y-STR loci with high mutation rates in Chinese father-son pairs. Sci Rep 2022; 12:15680. [PMID: 36127390 PMCID: PMC9489694 DOI: 10.1038/s41598-022-20014-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 09/07/2022] [Indexed: 11/08/2022] Open
Abstract
Rapidly mutating Y-STRs (RM Y-STRs) harbor great potential to distinguish male relatives and achieve male identification. However, forensic applications were greatly limited by the small number of the initially identified 14 RM Y-STRs. Recently, with the emergence of 12 novel RM Y-STRs, an integrated panel named RMplex was introduced, which contains all 26 RM Y-STRs and four fast mutating Y-STRs (FM Y-STRs). To obtain the first data on the mutation rates and father-son differentiation rates of the 30 newly proposed Y-STRs in Chinese populations, we performed an empirical mutation study on 307 DNA-confirmed Chinese paternal pairs. Previously reported mutation rates for 14 RM Y-STRs in Chinese and European populations were pooled and merged with our data. The highest meiosis number for the two groups reached 4771 and 2687, respectively. Five loci showed significant differences between the populations (DYS570, DYS399S1, DYS547, DYS612, and DYF403S1b). For the new panel covering 30 Y-STR loci, our results show extensive differences in the mutation rates between the two populations, as well. 10 RM Y-STR loci showed relatively low mutation rates (10-3-10-2 per meiosis) and 2 FM Y-STR loci had rapid mutation rates (> 10-2 per meiosis) in the Chinese population. Several-fold differences in mutation rates were found in nine Y-STR loci between the Chinese and reference populations, with two loci having significantly higher mutation rates and one locus with a significantly lower mutation rate in the Chinese population (P < 0.05). Eighteen RM Y-STRs (> 10-2 per meiosis), 8 FM Y-STR loci (5×10-3-10-2 per meiosis), 3 moderately mutating Y-STRs (MM Y-STRs, 10-3-5×10-3 per meiosis), and one locus with no observed mutation events were identified in the Chinese population. 40.06% of the Chinese paternity pairs were discriminated with RMplex while only 20.84% with the initial 14 RM Y-STRs, indicating that RMplex is beneficial for distinguishing paternally related males. Future studies on populations of different genetic backgrounds are necessary to obtain comprehensive estimates of mutation rates at these new loci.
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27
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Song M, Jiang L, Lyu Q, Ying J, Wang Z, Zhou Y, Song F, Luo H, Song X, Ying B. Developmental validation of the Microreader Group Y Direct ID System: A novel six‐dye typing system with 54 Y‐chromosomal loci for forensic application. Electrophoresis 2022; 43:2023-2032. [DOI: 10.1002/elps.202200109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 07/15/2022] [Accepted: 08/09/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Mengyuan Song
- Department of Laboratory Medicine West China Hospital Sichuan University Chengdu Sichuan P. R. China
| | - Lanrui Jiang
- Department of Forensic Genetics West China School of Basic Medical Sciences & Forensic Medicine Sichuan University Chengdu Sichuan P. R. China
| | - Qiang Lyu
- Department of Clinical Laboratory People's Hospital of Beichuan Qiang Autonomous County Beichuan Sichuan P. R. China
| | - Jun Ying
- Department of Clinical Laboratory Santai People's Hospital Santai Sichuan P. R. China
| | - Zefei Wang
- Department of Forensic Genetics West China School of Basic Medical Sciences & Forensic Medicine Sichuan University Chengdu Sichuan P. R. China
| | - Yuxiang Zhou
- Department of Forensic Genetics West China School of Basic Medical Sciences & Forensic Medicine Sichuan University Chengdu Sichuan P. R. China
| | - Feng Song
- Department of Forensic Genetics West China School of Basic Medical Sciences & Forensic Medicine Sichuan University Chengdu Sichuan P. R. China
| | - Haibo Luo
- Department of Forensic Genetics West China School of Basic Medical Sciences & Forensic Medicine Sichuan University Chengdu Sichuan P. R. China
| | - Xingbo Song
- Department of Laboratory Medicine West China Hospital Sichuan University Chengdu Sichuan P. R. China
- Department of Clinical Laboratory Karamay Hospital of Integrated Traditional Chinese and Western Medicine (Karamay People's Hospital) Karamay Xinjiang P. R. China
| | - Binwu Ying
- Department of Laboratory Medicine West China Hospital Sichuan University Chengdu Sichuan P. R. China
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Červenák Z, Červenák F, Baldovič M, Patlevičová A, Masnicová S. Mutational analysis of 16 STR markers in the Slovak population. Ann Hum Biol 2022; 49:248-253. [PMID: 35867540 DOI: 10.1080/03014460.2022.2105397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
BACKGROUND Short tandem repeats (STRs) are genetic markers frequently used for human identification and paternity testing. They are highly mutable, which may occasionally lead to inconsistencies between the genotypes of parents and their children. As the mutation rates of individual STR markers can vary among populations, population-specific data are of high importance. AIM To investigate the mutation rates of 16 STR markers in the Slovak population. SUBJECTS AND METHODS In this study, we analysed the germline mutation rates of 16 STR markers (TH01, D3S1358, vWA, D21S11, D16S539, D1S1656, D19S433, SE33, D10S1248, D22S1045, D12S391, D8S1179, D2S1338, D2S441, D18S51 and FGA) in the Slovak population. At these loci, we analysed 42 096 allelic transfers and identified 61 mutation events. RESULTS The loci with the highest overall mutation rates were SE33 and FGA, while no mutations were identified in TH01, D19S433 and D22S1045. The average paternal mutation rate was higher than the maternal mutation rate. All but one mutation consisted of gains or losses of a single repeat unit and the overall mutation rate was estimated to be 1.45 x10-3 per meiosis. CONCLUSION This study provides data which can be used to further strengthen the correct paternity index calculations and reliability of paternity testing in Slovakia.
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Affiliation(s)
- Zdenko Červenák
- Faculty of Medicine, Comenius University, Clinical Research Unit, 5. Department of Internal Medicine, Comenius University Science Park, Bratislava, Slovak Republic
| | - Filip Červenák
- Faculty of Natural Sciences, Comenius University, Department of Genetics, Bratislava, Slovak Republic
| | - Marian Baldovič
- Faculty of Natural Sciences, Comenius University, Department of Molecular Biology, Bratislava, Slovak Republic.,GHC GENETICS SK, Bratislava, Slovak Republic
| | - Andrea Patlevičová
- Department of Biology, Faculty of Natural Sciences, University of Ss. Cyril and Methodius in Trnava, Trnava, Slovak Republic.,GHC GENETICS SK, Bratislava, Slovak Republic
| | - Soňa Masnicová
- Department of Criminalistics and Forensic Sciences, Academy of Police Force in Bratislava, Bratislava, Slovak Republic
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Song F, Wei X, Zhou C, Wang S, Deng C, Liao M, Luo H. Resolving the recombination pattern of 38 X-STRs from Chinese Han three-generation pedigrees. Leg Med (Tokyo) 2022; 59:102135. [PMID: 36029693 DOI: 10.1016/j.legalmed.2022.102135] [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: 06/29/2022] [Revised: 07/26/2022] [Accepted: 08/17/2022] [Indexed: 11/18/2022]
Abstract
X-chromosomal markers have been proved as a useful tool for solving complex kinship cases due to its sex-linked inheriting feature. Among these markers, tightly linked X-STR clusters forming haplotypes are highly informative. The analysis of the haplotypes requires determination of linkage disequilibrium. In this study, genetic linkage, recombination fractions and mutation rates of 38 X-STR loci in 177 three-generation pedigrees were investigated. Genetic linkage analysis and calculation of recombination fractions were performed within each pair of markers and clusters. Then mutation rates were calculated. The results showed that, a) 22 recombination events happened within the tightly linked X-STR clusters, which span<1.0 Mb; b) significantly linked marker pairs were observed with the LOD (logarithm of the odds) scores > 2.0 (2.0104 to 54.8316); c) the average mutation rate of the 38 X-STR loci was 1.32 × 10-3 per meiosis in the Chinese Han population, with DXS10135 and DXS8377 presenting notably high mutation rate (6.5 × 10-3). Our results confirmed that meiotic recombination was not a simple function of physical distance, so that whether recombination occurred at the closely clustered X-STRs or not should be assumed cautiously considering the stability of haplotypes in inheritance process for kinship analysis. This study supplemented the existing database and laid an experimental foundation for the future study on genetic characteristics, recombination, and mutation of the X-STRs.
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Affiliation(s)
- Feng Song
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Xiaowen Wei
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Chengye Zhou
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Shuangshuang Wang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Chuncao Deng
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Miao Liao
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Haibo Luo
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China.
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30
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Otagiri T, Sato N, Asamura H, Parvanova E, Kayser M, Ralf A. RMplex reveals population differences in RM Y-STR mutation rates and provides improved father-son differentiation in Japanese. Forensic Sci Int Genet 2022; 61:102766. [PMID: 36007266 DOI: 10.1016/j.fsigen.2022.102766] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 08/15/2022] [Indexed: 11/29/2022]
Abstract
Rapidly mutating Y chromosomal short tandem repeat markers (RM Y-STRs) -characterized by at least one mutation per 100 generations- are suitable for differentiating both related and unrelated males. The recently introduced multiplex method RMplex allows for the efficient analysis of 30 Y-STRs with increased mutation rates, including all 26 currently known RM Y-STRs. While currently available RM Y-STR mutation rates were established mostly from European individuals, here we applied RMplex to DNA samples of 178 genetically confirmed father-son pairs from East Asia. For several Y-STRs, we found significantly higher mutation rates in Japanese compared to previous estimates. The consequent father-son differentiation rate based on RMplex was significantly higher (52%) in Japanese than previously reported for Europeans (42%), and much higher than with Yfiler Plus in both sample sets (14% and 13%, respectively). Further analysis suggests that the higher mutation and relative differentiation rates in Japanese can in part be explained by on average longer Y-STR alleles relative to Europeans. Moreover, we show that the most striking difference, which was found in DYS712, could be linked to a Y-SNP haplogroup (O1b2-P49) that is common in Japanese and rare in other populations. We encourage the forensic Y-STR community to generate more RMplex data from more population samples of sufficiently large sample size in combination with Y-SNP data to further investigate population effects on mutation and relative differentiation rates. Until more RMplex data from more populations become available, caution shall be placed when applying RM Y-STR mutation rate estimates established in one population, such as Europeans, to forensic casework involving male suspects of paternal origin from other populations, such as non-Europeans.
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Affiliation(s)
- Tomomi Otagiri
- Department of Legal Medicine, Shinshu University School of Medicine, Matsumoto, Nagano, Japan
| | - Noriko Sato
- Department of Legal Medicine, Shinshu University School of Medicine, Matsumoto, Nagano, Japan
| | - Hideki Asamura
- Department of Legal Medicine, Shinshu University School of Medicine, Matsumoto, Nagano, Japan
| | - Evelina Parvanova
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Arwin Ralf
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.
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31
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Nazir S, Adnan A, Rehman RA, Al-Qahtani WS, Alsaleh AB, Al-Harthi HS, Safhi FA, Almheiri R, Lootah R, Alreyami A, Almarri I, Wang CC, Rakha A, Hadi S. Mutation Rate Analysis of RM Y-STRs in Deep-Rooted Multi-Generational Punjabi Pedigrees from Pakistan. Genes (Basel) 2022; 13:genes13081403. [PMID: 36011314 PMCID: PMC9407599 DOI: 10.3390/genes13081403] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 08/03/2022] [Indexed: 11/30/2022] Open
Abstract
Y chromosome short tandem repeat polymorphisms (Y-STRs) are important in many areas of human genetics. Y chromosomal STRs, being normally utilized in the field of forensics, exhibit low haplotype diversity in consanguineous populations and fail to discriminate among male relatives from the same pedigree. Rapidly mutating Y-STRs (RM Y-STRs) have received much attention in the past decade. These 13 RM Y-STRs have high mutation rates (>10−2) and have considerably higher haplotype diversity and discrimination capacity than conventionally used Y-STRs, showing remarkable power when it comes to differentiation in paternal lineages in endogamous populations. Previously, we analyzed two to four generations of 99 pedigrees with 1568 pairs of men covering one to six meioses from all over Pakistan and 216 male relatives from 18 deep-rooted endogamous Sindhi pedigrees covering one to seven meioses. Here, we present 861 pairs of men from 62 endogamous pedigrees covering one to six meioses from the Punjabi population of Punjab, Pakistan. Mutations were frequently observed at DYF399 and DYF403, while no mutation was observed at DYS526a/b. The rate of differentiation ranged from 29.70% (first meiosis) to 80.95% (fifth meiosis), while overall (first to sixth meiosis) differentiation was 59.46%. Combining previously published data with newly generated data, the overall differentiation rate was 38.79% based on 5176 pairs of men related by 1−20 meioses, while Yfiler differentiation was 9.24% based on 3864 pairs. Using father−son pair data from the present and previous studies, we also provide updated RM Y-STR mutation rates.
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Affiliation(s)
- Shahid Nazir
- Department of Forensic Sciences, University of Health Sciences, Lahore 54600, Pakistan
| | - Atif Adnan
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen 361005, China
- Department of Forensic Sciences, College of Criminal Justice, Naïf Arab University of Security Sciences, Riyadh 11452, Saudi Arabia
- Correspondence: (A.A.); (C.-C.W.); (A.R.); (S.H.)
| | - Rahat Abdul Rehman
- Department of Forensic Sciences, University of Health Sciences, Lahore 54600, Pakistan
| | - Wedad Saeed Al-Qahtani
- Department of Forensic Sciences, College of Criminal Justice, Naïf Arab University of Security Sciences, Riyadh 11452, Saudi Arabia
| | - Abrar B. Alsaleh
- Department of Forensic Sciences, College of Criminal Justice, Naïf Arab University of Security Sciences, Riyadh 11452, Saudi Arabia
| | - Hussam S. Al-Harthi
- Prince Sultan Military Medical City, Makkah Al Mukarramah Road, Al-Sulimaniyah, Riyadh 12233, Saudi Arabia
| | - Fatmah Ahmed Safhi
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh 11671, Saudi Arabia
| | - Reem Almheiri
- General Department of Forensic Sciences and Criminology, Dubai Police General Headquarters, Dubai 1493, United Arab Emirates
| | - Reem Lootah
- General Department of Forensic Sciences and Criminology, Dubai Police General Headquarters, Dubai 1493, United Arab Emirates
| | - Afra Alreyami
- General Department of Forensic Sciences and Criminology, Dubai Police General Headquarters, Dubai 1493, United Arab Emirates
| | - Imran Almarri
- General Department of Forensic Sciences and Criminology, Dubai Police General Headquarters, Dubai 1493, United Arab Emirates
| | - Chuan-Chao Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen 361005, China
- Correspondence: (A.A.); (C.-C.W.); (A.R.); (S.H.)
| | - Allah Rakha
- Department of Forensic Sciences, University of Health Sciences, Lahore 54600, Pakistan
- Correspondence: (A.A.); (C.-C.W.); (A.R.); (S.H.)
| | - Sibte Hadi
- Department of Forensic Sciences, College of Criminal Justice, Naïf Arab University of Security Sciences, Riyadh 11452, Saudi Arabia
- Correspondence: (A.A.); (C.-C.W.); (A.R.); (S.H.)
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32
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Della Rocca C, Trombetta B, Barni F, D’Atanasio E, Hajiesmaeil M, Berti A, Hadi S, Cruciani F. Improving discrimination capacity through rapidly mutating Y-STRs in structured populations from the African continent. Forensic Sci Int Genet 2022; 61:102755. [DOI: 10.1016/j.fsigen.2022.102755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 07/21/2022] [Accepted: 07/31/2022] [Indexed: 11/16/2022]
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Antão-Sousa S, Conde-Sousa E, Gusmão L, Amorim A, Pinto N. Estimations of Mutation Rates Depend on Population Allele Frequency Distribution: The Case of Autosomal Microsatellites. Genes (Basel) 2022; 13:genes13071248. [PMID: 35886031 PMCID: PMC9323320 DOI: 10.3390/genes13071248] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/28/2022] [Accepted: 07/11/2022] [Indexed: 01/27/2023] Open
Abstract
Microsatellites (or short-tandem repeats (STRs)) are widely used in anthropology and evolutionary studies. Their extensive polymorphism and rapid evolution make them the ideal genetic marker for dating events, such as the age of a gene or a population. This usage requires the estimation of mutation rates, which are usually estimated by counting the observed Mendelian incompatibilities in one-generation familial configurations (typically parent(s)–child duos or trios). Underestimations are inevitable when using this approach, due to the occurrence of mutational events that do not lead to incompatibilities with the parental genotypes (‘hidden’ or ‘covert’ mutations). It is known that the likelihood that one mutation event leads to a Mendelian incompatibility depends on the mode of genetic transmission considered, the type of familial configuration (duos or trios) considered, and the genotype(s) of the progenitor(s). In this work, we show how the magnitude of the underestimation of autosomal microsatellite mutation rates varies with the populations’ allele frequency distribution spectrum. The Mendelian incompatibilities approach (MIA) was applied to simulated parent(s)/offspring duos and trios in different populational scenarios. The results showed that the magnitude and type of biases depend on the population allele frequency distribution, whatever the type of familial data considered, and are greater when duos, instead of trios, are used to obtain the estimates. The implications for molecular anthropology are discussed and a simple framework is presented to correct the naïf estimates, along with an informatics tool for the correction of incompatibility rates obtained through the MIA.
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Affiliation(s)
- Sofia Antão-Sousa
- Instituto de Investigação e Inovação em Saúde (i3S), 4200-135 Porto, Portugal; (E.C.-S.); (A.A.); (N.P.)
- Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP), 4200-465 Porto, Portugal
- Faculty of Sciences, University of Porto (FCUP), 4169-007 Porto, Portugal
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro 20550-013, Brazil;
- Correspondence:
| | - Eduardo Conde-Sousa
- Instituto de Investigação e Inovação em Saúde (i3S), 4200-135 Porto, Portugal; (E.C.-S.); (A.A.); (N.P.)
- Instituto de Engenharia Biomédica (INEB), 4200-135 Porto, Portugal
| | - Leonor Gusmão
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro 20550-013, Brazil;
| | - António Amorim
- Instituto de Investigação e Inovação em Saúde (i3S), 4200-135 Porto, Portugal; (E.C.-S.); (A.A.); (N.P.)
- Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP), 4200-465 Porto, Portugal
- Faculty of Sciences, University of Porto (FCUP), 4169-007 Porto, Portugal
| | - Nádia Pinto
- Instituto de Investigação e Inovação em Saúde (i3S), 4200-135 Porto, Portugal; (E.C.-S.); (A.A.); (N.P.)
- Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP), 4200-465 Porto, Portugal
- Center of Mathematics, University of Porto (CMUP), 4169-007 Porto, Portugal
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34
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Xiong C, Yang C, Wu W, Zeng Y, Lin T, Chen L, Liu H, Liu C, Du W, Wang M, Sun H, Liu C. Development and Validation of A Multiplex Typing System With 32 Y-STRs for Forensic Application. Forensic Sci Int 2022; 339:111409. [DOI: 10.1016/j.forsciint.2022.111409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/13/2022] [Accepted: 07/21/2022] [Indexed: 11/26/2022]
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35
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Hadi S, Yao J, Adnan A. Editorial: Role of Y Chromosome in Molecular Anthropology, Forensics, and Genetic Genealogy. Front Genet 2022; 13:863455. [PMID: 35754810 PMCID: PMC9218708 DOI: 10.3389/fgene.2022.863455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 05/09/2022] [Indexed: 12/03/2022] Open
Affiliation(s)
- Sibte Hadi
- Department of Forensic Sciences, College of Criminal Justice, Naif Arab University for Security Sciences, Riyadh, Kingdom of Saudi Arabia
| | - Jun Yao
- Department of Forensic Genetics, School of Forensic Medicine, China Medical University, Shenyang, China
| | - Atif Adnan
- Department of Forensic Genetics, School of Forensic Medicine, China Medical University, Shenyang, China
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Javed F, Shafique M, McNevin D, Javed MU, Shehzadi A, Shahid AA. Empirical Evidence on Enhanced Mutation Rates of 19 RM-YSTRs for Differentiating Paternal Lineages. Genes (Basel) 2022; 13:genes13060946. [PMID: 35741708 PMCID: PMC9222627 DOI: 10.3390/genes13060946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/13/2022] [Accepted: 05/20/2022] [Indexed: 11/21/2022] Open
Abstract
Rapidly mutating Y-chromosomal short tandem repeats (RM Y STRs) with mutation rates ≥ 10−2 per locus per generation are valuable for differentiating amongst male paternal relatives where standard Y STRs with mutation rates of ≤10−3 per locus per generation may not. Although the 13 RM Y STRs commonly found in commercial assays provide higher levels of paternal lineage differentiation than conventional Y STRs, there are many male paternal relatives that still cannot be differentiated. This can be improved by increasing the number of Y STRs or choosing those with high mutation rates. We present a RM Y STR multiplex comprising 19 loci with high mutation rates and its developmental validation (repeatability, sensitivity and male specificity). The multiplex was found to be robust, reproducible, specific and sensitive enough to generate DNA profiles from samples with inhibitors. It was also able to detect all contributor alleles of mixtures in ratios up to 9:1. We provide preliminary evidence for the ability of the multiplex to discriminate between male paternal relatives by analyzing large numbers of male relative pairs (536) separated by one to seven meioses. A total of 96 mutations were observed in 162 meioses of father–son pairs, and other closely related male pairs were able to be differentiated after 1, 2, 3, 4, 5, 6 and 7 meiosis in 44%, 69%, 68%, 85%, 0%, 100% and 100% of cases, respectively. The multiplex offers a noticeable enhancement in the ability to differentiate paternally related males compared with the 13 RM Y STR set. We envision the future application of our 19 RM Yplex in criminal cases for the exclusion of male relatives possessing matching standard Y STR profiles and in familial searching with unknown suspects. It represents a step towards the complete individualization of closely related males.
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Affiliation(s)
- Faqeeha Javed
- Forensic Research Laboratory, Centre of Excellence in Molecular Biology, University of the Punjab, Lahore 53700, Pakistan; (F.J.); (A.S.); (A.A.S.)
| | - Muhammad Shafique
- Forensic Research Laboratory, Centre of Excellence in Molecular Biology, University of the Punjab, Lahore 53700, Pakistan; (F.J.); (A.S.); (A.A.S.)
- Correspondence:
| | - Dennis McNevin
- Centre for Forensic Science, University of Technology Sydney, Sydney 2007, Australia;
| | - Muhammad Usama Javed
- Faculty of Medicine, Allama Iqbal Medical College, University of Health Sciences, Lahore 54700, Pakistan;
| | - Abida Shehzadi
- Forensic Research Laboratory, Centre of Excellence in Molecular Biology, University of the Punjab, Lahore 53700, Pakistan; (F.J.); (A.S.); (A.A.S.)
| | - Ahmad Ali Shahid
- Forensic Research Laboratory, Centre of Excellence in Molecular Biology, University of the Punjab, Lahore 53700, Pakistan; (F.J.); (A.S.); (A.A.S.)
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Labuda D, Harding T, Milot E, Vézina H. The effective family size of immigrant founders predicts their long-term demographic outcome: From Québec settlers to their 20th-century descendants. PLoS One 2022; 17:e0266079. [PMID: 35507549 PMCID: PMC9067642 DOI: 10.1371/journal.pone.0266079] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 03/14/2022] [Indexed: 11/19/2022] Open
Abstract
Population history reconstruction, using extant genetic diversity data, routinely relies on simple demographic models to project the past through ascending genealogical-tree branches. Because genealogy and genetics are intimately related, we traced descending genealogies of the Québec founders to pursue their fate and to assess their contribution to the present-day population. Focusing on the female and male founder lines, we observed important sex-biased immigration in the early colony years and documented a remarkable impact of these early immigrants on the genetic make-up of 20th-century Québec. We estimated the immigrants’ survival ratio as a proportion of lineages found in the 1931–60 Québec to their number introduced within the immigration period. We assessed the effective family size, EFS, of all immigrant parents and their Québec-born descendants. The survival ratio of the earliest immigrants was the highest and declined over centuries in association with the immigrants’ EFS. Parents with high EFS left plentiful married descendants, putting EFS as the most important variable determining the parental demographic success throughout time for generations ahead. EFS of immigrant founders appears to predict their long-term demographic and, consequently, their genetic outcome. Genealogically inferred immigrants’ "autosomal" genetic contribution to 1931–60 Québec from consecutive immigration periods follow the same yearly pattern as the corresponding maternal and paternal lines. Québec genealogical data offer much broader information on the ancestral diversity distribution than genetic scrutiny of a limited population sample. Genealogically inferred population history could assist studies of evolutionary factors shaping population structure and provide tools to target specific health interventions.
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Affiliation(s)
- Damian Labuda
- Centre de Recherche, CHU Sainte-Justine, Université de Montréal, Montreal, Québec, Canada
- Département de Pédiatrie, Université de Montréal, Montreal, Québec, Canada
- * E-mail:
| | - Tommy Harding
- Centre de Recherche, CHU Sainte-Justine, Université de Montréal, Montreal, Québec, Canada
- Département de chimie, biochimie et physique, Université du Québec à Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Emmanuel Milot
- Département de chimie, biochimie et physique, Université du Québec à Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Hélène Vézina
- Projet BALSAC, Université du Québec à Chicoutimi, Chicoutimi, Québec, Canada
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Sequence polymorphisms of forensic Y-STRs revealed by a 68-plex in-house massively parallel sequencing panel. Forensic Sci Int Genet 2022; 59:102727. [DOI: 10.1016/j.fsigen.2022.102727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 05/03/2022] [Accepted: 05/23/2022] [Indexed: 11/20/2022]
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39
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Lan Q, Zhao C, Chen C, Xu H, Fang Y, Yao H, Zhu B. Forensic Feature Exploration and Comprehensive Genetic Insights Into Yugu Ethnic Minority and Northern Han Population via a Novel NGS-Based Marker Set. Front Genet 2022; 13:816737. [PMID: 35601485 PMCID: PMC9121381 DOI: 10.3389/fgene.2022.816737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 03/08/2022] [Indexed: 12/02/2022] Open
Abstract
The MPS technology has expanded the potential applications of DNA markers and increased the discrimination power of the targeted loci by taking variations in their flanking regions into consideration. Here, a collection of nuclear and extranuclear DNA markers (totally six kinds of nuclear genetic markers and mtDNA hypervariable region variations) were comprehensively and systematically assessed for polymorphism detections, further employed to dissect the population backgrounds in the Yugu ethnic group from Gansu province (Yugu) and Han population from the Inner Mongolia Autonomous Region (NMH) of China. The elevated efficiencies of the marker set in separating full sibling and challenging half sibling determination cases in parentage tests (iiSNPs), as well as predicting ancestry origins of unknown individuals from at least four continental populations (aiSNPs) and providing informative characteristic-related clues for Chinese populations (piSNPs) are highlighted in the present study. To sum up, different sets of DNA markers revealed sufficient effciencies to serve as promising tools in forensic applications. Genetic insights from the perspectives of autosomal DNA, Y chromosomal DNA, and mtDNA variations yielded that the Yugu ethnic group was genetically close related to the Han populations of the northern region. But we admit that more reference populations (like Mongolian, Tibetan, Hui, and Tu) should be incorporated to gain a refined genetic background landscape of the Yugu group in future studies.
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Affiliation(s)
- Qiong Lan
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Congying Zhao
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Chong Chen
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi’an Jiaotong University, Xi’an, China
| | - Hui Xu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Yating Fang
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Hongbing Yao
- Belt and Road Research Center for Forensic Molecular Anthropology Gansu University of Political Science and Law, Lanzhou, China
| | - Bofeng Zhu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi’an Jiaotong University, Xi’an, China
- *Correspondence: Bofeng Zhu,
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Microhaplotype and Y-SNP/STR (MY): A novel MPS-based system for genotype pattern recognition in two-person DNA mixtures. Forensic Sci Int Genet 2022; 59:102705. [DOI: 10.1016/j.fsigen.2022.102705] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 03/10/2022] [Accepted: 04/10/2022] [Indexed: 12/13/2022]
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Jin X, Zhang H, Ren Z, Wang Q, Liu Y, Ji J, Zhang H, Yang M, Zhou Y, Huang J. Developmental Validation of a Rapidly Mutating Y-STR Panel Labeled by Six Fluoresceins for Forensic Research. Front Genet 2022; 13:777440. [PMID: 35309136 PMCID: PMC8927084 DOI: 10.3389/fgene.2022.777440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 01/20/2022] [Indexed: 11/23/2022] Open
Abstract
The male-specific region of the human Y chromosome is a useful genetic marker for genealogical searching, male inheritance testing, and male DNA mixture deconvolution in forensic studies. However, the Y chromosomal short tandem repeats (Y-STRs) are difficult to distinguish among related males due to their low/medium mutation rate. In contrast, rapidly mutating (RM) Y-STRs exhibit unusually high mutation rates and possess great potential for differentiating male lineages. In this study, we developed a novel Y-STRs multiplex amplification assay of 32 RM Y-STRs by fragment analysis using six dye-labeled technologies (FAM, HEX, TAMRA, ROX, VIG, and SIZ). The development and the validation of the kit were carried out in accordance with the Scientific Working Group guidelines on DNA Analysis Methods. Identical allelic profiles of the 32 RM Y-STRs using a DNA 9948 sample as the positive control could be observed at different concentrations of PCR reagents. Further, the RM Y-STRs did not show cross-reactions with other common animal species, and the developed assay could tolerate interferences from common PCR inhibitors and mixed DNA samples. More importantly, the kit showed relatively high sensitivity and could detect trace DNA samples. Genetic distributions of 32 RM Y-STRs in the Guizhou Han population revealed that these RM Y-STRs showed relatively high genetic diversities. In conclusion, the RM Y-STR assay developed here showed good species specificity, high sensitivity, tolerance to inhibitors, and sample compatibility, which can be viewed as a highly efficient tool with high discrimination capacity for forensic male differentiation.
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Affiliation(s)
- Xiaoye Jin
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Hongling Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Zheng Ren
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Qiyan Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Yubo Liu
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Jingyan Ji
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Han Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Meiqing Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Yongsong Zhou
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Jiang Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
- *Correspondence: Jiang Huang,
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A multi-dimensional evaluation of the 'NIST 1032' sample set across four forensic Y-STR multiplexes. Forensic Sci Int Genet 2022; 57:102655. [PMID: 35007854 PMCID: PMC9901497 DOI: 10.1016/j.fsigen.2021.102655] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/09/2021] [Accepted: 12/12/2021] [Indexed: 02/08/2023]
Abstract
This manuscript reports Y-chromosomal short tandem repeat (Y-STR) haplotypes for 1032 male U.S. population samples across 30 Y-STR loci characterized by three capillary electrophoresis (CE) length-based kits (PowerPlex Y23 System, Yfiler Plus PCR Amplification Kit, and Investigator Argus Y-28 QS Kit) and one sequence-based kit (ForenSeq DNA Signature Prep Kit): DYF387S1, DYS19, DYS385 a/b, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS460, DYS481, DYS505, DYS518, DYS522, DYS533, DYS549, DYS570, DYS576, DYS612, DYS627, DYS635, DYS643, and Y-GATA-H4. The length-based Y-STR haplotypes include six loci that are not reported in the sequence-based kit (DYS393, DYS449, DYS456, DYS458, DYS518, and DYS627), whereas three loci included in the sequence-based kit are not present in length-based kits (DYS505, DYS522, and DYS612). For the latter, a custom multiplex was used to generate CE length-based data, allowing 1032 samples to be evaluated for concordance across the 30 Y-STR loci included in these four commercial Y-STR typing kits. Discordances between typing methods were analyzed further to assess underlying causes such as primer binding site mutations and flanking region insertions/deletions. Allele-level frequency and statistical information is provided for sequenced loci, excluding the multi-copy loci DYF387S1 and DYS385 a/b, for which locus-specific haplotype-level frequencies are provided instead. The resulting data reveals the degree of information gained through sequencing: 88% of sequenced Y-STR loci contain additional sequence-based alleles compared to length-based data, with the DYS389II locus containing the most additional alleles (51) observed by sequencing. Despite these allelic increases, only minimal improvement was observed in haplotype resolution by sequence, with all four commercial kits providing a similar ability to differentiate length-based haplotypes in this sample set. Finally, a subset of 369 male samples were compared to their corresponding additionally sequenced father samples, revealing the sequence basis for the 50 length-based changes observed, and no additional sequence-based mutations. GenBank accession numbers are reported for each unique sequence, and associated records are available in the STRSeq Y-Chromosomal STR Loci National Center for Biotechnology Information (NCBI) BioProject, accession PRJNA380347. Haplotype data is updated in the Y-STR Haplotype Reference Database (YHRD) for the 'NIST 1032' data set to now achieve the level of maximal haplotype of YHRD. All supplementary files including revisions to previously published Y-STR data are available in the NIST Public Data Repository: U.S. population data for human identification markers, DOI 10.18434/t4/1500024.
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Moon MH, Hong SR, Shin KJ. Sequence Variations of 31 Υ-Chromosomal Short Tandem Repeats Analyzed by Massively Parallel Sequencing in Three U.S. Population Groups and Korean Population. J Korean Med Sci 2022; 37:e40. [PMID: 35166077 PMCID: PMC8845103 DOI: 10.3346/jkms.2022.37.e40] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 12/19/2021] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Rapidly mutating (RM) Y-chromosomal short tandem repeats (Y-STRs) have been demonstrated to increase the possibility of distinguishing between male relatives due to a higher mutation rate than conventional Y-STRs. Massively parallel sequencing (MPS) can be useful for forensic DNA typing as it allows the detection of sequence variants of many forensic markers. Here, we present sequence variations of 31 Y-STRs including nine RM Y-STRs (DYF387S1, DYF399S1, DYF404S1, DYS449, DYS518, DYS570, DYS576, DYS612, and DYS627), their frequencies, distribution, and the gain in the number of alleles using MPS. METHODS We constructed a multiplex MPS assay capable of simultaneously amplifying 32 Y-chromosomal markers, producing amplicons ranging from 85-274 bp. Barcoded libraries from 220 unrelated males from four populations-African Americans, Caucasians, Hispanics, and Koreans-were generated via two-step polymerase chain reaction and sequenced on a MiSeq system. Genotype concordance between the capillary electrophoresis (CE) and MPS method and sequence variation of Y-STRs were investigated. RESULTS In total, 195 alleles were increased by MPS compared to CE-based alleles (261 to 456). The DYS518 marker showed the largest increase due to repeat region variation (a 3.69-fold increase). The highest increase in the number of alleles due to single nucleotide polymorphisms in the flanking region was found in DYF399S1. RM Y-STRs had more diverse sequences than conventional Y-STRs. Furthermore, null alleles were observed in DYS576 due to primer-binding site mutation, and allele drop-outs in DYS449 resulted from low marker coverage of less than the threshold. CONCLUSION The results suggest that the expanded and discriminative MPS assay could provide more genetic information for Y-STRs, especially for RM Y-STRs, and could advance male individualization. Compiling sequence-based Y-STR data for worldwide populations would facilitate the application of MPS in the field of forensic genetics and could be applicable in solving male-related forensic cases.
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Affiliation(s)
- Mi Hyeon Moon
- Department of Forensic Medicine, Yonsei University College of Medicine, Seoul, Korea
- Graduate School of Medical Science and Brain Korea 21 Project, Yonsei University, Seoul, Korea
| | - Sae Rom Hong
- Department of Forensic Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Kyoung-Jin Shin
- Department of Forensic Medicine, Yonsei University College of Medicine, Seoul, Korea
- Graduate School of Medical Science and Brain Korea 21 Project, Yonsei University, Seoul, Korea.
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Kasu M, Cloete K, Pitere R, Tsiana K, D’Amato M. The Genetic Landscape of South African males: A Y-STR Perspective. Forensic Sci Int Genet 2022; 58:102677. [DOI: 10.1016/j.fsigen.2022.102677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 01/21/2022] [Accepted: 02/04/2022] [Indexed: 11/04/2022]
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Neuhuber F, Dunkelmann B, Grießner I, Helm K, Kayser M, Ralf A. Improving the differentiation of closely related males by RMplex analysis of 30 Y-STRs with high mutation rates. Forensic Sci Int Genet 2022; 58:102682. [DOI: 10.1016/j.fsigen.2022.102682] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/16/2022] [Accepted: 02/20/2022] [Indexed: 11/04/2022]
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46
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Wang F, Song F, Song M, Luo H, Hou Y. Genetic structure and paternal admixture of the modern Chinese Zhuang population based on 37 Y-STRs and 233 Y-SNPs. Forensic Sci Int Genet 2022; 58:102681. [DOI: 10.1016/j.fsigen.2022.102681] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 01/05/2022] [Accepted: 02/20/2022] [Indexed: 11/25/2022]
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47
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Zeng Y, Chen L, Wang M, Yang C, Liu H, Xiao C, Liu C, Li Y, Xu Q, Du W, Liu C. The Validation of a Single Multiplex Typing System With 45 Y-STR Markers for Familial Searching and Database Construction. Front Genet 2022; 13:842004. [PMID: 35154290 PMCID: PMC8829124 DOI: 10.3389/fgene.2022.842004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 01/07/2022] [Indexed: 11/13/2022] Open
Abstract
The Y-chromosomal short tandem repeat (Y-STR) is an effective forensic tool in familial searches and patrilineal relationship evaluation. However, currently available Y-STR panels often lack sufficient discriminatory power to resolve genetic relationships between distant relatives or within patrilocal populations. This study aims to establish a novel Y-STR amplification system for forensic casework analysis and database construction, which contains 44 slowly and moderately mutating and one rapidly mutating Y-STR. The validation of the assay was conducted following the recommendations of SWGDAM developmental validation guidelines. Different types of casework samples were tested and reliable profiles were obtained. Furthermore, we genotyped and analyzed 141 unrelated Han Chinese male samples. The results showed that this Y45 kit could improve the performance of identifying male individuals, higher haplotype diversity, and discrimination capacity when compared to the previous widely used Yfiler Plus kit. In general, the validation study demonstrated that the newly developed Y45 kit possesses high sensitivity, inhibitor tolerance, male specificity in a mixture, species specificity, and precision and is capable of forensic casework analysis and database construction.
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Affiliation(s)
- Ying Zeng
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Ling Chen
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Mengge Wang
- Guangzhou Forensic Science Institute, Guangzhou, China
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Chengliang Yang
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Hong Liu
- Guangzhou Forensic Science Institute, Guangzhou, China
| | - Cheng Xiao
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - ChangHui Liu
- Guangzhou Forensic Science Institute, Guangzhou, China
| | - Yue Li
- Guangzhou Forensic Science Institute, Guangzhou, China
| | - Quyi Xu
- Guangzhou Forensic Science Institute, Guangzhou, China
| | - Weian Du
- Guangdong Homy Genetics Incorporation, Foshan, China
| | - Chao Liu
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
- Guangzhou Forensic Science Institute, Guangzhou, China
- *Correspondence: Chao Liu,
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Improving the regional Y-STR haplotype resolution utilizing haplogroup-determining Y-SNPs and the application of machine learning in Y-SNP haplogroup prediction in a forensic Y-STR database: A pilot study on male Chinese Yunnan Zhaoyang Han population. Forensic Sci Int Genet 2021; 57:102659. [PMID: 35007855 DOI: 10.1016/j.fsigen.2021.102659] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 12/14/2021] [Accepted: 12/27/2021] [Indexed: 11/23/2022]
Abstract
Improving the resolution of the current widely used Y-chromosomal short tandem repeat (Y-STR) dataset is of great importance for forensic investigators, and the current approach is limited, except for the addition of more Y-STR loci. In this research, a regional Y-DNA database was investigated to improve the Y-STR haplotype resolution utilizing a Y-SNP Pedigree Tagging System that includes 24 Y-chromosomal single nucleotide polymorphism (Y-SNP) loci. This pilot study was conducted in the Chinese Yunnan Zhaoyang Han population, and 3473 unrelated male individuals were enrolled. Based on data on the male haplogroups under different panels, the matched or near-matching (NM) Y-STR haplotype pairs from different haplogroups indicated the critical roles of haplogroups in improving the regional Y-STR haplotype resolution. A classic median-joining network analysis was performed using Y-STR or Y-STR/Y-SNP data to reconstruct population substructures, which revealed the ability of Y-SNPs to correct misclassifications from Y-STRs. Additionally, population substructures were reconstructed using multiple unsupervised or supervised dimensionality reduction methods, which indicated the potential of Y-STR haplotypes in predicting Y-SNP haplogroups. Haplogroup prediction models were built based on nine publicly accessible machine-learning (ML) approaches. The results showed that the best prediction accuracy score could reach 99.71% for major haplogroups and 98.54% for detailed haplogroups. Potential influences on prediction accuracy were assessed by adjusting the Y-STR locus numbers, selecting Y-STR loci with various mutabilities, and performing data processing. ML-based predictors generally presented a better prediction accuracy than two available predictors (Nevgen and EA-YPredictor). Three tree models were developed based on the Yfiler Plus panel with unprocessed input data, which showed their strong generalization ability in classifying various Chinese Han subgroups (validation dataset). In conclusion, this study revealed the significance and application prospects of Y-SNP haplogroups in improving regional Y-STR databases. Y-SNP haplogroups can be used to discriminate NM Y-STR haplotype pairs, and it is important for forensic Y-STR databases to develop haplogroup prediction tools to improve the accuracy of biogeographic ancestry inferences.
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Bini C, Cilli E, Sarno S, Traversari M, Fontani F, Boattini A, Pelotti S, Luiselli D. Twenty-Seven Y-Chromosome Short Tandem Repeats Analysis of Italian Mummies of the 16th and 18th Centuries: An Interdisciplinary Research. Front Genet 2021; 12:720640. [PMID: 34659342 PMCID: PMC8514714 DOI: 10.3389/fgene.2021.720640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/12/2021] [Indexed: 11/13/2022] Open
Abstract
Roccapelago (MO) is a small village located in the Northern Central Apennines, with a population of 31 inhabitants (2014). In 2010, more than 400 individuals dated between the end of the 16th and the 18th century, many of which partially mummified, were discovered in the crypt of the church. This small village, because of its geographical location and surrounding environment, seems to possess the characteristics of a genetic isolate, useful for population genetics and genealogical analyses. Thus, a diachronic study of DNA aimed at investigating the structure and dynamics of the population of Roccapelago over the about 4 centuries, was conducted by analyzing ancient and modern inhabitants of the village. The 14 modern samples were selected by considering both the founder surnames of the village, identified thanks to the study of parish registers, and the grandparent's criterion. From 25 ancient mummies, morphologically assigned to male individuals, the petrous bone, that harbors high DNA amounts, was selected for the DNA extraction. The quantification and qualitative assessment of total human male DNA were evaluated by a real-time PCR assay using the Quantifiler Trio DNA Quantification Kit and multiplex PCR of 27 Y-chromosome short tandem repeat (Y-STR) markers included in the Yfiler Plus PCR Amplification Kit, with seven rapidly mutating Y-STR loci for improving discrimination of male lineages, was performed to genotype the samples. Y-STRs were analyzed according to the criteria of ancient DNA (aDNA) analysis to ensure that authentic DNA typing results were obtained from these ancient samples. The molecular analysis showed the usefulness of the Y chromosome to identify historically relevant remains and discover patterns of relatedness in communities moving from anthropology to genetic genealogy and forensics.
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Affiliation(s)
- Carla Bini
- Laboratory of Forensic Genetics, Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Elisabetta Cilli
- Laboratory of Ancient DNA (aDNALab), Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Stefania Sarno
- Laboratory of Molecular Anthropology and Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Mirko Traversari
- Laboratory of Ancient DNA (aDNALab), Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Francesco Fontani
- Laboratory of Ancient DNA (aDNALab), Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Alessio Boattini
- Laboratory of Molecular Anthropology and Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Susi Pelotti
- Laboratory of Forensic Genetics, Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Donata Luiselli
- Laboratory of Ancient DNA (aDNALab), Department of Cultural Heritage, University of Bologna, Ravenna, Italy
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50
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Lemos MP, Nandi V, Dragavon J, Fleming I, Krishnan K, Musuruana M, Kramer M, Glantz H, Andrasik M, Coombs RW, McElrath MJ, Tieu HV. HIV-1 Nucleic Acids Identify Rectal HIV Exposures in Self-Collected Rectal Swabs, Whereas Y-Chromosome Single Tandem Repeat Mixtures Are Not Reliable Biomarkers of Condomless Receptive Anal Intercourse. J Acquir Immune Defic Syndr 2021; 88:138-148. [PMID: 34506358 PMCID: PMC8439546 DOI: 10.1097/qai.0000000000002748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 05/10/2021] [Indexed: 11/26/2022]
Abstract
BACKGROUND To focus interventions, biomarkers of HIV-1 exposure could help in identifying subpopulations at highest risk of acquisition. We assessed whether Y-chromosome single tandem repeat (YSTR) mixtures obtained from rectal swabs could serve as a biomarker of condomless receptive anal intercourse (CRAI) among men who have sex with men and transgender women and evaluated the feasibility of detecting HIV-1 virions to assess exposures. METHODS Twenty-nine sexually active HIV-seronegative men who have sex with men and one transgender woman from New York City answered on-site and mobile app sexual behavior questionnaires. They were randomized to collecting self-administered rectal swabs every morning or after receptive anal intercourse (RAI). YSTR profiles were assessed from blood sample and swabs; HIV-1 exposure was measured by conducting quantitative polymerase chain reaction in swabs. RESULTS After 2 months, the daily mobile survey had 135%-201% more instances of anal sex acts and 170%-193% more RAI than on-site surveys. Daily mobile reporting had 11%-35% less CRAI events than those reported on-site (Pdaily = 0.001; Pper-sex = 0.047). The daily swabbing arm reported less RAI (P < 0.001) and CRAI (P < 0.038) and had 2.95 lower odds of detecting YSTR mixtures (P = 0.021) than the per-sex-event arm. Surprisingly, YSTR detection was not significantly modified by report of bowel movements and lubricant, enema, or condom use. No participant became HIV-1 infected, yet HIV-1 total nucleic acids were detected in 6 independent episodes of CRAI in 2 participants taking pre-exposure prophylaxis. CONCLUSIONS YSTR mixtures demonstrated 80% specificity but only 30% sensitivity as a biomarker of CRAI in self-collected rectal swabs. However, detection of HIV-1 exposures in self-collected swabs may help in identifying those needing further HIV risk reduction strategies.
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Affiliation(s)
- Maria P. Lemos
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Vijay Nandi
- Laboratory of Data Analytics, Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY
| | - Joan Dragavon
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Ira Fleming
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Keertana Krishnan
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Martin Musuruana
- Laboratory of Data Analytics, Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY
| | - Madeline Kramer
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Hayley Glantz
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Michele Andrasik
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Robert W. Coombs
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
- Department of Pathology, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - M. Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Global Health, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Hong-Van Tieu
- Laboratory of Infectious Disease Prevention, Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY
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