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Feng Y, Wang T, Yang Y, You J, He K, Zhang H, Wang Q, Yang M, Huang J, Ren Z, Jin X. Genetic features and phylogenetic relationship analyses of Guizhou Han population residing in Southwest China via 38 X-InDels. PeerJ 2023; 11:e14964. [PMID: 36915656 PMCID: PMC10007965 DOI: 10.7717/peerj.14964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 02/06/2023] [Indexed: 03/11/2023] Open
Abstract
Background The insertion/deletion polymorphism (InDel), an ideal forensic genetic marker with a low spontaneous mutation rate and small amplification product fragments, is widely distributed in the genome, combining the advantages of STR and SNP genetic markers. The X-chromosome has high application value in complex paternity testing, and it is an excellent system for evaluating population admixture and studying evolutionary anthropology. However, further research is needed on the population genetics of X-chromosome InDels (X-InDels). Methods In this article, a system composed of 38 X-InDel loci was utilized to analyse and evaluate the forensic parameters of the Guizhou Han population in order to explore its forensic application efficiency. Results The results showed that expected heterozygosities spanned from 0.0189 to 0.5715, and the cumulative power of discrimination of the 32 X-InDels and three linkage blocks was 0.9999999954 and 0.999999999999741 for males and females, respectively. The combined mean exclusion chance of these loci for trios and duos is 0.999999 and 0.999747, respectively. Multiple methods like principal component analysis, Fst genetic distance, and phylogenetic reconstruction were employed for dissecting the genetic structure of the Guizhou Han population by comparing it with previously reported populations. As expected, the studied Han population displayed relatively close genetic affinities with the East Asian populations. At the same time, there were obvious genetic differentiations between the Guizhou Han population and other continental populations that were discerned, especially for the African populations. Conclusions This study further verified the applicability of 38 X-InDels for human personal identification and kinship analyses of Han Chinese, and also showed the application potential of X-InDels in population genetics.
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Affiliation(s)
- Yuhang Feng
- Shanghai Key Lab of Forensic Medicine, Key Lab of Forensic Science, Ministry of Justice, China, Academy of Forensic Science, Shanghai, China.,Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Ting Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Yunteng Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Jiangtao You
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Kun He
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Hongling Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Qiyan Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Meiqing Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Jiang Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Zheng Ren
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Xiaoye Jin
- Shanghai Key Lab of Forensic Medicine, Key Lab of Forensic Science, Ministry of Justice, China, Academy of Forensic Science, Shanghai, China.,Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
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Chen L, Pan X, Wang Y, Du W, Wu W, Tang Z, Xiao C, Han X, Liu C, Liu C. Development and Validation of a Forensic Multiplex System With 38 X-InDel Loci. Front Genet 2021; 12:670482. [PMID: 34484288 PMCID: PMC8416044 DOI: 10.3389/fgene.2021.670482] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 07/13/2021] [Indexed: 11/17/2022] Open
Abstract
In the present study, a novel multiplex system, AGCU X-InDel 38 kit, was designed to amplify 38 X-InDel markers and amelogenin in a single Polymerase Chain Reaction (PCR). To demonstrate the suitability and efficiency for forensic applications, a series of validation experiments were conducted, including sensitivity, species specificity, reproducibility, stability, case samples, balance of peak height, size precision, as well as allele frequency and forensic parameter analysis. The results showed that AGCU X-InDel 38 kit was capable to get full profiles even with 62.5 pg of template DNA, and full profiles can be obtained when hematin concentration ≤25 μmol/L, or hemoglobin concentration ≤50 μmol/L, showing good tolerance to six common inhibitors. Moreover, the analyzed case samples indicated that AGCU X-InDel 38 kit had better performance for degraded and trace DNA samples. The 200 unrelated males from Guangdong Han population showed that the combined PDMale and PDFemale were both more than 0.999999999, and the combined MECKrüger, MECKishida, and MECDesmarais Duo were 0.999369481, 0.999999917, and 0.999941556, respectively. Robust discrimination capability of this novel multiplex system could be demonstrated through the high values of forensic parameters. In conclusion, AGCU X-InDel 38 kit is sensitive, precise, reproducible, and highly informative and could be used as a complementary tool for complex and challenging kinship cases.
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Affiliation(s)
- Ling Chen
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Xiyong Pan
- School of Forensic Medicine, Sun Yat-sen University, Guangzhou, China
| | - Yuan Wang
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Weian Du
- Guangdong Homy Genetics Incorporation, Foshan, China.,AGCU ScienTech Incorporation, Wuxi, China
| | - Weibin Wu
- Guangdong Homy Genetics Incorporation, Foshan, China.,AGCU ScienTech Incorporation, Wuxi, China
| | - Zhenya Tang
- Guangdong Provincial Forensic Science Center, Guangzhou, China
| | - Cheng Xiao
- Guangzhou Forensic Science Institute, Guangzhou, China
| | - Xiaolong Han
- Guangzhou Forensic Science Institute, Guangzhou, China
| | - Chao Liu
- School of Forensic Medicine, Southern Medical University, Guangzhou, China.,Guangzhou Forensic Science Institute, Guangzhou, China
| | - Changhui Liu
- School of Forensic Medicine, Southern Medical University, Guangzhou, China.,Guangzhou Forensic Science Institute, Guangzhou, China
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Gomes I, Pinto N, Antão-Sousa S, Gomes V, Gusmão L, Amorim A. Twenty Years Later: A Comprehensive Review of the X Chromosome Use in Forensic Genetics. Front Genet 2020; 11:926. [PMID: 33093840 PMCID: PMC7527635 DOI: 10.3389/fgene.2020.00926] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 07/24/2020] [Indexed: 12/12/2022] Open
Abstract
The unique structure of the X chromosome shaped by evolution has led to the present gender-specific genetic differences, which are not shared by its counterpart, the Y chromosome, and neither by the autosomes. In males, recombination between the X and Y chromosomes is limited to the pseudoautosomal regions, PAR1 and PAR2; therefore, in males, the X chromosome is (almost) entirely transmitted to female offspring. On the other hand, the X chromosome is present in females with two copies that recombine along the whole chromosome during female meiosis and that is transmitted to both female and male descendants. These transmission characteristics, besides the obvious clinical impact (sex chromosome aneuploidies are extremely frequent), make the X chromosome an irreplaceable genetic tool for population genetic-based studies as well as for kinship and forensic investigations. In the early 2000s, the number of publications using X-chromosomal polymorphisms in forensic and population genetic applications increased steadily. However, nearly 20 years later, we observe a conspicuous decrease in the rate of these publications. In light of this observation, the main aim of this article is to provide a comprehensive review of the advances and applications of X-chromosomal markers in population and forensic genetics over the last two decades. The foremost relevant topics are addressed as: (i) developments concerning the number and types of markers available, with special emphasis on short tandem repeat (STR) polymorphisms (STR nomenclatures and practical concerns); (ii) overview of worldwide population (frequency) data; (iii) the use of X-chromosomal markers in (complex) kinship testing and the forensic statistical evaluation of evidence; (iv) segregation and mutation studies; and (v) current weaknesses and future prospects.
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Affiliation(s)
- Iva Gomes
- Institute for Research and Innovation in Health Sciences (i3S), University of Porto, Porto, Portugal.,Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP), Porto, Portugal
| | - Nádia Pinto
- Institute for Research and Innovation in Health Sciences (i3S), University of Porto, Porto, Portugal.,Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP), Porto, Portugal.,Center of Mathematics, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Sofia Antão-Sousa
- Institute for Research and Innovation in Health Sciences (i3S), University of Porto, Porto, Portugal.,Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP), Porto, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal.,DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Verónica Gomes
- Institute for Research and Innovation in Health Sciences (i3S), University of Porto, Porto, Portugal.,Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP), Porto, Portugal
| | - Leonor Gusmão
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - António Amorim
- Institute for Research and Innovation in Health Sciences (i3S), University of Porto, Porto, Portugal.,Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP), Porto, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
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Ferragut JF, Pinto N, Amorim A, Picornell A. Improving publication quality and the importance of Post Publication Peer Review: The illustrating example of X chromosome analysis and calculation of forensic parameters. Forensic Sci Int Genet 2018; 38:e5-e7. [PMID: 30455113 DOI: 10.1016/j.fsigen.2018.11.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 10/22/2018] [Accepted: 11/06/2018] [Indexed: 01/17/2023]
Affiliation(s)
- J F Ferragut
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS) i Laboratori de Genètica, Departament de Biologia, Universitat de les Illes Balears, Spain.
| | - N Pinto
- IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal; I3s, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal; CMUP, Center of Mathematics of the University of Porto, Porto, Portugal
| | - A Amorim
- IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal; I3s, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal; FCUP - Faculty of Sciences of the University of Porto, Portugal
| | - A Picornell
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS) i Laboratori de Genètica, Departament de Biologia, Universitat de les Illes Balears, Spain
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Dong C, Fu L, Zhang X, Ma C, Yu F, Li S, Cong B. Development of three X-linked tetrameric microsatellite markers for forensic purposes. Mol Biol Rep 2014; 41:6429-32. [DOI: 10.1007/s11033-014-3523-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 06/19/2014] [Indexed: 11/27/2022]
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Medina-Acosta E, Machado FB. Eyes wide open: the (mis)use of combined power of discrimination for X-linked short tandem repeats. Mol Biol Rep 2010; 38:4003-6. [PMID: 21110111 DOI: 10.1007/s11033-010-0518-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Accepted: 11/13/2010] [Indexed: 01/15/2023]
Affiliation(s)
- Enrique Medina-Acosta
- Núcleo de Diagnóstico e Investigação Molecular, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Avenida Alberto Lamego 2000, Parque Califórnia, Campos dos Goytacazes, RJ, CEP 28013-602, Brazil.
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