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Wang X, Lan Q, Lin Y, Yuan X, Mei S, Lei F, Dong B, Zhao M, Cai M, Shen C, Zhu B. Investigating the effectiveness of forensic genetics and population genetic diversity using a multi-InDel system in Chinese Hezhou and Southern Shaanxi Han populations. Ann Hum Genet 2024. [PMID: 38766954 DOI: 10.1111/ahg.12553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 01/21/2024] [Accepted: 01/29/2024] [Indexed: 05/22/2024]
Abstract
INTRODUCTION Multiple insertion-deletion (multi-InDel) has greater potential in forensic genetics than InDel, and its efficacy in kinship testing, individual identification, DNA mixture detection and ancestry inference remains to be explored. METHODS Consequently, we designed an efficient and robust system consisting of 41 multi-InDels to evaluate its efficacy in forensic applications in Chinese Hezhou Han (HZH) and Southern Shaanxi Han (SNH) populations and explore the genetic relationships between the SNH, HZH, and 26 reference populations. RESULTS AND CONCLUSION The obtained results showed that 38 out of the 41 multi-InDels had fairly high genetic variations. The the cumulative probability of discrimination and exclusion values of the multi-InDels (except MI38) in HZH and SNH populations both exceeded 1-e-25 and 1-e-6, correspondingly. The genetic compositions of HZH and SNH individuals were similar to that of East Asians and the Naive Bayes model could well distinguish East Asians, Africans and Americans. These results indicated that the multi-InDel systerm can serve as an effective tool to provide important evidence for the development of multi-InDels in forensic practice and better analyse the genetic background of the Han Chinese populations.
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Affiliation(s)
- Xi Wang
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Qiong Lan
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Yifeng Lin
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Xi Yuan
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Shuyan Mei
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Fanzhang Lei
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Bonan Dong
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Ming Zhao
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Meiming Cai
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Chunmei Shen
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Bofeng Zhu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
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Du W, Zheng X, Jiang L, Li S, Lan S, Ye Y, Liu J. Forensic characteristics and genetic structure of the Chinese Tibetan population revealed by 38 X-chromosomal InDel loci. Forensic Sci Int 2024; 356:111961. [PMID: 38377671 DOI: 10.1016/j.forsciint.2024.111961] [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: 11/05/2023] [Revised: 01/04/2024] [Accepted: 02/04/2024] [Indexed: 02/22/2024]
Abstract
With the increasing importance of X-chromosome (Chr-X) genotyping in kinship identification, the exploitation of X chromosome genetic marker multiplex kits is increasing. The Human X-InDels amplification kit is a novel developed system which contained 38 X-chromosomal Insertion/deletion markers (X-InDels) and Amelogenin. Herein, we investigated the genetic diversity of the 38 X-InDels in the Tibetan ethnic minority (n = 792) from seven regions and evaluated the application potential of this novel panel. The rs16368 was the least variable locus, whereas the most polymorphic locus was the rs59605609 in Tibetan population. We confirmed three linkage groups with the haplotype diversities ranged from 0.5032 to 0.5976. The overall combined power of discrimination (PD) in males and females were 0.999999999582066 and 0.999999999999993, respectively. And the overall combined mean exclusion chance (MEC) values were not lower than 0.999125526990159. In addition, we explored the genetic relationships among the Tibetans in seven different regions via series of population comparison analyses, finding that the genetic relationship between the Ngari Tibetan and Chamdo Tibetan was the farthest, which was consistent with geographical distribution.
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Affiliation(s)
- Weian Du
- Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, Beijing 100088, China; Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China; Guangdong Homy Genetics Incorporation, Foshan 528000, China
| | - Xinyue Zheng
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Lirong Jiang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Suyu Li
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Shengnan Lan
- Department of Forensic Toxicological Analysis, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Yi Ye
- Department of Forensic Toxicological Analysis, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China.
| | - Jing Liu
- Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, Beijing 100088, China; Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China.
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Garcia FM, Trabach RSR, Stange VS, Cancian B, Zetum ASS, Casotti MC, Errera FIV, de Carvalho EF, Meira DD, Louro ID. Analysis of 12 X-STRs loci in a population from southeastern Brazil. Forensic Sci Int Genet 2024; 68:102974. [PMID: 37952485 DOI: 10.1016/j.fsigen.2023.102974] [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: 11/30/2022] [Revised: 10/24/2023] [Accepted: 10/28/2023] [Indexed: 11/14/2023]
Abstract
Short tandem repeat (STR) markers on the X chromosome have a high potential for solving complex kinship analysis and individual identification cases. To achieve such purposes, allele and haplotype frequencies for the specific population are necessary. Nonetheless, such frequencies are not always available. Therefore, we obtained haplotypes from 520 unrelated males from four different geographic regions of Espírito Santo - Brazil, using the Investigator Argus X-12 kit. Forensic parameters for linked groups of four X-STR loci are reported. Genetic distance analyzes suggest that ES population is genetically closer to the Italian population and farther from the Mexican one, among the populations analyzed in this study.
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Affiliation(s)
- Fernanda M Garcia
- Núcleo de Genética Humana e Molecular - Departamento de Ciências Biológicas - Universidade Federal do Espírito Santo, Vitória 29075-910, Espirito Santo, Brazil.
| | - Raquel S R Trabach
- Núcleo de Genética Humana e Molecular - Departamento de Ciências Biológicas - Universidade Federal do Espírito Santo, Vitória 29075-910, Espirito Santo, Brazil
| | - Victor S Stange
- Laboratório de DNA Forense - Polícia Civil do Espírito Santo, Vitória 29045-402, Espírito Santo, Brazil
| | - Bruno Cancian
- Núcleo de Genética Humana e Molecular - Departamento de Ciências Biológicas - Universidade Federal do Espírito Santo, Vitória 29075-910, Espirito Santo, Brazil
| | - Alexia S S Zetum
- Núcleo de Genética Humana e Molecular - Departamento de Ciências Biológicas - Universidade Federal do Espírito Santo, Vitória 29075-910, Espirito Santo, Brazil
| | - Matheus C Casotti
- Núcleo de Genética Humana e Molecular - Departamento de Ciências Biológicas - Universidade Federal do Espírito Santo, Vitória 29075-910, Espirito Santo, Brazil
| | - Flavia I V Errera
- Núcleo de Genética Humana e Molecular - Departamento de Ciências Biológicas - Universidade Federal do Espírito Santo, Vitória 29075-910, Espirito Santo, Brazil
| | - Elizeu F de Carvalho
- Laboratório de Diagnóstico por DNA - Instituto de Biologia Roberto Alcantara Gomes - Universidade Estadual do Rio de Janeiro
| | - Débora D Meira
- Núcleo de Genética Humana e Molecular - Departamento de Ciências Biológicas - Universidade Federal do Espírito Santo, Vitória 29075-910, Espirito Santo, Brazil
| | - Iuri D Louro
- Núcleo de Genética Humana e Molecular - Departamento de Ciências Biológicas - Universidade Federal do Espírito Santo, Vitória 29075-910, Espirito Santo, Brazil
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Yang C, He M, Liu C, Liu X, Lun M, Su Q, Han X, Liu H, Wang M, Chen L, Liu C. Development and validation of a custom panel including 114 InDels using massively parallel sequencing for forensic application. Electrophoresis 2023; 44:1704-1713. [PMID: 37622566 DOI: 10.1002/elps.202300044] [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: 02/27/2023] [Revised: 05/13/2023] [Accepted: 08/04/2023] [Indexed: 08/26/2023]
Abstract
Insertion/deletion polymorphisms (InDels) have particular characteristics, such as a relatively low mutation rate, small amplicon size, and no stutter artifacts when genotyped via the capillary electrophoresis platform. It would be an important complementary tool for individual identification and certain kinship analyses. At present, massively parallel sequencing (MPS) has shown excellent application value in forensic studies. Therefore, in this study, we developed a custom MPS InDel panel that contains 114 InDels [77 autosomal InDels (A-InDels), 32 X-chromosomal InDels (X-InDels), and 5 Y-chromosomal InDels) based on previous studies. To assess this panel's performance, several validation experiments were performed, including sensitivity, inhibitor, degraded DNA testing, species specificity, concordance, repeatability, case-type samples, and population studies. The results showed that the lowest DNA input was 0.25 ng. All genotypes were obtained in the presence of 80 ng/µL humic acid, 2000 µmol/L calcium, 3000 µmol/L EDTA and indigo. In degraded DNA testing, 90% of loci could be detected for 16-day-old formalin-fixed hearts. In addition, this panel has good species specificity. The values of combined power of discrimination and the combined power of exclusion for 77 A-InDels were 1-3.9951 × 10-32 and 1-4.2956 × 10-7 , respectively. The combined mean exclusion chance for 32 X-InDels was 0.99999 in trios and 0.99904 in duos. The validation results indicate that this newly developed MPS multiplex system is a robust tool for forensic applications.
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Affiliation(s)
- Chengliang Yang
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Meiyun He
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Changhui Liu
- Guangzhou Forensic Science Institute, Guangzhou, P. R. China
| | - Xueyuan Liu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Miaoqiang Lun
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Qin Su
- Guangzhou Forensic Science Institute, Guangzhou, P. R. China
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, P. R. China
| | - Xiaolong Han
- Guangzhou Forensic Science Institute, Guangzhou, P. R. China
| | - Hong Liu
- Guangzhou Forensic Science Institute, Guangzhou, P. R. China
| | - Mengge Wang
- Guangzhou Forensic Science Institute, Guangzhou, P. R. China
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, P. R. China
| | - Ling Chen
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Chao Liu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
- National Anti-Drug Laboratory Guangdong Regional Center, Guangzhou, P. R. China
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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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Forensic Applications of Markers Present on the X Chromosome. Genes (Basel) 2022; 13:genes13091597. [PMID: 36140765 PMCID: PMC9498577 DOI: 10.3390/genes13091597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/23/2022] [Accepted: 09/02/2022] [Indexed: 11/17/2022] Open
Abstract
Microsatellite genetic markers are the gold standard for human genetic identification. Forensic analyses around the world are carried out through protocols using the analysis of STR markers in autosomal chromosomes and in the Y chromosome to solve crimes. However, these analyses do not allow for the resolution of all cases, such as rape situations with suspicion of incest, paternity without a maternal sample for comparison, and biological traces with DNA mixture where the profile sought is female, among other situations. In these complex cases, the study of X-chromosome STR markers significantly increases the probability of identification by complementing the data obtained for autosomal and Y-chromosome markers, due to the unique structure of the X chromosome and its exclusive method of inheritance. However, there are currently no validated Brazilian protocols for this purpose, nor are there any population data necessary for statistical analyses that must be included in the issuance of expert reports. Thus, the aim of this article is to provide a literary review of the applications of X-chromosomal markers in population genetics.
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