1
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Zeng K, Zhao D. Genetic polymorphism analysis and forensic application evaluation of 57 insertion/deletion polymorphisms from Yi ethnic group in Yunnan. Ann Hum Biol 2024; 51:1-9. [PMID: 38251838 DOI: 10.1080/03014460.2023.2294743] [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: 05/23/2023] [Accepted: 11/29/2023] [Indexed: 01/23/2024]
Abstract
BACKGROUND As a new kind of diallelic genetic marker, insertion/deletion (InDel) polymorphisms have recently been used in forensic science. However, there are relatively few studies on the forensic evaluation of InDel genetic polymorphisms from different populations. AIM The aim of the present work is to assess the genetic polymorphism and forensic applicability of 57 InDels from the Yi ethnic group and explore the genetic background of this group. SUBJECTS AND METHODS A total sample of 122 unrelated individuals of Yi group from the Yunnan province were genotyped by the AGCU indel 60 Kit. Multiplex population genetic analyses on the same 57 InDels were carried out among the Yunnan Yi group and 29 reference populations. RESULTS The average allele frequency of these loci in the Yi ethnic group was 0.485. Heterozygosity, polymorphism information content, and the power of discrimination were 0.477, 0.362, and 0.612, respectively. The combined power of discrimination and the combined power of exclusion reached to 0.99999999999999999669 and 0.999962965, respectively. The results showed that 57 InDels polymorphisms have high genetic polymorphisms in the Yi ethnic group. CONCLUSIONS The 57 InDels could be used for forensic individual identification, paternity testing, and intercontinental population discrimination, with the potential for use in biogeographic ancestry inference.
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Affiliation(s)
- Kuo Zeng
- Institute of Evidence Law and Forensic Science, China University of Political Science and Law, Beijing, China
| | - Dong Zhao
- Institute of Evidence Law and Forensic Science, China University of Political Science and Law, Beijing, China
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2
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Ozyer S, Uslu ZS, Unsal Sapan T, Bulbul O, Filoglu G. The development of the novel 22 X- indel multiplex system for forensic genetics. Leg Med (Tokyo) 2023; 62:102224. [PMID: 36898282 DOI: 10.1016/j.legalmed.2023.102224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 01/28/2023] [Accepted: 02/23/2023] [Indexed: 03/06/2023]
Abstract
InDel (Insertions/deletion) markers have been used as an alternative, or as a complementary marker system, to STR markers in human identification due to their advantages such as low mutation rates, no stutter, and potential small amplicon sizes. In forensic sciences, sex chromosomes are widely used in forensic genetics for specific cases. For example, the relationship between father and daughter can be determined by using X-InDels. In this study, we developed a novel 22 X-InDel multiplex system that was identified by two separate assays with fluorescence amplification and capillary electrophoresis detection technology. We chose 22 X-InDel markers based on the following criteria: mean heterozygosity over 30% in Europeans; minimum of 250 Kb differences between each InDel loci; and an amplicon length that was less than 300 bp. We performed an optimization and validation study of 22 X-InDel systems under the following parameters: analytical threshold, sensitivity, precision and accuracy, stochastic threshold, repeatability, and reproducibility. We evaluated the allele frequency of this multiplex system in the Turkish population, and then the population comparisons were carried out on data from 1000 Genome populations (Europe, Africa, America, South Asia, and East Asia). The sensitivity test showed a complete genotyping profile with DNA concentrations as low as 0.5 ng. The heterozygosity ratio of 22 X-InDel loci was determined as 0.4690 and the discrimination power was defined as 0.99. The results show that the new 22 X-InDel multiplex system provides high polymorphism information, and it is a reproducible, accurate, sensitive, and robust system that could be used as an additional tool for kinship testing.
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Affiliation(s)
- Selen Ozyer
- Istanbul University- Cerrahpasa, Institute of Forensic Science and Legal Medicine, Istanbul, Turkey; Dogus University, Advanced Vocational School, Program of Autopsy Assistant, Istanbul, Turkey
| | - Zulal Seval Uslu
- Istanbul University- Cerrahpasa, Institute of Forensic Science and Legal Medicine, Istanbul, Turkey
| | - Tugba Unsal Sapan
- Uskudar University, Institute of Addiction and Forensic Science, Istanbul, Turkey
| | - Ozlem Bulbul
- Istanbul University- Cerrahpasa, Institute of Forensic Science and Legal Medicine, Istanbul, Turkey
| | - Gonul Filoglu
- Istanbul University- Cerrahpasa, Institute of Forensic Science and Legal Medicine, Istanbul, Turkey
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3
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Liu J, Du W, Jiang L, Liu C, Chen L, Zheng Y, Hou Y, Liu C, Wang Z. Development and validation of a forensic multiplex InDel assay: The AGCU InDel 60 kit. Electrophoresis 2022; 43:1871-1881. [PMID: 35859229 DOI: 10.1002/elps.202100376] [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: 12/02/2021] [Revised: 07/11/2022] [Accepted: 07/14/2022] [Indexed: 12/14/2022]
Abstract
Marker sets based on insertion/deletion polymorphisms (InDels) combine the characteristics of both short tandem repeats (STRs) and single nucleotide polymorphisms and have served as effective complementary or stand-alone systems for human identification in forensics. We developed a novel multiplex amplification detection system, designated the AGCU InDel 60 kit, containing 57 autosomal InDels, 2 Y-chromosomal InDels, and the amelogenin locus and validated the kit in a series of studies, which included tests of the PCR conditions; tests for sensitivity, species specificity, reproducibility, stability, and mock case samples; degradation studies; and a population study. The results indicated that the AGCU InDel 60 kit was accurate, specific, reproducible, stable, and robust. Complete DNA profiles were obtained even with 125 pg of human DNA. In tests of artificially degraded samples, we found that the number of alleles detected by the validated kit was considerably greater than that detected by the STR-based AGCU 21+1 kit, even as the degree of degradation increased. Additionally, 564 unrelated individuals from three Han groups were investigated using this novel system, and the values of combined power of discrimination and combined power of exclusion were not less than 1-4.9026 × 10-24 and 1-3.1123 × 10-5 , respectively. Thus, the results indicated that the novel kit was more powerful than the previous version of the InDel kit (the AGCU InDel 50 kit). Our results suggest that the AGCU InDel 60 kit can serve as an efficient tool for human forensics and a supplementary kit for population genetics research.
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Affiliation(s)
- Jing Liu
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Weian Du
- School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China.,AGCU ScienTech Incorporation, Wuxi, P. R. China
| | - Lirong Jiang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Changhui Liu
- School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China.,AGCU ScienTech Incorporation, Wuxi, P. R. China
| | - Ling Chen
- AGCU ScienTech Incorporation, Wuxi, P. R. China
| | - Yangyang Zheng
- School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China.,Guangdong Province Key Laboratory of Forensic Genetics, Guangzhou Forensic Science Institute, Guangzhou, P. R. China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Chao Liu
- School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China.,Guangdong Province Key Laboratory of Forensic Genetics, Guangzhou Forensic Science Institute, Guangzhou, P. R. China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China
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4
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Jin X, Liu Y, Zhang Y, Li Y, Chen C, Wang H. Autosomal deletion/insertion polymorphisms for global stratification analyses and ancestry origin inferences of different continental populations by machine learning methods. Electrophoresis 2021; 42:1473-1479. [PMID: 33948979 DOI: 10.1002/elps.202100044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 03/19/2021] [Accepted: 04/12/2021] [Indexed: 11/11/2022]
Abstract
A lot of population data of 30 deletion/insertion polymorphisms (DIPs) of the Investigator DIPplex kit in different continental populations have been reported. Here, we assessed genetic distributions of these 30 DIPs in different continental populations to pinpoint candidate ancestry informative DIPs. Besides, the effectiveness of machine learning methods for ancestry analysis was explored. Pairwise informativeness (In) values of 30 DIPs revealed that six loci displayed relatively high In values (>0.1) among different continental populations. Besides, more loci showed high population-specific divergence (PSD) values in African population. Based on the pairwise In and PSD values of 30 DIPs, 17 DIPs in the Investigator DIPplex kit were selected to ancestry analyses of African, European, and East Asian populations. Even though 30 DIPs provided better ancestry resolution of these continental populations based on the results of PCA and population genetic structure, we found that 17 DIPs could also distinguish these continental populations. More importantly, these 17 DIPs possessed more balanced cumulative PSD distributions in these populations. Six machine learning methods were used to perform ancestry analyses of these continental populations based on 17 DIPs. Obtained results revealed that naïve Bayes manifested the greatest performance; whereas, k nearest neighbor showed relatively low performance. To sum up, these machine learning methods, especially for naïve Bayes, could be used as the valuable tool for ancestry analysis.
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Affiliation(s)
- Xiaoye Jin
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, P. R. China.,Medical Genetics Institute of Henan Province, Henan Provincial People's Hospital,Zhengzhou University People's Hospital, Zhengzhou, P. R. China.,National Health Commission Key Laboratory of Birth Defects Prevention, Henan Key Laboratory of Population Defects Prevention, Zhengzhou, P. R. China
| | - Yuluo Liu
- Department of Forensic Science, Guangdong Police College, Guangzhou, P. R. China
| | - Yuanyuan Zhang
- School of Foreign Languages, Zhengzhou University of Industrial Technology, Zhengzhou, P. R. China
| | - Yongle Li
- National Health Commission Key Laboratory of Birth Defects Prevention, Henan Key Laboratory of Population Defects Prevention, Zhengzhou, P. R. China
| | - Chuanliang Chen
- Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, P. R. China
| | - Hongdan Wang
- Medical Genetics Institute of Henan Province, Henan Provincial People's Hospital,Zhengzhou University People's Hospital, Zhengzhou, P. R. China.,National Health Commission Key Laboratory of Birth Defects Prevention, Henan Key Laboratory of Population Defects Prevention, Zhengzhou, P. R. China
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5
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Jin X, Xing G, Yang C, Zhang X, Cui W, Chen C, Zhu B. Genetic polymorphisms of 44 Y chromosomal genetic markers in the Inner Mongolia Han population and its genetic relationship analysis with other reference populations. Forensic Sci Res 2021; 7:510-517. [PMID: 36353319 PMCID: PMC9639530 DOI: 10.1080/20961790.2020.1857509] [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] [Indexed: 12/09/2022] Open
Abstract
Y chromosomal genetic markers in the non-recombining region are commonly used for human evolution research, familial searching, and forensic male differentiation since they strictly follow paternal inheritance. Y chromosomal short tandem repeats (Y-STRs) possess extraordinarily advantages in forensic applications because of their high polymorphisms and special genetic pattern. Here, we assessed the genetic diversities of 41 Y-STRs and three Y chromosomal insertion/deletion (Y-InDels) loci in the Chinese Inner Mongolia Han population; besides, genetic differentiation analyses among the studied Han population and other previously reported populations were conducted based on 27 same Y-STRs. Totally, 425 alleles were observed in 324 Inner Mongolia Han individuals for these Y-markers. Gene diversities of these Y-markers distributed from 0.0306 to 0.9634. The haplotype diversity and discriminatory capacity of these Y-markers in the Inner Mongolia Han population were 0.9999 and 0.98457, respectively. Haplotype resolution comparisons of different Y-marker groups in the studied Han population revealed that higher haplotype resolution could be achieved for these 44 Y-markers. Population genetic analyses of the Inner Mongolia Han population and other reference populations demonstrated that the studied Han population had relatively closer genetic affinities with Northern Han Chinese populations than Southern Han and other minority groups. To sum up, these 44 Y-markers can be utilized as a valuable tool for male differentiation in the Inner Mongolia Han population.
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Affiliation(s)
- Xiaoye Jin
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an, China
- College of Forensic Science, Xi’an Jiaotong University Health Science Center, Xi’an, China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi’an Jiaotong University, Xi’an, China
| | - Guohui Xing
- People’s Hospital of Arong Banner, Hulun Buir City, China
| | - Chunhua Yang
- People’s Hospital of Arong Banner, Hulun Buir City, China
| | - Xingru Zhang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an, China
- College of Forensic Science, Xi’an Jiaotong University Health Science Center, Xi’an, China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi’an Jiaotong University, Xi’an, China
| | - Wei Cui
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an, China
- College of Forensic Science, Xi’an Jiaotong University Health Science Center, Xi’an, China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi’an Jiaotong University, Xi’an, China
| | - Chong Chen
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an, China
- College of Forensic Science, Xi’an Jiaotong University Health Science Center, Xi’an, China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi’an Jiaotong University, Xi’an, China
| | - Bofeng Zhu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an, China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi’an Jiaotong University, Xi’an, China
- Multi-Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, China
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6
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Liu Y, Jin X, Lan Q, Zhao C, Xu H, Xie T, Lan J, Tai Y, Zhu B. Forensic characteristic and population structure dissection of Shaanxi Han population in the light of diallelic deletion/insertion polymorphism data. Genomics 2020; 112:3837-3845. [PMID: 32574833 DOI: 10.1016/j.ygeno.2020.06.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/15/2020] [Accepted: 06/17/2020] [Indexed: 12/08/2022]
Abstract
The genetic polymorphisms of diallelic deletion/insertion polymorphic (DIP) loci in the Shaanxi Han population are still not clearly characterized. Herein, allele frequencies and forensic application efficiencies for 30 diallelic DIP loci were investigated in 506 unrelated healthy Han individuals from Chinese Shaanxi province. Based on population data of the same 30 diallelic DIP loci, the genetic differentiations, hierarchical clustering relationships and population architectures among Shaanxi Han and other 50 populations were further dissected through genetic and bioinformatics analyses. Results indicated that most of the 30 diallelic DIP loci were relatively high polymorphisms in the Shaanxi Han population; and there were the genetically intimate relationships between Shaanxi Han and the East Asian populations. In summary, this study provided significant insights into genetic background of Shaanxi Han population, and the multiplex amplification of these 30 diallelic DIP loci was appropriate for forensic individual identification and population genetic research in Shaanxi Han population.
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Affiliation(s)
- Yanfang Liu
- Multi-Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
| | - Xiaoye Jin
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, 710004 Xi'an, China; Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, 710004, Xi'an, China; College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, China
| | - Qiong Lan
- Multi-Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
| | - Congying Zhao
- Multi-Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
| | - Hui Xu
- Multi-Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
| | - Tong Xie
- Multi-Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
| | - Jiangwei Lan
- Multi-Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
| | - Yunchun Tai
- Multi-Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
| | - Bofeng Zhu
- Multi-Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China; Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, 710004 Xi'an, China; Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, 710004, Xi'an, China.
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7
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Wang F, He G, Wang Z, Wang M, Liu J, Zou X, Wang S, Song M, Ye Z, Xie M, Hou Y. Population genetics and forensic efficiency of 30 InDel markers in four Chinese ethnic groups residing in Sichuan. Forensic Sci Res 2020; 7:498-502. [DOI: 10.1080/20961790.2020.1737470] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Affiliation(s)
- Fei Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Guanglin He
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Mengge Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Jing Liu
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Xing Zou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Shouyu Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Mengyuan Song
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Ziwei Ye
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Mingkun Xie
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
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8
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Zhou B, Wen S, Sun H, Zhang H, Shi R. Genetic affinity between Ningxia Hui and eastern Asian populations revealed by a set of InDel loci. ROYAL SOCIETY OPEN SCIENCE 2020; 7:190358. [PMID: 32218926 PMCID: PMC7029925 DOI: 10.1098/rsos.190358] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 11/29/2019] [Indexed: 01/02/2023]
Abstract
According to historical records, ethnic Hui in China obtained substantial genetic components from western Eurasian populations during their Islamization. However, some scholars believed that the ancestry of Hui people were native Chinese populations. In this context, the formation of Hui is due to simple cultural diffusion rather than demic diffusion. In this study, we examined the forensic and population genetic application of the 30 InDel loci in Hui population from Ningxia Hui Autonomous Region, Northwest China. Genotype analysis of 129 unrelated individuals revealed that all loci were in the Hardy-Weinberg equilibrium in Ningxia Hui. Forensic indices calculated from genotypes demonstrated that this panel, Qiagen DIPplex® Investigator kit, was powerful enough to be used in individual identification but not in paternity cases. Through population genetic analysis, we found that Ningxia Hui received much more genetic contributions from East Asian populations than those from western Eurasian populations. Finally, we statistically identified the admixture signal of eastern and western Eurasians, although the latter is weak, in Ningxia Hui via the three-population test. All this evidence suggested that the formation of Ningxia Hui was mainly attributed to the cultural transformation of local Chinese residents with minor gene flow from western Eurasian populations.
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Affiliation(s)
- Boyan Zhou
- State Key Laboratory of Genetic Engineering and Institute of Biostatistics, School of Life Sciences, Fudan University, Shanghai 200438, People's Republic of China
- State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai 200438, People's Republic of China
| | - Shaoqing Wen
- State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai 200438, People's Republic of China
| | - Huilin Sun
- Department of Endocrinology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangdong 510080, People's Republic of China
| | - Hong Zhang
- The First Affiliated Hospital Health Center and School of Management, University of Science and Technology of China, Hefei 230026, People's Republic of China
| | - Ruiming Shi
- Department of Pediatrics, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, People's Republic of China
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Liu J, Ye Z, Wang Z, Zou X, He G, Wang M, Wang S, Hou Y. Genetic diversity and phylogenetic analysis of Chinese Han and Li ethnic populations from Hainan Island by 30 autosomal insertion/deletion polymorphisms. Forensic Sci Res 2019; 7:189-195. [PMID: 35784419 PMCID: PMC9245983 DOI: 10.1080/20961790.2019.1672933] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
With the characteristics of low mutation rate, length variation and short amplicon size, insertion/deletion polymorphisms (InDels) have the advantages of both short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs). Herein, people of two ethnicities from Hainan Island were genotyped for the first time using the Investigator DIPplex kit. We investigated the forensic parameters of the 30 InDels and the phylogenetic relationships among different populations. The accumulated powers of discrimination and powers of exclusion were 0.999 999 999 9646 and 0.9897 in the Hainan Han population and 0.999 999 999 9292 and 0.9861 in the Hainan Li population, respectively. Additionally, population comparisons among geographically, ethnically and linguistically diverse populations via cluster heatmap, multidimensional scaling, principal component analysis, phylogenetic tree and STRUCTURE analyses demonstrated that the Hainan Han population had genetic similarities to the other Han, She and Tujia populations, while the Hainan Li population had close genetic relationships to the Zhuang and Miao groups; both populations had a high degree of genetic differentiation from most Turkic-speaking populations. Aforementioned results suggested that the 30 autosomal InDels are highly polymorphic and informative, which are suitable for human identification and population genetics. Four hundred and forty-five Chinese individuals from two ethnicities (Hainan Han and Hainan Li) were firstly analyzed by 30 autosomal InDels included in the Investigator DIPplex panel. Forensic parameters of the 30 InDels in the two populations showed high polymorphism and universality for human identification purposes. The Investigator DIPplex panel had a certain capacity of differentiating intercontinental populations and different language populations.
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Affiliation(s)
- Jing Liu
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Ziwei Ye
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Xing Zou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Guanglin He
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Mengge Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Shouyu Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
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10
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Nagai A, Yamamoto T, Hara M, Michiue T. Genetic polymorphisms of 30 insertion/deletion markers in the populations of Japan, Bangladesh, and Indonesia. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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11
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A comprehensive exploration of the genetic legacy and forensic features of Afghanistan and Pakistan Mongolian-descent Hazara. Forensic Sci Int Genet 2019; 42:e1-e12. [DOI: 10.1016/j.fsigen.2019.06.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 06/23/2019] [Accepted: 06/23/2019] [Indexed: 01/09/2023]
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12
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Population genetics, diversity and forensic characteristics of Tai–Kadai-speaking Bouyei revealed by insertion/deletions markers. Mol Genet Genomics 2019; 294:1343-1357. [DOI: 10.1007/s00438-019-01584-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Accepted: 05/30/2019] [Indexed: 12/13/2022]
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13
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Chen L, Du W, Wu W, Yu A, Pan X, Feng P, Feng C, Li C, Xu L, Liu C, Liu C. Developmental validation of a novel six-dye typing system with 47 A-InDels and 2 Y-InDels. Forensic Sci Int Genet 2019; 40:64-73. [DOI: 10.1016/j.fsigen.2019.02.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 11/17/2018] [Accepted: 02/10/2019] [Indexed: 10/27/2022]
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14
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Jin X, Wei Y, Cui W, Chen C, Guo Y, Zhang W, Zhu B. Development of a novel multiplex polymerase chain reaction system for forensic individual identification using insertion/deletion polymorphisms. Electrophoresis 2019; 40:1691-1698. [DOI: 10.1002/elps.201800412] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 03/12/2019] [Accepted: 03/21/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Xiao‐Ye Jin
- Key laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of StomatologyXi'an Jiaotong University Xi'an P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial DiseasesCollege of StomatologyXi'an Jiaotong University Xi'an P. R. China
- College of Forensic MedicineXi'an Jiaotong University Health Science Center Xi'an P. R. China
| | - Yuan‐Yuan Wei
- Key laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of StomatologyXi'an Jiaotong University Xi'an P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial DiseasesCollege of StomatologyXi'an Jiaotong University Xi'an P. R. China
| | - Wei Cui
- Key laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of StomatologyXi'an Jiaotong University Xi'an P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial DiseasesCollege of StomatologyXi'an Jiaotong University Xi'an P. R. China
- College of Forensic MedicineXi'an Jiaotong University Health Science Center Xi'an P. R. China
| | - Chong Chen
- Key laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of StomatologyXi'an Jiaotong University Xi'an P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial DiseasesCollege of StomatologyXi'an Jiaotong University Xi'an P. R. China
- College of Forensic MedicineXi'an Jiaotong University Health Science Center Xi'an P. R. China
| | - Yu‐Xin Guo
- Key laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of StomatologyXi'an Jiaotong University Xi'an P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial DiseasesCollege of StomatologyXi'an Jiaotong University Xi'an P. R. China
- College of Forensic MedicineXi'an Jiaotong University Health Science Center Xi'an P. R. China
| | - Wen‐Qing Zhang
- Key laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of StomatologyXi'an Jiaotong University Xi'an P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial DiseasesCollege of StomatologyXi'an Jiaotong University Xi'an P. R. China
| | - Bo‐Feng Zhu
- Key laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of StomatologyXi'an Jiaotong University Xi'an P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial DiseasesCollege of StomatologyXi'an Jiaotong University Xi'an P. R. China
- Department of Forensic GeneticsSchool of Forensic MedicineSouthern Medical University Guangzhou P. R. China
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15
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Yang CH, Jin XY, Guo YX, Cui W, Chen C, Meng HT, Zhu BF. Genetic distribution analyses and population background explorations of Gansu Yugur and Guizhou Miao groups via InDel markers. J Hum Genet 2019; 64:535-543. [PMID: 30944401 DOI: 10.1038/s10038-019-0595-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 03/01/2019] [Accepted: 03/15/2019] [Indexed: 12/27/2022]
Abstract
Insertion and deletion markers (InDels) have gained considerable attentions in population genetics and forensic research. In this study, we investigated genetic distributions of 30 InDels in Gansu Yugur and Guizhou Miao groups and evaluated their forensic application values. Genetic relationship analyses between Gansu Yugur, Guizhou Miao groups and other published populations were conducted based on these 30 InDels. Power of discrimination and power of exclusion in trio and duo cases of 30 InDels ranged from 0.3528 to 0.6247, 0.0937 to 0.1873, and 0.0219 to 0.1247 in Gansu Yugur group; and they ranged from 0.2579 to 0.6247, 0.0671 to 0.1874, and 0.0105 to 0.1247 in Guizhou Miao group. Obtained cumulative power of discrimination values indicated these InDels could be used for forensic individual identifications in both ethnic groups. Principal component analysis and phylogenetic reconstruction revealed that Gansu Yugur and Guizhou Miao groups had close affinities with their neighboring populations. Genetic structure analyses among these populations also indicated that studied Gansu Yugur and Guizhou Miao groups showed similar genetic structure with their neighboring populations. Further analyses of Y-STR, mtDNA, and ancestry informative markers should be conducted to better understand genetic backgrounds of Gansu Yugur and Guizhou Miao groups in the future.
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Affiliation(s)
- Chun-Hua Yang
- Key laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, 710004, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, 710004, Xi'an, China.,College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, 710061, Xi'an, China
| | - Xiao-Ye Jin
- Key laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, 710004, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, 710004, Xi'an, China.,College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, 710061, Xi'an, China
| | - Yu-Xin Guo
- Key laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, 710004, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, 710004, Xi'an, China.,College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, 710061, Xi'an, China
| | - Wei Cui
- Key laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, 710004, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, 710004, Xi'an, China.,College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, 710061, Xi'an, China
| | - Chong Chen
- Key laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, 710004, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, 710004, Xi'an, China.,College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, 710061, Xi'an, China
| | - Hao-Tian Meng
- Key laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, 710004, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, 710004, Xi'an, China
| | - Bo-Feng Zhu
- Key laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, 710004, Xi'an, China. .,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, 710004, Xi'an, China. .,Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, 510515, Guangzhou, China.
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16
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Li L, Ye Y, Song F, Wang Z, Hou Y. Genetic structure and forensic parameters of 30 InDels for human identification purposes in 10 Tibetan populations of China. Forensic Sci Int Genet 2019; 40:e219-e227. [PMID: 30744985 DOI: 10.1016/j.fsigen.2019.02.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 02/02/2019] [Accepted: 02/03/2019] [Indexed: 01/21/2023]
Abstract
Insertion/deletion analysis can serve as a promising and useful supporting tool in forensic research. The Qiagen Investigator® DIPplex Kit contained 30 well-chosen autosomal InDels was targeted to reveal the population genetic variation. In the present study, 10 Tibetan populations residing in different geographic areas of China were recruited and genotyped by Investigator® DIPplex Kit. Allele frequencies and forensic parameters were determined. No significant departures from Hard-Weinberg equilibrium (HWE) in all loci/populations after Bonferroni correction. The combined matching probability values range from 1.7148 × 10-11 to 5.3516 × 10-1° in 10 Tibetan populations. Our results revealed 10 Tibetan populations in China are genetically very similar. Intercontinental population differentiation analysis indicated Tibetan populations had a close genetic relationship with East Asian populations using Hierarchical clustering, multi-dimensional scaling (MDS), principal component analysis (PCA) and STRUCTURE. Comprehensive population genetic studies revealed that the 30-InDels assay was similarly efficient in forensic personal identification and could be regarded as an effective supplementary protocol for kinship testing.
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Affiliation(s)
- Luyao Li
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Yi Ye
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Feng Song
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China.
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17
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Forensic efficiency and genetic divergence of 30 autosomal InDels in Chinese Han population from Jiangsu province. Forensic Sci Int Genet 2018; 37:e17-e19. [DOI: 10.1016/j.fsigen.2018.08.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 08/09/2018] [Accepted: 08/12/2018] [Indexed: 12/19/2022]
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18
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Guo Y, Chen C, Jin X, Cui W, Wei Y, Wang H, Kong T, Mu Y, Zhu B. Autosomal DIPs for population genetic structure and differentiation analyses of Chinese Xinjiang Kyrgyz ethnic group. Sci Rep 2018; 8:11054. [PMID: 30038288 PMCID: PMC6056483 DOI: 10.1038/s41598-018-29010-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 07/04/2018] [Indexed: 11/09/2022] Open
Abstract
In recent years, deletion and insertion polymorphisms (DIPs) were treated as a novel complementary tool with huge potential for forensic applications. In this study, we utilized 30 DIP loci to make a comprehensive research of allele frequency distribution and compute forensic parameters to evaluate the efficiency of forensic applications in the 295 unrelated healthy individuals of Kyrgyz group, and in addition, infer the genetic relationships between Kyrgyz group and 24 other previously studied groups. No significant departures from Hardy-Weinberg equilibrium and linkage disequilibrium were observed at these 30 DIP loci. The combined power of discrimination and the combined probability of exclusion for all 30 DIP loci in Kyrgyz group were 0.9999999999989 and 0.9939, respectively. Furthermore, the results of the interpopulation differentiations, phylogenetic reconstruction, population genetic structure and principal component analyses suggested that Kyrgyz group had relatively close genetic relationships with Kazakh and Uygur groups. However, it was also important to stress that 15 loci were selected out from these 30 DIP loci using the method of selecting ancestry markers, which could be utilized for further ancestry inference study relatively.
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Affiliation(s)
- Yuxin Guo
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, P. R. China
- College of Medicine & Forensics, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, P. R. China
| | - Chong Chen
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, P. R. China
- College of Medicine & Forensics, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, P. R. China
| | - Xiaoye Jin
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, P. R. China
- College of Medicine & Forensics, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, P. R. China
| | - Wei Cui
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, P. R. China
- College of Medicine & Forensics, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, P. R. China
| | - Yuanyuan Wei
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, P. R. China
| | - Hongdan Wang
- Medical Genetics Institute of Henan Province, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, 450003, P. R. China
| | - Tingting Kong
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, P. R. China
| | - Yuling Mu
- College of Medicine & Forensics, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, P. R. China
| | - Bofeng Zhu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, P. R. China.
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, P. R. China.
- College of Medicine & Forensics, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, P. R. China.
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19
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He G, Wang Z, Zou X, Chen X, Liu J, Wang M, Hou Y. Genetic diversity and phylogenetic characteristics of Chinese Tibetan and Yi minority ethnic groups revealed by non-CODIS STR markers. Sci Rep 2018; 8:5895. [PMID: 29651125 PMCID: PMC5897523 DOI: 10.1038/s41598-018-24291-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 03/13/2018] [Indexed: 12/16/2022] Open
Abstract
Non-CODIS STRs, with high polymorphism and allele frequency difference among ethnically and geographically different populations, play a crucial role in population genetics, molecular anthropology, and human forensics. In this work, 332 unrelated individuals from Sichuan Province (237 Tibetan individuals and 95 Yi individuals) are firstly genotyped with 21 non-CODIS autosomal STRs, and phylogenetic relationships with 26 previously investigated populations (9,444 individuals) are subsequently explored. In the Sichuan Tibetan and Yi, the combined power of discrimination (CPD) values are 0.9999999999999999999 and 0.9999999999999999993, and the combined power of exclusion (CPE) values are 0. 999997 and 0.999999, respectively. Analysis of molecular variance (AMOVA), principal component analysis (PCA), multidimensional scaling plots (MDS) and phylogenetic analysis demonstrated that Sichuan Tibetan has a close genetic relationship with Tibet Tibetan, and Sichuan Yi has a genetic affinity with Yunnan Bai group. Furthermore, significant genetic differences have widely existed between Chinese minorities (most prominently for Tibetan and Kazakh) and Han groups, but no population stratifications rather a homogenous group among Han populations distributed in Northern and Southern China are observed. Aforementioned results suggested that these 21 STRs are highly polymorphic and informative in the Sichuan Tibetan and Yi, which are suitable for population genetics and forensic applications.
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Affiliation(s)
- Guanglin He
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Xing Zou
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Xu Chen
- Department of Clinical Laboratory, the First People's Hospital of Liangshan Yi Autonomous Prefecture, Xichang, Sichuan, China
| | - Jing Liu
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Mengge Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, China.
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20
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Yang CH, Yin CY, Shen CM, Guo YX, Dong Q, Yan JW, Wang HD, Zhang YD, Meng HT, Jin R, Chen F, Zhu BF. Genetic variation and forensic efficiency of autosomal insertion/deletion polymorphisms in Chinese Bai ethnic group: phylogenetic analysis to other populations. Oncotarget 2018; 8:39582-39591. [PMID: 28465476 PMCID: PMC5503634 DOI: 10.18632/oncotarget.17137] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 02/17/2017] [Indexed: 01/01/2023] Open
Abstract
Thirty insertion/deletion loci were utilized to study the genetic diversities of 125 bloodstain samples collected from Bai group in Yunnan Dali region, China. The observed heterozygosity and expected heterozygosity of the 30 loci ranged from 0.1520 to 0.5680, and 0.1927 to 0.4997, respectively. No deviations from Hardy-Weinberg equilibrium tests after Bonferroni correction were found at all 30 loci in Bai group. The cumulative probability of exclusion and combined discrimination power were 0.9859 and 0.9999999999887, respectively, which indicated the 30 loci could be used as complementary genetic markers for paternity testing and were qualified for personal identification in forensic cases. We found the studied Bai group had close relationships with Tibetan, Yi and Han groups from China by the population structure, principal component analysis, population differentiations, and phylogenetic reconstruction studies. Even so, for a better understanding of Bai ethnicity's genetic milieu, DNA genotyping at various genetic markers is necessary in future studies.
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Affiliation(s)
- Chun-Hua Yang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China.,Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, P. R. China
| | - Cai-Yong Yin
- Department of Forensic Medicine, Nanjing Medical University, Nanjing, Jiangsu, P. R. China
| | - Chun-Mei Shen
- Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, P. R. China.,Institute of Brain and Behavioral Sciences, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, P. R. China
| | - Yu-Xin Guo
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Qian Dong
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Jiang-Wei Yan
- Key Laboratory of Genome Sciences, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, P. R. China
| | - Hong-Dan Wang
- Medical Genetic Institute of Henan Province, People's Hospital of Henan Province, Zhengzhou, Henan, P. R. China
| | - Yu-Dang Zhang
- Institue of Forensic Sciences of Anhui Public Security Department, Hefei, Anhui, P. R. China
| | - Hao-Tian Meng
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Rui Jin
- Department of Radiology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Feng Chen
- Department of Forensic Medicine, Nanjing Medical University, Nanjing, Jiangsu, P. R. China
| | - Bo-Feng Zhu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China.,Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, P. R. China
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21
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Xie T, Guo Y, Chen L, Fang Y, Tai Y, Zhou Y, Qiu P, Zhu B. A set of autosomal multiple InDel markers for forensic application and population genetic analysis in the Chinese Xinjiang Hui group. Forensic Sci Int Genet 2018; 35:1-8. [PMID: 29602069 DOI: 10.1016/j.fsigen.2018.03.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 03/01/2018] [Accepted: 03/12/2018] [Indexed: 01/01/2023]
Abstract
In recent years, insertion/deletion (InDel) markers have become a promising and useful supporting tool in forensic identification cases and biogeographic research field. In this study, 30 InDel loci were explored to reveal the genetic diversities and genetic relationships between Chinese Xinjiang Hui group and the 25 previously reported populations using various biostatistics methods such as forensic statistical parameter analysis, phylogenetic reconstruction, multi-dimensional scaling, principal component analysis, and STRUCTURE analysis. No deviations from Hardy-Weinberg equilibrium tests were found at all 30 loci in the Chinese Xinjiang Hui group. The observed heterozygosity and expected heterozygosity ranged from 0.1971 (HLD118) to 0.5092 (HLD92), 0.2222 (HLD118) to 0.5000 (HLD6), respectively. The cumulative probability of exclusion and combined power of discrimination were 0.988849 and 0.99999999999378, respectively, which indicated that these 30 loci could be qualified for personal identification and used as complementary genetic markers for paternity tests in forensic cases. The results of present research based on the different methods of population genetic analysis revealed that the Chinese Xinjiang Hui group had close relationships with most Chinese groups, especially Han populations. In spite of this, for a better understanding of genetic background of the Chinese Xinjiang Hui group, more molecular genetic markers such as ancestry informative markers, single nucleotide polymorphisms (SNPs), and copy number variations will be conducted in future studies.
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Affiliation(s)
- Tong Xie
- Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, PR China
| | - Yuxin Guo
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, PR China; Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
| | - Ling Chen
- Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, PR China
| | - Yating Fang
- Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, PR China
| | - Yunchun Tai
- Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, PR China
| | - Yongsong Zhou
- Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, PR China
| | - Pingming Qiu
- Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, PR China
| | - Bofeng Zhu
- Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, PR China; Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, PR China; Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, PR China.
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22
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Forensic efficiency and genetic variation of 30 InDels in Vietnamese and Nigerian populations. Oncotarget 2017; 8:88934-88940. [PMID: 29179488 PMCID: PMC5687658 DOI: 10.18632/oncotarget.21494] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 08/23/2017] [Indexed: 01/28/2023] Open
Abstract
Insertion/deletion polymorphisms (InDels) are ubiquitous diallelic genetic markers that have drawn increasing attention from forensic researchers. Here, we investigated 30 InDel loci in Vietnamese and Nigerian populations and evaluated their usefulness in forensic genetics. The polymorphic information content of these populations ranged, respectively, from 0.164 to 0.375 and from 0.090 to 0.375 across loci. After Bonferroni correction, no significant deviation from Hardy-Weinberg equilibrium was found, except for HLD97 in the Nigerian population. The cumulative power of exclusion for all 30 loci in the Vietnamese and Nigerian populations was 0.9870 and 0.9676, respectively, indicating that this InDel set is not suitable for paternity testing in these populations, but could be included as a supplement. For the Vietnamese and the Nigerian populations, the mean observed heterozygosity was 0.5917 and 0.6268, and the combined discrimination power of the 30 loci was 0.9999999999767 and 0.9999999999603, respectively. These findings indicated that these InDels may be suitable for personal forensic identification in the studied populations. The results of DA distance, phylogenetic tree, principal component, and cluster analyses were consistent and indicated a clear pattern of regional distribution. Moreover, the Vietnamese population was shown to have close genetic relationships with the Guangdong Han and Shanghai Han populations.
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23
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Kong T, Chen Y, Guo Y, Wei Y, Jin X, Xie T, Mu Y, Dong Q, Wen S, Zhou B, Zhang L, Shen C, Zhu B. Autosomal InDel polymorphisms for population genetic structure and differentiation analysis of Chinese Kazak ethnic group. Oncotarget 2017; 8:56651-56658. [PMID: 28915619 PMCID: PMC5593590 DOI: 10.18632/oncotarget.17838] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 04/12/2017] [Indexed: 01/25/2023] Open
Abstract
In the present study, we assessed the genetic diversities of the Chinese Kazak ethnic group on the basis of 30 well-chosen autosomal insertion and deletion loci and explored the genetic relationships between Kazak and 23 reference groups. We detected the level of the expected heterozygosity ranging from 0.3605 at HLD39 locus to 0.5000 at HLD136 locus and the observed heterozygosity ranging from 0.3548 at HLD39 locus to 0.5283 at HLD136 locus. The combined power of discrimination and the combined power of exclusion for all 30 loci in the studied Kazak group were 0.999999999999128 and 0.9945, respectively. The dataset generated in this study indicated the panel of 30 InDels was highly efficient in forensic individual identifcation but may not have enough power in paternity cases. The results of the interpopulation differentiations, PCA plots, phylogenetic trees and STRUCTURE analyses showed a close genetic affiliation between the Kazak and Uigur group.
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Affiliation(s)
- Tingting Kong
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an, P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi’an Jiaotong University, Xi’an, P. R. China
- Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Yahao Chen
- Laboratory Medicine Center, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, P. R. China
| | - Yuxin Guo
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an, P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi’an Jiaotong University, Xi’an, P. R. China
- College of Medicine & Forensics, Xi’an Jiaotong University Health Science Center, Xi’an, P. R. China
| | - Yuanyuan Wei
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an, P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi’an Jiaotong University, Xi’an, P. R. China
| | - Xiaoye Jin
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an, P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi’an Jiaotong University, Xi’an, P. R. China
- College of Medicine & Forensics, Xi’an Jiaotong University Health Science Center, Xi’an, P. R. China
| | - Tong Xie
- Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Yuling Mu
- College of Medicine & Forensics, Xi’an Jiaotong University Health Science Center, Xi’an, P. R. China
| | - Qian Dong
- College of Medicine & Forensics, Xi’an Jiaotong University Health Science Center, Xi’an, P. R. China
| | - Shaoqing Wen
- State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, P. R. China
| | - Boyan Zhou
- State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, P. R. China
- State Key Laboratory of Genetic Engineering and Institute of Biostatistics, School of Life Sciences, Fudan University, Shanghai, P. R. China
| | - Li Zhang
- Department of Gastroenterology, Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, P. R. China
| | - Chunmei Shen
- Institute of Brain and Behavioral Sciences, College of Life Sciences, Shaanxi Normal University, Xi’an, P. R. China
| | - Bofeng Zhu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an, P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi’an Jiaotong University, Xi’an, P. R. China
- Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
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Liu X, Chen F, Niu Y, Bian Y, Zhang S, Zhu R, Li C. Population genetics of 30 insertion/deletion polymorphisms in Han Chinese population from Zhejiang Province. Forensic Sci Int Genet 2017; 28:e33-e35. [DOI: 10.1016/j.fsigen.2017.02.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 02/08/2017] [Accepted: 02/19/2017] [Indexed: 12/30/2022]
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Guo Y, Shen C, Meng H, Dong Q, Kong T, Yang C, Wang H, Jin R, Zhu B. Population Differentiations and Phylogenetic Analysis of Tibet and Qinghai Tibetan Groups Based on 30 InDel Loci. DNA Cell Biol 2016; 35:787-794. [DOI: 10.1089/dna.2016.3395] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Yuxin Guo
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
| | - Chunmei Shen
- College of Life Sciences, Shaanxi Normal University, Xi'an, People's Republic of China, China
- Blood Center of Shaanxi Province, Xi'an, People's Republic of China, China
| | - Haotian Meng
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
| | - Qian Dong
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
| | - Tingting Kong
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
| | - Chunhua Yang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
- People's Hospital of Arong Banner, Hulun Buir City, People's Republic of China, China
| | - Hongdan Wang
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, People's Republic of China, China
| | - Rui Jin
- Department of Radiology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, People's Republic of China, China
| | - Bofeng Zhu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
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Shen C, Zhu B, Yao T, Li Z, Zhang Y, Yan J, Wang B, Bie X, Tai F. A 30-InDel Assay for Genetic Variation and Population Structure Analysis of Chinese Tujia Group. Sci Rep 2016; 6:36842. [PMID: 27833167 PMCID: PMC5104975 DOI: 10.1038/srep36842] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 10/19/2016] [Indexed: 01/10/2023] Open
Abstract
In the present study, thirty autosomal insertion and deletion polymorphic loci were simultaneously amplified and genotyped in a multiplex system, and their allelic frequencies as well as several forensic parameters were obtained in a sample of 236 unrelated healthy Tujia individuals. All the loci were in Hardy-Weinberg equilibrium after applying a Bonferroni correction and all pair-wise loci showed no significant linkage disequilibrium. These loci were observed to be relatively informative and discriminating, quite efficient for forensic applications. Allelic frequencies of 30 loci were compared between the Tujia group and other reference populations, and the results of analysis of molecular variance indicated the Tujia group showed the least significant differences with the Shanghai Han at one locus, and the most with Central Spanish population at 22 loci. We analyzed the population genetic structure by the principal component analysis, the clustering of STRUCTURE program and a Neighbor-Joining tree, and then evaluated the genetic relationships among Tujia and other 15 populations.
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Affiliation(s)
- Chunmei Shen
- Blood Center of Shaanxi Province, Xi'an, Shaanxi 710061, P. R. China.,Institute of Brain and Behavioral Sciences, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710062, P. R. China
| | - Bofeng Zhu
- Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, P. R. China.,Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P. R. China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P. R. China
| | - Tianhua Yao
- Department of General Dentistry, Stomatological Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P. R. China
| | - Zhidan Li
- Department of Endodontics, Stomatological Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P. R. China
| | - Yudang Zhang
- Institute of Forensic Science of Anhui Public Security Department, Hefei, Anhui 230061, P. R. China
| | - Jiangwei Yan
- Key Laboratory of Genome Sciences, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, P. R. China
| | - Bo Wang
- College of Biological Technology, Xi'an University, Xi'an, Shaanxi 710065, P. R. China
| | - Xiaohua Bie
- Department of Neurosurgery, Hong-hui Hospital, Xi'an Jiaotong University College of Medicine, Xi'an, Shaanxi 710054, P. R. China
| | - Fadao Tai
- Institute of Brain and Behavioral Sciences, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710062, P. R. China
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27
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Mei T, Shen CM, Liu YS, Meng HT, Zhang YD, Guo YX, Dong Q, Wang XX, Yan JW, Zhu BF, Zhang LP. Population genetic structure analysis and forensic evaluation of Xinjiang Uigur ethnic group on genomic deletion and insertion polymorphisms. SPRINGERPLUS 2016; 5:1087. [PMID: 27468387 PMCID: PMC4947079 DOI: 10.1186/s40064-016-2730-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 06/30/2016] [Indexed: 02/07/2023]
Abstract
Background The Uigur ethnic minority is the largest ethnic group in the Xinjiang Uygur Autonomous Region of China, and valuable resource for the study of ethnogeny. The objective of this study was to estimate the genetic diversities and forensic parameters of 30 insertion-deletion loci in Uigur ethnic group from Xinjiang Uigur Autonomous Region of China and to analyze the genetic relationships between Xinjiang Uigur group and other previously published groups based on population data of these loci. Results All the tested loci were conformed to Hardy–Weinberg equilibrium after Bonferroni correction. The observed and expected heterozygosity ranged from 0.3750 to 0.5515; and 0.4057 to 0.5037, respectively. The combined power of discrimination and probability of exclusion in the group were 0.99999999999940 and 0.9963, respectively. We analyzed the DA distance, interpopulation differentiations and population structure, conducted principal component analysis and neighbor-joining tree based on our studied group and 21 reference groups. The present results indicated that the studied Xinjiang Uigur group (represented our samples from the whole territory of Xinjiang Uigur Autonomous Region) had a close relationships with Urumchi Uigur (represented previously reported samples from Urumchi of Xinjiang) and Kazak groups. Conclusions The present study may provide novel biological information for the study of population genetics, and can also increase our understanding of the genetic relationships between Xinjiang Uigur group and other groups. Electronic supplementary material The online version of this article (doi:10.1186/s40064-016-2730-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ting Mei
- Department of Biochemistry and Molecular Biology, Basic Medicine College, Xinjiang Medical University, Urumqi, 830011 People's Republic of China.,Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004 People's Republic of China.,Clinical Reaserch Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004 People's Republic of China
| | - Chun-Mei Shen
- Institute of Brain and Behavioral Sciences, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710062 China.,Blood Center of Shaanxi Province, Xi'an, 710061 People's Republic of China
| | - Yao-Shun Liu
- Department of Biochemistry and Molecular Biology, Basic Medicine College, Xinjiang Medical University, Urumqi, 830011 People's Republic of China.,Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004 People's Republic of China.,Clinical Reaserch Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004 People's Republic of China
| | - Hao-Tian Meng
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004 People's Republic of China.,Clinical Reaserch Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004 People's Republic of China
| | - Yu-Dang Zhang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004 People's Republic of China.,Clinical Reaserch Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004 People's Republic of China
| | - Yu-Xin Guo
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004 People's Republic of China.,Clinical Reaserch Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004 People's Republic of China
| | - Qian Dong
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004 People's Republic of China.,Clinical Reaserch Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004 People's Republic of China
| | - Xin-Xin Wang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004 People's Republic of China.,Clinical Reaserch Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004 People's Republic of China
| | - Jiang-Wei Yan
- Key Laboratory of Genome Sciences, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101 People's Republic of China
| | - Bo-Feng Zhu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004 People's Republic of China.,Clinical Reaserch Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004 People's Republic of China
| | - Li-Ping Zhang
- Department of Biochemistry and Molecular Biology, Basic Medicine College, Xinjiang Medical University, Urumqi, 830011 People's Republic of China
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Hefke G, Davison S, D'Amato ME. Forensic performance of Investigator DIPplex indels genotyping kit in native, immigrant, and admixed populations in South Africa. Electrophoresis 2015; 36:3018-25. [DOI: 10.1002/elps.201500243] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 08/09/2015] [Accepted: 08/27/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Gwynneth Hefke
- Forensic DNA Laboratory, Department of Biotechnology; University of the Western Cape; Bellville South Africa
- South African Police Service Forensic Science Laboratory; Biology Unit; Panorama South Africa
| | - Sean Davison
- Forensic DNA Laboratory, Department of Biotechnology; University of the Western Cape; Bellville South Africa
| | - Maria Eugenia D'Amato
- Forensic DNA Laboratory, Department of Biotechnology; University of the Western Cape; Bellville South Africa
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29
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D’ Amato M, Hefke G, Davison S. Evaluation of DIPplex investigator kit in European, Asian and African populations. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2015. [DOI: 10.1016/j.fsigss.2015.09.186] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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