1
|
Yang M, Yang X, Ren Z, He G, Zhang H, Wang Q, Liu Y, Zhang H, Ji J, Chen J, Guo J, Huang J, Wang CC. Genetic Admixture History and Forensic Characteristics of Guizhou Sui People Inferred From Autosomal Insertion/Deletion and Genome-Wide Single-Nucleotide Polymorphisms. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.844761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Insertion-deletion (Indel) serves as one of the important markers in forensic personal identification and parentage testing, especially for cases with degraded samples. However, the genetic diversity and forensic features in ethnolinguistically diverse southwestern Chinese populations remain to be explored. Sui, one Tai-Kadai-speaking population residing in Guizhou, has a complex genetic history based on linguistic, historic, and anthropological evidence. In this study, we genotyped 30 Indels from 511 Guizhou Sui individuals and obtained approximately 700,000 genome-wide single-nucleotide polymorphisms (SNPs) in 15 representative Sui individuals to comprehensively characterize the genetic diversity, forensic characteristics, and genomic landscape of Guizhou Sui people. The estimated forensic statistically allele frequency spectrum and parameters demonstrated that this Indels panel was polymorphic and informative in Tai-Kadai populations in southern China. Results of principal component analysis (PCA), STRUCTURE, and phylogenetic trees showed that Guizhou Sui had a close genetic relationship with geographically close Tai-Kadai and Hmong-Mien people. Furthermore, genomic analysis based on the Fst and f4-statistics further suggested the genetic affinity within southern Chinese Tai-Kadai-speaking populations and a close relationship with geographically adjoining Guizhou populations. Admixture models based on the ADMIXTURE, f4, three-way qpAdm, and ALDER results demonstrated the interaction between the common ancestor for Tai-Kadai/Austronesian, Hmong-Mien, and Austroasiatic speaking populations played a significant role in the formation of modern Tai-Kadai people. We observed a sex-biased influence in Sui people by finding that the dominant Y chromosomal type was a Hmong-Mien specific lineage O2a2a1a2a1a2-N5 but the mtDNA lineages were commonly found in Tai-Kadai populations. The additional southward expansion of millet farmers in the Yellow River Basin has impacted the gene pool of southern populations including Tai-Kadai. The whole-genome sequencing in the future will shed more light on the finer genetic profile of Guizhou populations.
Collapse
|
2
|
Xu H, Zhao C, Lan Q, Li S, Liu Y, Mei S, Fang Y, Zhu B. Forensic features and genetic structure revealed by 47 Individual Identification InDels in the Shaanxi Han population. Leg Med (Tokyo) 2022; 56:102030. [DOI: 10.1016/j.legalmed.2022.102030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 12/21/2021] [Accepted: 01/25/2022] [Indexed: 10/19/2022]
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Cui W, Jin X, Guo Y, Chen C, Zhang W, Kong T, Wang Y, Huang J, Zhu B. Forensic applicability of autosomal insertion/deletion loci in Chinese Daur ethnic group and genetic affinity evaluations between Daur group and reference populations. Leg Med (Tokyo) 2020; 47:101741. [PMID: 32682294 DOI: 10.1016/j.legalmed.2020.101741] [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: 06/27/2019] [Revised: 04/01/2020] [Accepted: 06/26/2020] [Indexed: 12/25/2022]
Abstract
In present study, we evaluated the genetic diversities of 30 insertion/deletion (InDel) loci and analyzed the genetic relationships between Daur and other comparison populations. In the studied Daur group, any two InDel loci showed no linkage disequilibrium, and all loci showed no deviations from exact tests of Hardy-Weinberg equilibrium. Insertion allele frequencies at 30 InDel loci ranged from 0.1459 (HLD39) to 0.8774 (HLD118). The observed heterozygosity and expected heterozygosity values were ranged from 0.1984 (HLD118) to 0.5564 (HLD6) and 0.2155 (HLD118) to 0.5000 (HLD92 and HLD6), respectively. The combined power of discrimination and power of exclusion values were 0.999999999993428 and 0.9878, respectively, which indicated that this panel of 30 InDels could be used for individual identifications in Daur group. Population genetic analyses including pairwise fixation index, STRUCTURE analysis, principal component analysis, genetic distance, multidimensional scaling analysis and phylogenetic analysis demonstrated that the Daur group had the closer genetic relationships with the groups from western China in comparison with other continental populations.
Collapse
Affiliation(s)
- Wei Cui
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an 710004, China; Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an 710004, China; College of Medicine and Forensics, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China
| | - Xiaoye Jin
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an 710004, China; Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an 710004, China; College of Medicine and Forensics, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China
| | - Yuxin Guo
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an 710004, China; Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an 710004, China; College of Medicine and Forensics, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China
| | - Chong Chen
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an 710004, China; Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an 710004, China; College of Medicine and Forensics, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China
| | - Wenqing Zhang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an 710004, China; Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an 710004, China
| | - Tingting Kong
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an 710004, China; Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an 710004, China
| | - Yijie Wang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an 710004, China; Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an 710004, China
| | - Jingfeng Huang
- College of Medicine and Forensics, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China
| | - Bofeng Zhu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an 710004, China; Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an 710004, China; Multi-Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics; School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China.
| |
Collapse
|
5
|
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.
Collapse
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.
| |
Collapse
|
6
|
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
| |
Collapse
|
7
|
Gomes C, Quintero-Brito JD, Martínez-Gómez J, Pereira R, Baeza-Richer C, Aler Gay M, Díez-Juárez L, Palomo-Díez S, López-Parra AM, Labajo-González E, Esteban-Ramos VJ, Perea-Pérez B, Arroyo-Pardo E. Spanish allele and haplotype database for 32 X-chromosome Insertion-Deletion polymorphisms. Forensic Sci Int Genet 2020; 46:102262. [PMID: 32088644 DOI: 10.1016/j.fsigen.2020.102262] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 01/27/2020] [Accepted: 02/08/2020] [Indexed: 01/21/2023]
Abstract
X-chromosome markers have been proved to be decisive both complementing and solving kinship analysis, particularly when autosomal markers are not able to produce adequate likelihood ratios between different hypothesis. On the other hand, Pereira et al., (2012) have demonstrated that 32 Insertion/Deletion (InDel) markers located on the X-Chromosome have a very important power of discrimination in human populations, being a novel tool in the forensic and population fields. So, the aim of the present work was testing the forensic and population genetic efficiency of the 32 X-InDel polymorphisms in the Spanish population, and subsequently build an allele/haplotype frequencies database. To accomplish this objective, a total of 555 samples comprising male individuals from 13 Spanish regions were analysed for the above mentioned 32 X-InDels in two independent laboratories. A pairwise FST analysis was performed in order to understand if the studied Spanish sub-populations present significant differences among them, detecting possible population substructure. Also, linkage disequilibrium analyses were computed to investigate the presence of association between markers in the Spanish population. After Bonferroni correction, the absence of significant differences among the studied regions supports a global Spanish population database. Concerning LD, besides previously reported linked markers MID356-MID357 and MID3690-MID3719-MID2089, we also detected significant association between MID3703-MID3774, even after Bonferroni correction. Finally, after computing allele and haplotype frequencies, forensic efficiency parameters were calculated (PDmales = 99.999976 %; PDfemales = 99.99999999998 %). Mean exclusion chance values for duos were 0.999 and trios 0.99999. These results reinforce the suitability of the 32 X-InDels marker set both in identification and kinship studies.
Collapse
Affiliation(s)
- Cláudia Gomes
- Laboratory of Forensic and Population Genetics, Legal Medicine, Psychiatry and Pathology Department, Medicine School, Complutense University of Madrid (UCM), Pza. Ramón y Cajal s/n 28040 Madrid, Spain; Legal Medicine, Psychiatry and Pathology Department, Medicine School, Complutense University of Madrid (UCM), Madrid, Spain; Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Madrid, Spain.
| | | | - Jesús Martínez-Gómez
- Laboratory of the Biology Department, Criminalistics Service, Civil Guard, Madrid, Spain
| | - Rui Pereira
- Instituto de Investigação e Inovação em Saúde da Universidade do Porto (i3S), Porto, Portugal; Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
| | - Carlos Baeza-Richer
- Laboratory of Forensic and Population Genetics, Legal Medicine, Psychiatry and Pathology Department, Medicine School, Complutense University of Madrid (UCM), Pza. Ramón y Cajal s/n 28040 Madrid, Spain; Legal Medicine, Psychiatry and Pathology Department, Medicine School, Complutense University of Madrid (UCM), Madrid, Spain; Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Madrid, Spain
| | - Mercedes Aler Gay
- Sección de Genética y Criminalística, Servicio de Laboratorio, Instituto de Medicina Legal y Ciencias Forenses de Valencia, Spain
| | - Laura Díez-Juárez
- Laboratory of the Biology Department, Criminalistics Service, Civil Guard, Madrid, Spain
| | - Sara Palomo-Díez
- Laboratory of Forensic and Population Genetics, Legal Medicine, Psychiatry and Pathology Department, Medicine School, Complutense University of Madrid (UCM), Pza. Ramón y Cajal s/n 28040 Madrid, Spain; Legal Medicine, Psychiatry and Pathology Department, Medicine School, Complutense University of Madrid (UCM), Madrid, Spain; Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Madrid, Spain
| | - Ana María López-Parra
- Laboratory of Forensic and Population Genetics, Legal Medicine, Psychiatry and Pathology Department, Medicine School, Complutense University of Madrid (UCM), Pza. Ramón y Cajal s/n 28040 Madrid, Spain; Legal Medicine, Psychiatry and Pathology Department, Medicine School, Complutense University of Madrid (UCM), Madrid, Spain; Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Madrid, Spain
| | - Elena Labajo-González
- Legal Medicine School, Complutense University of Madrid, Pza Ramón y Cajal s/n, 28040 Madrid, Spain
| | | | - Bernardo Perea-Pérez
- Legal Medicine School, Complutense University of Madrid, Pza Ramón y Cajal s/n, 28040 Madrid, Spain
| | - Eduardo Arroyo-Pardo
- Laboratory of Forensic and Population Genetics, Legal Medicine, Psychiatry and Pathology Department, Medicine School, Complutense University of Madrid (UCM), Pza. Ramón y Cajal s/n 28040 Madrid, Spain; Legal Medicine, Psychiatry and Pathology Department, Medicine School, Complutense University of Madrid (UCM), Madrid, Spain; Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Madrid, Spain
| |
Collapse
|
8
|
Cui W, Jin X, Guo Y, Chen C, Zhang W, Kong T, Meng H, Zhu B. An innovative panel containing a set of insertion/deletion loci for individual identification and its forensic efficiency evaluations in Chinese Hui ethnic minority. Mol Genet Genomic Med 2020; 8:e1074. [PMID: 31865639 PMCID: PMC7005628 DOI: 10.1002/mgg3.1074] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 10/25/2019] [Accepted: 11/15/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Individual identification is one of the most important tasks in the field of forensic genetics. Insertion/Deletion (InDel) polymorphism marker has been a promising marker for individual identification. However, a part of InDel loci in commonly used commercial kit show low polymorphisms in Chinese populations. METHODS We evaluated a panel of 35 InDel loci constructed previously for individual identifications in Hui group. Subsequently, population data of three Chinese populations from 1,000 Genomes Project database were used to evaluate individual identification performance of these 35 InDels. Forensic parameters, such as heterozygosity, power of exclusion, match probability and power of discrimination, were calculated to evaluate the forensic efficiency of these loci in Hui group. The heatmap of insertion allelic frequencies, Nei's genetic distances, pairwise fixation index values, principal component analyses and admixture analyses were used to analyze the genetic differentiations and structure between Hui group and other populations. RESULTS In studied Hui group, besides rs3054057, polymorphism information content values of the remaining loci were greater than 0.3. Values of expected heterozygosity of these loci were close to 0.5. The combined power of discrimination and power of exclusion values were 0.99999999999999659609 and 0.998682, respectively. Analyses of population genetics revealed that Chinese Hui group had closer genetic relationships with East Asian populations than other intercontinental populations. CONCLUSION The forensic statistical analyses revealed these loci showed relatively high genetic polymorphisms in Chinese Hui group, and could be served as a useful tool for individual identifications in Hui group. Population genetic evaluations indicated that Chinese Hui group had close genetic relationships with East Asian populations.
Collapse
Affiliation(s)
- Wei Cui
- Key laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of StomatologyXi’an Jiaotong UniversityXi’anChina
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial DiseasesCollege of StomatologyXi’an Jiaotong UniversityXi’anChina
- College of Medicine and ForensicsXi’an Jiaotong University Health Science CenterXi’anChina
| | - Xiaoye Jin
- Key laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of StomatologyXi’an Jiaotong UniversityXi’anChina
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial DiseasesCollege of StomatologyXi’an Jiaotong UniversityXi’anChina
- College of Medicine and ForensicsXi’an Jiaotong University Health Science CenterXi’anChina
| | - Yuxin Guo
- Key laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of StomatologyXi’an Jiaotong UniversityXi’anChina
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial DiseasesCollege of StomatologyXi’an Jiaotong UniversityXi’anChina
- College of Medicine and ForensicsXi’an Jiaotong University Health Science CenterXi’anChina
| | - Chong Chen
- Key laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of StomatologyXi’an Jiaotong UniversityXi’anChina
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial DiseasesCollege of StomatologyXi’an Jiaotong UniversityXi’anChina
- College of Medicine and ForensicsXi’an Jiaotong University Health Science CenterXi’anChina
| | - Wenqing Zhang
- Key laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of StomatologyXi’an Jiaotong UniversityXi’anChina
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial DiseasesCollege of StomatologyXi’an Jiaotong UniversityXi’anChina
| | - Tingting Kong
- Key laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of StomatologyXi’an Jiaotong UniversityXi’anChina
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial DiseasesCollege of StomatologyXi’an Jiaotong UniversityXi’anChina
| | - Haotian Meng
- Key laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of StomatologyXi’an Jiaotong UniversityXi’anChina
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial DiseasesCollege of StomatologyXi’an Jiaotong UniversityXi’anChina
| | - Bofeng Zhu
- Key laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of StomatologyXi’an Jiaotong UniversityXi’anChina
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial DiseasesCollege of StomatologyXi’an Jiaotong UniversityXi’anChina
- Department of Forensic GeneticsSchool of Forensic MedicineSouthern Medical UniversityGuangzhouChina
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
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.
Collapse
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.
| |
Collapse
|