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Chen C, Jin X, Zhang X, Zhang W, Guo Y, Tao R, Chen A, Xu Q, Li M, Yang Y, Zhu B. Comprehensive Insights Into Forensic Features and Genetic Background of Chinese Northwest Hui Group Using Six Distinct Categories of 231 Molecular Markers. Front Genet 2021; 12:705753. [PMID: 34721519 PMCID: PMC8555763 DOI: 10.3389/fgene.2021.705753] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 09/07/2021] [Indexed: 11/13/2022] Open
Abstract
The Hui minority is predominantly composed of Chinese-speaking Islamic adherents distributed throughout China, of which the individuals are mainly concentrated in Northwest China. In the present study, we employed the length and sequence polymorphisms-based typing system of 231 molecular markers, i.e., amelogenin, 22 phenotypic-informative single nucleotide polymorphisms (PISNPs), 94 identity-informative single nucleotide polymorphisms (IISNPs), 24 Y-chromosomal short tandem repeats (Y-STRs), 56 ancestry-informative single nucleotide polymorphisms (AISNPs), 7 X-chromosomal short tandem repeats (X-STRs), and 27 autosomal short tandem repeats (A-STRs), into 90 unrelated male individuals from the Chinese Northwest Hui group to comprehensively explore its forensic characteristics and genetic background. Total of 451 length-based and 652 sequence-based distinct alleles were identified from 58 short tandem repeats (STRs) in 90 unrelated Northwest Hui individuals, denoting that the sequence-based genetic markers could pronouncedly provide more genetic information than length-based markers. The forensic characteristics and efficiencies of STRs and IISNPs were estimated, both of which externalized high polymorphisms in the Northwest Hui group and could be further utilized in forensic investigations. No significant departure from the Hardy-Weinberg equilibrium (HWE) expectation was observed after the Bonferroni correction. Additionally, four group sets of reference population data were exploited to dissect the genetic background of the Northwest Hui group separately from different perspectives, which contained 26 populations for 93 IISNPs, 58 populations for 17 Y-STRs, 26 populations for 55 AISNPs (raw data), and 109 populations for 55 AISNPs (allele frequencies). As a result, the analyses based on the Y-STRs indicated that the Northwest Hui group primarily exhibited intimate genetic relationships with reference Hui groups from Chinese different regions except for the Sichuan Hui group and secondarily displayed close genetic relationships with populations from Central and West Asia, as well as several Chinese groups. However, the AISNP analyses demonstrated that the Northwest Hui group shared more intimate relationships with current East Asian populations apart from reference Hui group, harboring the large proportion of ancestral component contributed by East Asia.
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Affiliation(s)
- Chong Chen
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an, China
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Xiaoye Jin
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an, China
| | - Xingru Zhang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an, China
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Wenqing Zhang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an, China
| | - Yuxin Guo
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an, China
| | - Ruiyang Tao
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
| | - Anqi Chen
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
- Department of Forensic Medicine, Shanghai Medical College of Fudan University, Shanghai, China
| | - Qiannan Xu
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
- Institute of Forensic Medicine, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Min Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
- Institute of Forensic Medicine, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Yue Yang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
- School of Basic Medicine, Inner Mongolia Medical University, Hohhot, China
| | - Bofeng Zhu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an, China
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
- Department of Forensic Genetics, Multi-Omics Innovative Research Center of Forensic Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
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2
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Liu L, Yao J, Huang Y, Gao L, Dai J, Yuan X, Zhang X, Nie S, Hu L. Genetic polymorphisms of 16 X-STR loci in the Hani population from Southwest China. Forensic Sci Res 2021; 7:196-201. [PMID: 35784423 PMCID: PMC9246014 DOI: 10.1080/20961790.2021.1877389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Affiliation(s)
- Linlin Liu
- School of Forensic Medicine, Kunming Medical University, Kunming, China
- Judicial Expertise Center, Kunming Medical University, Kunming, China
| | - Jinyong Yao
- Honghe Public Security Bureau, Honghe, China
| | | | - Lei Gao
- Honghe Public Security Bureau, Honghe, China
| | - Jiameng Dai
- School of Forensic Medicine, Kunming Medical University, Kunming, China
| | | | - Xiufeng Zhang
- School of Forensic Medicine, Kunming Medical University, Kunming, China
- Judicial Expertise Center, Kunming Medical University, Kunming, China
| | - Shengjie Nie
- School of Forensic Medicine, Kunming Medical University, Kunming, China
- Judicial Expertise Center, Kunming Medical University, Kunming, China
| | - Liping Hu
- School of Forensic Medicine, Kunming Medical University, Kunming, China
- Judicial Expertise Center, Kunming Medical University, Kunming, China
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3
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Ma X, Yang W, Gao Y, Pan Y, Lu Y, Chen H, Lu D, Xu S. Genetic origins and sex-biased admixture of the Huis. Mol Biol Evol 2021; 38:3804-3819. [PMID: 34021754 PMCID: PMC8382924 DOI: 10.1093/molbev/msab158] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The Hui people are unique among Chinese ethnic minorities in that they speak the same language as Han Chinese (HAN) but practice Islam. However, as the second-largest minority group in China numbering well over 10 million, the Huis are under-represented in both global and regional genomic studies. Here, we present the first whole-genome sequencing effort of 234 Hui individuals (NXH) aged over 60 who have been living in Ningxia, where the Huis are mostly concentrated. NXH are genetically more similar to East Asian than to any other global populations. In particular, the genetic differentiation between NXH and HAN (FST = 0.0015) is only slightly larger than that between northern and southern HAN (FST = 0.0010), largely attributed to the western ancestry in NXH (∼10%). Highly differentiated functional variants between NXH and HAN were identified in genes associated with skin pigmentation (e.g., SLC24A5), facial morphology (e.g., EDAR), and lipid metabolism (e.g., ABCG8). The Huis are also distinct from other Muslim groups such as the Uyghurs (FST = 0.0187), especially, NXH derived much less western ancestry (∼10%) compared with the Uyghurs (∼50%). Modeling admixture history indicated that NXH experienced an episode of two-wave admixture. An ancient admixture occurred ∼1,025 years ago, reflecting the intensive west-east contacts during the late Tang Dynasty, and the Five Dynasties and Ten Kingdoms period. A recent admixture occurred ∼500 years ago, corresponding to the Ming Dynasty. Notably, we identified considerable sex-biased admixture, i.e., excess of western males and eastern females contributing to the NXH gene pool. The origins and the genomic diversity of the Hui people imply the complex history of contacts between western and eastern Eurasians.
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Affiliation(s)
- Xixian Ma
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Wenjun Yang
- Key Laboratory of Fertility Preservation and Maintenance, the General Hospital, Ningxia Medical University, Yinchuan, Ningxia 750004 China
| | - Yang Gao
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yuwen Pan
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yan Lu
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Hao Chen
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Dongsheng Lu
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shuhua Xu
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.,Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450052, China.,Human Phenome Institute, Fudan University, Shanghai 201203, China
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Chen C, Li Y, Tao R, Jin X, Guo Y, Cui W, Chen A, Yang Y, Zhang X, Zhang J, Li C, Zhu B. The Genetic Structure of Chinese Hui Ethnic Group Revealed by Complete Mitochondrial Genome Analyses Using Massively Parallel Sequencing. Genes (Basel) 2020; 11:E1352. [PMID: 33202591 PMCID: PMC7698084 DOI: 10.3390/genes11111352] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 11/03/2020] [Accepted: 11/09/2020] [Indexed: 01/10/2023] Open
Abstract
Mitochondrial DNA (mtDNA), coupled with maternal inheritance and relatively high mutation rates, provides a pivotal way for us to investigate the formation histories of populations. The Hui minority with Islamic faith is one of the most widely distributed ethnic groups in China. However, the exploration of Hui's genetic architecture from the complete mitochondrial genome perspective has not been detected yet. Therefore, in this study, we employed the complete mitochondrial genomes of 98 healthy and unrelated individuals from Northwest China, as well as 99 previously published populations containing 7274 individuals from all over the world as reference data, to comprehensively dissect the matrilineal landscape of Hui group. Our results demonstrated that Hui group exhibited closer genetic relationships with Chinese Han populations from different regions, which was largely attributable to the widespread of haplogroups D4, D5, M7, B4, and F1 in these populations. The demographic expansion of Hui group might occur during the Late Pleistocene. Finally, we also found that Hui group might have gene exchanges with Uygur, Tibetan, and Tajik groups in different degrees and retained minor genetic imprint of European-specific lineages, therefore, hinting the existence of multi-ethnic integration events in shaping the genetic landscape of Chinese Hui group.
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Affiliation(s)
- Chong Chen
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China; (C.C.); (X.J.); (Y.G.); (X.Z.)
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, China; (R.T.); (A.C.); (Y.Y.); (J.Z.)
- Multi-Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China;
| | - Yuchun Li
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China;
| | - Ruiyang Tao
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, China; (R.T.); (A.C.); (Y.Y.); (J.Z.)
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610017, China
| | - Xiaoye Jin
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China; (C.C.); (X.J.); (Y.G.); (X.Z.)
| | - Yuxin Guo
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China; (C.C.); (X.J.); (Y.G.); (X.Z.)
| | - Wei Cui
- Multi-Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China;
| | - Anqi Chen
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, China; (R.T.); (A.C.); (Y.Y.); (J.Z.)
- Department of Forensic Medicine, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Yue Yang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, China; (R.T.); (A.C.); (Y.Y.); (J.Z.)
- School of Basic Medicine, Inner Mongolia Medical University, Hohhot 010030, China
| | - Xingru Zhang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China; (C.C.); (X.J.); (Y.G.); (X.Z.)
| | - Jingyi Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, China; (R.T.); (A.C.); (Y.Y.); (J.Z.)
| | - Chengtao Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, China; (R.T.); (A.C.); (Y.Y.); (J.Z.)
- Multi-Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China;
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610017, China
- Department of Forensic Medicine, Shanghai Medical College of Fudan University, Shanghai 200032, China
- School of Basic Medicine, Inner Mongolia Medical University, Hohhot 010030, China
| | - Bofeng Zhu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China; (C.C.); (X.J.); (Y.G.); (X.Z.)
- Multi-Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China;
- College of Forensic Medicine, Xi’an Jiaotong University Health Science Center, Xi’an 710061, China
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Ancestry Prediction Comparisons of Different AISNPs for Five Continental Populations and Population Structure Dissection of the Xinjiang Hui Group via a Self-Developed Panel. Genes (Basel) 2020; 11:genes11050505. [PMID: 32375366 PMCID: PMC7288656 DOI: 10.3390/genes11050505] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 04/28/2020] [Accepted: 04/30/2020] [Indexed: 01/23/2023] Open
Abstract
Ancestry informative markers are genetic markers that show distinct genetic divergences among different populations. These markers can be utilized to discern population substructures and estimate the ancestral origins of unknown individuals. Previously, we developed a multiplex system of 30 ancestry informative single nucleotide polymorphism (AISNP) loci to facilitate ancestral inferences in different continental populations. In the current study, we first compared the ancestry resolutions of the 30 AISNPs and the other previously reported AISNP panels for African, European, East Asian, South Asian and American populations. Next, the genetic components of the Xinjiang Hui group were further explored in comparison to these continental populations based on the 30 AISNPs. Genetic divergence analyses of the 30 AISNPs in these five continental populations revealed that most of the AISNPs showed high genetic differentiations between these populations. Ancestry analysis comparisons of the 30 AISNPs and other published AISNPs revealed that these 30 AISNPs had comparable efficiency to other AISNP panels. Genetic relationship analyses among the studied Hui group and other continental populations demonstrated that the Hui group had close genetic affinities with East Asian populations and might share the genetic ancestries with East Asian populations. Overall, the 30 AISNPs can be used to predict the bio-geographical origins of different continental populations. Moreover, the obtained genetic data of 30 AISNPs in the Hui group can further enrich the extant reference data, which can be used as reference data for ancestry analyses of the Hui group.
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Sun S, Yang Z, Wen D, Lan L, Xie P, Xiao J, Li G, Zhu W, Zha L. Genetic polymorphism investigation of 16 X-STR loci in a Han population in Central South China. Forensic Sci Int Genet 2018; 39:e21-e23. [PMID: 30538076 DOI: 10.1016/j.fsigen.2018.11.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 10/07/2018] [Accepted: 11/25/2018] [Indexed: 11/19/2022]
Affiliation(s)
- Shule Sun
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, PR China
| | - Zedeng Yang
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, PR China
| | - Dan Wen
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, PR China
| | - Lingmei Lan
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, PR China
| | - Pingli Xie
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, PR China
| | - Junxin Xiao
- Center of Forensic Services of Xiangya of Hunan Province, Changsha, 410013, Hunan, PR China
| | - Guanlin Li
- Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Key Clinical Laboratory of Henan Province, Zhengzhou, 450052, PR China
| | - Wenbing Zhu
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medicine, Central South University, Changsha, 410013, Hunan, PR China.
| | - Lagabaiyila Zha
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, PR China.
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Chen L, Guo Y, Xiao C, Wu W, Lan Q, Fang Y, Chen J, Zhu B. Genetic polymorphisms and forensic efficiency of 19 X-chromosomal STR loci for Xinjiang Mongolian population. PeerJ 2018; 6:e5117. [PMID: 30002965 PMCID: PMC6034600 DOI: 10.7717/peerj.5117] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 06/05/2018] [Indexed: 01/10/2023] Open
Abstract
Aim X-chromosomal short tandem repeat (X-STR) loci are playing an increasingly important role in some complex kinship cases in recent years. To investigate the forensic efficiency of X-STRs of Mongolian minority group from Xinjiang Uygur Autonomous Region, China, and further depict the genetic relationship among Xinjiang Mongolians and other populations, 267 blood samples from unrelated healthy Xinjiang Mongolians were amplified by an AGCU X-19 STR kit. Results No deviations for all 19 X-STR loci were observed from the Hardy-Weinberg equilibrium after Bonferroni correction (p > 0.0026) in female samples. The most frequent allele was allele 10 at locus DXS10164 with the frequency 0.5663. The polymorphism information content values of the 19 X-STR loci were more than 0.5 with the highest polymorphism at the locus DXS10135. The cumulative power of discrimination were 0.99999999999999999999988761005481 in females and 0.999999999999903 in males, respectively; and the cumulative mean exclusion chances were 0.9999999969738068321121 in duos and 0.999999999998952 in trios, respectively. The seven linkage groups were extremely informative, with all the haplotype diversities greater than 0.9487. No linkage disequilibrium was observed for a significance level of 0.00029 (p = 0.05/171) after Bonferroni correction. The DA distances, multidimensional scaling plot and phylogenetic tree based on the 11 overlapping X-STR loci all presented that the Xinjiang Mongolian population was genetically different from other Asian populations, including the Mongolian population from Inner Mongolia Autonomous Region, China. Conclusion This study indicated that the 19 X-STR multiplex PCR system was of high utility value for both forensic practices and population genetic research in Xinjiang Mongolian group.
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Affiliation(s)
- Ling Chen
- Department of Forensic Biology, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Yuxin Guo
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Cheng Xiao
- Department of Forensic Biology, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Weibin Wu
- Department of Forensic Biology, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Qiong Lan
- Department of Forensic Biology, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Yating Fang
- Department of Forensic Biology, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Jiangang Chen
- Institute of Forensic Science, Ministry of Public Security, Beijing, China
| | - Bofeng Zhu
- Department of Forensic Biology, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, China.,Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
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8
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Meng HT, Shen CM, Zhang YD, Dong Q, Guo YX, Yang G, Yan JW, Liu YS, Mei T, Shi JF, Zhu BF. Chinese Xibe population genetic composition according to linkage groups of X-chromosomal STRs: population genetic variability and interpopulation comparisons. Ann Hum Biol 2017; 44:546-553. [PMID: 28412872 DOI: 10.1080/03014460.2017.1318951] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
BACKGROUND The Xibe population is one of China's officially recognised populations and is now distributed separately from west to east in the northern part of China. X-chromosomal short tandem repeats have a special inheritance pattern, and could be used as complements in forensic application, especially for complex or deficiency cases. SUBJECTS AND METHODS This study obtained the allelic and haplotypic frequencies of 19 X-STR loci in the Xibe population from Xinjiang Uygur Autonomous Region, China, and studied the genetic differentiations between the Xibe and other populations. RESULTS The combined power of discrimination in females and males and mean exclusion chances in deficiency cases, normal trios and duo cases was at least 0.999 999 994. In the haplotypic study, the Xibe population showed a more similar pattern of haplotype distribution with Asian populations than populations from other continents, while allelic study also indicated a closer relationship between the Xibe and Asian populations. CONCLUSIONS The 19 X-STR loci would be useful in forensic application in the studied population. The Xibe population showed a closer genetic relationship with Asian populations in the study, and more population data would be necessary for more detailed genetic relationship studies.
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Affiliation(s)
- Hao-Tian Meng
- a Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology , Xi'an Jiaotong University , Xi'an , PR China.,b Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology , Xi'an Jiaotong University , Xi'an , PR China.,c Department of Forensic Genetics, School of Forensic Medicine , Southern Medical University , Guangzhou , PR China
| | - Chun-Mei Shen
- d Blood Center of Shaanxi Province , Xi'an , PR China.,e Institute of Brain and Behavioral Sciences, College of Life Sciences , Shaanxi Normal University , Xi'an , PR China
| | - Yu-Dang Zhang
- a Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology , Xi'an Jiaotong University , Xi'an , PR China.,b Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology , Xi'an Jiaotong University , Xi'an , PR China.,f Institute of Forensic Sciences of Anhui Public Security Department , Hefei , PR China
| | - Qian Dong
- a Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology , Xi'an Jiaotong University , Xi'an , PR China.,b Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology , Xi'an Jiaotong University , Xi'an , PR China
| | - Yu-Xin Guo
- a Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology , Xi'an Jiaotong University , Xi'an , PR China.,b Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology , Xi'an Jiaotong University , Xi'an , PR China
| | - Guang Yang
- g Department of Pathology , Laboratory of Medicine, Loma Linda University Medical Center , Loma Linda , CA , USA
| | - Jiang-Wei Yan
- h Key Laboratory of Genome Sciences , Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing , PR China
| | - Yao-Shun Liu
- i Department of Biochemistry , Preclinical Medicine College, Xinjiang Medical University , Urumqi , PR China
| | - Ting Mei
- i Department of Biochemistry , Preclinical Medicine College, Xinjiang Medical University , Urumqi , PR China
| | - Jian-Feng Shi
- a Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology , Xi'an Jiaotong University , Xi'an , PR China.,b Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology , Xi'an Jiaotong University , Xi'an , PR China
| | - Bo-Feng Zhu
- a Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology , Xi'an Jiaotong University , Xi'an , PR China.,b Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology , Xi'an Jiaotong University , Xi'an , PR China.,c Department of Forensic Genetics, School of Forensic Medicine , Southern Medical University , Guangzhou , PR China
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9
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Forensic effectiveness and population differentiations study of AGCU 21 + 1 fluorescence multiplex in Chinese Henan Han population. Forensic Sci Int Genet 2017; 28:e18-e21. [DOI: 10.1016/j.fsigen.2017.01.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 12/10/2016] [Accepted: 01/24/2017] [Indexed: 01/10/2023]
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10
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Liu YS, Meng HT, Mei T, Zhang LP, Chen JG, Zhang YD, Chen J, Guo YX, Dong Q, Yan JW, Zhu BF. Genetic diversity and haplotypic structure of Chinese Kazak ethnic group revealed by 19 STRs on the X chromosome. Gene 2016; 600:64-69. [PMID: 27840163 DOI: 10.1016/j.gene.2016.11.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 10/31/2016] [Accepted: 11/08/2016] [Indexed: 01/10/2023]
Abstract
X-chromosomal short tandem repeats (X-STRs) have been widely used in forensic practices involving complicated ties of kinship over the past years, and also play an increasingly important role in population genetics. To study the genetic polymorphisms of 19 STR loci on X chromosome in Chinese Kazak ethnic group, we investigated the allelic and haplotypic frequencies of the 19 loci in 300 (149 males and 151 females) unrelated healthy individuals from Ili Kazak Autonomous Prefecture, Xinjiang Uigur Autonomous Region of China after having evaluated the forensic application value of these loci in forensic sciences, and then compared the population distinctions between the Kazak group and other reference groups. We observed a total of 240 alleles at these X-STR loci with the corresponding allelic frequencies ranging from 0.0017 to 0.5917. In the study, the highest polymorphism was found at DXS10135 locus. The combined power of discrimination in females was 0.999999999999999999999985 and in males 0.999999999999968. The present study indicates that the 19 X-STR loci are very useful for both forensic identification cases and kinship analyses involving a female offspring.
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Affiliation(s)
- Yao-Shun Liu
- Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong 510515, PR China; Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004, PR China; Department of Biochemistry, Preclinical Medicine College, Xinjiang Medical University, Urumqi 830011, PR 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, PR China
| | - Ting Mei
- Department of Biochemistry, Preclinical Medicine College, Xinjiang Medical University, Urumqi 830011, PR China
| | - Li-Ping Zhang
- Department of Biochemistry, Preclinical Medicine College, Xinjiang Medical University, Urumqi 830011, PR China
| | - Jian-Gang Chen
- Department of Biochemistry, Preclinical Medicine College, Xinjiang Medical University, Urumqi 830011, PR China
| | - Yu-Dang Zhang
- Anhui Public Security Bureau Evidence Identification Center, Anhui 518054, PR China
| | - Jing Chen
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, PR 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, PR China
| | - Qian Dong
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004, PR China
| | - Jiang-Wei Yan
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Bo-Feng Zhu
- Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong 510515, PR China.
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11
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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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12
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Zhang YD, Shen CM, Meng HT, Guo YX, Dong Q, Yang G, Yan JW, Liu YS, Mei T, Huang RZ, Zhu BF. Allele and haplotype diversity of new multiplex of 19 ChrX-STR loci in Han population from Guanzhong region (China). Electrophoresis 2016; 37:1669-75. [PMID: 27063464 DOI: 10.1002/elps.201500425] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Revised: 02/29/2016] [Accepted: 03/30/2016] [Indexed: 12/12/2022]
Abstract
X-chromosomal short tandem repeats (X-STRs) have been proved to be useful for some deficiency paternity cases in recent years. Here, we studied the genetic polymorphisms of 19 X-STR loci (DXS10148-DXS10135-DXS8378, DXS10159-DXS10162-DXS10164, DXS7132-DXS10079-DXS10074-DXS10075, DXS6809-DXS6789, DXS7424-DXS101, DXS10103-HPRTB-DXS10101 and DXS7423-DXS10134) in 252 male and 222 female individuals from Guanzhong Han population, China. No deviation for all 19 loci was observed from the Hardy-Weinberg equilibrium. The polymorphism information content values of the panel of 19 loci were more than 0.5 with the exception of the locus DXS7423. The combined power of discrimination were 0.9999999999999999999994340 in females and 0.9999999999997662 in males, respectively; and the combined mean exclusion chances were 0.999999993764 in duos and 0.999999999997444 in trios, respectively. The haplotype diversities for all the seven clusters of linked loci were more than 0.9. The results showed that the panel of 19 X-STR loci were powerful for forensic applications in Guanzhong Han population. Locus by locus population comparisons showed significant differences at more than seven loci between Guanzhong Han population and the groups from North America, Europe and Africa.
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Affiliation(s)
- Yu-Dang Zhang
- 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.,Research Center of Stomatology, Stomatological Hospital, Xi'an Jiaotong University, Xi'an, P. R. China.,Xi'an Jiaotong University Health Science Center, Xi'an, P. R. China
| | - Chun-Mei Shen
- Blood Center of Shaanxi Province, Xi'an, P. R. China.,College of Life Sciences, Shaanxi Normal University, Xi'an, 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, 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.,Research Center of Stomatology, Stomatological Hospital, Xi'an Jiaotong University, Xi'an, P. R. China.,Xi'an Jiaotong University Health Science Center, Xi'an, 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, 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.,Research Center of Stomatology, Stomatological Hospital, Xi'an Jiaotong University, Xi'an, P. R. China.,Xi'an Jiaotong University Health Science Center, Xi'an, P. R. China
| | - Qian Dong
- 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.,Research Center of Stomatology, Stomatological Hospital, Xi'an Jiaotong University, Xi'an, P. R. China.,Xi'an Jiaotong University Health Science Center, Xi'an, P. R. China
| | - Guang Yang
- Department of Pathology and Laboratory Medicine, Loma Linda University Medical Center, Loma Linda, CA, USA
| | - Jiang-Wei Yan
- Key Laboratory of Genome Sciences, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, P. R. China
| | - Yao-Shun Liu
- 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.,Research Center of Stomatology, Stomatological Hospital, Xi'an Jiaotong University, Xi'an, P. R. China.,Department of Biochemistry, Preclinical Medicine College, Xinjiang Medical University, Urumqi, P. R. China
| | - Ting Mei
- 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.,Research Center of Stomatology, Stomatological Hospital, Xi'an Jiaotong University, Xi'an, P. R. China.,Department of Biochemistry, Preclinical Medicine College, Xinjiang Medical University, Urumqi, P. R. China
| | - Rui-Zhe Huang
- 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
| | - Bo-Feng 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.,Research Center of Stomatology, Stomatological Hospital, Xi'an Jiaotong University, Xi'an, P. R. China
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