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Tao R, Dong X, Zhen X, Xia R, Qu Y, Liu S, Zhang S, Li C. Population genetic analyses of Eastern Chinese Han nationality using ForenSeq™ DNA Signature Prep Kit. Mol Genet Genomics 2024; 299:9. [PMID: 38374461 DOI: 10.1007/s00438-024-02121-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 01/31/2024] [Indexed: 02/21/2024]
Abstract
Currently, the most commonly used method for human identification and kinship analysis in forensic genetics is the detection of length polymorphism in short tandem repeats (STRs) using polymerase chain reaction (PCR) and capillary electrophoresis (CE). However, numerous studies have shown that considerable sequence variations exist in the repeat and flanking regions of the STR loci, which cannot be identified by CE detection. Comparatively, massively parallel sequencing (MPS) technology can capture these sequence differences, thereby enhancing the identification capability of certain STRs. In this study, we used the ForenSeq™ DNA Signature Prep Kit to sequence 58 STRs and 94 individual identification SNPs (iiSNPs) in a sample of 220 unrelated individuals from the Eastern Chinese Han population. Our aim is to obtain MPS-based STR and SNP data, providing further evidence for the study of population genetics and forensic applications. The results showed that the MPS method, utilizing sequence information, identified a total of 486 alleles on autosomal STRs (A-STRs), 97 alleles on X-chromosome STRs (X-STRs), and 218 alleles on Y-chromosome STRs (Y-STRs). Compared with length polymorphism, we observed an increase of 260 alleles (157, 31, and 72 alleles on A-STRs, X-STRs, and Y-STRs, respectively) across 36 STRs. The most substantial increments were observed in DYF387S1 and DYS389II, with increases of 287.5% and 250%, respectively. The most increment in the number of alleles was found at DYF387S1 and DYS389II (287.5% and 250%, respectively). The length-based (LB) and sequence-based (SB) combined random match probability (RMP) of 27 A-STRs were 6.05E-31 and 1.53E-34, respectively. Furthermore, other forensic parameters such as total discrimination power (TDP), cumulative probability of exclusion of trios (CPEtrio), and duos (CPEduo) were significantly improved when using the SB data, and informative data were obtained for the 94 iiSNPs. Collectively, these findings highlight the advantages of MPS technology in forensic genetics, and the Eastern Chinese Han genetic data generated in this study could be used as a valuable reference for future research in this field.
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Affiliation(s)
- Ruiyang Tao
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Key Laboratory of Forensic Science, Shanghai, 200063, China
| | - Xinyu Dong
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Key Laboratory of Forensic Science, Shanghai, 200063, China
- Minhang Branch of Shanghai Public Security Bureau, Shanghai, 201108, China
| | - Xiaoyuan Zhen
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Key Laboratory of Forensic Science, Shanghai, 200063, China
- Department of Forensic Science, Medical School of Soochow University, Suzhou, 215123, China
| | - Ruocheng Xia
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Key Laboratory of Forensic Science, Shanghai, 200063, China
| | - Yiling Qu
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Key Laboratory of Forensic Science, Shanghai, 200063, China
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Shiquan Liu
- Institute of Evidence Law and Forensic Science, China University of Political Science and Law, Beijing, 100088, China.
| | - Suhua Zhang
- Shanghai Medical College, Fudan University, Shanghai, 200032, China.
| | - Chengtao Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Key Laboratory of Forensic Science, Shanghai, 200063, China.
- Shanghai Medical College, Fudan University, Shanghai, 200032, China.
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Cheffi K, El Khair A, Dahbi N, Talbi J, Hilali A, El Ossmani H. Genetic analysis based on 15 autosomal short tandem repeats (STRs) in the Chaouia population, western center Morocco, and genetic relationships with worldwide populations. Mol Genet Genomics 2023; 298:931-941. [PMID: 37162566 DOI: 10.1007/s00438-023-02028-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 04/29/2023] [Indexed: 05/11/2023]
Abstract
The complex demographic history of human populations in North Africa has resulted in a high degree of genetic heterogeneity across the region. However, little is known about the pattern of these genetic variations in its current populations. The present study provides new data on the genetic background of Chaouia, an Arabic-speaking North African population in the western center of Morocco. A random sample of 150 unrelated healthy individuals from Chaouia was assessed using the AmpFLSTR Identifiler kit. The most polymorphic markers were D21S11 and D18S51, with 23 and 22 alleles, respectively. After Bonferroni's correction, two loci (TH01 and D18S51) deviated from Hardy-Weinberg equilibrium. The phylogeny analysis separated North African populations into northeastern and northwestern groups. The Chaouia population was clustered with northwestern Africans. It was the closest to the Berbers of Azrou. The Chaouia shared close genetic affinities with populations from North Africa, the Middle East, and Europe, particularly Iberians, and to a lesser extent with sub-Saharan populations. The pattern of genetic admixture varied across North African populations without a clear correlation between their geographic (northeastern or northwestern) or linguistic identities (Arab or Berber), however, genetic heterogeneity among Berbers was observed. These findings suggest that the diversity observed in North African populations extends geographical and linguistic boundaries. It is further linked to each population's unique and complex demographic history. Human North African population genetics seems to present an intriguing landscape for future studies in the region and its surrounding populations to trace the origins of the genetic heterogeneity observed in these populations.
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Affiliation(s)
- Khadija Cheffi
- Hassan First University of Settat, Higher Institute of Health Sciences, Laboratory of Health Sciences and Technologies, Settat, Morocco.
| | - Abderrazak El Khair
- Hassan First University of Settat, Higher Institute of Health Sciences, Laboratory of Health Sciences and Technologies, Settat, Morocco
| | - Noura Dahbi
- Hassan First University of Settat, Higher Institute of Health Sciences, Laboratory of Health Sciences and Technologies, Settat, Morocco
| | - Jalal Talbi
- General Directorate of National Security, National Laboratory of the Scientific and Technical Police, Casablanca, Morocco
| | - Abderraouf Hilali
- Hassan First University of Settat, Higher Institute of Health Sciences, Laboratory of Health Sciences and Technologies, Settat, Morocco
| | - Hicham El Ossmani
- Institut de Criminalistique de la Gendarmerie Royale, Rabat, Morocco
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Biogeographic origin and genetic characteristics of the peopling of Jeju Island based on lineage markers. Genes Genomics 2023; 45:307-318. [PMID: 36607592 DOI: 10.1007/s13258-022-01363-5] [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: 07/31/2022] [Accepted: 12/26/2022] [Indexed: 01/07/2023]
Abstract
BACKGROUND Jeju Island is the largest island of South Korea, located southwest far from the mainland of Korea, and has a unique history and its own cultures that are distinguished from those of the other regions of the Korean mainland. However, the Jeju population has not been deeply investigated to date to understand their genetic structure, which may reflect their historical and geographical background. OBJECTIVE To identify the genetic characteristics and biogeographic origin of people of Jeju Island based on the statistical analysis of genetic data using lineage markers. METHODS 17 Y-STRs data for 615 unrelated males and mitochondrial DNA haplogroup data for 799 unrelated individuals residing on Jeju Island were generated, and analyzed to investigate genetic diversity and genetic characteristics using statistical methods including pairwise Fst or Rst, Analysis of molecular variance (AMOVA) and Multidimensional scaling (MDS). RESULTS For male individuals of Jeju Island, unique genetic characteristics were observed in the analysis of Y-STRs, including low haplotype diversity, strong association with surnames, genetic difference from other regions of Korea, and common genetic variation of the Y-STR loci known to be predominant in Northern populations, such as Mongolians. Statistical analysis of the mitochondrial DNA haplogroups also revealed similar results that showed low haplogroup diversity and high frequency of haplogroup Y prevalent mostly in ethnic populations around the Sea of Okhotsk in Northeastern Asia. All these results suggest that Jeju Island is genetically distinct from other regions of Korea, possibly being a subpopulation in Korea, and related closely to Northern Asian populations. CONCLUSION The findings in the genetic approach could support understanding of the historical background of Jeju Island that is consistent with evidence from other multidisciplinary studies.
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Fan GY, Jiang DZ, Jiang YH, Song W, He YY, Wuo NA. Phylogenetic analyses of 41 Y-STRs and machine learning-based haplogroup prediction in the Qingdao Han population from Shandong province, Eastern China. Ann Hum Biol 2023; 50:35-41. [PMID: 36636009 DOI: 10.1080/03014460.2023.2168057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
BACKGROUND Known for its rich history and culture, Qingdao is a typical symbol of Chinese maritime culture. Its unique genetic landscape has aroused interest among geneticists and forensic scientists. However, the genetic landscape of Qingdao has never been uncovered. AIM This investigation intends to provide light on Qingdao's paternal genetic diversity and its evolutionary connections to other Han subgroups. SUBJECTS AND METHODS The genetic polymorphisms of 41 Y-chromosomal short tandem repeat (STR) loci in the Qingdao Han were investigated using SureID® PathFinder Plus Kit. Phylogenetic studies were performed using genotype data from 52 East Asian groups at 23 common Y-STR loci. A multidimensional scaling plot and cladogram were constructed. Linear Discriminant Analysis (LDA) was carried out for predicting categories among the Han people. The k-nearest neighbour (kNN) algorithm was utilised to designate Y-SNP haplogroups for each haplotype. RESULTS The Qingdao Han were genetically far from the Tibeto-Burman populations and close with the Han people from northern China. LDA indicated a deep integration among the present-day Han people. By the kNN model, the predicted O2a2 and O2a1 were shown to be the predominant Y-SNP haplogroups. CONCLUSIONS This study would be helpful for reconstructing the patrilineal history in China and establishing a more comprehensive Y-STR database.
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Affiliation(s)
- Guang-Yao Fan
- Forensic Center, College of Medicine, Shaoxing University, Shaoxing, China
| | - De-Zhi Jiang
- Criminal Technology Department, Qingdao Public Security Bureau, Shandong, China
| | - Yao-Heng Jiang
- Criminal Technology Department, Qingdao Public Security Bureau, Shandong, China
| | - Wei Song
- Criminal Technology Department, Qingdao Public Security Bureau, Shandong, China
| | - Ying-Yun He
- Ningbo Health Gene Technologies Co. Ltd, Ningbo, China
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Zhou J, Zhang X, Li X, Sui J, Zhang S, Zhong H, Zhang Q, Zhang X, Huang H, Wen Y. Genetic structure and demographic history of Northern Han people in Liaoning Province inferred from genome-wide array data. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1014024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In this study, we used typical and advanced population genetic analysis methods [principal component analysis (PCA), ADMIXTURE, FST, f3-statistics, f4-statistics, qpAdm/qpWave, qpGraph, ALDER (Admixture-induced Linkage Disequilibrium for Evolutionary Relationships) and TreeMix] to explore the genetic structure of 80 Han individuals from four different cities in Liaoning Province and reconstruct their demographic history based on the newly generated genome-wide data. We found that Liaoning Han people have genetic similarities with other northern Han people (Shandong, Henan, and Shanxi) and Liaoning Manchu people. Millet farmers in the Yellow River Basin (YRB) and the West Liao River Basin (WLRB) (57–98%) and hunter-gatherers in the Mongolian Plateau (MP) and the Amur River Basin (ARB) (40–43%) are the main ancestral sources of the Liaoning Han people. Our study further supports the “northern origin hypothesis”; YRB-related ancestry accounts for 83–98% of the genetic makeup of the Liaoning Han population. There are clear genetic influences of northern East Asian populations in the Liaoning Han people, ancient Northeast Asian-related ancestry is another dominant ancestral component, and large-scale population admixture has happened between Tungusic Manchu people and Han people. There are genetic differences among the Liaoning Han people, and we found that these differences are associated with different migration routes of Hans during the “Chuang Guandong” period in historical records.
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Wang H, Xin C, Meng X, Xing S, Guo B, Chen Y, Wang BJ, Yao J. Genetic polymorphism and forensic application of 23 autosomal STR loci in the Han population of Panjin City, Liaoning Province, Northeastern China. Ann Hum Biol 2022; 49:254-259. [PMID: 35815629 DOI: 10.1080/03014460.2022.2100479] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
BACKGROUND Short tandem repeats (STRs) are consecutive repetition of a repeat motif and widely used in forensic medicine and human genetics because of their high polymorphism. SUBJECTS AND METHODS In the current study, 23 autosomal STR loci were genotyped from 1263 unrelated healthy individuals living in Panjin City, Liaoning Province, Northeastern China using the VeriFilerTM Express PCR Amplification Kit. The population comparison was performed between the Panjin Han population and the other relevant groups to further explore the structure of Panjin Han and its relationship with the other groups. RESULTS The results found 316 alleles across the 23 STRs and the corresponding allelic frequencies ranged from 0.5198 to 0.0004. Except for D3S1358, TPOX, TH01, and D3S1358, all STR loci were highly polymorphic (PIC > 0.7), with the Penta E locus having the highest degree of polymorphism (0.9147). For population comparison, the exact test of population differentiation found that no significant difference was observed between the Panjin Han and the other Han populations, except for Guangdong Han and Jiangxi Han. CONCLUSION The Panjin Han population showed significant differences with the other ethnic groups in China (Bouyei, Dong, Hui, Miao, Tibetan, and Uygur) and the foreign ethnic groups.
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Affiliation(s)
- Hongbo Wang
- Department of Anatomy, Shenyang Medical College, Shenyang, China
| | | | - Xinyao Meng
- Department of Anatomy, Shenyang Medical College, Shenyang, China
| | - Shihan Xing
- Department of Anatomy, Shenyang Medical College, Shenyang, China
| | - Baotong Guo
- Department of Anatomy, Shenyang Medical College, Shenyang, China
| | - Yuhan Chen
- Department of Anatomy, Shenyang Medical College, Shenyang, China
| | - Bao-Jie Wang
- School of Forensic Medicine, China Medical University, Shenyang, China
| | - Jun Yao
- School of Forensic Medicine, China Medical University, Shenyang, China
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Zhao C, Xu H, Mei S, Lan Q, Liu Y, Fang Y, Zhu B. Polymorphic investigation and interpopulation genetic differentiation analyses of 20 STR loci in Inner Mongolia Han population. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Zhang X, He G, Li W, Wang Y, Li X, Chen Y, Qu Q, Wang Y, Xi H, Wang CC, Wen Y. Genomic Insight Into the Population Admixture History of Tungusic-Speaking Manchu People in Northeast China. Front Genet 2021; 12:754492. [PMID: 34659368 PMCID: PMC8515022 DOI: 10.3389/fgene.2021.754492] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 08/30/2021] [Indexed: 11/13/2022] Open
Abstract
Manchu is the third-largest ethnic minority in China and has the largest population size among the Tungusic-speaking groups. However, the genetic origin and admixture history of the Manchu people are far from clear due to the sparse sampling and a limited number of markers genotyped. Here, we provided the first batch of genome-wide data of genotyping approximate 700,000 single-nucleotide polymorphisms (SNPs) in 93 Manchu individuals collected from northeast China. We merged the newly generated data with data of publicly available modern and ancient East Asians to comprehensively characterize the genetic diversity and fine-scale population structure, as well as explore the genetic origin and admixture history of northern Chinese Manchus. We applied both descriptive methods of ADMIXTURE, fineSTRUCTURE, F ST , TreeMix, identity by decedent (IBD), principal component analysis (PCA), and qualitative f-statistics (f 3, f 4, qpAdm, and qpWave). We found that Liaoning Manchus have a close genetic relationship and significant admixture signal with northern Han Chinese, which is in line with the cluster patterns in the haplotype-based results. Additionally, the qpAdm-based admixture models showed that modern Manchu people were formed as major ancestry related to Yellow River farmers and minor ancestry linked to ancient populations from Amur River Bain, or others. In summary, the northeastern Chinese Manchu people in Liaoning were an exception to the coherent genetic structure of Tungusic-speaking populations, probably due to the large-scale population migrations and genetic admixtures in the past few hundred years.
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Affiliation(s)
- Xianpeng Zhang
- Institute of Biological Anthropology, Jinzhou Medical University, Jinzhou, China
| | - Guanglin He
- State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, Xiamen, China
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
- School of Humanities, Nanyang Technological University, Singapore, Singapore
| | - Wenhui Li
- Institute of Biological Anthropology, Jinzhou Medical University, Jinzhou, China
| | - Yunfeng Wang
- Xinbin Manchu Autonomous County People’s Hospital, Fushun, China
| | - Xin Li
- Institute of Biological Anthropology, Jinzhou Medical University, Jinzhou, China
| | - Ying Chen
- Institute of Biological Anthropology, Jinzhou Medical University, Jinzhou, China
| | - Quanying Qu
- Institute of Biological Anthropology, Jinzhou Medical University, Jinzhou, China
| | - Ying Wang
- Institute of Biological Anthropology, Jinzhou Medical University, Jinzhou, China
| | - Huanjiu Xi
- Institute of Biological Anthropology, Jinzhou Medical University, Jinzhou, China
| | - Chuan-Chao Wang
- State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, Xiamen, China
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Youfeng Wen
- Institute of Biological Anthropology, Jinzhou Medical University, Jinzhou, China
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Zhou Y, Huang L, Liu H, Liu M, Fan G. Population genetic characteristics for populations on the Shandong Peninsula revealed by autosomal STR. Ann Hum Biol 2021; 48:157-159. [PMID: 33487040 DOI: 10.1080/03014460.2021.1879264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The Shandong Peninsula is the largest peninsula in China and has played a vital part in Chinese civilisation. The ancient independent Laizi kingdom was located on the Shandong peninsula. While large demographic changes have happened at this peninsula throughout history, the genetic landscape of modern populations on this peninsula has never been clarified. The aims of our study were to investigate population genetic characteristics of the populations on the Shandong peninsula and to reveal their genetic affinities with other populations around the world. Allele frequencies, Hardy-Weinberg equilibrium, and forensic parameters of 15 autosomal STRs in the AmpFlSTR® Identifiler system were obtained from the studied populations with 2441 individuals in total. Allele frequencies were used to reveal the phylogenetic relationships among 287 worldwide populations. The combined power of discrimination (CPD) and the combined power of exclusion (CPE) in the whole of the Han population on the Shandong Peninsula were 0.999999999999999983 and 0.999998155, respectively. The 15 autosomal loci were polymorphic and informative among our studied populations. Genetic homogeneities were revealed between the modern populations on the Shandong Peninsula and Han nationalities from Northeastern China as well as East China.
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Affiliation(s)
- Yijun Zhou
- College of Medicine, Shaoxing University, Shaoxing, China
| | - Lei Huang
- Shandong Public Security Bureau, Shandong, China
| | - Haidong Liu
- Jining Municipal Public Security Bureau, Shandong, China
| | - Mengnan Liu
- College of Medicine, Shaoxing University, Shaoxing, China
| | - Guangyao Fan
- Forensic Center, College of Medicine, Shaoxing University, Shaoxing, China
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Wen D, Sun S, Liu Y, Li J, Yang Z, Kureshi A, Fu Y, Li H, Jiang B, Jin C, Cai J, Zha L. Considering the flanking region variants of nonbinary SNP and phenotype-informative SNP to constitute 30 microhaplotype loci for increasing the discriminative ability of forensic applications. Electrophoresis 2021; 42:1115-1126. [PMID: 33483973 DOI: 10.1002/elps.202000341] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 12/22/2020] [Accepted: 01/15/2021] [Indexed: 12/15/2022]
Abstract
The flanking region variants of nonbinary SNPs and phenotype-informative SNPs (piSNPs) have been observed, which may greatly improve the discriminative ability after constituting microhaplotype. In this study, 30 microhaplotype loci based on the nonbinary SNPs and piSNPs (shown to be related to phenotypes such as hair and eye color) were selected. Genotyping were conducted on 100 unrelated northern Han Chinese, and the 26 populations from the 1000 Genome Project were also included for comparison of populations differentiation. The simulated study was conducted for evaluating the efficiency of kinship testing. These 30 microhaplotype loci we selected had good polymorphism, with a mean effective number of alleles (Ae) of 3.46. The average Ae increase was 1.27 compared with the target SNPs. The populations from the five regions worldwide could also be distinguished using these loci. The results of kinship testing showed that these microhaplotype loci had the similar ability as 15 STR loci of AmpFlSTRR IdentifilerR PCR Amplification Kit to identify the biological parent and a stronger ability to exclude the nonbiological parents. So, these 30 microhaplotype loci may be multifunctional for forensic application, including the ability of personal identification and kinship testing equivalent to 15 STR loci, and the power of ancestry inference for distinguishing the main intercontinental population. Moreover, our selected phenotypic microhaplotype loci may theoretically have phenotype prediction capabilities. But the phenotype prediction efficiency of these phenotypic microhaplotype loci may be worse than that of piSNPs and the detailed prediction accuracy of different populations needs to be further studied.
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Affiliation(s)
- Dan Wen
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, P. R. China
| | - Shule Sun
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, P. R. China
| | - Ying Liu
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, P. R. China
| | - Jienan Li
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, P. R. China
| | - Zedeng Yang
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, P. R. China
| | - Aliye Kureshi
- School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, P. R. China
| | - Yan Fu
- Huazhi Biotech Co., Ltd, Changsha, P. R. China
| | - Henan Li
- Microanaly Gene Technologies Co., Ltd, Hefei, P. R. China
| | - Bowei Jiang
- The First Research Institute of the Ministry of Public Security P.R.C, Beijing, P. R. China
| | - Chuan Jin
- The First Research Institute of the Ministry of Public Security P.R.C, Beijing, P. R. China
| | - Jifeng Cai
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, P. R. China
| | - Lagabaiyila Zha
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, P. R. China
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Wang H, Xin C, Cao H. Forensic features and genetic structure of 20 autosomal STR loci in the Han population of Ningde City, Southeastern China. Ann Hum Biol 2021; 48:56-61. [PMID: 33225750 DOI: 10.1080/03014460.2020.1854344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
BACKGROUND Short tandem repeat (STR) loci are widely used in forensic medicine and population genetics. AIM To profile 20 autosomal STR loci using the SureID® 21 G Human STR Identification Kit. SUBJECTS AND METHODS Samples were obtained from 1412 unrelated Chinese Han individuals from Ningde City, Southeastern China and 20 autosomal STR loci were profiled using the SureID® 21 G Human STR Identification Kit. RESULTS A total of 261 alleles were observed among 1412 unrelated individuals and the corresponding allelic frequencies ranged from 0.5464 to 0.0004. The combined power of discrimination and exclusion of the 20 autosomal STR loci were 0.99999999999999999922 and 0.999999340285752, respectively. There was no significant deviation from Hardy-Weinberg equilibrium (HWE) and minimal departure from linkage equilibrium (LE) for two pairwise combinations of loci after sequential Bonferroni correction. In the population comparison, phylogenetic analysis was performed between the Han population and other relevant populations on the basis of the shared autosomal STR genotyping. Moreover, the neighbor-joining tree and principal component analysis were analysed based on the Nei's standard genetic distance. CONCLUSION The population comparison revealed that the structure of the Ningde Han population was similar to the structure of southern Han populations in China and was significantly different to the other Chinese ethnic groups, such as Kyrgyz, Uzbek, Kazakh, Uyghur, Manchu from Xinjiang and Mongols.
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Affiliation(s)
- Hongbo Wang
- Department of Anatomy, Shenyang Medical College, Shenyang, China
| | | | - Hongyi Cao
- Department of Pathology, College of Basic Medical Science, China Medical University, Shenyang, China
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Population-genetic and comparative interpopulation studies of Azerbaijan population based on the 15 autosomal STR markers. Gene 2020; 753:144804. [PMID: 32445920 DOI: 10.1016/j.gene.2020.144804] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 05/15/2020] [Accepted: 05/20/2020] [Indexed: 11/21/2022]
Abstract
We have investigated 765 unrelated individuals from Azerbaijan using AmpFlSTR® Identifiler® Plus PCR Amplification Kit. For each STR locus basic population-genetic and forensic parameters were determined. The calculated P-values (PHWE) for the accuracy of the Hardy-Weinberg equilibrium (HWE) tests, showed that this parameter had a statistically significant value (PHWE = 0.0000) only for the THO1, D18S51 and FGA loci. The values of parameters for the set of 15 STR loci such as CPE, CPD, CTPI and the PP showed that the given set of loci can be confidently used to solve identification problems for the studied population. Multiple population differentiation tests performed between Azerbaijan and other 17 world populations revealed that between Azerbaijan and Iraqi, Iranian, Turkish populations there were no significant differences on all STR loci. Additionally, comparisons of Fischer genetic distance indices (FST) P-values did not reveal any statistically significant difference between Azerbaijan and Iranian populations at P < 0.05. However, with South African black population differences at all STR loci were detected. Both tests did not reveal a locus by which our population would differ from all the other compared populations. PCA and PCoA analyzes showed that the Azerbaijani population was grouped with different populations in different quarters, showing a negative and zero correlation, respectively. Regarding the location of the Azerbaijan population, there are some differences between NJ and UPGMA phylogenetic trees. For example, in the NJ tree, Azerbaijan population was grouped with Iranian, but in the UPGMA tree, it was grouped with the Turkish population. Based on Nei's genetic distance between populations the second tree has a more realistic outcome.
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Lu Y, Sun HJ, Zhou JC, Wu X. Genetic polymorphisms, forensic efficiency and phylogenetic analysis of 17 autosomal STR loci in the Han population of Wuxi, Eastern China. Ann Hum Biol 2019; 46:601-605. [DOI: 10.1080/03014460.2019.1693628] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Yan Lu
- School of Forensic Medicine, China Medical University, Shenyang, PR China
- Key Laboratory of Health Ministry in Congenital Malformation, the Affiliated Shengjing Hospital of China Medical University, Shenyang, PR China
| | - Hong-jie Sun
- Institute of Criminal Science and Technology, Wuxi Public Security Bureau, Wuxi, PR China
| | - Ji-chuan Zhou
- School of Forensic Medicine, China Medical University, Shenyang, PR China
| | - Xu Wu
- School of Forensic Medicine, China Medical University, Shenyang, PR China
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14
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Xu X, Zheng J, Lou Y, Wei X, Wang B, Yao J. Population genetics of 24 Y-STR loci in Chinese Han population from Jilin Province, Northeast China. Mol Genet Genomic Med 2019; 7:e984. [PMID: 31566932 PMCID: PMC6825842 DOI: 10.1002/mgg3.984] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 08/27/2019] [Accepted: 09/03/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND It is meaningful to expand the available population information on forensic medicine and to investigate the genetic characteristics of Han population from Jilin Province, Northeast China. METHODS In this study, we investigated the genetic characteristics of 24 Y-chromosomal short tandem repeat (STR) loci in 1,088 unrelated Chinese Han male individuals from Jilin Province, using DNATyperTM Y24 amplification kit. Additionally, we performed the population comparison between the Jilin population and the other nine reported populations based on the Y-STR genotyping haplotypes. RESULTS A total of 1,067 different haplotypes were found from 1,088 unrelated individuals, of which 1,046 were unique and 21 were shared by two individuals. The gene diversity values of 22 loci ranged from 0.3870 (DYS391) to 0.9668 (DYS385ab). The random match probability was 0.0010 with the discrimination capacity of 0.9807. Population comparison showed that there were minor differences compared to Beijing Chinese Han, China Manchu, Gansu Chinese Han, and Jiangsu Chinese Han, but major differences with respect to the populations of Guangdong Chinese Han, Yunnan Chinese Han, China Hui, China Korean, and China Tibetan. CONCLUSION Our results showed that the 24 Y-STR loci in Jilin Han population are valuable for forensic application and human genetics.
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Affiliation(s)
- Xiao‐ming Xu
- School of Forensic MedicineChina Medical UniversityShenyangChina
| | - Ji‐long Zheng
- Department of Forensic MedicineCriminal Investigation Police University of ChinaShenyangChina
| | - Yin Lou
- School of Forensic MedicineChina Medical UniversityShenyangChina
| | - Xiao‐han Wei
- School of Forensic MedicineChina Medical UniversityShenyangChina
| | - Bao‐jie Wang
- School of Forensic MedicineChina Medical UniversityShenyangChina
| | - Jun Yao
- School of Forensic MedicineChina Medical UniversityShenyangChina
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15
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Adnan A, Rakha A, Nazir S, Rehman Z, Lu J, Xuan JF. Genetic characterization of 15 autosomal STRs in the interior Sindhi population of Pakistan and their phylogenetic relationship with other populations. Int J Immunogenet 2019; 47:149-157. [PMID: 31657139 DOI: 10.1111/iji.12458] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 09/02/2019] [Accepted: 09/18/2019] [Indexed: 11/28/2022]
Abstract
Genetic structure of a population can be influenced by evolutionary processes and cultural histories which can alter the frequencies of different variants at particular genetic markers. These characteristics make DNA evidence suitable for forensic applications. Little relevant data are available from the interior Sindhi population; thus, in the current study, we have investigated 15 autosomal STRs in 181 unrelated individuals belonging to the interior parts of Sindh Pakistan, to establish its lineage and parameters of forensic interest. These STRs revealed a high power of discrimination (CPD), power of exclusion (CPE) and matching probability (CMP) are 0.9999999999999999968997, 0.99998612 and 3.1003 × 10-18 respectively. The genetic distances, neighbour-joining (NJ) tree, interactivity test and principal component analysis (PCA) based on 15 autosomal STR loci showed that the interior Sindhi population had a closer genetic relationship with Pakistani populations and distant relationships with regional (India and Afghanistan) populations. The present findings exhibited that STRs included in AmpFLSTR Identifiler kit (Applied Biosystems) are genetically polymorphic in the interior Sindhi population of Pakistan. This study provides valuable population genetic data for the genetic information study, forensic human individual identification and paternity testing.
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Affiliation(s)
- Atif Adnan
- Department of Human Anatomy, School of Basic Medicine, China Medical University, Shenyang, China
| | - Allah Rakha
- Department of Forensic Sciences, University of Health Sciences, Lahore, Pakistan
| | - Shahid Nazir
- Department of Forensic Sciences, University of Health Sciences, Lahore, Pakistan
| | - Ziaur Rehman
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Lahore, Pakistan
| | - Jie Lu
- Department of Human Anatomy, School of Basic Medicine, China Medical University, Shenyang, China
| | - Jin-Feng Xuan
- Department of Forensic Genetics and Biology, School of Forensic Medicine, China Medical University, Shenyang, China
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16
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Li XN, Al-Sabri A, Ameen F, Al-Dayan N, Adnan A, Yao J. Genetic polymorphisms of 20 autosomal STR loci in the Han population of Putian City, Southeastern China. Ann Hum Biol 2019; 46:509-513. [DOI: 10.1080/03014460.2019.1674379] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Xiao-Na Li
- School of Fundamental Sciences, China Medical University, Shenyang, China
| | - Ahmad Al-Sabri
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Faud Ameen
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Noura Al-Dayan
- Department of Medical Laboratory, College of Applied Medical Science, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Atif Adnan
- School of Forensic Medicine, China Medical University, Shenyang, China
| | - Jun Yao
- School of Forensic Medicine, China Medical University, Shenyang, China
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17
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Genetic substructure and forensic characteristics of Chinese Hui populations using 157 Y-SNPs and 27 Y-STRs. Forensic Sci Int Genet 2019; 41:11-18. [DOI: 10.1016/j.fsigen.2019.03.022] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Revised: 03/20/2019] [Accepted: 03/23/2019] [Indexed: 01/10/2023]
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18
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Wang D, Zhang T, Xu R, Dong Z, Li C, Cui W. Genetic polymorphisms of 23 STR loci of Goldeneye™ 25A kit in Shandong Han population. Forensic Sci Int Genet 2019; 40:e256-e258. [PMID: 30826257 DOI: 10.1016/j.fsigen.2019.02.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 12/27/2018] [Accepted: 02/03/2019] [Indexed: 10/27/2022]
Affiliation(s)
- Dan Wang
- Institute of Forensic Medicine and Laboratory Medicine, Jining Medical School, PR China
| | - Ting Zhang
- Yanzhou Hospital of Traditional Chinese Medicine, PR China
| | - Ruoyang Xu
- Yanzhou Public Security Bureau, PR China
| | | | - Changzheng Li
- Institute of Forensic Medicine and Laboratory Medicine, Jining Medical School, PR China
| | - Wen Cui
- Institute of Forensic Medicine and Laboratory Medicine, Jining Medical School, PR China.
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19
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Tao R, Wang S, Zhang J, Zhang J, Yang Z, Zhang S, Li C. Genetic characterization of 27 Y-STR loci analyzed in the Nantong Han population residing along the Yangtze Basin. Forensic Sci Int Genet 2019; 39:e10-e13. [DOI: 10.1016/j.fsigen.2018.11.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 09/25/2018] [Accepted: 11/26/2018] [Indexed: 10/27/2022]
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20
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Xuan JF, Adnan A, Khan RA, Xing JX, Yao J, Wang BJ. Population genetics of 19 Y-STR loci in Yanbian Korean samples from China. Ann Hum Genet 2018; 83:134-140. [PMID: 30506867 DOI: 10.1111/ahg.12296] [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: 06/14/2018] [Revised: 10/18/2018] [Accepted: 11/20/2018] [Indexed: 11/28/2022]
Abstract
BACKGROUND China harbors 56 ethnic groups, including Korean, with a population size of approximately 1.92 million at the 2010 census. Most of the Koreans live in Northeastern parts of China, including Jilin (59.64%), Heilongjiang (20.21%), and Liaoning (12.55%) provinces, and the rest are spread to other parts of China. Koreans across China share a common culture, which is similar to Korea. METHODS We have explored the genetic characteristics of 20 Y-chromosomal short tandem repeat (Y-STR) loci in 252 unrelated Chinese Korean male individuals from Jilin Province, using a Goldeneye 20Y amplification kit. Moreover, phylogenetic analysis was performed between the Korean population and other relevant populations based on the Y-STR haplotypes. RESULTS We have found 237 different haplotypes among 252 unrelated individuals. The haplotype frequencies ranged from 0.0238 to 0.0040, while gene diversity ranged from 0.9666 (DYS385a/b) to 0.2260 (DYS391). The random match probability was 0.0048, the haplotype diversity was 0.9992 ± 0.0006 and discrimination capacity was 0.9405. Population comparison revealed that Korean populations are lining up together with other Korean populations from East Asia. CONCLUSION Our results showed that the 20 Y-STR loci in the Yanbian Korean population are valuable for forensic application and human genetics. The Yanbian Koreans have lined up with other Korean population from China and Korea while showing significant differences from other East Asian populations.
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Affiliation(s)
- Jin-Feng Xuan
- School of Forensic Medicine, China Medical University, Shenyang, 110122, China
| | - Atif Adnan
- School of Forensic Medicine, China Medical University, Shenyang, 110122, China
| | - Rehan Ali Khan
- School of International Education, China Medical University, Shenyang, 110122, China
| | - Jia-Xin Xing
- School of Forensic Medicine, China Medical University, Shenyang, 110122, China
| | - Jun Yao
- School of Forensic Medicine, China Medical University, Shenyang, 110122, China
| | - Bao-Jie Wang
- School of Forensic Medicine, China Medical University, Shenyang, 110122, China
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21
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Feng C, Wang X, Yu H, Wang X, Zhang G. Genetic polymorphisms, forensic efficiency, and phylogenetic analysis of 15 autosomal STR loci in the Uygur population of Ili Kazakh Autonomous Prefecture, Northwestern China. Ann Hum Genet 2018; 83:46-53. [DOI: 10.1111/ahg.12283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Revised: 07/30/2018] [Accepted: 07/31/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Chun‐Mei Feng
- School of Forensic Medicine China Medical University Shenyang P.R. China
- Department of Biotechnology Laboratory Mudanjiang Medical College Mudanjiang P.R. China
| | - Xin Wang
- DNA Laboratory of Criminal Police Detachment Suzhou Public Security Bureau Suzhou P.R. China
| | - Hao Yu
- School of Forensic Medicine China Medical University Shenyang P.R. China
| | - Xiao‐Long Wang
- School of Forensic Medicine China Medical University Shenyang P.R. China
| | - Guo‐Hua Zhang
- School of Forensic Medicine China Medical University Shenyang P.R. China
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22
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Zhan X, Adnan A, Zhou Y, Khan A, Kasim K, McNevin D. Forensic characterization of 15 autosomal STRs in four populations from Xinjiang, China, and genetic relationships with neighboring populations. Sci Rep 2018; 8:4673. [PMID: 29549272 PMCID: PMC5856808 DOI: 10.1038/s41598-018-22975-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 03/05/2018] [Indexed: 11/29/2022] Open
Abstract
The Xinjiang Uyghur Autonomous Region of China (XUARC) harbors 47 ethnic groups including the Manchu (MCH: 0.11%), Mongols (MGL: 0.81%), Kyrgyz (KGZ: 0.86%) and Uzbek (UZK: 0.066%). To establish DNA databases for these populations, allele frequency distributions for 15 autosomal short tandem repeat (STR) loci were determined using the AmpFlSTR Identifiler PCR amplification kit. There was no evidence of departures from Hardy-Weinberg equilibrium (HWE) in any of the four populations and minimal departure from linkage equilibrium (LE) for a very small number of pairwise combinations of loci. The probabilities of identity for the different populations ranged from 1 in 1.51 × 1017 (MCH) to 1 in 9.94 × 1018 (MGL), the combined powers of discrimination ranged from 0.99999999999999999824 (UZK) to 0.9999999999999999848 (MCH) and the combined probabilities of paternal exclusion ranged from 0.9999979323 (UZK) to 0.9999994839 (MCH). Genetic distances, a phylogenetic tree and principal component analysis (PCA) revealed that the MCH, KGZ and UZK are genetically closer to the Han population of Liaoning and the Mongol population of Mongolia while the MGL are closer to Han, Japanese, Korean, Malaysian, Hong Kong Han and Russians living in China.
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Affiliation(s)
- Xiaoni Zhan
- Department of Forensic Genetics, School of Forensic Medicine, China Medical University, Shenyang, 110122, P.R. China
| | - Atif Adnan
- Department of Forensic Genetics, School of Forensic Medicine, China Medical University, Shenyang, 110122, P.R. China.
| | - Yuzhang Zhou
- Department of Forensic Genetics, School of Forensic Medicine, China Medical University, Shenyang, 110122, P.R. China
| | - Amjad Khan
- Department of Forensic Genetics, School of Forensic Medicine, China Medical University, Shenyang, 110122, P.R. China
| | - Kadirya Kasim
- Department of Forensic Genetics, School of Forensic Medicine, China Medical University, Shenyang, 110122, P.R. China
| | - Dennis McNevin
- National Centre for Forensic Studies, Faculty of Science & Technology, University of Canberra, Canberra, Australia
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23
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Feng C, Wang X, Wang X, Yu H, Zhang G. Genetic polymorphisms, forensic efficiency and phylogenetic analysis of 15 autosomal STR loci in the Kazak population of Ili Kazak Autonomous Prefecture, northwestern China. Ann Hum Biol 2018; 45:160-165. [DOI: 10.1080/03014460.2018.1445289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Chunmei Feng
- School of Forensic Medicine, China Medical University, Shenyang, Liaoning, PR China
- Department of Biotechnology Laboratory, Mudanjiang Medical College, Mudanjiang, Heilongjiang, PR China
| | - Xin Wang
- DNA Laboratory of Criminal Police Detachment, Suzhou Public Security Bureau, Suzhou, Jiangsu, PR China
| | - Xiaolong Wang
- School of Forensic Medicine, China Medical University, Shenyang, Liaoning, PR China
| | - Hao Yu
- School of Forensic Medicine, China Medical University, Shenyang, Liaoning, PR China
| | - Guohua Zhang
- School of Forensic Medicine, China Medical University, Shenyang, Liaoning, PR China
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24
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Li J, Shao Z, Liu G, Bai X, Borrow R, Chen M, Guo Q, Han Y, Li Y, Taha MK, Xu X, Xu X, Zheng H. Meningococcal disease and control in China: Findings and updates from the Global Meningococcal Initiative (GMI). J Infect 2018; 76:429-437. [PMID: 29406154 DOI: 10.1016/j.jinf.2018.01.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 12/22/2017] [Accepted: 01/03/2018] [Indexed: 10/18/2022]
Abstract
The Global Meningococcal Initiative (GMI) is a global expert group, including scientists, clinicians and public health officials from a wide range of specialities. The goal of the GMI is to prevent meningococcal disease worldwide through education, research, and co-operation. The Chinese GMI roundtable meeting was held in June 2017. The GMI met with local experts to gain insight into the meningococcal disease burden in China and current prevention and vaccination strategies in place. China experienced five epidemics of serogroup A meningococcal disease (MenA) between 1938 and 1977, with peak incidence of 403/100,000 recorded in 1967. MenA incidence rates have significantly declined following the universal introduction of the MenA polysaccharide vaccine in China in the 1980s. Further, surveillance data indicates changing meningococcal epidemiology in China with the emergence of new clones of serogroup B from serogroup C clonal complex (cc) 4821 due to capsular switching, and the international spread of serogroup W cc11. The importance of carriage and herd protection for controlling meningococcal disease was highlighted with the view to introduce conjugate vaccines and serogroup B vaccines into the national immunization schedule. Improved disease surveillance and standardized laboratory techniques across and within provinces will ensure optimal epidemiological monitoring.
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Affiliation(s)
- Junhong Li
- National Immunisation Programme Department, Chinese Center for Disease Control and Prevention, Beijing, China.
| | - Zhujun Shao
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
| | - Gang Liu
- Department of Infectious Disease, Beijing Children's Hospital, Beijing, China.
| | - Xilian Bai
- Meningococcal Reference Unit, Public Health England, Manchester Royal Infirmary, Manchester, UK.
| | - Ray Borrow
- Meningococcal Reference Unit, Public Health England, Manchester Royal Infirmary, Manchester, UK.
| | - Min Chen
- Department of Microbiology, Center for Disease Control and Prevention, Shanghai, China.
| | - Qinglan Guo
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China.
| | - Yue Han
- Department of Immunology, Center for Disease Control and Prevention, Liaoning, China.
| | - Yixing Li
- National Immunisation Programme Department, Chinese Center for Disease Control and Prevention, Beijing, China.
| | - Muhamed-Kheir Taha
- National Reference Centre for Meningococci, Institute Pasteur, Paris, France.
| | - Xihai Xu
- Department of Infectious Diseases, the First Affiliated Hospital of Anhui Medical University, China.
| | - Xin Xu
- Department of Immunization Programme, Center for Disease Control and Prevention, Guangdong, China.
| | - Huizhen Zheng
- Department of Immunization Programme, Center for Disease Control and Prevention, Guangdong, China.
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25
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Lan Q, Chen J, Guo Y, Xie T, Fang Y, Jin X, Cui W, Zhou Y, Zhu B. Genetic structure and polymorphism analysis of Xinjiang Hui ethnic minority based on 21 STRs. Mol Biol Rep 2018; 45:99-108. [PMID: 29372494 DOI: 10.1007/s11033-018-4143-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 12/27/2017] [Indexed: 01/23/2023]
Abstract
In the present study, we calculated the allelic frequencies and forensic descriptive parameters of Hui ethnic minority on the basis of 21 short tandem repeat (STR) loci aiming at understanding population structure better and enriching population genetic database. Bloodstain samples of 506 unrelated healthy Hui individuals in Xinjiang Uygur Autonomous Region were collected. Altogether 268 alleles were observed and the allelic frequencies ranged from 0.0010 to 0.5306. The combined power of discrimination and the cumulative probability of exclusion of the 21 STR loci in Hui ethnic minority were 0.9999999999999999999999998697 and 0.9999999968, respectively. Population data obtained manifested that the panel of 21 STR loci could provide robust genetic information for individual identification and paternity testing involved in forensic applications for Huis of Xinjiang Region. Furthermore, the present results of interpopulation differentiations, phylogenetic trees and principal component analysis which were conducted based on the overlapping 16 STR loci revealed that Hui group was genetically close to Xibe ethnic group and Han populations from different regions.
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Affiliation(s)
- Qiong Lan
- Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, Guangdong, People's Republic of China
| | - Jiangang Chen
- Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, People's Republic of China
| | - Yuxin Guo
- Key laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, Shaanxi, People's Republic of China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, Shaanxi, People's Republic of China
| | - Tong Xie
- Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, Guangdong, People's Republic of China
| | - Yating Fang
- Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, Guangdong, People's Republic of China
| | - Xiaoye Jin
- Key laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, Shaanxi, People's Republic of China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, Shaanxi, People's Republic of China
| | - Wei Cui
- Key laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, Shaanxi, People's Republic of China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, Shaanxi, People's Republic of China
| | - Yongsong Zhou
- Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, Guangdong, People's Republic of China
| | - Bofeng Zhu
- Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, Guangdong, People's Republic of China.
- Key laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, Shaanxi, People's Republic of China.
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, Shaanxi, People's Republic of China.
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26
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Zhou Y, Shao C, Li L, Zhang Y, Liu B, Yang Q, Tang Q, Li S, Xie J. Genetic analysis of 29 Y-STR loci in the Chinese Han population from Shanghai. Forensic Sci Int Genet 2018; 32:e1-e4. [DOI: 10.1016/j.fsigen.2017.11.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Revised: 09/27/2017] [Accepted: 11/09/2017] [Indexed: 10/18/2022]
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27
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Wang H, Ba H, Yang C, Zhang J, Tai Y. Inner and inter population structure construction of Chinese Jiangsu Han population based on Y23 STR system. PLoS One 2017; 12:e0180921. [PMID: 28704439 PMCID: PMC5509181 DOI: 10.1371/journal.pone.0180921] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 06/25/2017] [Indexed: 01/22/2023] Open
Abstract
In this study, we analyzed the genetic polymorphisms of 23 Y-STR loci from PowerPlex® Y23 system in 916 unrelated healthy male individuals from Chinese Jiangsu Han, and observed 912 different haplotypes including 908 unique haplotypes and 4 duplicate haplotypes. The haplotype diversity reached 0.99999 and the discrimination capacity and match probability were 0.9956 and 0.0011, respectively. The gene diversity values ranged from 0.3942 at DYS438 to 0.9607 at DYS385a/b. Population differentiation within 10 Jiangsu Han subpopulations were evaluated by RST values and visualized in Neighbor-Joining trees and Multi-Dimensional Scaling plots as well as population relationships between the Jiangsu Han population and other 18 Eastern Asian populations. Such results indicated that the 23 Y-STR loci were highly polymorphic in Jiangsu Han population and played crucial roles in forensic application as well as population genetics. For the first time, we reported the genetic diversity of male lineages in Jiangsu Han population at a high-resolution level of 23 Y-STR set and consequently contributed to familial searching, offender tracking, and anthropology analysis of Jiangsu Han population.
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Affiliation(s)
- Huipin Wang
- Zhongshan City People's Hospital, Zhongshan, Guangdong, P. R., China
| | - Huajie Ba
- DNA Laboratory, Public Security Bureau of Changzhou, Changzhou, Jiangsu, P. R., China
| | - Chun Yang
- Department of Psychiatry, Psychiatry Center of Chinese People’s Liberation Army, No. 102 Hospital of People’s Liberation Army, Changzhou, Jiangsu, P. R., China
| | - Jianqiu Zhang
- DNA Laboratory, Public Security Bureau of Yangzhou, Yangzhou, Jiangsu, P. R., China
| | - Yunchun Tai
- School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, P. R., China
- * E-mail:
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28
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Genetic polymorphism and evolutionary differentiation of Eastern Chinese Han: a comprehensive and comparative analysis on KIRs. Sci Rep 2017; 7:42486. [PMID: 28205529 PMCID: PMC5311978 DOI: 10.1038/srep42486] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 01/10/2017] [Indexed: 11/23/2022] Open
Abstract
Killer cell immunoglobulin-like receptor genes, namely KIRs, cluster together within the 160 kb genomic DNA region. In this study, we used PCR-SSP approach and successfully identified the genotype of 17 KIR genes in 123 independent healthy donors residing in the Jiangsu province, China. All individuals were positive at the 7 genes. The observed carrier gene frequencies (OFs) of remaining 10 KIRs ranged from 14.63% (KIR2DS3) to 95.93% (KIR3DL1). We found 27 distinct genotypes excluding KIR1D. The most frequent occurred in 63 individuals (51.22%). The linkage disequilibrium analysis signified 29 positive and 6 negative relations in 45 pairwise comparisons. To study population differentiation, we drew a Heatmap based on the data of KIRs from 59 populations and conducted Hierarchical Clustering by Euclidean distances. We next validated our results by estimating pairwise DA distances and illustrating a Neighbor-Joining tree, as well as a MDS plot covering 3 additional Chinese Han groups. The phylogenetic reconstruction and cluster analysis strongly indicated a genetically close relationship between Eastern and Jilin Hans. In conclusion, the present study provided a meritorious resource of KIR genotyping for population genetics, and could be helpful to uncover the genetic mechanism of KIRs in immune disease in the future.
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