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Alinaghi S, Mohseni M, Fattahi Z, Beheshtian M, Ghodratpour F, Zare Ashrafi F, Arzhangi S, Jalalvand K, Najafipour R, Khorram Khorshid HR, Kahrizi K, Najmabadi H. Genetic Analysis of 27 Y-STR Haplotypes in 11 Iranian Ethnic Groups. ARCHIVES OF IRANIAN MEDICINE 2024; 27:79-88. [PMID: 38619031 PMCID: PMC11017261 DOI: 10.34172/aim.2024.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 01/23/2024] [Indexed: 04/16/2024]
Abstract
BACKGROUND The study of Y-chromosomal variations provides valuable insights into male susceptibility in certain diseases like cardiovascular disease (CVD). In this study, we analyzed paternal lineage in different Iranian ethnic groups, not only to identify developing medical etiology, but also to pave the way for gender-specific targeted strategies and personalized medicine in medical genetic research studies. METHODS The diversity of eleven Iranian ethnic groups was studied using 27 Y-chromosomal short tandem repeat (Y-STR) haplotypes from Y-filer® Plus kit. Analysis of molecular variance (AMOVA) based on pair-wise RST along with multidimensional scaling (MDS) calculation and Network phylogenic analysis was employed to quantify the differences between 503 unrelated individuals from each ethnicity. RESULTS Results from AMOVA calculation confirmed that Gilaks and Azeris showed the largest genetic distance (RST=0.35434); however, Sistanis and Lurs had the smallest considerable genetic distance (RST=0.00483) compared to other ethnicities. Although Azeris had a considerable distance from other ethnicities, they were still close to Turkmens. MDS analysis of ethnic groups gave the indication of lack of similarity between different ethnicities. Besides, network phylogenic analysis demonstrated insignificant clustering between samples. CONCLUSION The AMOVA analysis results explain that the close distance of Azeris and Turkmens may be the effect of male-dominant expansions across Central Asia that contributed to historical and demographics of populations in the region. Insignificant differences in network analysis could be the consequence of high mutation events that happened in the Y-STR regions over the years. Considering the ethnic group affiliations in medical research, our results provided an understanding and characterization of Iranian male population for future medical and population genetics studies.
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Affiliation(s)
- Somayeh Alinaghi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Marzieh Mohseni
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Zohreh Fattahi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Maryam Beheshtian
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Fatemeh Ghodratpour
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Farzane Zare Ashrafi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Sanaz Arzhangi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Khadijeh Jalalvand
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Reza Najafipour
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | | | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
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Chai S, Li M, Tao R, Xia R, Kong Q, Qu Y, Chen L, Liu S, Li C, Chen P, Zhang S. Internal validation of an improved system for forensic application: a 41-plex Y-STR panel. Forensic Sci Res 2023; 8:70-78. [PMID: 37415794 PMCID: PMC10265952 DOI: 10.1093/fsr/owad012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 03/22/2023] [Indexed: 07/08/2023] Open
Abstract
Y-chromosome short tandem repeats (Y-STRs) have a unique role in forensic investigation. However, low-medium mutating Y-STRs cannot meet the requirements for male lineage differentiation in inbred populations, whereas rapidly mutating (RM) high-resolution Y-STRs might cause unexpected exclusion of paternal lineages. Thus, combining Y-STRs with low and high mutation rates helps to distinguish male individuals and lineages in family screening and analysis of genetic relationships. In this study, a novel 6-dye, 41-plex Y-STR panel was developed and validated, which included 17 loci from the Yfiler kit, nine RM Y-STR loci, 15 low-medium mutating Y-STR loci, and three Y-InDels. Developmental validation was performed for this panel, including size precision testing, stutter analysis, species specificity analysis, male specificity testing, sensitivity testing, concordance evaluation, polymerase chain reaction inhibitors analysis, and DNA mixture examination. The results demonstrated that the novel 41-plex Y-STR panel, developed in-house, was time efficient, accurate, and reliable. It showed good adaptability to directly amplify a variety of case-type samples. Furthermore, adding multiple Y-STR loci significantly improved the system's ability to distinguish related males, making it highly informative for forensic applications. In addition, the data obtained were compatible with the widely used Y-STR kits, facilitating the search and construction of population databases. Moreover, the addition of Y-Indels with short amplicons improves the analyses of degraded samples. Key Points A novel multiplex comprising 41 Y-STR and 3 Y-InDel was developed for forensic application.The multiplex included rapidly mutating Y-STRs and low-medium mutating Y-STRs, which is compatible with many commonly used Y-STR kits.The multiplex is a powerful tool for distinguishing related males, familial searching, and constructing DNA databases.
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Affiliation(s)
| | | | - Ruiyang Tao
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, China, Shanghai, China
| | - Ruocheng Xia
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, China, Shanghai, China
| | - Qianqian Kong
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, China, Shanghai, China
- Department of Forensic Medicine, Inner Mongolia Medical University, Hohhot, China
| | - Yiling Qu
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, China, Shanghai, China
- Department of Forensic Science, Medical School of Soochow University, Suzhou, China
| | - Liqin Chen
- Department of Forensic Medicine, Inner Mongolia Medical University, Hohhot, China
| | - Shiquan Liu
- Institute of Evidence Law and Forensic Science, China University of Political Science and Law, Beijing, China
| | - Chengtao Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, China, Shanghai, China
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Ran P, Ou S, Hadi S, Safhi FA, Al-Qahtani WS, Xuan JF, Adnan A, Pei B. Genetic characteristics and forensic features of Xibe ethnic group revealed via extended set of Y-STRs. Ann Hum Biol 2022; 49:204-209. [PMID: 35815603 DOI: 10.1080/03014460.2022.2100478] [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: 11/01/2022]
Abstract
BACKGROUND Xibe is the fifth largest minority population of Liaoning province. Predominately they live in Liaoning province (69.52%), followed by Xinjiang (18.06%), Heilongjiang (3.99%), Jilin (1.63%) and Inner Mongolia provinces (1.57%). AIM To provide an updated and precise population database on an extended set of Y STRs not available before and explore the forensic characteristics of 26 Y chromosomal STRs. SUBJECTS & METHODS In this study, we genotyped 406 unrelated Xibe male individuals from Liaoning province using Goldeneye® 26Y System kit and calculated the forensic parameters of these 26 Y STRs loci. RESULTS All haplotypes generated for 406 Xibe samples using Goldeneye® 26Y kit were unique with a discrimination capacity (DC) of 1. On restricting the haplotypes to the Y-filer® set of 17 Y-STRs, we observed 392 haplotypes. Among them 93.53% (380) were unique with a DC of 0.9655 and haplotype diversity (HD) of 0.9998, showing high discrimination power of the extended set of markers in this population. Allelic frequencies ranged from 0.0024 to 0.7684 across 26 Y STRs loci. DYS385 showed the highest gene diversity (0.9691) among all markers. CONCLUSION According to pairwise RST genetic distances among Xibe populations from China, the Liaoning Xibe population showed the closest genetic distance (0.0035) followed by Xinjiang Xibe population (0.0218). Multidimensional scaling (MDS) analysis among Xibe and 29 other Chinese populations showed that local populations such as Manchu from Liaoning and Han from Beijing had a close affinity while Tibetans from Aba, China, were most distant from Xibe populations. Moreover, 12 individuals showed a null allele at DYS448 in Xibe population samples. We submitted Y-STRs data in the Y-Chromosome Haplotype Reference Database (YHRD) for future forensic and other usage.
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Affiliation(s)
- Peng Ran
- Xiamen Blood Center, Xiamen, Fujian province 361004, P.R. China
| | - Shanhai Ou
- Xiamen Blood Center, Xiamen, Fujian province 361004, P.R. China
| | - Sibte Hadi
- Department of Forensic Sciences, College of Criminal Justice, Naif Arab University of Security Sciences, Riyadh, 11452, Kingdom of Saudi Arabia
| | - Fatmah Ahmed Safhi
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Wedad Saeed Al-Qahtani
- Department of Forensic Sciences, College of Criminal Justice, Naif Arab University of Security Sciences, Riyadh, 11452, Kingdom of Saudi Arabia
| | - Jin-Feng Xuan
- Department of Forensic Genetics, School of Forensic Medicine, China Medical University, Shenyang, Liaoning, P.R. China
| | - Atif Adnan
- Department of Forensic Sciences, College of Criminal Justice, Naif Arab University of Security Sciences, Riyadh, 11452, Kingdom of Saudi Arabia
| | - Bin Pei
- Xiamen Blood Center, Xiamen, Fujian province 361004, P.R. China
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Li L, Yao L, Gong H, Luo L, Liang H, Zhang J, Wang Y, He G, Jia F, Chen P. Genetic characterisation for Yan'an Han population in Northern Shaanxi Province, China, via 38Y-STRs using Yfiler™ Platinum. Ann Hum Biol 2021; 48:327-334. [PMID: 34308740 DOI: 10.1080/03014460.2021.1951350] [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: 10/20/2022]
Abstract
BACKGROUND Haplotype/allele frequency data of Y-chromosomal STR loci in ethnically diverse populations are essential for forensics, anthropology and genealogy. However, genetic structure and forensic characterisation of the Chinese Han population residing in Yan'an, in the Northern Shaanxi Province, remain unclear. AIM To assess forensic efficiency for 38 Y-Chromosomal STR loci in Yan'an Han population and reveal the population genetic relationships between Yan'an Han and other populations at a nationwide and worldwide level. SUBJECTS AND METHODS 719 healthy unrelated males were genotyped using the Yfiler™ Platinum system. Haplotype/allele frequencies and forensic parameters were calculated. Multi-dimensional scaling plots (MDS) and neighbor-joining (N-J) tree were used to explore the population structure based on the pairwise gene distances (Rst). RESULTS A total of 707 haplotypes were identified, among which 697 unique haplotypes were observed (98.59%). The overall haplotype diversity (HD) and discrimination capacity (DC) were 0.9999 and 0.9833, respectively. Comprehensive population comparisons showed Yan'an Han is genetically closer to linguistically similar populations in China, and more related to East Asian populations around the world. CONCLUSION The present results give a unique insight into the Yan'an Han population via the set of 38 Y-STRs, which can be used for forensic practice and human genetics research.
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Affiliation(s)
- Luyao Li
- Department of Pathology, The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, China
| | - Lilan Yao
- Key Laboratory of Cell Engineering in Guizhou Province, Affiliated Hospital of Zunyi Medical University, Guizhou, China.,Center of Forensic Expertise, Affiliated hospital of Zunyi Medical University, Guizhou, China
| | - Huilin Gong
- Department of Pathology, The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, China
| | - Li Luo
- Key Laboratory of Cell Engineering in Guizhou Province, Affiliated Hospital of Zunyi Medical University, Guizhou, China.,Center of Forensic Expertise, Affiliated hospital of Zunyi Medical University, Guizhou, China
| | - Hau Liang
- Department of Pathology, The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, China
| | - Jiaojiao Zhang
- Department of Pathology, The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, China
| | - Yuanyuan Wang
- Department of Pathology, The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, China
| | - Guanglin He
- Institute of Forensic medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Sichuan, China
| | - Fuquan Jia
- Department of Forensic Medicine, Inner Mongolia Medical University, Inner Mongolia Autonomous Region, Hohhot, China
| | - Pengyu Chen
- Key Laboratory of Cell Engineering in Guizhou Province, Affiliated Hospital of Zunyi Medical University, Guizhou, China.,Center of Forensic Expertise, Affiliated hospital of Zunyi Medical University, Guizhou, China
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5
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Fan H, Xie Q, Li Y, Wang L, Wen SQ, Qiu P. Insights Into Forensic Features and Genetic Structures of Guangdong Maoming Han Based on 27 Y-STRs. Front Genet 2021; 12:690504. [PMID: 34220963 PMCID: PMC8253533 DOI: 10.3389/fgene.2021.690504] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 05/14/2021] [Indexed: 11/13/2022] Open
Abstract
Maoming is located in the southwest region of Guangdong Province and is the cradle of Gaoliang culture, which is the representative branch of Lingnan cultures. Historical records showed that the amalgamations between Gaoliang aborigines and distinct ethnic minorities had some influences on the shaping of Gaoliang culture, especially for the local Tai-kadai language-speaking Baiyue and Han Chinese from Central China. However, there is still no exact genetic evidence for the influences on the genetic pool of Maoming Han, and the genetic relationships between Maoming Han and other Chinese populations are still unclear. Hence, in order to get a better understanding of the paternal genetic structures and characterize the forensic features of 27 Y-chromosomal short tandem repeats (Y-STRs) in Han Chinese from Guangdong Maoming, we firstly applied the AmpFLSTR® Yfiler® Plus PCR Amplification Kit (Thermo Fisher Scientific, Waltham, MA, United States) to genotype the haplotypes in 431 Han males residing in Maoming. A total of 263 different alleles were determined across all 27 Y-STRs with the corresponding allelic frequencies from 0.0004 to 0.7401, and the range of genetic diversity (GD) was 0.4027 (DYS391) to 0.9596 (DYS385a/b). In the first batch of 27 Yfiler data in Maoming Han, 417 distinct haplotypes were discovered, and nine off-ladder alleles were identified at six Y-STRs; in addition, no copy number variant or null allele was detected. The overall haplotype diversity (HD) and discrimination capacity (DC) of 27 Yfiler were 0.9997 and 0.9675, respectively, which demonstrated that the 6-dye and 27-plex system has sufficient system effectiveness for forensic applications in Maoming Han. What is more, the phylogenetic analyses indicated that Maoming Han, which is a Southern Han Chinese population, has a close relationship with Meizhou Kejia, which uncovered that the role of the gene flows from surrounding Han populations in shaping the genetic pool of Maoming Han cannot be ignored. From the perspectives of genetics, linguistics, and geographies, the genetic structures of Han populations correspond to the patterns of the geographical-scale spatial distributions and the relationships of language families. Nevertheless, no exact genetic evidence supports the intimate relationships between Maoming Han and Tai-Kadai language-speaking populations and Han populations of Central Plains in the present study.
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Affiliation(s)
- Haoliang Fan
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
- Institute of Archaeological Science, Fudan University, Shanghai, China
- School of Basic Medicine and Life Science, Hainan Medical University, Haikou, China
| | - Qiqian Xie
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Yanning Li
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
- School of Basic Medicine, Gannan Medical University, Ganzhou, China
| | - Lingxiang Wang
- Institute of Archaeological Science, Fudan University, Shanghai, China
| | - Shao-Qing Wen
- Institute of Archaeological Science, Fudan University, Shanghai, China
| | - Pingming Qiu
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
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6
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Shang L, Ding G, Mo X, Sun J, Sun H, Yu Z, Li W. A novel multiplex of 12 multicopy Y-STRs for forensic application. J Forensic Sci 2021; 66:1901-1907. [PMID: 34110021 DOI: 10.1111/1556-4029.14774] [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: 01/05/2021] [Revised: 05/08/2021] [Accepted: 05/18/2021] [Indexed: 11/28/2022]
Abstract
Y chromosomal short tandem repeats (Y-STRs) have been applied overwhelmingly in forensic areas for solving paternity identification and sexual assault cases. Yet the widely used Y-STR kits contain mostly single-copy markers, which may restrict the discrimination power. Here, a novel Y-STR multiplex was developed and validated in order to complement the currently available Y-STR kits, especially on differentiating male relatives. The assay includes twelve multicopy Y-STR loci (DYF371, DYF383S1, DYS385, DYF387S1, DYS389I/II, DYF399S1, DYF404S1, DYF409S1, DYF411S1, DYS464, DYS526, DYS527; four of them are rapidly mutating ones), 1 single-copy Y-STR (DYS391), and Amelogenin, and was optimized to amplify at annealing temperature of 59°C and 28 cycles. Validation studies show that full profiles are obtained with 0.125 ng of male DNA. The system is capable of overcoming high concentrations of inhibitors such as hematin, EDTA, and humic acid. Besides, the results demonstrate good sizing precision and the ability to detect male-specific profiles in male/female DNA mixtures at a ratio of 1:800. Excellent species specificity was also observed in microorganisms and non-primates, while detectable peaks were found in some primates. Based on published genetic data, gene diversity values were above 0.7 for most of the loci in our multiplex, inferring a high capacity in discriminating unrelated and related male individuals. The kit is of great potential for forensic application.
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Affiliation(s)
- Lei Shang
- National Engineering Laboratory for Forensic Science, Beijing Engineering Research Center of Crime Scene Evidence Examination, Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing, China
| | - Guangshu Ding
- National Engineering Laboratory for Forensic Science, Beijing Engineering Research Center of Crime Scene Evidence Examination, Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing, China
| | - Xiaoting Mo
- National Engineering Laboratory for Forensic Science, Beijing Engineering Research Center of Crime Scene Evidence Examination, Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing, China
| | - Jing Sun
- National Engineering Laboratory for Forensic Science, Beijing Engineering Research Center of Crime Scene Evidence Examination, Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing, China
| | - Hui Sun
- National Engineering Laboratory for Forensic Science, Beijing Engineering Research Center of Crime Scene Evidence Examination, Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing, China
| | - Zhengliang Yu
- National Engineering Laboratory for Forensic Science, Beijing Engineering Research Center of Crime Scene Evidence Examination, Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing, China
| | - Wanshui Li
- National Engineering Laboratory for Forensic Science, Beijing Engineering Research Center of Crime Scene Evidence Examination, Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing, China
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7
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Luo C, Duan L, Li Y, Xie Q, Wang L, Ru K, Nazir S, Jawad M, Zhao Y, Wang F, Du Z, Peng D, Wen SQ, Qiu P, Fan H. Insights From Y-STRs: Forensic Characteristics, Genetic Affinities, and Linguistic Classifications of Guangdong Hakka and She Groups. Front Genet 2021; 12:676917. [PMID: 34108995 PMCID: PMC8181459 DOI: 10.3389/fgene.2021.676917] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 04/06/2021] [Indexed: 12/02/2022] Open
Abstract
Guangdong province is situated in the south of China with a population size of 113.46 million. Hakka is officially recognized as a branch of Han Chinese, and She is the official minority group in mainland China. There are approximately 25 million Hakka people who mainly live in the East and North regions of China, while there are only 0.7 million She people. The genetic characterization and forensic parameters of these two groups are poorly defined (She) or still need to be explored (Hakka). In this study, we have genotyped 475 unrelated Guangdong males (260 Hakka and 215 She) with Promega PowerPlex® Y23 System. A total of 176 and 155 different alleles were observed across all 23 Y-STRs for Guangdong Hakka (with a range of allele frequencies from 0.0038 to 0.7423) and Guangdong She (0.0047–0.8605), respectively. The gene diversity ranged from 0.4877 to 0.9671 (Guangdong Hakka) and 0.3277–0.9526 (Guangdong She), while the haplotype diversities were 0.9994 and 0.9939 for Guangdong Hakka and Guangdong She, with discrimination capacity values of 0.8885 and 0.5674, respectively. With reference to geographical and linguistic scales, the phylogenetic analyses showed us that Guangdong Hakka has a close relationship with Southern Han, and the genetic pool of Guangdong Hakka was influenced by surrounding Han populations. The predominant haplogroups of the Guangdong She group were O2-M122 and O2a2a1a2-M7, while Guangdong She clustered with other Tibeto-Burman language-speaking populations (Guizhou Tujia and Hunan Tujia), which shows us that the Guangdong She group is one of the branches of Tibeto-Burman populations and the Huonie dialect of She languages may be a branch of Tibeto-Burman language families.
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Affiliation(s)
- Chunfang Luo
- School of Forensic Medicine, Southern Medical University, Guangzhou, China.,Heyuan Municipal Public Security Bureau, Heyuan, China
| | - Lizhong Duan
- Beijing Municipal Public Security Bureau, Beijing, China
| | - Yanning Li
- School of Forensic Medicine, Southern Medical University, Guangzhou, China.,School of Basic Medicine, Gannan Medical University, Ganzhou, China
| | - Qiqian Xie
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Lingxiang Wang
- Institute of Archaeological Science, Fudan University, Shanghai, China
| | - Kai Ru
- Institute of Archaeological Science, Fudan University, Shanghai, China
| | - Shahid Nazir
- Department of Forensic Sciences, University of Health Sciences, Lahore, Pakistan
| | - Muhammad Jawad
- Department of Forensic Sciences, University of Health Sciences, Lahore, Pakistan
| | - Yifeng Zhao
- Nanjing Zhenghong Judicial Identification Institute, Nanjing, China
| | - Fenfen Wang
- First Clinical Medical College, Hainan Medical University, Haikou, China
| | - Zhengming Du
- First Clinical Medical College, Hainan Medical University, Haikou, China
| | - Dehua Peng
- Heyuan Municipal Public Security Bureau, Heyuan, China
| | - Shao-Qing Wen
- Institute of Archaeological Science, Fudan University, Shanghai, China
| | - Pingming Qiu
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Haoliang Fan
- School of Forensic Medicine, Southern Medical University, Guangzhou, China.,Institute of Archaeological Science, Fudan University, Shanghai, China.,School of Basic Medicine and Life Science, Hainan Medical University, Haikou, China
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8
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Jin X, Xing G, Yang C, Zhang X, Cui W, Chen C, Zhu B. Genetic polymorphisms of 44 Y chromosomal genetic markers in the Inner Mongolia Han population and its genetic relationship analysis with other reference populations. Forensic Sci Res 2021; 7:510-517. [PMID: 36353319 PMCID: PMC9639530 DOI: 10.1080/20961790.2020.1857509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022] Open
Abstract
Y chromosomal genetic markers in the non-recombining region are commonly used for human evolution research, familial searching, and forensic male differentiation since they strictly follow paternal inheritance. Y chromosomal short tandem repeats (Y-STRs) possess extraordinarily advantages in forensic applications because of their high polymorphisms and special genetic pattern. Here, we assessed the genetic diversities of 41 Y-STRs and three Y chromosomal insertion/deletion (Y-InDels) loci in the Chinese Inner Mongolia Han population; besides, genetic differentiation analyses among the studied Han population and other previously reported populations were conducted based on 27 same Y-STRs. Totally, 425 alleles were observed in 324 Inner Mongolia Han individuals for these Y-markers. Gene diversities of these Y-markers distributed from 0.0306 to 0.9634. The haplotype diversity and discriminatory capacity of these Y-markers in the Inner Mongolia Han population were 0.9999 and 0.98457, respectively. Haplotype resolution comparisons of different Y-marker groups in the studied Han population revealed that higher haplotype resolution could be achieved for these 44 Y-markers. Population genetic analyses of the Inner Mongolia Han population and other reference populations demonstrated that the studied Han population had relatively closer genetic affinities with Northern Han Chinese populations than Southern Han and other minority groups. To sum up, these 44 Y-markers can be utilized as a valuable tool for male differentiation in the Inner Mongolia Han population.
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Affiliation(s)
- Xiaoye Jin
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an, China
- College of Forensic Science, Xi’an Jiaotong University Health Science Center, Xi’an, China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi’an Jiaotong University, Xi’an, China
| | - Guohui Xing
- People’s Hospital of Arong Banner, Hulun Buir City, China
| | - Chunhua Yang
- People’s Hospital of Arong Banner, Hulun Buir City, China
| | - Xingru Zhang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an, China
- College of Forensic Science, Xi’an Jiaotong University Health Science Center, Xi’an, China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi’an Jiaotong University, Xi’an, China
| | - Wei Cui
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an, China
- College of Forensic Science, Xi’an Jiaotong University Health Science Center, Xi’an, China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi’an Jiaotong University, Xi’an, China
| | - Chong Chen
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an, China
- College of Forensic Science, Xi’an Jiaotong University Health Science Center, Xi’an, China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi’an Jiaotong University, Xi’an, China
| | - Bofeng Zhu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an, China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi’an Jiaotong University, Xi’an, China
- Multi-Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, China
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Simayijiang H, Morling N, Børsting C. Sequencing of human identification markers in an Uyghur population using the MiSeq FGxTM Forensic Genomics System. Forensic Sci Res 2020; 7:154-162. [PMID: 35784409 PMCID: PMC9246034 DOI: 10.1080/20961790.2020.1779967] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Massively parallel sequencing (MPS) offers a useful alternative to capillary electrophoresis (CE) based analysis of human identification markers in forensic genetics. By sequencing short tandem repeats (STRs) instead of determining the fragment lengths by CE, the sequence variation within the repeat region and the flanking regions may be identified. In this study, we typed 264 Uyghur individuals using the MiSeq FGx™ Forensic Genomics System and Primer Mix A of the ForenSeq™ DNA Signature Prep Kit that amplifies 27 autosomal STRs, 25 Y-STRs, seven X-STRs, and 94 HID-SNPs. STRinNGS v.1.0 and GATK 3.6 were used to analyse the STR regions and HID-SNPs, respectively. Increased allelic diversity was observed for 33 STRs with the PCR-MPS assay. The largest increases were found in DYS389II and D12S391, where the numbers of sequenced alleles were 3–4 times larger than those of alleles determined by repeat length alone. A relatively large number of flanking region variants (28 SNPs and three InDels) were observed in the Uyghur population. Seventeen of the flanking region SNPs were rare, and 12 of these SNPs had no accession number in dbSNP. The combined mean match probability and typical paternity index based on 26 sequenced autosomal STRs were 3.85E−36 and 1.49E + 16, respectively. This was 10 000 times lower and 1 000 times higher, respectively, than the same parameters calculated from STR repeat lengths.Key Points Sequencing data on STRs and SNPs used for human identification are presented for the Uyghur population. STRinNGS v.1.0 was used to analyse the flanking regions of STRs. The concordance between PCR-CE and PCR-MPS results was 99.86%. Detection of sequence variation in STRs and their flanking regions increased the allelic diversity.
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Affiliation(s)
- Halimureti Simayijiang
- Faculty of Health and Medical Sciences, Section of Forensic Genetics, Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark
- Faculty of Criminal Science and Technology, Xinjiang Police College, Xinjiang, China
| | - Niels Morling
- Faculty of Health and Medical Sciences, Section of Forensic Genetics, Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Claus Børsting
- Faculty of Health and Medical Sciences, Section of Forensic Genetics, Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark
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10
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Kumawat R, Shrivastava P, Shrivastava D, Mathur G. Molecular diversity of 23 Y-STR genetic markers in the population of Rajasthan, India. Meta Gene 2020. [DOI: 10.1016/j.mgene.2020.100694] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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11
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Joint Genetic Analyses of Mitochondrial and Y-Chromosome Molecular Markers for a Population from Northwest China. Genes (Basel) 2020; 11:genes11050564. [PMID: 32443545 PMCID: PMC7290686 DOI: 10.3390/genes11050564] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/09/2020] [Accepted: 05/11/2020] [Indexed: 12/27/2022] Open
Abstract
The genetic markers on mitochondria DNA (mtDNA) and Y-chromosome can be applied as a powerful tool in population genetics. We present a study to reveal the genetic background of Kyrgyz group, a Chinese ethnic group living in northwest China, and genetic polymorphisms of 60 loci on maternal inherited mtDNA and 24 loci on paternal inherited Y-chromosome short tandem repeats (Y-STRs) were investigated. The relationship between the two systems was tested, and the result indicated that they were statistically independent from each other. The genetic distances between Kyrgyz group and 11 reference populations for mtDNA, and 13 reference populations for Y-STRs were also calculated, respectively. The present results demonstrated that the Kyrgyz group was genetically closer to East Asian populations than European populations based on the mtDNA loci but the other way around for the Y-STRs. The genetic analyses could largely strengthen the understanding for the genetic background of the Kyrgyz group.
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12
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Adnan A, Kasimu K, Rakha A, He G, Yang T, Wang C, Lu J, Xuan J. Comprehensive genetic structure analysis of Han population from Dalian City revealed by 20 Y-STRs. Mol Genet Genomic Med 2020; 8:e1149. [PMID: 31989793 PMCID: PMC7057124 DOI: 10.1002/mgg3.1149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 11/15/2019] [Accepted: 01/08/2020] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Dalian is a city formed in the 1880s in Liaoning province, Northeastern China with a population of 6.69 million now. Han is the largest ethnic group not only across Mainland China (92%) and Taiwan (97%) but also considered to be the largest ethnic group of the world contributing to above 18% of world's population. METHODS In the current study, we genotyped Goldeneye® 20Y System loci in 879 unrelated male individuals from the Han ethnic group in Dalian city and calculated the forensic parameters of the 20 Y-STR loci. RESULTS In total, we observed 855 haplotypes, among which 835 (94.99%) were unique. The discrimination capacity (DC) of overall Goldeneye® 20Y System is 97.27% and it slightly reduces to 96.93% when only Y-filer® set of 17 Y-STRs were used, which mitigates using the extended set of markers in this population. We found DYS388 showed the lowest gene diversity (0.5151), whereas DYS389II showed the highest gene diversity (0.7621) in single copy Y-STR, and DYS385 showed the highest gene diversity (0.9683) among all. CONCLUSION Multidimensional scaling (MDS) analysis based upon pairwise Rst genetic distance showed difference among Han population from the east to the west and from the north to the south. We also predicted haplogroups using Y-STR haplotypes, which showed the dominance of Haplogroup O (65.2%) followed by Haplogroup C (14.5%) in Dalian Han population. Moreover, we found 10 individuals showed a null allele at the DYS448 in our samples. We also performed linear discriminatory analysis (LDA) between Han and other prominent Chinese minority ethnic groups. We presented Y-STRs data in the Y-Chromosome Haplotype Reference Database (YHRD) for the future forensic and other usage.
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Affiliation(s)
- Atif Adnan
- Department of Forensic Genetics and BiologySchool of Forensic MedicineChina Medical UniversityShenyangP.R. China
- Department of Human AnatomyCollege of Basic Medical ScienceChina Medical UniversityShenyangP.R. China
| | - Kaidirina Kasimu
- School of Clinical MedicineChina Medical UniversityShenyangP.R. China
| | - Allah Rakha
- Department of Forensic SciencesUniversity of Health Sciences LahoreLahorePakistan
| | - Guanglin He
- Department of Anthropology and EthnologyXiamen UniversityXiamenChina
| | - Tongya Yang
- Department of Human AnatomyCollege of Basic Medical ScienceChina Medical UniversityShenyangP.R. China
| | - Chuan‐Chao Wang
- Department of Anthropology and EthnologyXiamen UniversityXiamenChina
| | - Jie Lu
- Department of Human AnatomyCollege of Basic Medical ScienceChina Medical UniversityShenyangP.R. China
| | - Jin‐feng Xuan
- Department of Forensic Genetics and BiologySchool of Forensic MedicineChina Medical UniversityShenyangP.R. China
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13
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Li M, Zhou W, Zhang Y, Huang L, Wang X, Wu J, Meng M, Wang H, Li C, Bian Y. Development and validation of a novel 29-plex Y-STR typing system for forensic application. Forensic Sci Int Genet 2020; 44:102169. [DOI: 10.1016/j.fsigen.2019.102169] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 09/24/2019] [Accepted: 09/29/2019] [Indexed: 11/29/2022]
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14
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Genetic polymorphism of 190 Y-SNPs in Han population from Jiangsu province, China. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.10.087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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15
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Genetic polymorphism and population structure of Torghut Mongols and comparison with a Mongolian population 3000 kilometers away. Forensic Sci Int Genet 2019; 42:235-243. [DOI: 10.1016/j.fsigen.2019.07.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 07/28/2019] [Accepted: 07/28/2019] [Indexed: 12/17/2022]
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16
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Haplotypes of 27 Y-STRs analyzed in Gelao and Miao ethnic minorities from Guizhou Province, Southwest China. Forensic Sci Int Genet 2019; 40:e264-e267. [DOI: 10.1016/j.fsigen.2019.03.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 02/18/2019] [Accepted: 03/02/2019] [Indexed: 11/17/2022]
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17
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Wang CZ, Su MJ, Li Y, Chen L, Jin X, Wen SQ, Tan J, Shi MS, Li H. Genetic polymorphisms of 27 Yfiler® Plus loci in the Daur and Mongolian ethnic minorities from Hulunbuir of Inner Mongolia Autonomous Region, China. Forensic Sci Int Genet 2019; 40:e252-e255. [DOI: 10.1016/j.fsigen.2019.02.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 01/22/2019] [Accepted: 02/03/2019] [Indexed: 11/28/2022]
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18
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Lan Q, Shen C, Jin X, Guo Y, Xie T, Chen C, Cui W, Fang Y, Yang G, Zhu B. Distinguishing three distinct biogeographic regions with an in‐house developed 39‐AIM‐InDel panel and further admixture proportion estimation for Uyghurs. Electrophoresis 2019; 40:1525-1534. [DOI: 10.1002/elps.201800448] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 01/27/2019] [Accepted: 02/03/2019] [Indexed: 01/09/2023]
Affiliation(s)
- Qiong Lan
- Department of Forensic GeneticsSchool of Forensic MedicineSouthern Medical University Guangzhou P. R. China
| | - Chunmei Shen
- Institute of Brain and Behavioral SciencesCollege of Life SciencesShaanxi Normal University Xi'an P. R. China
| | - Xiaoye Jin
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of StomatologyXi'an Jiaotong University Xi'an P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial DiseasesCollege of StomatologyXi'an Jiaotong University Xi'an P. R. China
| | - Yuxin Guo
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of StomatologyXi'an Jiaotong University Xi'an P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial DiseasesCollege of StomatologyXi'an Jiaotong University Xi'an P. R. China
| | - Tong Xie
- Department of Forensic GeneticsSchool of Forensic MedicineSouthern Medical University Guangzhou P. R. China
| | - Chong Chen
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of StomatologyXi'an Jiaotong University Xi'an P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial DiseasesCollege of StomatologyXi'an Jiaotong University Xi'an P. R. China
| | - Wei Cui
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of StomatologyXi'an Jiaotong University Xi'an P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial DiseasesCollege of StomatologyXi'an Jiaotong University Xi'an P. R. China
| | - Yating Fang
- Department of Forensic GeneticsSchool of Forensic MedicineSouthern Medical University Guangzhou P. R. China
| | - Guang Yang
- Department of Laboratory Medicine and PathologyMayo Clinic Rochester Minnesota USA
| | - Bofeng Zhu
- Department of Forensic GeneticsSchool of Forensic MedicineSouthern Medical University Guangzhou P. R. China
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of StomatologyXi'an Jiaotong University Xi'an P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial DiseasesCollege of StomatologyXi'an Jiaotong University Xi'an P. R. China
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19
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Fan H, Wang X, Chen H, Long R, Liang A, Li W, Chen J, Wang W, Qu Y, Song T, Zhang P, Deng J. The evaluation of forensic characteristics and the phylogenetic analysis of the Ong Be language-speaking population based on Y-STR. Forensic Sci Int Genet 2018; 37:e6-e11. [DOI: 10.1016/j.fsigen.2018.09.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 08/24/2018] [Accepted: 09/24/2018] [Indexed: 11/25/2022]
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20
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A comprehensive portrait of Y-STR diversity of Indian populations and comparison with 129 worldwide populations. Sci Rep 2018; 8:15421. [PMID: 30337554 PMCID: PMC6194109 DOI: 10.1038/s41598-018-33714-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 10/05/2018] [Indexed: 11/28/2022] Open
Abstract
India, known for its rich cultural, linguistic and ethnic diversity, has attracted the attention of population geneticists to understand its genetic diversity employing autosomal, Y-chromosomal and mitochondrial DNA markers. Y-chromosomal short tandem repeats (Y-STRs) are useful in understanding population substructures and reveal the patrilineal affinities among populations. Previous studies on Indian populations based on Y-STR markers were either limited to restricted number of markers or focused on few selected populations. In this study we genotyped 407 unrelated male individuals from 12 states in India employing the suite of Y-STRs present in PowerPlex Y23 (Promega, Madison, WI, USA). These populations clustered genetically close to each other irrespective of their geographic co-ordinates and were characterized primarily by R1a, H and L haplogroups. Interestingly, comparison with 129 worldwide populations showed genetic affinity of the Indian populations with few populations from Europe and Levantine. This study presents the first pan-Indian landscape of 23 Y-STRs and serves as a useful resource for construction of an Indian Y-STR database.
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21
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Genetic diversity of 21 forensic autosomal STRs and DYS391 in the Han population from Shanghai, Eastern China. Forensic Sci Int Genet 2018; 37:e23-e25. [PMID: 30181102 DOI: 10.1016/j.fsigen.2018.08.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 08/13/2018] [Accepted: 08/26/2018] [Indexed: 01/11/2023]
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22
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Zhang J, Mo X, Zhang Y, Ding G, Wang X, Li W, Zhao X, Ye J. Genetic analysis of 26 Y-STR loci in Han population from Leshan, Southwest China. Forensic Sci Int Genet 2018; 37:e15-e16. [PMID: 30100390 DOI: 10.1016/j.fsigen.2018.07.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 07/27/2018] [Accepted: 07/30/2018] [Indexed: 12/09/2022]
Affiliation(s)
- Jian Zhang
- Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China; National Engineering Laboratory for Forensic Science, Beijing 100038, China
| | - Xiaoting Mo
- Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China; National Engineering Laboratory for Forensic Science, Beijing 100038, China
| | - Yiwen Zhang
- Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China; National Engineering Laboratory for Forensic Science, Beijing 100038, China
| | - Guangshu Ding
- Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China; National Engineering Laboratory for Forensic Science, Beijing 100038, China
| | - Xi Wang
- Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China; National Engineering Laboratory for Forensic Science, Beijing 100038, China
| | - Wanshui Li
- Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China; National Engineering Laboratory for Forensic Science, Beijing 100038, China
| | - Xingchun Zhao
- Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China; National Engineering Laboratory for Forensic Science, Beijing 100038, China.
| | - Jian Ye
- Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China; National Engineering Laboratory for Forensic Science, Beijing 100038, China.
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23
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Zhang J, Mo X, Shang L, Jin X, Chen D, Zhu H, Zhang Y, Kang B, Li W, Ye J. Genetic analysis of 29 Y-STR loci in Han population from Dongfang, Southern China. Int J Legal Med 2018; 133:1033-1035. [PMID: 30032460 DOI: 10.1007/s00414-018-1899-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Accepted: 07/17/2018] [Indexed: 11/29/2022]
Abstract
In the present study, blood samples of 984 unrelated Han individuals were collected from Dongfang, Southern China, after informed consent. A total of 29 Y-chromosomal short tandem repeat (Y-STR) were analyzed, including DYF387S1, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS444, DYS447, DYS448, DYS449, DYS456, DYS458, DYS460, DYS481, DYS508, DYS518, DYS533, DYS576, DYS635, DYS643 and GATAH4. A total of 749 different haplotypes were found among 984 individuals, of which 645 were unique. The haplotype diversity was 0.9988 and the discrimination capacity was 0.7612, while the match probability was 0.0025. The smallest genetic distance (RST = 0.0155) was found between the Dongfang Han population and Guizhou Han population, while the largest genetic distance (RST = 0.1284) was observed with Gansu Tibetan.
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Affiliation(s)
- Jian Zhang
- National Engineering Laboratory for Forensic Science, Beijing Engineering Research Center of Crime Scene Evidence Examination, Key Laboratory of Forensic Genetics, Ministry of Public Security, Institute of Forensic Science, Beijing, 100038, China
| | - Xiaoting Mo
- National Engineering Laboratory for Forensic Science, Beijing Engineering Research Center of Crime Scene Evidence Examination, Key Laboratory of Forensic Genetics, Ministry of Public Security, Institute of Forensic Science, Beijing, 100038, China
| | - Lei Shang
- National Engineering Laboratory for Forensic Science, Beijing Engineering Research Center of Crime Scene Evidence Examination, Key Laboratory of Forensic Genetics, Ministry of Public Security, Institute of Forensic Science, Beijing, 100038, China
| | - Xiuwen Jin
- Dongfang Public Security Bureau, Dongfang, 000253, China
| | - Dong Chen
- Dongfang Public Security Bureau, Dongfang, 000253, China
| | - Hongshan Zhu
- Hainan Public Security Department, Haikou, China
| | - Yiwen Zhang
- National Engineering Laboratory for Forensic Science, Beijing Engineering Research Center of Crime Scene Evidence Examination, Key Laboratory of Forensic Genetics, Ministry of Public Security, Institute of Forensic Science, Beijing, 100038, China
| | - Bin Kang
- National Engineering Laboratory for Forensic Science, Beijing Engineering Research Center of Crime Scene Evidence Examination, Key Laboratory of Forensic Genetics, Ministry of Public Security, Institute of Forensic Science, Beijing, 100038, China
| | - Wanshui Li
- National Engineering Laboratory for Forensic Science, Beijing Engineering Research Center of Crime Scene Evidence Examination, Key Laboratory of Forensic Genetics, Ministry of Public Security, Institute of Forensic Science, Beijing, 100038, China
| | - Jian Ye
- National Engineering Laboratory for Forensic Science, Beijing Engineering Research Center of Crime Scene Evidence Examination, Key Laboratory of Forensic Genetics, Ministry of Public Security, Institute of Forensic Science, Beijing, 100038, China.
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24
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He G, Wang Z, Wang M, Luo T, Liu J, Zhou Y, Gao B, Hou Y. Forensic ancestry analysis in two Chinese minority populations using massively parallel sequencing of 165 ancestry-informative SNPs. Electrophoresis 2018; 39:2732-2742. [PMID: 29869338 DOI: 10.1002/elps.201800019] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Revised: 04/28/2018] [Accepted: 05/21/2018] [Indexed: 11/08/2022]
Abstract
Ancestry inference based on SNPs with marked allele frequency differences in diverse populations (called ancestry-informative SNP (AISNP)) is rapidly developed with the technology advancements of massively parallel sequencing. Despite the decade of exploration and broad public interest in the peopling of East-Asians, the genetic landscape of Chinese Silk Road populations based on the AISNPs is still little known. In this work, 206 unrelated individuals from Chinese Uyghur and Hui populations were firstly genotyped by 165 AISNPs (The Precision ID Ancestry Panel) using the Ion Torrent Personal Genome Machine system. The ethnic origin of two investigated populations and population structures and genetic relationships were subsequently investigated. The 165 AISNPs panel not only can differentiate Uyghur and Hui populations but also has potential applications in individual identification. Comprehensive population comparisons and admixture estimates demonstrated a predominantly higher European-related ancestry (36.30%) in Uyghurs than Huis (3.66%). Overall, the Precision ID Ancestry Panel can provide good resolution at the intercontinental level, but has limitations on the genetic homogeneous populations, such as the Hui and Han. Additional population-specific AISNPs remain necessary to get better-scale resolution within geographically proximate populations in East Asia.
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Affiliation(s)
- Guanglin He
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Mengge Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Tao Luo
- Laboratory of Infection and Immunity, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Jing Liu
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - You Zhou
- Kumul Public Security Bureau, Xinjiang Uygur Autonomous Region, P. R. China
| | - Bo Gao
- Yili Public Security Bureau, Xinjiang Uygur Autonomous Region, P. R. China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China
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25
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Technical note: developmental validation of a novel 6-dye typing system with 36 Y-STR loci. Int J Legal Med 2018; 133:1015-1027. [DOI: 10.1007/s00414-018-1864-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Accepted: 05/14/2018] [Indexed: 10/16/2022]
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26
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Zhang J, Li Z, Mo X, Ma W, Zhang H, Lin Z, Ye J. Allele frequencies of 18 autosomal STR loci in the Uyghur population living in Kashgar Prefecture, Northwest China. Int J Legal Med 2018. [PMID: 29526015 DOI: 10.1007/s00414-018-1821-9] [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: 11/30/2022]
Abstract
There is currently no large population data-based data set in Kashgar Prefecture Uyghur. The allele frequencies of 18 autosomal short tandem repeat (STR) loci included in the DNATyper™ 19 kit were evaluated in 2600 Uyghur individuals living in Kashgar Prefecture, Northwest China. The values of combined power of discrimination (CPD) and combined probability of exclusion (CPE) of all 18 autosomal STR loci were 0.99999999999999999998235 and 0.99999998670, respectively. Phylogenetic analyses revealed that the Uyghur population has a closer relationship with the Xinjiang-Kazakh, Inner Mongolia-Mongolian, and other three Uyghur populations. In addition, our results are consistent with the hypothesis that Uyghur population is an admixture of Eastern Asian and European populations.
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Affiliation(s)
- Jian Zhang
- Institute of Forensic Science, Ministry of public security, Beijing, 100038, China.,National Engineering Laboratory for Forensic Science, Beijing, 100038, China
| | - Zhenghui Li
- Department of Forensic Medicine, Criminal Investigation Police University of China, No. 83, Tawan Street, Huanggu District, Shenyang, Liaoning, 110854, China
| | - Xiaoting Mo
- Institute of Forensic Science, Ministry of public security, Beijing, 100038, China.,National Engineering Laboratory for Forensic Science, Beijing, 100038, China
| | - Wenhua Ma
- Institute of Forensic Science, Ministry of public security, Beijing, 100038, China.,National Engineering Laboratory for Forensic Science, Beijing, 100038, China
| | - Hantao Zhang
- Department of Forensic Medicine, Criminal Investigation Police University of China, No. 83, Tawan Street, Huanggu District, Shenyang, Liaoning, 110854, China
| | - Ziqing Lin
- Department of Forensic Medicine, Criminal Investigation Police University of China, No. 83, Tawan Street, Huanggu District, Shenyang, Liaoning, 110854, China
| | - Jian Ye
- Institute of Forensic Science, Ministry of public security, Beijing, 100038, China. .,National Engineering Laboratory for Forensic Science, Beijing, 100038, China.
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27
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Genetic diversity of 21 autosomal STR loci in the Han population from Sichuan province, Southwest China. Forensic Sci Int Genet 2017; 31:e33-e35. [PMID: 28743451 DOI: 10.1016/j.fsigen.2017.07.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 07/09/2017] [Accepted: 07/12/2017] [Indexed: 11/22/2022]
Abstract
Exploration of the ethnic origin and genetic differentiation of 56 Chinese officially recognized nationalities populations played a fundamental role in the research field of population genetics, forensic science, linguistics, anthropology, and archaeology. In the present study, population data of 21 autosomal STR loci (CSF1PO, D10S1248, D12S391, D13S317, D16S539, D18S51, D19S433, D21S11, D2S1338, D2S441, D3S1358, D5S818, D6S1043, D7S820, D8S1179, FGA, Penta D, Penta E, TH01, TPOX, and vWA) included in the AGCU EX22 kit in 2793 Southwest Han Chinese individuals was obtained and population genetic relationships among 28 Chinese populations were investigated. Our study indicated that the twenty-one autosomal STRs are highly polymorphic in the Sichuan Han population and can be used as a powerful tool in the routine forensic usage. MDS and phylogenetic analysis suggested that the Sichuan Han population kept a close genetic relationship with the southwest populations.
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Jin X, Wei Y, Chen J, Kong T, Mu Y, Guo Y, Dong Q, Xie T, Meng H, Zhang M, Li J, Li X, Zhu B. Phylogenic analysis and forensic genetic characterization of Chinese Uyghur group via autosomal multi STR markers. Oncotarget 2017; 8:73837-73845. [PMID: 29088750 PMCID: PMC5650305 DOI: 10.18632/oncotarget.17992] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 05/06/2017] [Indexed: 01/10/2023] Open
Abstract
We investigated the allelic frequencies and forensic descriptive parameters of 23 autosomal short tandem repeat loci in a randomly selected sample of 1218 unrelated healthy Uyghur individuals residing in the Xinjiang Uyghur Autonomous Region, northwest China. A total of 281 alleles at these loci were identified and their corresponding allelic frequencies ranged from 0.0004 to 0.5390. The combined match probability and combined probability of exclusion of all loci were 5.192 × 10−29 and 0.9999999996594, respectively. The results of population genetic study manifested that Uyghur had close relationships with those contiguous populations, such as Xibe and Hui groups. In a word, these autosomal short tandem repeat loci were highly informative in Uyghur group and the multiplex PCR system could be used as a valuable tool for forensic caseworks and population genetic analysis.
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Affiliation(s)
- Xiaoye Jin
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, Shaanxi, PR China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, Shaanxi, PR China.,College of Medicine and Forensics, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, Shaanxi, PR China
| | - Yuanyuan Wei
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, Shaanxi, PR China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, Shaanxi, PR China
| | - Jiangang Chen
- Department of Biochemistry, Preclinical Medicine College, Xinjiang Medical University, Urumqi, 830011, Xinjiang, PR China
| | - Tingting Kong
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, Shaanxi, PR China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, Shaanxi, PR China
| | - Yuling Mu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, Shaanxi, PR China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, Shaanxi, PR China.,College of Medicine and Forensics, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, Shaanxi, PR China
| | - Yuxin Guo
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, Shaanxi, PR China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, Shaanxi, PR China.,College of Medicine and Forensics, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, Shaanxi, PR China
| | - Qian Dong
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, Shaanxi, PR China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, Shaanxi, PR China.,College of Medicine and Forensics, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, Shaanxi, PR China
| | - Tong Xie
- Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, Guangdong, PR China
| | - Haotian Meng
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, Shaanxi, PR China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, Shaanxi, PR China
| | - Meng Zhang
- Department of Orthopaedics, Ankang City Central Hospital, Ankang, 725000, Shaanxi, PR China
| | - Jianfei Li
- Xi'an Jiaotong University, Xi'an, 710049, Shaanxi, PR China
| | - Xiaopeng Li
- Department of Ultrasound, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710004, Shaanxi, PR China
| | - Bofeng Zhu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, Shaanxi, PR China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, Shaanxi, PR China.,Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, Guangdong, PR China
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29
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He GL, Chen PY, Gao B, Han YY, Zou X, Song F, Yan J, Hou YP. Phylogenetic analysis among 27 Chinese populations and genetic polymorphisms of 20 autosomal STR loci in a Chinese Uyghur ethnic minority group. AUST J FORENSIC SCI 2017. [DOI: 10.1080/00450618.2016.1275793] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Guang-Lin He
- Department of Forensic Genetics, West China School of Basic Science and Forensic Medicine, Sichuan University (West China University of Medical Sciences) , Chengdu, China
| | - Peng-Yu Chen
- Center of Forensic Expertise, Affiliated Hospital of Zunyi Medical University , Zunyi, China
- Department of Forensic Medicine, Zunyi Medical University , Zunyi, China
| | - Bo Gao
- Institute of Forensic Science, Yili Public Security Bureau of Xinjiang , Kuitun, China
| | - Yan-Yan Han
- Department of Nutrition and Food Hygiene, School of Public Health, Zunyi Medical University , Zunyi, China
| | - Xing Zou
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University , Chongqing, China
| | - Feng Song
- Department of Forensic Genetics, West China School of Basic Science and Forensic Medicine, Sichuan University (West China University of Medical Sciences) , Chengdu, China
| | - Jing Yan
- Department of Forensic Genetics, West China School of Basic Science and Forensic Medicine, Sichuan University (West China University of Medical Sciences) , Chengdu, China
| | - Yi-Ping Hou
- Department of Forensic Genetics, West China School of Basic Science and Forensic Medicine, Sichuan University (West China University of Medical Sciences) , Chengdu, China
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Babić N, Dogan S, Čakar J, Pilav A, Marjanović D, Hadžiavdić V. Molecular diversity of 23 Y-chromosome short tandem repeat loci in the population of Tuzla Canton, Bosnia and Herzegovina. Ann Hum Biol 2016; 44:419-426. [PMID: 27826995 DOI: 10.1080/03014460.2016.1259430] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
BACKGROUND Tuzla Canton is the most populated region in the ethnically mixed territory of Bosnia and Herzegovina, whose genetic analysis could provide an insight into past demographic events. AIM Analysis of 23 Y-chromosome STR markers in the population of Tuzla Canton and investigation of the genetic relationship of the male population of the Tuzla Canton and that of the larger Bosnian and Herzegovinian population as well as neighbouring and other European populations. SUBJECTS AND METHODS The study was conducted among 100 unrelated healthy adult males from Tuzla Canton that have been genotyped using 23 Y-STR loci included in the PowerPlex Y23 kit. Statistical parameters such as haplotype diversity and allele frequencies were calculated, as well as the Rst-based genetic distances between the new dataset and those from Bosnia and Herzegovina and elsewhere, which were then visualised through multi-dimensional scaling plot and neighbour-joining phylogenetic tree analyses. RESULTS The PowerPlex Y23 kit has shown high discrimination capacity, as all 100 individuals have unique haplotypes. The newly incorporated loci seem to be highly informative. Population comparison reveals no statistically significant differences between the study population and the general Bosnian-Herzegovinian population, and between the study population and neighbouring populations. CONCLUSION These results could be used as an additional investigation of the genetic relationship between the regional populations in Bosnia and Herzegovina and neighbouring human populations, as well as for further human population and forensic genetics studies.
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Affiliation(s)
- Naida Babić
- a Department of Biology, Faculty of Natural Sciences and Mathematics , University of Tuzla , Tuzla , Bosnia and Herzegovina
| | - Serkan Dogan
- b Department of Genetics and Bioengineering , International Burch University , Sarajevo , Bosnia and Herzegovina
| | - Jasmina Čakar
- c Institute for Genetic Engineering and Biotechnology, University of Sarajevo , Sarajevo , Bosnia and Herzegovina
| | - Amela Pilav
- c Institute for Genetic Engineering and Biotechnology, University of Sarajevo , Sarajevo , Bosnia and Herzegovina
| | - Damir Marjanović
- b Department of Genetics and Bioengineering , International Burch University , Sarajevo , Bosnia and Herzegovina.,d Institute for Anthropological Researches , Zagreb , Croatia
| | - Vesna Hadžiavdić
- a Department of Biology, Faculty of Natural Sciences and Mathematics , University of Tuzla , Tuzla , Bosnia and Herzegovina
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