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Zhang H, Huang X, Jin X, Ren Z, Wang Q, Yang M, Xu R, Yuan X, Yang D, Liu H, Shen W, Zhang H, Que Y, Huang J. Comprehensive analyses of genetic diversities and population structure of the Guizhou Dong group based on 44 Y-markers. PeerJ 2023; 11:e16183. [PMID: 37780380 PMCID: PMC10538297 DOI: 10.7717/peerj.16183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 09/05/2023] [Indexed: 10/03/2023] Open
Abstract
Background The non-recombining region of the human Y chromosome (NRY) is a strictly paternally inherited genetic marker and the best material to trace the paternal lineages of populations. Y chromosomal short tandem repeat (Y-STR) is characterized by high polymorphism and paternal inheritance pattern, so it has been widely used in forensic medicine and population genetic research. This study aims to understand the genetic distribution of Y-STRs in the Guizhou Dong population, provide reference data for forensic application, and explore the phylogenetic relationships between the Guizhou Dong population and other comparison populations. Methods Based on the allele profile of 44 Y-markers in the Guizhou Dong group, we estimate their allele frequencies and haplotype frequencies. In addition, we also compare the forensic application efficiency of different Y-STR sets in the Guizhou Dong group. Finally, genetic relationships among Guizhou Dong and other reference populations are dissected by the multi-dimensional scaling and the phylogenetic tree. Results A total of 393 alleles are observed in 312 Guizhou Dong individuals for these Y-markers, with allele frequencies ranging from 0.0032 to 0.9679. The haplotype diversity and discriminatory capacity for these Y-markers in the Guizhou Dong population are 0.99984 and 0.97440, respectively. The population genetic analyses of the Guizhou Dong group and other reference populations show that the Guizhou Dong group has the closest genetic relationship with the Hunan Dong population, and followed by the Guizhou Tujia population. Conclusions In conclusion, these 44 Y-markers can be used as an effective tool for male differentiation in the Guizhou Dong group. The haplotype data in this study not only enrich the Y-STR data of different ethnic groups in China, but also have important significance for population genetics and forensic research.
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Affiliation(s)
- Hongling Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Xiaolan Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Xiaoye Jin
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Zheng Ren
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Qiyan Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Meiqing Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Ronglan Xu
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Xiang Yuan
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Daiquan Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Hongyan Liu
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Wanyi Shen
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Huiying Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Yangjie Que
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Jiang Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, 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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Panda M, Kumawat R, Dixit S, Sharma AN, Shankar H, Chaubey G, Shrivastava P. Forensic features and phylogenetic analyses of the population of Nayagarh (Odisha), India using 23 Y-STRs. Ann Hum Biol 2022; 49:54-68. [PMID: 35499241 DOI: 10.1080/03014460.2022.2039762] [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
AIM The present study was designed to explore the STR diversity and genomic history of the inhabitants of Nayagarh district of Odisha, India. We also tested the proficiency of the most recent, new generation PowerPlexR Y23 multiplex system for forensic characterisation and to decipher the phylogenetic affinities. SUBJECTS AND METHODS The genetic diversity and polymorphism among 236 healthy unrelated male volunteers from Nayagarh district of Odisha, India was investigated. This investigation was carried out via 23 Y-chromosomal STRs using capillary electrophoresis. RESULT A total 223 unique haplotypes were reported. Discrimination capacity (DC), gene diversity (GD) and power of discrimination (PD) were observed as 0.945, 0.999999999998333, and 0.99999999999794, respectively. Polymorphic information content (PIC) and matching probability (PM) were reported as 0.999999999925535 and 2.06 × 10-12, respectively. Simultaneously, the haplogroup analysis characterised with C2, E1b1a, E1b1b, G2a, H1, I2a, J2a, J2b, L, O, O1, O2, Q, R1a, R2, and T haplogroups, disclosing the possible geographical relatedness of the studied population to different areas of the world. CONCLUSION Phylogenetic analysis with previously reported Indian and Asian populations showed the genetic closeness of the studied population to different Indian populations and the Bangladeshi population of Dhaka, whereas the Bhotra population of Odisha and Han population of China showed much less genetic affinity.
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Affiliation(s)
- Muktikanta Panda
- Department of Home (Police), DNA Fingerprinting Unit, State Forensic Science Laboratory, Government of MP, Sagar, India.,Department of Anthropology, Dr. Harisingh Gour Vishwavidyalaya (A Central University), Sagar, Madhya Pradesh, India
| | - Ramkishan Kumawat
- DNA Division, State Forensic Science Laboratory, Jaipur, Rajasthan, India
| | - Shivani Dixit
- Department of Home (Police), DNA Fingerprinting Unit, State Forensic Science Laboratory, Government of MP, Sagar, India
| | - Awdhesh Narayan Sharma
- Department of Anthropology, Dr. Harisingh Gour Vishwavidyalaya (A Central University), Sagar, Madhya Pradesh, India
| | - Hari Shankar
- Department of Home (Police), DNA Fingerprinting Unit, State Forensic Science Laboratory, Government of MP, Sagar, India
| | - Gyaneshwer Chaubey
- Department of Zoology, Cytogenetics Laboratory, Banaras Hindu University, Varanasi, India
| | - Pankaj Shrivastava
- Department of Home (Police), DNA Fingerprinting Unit, State Forensic Science Laboratory, Government of MP, Sagar, India.,Department of Anthropology, Dr. Harisingh Gour Vishwavidyalaya (A Central University), Sagar, Madhya Pradesh, India
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4
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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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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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6
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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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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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Mansour H, Sperhake JP, Bekaert B, Krebs O, Friedrich P, Fuhrmann A, Püschel K. New aspects of dental implants and DNA technology in human identification. Forensic Sci Int 2019; 302:109926. [PMID: 31444040 DOI: 10.1016/j.forsciint.2019.109926] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 07/11/2019] [Accepted: 08/05/2019] [Indexed: 01/29/2023]
Abstract
Missing, ineligible or delayed reference data to establish conventional dental or DNA identification are common scenarios in forensic practice. Therefore, it is worthwhile to explore new avenues that facilitate human identification. Due to the recent remarkable evolution in the prosthetic dental restorations based on dental implants and the emergence of novel DNA technologies utilized to infer the biological profile, the identification process has become easier than ever before. We report on a characteristic case, which highlights the particular importance of dental implants and DNA approaches in the prospective investigations for human identification. The aim of this publication is to focus on the possibility of identifying the batch numbers, even if they were not engraved in dental implants, making antemortem dental records of dental implants more easily accessible to establish a comparative dental identification. In addition, the reported case presents the supplementary data yielded through estimating the epigenetic age using DNA methylation as well as the biogeographical origin using Y-Haplotype and mitochondrial DNA analyses. Our results demonstrate that expanded oral implant investigations that also include implants extraction and comprehensive microscopic measurements can lead to identifying their batch numbers despite the numerous number of implants systems manufactured and distributed worldwide. Data saved by dental implant manufacturers can be very supportive and represent additional reference data for dental identification, when antemortem dental records are still missing. Furthermore, DNA methylation and mitochondrial DNA analyses can support the progress of investigation.
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Affiliation(s)
- Hussam Mansour
- University Medical Center Hamburg-Eppendorf, Institute of Legal Medicine, Butenfeld34, 22529 Hamburg, Germany.
| | - Jan Peter Sperhake
- University Medical Center Hamburg-Eppendorf, Institute of Legal Medicine, Butenfeld34, 22529 Hamburg, Germany.
| | - Bram Bekaert
- KU Leuven - University of Leuven, Department of Imaging & Pathology, Campus St-Rafaël, Kapucijnenvoer 33, Leuven, Belgium; KU-Leuven - University of Leuven, University Hospitals Leuven, Department of Forensic Medicine, Laboratory of Forensic Genetics and Molecular Archeology, Campus St-Rafaël, Kapucijnenvoer 33, Leuven, Belgium.
| | - Oliver Krebs
- University Medical Center Hamburg-Eppendorf, Institute of Legal Medicine, Butenfeld34, 22529 Hamburg, Germany.
| | - Peter Friedrich
- State Criminal Investigation Department of the City of Hamburg (LKA 41), Bruno-Georges-Platz 1, 22297 Hamburg, Germany.
| | - Andreas Fuhrmann
- University Medical Center Hamburg-Eppendorf, Institute of Legal Medicine, Butenfeld34, 22529 Hamburg, Germany.
| | - Klaus Püschel
- University Medical Center Hamburg-Eppendorf, Institute of Legal Medicine, Butenfeld34, 22529 Hamburg, Germany.
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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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10
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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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Fan H, Zhang X, Wang X, Ren Z, Li W, Long R, Liang A, Chen J, Song T, Qu Y, Deng J. Genetic analysis of 27 Y-STR loci in Han population from Hainan province, southernmost China. Forensic Sci Int Genet 2018; 33:e9-e10. [DOI: 10.1016/j.fsigen.2017.12.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Revised: 12/16/2017] [Accepted: 12/18/2017] [Indexed: 11/24/2022]
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12
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Lim S, Youn JP, Hong S, Choi D, Moon S, Kim W, Han M, Hwang SY. Customized multiplexing SNP panel for Korean-specific DNA phenotyping in forensic applications. Genes Genomics 2017. [DOI: 10.1007/s13258-016-0509-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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13
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Seyedebrahimi R, Esfandiari E, Rashidi B, Salehi R, Dahghi AG, Dabiri S, Kheirollahi M. Comparison of the Frequency of Y-short Tandem Repeats Markers between Sadat and Non-Sadat Populations in Isfahan Province of Iran. Adv Biomed Res 2017; 6:33. [PMID: 28401080 PMCID: PMC5360006 DOI: 10.4103/2277-9175.188493] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Y chromosome is one of the two sex chromosomes and is male specific. Due to limited genetic exchange, the main part of that is passed virtually unchanged from one generation to next generation. The short tandem repeats (STRs) are almost constant on chromosomes that make them as an appropriate factor for use in population genetic studies. In this study, we used the STRs of Y chromosome markers in Sadat families and comparison with other families was investigated. MATERIALS AND METHODS In this study, sampling was done from fifty unrelated males of Sadat families and fifty unrelated males of non-Sadat families. After the extraction of DNA from blood samples and primer design, polymerase chain reaction (PCR) was performed for each primer pairs separately. The PCR products were run on agarose gel that followed by running on polyacrylamide gel for better resolution. In addition, some sequenced samples were used as identified markers to determine the length of other alleles in polyacrylamide gel. RESULTS The survey of six STR in two case and control groups was carried out, and analysis revealed that the frequency of some alleles is different in case group compared to control group. Allele frequency of the markers DYS392, DYS393, DYS19, DYS390, DYS388, and DYS437 on the Y chromosome in Sadat families was quite different in comparison with other families. CONCLUSIONS The reason for these differences in allele frequencies of the Sadat family in comparison with other families is having a common ancestor.
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Affiliation(s)
- Reihaneh Seyedebrahimi
- From the Department of Anatomy, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Ebrahim Esfandiari
- From the Department of Anatomy, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Bahman Rashidi
- From the Department of Anatomy, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Rasoul Salehi
- Department of Genetics and Molecular Biology, Research Institute for Primordial Prevention of Noncommunicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
- Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Noncommunicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Ali Gholami Dahghi
- Department of Islamic Studies, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Shahriar Dabiri
- Department of Pathology, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Majid Kheirollahi
- Department of Genetics and Molecular Biology, Research Institute for Primordial Prevention of Noncommunicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
- Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Noncommunicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
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Ji J, Ren Z, Zhang H, Wang Q, Wang J, Kong Z, Xu C, Tian M, Huang J. Genetic profile of 23 Y chromosomal STR loci in Guizhou Shui population, southwest China. Forensic Sci Int Genet 2017; 28:e16-e17. [PMID: 28209446 DOI: 10.1016/j.fsigen.2017.01.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 01/05/2017] [Accepted: 01/21/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Jingyan Ji
- Department of Forensic Genetics, Guizhou Medical University, Guiyang 550004, Guizhou, China; Public Security Bureau, QIanNan Buyi and Miao Autonomous Prefecture, Duyun 558800, Guizhou, China; Department of Forensic Genetics, Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Zheng Ren
- Department of Forensic Genetics, Guizhou Medical University, Guiyang 550004, Guizhou, China; Public Security Bureau, QIanNan Buyi and Miao Autonomous Prefecture, Duyun 558800, Guizhou, China; Department of Forensic Genetics, Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Hongling Zhang
- Department of Forensic Genetics, Guizhou Medical University, Guiyang 550004, Guizhou, China; Public Security Bureau, QIanNan Buyi and Miao Autonomous Prefecture, Duyun 558800, Guizhou, China; Department of Forensic Genetics, Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Qiyan Wang
- Department of Forensic Genetics, Guizhou Medical University, Guiyang 550004, Guizhou, China; Public Security Bureau, QIanNan Buyi and Miao Autonomous Prefecture, Duyun 558800, Guizhou, China; Department of Forensic Genetics, Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Jie Wang
- Department of Forensic Genetics, Guizhou Medical University, Guiyang 550004, Guizhou, China; Public Security Bureau, QIanNan Buyi and Miao Autonomous Prefecture, Duyun 558800, Guizhou, China; Department of Forensic Genetics, Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Zhiming Kong
- Department of Forensic Genetics, Guizhou Medical University, Guiyang 550004, Guizhou, China; Public Security Bureau, QIanNan Buyi and Miao Autonomous Prefecture, Duyun 558800, Guizhou, China; Department of Forensic Genetics, Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Chunmei Xu
- Department of Forensic Genetics, Guizhou Medical University, Guiyang 550004, Guizhou, China; Public Security Bureau, QIanNan Buyi and Miao Autonomous Prefecture, Duyun 558800, Guizhou, China; Department of Forensic Genetics, Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Mi Tian
- Department of Forensic Genetics, Guizhou Medical University, Guiyang 550004, Guizhou, China; Public Security Bureau, QIanNan Buyi and Miao Autonomous Prefecture, Duyun 558800, Guizhou, China; Department of Forensic Genetics, Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Jiang Huang
- Department of Forensic Genetics, Guizhou Medical University, Guiyang 550004, Guizhou, China; Public Security Bureau, QIanNan Buyi and Miao Autonomous Prefecture, Duyun 558800, Guizhou, China; Department of Forensic Genetics, Guizhou Medical University, Guiyang 550004, Guizhou, China.
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Choi EJ, Park KW, Lee YH, Nam YH, Suren G, Ganbold U, Kim JA, Kim SY, Kim HM, Kim K, Kim W. Forensic and population genetic analyses of the GlobalFiler STR loci in the Mongolian population. Genes Genomics 2017. [DOI: 10.1007/s13258-016-0511-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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16
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Bian Y, Zhang S, Wang Z, Zhu R, Zhao Q, Li C. Phylogenetic analysis of She population from Fujian Province in China based on 26 Y-STR Loci*. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2015. [DOI: 10.1016/j.fsigss.2015.09.206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Shrivastava P, Gupta U, Jain T, Trivedi VB. Y STR haplotype diversity in central Indian population. Ann Hum Biol 2015; 43:480-7. [PMID: 26381716 DOI: 10.3109/03014460.2015.1071425] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
AIMS Seventeen Y-STR loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385a/b, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635 and Y-GATA-H4) were analysed in 173 males belonging to the central Indian population with the aim of studying genetic diversity and adding to the population database. METHODS Multiplexed PCR amplifications of the 17 Y STR loci were performed using AmpFlSTR® Yfiler® Kit. Amplified products were genotyped using a multi capillary electrophoresis with POP-4 polymer in ABI Prism 3100 Genetic Analyzer. Population genetic diversity and allele frequencies were calculated. The haplotype data obtained in the study was compared with the Y-STR haplotypes reference database (YHRD, http://www.yhrd.org ) and with previously published population data using the AMOVA tool and visualised in two-dimensional multidimensional scaling (MDS) plots. RESULTS A total of 147 haplotypes were observed, out of which 125 were unique. Haplotype diversity and discriminating capacity were found to be 0.9979 and 0.8497, respectively. The gene diversity at the loci ranged from 0.398-0.785. Genotype diversity at the locus DYS385a/b was found to be 0.869. CONCLUSIONS The population of central India was found to be significantly different (p < 0.05) when compared with populations from other parts of the Indian sub-continent and the population data of other countries. The population data generated in this study are useful for forensic, anthropological and demographic studies.
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Affiliation(s)
- Pankaj Shrivastava
- a DNA Fingerprinting Unit, State Forensic Science Laboratory, Department of Home (Police), Government of Madhya Pradesh , Sagar (MP) , India
| | - Umang Gupta
- a DNA Fingerprinting Unit, State Forensic Science Laboratory, Department of Home (Police), Government of Madhya Pradesh , Sagar (MP) , India
| | - Toshi Jain
- a DNA Fingerprinting Unit, State Forensic Science Laboratory, Department of Home (Police), Government of Madhya Pradesh , Sagar (MP) , India
| | - Veena Ben Trivedi
- a DNA Fingerprinting Unit, State Forensic Science Laboratory, Department of Home (Police), Government of Madhya Pradesh , Sagar (MP) , India
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18
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Shang J, Hu SP. Haplotype data of 23 Y-chromosome markers in Minnan Han Chinese and comparison with those of 12 Y-chromosome markers. JOURNAL OF HUAZHONG UNIVERSITY OF SCIENCE AND TECHNOLOGY. MEDICAL SCIENCES = HUA ZHONG KE JI DA XUE XUE BAO. YI XUE YING DE WEN BAN = HUAZHONG KEJI DAXUE XUEBAO. YIXUE YINGDEWEN BAN 2015; 35:456-463. [PMID: 26072089 DOI: 10.1007/s11596-015-1453-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 12/10/2014] [Indexed: 02/05/2023]
Abstract
We genotyped 23 Y-STR loci (DYS576, DYS389I, DYS448, DYS389II, DYS19, DYS391, DYS481, DYS549, DYS533, DYS438, DYS437, DYS570, DYS635, DYS390, DYS439, DYS392, DYS643, DYS393, DYS458, DYS385a/b, DYS456, and GATA-H4) in a sample of 109 unrelated male Chinese people residing in Minnan area and compared the results with those from our previous study on 12 Y-STR. The haplotype diversity and the discrimination capacity of the 23 Y-STR reached 0.9903 and 0.9725, respectively, and the genetic diversity for each locus ranged from 0.321 (DYS391) to 0.955 (DYS385). Besides, we observed a strong correlation between the number of Y-STR markers and the substantial improvement of forensic parameters used to discriminate between individuals. The results indicated that these highly polymorphic Y-STR markers were useful for human identification in forensic cases and paternity tests within the Minnan Han Chinese population.
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Affiliation(s)
- Jie Shang
- Molecular Biology and Forensic Genetics Laboratory, Shantou University Medical College, Shantou, 515031, China
| | - Sheng-Ping Hu
- Molecular Biology and Forensic Genetics Laboratory, Shantou University Medical College, Shantou, 515031, China.
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Vongpaisarnsin K, Saengkaeotrakul P, Boonlert A, Tansrisawad N. Gene and haplotype diversity of 23 Y-chromosomal short tandem repeat loci in the central Thai population. Forensic Sci Int Genet 2015; 14:191-3. [DOI: 10.1016/j.fsigen.2014.10.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 10/16/2014] [Accepted: 10/20/2014] [Indexed: 11/26/2022]
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20
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Harayama Y, Kamei S, Sato N, Hayashi T, Shiozaki T, Ota M, Asamura H. Analysis of Y chromosome haplogroups in Japanese population using short amplicons and its application in forensic analysis. Leg Med (Tokyo) 2014; 16:20-5. [DOI: 10.1016/j.legalmed.2013.10.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2013] [Revised: 08/23/2013] [Accepted: 10/22/2013] [Indexed: 10/26/2022]
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21
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Roewer L, Nothnagel M, Gusmão L, Gomes V, González M, Corach D, Sala A, Alechine E, Palha T, Santos N, Ribeiro-Dos-Santos A, Geppert M, Willuweit S, Nagy M, Zweynert S, Baeta M, Núñez C, Martínez-Jarreta B, González-Andrade F, Fagundes de Carvalho E, da Silva DA, Builes JJ, Turbón D, Lopez Parra AM, Arroyo-Pardo E, Toscanini U, Borjas L, Barletta C, Ewart E, Santos S, Krawczak M. Continent-wide decoupling of Y-chromosomal genetic variation from language and geography in native South Americans. PLoS Genet 2013; 9:e1003460. [PMID: 23593040 PMCID: PMC3623769 DOI: 10.1371/journal.pgen.1003460] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 03/04/2013] [Indexed: 01/07/2023] Open
Abstract
Numerous studies of human populations in Europe and Asia have revealed a concordance between their extant genetic structure and the prevailing regional pattern of geography and language. For native South Americans, however, such evidence has been lacking so far. Therefore, we examined the relationship between Y-chromosomal genotype on the one hand, and male geographic origin and linguistic affiliation on the other, in the largest study of South American natives to date in terms of sampled individuals and populations. A total of 1,011 individuals, representing 50 tribal populations from 81 settlements, were genotyped for up to 17 short tandem repeat (STR) markers and 16 single nucleotide polymorphisms (Y-SNPs), the latter resolving phylogenetic lineages Q and C. Virtually no structure became apparent for the extant Y-chromosomal genetic variation of South American males that could sensibly be related to their inter-tribal geographic and linguistic relationships. This continent-wide decoupling is consistent with a rapid peopling of the continent followed by long periods of isolation in small groups. Furthermore, for the first time, we identified a distinct geographical cluster of Y-SNP lineages C-M217 (C3*) in South America. Such haplotypes are virtually absent from North and Central America, but occur at high frequency in Asia. Together with the locally confined Y-STR autocorrelation observed in our study as a whole, the available data therefore suggest a late introduction of C3* into South America no more than 6,000 years ago, perhaps via coastal or trans-Pacific routes. Extensive simulations revealed that the observed lack of haplogroup C3* among extant North and Central American natives is only compatible with low levels of migration between the ancestor populations of C3* carriers and non-carriers. In summary, our data highlight the fact that a pronounced correlation between genetic and geographic/cultural structure can only be expected under very specific conditions, most of which are likely not to have been met by the ancestors of native South Americans. In the largest population genetic study of South Americans to date, we analyzed the Y-chromosomal makeup of more than 1,000 male natives. We found that the male-specific genetic variation of Native Americans lacks any clear structure that could sensibly be related to their geographic and/or linguistic relationships. This finding is consistent with a rapid initial peopling of South America, followed by long periods of isolation in small tribal groups. The observed continent-wide decoupling of geography, spoken language, and genetics contrasts strikingly with previous reports of such correlation from many parts of Europe and Asia. Moreover, we identified a cluster of Native American founding lineages of Y chromosomes, called C-M217 (C3*), within a restricted area of Ecuador in North-Western South America. The same haplogroup occurs at high frequency in Central, East, and North East Asia, but is virtually absent from North (except Alaska) and Central America. Possible scenarios for the introduction of C-M217 (C3*) into Ecuador may thus include a coastal or trans-Pacific route, an idea also supported by occasional archeological evidence and the recent coalescence of the C3* haplotypes, estimated from our data to have occurred some 6,000 years ago.
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Affiliation(s)
- Lutz Roewer
- Institute of Legal Medicine and Forensic Sciences, Department of Forensic Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany.
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22
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AMORUSO IRENE, CAENAZZO LUCIANA, PRESCIUTTINI SILVANO, GREGIANIN ELISA, BOZZATO ANDREA, CARAVELLO GIANUMBERTO. Y-chromosome haplotypes and clan structure of the Sherpa of the Solukhumbu (Nepal): preliminary ethnogenetic considerations. ANTHROPOL SCI 2013. [DOI: 10.1537/ase.121122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- IRENE AMORUSO
- University of Padua, Department of Molecular Medicine—Public Health Unit, Padova
| | - LUCIANA CAENAZZO
- University of Padua, Deptartment of Molecular Medicine—Legal Medicine Unit, Padova
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Brucato N, Mazières S, Guitard E, Giscard PH, Bois E, Larrouy G, Dugoujon JM. The Hmong Diaspora: preserved South-East Asian genetic ancestry in French Guianese Asians. C R Biol 2012. [PMID: 23199638 DOI: 10.1016/j.crvi.2012.10.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
The Hmong Diaspora is one of the widest modern human migrations. Mainly localised in South-East Asia, the United States of America, and metropolitan France, a small community has also settled the Amazonian forest of French Guiana. We have biologically analysed 62 individuals of this unique Guianese population through three complementary genetic markers: mitochondrial DNA (HVS-I/II and coding region SNPs), Y-chromosome (SNPs and STRs), and the Gm allotypic system. All genetic systems showed a high conservation of the Asian gene pool (Asian ancestry: mtDNA=100.0%; NRY=99.1%; Gm=96.6%), without a trace of founder effect. When compared across various Asian populations, the highest correlations were observed with Hmong-Mien groups still living in South-East Asia (Fst<0.05; P-value<0.05). Despite a long history punctuated by exodus, the French Guianese Hmong have maintained their original genetic diversity.
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Affiliation(s)
- Nicolas Brucato
- UMR 5288 CNRS, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Paul-Sabatier Toulouse III, Toulouse, France
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24
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Gayden T, Bukhari A, Chennakrishnaiah S, Stojkovic O, Herrera RJ. Y-chromosomal microsatellite diversity in three culturally defined regions of historical Tibet. Forensic Sci Int Genet 2011; 6:437-46. [PMID: 22005116 DOI: 10.1016/j.fsigen.2011.09.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2011] [Revised: 08/08/2011] [Accepted: 09/13/2011] [Indexed: 12/19/2022]
Abstract
In the present study, we analyzed 17 Y-STR loci in 350 Tibetan males from three culturally defined regions of historical Tibet: Amdo (88), Kham (109) and U-Tsang (153). A total of 299 haplotypes were observed, 272 (90.9%) of which were unique. Only one Y-STR profile is shared across the three Tibetan groups and, incidentally, is also the most frequent haplotype (4.0%), represented by two, five and seven individuals from U-Tsang, Kham and Amdo, respectively. The overall haplotype diversity for the three Tibetan populations at 17 Y-STR loci was 0.9978 and the corresponding values for the extended (11-loci) and minimal (9-loci) haplotypes were 0.9935 and 0.9909, respectively. Both neighbor-joining and Rst pairwise analyses suggest a close genetic relationship between the Amdo and Kham populations, while U-Tsang is genetically distinct from the aforementioned groups. The results demonstrate that the 17 Y-STR loci analyzed are highly polymorphic in all three Tibetan populations examined and hence useful for forensic cases, paternity testing and population genetic studies.
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Affiliation(s)
- Tenzin Gayden
- Department of Molecular and Human Genetics, College of Medicine, Florida International University, Miami, FL 33199, USA
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25
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Hu SP, Li H, Zhang FH, Huang LQ, Lu Y. Dominant contribution of northern chinese to the paternal genetic structure of Chaoshanese in South China. Biochem Genet 2011; 49:483-98. [PMID: 21360052 DOI: 10.1007/s10528-011-9424-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2010] [Accepted: 11/22/2010] [Indexed: 02/05/2023]
Abstract
We investigated the Y chromosome of various Chinese populations to determine the patrilineal origin of the Chaoshanese population. Admixture analysis of six specific Y short tandem repeat (STR) loci in 6,292 individual samples taken from 51 populations, including Chaoshanese and Minnanese of our earlier studies, showed that over 85% of the Chaoshanese Y chromosomes were derived from the Central China Han (M (RH): 0.8614; M (BE): 1.1868 ± 0.2054), and a very small portion were from the southern aborigines. These results support a Central China Han origin of the Chaoshanese and additionally reveal that males from the Central China Han were the predominant contributor to the patrilineal genetics of the Chaoshanese. A phylogenetic tree and analysis of molecular variance signified a strong association between Y chromosomes of Chinese populations and their linguistic affiliations, revealing a coevolution of Y chromosome diversity and languages in East Asia.
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Affiliation(s)
- Sheng-Ping Hu
- Molecular Biology Laboratory, Shantou University Medical College, Guangdong, China.
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Yang JH, Sohn YH, Ko SY, Choi SE, Kim MH, Oh HB. Anthropological analysis of Koreans using HLA class II diversity among East Asians. ACTA ACUST UNITED AC 2011; 76:282-8. [PMID: 20522202 DOI: 10.1111/j.1399-0039.2010.01511.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Human leukocyte antigens (HLAs) are useful markers for anthropological investigations because the allele and haplotype distributions at these loci vary widely among ethnic groups. HLA frequencies in Koreans, however, have not previously been analyzed on a phylogenetic basis. We determined the allele frequencies of four HLA class II (HLA-DRB1, -DQA1, -DQB1, and -DPB1) loci in 149 unrelated Korean individuals using a sequence-based typing method. A total of 29 HLA-DRB1, 17 HLA-DQA1, 16 HLA-DQB1, and 15 HLA-DPB1 alleles were identified. The most common allele at each locus was DRB1*0901, DQA1*0102, DQB1*0301, and DPB1*0501, respectively. Four-locus allelic association analysis showed the existence of 25 DRB1-DQA1-DQB1-DPB1 haplotypes with a frequency greater than 0.010. A dataset comprising ethnicity-specific information from published literature and the dbMHC database, as well as the allele frequencies determined in this study, was subjected to phylogenetic analysis. The analysis showed that Koreans are most closely related to Japanese and Han Chinese from Shandong province. Correspondence analyses showed that the current Korean population is located in a position intermediate between the northern and southern East Asian groups, supporting the theory of a bi- and/or multidirectional route of migration of early Korean settlers. This report can be used for anthropological studies, and may also be of use in the International Hematopoietic Stem Cell Sharing program.
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Affiliation(s)
- J H Yang
- Department of Laboratory Medicine, Korea University Medical College, Seoul, Korea
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27
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Lacau H, Bukhari A, Gayden T, La Salvia J, Regueiro M, Stojkovic O, Herrera RJ. Y-STR profiling in two Afghanistan populations. Leg Med (Tokyo) 2011; 13:103-8. [DOI: 10.1016/j.legalmed.2010.11.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2010] [Revised: 11/24/2010] [Accepted: 11/25/2010] [Indexed: 11/15/2022]
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28
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Gršković B, Mršić G, Polašek O, Vrdoljak A, Merkaš S, Anđelinović S. Genetic polymorphisms of 17 short tandem repeat loci on Y chromosome in central Croatian population. Forensic Sci Med Pathol 2011; 7:155-61. [PMID: 21279707 DOI: 10.1007/s12024-010-9216-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/13/2010] [Indexed: 11/25/2022]
Abstract
In forensic casework, Y-chromosome short tandem repeat (STR) haplotyping is used in human identification, paternity testing and sexual assault cases where Y-STRs provide a male-specific DNA profile. The aim of this study was to describe the genetic structure of Y chromosome in a central Croatian population. We carried out a statistical analysis of the data from previously performed genetic analyses collected during routine forensic work by the Forensic Science Centre "Ivan Vučetić". A total of 220 unrelated healthy men from central Croatia were selected for the purpose of this study. Genomic DNA was extracted using a Chelex procedure from FTA(®) cards. Y-chromosomal STRs were determined using the AmpFISTR Yfiler PCR amplification kit. The haplotype frequencies were determined by direct counting and analyzed using Arlequin 3.1 and analysis of molecular variance calculated with the Y chromosome haplotype reference database online analysis tool. A total of 212 haplotypes were identified, 204 of which were unique. Total haplotype diversity was 0.993. Locus diversity varied from 0.325 for DYS392 to 0.786 for DYS385. Discrimination capacity was 92.7%. Allele frequencies diversity was 0.615. Intermediate alleles 17.2, 18.2 and 19.2 were found at DYS458 locus. A comparison with published data for the European minimal haplotype set showed the closest relationship to the Croatian capital of Zagreb and Bosnia and Herzegovina with significant genetic distance from Slovenia and Austria. The central Croatian population is now well characterized in terms of Y-chromosome STRs, thus providing a solid basis for further forensic and genetic epidemiology studies.
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Affiliation(s)
- Branka Gršković
- Department of Biology and Fibers, Division of Biology, Forensic Science Centre Ivan Vučetić, General Police Directorate, Ministry of Interior, Ilica Zagreb, Croatia.
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Kim SH, Chun BW, Jung J, Kemp BM, Kwak KD, Cho NS, Kim JJ, Han MS, Kim W. A preliminary study on the origin of Koreans based on Y-STR variation. Genes Genomics 2010. [DOI: 10.1007/s13258-010-0030-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Gayden T, Chennakrishnaiah S, La Salvia J, Jimenez S, Regueiro M, Maloney T, Persad PJ, Bukhari A, Perez A, Stojkovic O, Herrera RJ. Y-STR diversity in the Himalayas. Int J Legal Med 2010; 125:367-75. [PMID: 20652582 DOI: 10.1007/s00414-010-0485-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2010] [Accepted: 06/28/2010] [Indexed: 11/24/2022]
Abstract
Linguistic and ethnic diversity throughout the Himalayas suggests that this mountain range played an important role in shaping the genetic landscapes of the region. Previous Y-chromosome work revealed that the Himalayas acted as a biased bidirectional barrier to gene flow across the cordillera. In the present study, 17 Y-chromosomal short tandem repeat (Y-STR) loci included in the AmpFlSTR® Yfiler kit were analyzed in 344 unrelated males from three Nepalese populations (Tamang, Newar, and Kathmandu) and a general collection from Tibet. The latter displays the highest haplotype diversity (0.9990) followed by Kathmandu (0.9977), Newar (0.9570), and Tamang (0.9545). The overall haplotype diversity for the Himalayan populations at 17 Y-STR loci was 0.9973, and the corresponding values for the extended (11 loci) and minimal (nine loci) haplotypes were 0.9955 and 0.9942, respectively. No Y-STR profiles are shared across the four Himalayan collections at the 17-, 11-, and nine-locus resolutions considered, indicating a lack of recent gene flow among them. Phylogenetic analyses support our previous findings that Kathmandu, and to some extent Newar, received significant genetic influence from India while Tamang and Tibet exhibit limited or no gene flow from the subcontinent. A median-joining network of haplogroup O3a3c-M134 based on 15 Y-STR loci from our four Himalayan populations suggests either a male founder effect in Tamang, possibly from Tibet, or a recent bottleneck following their arrival south of the Himalayas from Tibet leading to their highly reduced Y single-nucleotide polymorphism and Y-STR diversity. The genetic uniqueness of the four Himalayan populations examined in this study merits the creation of separate databases for individual identification, parentage analysis, and population genetic studies.
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Affiliation(s)
- Tenzin Gayden
- Department of Biological Sciences, Florida International University, Miami, FL 33199, USA
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31
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McGinnis RE, Deloukas P, McLaren WM, Inouye M. Visualizing chromosome mosaicism and detecting ethnic outliers by the method of "rare" heterozygotes and homozygotes (RHH). Hum Mol Genet 2010; 19:2539-53. [PMID: 20211853 PMCID: PMC2883336 DOI: 10.1093/hmg/ddq102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We describe a novel approach for evaluating SNP genotypes of a genome-wide association scan to identify “ethnic outlier” subjects whose ethnicity is different or admixed compared to most other subjects in the genotyped sample set. Each ethnic outlier is detected by counting a genomic excess of “rare” heterozygotes and/or homozygotes whose frequencies are low (<1%) within genotypes of the sample set being evaluated. This method also enables simple and striking visualization of non-Caucasian chromosomal DNA segments interspersed within the chromosomes of ethnically admixed individuals. We show that this visualization of the mosaic structure of admixed human chromosomes gives results similar to another visualization method (SABER) but with much less computational time and burden. We also show that other methods for detecting ethnic outliers are enhanced by evaluating only genomic regions of visualized admixture rather than diluting outlier ancestry by evaluating the entire genome considered in aggregate. We have validated our method in the Wellcome Trust Case Control Consortium (WTCCC) study of 17,000 subjects as well as in HapMap subjects and simulated outliers of known ethnicity and admixture. The method's ability to precisely delineate chromosomal segments of non-Caucasian ethnicity has enabled us to demonstrate previously unreported non-Caucasian admixture in two HapMap Caucasian parents and in a number of WTCCC subjects. Its sensitive detection of ethnic outliers and simple visual discrimination of discrete chromosomal segments of different ethnicity implies that this method of rare heterozygotes and homozygotes (RHH) is likely to have diverse and important applications in humans and other species.
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Hwa HL, Tseng LH, Ko TM, Chang YY, Yin HY, Su YN, Lee JCI. Seventeen Y-chromosomal short tandem repeat haplotypes in seven groups of population living in Taiwan. Int J Legal Med 2010; 124:295-300. [DOI: 10.1007/s00414-010-0425-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2009] [Accepted: 01/21/2010] [Indexed: 10/19/2022]
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Thèves C, Balaresque P, Evdokimova LE, Timofeev IV, Alekseev AN, Sevin A, Crubézy E, Gibert M. Population genetics of 17 Y-chromosomal STR loci in Yakutia. Forensic Sci Int Genet 2010; 4:e129-30. [PMID: 20457087 DOI: 10.1016/j.fsigen.2010.01.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2009] [Revised: 01/25/2010] [Accepted: 01/26/2010] [Indexed: 10/19/2022]
Abstract
Haplotype and allele frequencies of 17 Y-chromosomal short tandem repeat (Y-STR) markers in a population sample of 133 Yakut male volunteers from two regions: Central (n=41) and Western Yakutia (n=92) were determined using the AmpFlSTR Yfiler PCR Amplification Kit (Applied Biosystems). A total of 65 haplotypes were identified in the Yakut population, with 15 haplotypes in Central sample and 54 haplotypes in Western sample. Haplotype diversity values of 0.79 and 0.96, and average gene diversity values of 0.14 and 0.41 were calculated for Central and Western samples, respectively. The Fst distances between both our Yakut populations with other Russian, Siberian and Chinese populations were represented by MDS plot. The graphical view demonstrated close distances between most Yakut populations and differences with other Siberian populations.
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Affiliation(s)
- Catherine Thèves
- Laboratory AMIS, FRE N°2960, CNRS/UPS, 37 Allées Jules Guesde, 31000 Toulouse, France.
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Choi JY, Seo TS. An integrated microdevice for high-performance short tandem repeat genotyping. Biotechnol J 2010; 4:1530-41. [PMID: 19844914 DOI: 10.1002/biot.200900202] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Short tandem repeat (STR) analysis provides genetic fingerprinting of individuals, and is considered as a powerful and indispensable technique for forensic human identification. However, the current state-of-the-art STR genotyping processes and instruments are labor intensive, expensive, time consuming, and lack portability. Micro-total-analysis systems or lab-on-a-chip platforms based on microfabrication technologies have the capability to miniaturize and integrate bioanalysis steps in a single format. Recent progress in microsystems has demonstrated their successful performance for the forensic STR typing with a reduced cost, high speed, and improved high throughput. The purpose of this review article is to highlight up-to-date work on advanced microdevices for high-throughput STR genotyping, and a portable integrated microsystem for on-site forensic DNA analysis.
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Affiliation(s)
- Jong Young Choi
- Department of Chemical and Biomolecular Engineering (BK21 Program), Institute for the BioCentury, KAIST, Daejeon, Korea
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Wu FC, Ho CW, Pu CE, Hu KY, Willuweit S, Roewer L, Liu DH. Y-chromosomal STRs haplotypes in the Taiwanese Paiwan population. Int J Legal Med 2010; 125:39-43. [PMID: 20107827 PMCID: PMC3016148 DOI: 10.1007/s00414-009-0416-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2008] [Accepted: 12/22/2009] [Indexed: 11/24/2022]
Abstract
The distribution of Y-chromosomal short tandem repeat (Y-STR) haplotypes was determined in a population of Taiwanese Paiwan aboriginals. Using 17 Y-STR markers, a total of 135 haplotypes were observed, 102 of which were unique. The overall haplotype diversity for the 17 Y-STR loci tested was 0.9922 and the discrimination capacity was 0.6490. In addition, three novel intermediate alleles at the DYS448 locus were also found.
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Affiliation(s)
- Fang-Chin Wu
- Department of Forensic Science, Investigation Bureau, Ministry of Justice, Taipei County, Taiwan, Republic of China.
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Myres NM, Ritchie KH, Lin AA, Hughes RH, Woodward SR, Underhill PA. Y-chromosome short tandem repeat intermediate variant alleles DYS392.2, DYS449.2, and DYS385.2 delineate new phylogenetic substructure in human Y-chromosome haplogroup tree. Croat Med J 2009; 50:239-49. [PMID: 19480020 DOI: 10.3325/cmj.2009.50.239] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
AIM To determine the human Y-chromosome haplogroup backgrounds of intermediate-sized variant alleles displayed by short tandem repeat (STR) loci DYS392, DYS449, and DYS385, and to evaluate the potential of each intermediate variant to elucidate new phylogenetic substructure within the human Y-chromosome haplogroup tree. METHODS Molecular characterization of lineages was achieved using a combination of Y-chromosome haplogroup defining binary polymorphisms and up to 37 short tandem repeat loci. DNA sequencing and median-joining network analyses were used to evaluate Y-chromosome lineages displaying intermediate variant alleles. RESULTS We show that DYS392.2 occurs on a single haplogroup background, specifically I1*-M253, and likely represents a new phylogenetic subdivision in this European haplogroup. Intermediate variants DYS449.2 and DYS385.2 both occur on multiple haplogroup backgrounds, and when evaluated within specific haplogroup contexts, delineate new phylogenetic substructure, with DYS449.2 being informative within haplogroup A-P97 and DYS385.2 in haplogroups D-M145, E1b1a-M2, and R1b*-M343. Sequence analysis of variant alleles observed within the various haplogroup backgrounds showed that the nature of the intermediate variant differed, confirming the mutations arose independently. CONCLUSIONS Y-chromosome short tandem repeat intermediate variant alleles, while relatively rare, typically occur on multiple haplogroup backgrounds. This distribution indicates that such mutations arise at a rate generally intermediate to those of binary markers and STR loci. As a result, intermediate-sized Y-STR variants can reveal phylogenetic substructure within the Y-chromosome phylogeny not currently detected by either binary or Y-STR markers alone, but only when such variants are evaluated within a haplogroup context.
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Affiliation(s)
- Natalie M Myres
- Sorenson Molecular Genealogy Foundation, Salt Lake City, Utah, USA
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Tofanelli S, Bertoncini S, Castrì L, Luiselli D, Calafell F, Donati G, Paoli G. On the origins and admixture of Malagasy: new evidence from high-resolution analyses of paternal and maternal lineages. Mol Biol Evol 2009; 26:2109-24. [PMID: 19535740 DOI: 10.1093/molbev/msp120] [Citation(s) in RCA: 132] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Malagasy have been shown to be a genetically admixed population combining parental lineages with African and South East Asian ancestry. In the present paper, we fit the Malagasy admixture history in a highly resolved phylogeographic framework by typing a large set of mitochondrial DNA and Y DNA markers in unrelated individuals from inland (Merina) and coastal (Antandroy, Antanosy, and Antaisaka) ethnic groups. This allowed performance of a multilevel analysis in which the diversity among main ethnic divisions, lineage ancestries, and modes of inheritance could be concurrently evaluated. Admixture was confirmed to result from the encounter of African and Southeast Asian people with minor recent male contributions from Europe. However, new scenarios are depicted about Malagasy admixture history. The distribution of ancestral components was ethnic and sex biased, with the Asian ancestry appearing more conserved in the female than in the male gene pool and in inland than in coastal groups. A statistic based on haplotype sharing (D(HS)), showing low sampling error and time linearity over the last 200 generations, was introduced here for the first time and helped to integrate our results with linguistic and archeological data. The focus about the origin of Malagasy lineages was enlarged in space and pushed back in time. Homelands could not be pinpointed but appeared to comprise two vast areas containing different populations from sub-Saharan Africa and South East Asia. The pattern of diffusion of uniparental lineages was compatible with at least two events: a primary admixture of proto-Malay people with Bantu speakers bearing a western-like pool of haplotypes, followed by a secondary flow of Southeastern Bantu speakers unpaired for gender (mainly male driven) and geography (mainly coastal).
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Affiliation(s)
- Sergio Tofanelli
- Dipartimento di Biologia, Unità di Antropologia, Università di Pisa, Pisa, Italy.
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Jin HJ, Tyler-Smith C, Kim W. The peopling of Korea revealed by analyses of mitochondrial DNA and Y-chromosomal markers. PLoS One 2009; 4:e4210. [PMID: 19148289 PMCID: PMC2615218 DOI: 10.1371/journal.pone.0004210] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2008] [Accepted: 12/08/2008] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The Koreans are generally considered a northeast Asian group because of their geographical location. However, recent findings from Y chromosome studies showed that the Korean population contains lineages from both southern and northern parts of East Asia. To understand the genetic history and relationships of Korea more fully, additional data and analyses are necessary. METHODOLOGY AND RESULTS We analyzed mitochondrial DNA (mtDNA) sequence variation in the hypervariable segments I and II (HVS-I and HVS-II) and haplogroup-specific mutations in coding regions in 445 individuals from seven east Asian populations (Korean, Korean-Chinese, Mongolian, Manchurian, Han (Beijing), Vietnamese and Thais). In addition, published mtDNA haplogroup data (N = 3307), mtDNA HVS-I sequences (N = 2313), Y chromosome haplogroup data (N = 1697) and Y chromosome STR data (N = 2713) were analyzed to elucidate the genetic structure of East Asian populations. All the mtDNA profiles studied here were classified into subsets of haplogroups common in East Asia, with just two exceptions. In general, the Korean mtDNA profiles revealed similarities to other northeastern Asian populations through analysis of individual haplogroup distributions, genetic distances between populations or an analysis of molecular variance, although a minor southern contribution was also suggested. Reanalysis of Y-chromosomal data confirmed both the overall similarity to other northeastern populations, and also a larger paternal contribution from southeastern populations. CONCLUSION The present work provides evidence that peopling of Korea can be seen as a complex process, interpreted as an early northern Asian settlement with at least one subsequent male-biased southern-to-northern migration, possibly associated with the spread of rice agriculture.
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Affiliation(s)
- Han-Jun Jin
- Department of Biological Sciences, Dankook University, Cheonan, Korea
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Chris Tyler-Smith
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Wook Kim
- Department of Biological Sciences, Dankook University, Cheonan, Korea
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Valle Y, Padilla-Gutiérrez JR, Rodarte K, Quintero-Ramos A, Ortiz R, Hernández-Zaragoza G, Rivas F. Five X-chromosome short tandem repeats in a Western Mexican population. Clin Chem Lab Med 2008; 46:1388-90. [PMID: 18844492 DOI: 10.1515/cclm.2008.279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND X-linked microsatellites represent an efficient complement of autosomal and Y-chromosomal markers in forensic and kinship analysis. METHODS DXS337 (n=208), DXS101 (n=208), HPRTB (n=206), DXS8377 (n=220), and DXS7423 (n=213) were genotyped in male and female samples from a Western Mexican Mestizo population using singleplex systems and polyacrylamide gel electrophoresis. RESULTS Genotype distributions did not deviate from Hardy-Weinberg expectations, and pairwise allele combination analysis was consistent with independent segregation for every marker (p>0.05). Allele frequencies were not different by gender. Differences in allele distribution with respect to Caucasian population data (DXS101, HPRTB, DXS8377, DXS7423) seem attributable to the native Mexican component. For the set of five markers, the combined power of discrimination and the probability of exclusion in paternity tests in trios were greater than 0.999. CONCLUSIONS The present data reveal that the panel of five X-short tandem repeats analyzed is highly informative in forensic identity and parentage studies in Western Mexico.
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Affiliation(s)
- Yeminia Valle
- Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara, Jalisco, Mexico.
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Shi MS, Tang JP, Bai RF, Yu XJ, Lv JY, Hu B. Haplotypes of 20 Y-chromosomal STRs in a population sample from southeast China (Chaoshan area). Int J Legal Med 2007; 121:455-62. [PMID: 17641908 DOI: 10.1007/s00414-007-0186-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2006] [Accepted: 04/13/2007] [Indexed: 02/05/2023]
Abstract
In this study, 20 Y-specific short tandem repeat (STR) loci (DYS434, Y-GATA-A10, Y-GATA-H4, DYS438, DYS439, DYS443, DYS444, DYS446, DYS447, DYS448, DYS456, DYS458, DYS460, DYS520, DYS531, DYS557, DYS622, DYS630, DYS635(Y-GATA-C4), and DYS709) were analyzed in 158 unrelated healthy men from southeast China by three fluorescence-labeled multiplex polymerase chain reaction systems. The Y-STR multiplexes developed have followed the published nomenclature and International Society for Forensic Genetics (ISFG) guidelines for STR analysis. Gene diversity ranged from 0.2506 at DYS434 to 0.8034 at DYS447. A total of 157 different haplotypes were observed, and among these, 156 were unique, while 1 was found two times. The haplotype diversity value calculated from all 20 loci combined was 0.9997, which is informative. Furthermore, 80 father-son pairs, previously confirmed by autosomal STR analysis, were typed using the same 20 Y-STR loci, and four mutation events were identified at the Y-GATA-H4, DYS439, DYS456, and DYS458 loci, giving an average mutation rate of 0.25% per locus per generation (95% confidence interval 0.09-0.54). These results including the haplotype data at 20 Y-STR loci would enrich Chinese genetic informational resources and provide useful information in forensic practice.
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Affiliation(s)
- Mei Sen Shi
- Department of Forensic Medicine, Shantou University Medical College, Shantou 515031, Guangdong, People's Republic of China.
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41
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Kang LL, Liu K, Ma Y. Y chromosome STR haplotypes of Tibetan Living Tibet Lassa. Forensic Sci Int 2007; 172:79-83. [PMID: 17008038 DOI: 10.1016/j.forsciint.2006.08.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2006] [Revised: 07/28/2006] [Accepted: 08/18/2006] [Indexed: 10/24/2022]
Abstract
Allele frequencies and haplotypes of the 17 Y-chromosome STRs loci, namely DYS19, DYS385a/b, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635 (YGATA C4), and YGATA H4 were determined in a sample of 131 healthy unrelated males from the Lassa area of Tibet Autonomy Region of China (SW China). In 131 samples 106 different haplotypes were encountered, of which 105 were observed only once. The overall haplotype diversity was 0.9998. The results demonstrate that these loci will be very useful for human identification in forensic cases and paternity tests in the Lassa region.
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Affiliation(s)
- Long Li Kang
- Medicine Department of Tibet Nationality College, No. 6 East Wenhui Road, 712082 Xianyang City, Shaan Xi Province, PR China.
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Ayadi I, Mahfoudh-Lahiani N, Makni H, Ammar-Keskes L, Rebaï A. Combining Autosomal and Y-Chromosomal Short Tandem Repeat Data in Paternity Testing with Male Child: Methods and Application. J Forensic Sci 2007; 52:1068-72. [PMID: 17645485 DOI: 10.1111/j.1556-4029.2007.00513.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Paternity testing is being increasingly requested with the aim of challenging presumptive fatherhood. The ability to establish the biological father is usually based on the genotyping of autosomal short tandem repeat (STR) in alleged father, mother and child, but the use of Y-chromosomal STR has gained interest in the last few years. In this work, we propose a new probabilistic approach that combines autosomal and Y-chromosomal STR data in paternity testing with father/son pairs taking into account mutation events. We also suggest a new two-stage approach where we first type Y-STRs and possibly autosomal STR for the putative father and son, conditional on Y-STR results. We applied this approach to 22 cases. Our results show that Y-STRs can identify nonpaternity cases with high accuracy but need to be validated with autosomal STR to establish paternity. Moreover, the two-stage approach is less costly than the standard approach and is very useful in motherless cases.
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Affiliation(s)
- Imen Ayadi
- Bioinformatics Unit, Centre de Biotechnologie de Sfax, PO Box K, 3038 Sfax, Tunisia
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Chang YM, Perumal R, Keat PY, Kuehn DLC. Haplotype diversity of 16 Y-chromosomal STRs in three main ethnic populations (Malays, Chinese and Indians) in Malaysia. Forensic Sci Int 2007; 167:70-6. [PMID: 16457976 DOI: 10.1016/j.forsciint.2006.01.002] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2005] [Revised: 01/02/2006] [Accepted: 01/02/2006] [Indexed: 11/16/2022]
Abstract
We have analyzed 16 Y-STR loci (DYS456, DYS389I, DYS390, DYS389II, DYS458, DYS19, DYS385a/b, DYS393, DYS391, DYS439, DYS635 or Y-GATA C4, DYS392, Y-GATA H4, DYS437, DYS438 and DYS448) from the non-recombining region of the human Y-chromosome in 980 male individuals from three main ethnic populations in Malaysia (Malay, Chinese, Indian) using the AmpFlSTR((R)) Y-filertrade mark (Applied Biosystems, Foster City, CA). The observed 17-loci haplotypes and the individual allele frequencies for each locus were estimated, whilst the locus diversity, haplotype diversity and discrimination capacity were calculated in the three ethnic populations. Analysis of molecular variance indicated that 88.7% of the haplotypic variation is found within population and 11.3% is between populations (fixation index F(ST)=0.113, p=0.000). This study has revealed Y-chromosomes with null alleles at several Y-loci, namely DYS458, DYS392, DYS389I, DYS389II, DYS439, DYS448 and Y-GATA H4; and several occurrences of duplications at the highly polymorphic DYS385 loci. Some of these deleted loci were in regions of the Y(q) arm that have been implicated in the occurrence of male infertility.
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Affiliation(s)
- Yuet Meng Chang
- Forensic DNA Laboratory, Department of Chemistry, Petaling Jaya, Malaysia
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44
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Roewer L, Krüger C, Willuweit S, Nagy M, Rodig H, Kokshunova L, Rothämel T, Kravchenko S, Jobling MA, Stoneking M, Nasidze I. Y-chromosomal STR haplotypes in Kalmyk population samples. Forensic Sci Int 2007; 173:204-9. [PMID: 17314020 DOI: 10.1016/j.forsciint.2006.11.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2006] [Revised: 11/14/2006] [Accepted: 11/19/2006] [Indexed: 10/23/2022]
Abstract
Seventeen Y-chromosomal short tandem repeats (STRs), DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, GATA-H4, DYS448, DYS456, DYS458, DYS635 were typed in DNA samples from the Kalmyk population (n=99). The population is characterized by a high proportion of duplicated DYS19 alleles and deletions of the locus DYS448 on the background of the Central Asian haplogroup C*. AMOVA analysis reveals a close vicinity to Mongolian and Kazakh populations and large genetic distance to geographical neighbours from Russia, Ukraine and the Caucasus.
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Affiliation(s)
- Lutz Roewer
- Institute of Legal Medicine, Charité, University Medicine Berlin, Hannoversche Str. 6, 10115 Berlin, Germany.
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45
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Onofri V, Alessandrini F, Turchi C, Fraternale B, Buscemi L, Pesaresi M, Tagliabracci A. Y-chromosome genetic structure in sub-Apennine populations of Central Italy by SNP and STR analysis. Int J Legal Med 2007; 121:234-7. [PMID: 17287987 DOI: 10.1007/s00414-007-0153-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2006] [Accepted: 12/22/2006] [Indexed: 11/27/2022]
Abstract
To define the Y-chromosome genetic structure in Apennine populations, 17 Y-chromosome short tandem repeats (Y-STRs) and 37 Y-single nucleotide polymorphisms (Y-SNPs) were typed in 162 subjects living in the upland area of the Marches (Central Italy). A total number of 155 haplotypes (haplotype diversity was 0.9994) and 14 SNP haplogroups were observed. Testing high-resolution Y-chromosome data sets, e.g. using Yfiler and SNPs, increases the discriminatory capacity in individual identification for forensic purposes. It is also useful in autochthonous population and micro-population studies to highlight the most informative loci for evolutionary aims.
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Affiliation(s)
- Valerio Onofri
- Institute of Legal Medicine, Università Politecnica delle Marche, Ancona, Italy
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46
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Woźniak M, Derenko M, Malyarchuk B, Dambueva I, Grzybowski T, Miścicka-Sliwka D. Allelic and haplotypic frequencies at 11 Y-STR loci in Buryats from South-East Siberia. Forensic Sci Int 2006; 164:271-5. [PMID: 16473487 DOI: 10.1016/j.forsciint.2005.11.023] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2005] [Revised: 11/23/2005] [Accepted: 11/23/2005] [Indexed: 10/25/2022]
Abstract
We have obtained Y-STR haplotypes in 12 loci (DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438 and DYS439) from 215 Buryat males. We have found that one haplotype (15-11,18-13-28-23-10-11-14-14-10-12) comprises more than 30% of Y chromosomes in this population while another haplotype (14-11,13-14-30-23-10-14-14-14-10-10) comprises additional 14% of chromosomes. The population under study seems to be very homogenous as far as Y chromosome is regarded and the most frequent haplotype seems to be the modal haplotype for Buryats.
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Affiliation(s)
- Marcin Woźniak
- Institute of Molecular and Forensic Genetics, Nicolaus Copernicus University, Collegium Medicum in Bydgoszcz, M Sklodowskiej-Curie 9, 85-094 Bydgoszcz, Poland.
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Park MJ, Lee HY, Chung U, Kang SC, Shin KJ. Y-STR analysis of degraded DNA using reduced-size amplicons. Int J Legal Med 2006; 121:152-7. [PMID: 17106735 DOI: 10.1007/s00414-006-0133-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2006] [Accepted: 09/20/2006] [Indexed: 11/30/2022]
Abstract
To increase the success rate of Y-STR genotyping for degraded DNA, we have developed two multiplex PCR sets for 21 Y-STR loci. Besides the 17 Y-STR loci of DYS19, DYS385, DYS389-I, DYS389-II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, and GATA H4.1 contained in a commercial Y-STR kit, AmpFlSTR Yfiler, the other four loci of DYS388, DYS446, DYS447, and DYS449 were also included in the multiplexes to increase the discrimination capacity. Among a total of 21 Y-STR loci, the primers for eight loci (DYS385, DYS390, DYS438, DYS446, DYS448, DYS449, and DYS635) were newly designed in the present study and nine loci (DYS385, DYS390, DYS391, DYS392, DYS438, DYS439, DYS448, and DYS635) have PCR amplicons smaller than those of the AmpFlSTR Yfiler kit. A sensitivity test using serially diluted standard 9948 male DNA showed that all the values of Y-STR loci in the Y-miniplexes are reliable at template concentrations as low as 30 pg. We compared the effectiveness of the two multiplexes with the AmpFlSTR Yfiler kit by using both enzymatically degraded DNA and 30 samples of 50-year-old skeletal remains. This comparison demonstrated that the new Y-miniplex sets can produce a better signal from degraded DNA than the AmpFlSTR Yfiler kit.
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Affiliation(s)
- Myung Jin Park
- Department of Forensic Medicine, Yonsei University College of Medicine, 134 Sinchon-Dong, Seodaemun-Gu, Seoul, 120-752, South Korea
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Lee HY, Park MJ, Chung U, Lee HY, Yang WI, Cho SH, Shin KJ. Haplotypes and mutation analysis of 22 Y-chromosomal STRs in Korean father-son pairs. Int J Legal Med 2006; 121:128-35. [PMID: 17106736 DOI: 10.1007/s00414-006-0130-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2006] [Accepted: 09/11/2006] [Indexed: 11/29/2022]
Abstract
We analyzed 369 Korean father/son haplotype transfers in 355 families at 22 Y-STRs (DYS19, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS385, DYS388, DYS437, DYS438, DYS439, DYS446, DYS447, DYS448, DYS449, DYS456, DYS458, DYS464, DYS635, and GATA H4.1). A total of 350 haplotypes were observed with an overall haplotype diversity of 0.9999. Among these, 345 were unique and five were found twice. Furthermore, 36 mutations were identified, giving locus-specific mutation rate estimates between 0.0 and 19.0 x 10(-3) per generation and an average mutation rate estimate of 3.9 x 10(-3) (95% CI 2.7-5.4 x 10(-3)). The compilation of Y-STR mutation events for the present study and previous studies demonstrates that DYS449, DYS458, DYS635, DYS456 and DYS439 are the most prone to mutations and that their overall average mutation rate estimate is 2.36 x 10(-3) (95% CI 2.03-2.73 x 10(-33)).
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Affiliation(s)
- Hwan Young Lee
- Department of Forensic Medicine and BK21 Project for Medical Science, Yonsei University College of Medicine, 134 Sinchon-Dong, Seodaemun-Gu, Seoul, 120-752, South Korea
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Zhang Q, Yan J, Tang H, Jiao Z, Liu Y. Genetic polymorphisms of 17 Y-STRs haplotypes in Tibetan ethnic minority group of China. Leg Med (Tokyo) 2006; 8:300-5. [PMID: 16978904 DOI: 10.1016/j.legalmed.2006.07.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2006] [Revised: 06/29/2006] [Accepted: 07/04/2006] [Indexed: 10/24/2022]
Abstract
Haplotypes and allele frequencies for the 17 Y-chromosomal STRs loci, namely DYS456, DYS389I, DYS390, DYS389II, DYS458, DYS19, DYS385a,b, DYS393, DYS391, DYS439, DYS635, DYS392, Y GATA H4, DYS437, DYS438, DYS448 were determined in a population sample of 112 healthy unrelated autochthonous Tibetan ethnic male individuals from Tibet of China. No shared haplotypes were observed. The gene diversity values for the Y-STRs loci ranged from 0.2052(DYS391) to 0.9301(DYS385a,b). The results demonstrate that these loci will be very useful for human identification in forensic cases and paternity tests in Tibetan population of China.
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Affiliation(s)
- Qingxia Zhang
- Graduate University of Chinese Academy of Sciences, Beijing 100049, China.
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Asamura H, Sakai H, Ota M, Fukushima H. Japanese population data for eight X-STR loci using two new quadruplex systems. Int J Legal Med 2006; 120:303-9. [PMID: 16758231 DOI: 10.1007/s00414-006-0103-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2006] [Accepted: 04/25/2006] [Indexed: 11/27/2022]
Abstract
Using two new X-chromosome short tandem repeats (X-STR) multiplex (quadruplex) systems, we investigated Japanese population data (drawn from 401 individuals) for eight X-STR loci (DXS10011, DXS9898, DXS8377, HPRTB, DXS7132, DXS6797, GATA172D05, and DXS6807). Allele typing with the systems was successful for all loci. The combined powers of discrimination of the eight loci in men and women were 0.999997 and 0.9999999996, respectively. We conclude that combined analyses of the eight X-STR loci using these two quadruplex polymerase chain reaction systems represent a powerful tool for Japanese forensic practice.
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Affiliation(s)
- H Asamura
- Department of Legal Medicine, Shinshu University School of Medicine, Asahi 3-1-1, Matsumoto, Nagano, 390-8621, Japan.
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