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Fan H, Xu Y, Zhao Y, Feng K, Hong L, Zhao Q, Lu X, Shi M, Li H, Wang L, Wen S. Development and validation of YARN: A novel SE-400 MPS kit for East Asian paternal lineage analysis. Forensic Sci Int Genet 2024; 71:103029. [PMID: 38518712 DOI: 10.1016/j.fsigen.2024.103029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 02/12/2024] [Accepted: 03/03/2024] [Indexed: 03/24/2024]
Abstract
Y-chromosomal short tandem repeat polymorphisms (Y-STRs) and Y-chromosomal single nucleotide polymorphisms (Y-SNPs) are valuable genetic markers used in paternal lineage identification and population genetics. Currently, there is a lack of an effective panel that integrates Y-STRs and Y-SNPs for studying paternal lineages, particularly in East Asian populations. Hence, we developed a novel Y-chromosomal targeted panel called YARN (Y-chromosome Ancestry and Region Network) based on multiplex PCR and a single-end 400 massive parallel sequencing (MPS) strategy, consisting of 44 patrilineage Y-STRs and 260 evolutionary Y-SNPs. A total of 386 reactions were validated for the effectiveness and applicability of YARN according to SWGDAM validation guidelines, including sensitivity (with a minimum input gDNA of 0.125 ng), mixture identification (ranging from 1:1-1:10), PCR inhibitor testing (using substances such as 50 μM hematin, 100 μM hemoglobin, 100 μM humic acid, and 2.5 mM indigo dye), species specificity (successfully distinguishing humans from other animals), repeatability study (achieved 100% accuracy), and concordance study (with 99.91% accuracy for 1121 Y-STR alleles). Furthermore, we conducted a pilot study using YARN in a cohort of 484 Han Chinese males from Huaiji County, Zhaoqing City, Guangdong, China (GDZQHJ cohort). In this cohort, we identified 52 different Y-haplogroups and 73 different surnames. We found weak to moderate correlations between the Y-haplogroups, Chinese surnames, and geographical locations of the GDZQHJ cohort (with λ values ranging from 0.050 to 0.340). However, when we combined two different categories into a new independent variable, we observed stronger correlations (with λ values ranging from 0.617 to 0.754). Overall, the YARN panel, which combines Y-STR and Y-SNP genetic markers, meets forensic DNA quality assurance guidelines and holds potential for East Asian geographical origin inference and paternal lineage analysis.
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Affiliation(s)
- Haoliang Fan
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China; School of Forensic Medicine, Shanxi Medical University, Taiyuan 030001, China.
| | - Yiran Xu
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China.
| | - Yutao Zhao
- Public Security Bureau of Zhaoqing Municipality, Zhaoqing 526000, China.
| | - Kai Feng
- Duanzhou Branch of Zhaoqing Public Security Bureau, Zhaoqing 526060, China.
| | - Liuxi Hong
- Sihui Public Security Bureau of Guangdong Province, Zhaoqing 526299, China.
| | - Qiancheng Zhao
- Public Security Bureau of Zhaoqing Municipality, Zhaoqing 526000, China.
| | - Xiaoyu Lu
- Deepreads Biotech Company Limited, Guangzhou 510663, China.
| | - Meisen Shi
- Criminal Justice College of China University of Political Science and Law, Beijing 100088, China.
| | - Haiyan Li
- Criminal Technology Center of Guangdong Provincial Public Security Department, Guangzhou 510050, China.
| | - Lingxiang Wang
- MOE Laboratory for National Development and Intelligent Governance, Fudan University, Shanghai 200433, China.
| | - Shaoqing Wen
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China; Institute of Archaeological Science, Fudan University, Shanghai 200433, China; MOE Laboratory for National Development and Intelligent Governance, Fudan University, Shanghai 200433, China.
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Song M, Zhou Y, Zhao C, Song F, Hou Y. YHP: Y-chromosome Haplogroup Predictor for predicting male lineages based on Y-STRs. Forensic Sci Int 2024; 361:112113. [PMID: 38936202 DOI: 10.1016/j.forsciint.2024.112113] [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: 03/18/2024] [Revised: 05/24/2024] [Accepted: 06/16/2024] [Indexed: 06/29/2024]
Abstract
Human Y chromosome reflects the evolutionary process of males. Male lineage tracing by Y chromosome is of great use in evolutionary, forensic, and anthropological studies. Identifying the male lineage based on the specific distribution of Y haplogroups narrows down the investigation scope, which has been used in forensic scenarios. However, existing software aids in familial searching using Y-STRs (Y-chromosome short tandem repeats) to predict Y-SNP (Y-chromosome single nucleotide polymorphism) haplogroups, they often lack resolution. In this study, we developed YHP (Y Haplogroup Predictor), a novel software offering high-resolution haplogroup inference without requiring extensive Y-SNP sequencing. Leveraging existing datasets (219 haplogroups, 4064 samples in total), YHP predicts haplogroups with 0.923 accuracy under the highest haplogroup resolution, employing a random forest algorithm. YHP, available on Github (https://github.com/cissy123/YHP-Y-Haplogroup-Predictor-), facilitates high-resolution haplogroup prediction, haplotype mismatch analysis, and haplotype similarity comparison. Notably, it demonstrates efficacy in East Asian populations, benefiting from training data from eight distinct East Asian ethnic populations. Moreover, it enables seamless integration of additional training sets, extending its utility to diverse populations.
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Affiliation(s)
- Mengyuan Song
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China; Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Yuxiang Zhou
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Chenxi Zhao
- College of Computer Science, Sichuan University, Chengdu, China
| | - Feng Song
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China.
| | - Yiping Hou
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China.
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Jia L, Wang M, Duan S, Chen J, Zhao M, Ji S, Lv B, Jiang X, He G, Yang J. Genetic history of esophageal cancer group in southwestern China revealed by Y-chromosome STRs and genomic evolutionary connection analysis. Heliyon 2024; 10:e29867. [PMID: 38720733 PMCID: PMC11076658 DOI: 10.1016/j.heliyon.2024.e29867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 04/09/2024] [Accepted: 04/16/2024] [Indexed: 05/12/2024] Open
Abstract
Genetic and environmental factors play crucial roles in the development of esophageal cancer (EC) and contribute uniquely or cooperatively to human cancer susceptibility. Sichuan is located in the interior of southwestern China, and the northern part of Sichuan is one of the regions with a high occurrence of EC. However, the factors influencing the high incidence rate of EC in the Sichuan Han Chinese population and its corresponding genetic background and origins are still poorly understood. Here, we utilized genome-wide single nucleotide polymorphisms (SNPs) and Y-chromosome short tandem repeats (Y-STRs) to characterize the genetic structure, connection, and origin of cancer groups and general populations. We generated Y-STR-based haplotype data from 214 Sichuan individuals, including the Han Chinese EC population and a control group of Han Chinese individuals. Our results, obtained from Y-STR-based population statistical methods (analysis of molecular variance (AMOVA), principal component analysis (PCA), and phylogenetic analysis), demonstrated that there was a genetic substructure difference between the EC population in the high-incidence area of northern Sichuan Province and the control population. Additionally, there was a strong genetic relationship between the EC population in the northern Sichuan high-incidence area and those at high risk in both the Fujian and Chaoshan areas. In addition, we obtained high-density SNP data from saliva samples of 60 healthy Han Chinese individuals from three high-prevalence areas of EC in China: Sichuan Nanchong, Fujian Quanzhou, and Henan Xinxiang. As inferred from the allele frequency of SNPs and sharing patterns of haplotype segments, the evolutionary history and admixture events suggested that the Han population from Nanchong in northern Sichuan Province shared a close genetic relationship with the Han populations from Xinxiang in Henan Province and Quanzhou in Fujian Province, both of which are regions with a high prevalence of EC. Our study illuminated the genetic profile and connection of the Northern Sichuan Han population and enriched the genomic resources and features of the Han Chinese populations in China, especially for the Y-STR genetic data of the Han Chinese EC population. Populations living in different regions with high incidences of EC may share similar genetic backgrounds, which offers new insights for further exploring the genetic mechanisms underlying EC.
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Affiliation(s)
- Lihua Jia
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College and Center for Genetics and Prenatal diagnosis, Affiliated Hospital of Northern Sichuan Medical College, Nanchong, Sichuan, 637007, China
| | - Mengge Wang
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
| | - Shuhan Duan
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College and Center for Genetics and Prenatal diagnosis, Affiliated Hospital of Northern Sichuan Medical College, Nanchong, Sichuan, 637007, China
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
| | - Jianghua Chen
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College and Center for Genetics and Prenatal diagnosis, Affiliated Hospital of Northern Sichuan Medical College, Nanchong, Sichuan, 637007, China
| | - Mei Zhao
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College and Center for Genetics and Prenatal diagnosis, Affiliated Hospital of Northern Sichuan Medical College, Nanchong, Sichuan, 637007, China
| | - Simeng Ji
- School of Laboratory Medicine, North Sichuan Medical College, Nanchong, Sichuan, 637000, China
| | - Bingbing Lv
- School of Laboratory Medicine, North Sichuan Medical College, Nanchong, Sichuan, 637000, China
| | - Xiucheng Jiang
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College and Center for Genetics and Prenatal diagnosis, Affiliated Hospital of Northern Sichuan Medical College, Nanchong, Sichuan, 637007, China
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
| | - Guanglin He
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
| | - Junbao Yang
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College and Center for Genetics and Prenatal diagnosis, Affiliated Hospital of Northern Sichuan Medical College, Nanchong, Sichuan, 637007, China
- School of Laboratory Medicine, North Sichuan Medical College, Nanchong, Sichuan, 637000, China
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Sun Q, Wang M, Lu T, Duan S, Liu Y, Chen J, Wang Z, Sun Y, Li X, Wang S, Lu L, Hu L, Yun L, Yang J, Yan J, Nie S, Zhu Y, Chen G, Wang CC, Liu C, He G, Tang R. Differentiated adaptative genetic architecture and language-related demographical history in South China inferred from 619 genomes from 56 populations. BMC Biol 2024; 22:55. [PMID: 38448908 PMCID: PMC10918984 DOI: 10.1186/s12915-024-01854-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 02/26/2024] [Indexed: 03/08/2024] Open
Abstract
BACKGROUND The underrepresentation of human genomic resources from Southern Chinese populations limited their health equality in the precision medicine era and complete understanding of their genetic formation, admixture, and adaptive features. Besides, linguistical and genetic evidence supported the controversial hypothesis of their origin processes. One hotspot case was from the Chinese Guangxi Pinghua Han people (GPH), whose language was significantly similar to Southern Chinese dialects but whose uniparental gene pool was phylogenetically associated with the indigenous Tai-Kadai (TK) people. Here, we analyzed genome-wide SNP data in 619 people from four language families and 56 geographically different populations, in which 261 people from 21 geographically distinct populations were first reported here. RESULTS We identified significant population stratification among ethnolinguistically diverse Guangxi populations, suggesting their differentiated genetic origin and admixture processes. GPH shared more alleles related to Zhuang than Southern Han Chinese but received more northern ancestry relative to Zhuang. Admixture models and estimates of genetic distances showed that GPH had a close genetic relationship with geographically close TK compared to Northern Han Chinese, supporting their admixture origin hypothesis. Further admixture time and demographic history reconstruction supported GPH was formed via admixture between Northern Han Chinese and Southern TK people. We identified robust signatures associated with lipid metabolisms, such as fatty acid desaturases (FADS) and medically relevant loci associated with Mendelian disorder (GJB2) and complex diseases. We also explored the shared and unique selection signatures of ethnically different but linguistically related Guangxi lineages and found some shared signals related to immune and malaria resistance. CONCLUSIONS Our genetic analysis illuminated the language-related fine-scale genetic structure and provided robust genetic evidence to support the admixture hypothesis that can explain the pattern of observed genetic diversity and formation of GPH. This work presented one comprehensive analysis focused on the population history and demographical adaptative process, which provided genetic evidence for personal health management and disease risk prediction models from Guangxi people. Further large-scale whole-genome sequencing projects would provide the entire landscape of southern Chinese genomic diversity and their contributions to human health and disease traits.
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Affiliation(s)
- Qiuxia Sun
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331, China
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
| | - Mengge Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China.
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China.
| | - Tao Lu
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331, China
| | - Shuhan Duan
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, 637100, China
| | - Yan Liu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, 637100, China
| | - Jing Chen
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030001, China
| | - Zhiyong Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Yuntao Sun
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Xiangping Li
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Shaomei Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Department of Public Health, Chengdu Medical College, Chengdu, 610500, China
| | - Liuyi Lu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- School of Clinical Medical Sciences, North Sichuan Medical College, Nanchong, 637100, China
| | - Liping Hu
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Libing Yun
- West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Junbao Yang
- School of Clinical Medical Sciences, North Sichuan Medical College, Nanchong, 637100, China
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030001, China
| | - Shengjie Nie
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Yanfeng Zhu
- Department of Public Health, Chengdu Medical College, Chengdu, 610500, China
| | - Gang Chen
- Hunan Key Lab of Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, 410075, China
| | - Chuan-Chao Wang
- State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, Xiamen, 361005, Fujian, China
| | - Chao Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510275, China
- Guangzhou Forensic Science Institute, Guangzhou, 510055, China
- Anti-Drug Technology Center of Guangdong Province, Guangzhou, 510230, China
| | - Guanglin He
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China.
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China.
| | - Renkuan Tang
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331, China.
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Watahiki H, Fujii K, Fukagawa T, Mita Y, Kitayama T, Mizuno N. Y chromosome haplogroup N in a Japanese population is classified into three subclades, and two DYS385 loci, a duplicated Y-STR, are duplicated again in subclade N-M1819. Leg Med (Tokyo) 2024; 67:102390. [PMID: 38190775 DOI: 10.1016/j.legalmed.2023.102390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/21/2023] [Accepted: 12/28/2023] [Indexed: 01/10/2024]
Abstract
DYS385 is one of the major Y chromosome short tandem repeats (Y-STRs) in forensic genetics and exists as 2 copies in the human Y chromosome palindrome P4 region. In this study, we found that some samples were estimated to have ≥ 4 copies of DYS385 in Y chromosome haplogroup N in a Japanese population. Y chromosome haplogroup N is distributed widely in eastern/central Asia, Siberia, and eastern/northern Europe, and is also observed in Japan; however, little is known about haplogroup N subclades in the Japanese population. To reveal the link between increased DYS385 copy number and haplogroup N subclades, we sequenced single nucleotide polymorphisms to classify the subclades. As a result, the Japanese Y chromosomes of haplogroup N were classified into three subclades, and an increased DYS385 copy number was specific to subclade N-M1819* (N1b2*). These results are of use in forensic DNA analysis because Y-STR copy number is important for the interpretation of Y-STR typing results of male DNA mixtures and kinship analysis. We also found that DYS458.1 microvariants (DYS458 intermediate alleles with single-nucleotide insertion) were observed only in subclade N-CTS962 (N1b1b∼) samples. Given that previous studies reported that DYS458.1 microvariants are observed in Y chromosomes of haplogroup N in other populations, DYS458.1 might be used to infer haplogroup N subclades without limitation to the Japanese population. The results of this study will be beneficial not only to forensic genetics but also to anthropological studies.
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Affiliation(s)
- Haruhiko Watahiki
- National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa, Chiba 277-0882, Japan.
| | - Koji Fujii
- National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Takashi Fukagawa
- National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Yusuke Mita
- National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Tetsushi Kitayama
- National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Natsuko Mizuno
- National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
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Yang Y, Li Q, Yang X, Zhang Z, Hu Y, Zhang Y, He F. Forensic parameters and population analysis of 21 autosomal STR loci in the Wuhu Han population from Anhui Province, East China. Ann Hum Biol 2024; 51:1-6. [PMID: 38251837 DOI: 10.1080/03014460.2023.2298470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 12/18/2023] [Indexed: 01/23/2024]
Abstract
BACKGROUND At present, there are no available genetic data on the AGCU EX22 Kit from the Wuhu Han population. AIM This study investigates the applicability of the AGCU EX22 kit, designed for the Chinese population for forensic analysis and population genetics of the Wuhu Han population. SUBJECTS AND METHODS Bloodstains from 1565 unrelated healthy individuals in Wuhu city, Anhui Province, were collected for analysis. The AGCU EX22 kit was used for amplification, and capillary electrophoresis was used to separate the amplification products. Allele frequencies and forensic parameters were determined. The Wuhu Han population was compared to 10 reference populations through genetic distance, a phylogenetic neighbor-joining tree and principal component analysis. RESULTS In total, 281 alleles and 1187 genotypes were observed. No significant deviations from Hardy-Weinberg equilibrium at any locus were found after Bonferroni's correction. The 21 autosomal short tandem repeat (STR) genetic markers exhibited high informativeness and polymorphism. The cumulative power of discrimination and power of exclusion were 0.999999999999999999999999913380 and 0.999999996752339, respectively. Population comparisons revealed a genetic affinity between Wuhu Han and southern Han populations, except for the Guangdong Han population, which aligned with the traditional geographical division in China. CONCLUSION The AGCU EX22 Kit, containing 21 STR loci, is suitable for forensic application and population genetics studies in the Wuhu Han population.
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Affiliation(s)
- Yanyan Yang
- Department of Forensic Genetics, Wannan Medical College, Wuhu, PR China
| | - Qianqian Li
- Department of Forensic Genetics, Wannan Medical College, Wuhu, PR China
| | - Xinrui Yang
- Department of Forensic Genetics, Wannan Medical College, Wuhu, PR China
| | - Ziwei Zhang
- Department of Forensic Genetics, Wannan Medical College, Wuhu, PR China
| | - Yongliang Hu
- Department of Forensic Genetics, Wannan Medical College, Wuhu, PR China
| | - Yue Zhang
- Department of Forensic Genetics, Wannan Medical College, Wuhu, PR China
| | - Fang He
- Department of Forensic Genetics, Wannan Medical College, Wuhu, PR China
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Fu D, Adnan A, Yao J, Aldayan NH, Wang CC, Hongyi C. Unraveling the paternal genetic structure and forensic traits of the Hui population in Liaoning Province, China using Y-chromosome analysis. BMC Genomics 2023; 24:691. [PMID: 37978341 PMCID: PMC10655310 DOI: 10.1186/s12864-023-09774-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 10/30/2023] [Indexed: 11/19/2023] Open
Abstract
The Hui people are the second-largest ethnic minority in China, and they are distributed throughout the country. A previous study explored the paternal genetic structure of the Hui population in nine different regions of China, but it overlooked the Liaoning province. In this study, we examined the paternal genetic makeup and forensic traits of the Hui population in Liaoning province by analyzing 157 Y-chromosome single nucleotide polymorphisms (Y-SNPs) and 26 short tandem repeats (Y-STRs). We successfully genotyped 282 unrelated male individuals from the Hui population of Liaoning province using the SNaPshot® single base extension assay and Goldeneye™ Y26 system kit (PEOPLESPOT R&D, Beijing, China). The results revealed high haplotypic diversity (0.9998) and identified 46 terminal haplogroups for the Hui population. Additional analyses, such as heat maps, principal component analysis (PCA), genetic distance (FST), Multidimensional scaling (MDS) analysis, and median-joining network (MJ) analysis, showed that the Hui population could be classified into three groups: Northwest Hui populations (NWH), including Liaoning, Xinjiang, Qinghai, Gansu, Ningxia, Shaanxi, and Henan; Hui populations from Sichuan and Shandong (SSH); and Yunnan Hui populations (YNH). Pairwise genetic distance (Rst) comparisons with other Chinese populations revealed that the Hui population displayed genetic affinity with the Han population. The comprehensive understanding of the Hui population in Liaoning province, explored by Y-SNPs and Y-STRs, can be utilized to interpret their genetic structure and enhance the accuracy of forensic databases.
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Affiliation(s)
- Dazhi Fu
- First Affiliated Hospital of China Medical University, 155 Heping District, Shenyang, 110001, China
| | - Atif Adnan
- Department of Forensic Sciences, Collage of Criminal Justice, Naif Arab University for Security Sciences, Riyadh, Saudi Arabia.
| | - Jun Yao
- Department of Forensic Biology and Genetics, School of Forensic Medicine, China Medical University, Shenyang, 110001, China
| | - Noura H Aldayan
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam Ibn Abdulaziz University, Al-Kharj, 16273, Saudi Arabia
| | - Chuan-Chao Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, Fujian, People's Republic of China.
| | - Cao Hongyi
- First Affiliated Hospital of China Medical University, 155 Heping District, Shenyang, 110001, China.
- Department of Pathology, School of Basic Medical Sciences, China Medical University, Shenyang, 110001, China.
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Fu J, Song B, Qian J, He T, Chen H, Cheng J, Fu J. Genetic Polymorphism Analysis of 24 Y-STRs in a Han Chinese Population in Luzhou, Southwest China. Genes (Basel) 2023; 14:1904. [PMID: 37895253 PMCID: PMC10606688 DOI: 10.3390/genes14101904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 09/27/2023] [Accepted: 09/30/2023] [Indexed: 10/29/2023] Open
Abstract
Han is the largest of China's 56 ethnic groups and the most populous ethnic group in the world. The Luzhou region is located in southwest China, at the junction of three provinces. The unique historical factors contribute to the genetic polymorphism information. Short tandem repeats (STRs) are highly polymorphic, but the polymorphism of the Y chromosomal STRs (Y-STRs) loci in the Luzhou region is still unclear. It is of great significance to provide Y-STRs genetic data for the Han population from the Luzhou areas of southwest China. A total of 910 unrelated male individuals of the Han population from the Luzhou area were recruited, and 24 Y-STRs were analyzed. The population structure and phylogenetic relationships were compared with those of another 11 related Han populations. A total of 893 different haplotypes were achieved from 910 samples, of which 877 (98.21%) haplotypes were unique. Haplotype diversity and discrimination were 0.999956 and 0.981319, respectively. The lowest genetic diversity of DYS437 is 0.4321, and the highest genetic diversity of DYS385a/b is 0.9642. Pair-to-pair genetic distance and relative probability values indicate that Luzhou Han people are close to Sichuan Han people, Guangdong Han people, and Hunan Han people, which is consistent with geographical distribution, historical influence, and economic development. The 24 Y-STR markers of the southwest Luzhou Han population were highly polymorphic, which provided us with genetic polymorphism information and enriched the population genetic database. Therefore, it is of great value to our forensic applications and population genetics research.
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Affiliation(s)
- Jiewen Fu
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, China; (J.F.); (B.S.); (J.Q.); (T.H.); (J.C.)
- School for Basic Medicine, Southwest Medical University, Luzhou 646000, China
- Laboratory of Forensic DNA, The Judicial Authentication Center, Southwest Medical University, Luzhou 646000, China
| | - Binghui Song
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, China; (J.F.); (B.S.); (J.Q.); (T.H.); (J.C.)
- Laboratory of Forensic DNA, The Judicial Authentication Center, Southwest Medical University, Luzhou 646000, China
| | - Jie Qian
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, China; (J.F.); (B.S.); (J.Q.); (T.H.); (J.C.)
| | - Ting He
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, China; (J.F.); (B.S.); (J.Q.); (T.H.); (J.C.)
| | - Hanchun Chen
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Central South University, Changsha 410013, China;
| | - Jingliang Cheng
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, China; (J.F.); (B.S.); (J.Q.); (T.H.); (J.C.)
- Laboratory of Forensic DNA, The Judicial Authentication Center, Southwest Medical University, Luzhou 646000, China
| | - Junjiang Fu
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, China; (J.F.); (B.S.); (J.Q.); (T.H.); (J.C.)
- Laboratory of Forensic DNA, The Judicial Authentication Center, Southwest Medical University, Luzhou 646000, China
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9
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Li J, Song F, Lang M, Xie M. Comprehensive insights into the genetic background of Chinese populations using Y chromosome markers. ROYAL SOCIETY OPEN SCIENCE 2023; 10:230814. [PMID: 37736526 PMCID: PMC10509572 DOI: 10.1098/rsos.230814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 09/01/2023] [Indexed: 09/23/2023]
Abstract
China is located in East Asia. With a high genetic and cultural diversity, human migration in China has always been a hot topic of genetics research. To explore the origins and migration routes of Chinese males, 3333 Chinese individuals (Han, Hui, Mongolia, Yi and Kyrgyz) with 27 Y-STRs and 143 Y-SNPs from published literature were analysed. Our data showed that there are five dominant haplogroups (O2-M122, O1-F265, C-M130, N-M231, R-M207) in China. Combining analysis of haplogroup frequencies, geographical positions and time with the most recent common ancestor (TMRCA), we found that haplogroups C-M130, N-M231 and R1-M173 and O1a-M175 probably migrated into China via the northern route. Interestingly, we found that haplogroup C*-M130 in China may originate in South Asia, whereas the major subbranches C2a-L1373 and C2b-F1067 migrated from northern China. The results of BATWING showed that the common ancestry of Y haplogroup in China can be traced back to 17 000 years ago, which was concurrent with global temperature increases after the Last Glacial Maximum.
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Affiliation(s)
- Jienan Li
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan Province, People's Republic of China
| | - Feng Song
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, People's Republic of China
| | - Min Lang
- Sichuan University Law School, Sichuan University, Chengdu, People's Republic of China
| | - Mingkun Xie
- Department of Obstetrics, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, People's Republic of China
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10
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He G, Wang M, Miao L, Chen J, Zhao J, Sun Q, Duan S, Wang Z, Xu X, Sun Y, Liu Y, Liu J, Wang Z, Wei L, Liu C, Ye J, Wang L. Multiple founding paternal lineages inferred from the newly-developed 639-plex Y-SNP panel suggested the complex admixture and migration history of Chinese people. Hum Genomics 2023; 17:29. [PMID: 36973821 PMCID: PMC10045532 DOI: 10.1186/s40246-023-00476-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 03/15/2023] [Indexed: 03/29/2023] Open
Abstract
BACKGROUND Non-recombining regions of the Y-chromosome recorded the evolutionary traces of male human populations and are inherited haplotype-dependently and male-specifically. Recent whole Y-chromosome sequencing studies have identified previously unrecognized population divergence, expansion and admixture processes, which promotes a better understanding and application of the observed patterns of Y-chromosome genetic diversity. RESULTS Here, we developed one highest-resolution Y-chromosome single nucleotide polymorphism (Y-SNP) panel targeted for uniparental genealogy reconstruction and paternal biogeographical ancestry inference, which included 639 phylogenetically informative SNPs. We genotyped these loci in 1033 Chinese male individuals from 33 ethnolinguistically diverse populations and identified 256 terminal Y-chromosomal lineages with frequency ranging from 0.0010 (singleton) to 0.0687. We identified six dominant common founding lineages associated with different ethnolinguistic backgrounds, which included O2a2b1a1a1a1a1a1a1-M6539, O2a1b1a1a1a1a1a1-F17, O2a2b1a1a1a1a1b1a1b-MF15397, O2a2b2a1b1-A16609, O1b1a1a1a1b2a1a1-F2517, and O2a2b1a1a1a1a1a1-F155. The AMOVA and nucleotide diversity estimates revealed considerable differences and high genetic diversity among ethnolinguistically different populations. We constructed one representative phylogenetic tree among 33 studied populations based on the haplogroup frequency spectrum and sequence variations. Clustering patterns in principal component analysis and multidimensional scaling results showed a genetic differentiation between Tai-Kadai-speaking Li, Mongolic-speaking Mongolian, and other Sinitic-speaking Han Chinese populations. Phylogenetic topology inferred from the BEAST and Network relationships reconstructed from the popART further showed the founding lineages from culturally/linguistically diverse populations, such as C2a/C2b was dominant in Mongolian people and O1a/O1b was dominant in island Li people. We also identified many lineages shared by more than two ethnolinguistically different populations with a high proportion, suggesting their extensive admixture and migration history. CONCLUSIONS Our findings indicated that our developed high-resolution Y-SNP panel included major dominant Y-lineages of Chinese populations from different ethnic groups and geographical regions, which can be used as the primary and powerful tool for forensic practice. We should emphasize the necessity and importance of whole sequencing of more ethnolinguistically different populations, which can help identify more unrecognized population-specific variations for the promotion of Y-chromosome-based forensic applications.
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Affiliation(s)
- Guanglin He
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610041, China.
| | - Mengge Wang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Lei Miao
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Jing Chen
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030001, China
| | - Jie Zhao
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Qiuxia Sun
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610041, China
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331, China
| | - Shuhan Duan
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610041, China
- School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, 637000, China
| | - Zhiyong Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610041, China
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Xiaofei Xu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610041, China
| | - Yuntao Sun
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610041, China
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Yan Liu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610041, China
- School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, 637000, China
| | - Jing Liu
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Lanhai Wei
- School of Ethnology and Anthropology, Inner Mongolia Normal University, Hohhot, 010028, Inner Mongolia, China
| | - Chao Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510275, China
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Jian Ye
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China.
| | - Le Wang
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China.
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11
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Li LY, Fan SG, Gong H, Fan X, Wang DC, Li NX, Jia FQ. Haplotype and Genetic Analysis of 41 Y-STR Loci in the Wuwei Han Population from Gansu Province, China. Curr Med Sci 2023; 43:184-190. [PMID: 36544037 DOI: 10.1007/s11596-022-2664-7] [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: 05/19/2022] [Accepted: 09/06/2022] [Indexed: 12/24/2022]
Abstract
OBJECTIVE Y-Chromosomal short tandem repeat polymorphism (Y-STR) analysis plays an indispensable role in the identification of male individuals, population genetics, and biogeographic research. While profiles of many populations based on Y-STR markers in human genomes are ample, haplotype data for the Wuwei Han are still scarce. METHODS In this study, 2180 unrelated Wuwei Han male individuals residing in Gansu Province, China were collected and genotyped using the novel Microreader™ 40Y Plus ID system. Phylogenetic relationship reconstructions, multidimensional scaling (MDS), and heatmap analysis were performed based on the genetic distance (Rst) values between our studied population and other populations of the Ymax module in the Y-STR Haplotype Reference Database (YHRD). RESULTS A total of 2129 unique haplotypes were obtained, and the haplotype diversity (HD) and discrimination capacity (DC) for the Wuwei Han were 0.9999 and 0.9931, respectively. CONCLUSION Our results demonstrate that the Wuwei Han population had intimate genetic relationships with East Asians, especially the geographically close Han populations. Overall, this Y-Chromosomal assay gives valuable information about paternal lineages in male individual tracking and genealogical database construction.
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Affiliation(s)
- Lu-Yao Li
- Department of Pathology, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Sheng-Gui Fan
- The Judicial Authentication Center, Wuwei Public Security Bureau, Wuwei, 733000, China
| | - Hui Gong
- Department of Pathology, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Xing Fan
- Department of Pathology, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - De-Chun Wang
- The Judicial Authentication Center, Wuwei Public Security Bureau, Wuwei, 733000, China
| | - Neng-Xiu Li
- The Judicial Authentication Center, Wuwei Public Security Bureau, Wuwei, 733000, China
| | - Fu-Quan Jia
- Department of Forensic Medicine, Inner Mongolia Medical University, Hohhot, 010059, China.
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12
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Xu C, Wei W, Zuo M, Zuo W, Li K, Lian X, Wang S, Zhou X, Zhang X, Zhong S. Genetic polymorphisms and phylogenetic characteristics of Tibeto-Burman-speaking Lahu population from southwest China based on 41 Y-STR loci. Ann Hum Biol 2023; 50:75-81. [PMID: 36688851 DOI: 10.1080/03014460.2023.2171123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
BACKGROUND Male sex-linked Y-chromosome short tandem repeats (Y-STRs) have been widely used in forensic cases and population genetics research. At present, the forensic-related Y-STR data in the Chinese Lahu population are still poorly understood. AIM To enrich the available Y-STR data of this Chinese minority population and investigate its phylogenetic relationships with other reported populations. SUBJECTS AND METHODS The genetic polymorphisms of 41 Y-STR loci were analysed in 299 unrelated healthy Lahu male individuals from Southwest China. Phylogenetic analyses were performed by multidimensional scaling analysis and neighbor-joining phylogenetic tree construction. RESULTS A total of 379 alleles were observed at the 41 Y-STR loci. The allele frequencies ranged from 0.0033 to 0.9666. The genetic diversity values ranged from 0.0653 to 0.9072. A total of 254 different haplotypes of the 41 Y-STR loci were observed in 299 individuals. The values of haplotype diversity, haplotype match probability, and discrimination capacity were 0.9987, 0.0047, and 0.8495, respectively. The phylogenetic analysis indicated that the Tibeto-Burman-speaking Lahu population showed a close genetic relationship with the Yunnan Yi population. CONCLUSIONS The haplotype data of the present study can enrich the forensic databases of this Chinese minority population and will be useful for population genetics and forensic DNA application.
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Affiliation(s)
- Chongchong Xu
- School of Forensic Medicine, Kunming Medical University, Kunming, China
| | - Wei Wei
- School of Forensic Medicine, Kunming Medical University, Kunming, China
| | - Mingxin Zuo
- School of Forensic Medicine, Kunming Medical University, Kunming, China
| | - Wu Zuo
- Institute of Criminal Science and Technology, Yuxi Municipal Public Security Bureau, Yuxi, China
| | - Kuan Li
- School of Forensic Medicine, Kunming Medical University, Kunming, China
| | - Xinqing Lian
- School of Forensic Medicine, Kunming Medical University, Kunming, China
| | - Shixu Wang
- School of Forensic Medicine, Kunming Medical University, Kunming, China
| | - Xuemei Zhou
- School of Forensic Medicine, Kunming Medical University, Kunming, China
| | - Xiufeng Zhang
- School of Forensic Medicine, Kunming Medical University, Kunming, China.,Judicial Expertise Center of Kunming Medical University, Kunming, China
| | - Shurong Zhong
- School of Forensic Medicine, Kunming Medical University, Kunming, China.,Judicial Expertise Center of Kunming Medical University, Kunming, China
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13
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Wang CZ, Wei LH, Zhang JS, Yu XE, Bai RF, Li H, Shi MS, Ma SH. Forensic characteristics and genetic substructure analysis of the Handan Han population, Northern China. Ann Hum Biol 2023; 50:123-125. [PMID: 36803234 DOI: 10.1080/03014460.2023.2181985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/22/2022] [Accepted: 01/27/2023] [Indexed: 02/22/2023]
Abstract
We analysed the forensic characteristics and substructure of the Handan Han population based on 36 Y-STR (short tandem repeat) and Y-SNP (single nucleotide polymorphism) markers. The two most dominant haplogroups in Handan Han, O2a2b1a1a1-F8 (17.95%) and O2a2b1a2a1a (21.51%), and their abundant downstream branches, reflected the strong expansion of the precursor of the Hans in Handan. The present results enrich the forensic database and explore the genetic relationships between Handan Han and other neighbouring and/or linguistically close populations, which suggests that the current concise overview of the Han intricate substructure remains oversimplified.
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Affiliation(s)
- Chi-Zao Wang
- Department of Radiology, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
- Shantou University Medical College, Shantou, China
- Laboratory of Medical Molecular Imaging, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Lan-Hai Wei
- School of Ethnology and Anthropology, Inner Mongolia Normal University, Hohhot, China
| | | | - Xue-Er Yu
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai, China
| | - Ru-Feng Bai
- Criminal Justice College of China University of Political Science and Law, Beijing, China
| | - Hui Li
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai, China
- Shanxi Academy of Advanced Research and Innovation, Fudan-Datong Institute of Chinese Origin, Datong, China
| | - Mei-Sen Shi
- Criminal Justice College of China University of Political Science and Law, Beijing, China
| | - Shu-Hua Ma
- Department of Radiology, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
- Shantou University Medical College, Shantou, China
- Laboratory of Medical Molecular Imaging, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
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14
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Fan GY, Jiang DZ, Jiang YH, Song W, He YY, Wuo NA. Phylogenetic analyses of 41 Y-STRs and machine learning-based haplogroup prediction in the Qingdao Han population from Shandong province, Eastern China. Ann Hum Biol 2023; 50:35-41. [PMID: 36636009 DOI: 10.1080/03014460.2023.2168057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
BACKGROUND Known for its rich history and culture, Qingdao is a typical symbol of Chinese maritime culture. Its unique genetic landscape has aroused interest among geneticists and forensic scientists. However, the genetic landscape of Qingdao has never been uncovered. AIM This investigation intends to provide light on Qingdao's paternal genetic diversity and its evolutionary connections to other Han subgroups. SUBJECTS AND METHODS The genetic polymorphisms of 41 Y-chromosomal short tandem repeat (STR) loci in the Qingdao Han were investigated using SureID® PathFinder Plus Kit. Phylogenetic studies were performed using genotype data from 52 East Asian groups at 23 common Y-STR loci. A multidimensional scaling plot and cladogram were constructed. Linear Discriminant Analysis (LDA) was carried out for predicting categories among the Han people. The k-nearest neighbour (kNN) algorithm was utilised to designate Y-SNP haplogroups for each haplotype. RESULTS The Qingdao Han were genetically far from the Tibeto-Burman populations and close with the Han people from northern China. LDA indicated a deep integration among the present-day Han people. By the kNN model, the predicted O2a2 and O2a1 were shown to be the predominant Y-SNP haplogroups. CONCLUSIONS This study would be helpful for reconstructing the patrilineal history in China and establishing a more comprehensive Y-STR database.
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Affiliation(s)
- Guang-Yao Fan
- Forensic Center, College of Medicine, Shaoxing University, Shaoxing, China
| | - De-Zhi Jiang
- Criminal Technology Department, Qingdao Public Security Bureau, Shandong, China
| | - Yao-Heng Jiang
- Criminal Technology Department, Qingdao Public Security Bureau, Shandong, China
| | - Wei Song
- Criminal Technology Department, Qingdao Public Security Bureau, Shandong, China
| | - Ying-Yun He
- Ningbo Health Gene Technologies Co. Ltd, Ningbo, China
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15
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Zhou Z, Li Z, Yao Y, Qian J, Ji Q, Shao C, Xie J. Validation of phylogenetic informative Y-InDels in Y-chromosomal haplogroup O-M175. Front Genet 2023; 14:1182028. [PMID: 37205119 PMCID: PMC10185902 DOI: 10.3389/fgene.2023.1182028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 04/17/2023] [Indexed: 05/21/2023] Open
Abstract
The Y-chromosomal haplogroup tree, which consists of a group of Y-chromosomal loci with phylogenetic information, has been widely applied in anthropology, archaeology and population genetics. With the continuous updating of the phylogenetic structure, Y-chromosomal haplogroup tree provides more information for recalling the biogeographical origin of Y chromosomes. Generally, Y-chromosomal insertion-deletion polymorphisms (Y-InDels) are genetically stable as Y-chromosomal single nucleotide polymorphisms (Y-SNPs), and therefore carry mutations that can accumulate over generations. In this study, potential phylogenetic informative Y-InDels were filtered out in haplogroup O-M175, which is dominant in East Asia, based on population data retrieved from the 1000 Genomes Project. A group of 22 phylogenetic informative Y-InDels were identified and then assigned to their corresponding subclades of haplogroup O-M175, which provided a supplement for the update and application of Y-chromosomal markers. Especially, four Y-InDels were introduced to define subclades determined using a single Y-SNP.
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16
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Song M, Wang X, Zhao C, Qian X, Lang M, Hou Y, Song F. Inference of population structure and admixture proportion from Y chromosomal data of Chinese population. Electrophoresis 2022; 43:2351-2362. [PMID: 35973689 DOI: 10.1002/elps.202200041] [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: 02/18/2022] [Revised: 07/14/2022] [Accepted: 08/11/2022] [Indexed: 12/14/2022]
Abstract
In the past two decades, Y chromosome data has been generated for human population genetic studies. These Y chromosome datasets were produced with various testing methods and markers, thus difficult to combine them for a comprehensive analysis. In this study, we combine four human Y chromosomal datasets of Han, Tibetan, Hui, and Li ethnic groups. The dataset contains 27 microsatellites and 137 single nucleotide polymorphisms these populations share in common. We assembled a single dataset containing 2439 individuals from 25 nationwide populations in China. A systematic analysis of genetic distance and clustering was performed. To determine the gene flow of the studied population with worldwide populations, we modeled the ancestry informative markers. The reference panel was regarded as a mixture of South Asian (SAS), East Asian (EAS), European (EUR), African (AFR), and American (AMR) populations from 1000 Genomes data of Y chromosome using nonlinear data-fitting. We then calculated the admixture proportion of these four studied populations with 26 worldwide populations. The results showed that the Han and Hui have great genetic affinity, and Hui is the most admixed ethnic group, with 61.53% EAS, 34.65% SAS, 1.91% AFR, 1.56% AMR, and 0.04% EUR ancestry component (the AMR is highly admixed and thus should be ignored). All the other three ethnic groups contained more than 97% EAS ancestry component. The Li is the least admixed population in this study. The combined dataset in this study is the largest of this kind reported to date and proposes reference population data for use in future paternal genetic studies and forensic genealogical identification.
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Affiliation(s)
- Mengyuan Song
- Department of Laboratory Medicine, West China Hospital, Sichuan University; Med+Molecular Diagnostics Institute of West China Hospital/West China School of Medicine, Chengdu, P. R. China.,Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Xindi Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Chenxi Zhao
- College of Computer Science, Sichuan University, Chengdu, P. R. China
| | - Xiaoqin Qian
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Min Lang
- Law School, Sichuan University, Chengdu, P. R. China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Feng Song
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China
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17
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Liu J, Jiang L, Zhao M, Du W, Wen Y, Li S, Zhang S, Fang F, Shen J, He G, Wang M, Dai H, Hou Y, Wang Z. Development and validation of a custom panel including 256 Y-SNPs for Chinese Y-chromosomal haplogroups dissection. Forensic Sci Int Genet 2022; 61:102786. [DOI: 10.1016/j.fsigen.2022.102786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 08/25/2022] [Accepted: 10/04/2022] [Indexed: 11/04/2022]
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18
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Hou X, Zhang X, Li X, Huang T, Li W, Zhang H, Huang H, Wen Y. Genomic insights into the genetic structure and population history of Mongolians in Liaoning Province. Front Genet 2022; 13:947758. [PMID: 36313460 PMCID: PMC9596793 DOI: 10.3389/fgene.2022.947758] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 09/26/2022] [Indexed: 11/29/2022] Open
Abstract
The Mongolian population exceeds six million and is the largest population among the Mongolic speakers in China. However, the genetic structure and admixture history of the Mongolians are still unclear due to the limited number of samples and lower coverage of single-nucleotide polymorphism (SNP). In this study, we genotyped genome-wide data of over 700,000 SNPs in 38 Mongolian individuals from Fuxin in Liaoning Province to explore the genetic structure and population history based on typical and advanced population genetic analysis methods [principal component analysis (PCA), admixture, FST, f3-statistics, f4-statistics, qpAdm/qpWave, qpGraph, ALDER, and TreeMix]. We found that Fuxin Mongolians had a close genetic relationship with Han people, northern Mongolians, other Mongolic speakers, and Tungusic speakers in East Asia. Also, we found that Neolithic millet farmers in the Yellow River Basin and West Liao River Basin and Neolithic hunter–gatherers in the Mongolian Plateau and Amur River Basin were the dominant ancestral sources, and there were additional gene flows related to Eurasian Steppe pastoralists and Neolithic Iranian farmers in the gene pool of Fuxin Mongolians. These results shed light on dynamic demographic history, complex population admixture, and multiple sources of genetic diversity in Fuxin Mongolians.
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19
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Fan GY. Assessing the factors influencing the performance of machine learning for classifying haplogroups from Y-STR haplotypes. Forensic Sci Int 2022; 340:111466. [PMID: 36150277 DOI: 10.1016/j.forsciint.2022.111466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/01/2022] [Accepted: 09/12/2022] [Indexed: 11/29/2022]
Abstract
Two distinct genetic markers, single nucleotide polymorphisms (Y-SNPs) and short tandem repeats (Y-STRs), exist simultaneously in the non-recombining portion of the Y chromosome. Because of their different rates of mutation, Y-STRs and Y-SNPs play distinct roles in forensic and evolutionary genetics. Current approaches to infer haplogroup status rely on genotyping lots of Y-SNP loci. Given the relationship between haplotype and haplogroup of a Y chromosome, a cost-effective strategy of Y-STRs typing had an advantage in haplogroup prediction. Many machine learning algorithms have sprung up for assigning a Y-STR haplotype to a haplogroup. However, a series of issues must be solved before the using of machine learning method in practice. Thus, the k-nearest neighbor (kNN) classifier was built respectively based on different situations in this study. We assessed different factors which may influence the performance of the kNN prediction model for classifying haplogroups. The training set was based on a diverse ground-truth data set comprising Y-STR haplotypes and corresponding Y-SNP haplogroups. Our results showed that combining different levels of haplogroups into the observations or transracial prediction was impractical. Moreover, using more slow mutation Y-STR loci in the category is good for promoting classification accuracy. The preconditions for an effective and accurate haplogroup assignment by the kNN classifier were revealed.
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Affiliation(s)
- Guang-Yao Fan
- Forensic Center, College of Medicine, Shaoxing University, Shaoxing 312000, China.
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Song M, Wang Z, Lyu Q, Ying J, Wu Q, Jiang L, Wang F, Zhou Y, Song F, Luo H, Hou Y, Song X, Ying B. Paternal genetic structure of the Qiang ethnic group in China revealed by high-resolution Y-chromosome STRs and SNPs. Forensic Sci Int Genet 2022; 61:102774. [PMID: 36156385 DOI: 10.1016/j.fsigen.2022.102774] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 08/02/2022] [Accepted: 09/11/2022] [Indexed: 11/18/2022]
Abstract
The Qiang population mainly lived in Beichuan Qiang Autonomous County of Sichuan Province. It is one of the nomads in China, distributed along the Minjiang River. The Qiang population was assumed to have great affinity with the Han, the largest ethnic group in China, when it refers to the genetic origin. Whereas, it is deeply understudied, especially from the Y chromosome. Here in this study, we used validated high-resolution Y-chromosome single nucleotide polymorphisms (Y-SNPs) and short tandem repeats (Y-STRs) panels to study the Qiang ethnic group to unravel their paternal genetic, forensic and phylogenetic characteristics. A total of 422 male samples of the Qiang ethnic group were genotyped by 233 Y-SNPs and 29 Y-STRs. Haplogroup O-M175 (N = 312) was the most predominant haplogroup in the Qiang ethnic group, followed by D-M174 (N = 32) and C-M130 (N = 32), N-M231 (N = 27), and Q-M242 (N = 15). After further subdivision, O2a-M324 (N = 213) accounted for the majority of haplogroup O. Haplogroup C2b-Z1338 (N = 29), D1a-CTS11577 (N = 30). O2a2b1a1a1-F42 (N = 48), O2a1b1a1a1a-F11 (N = 35), and O2a2b1a1-M117 (N = 21) represented other large terminal haplogroups. The results unveiled that Qiang ethnic group was a population with a high percentage of haplogroup O2a2b1a1a1-F42 (48/422) and O2a1b1a1a1a-F11 (35/422), and O2a2b1a1-M117 (21/422), which has never been reported. Its haplogroup distribution pattern was different from any of the Han populations, implying that the Qiang ethnic group had its unique genetic pattern. Mismatch analysis indicated that the biggest mismatch number in haplogroup O2a2b1a1a1-F42 was 21, while that of haplogroup O2a1b1a1a1a-F11 was 20. The haplotype diversity of the Qiang ethnic group equaled 0.999788, with 392 haplotypes observed, of which 367 haplotypes were unique. The haplogroup diversity of the Qiang ethnic group reached 0.9767, and 53 terminal haplogroups were observed (The haplogroup diversity of the Qiang ethnic group was the highest among Qiang and all Han subgroups, indicating the larger genetic diversity of the Qiang ethnic group.). Haplogroup O2a2b1a1a1-F42 was the most predominant haplogroup, including 11.37 % of the Qiang individuals. Median-joining trees showed gene flow between the Qiang and Han individuals. Our results indicated that 1) the highest genetic diversity was observed in the Qiang ethnic group compared to any of the former studied Chinese population, suggesting that the Qiang might be an older paternal branch; 2) the haplogroup D-M174 individuals of Qiang, Tibetans and Japanese distributed in three different subclades, which was unable to identify through low-resolution Y-SNP panel; and 3) the Qiang had lower proportion of haplogroup D compared to Yi and Tibetan ethnic groups, showing that the Qiang had less genetic communication with them than with Han Chinese.
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Affiliation(s)
- Mengyuan Song
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Zefei Wang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China
| | - Qiang Lyu
- Department of Clinical Laboratory, People's Hospital of Beichuan Qiang Autonomous County, Beichuan 622750, Sichuan, China
| | - Jun Ying
- Department of Clinical Laboratory, Santai People's Hospital, Santai 621100, Sichuan, China
| | - Qian Wu
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei, China
| | - Lanrui Jiang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China
| | - Fei Wang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China
| | - Yuxiang Zhou
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China
| | - Feng Song
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China
| | - Haibo Luo
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China
| | - Yiping Hou
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China.
| | - Xingbo Song
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China.
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China.
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Otagiri T, Sato N, Asamura H, Parvanova E, Kayser M, Ralf A. RMplex reveals population differences in RM Y-STR mutation rates and provides improved father-son differentiation in Japanese. Forensic Sci Int Genet 2022; 61:102766. [PMID: 36007266 DOI: 10.1016/j.fsigen.2022.102766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 08/15/2022] [Indexed: 11/29/2022]
Abstract
Rapidly mutating Y chromosomal short tandem repeat markers (RM Y-STRs) -characterized by at least one mutation per 100 generations- are suitable for differentiating both related and unrelated males. The recently introduced multiplex method RMplex allows for the efficient analysis of 30 Y-STRs with increased mutation rates, including all 26 currently known RM Y-STRs. While currently available RM Y-STR mutation rates were established mostly from European individuals, here we applied RMplex to DNA samples of 178 genetically confirmed father-son pairs from East Asia. For several Y-STRs, we found significantly higher mutation rates in Japanese compared to previous estimates. The consequent father-son differentiation rate based on RMplex was significantly higher (52%) in Japanese than previously reported for Europeans (42%), and much higher than with Yfiler Plus in both sample sets (14% and 13%, respectively). Further analysis suggests that the higher mutation and relative differentiation rates in Japanese can in part be explained by on average longer Y-STR alleles relative to Europeans. Moreover, we show that the most striking difference, which was found in DYS712, could be linked to a Y-SNP haplogroup (O1b2-P49) that is common in Japanese and rare in other populations. We encourage the forensic Y-STR community to generate more RMplex data from more population samples of sufficiently large sample size in combination with Y-SNP data to further investigate population effects on mutation and relative differentiation rates. Until more RMplex data from more populations become available, caution shall be placed when applying RM Y-STR mutation rate estimates established in one population, such as Europeans, to forensic casework involving male suspects of paternal origin from other populations, such as non-Europeans.
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Affiliation(s)
- Tomomi Otagiri
- Department of Legal Medicine, Shinshu University School of Medicine, Matsumoto, Nagano, Japan
| | - Noriko Sato
- Department of Legal Medicine, Shinshu University School of Medicine, Matsumoto, Nagano, Japan
| | - Hideki Asamura
- Department of Legal Medicine, Shinshu University School of Medicine, Matsumoto, Nagano, Japan
| | - Evelina Parvanova
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Arwin Ralf
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.
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Forensic Analysis and Genetic Structure Construction of Chinese Chongming Island Han Based on Y Chromosome STRs and SNPs. Genes (Basel) 2022; 13:genes13081363. [PMID: 36011274 PMCID: PMC9407086 DOI: 10.3390/genes13081363] [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] [Received: 04/17/2022] [Revised: 07/26/2022] [Accepted: 07/27/2022] [Indexed: 02/01/2023] Open
Abstract
Y-chromosome short tandem repeat (Y-STR) and Y-chromosome single nucleotide polymorphism (Y-SNP) are genetic markers on the male Y chromosome for individual identification, forensic applications, and paternal genetic history analysis. In this study we successfully genotyped 38 Y-STR loci and 24 Y-SNP loci of Pudong Han (n = 689) and Chongming Han (n = 530) in Shanghai. The haplotype diversity of the Y filer platinum genotyping system was the highest in the Han population in the Pudong area of Shanghai (0.99996) and Chongming Island (0.99997). The proportion of unique haplotypes was 97.10% (Pudong) and 98.49% (Chongming), respectively. The multidimensional scaling analysis and phylogenetic analysis were performed according to the genetic distance Rst, which was calculated based on the Y-STR gene frequency data. Moreover, we made a comparison on the frequency distribution analysis and principal component analysis of haplogroups in both populations. As a result, Shanghai Pudong Han, Chongming Island Han, and Jiangsu Han were determined to have a strong genetic affinity. The haplogroup distribution characteristics of the Pudong Han and Chongming Han populations were similar to those of the southern Han population. The results of haplotype network analysis showed that Jiangsu Wujiang Han and Jiangsu Changshu Han had more paternal genetic contributions to the formation of Shanghai Pudong Han and Chongming Island Han. Through the joint analysis of SNPs and STRs, this study deeply analyzed the paternal genetic structure of the Pudong Han and Chongming Han populations. The addition of Y-SNP haplogroups to forensic applications can provide information for pedigree investigation.
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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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Xiong J, Tao Y, Ben M, Yang Y, Du P, Allen E, Wang H, Xu Y, Yu Y, Meng H, Bao H, Zhou B, Chen G, Li H, Wen S. Uniparental Genetic Analyses Reveal Multi-Ethnic Background of Dunhuang Foyemiaowan Population (220–907 CE) With Typical Han Chinese Archaological Culture. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.901295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The relationship between archeological culture and ethnicity is invariably complex. This is especially the case for periods of national division and rapid inter-ethnic exchange, such as China’s Sixteen Kingdoms (304–439 CE) and Northern and Southern Dynasties (420–589 CE). Going by tomb shape and grave goods, the Foyemiaowan cemetery at Dunhuang exhibits a typical third–tenth century Han style. Despite this, the ethnic makeup of the Foyemiaowan population has remained unclear. We therefore analyzed 485 Y-chromosomal SNPs and entire mitochondrial genomes of 34 Foyemiaowan samples. Our study yielded the following discoveries: (1) principal component analysis revealed that the Foyemiaowan population was closely clustered with Tibeto-Burman populations on the paternal side and close to Mongolic-speaking populations on the maternal side; (2) lineage comparisons at the individual level showed that the Foyemiaowan population consisted of primarily Tibeto-Burman and Han Chinese related lineages (Oα-M117, 25%;Oβ-F46, 18.75%), partially Altaic speaking North Eurasian lineages (N-F1206, 18.75%) and a slight admixture of southern East Asian lineages (O1b1a2-Page59, 6.25%; O1b1a1-PK4, 3.13%). Similarly, the maternal gene pool of Foyemiaowan contained northern East Asian (A, 4.17%; CZ, 16.67%; D, 20.83%; G, 4.17%; M9, 4.17%), southern East Asian (B, 12.51%; F, 20.83%) and western Eurasian (H, 4.17%; J, 4.17%) related lineages; (3) we discovered a relatively high genetic diversity among the Foyemiaowan population (0.891) in our ancient reference populations, indicating a complex history of population admixture. Archeological findings, stable isotope analysis and historical documents further corroborated our results. Although in this period China’s central government had relinquished control of the Hexi Corridor and regional non-Han regimes became the dominant regional power, Foyemiaowan’s inhabitants remained strongly influenced by Han culture.
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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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Improving DNA Data Capacity: Forensic Parameters and Genetic Structure Analysis of Jinjiang Han Population with the Microreader™ Y Prime Plus ID System. Curr Med Sci 2022; 42:462-466. [PMID: 35403953 DOI: 10.1007/s11596-022-2570-z] [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: 04/12/2021] [Accepted: 11/01/2021] [Indexed: 12/14/2022]
Abstract
OBJECTIVE Population genetic analysis based on genetic markers harbors valuable forensic applications. In this regard, it is informative and imperative to explore Han groups as they are the largest population of China. In particular, there is a largely underrepresented amount of information from recent decades regarding the southeast costal Han Chinese. Therefore, the aim of this study is to investigate the available genetic characteristics of the Han population living in the Jinjiang, Fujian Province, Southeastern China. METHODS We sampled 858 saliva samples and used the commercially available Microreader™ Y Prime Plus ID System to identify population data of Y-short tandem repeat (STR) loci of this region. RESULTS A total of 822 different haplotypes were observed. The overall haplotype diversity, discriminatory power and haplotype match probability were 0.9999, 0.9999 and 0.0012, respectively. CONCLUSION Our results showed that the Jinjiang Han population was closely genetically related to Han groups of China. Overall, we identified a set of 37 Y-STRs that are highly polymorphic, and that can provide meaningful information in forensic practice and human genetic research.
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Zhou Y, Jin X, Wu B, Zhu B. Development and Performance Evaluation of a Novel Ancestry Informative DIP Panel for Continental Origin Inference. Front Genet 2022; 12:801275. [PMID: 35251118 PMCID: PMC8891605 DOI: 10.3389/fgene.2021.801275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/01/2021] [Indexed: 11/13/2022] Open
Abstract
Ancestry informative markers (AIMs) are useful to infer individual biogeographical ancestry and to estimate admixture proportions of admixed populations or individuals. Although a growing number of AIM panels for forensic ancestry origin analyses were developed, they may not efficiently infer the ancestry origins of most populations in China. In this study, a set of 52 ancestry informative deletion/insertion polymorphisms (AIDIPs) were selected with the aim of effectively differentiate continental and partial Chinese populations. All of the selected markers were successfully incorporated into a single multiplex PCR panel, which could be conveniently and efficiently detected on capillary electrophoresis platforms. Genetic distributions of the same 50 AIDIPs in different continental populations revealed that most loci showed high genetic differentiations between East Asian populations and other continental populations. Population genetic analyses of different continental populations indicated that these 50 AIDIPs could clearly discriminate East Asian, European, and African populations. In addition, the 52 AIDIPs also exhibited relatively high cumulative discrimination power in the Eastern Han population, which could be used as a supplementary tool for forensic investigation. Furthermore, the Eastern Han population showed close genetic relationships with East Asian populations and high ancestral components from East Asian populations. In the future, we need to investigate genetic distributions of these 52 AIDIPs in Chinese Han populations in different regions and other ethnic groups, and further evaluate the power of these loci to differentiate different Chinese populations.
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Affiliation(s)
- Yongsong Zhou
- Shenzhen Stomatology Hospital (Pingshan), Southern Medical University, Shenzhen, China
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Xiaoye Jin
- School of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Buling Wu
- Shenzhen Stomatology Hospital (Pingshan), Southern Medical University, Shenzhen, China
- *Correspondence: Buling Wu, ; Bofeng Zhu,
| | - Bofeng Zhu
- Shenzhen Stomatology Hospital (Pingshan), Southern Medical University, Shenzhen, China
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
- 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
- *Correspondence: Buling Wu, ; Bofeng Zhu,
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28
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Moon MH, Hong SR, Shin KJ. Sequence Variations of 31 Υ-Chromosomal Short Tandem Repeats Analyzed by Massively Parallel Sequencing in Three U.S. Population Groups and Korean Population. J Korean Med Sci 2022; 37:e40. [PMID: 35166077 PMCID: PMC8845103 DOI: 10.3346/jkms.2022.37.e40] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 12/19/2021] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Rapidly mutating (RM) Y-chromosomal short tandem repeats (Y-STRs) have been demonstrated to increase the possibility of distinguishing between male relatives due to a higher mutation rate than conventional Y-STRs. Massively parallel sequencing (MPS) can be useful for forensic DNA typing as it allows the detection of sequence variants of many forensic markers. Here, we present sequence variations of 31 Y-STRs including nine RM Y-STRs (DYF387S1, DYF399S1, DYF404S1, DYS449, DYS518, DYS570, DYS576, DYS612, and DYS627), their frequencies, distribution, and the gain in the number of alleles using MPS. METHODS We constructed a multiplex MPS assay capable of simultaneously amplifying 32 Y-chromosomal markers, producing amplicons ranging from 85-274 bp. Barcoded libraries from 220 unrelated males from four populations-African Americans, Caucasians, Hispanics, and Koreans-were generated via two-step polymerase chain reaction and sequenced on a MiSeq system. Genotype concordance between the capillary electrophoresis (CE) and MPS method and sequence variation of Y-STRs were investigated. RESULTS In total, 195 alleles were increased by MPS compared to CE-based alleles (261 to 456). The DYS518 marker showed the largest increase due to repeat region variation (a 3.69-fold increase). The highest increase in the number of alleles due to single nucleotide polymorphisms in the flanking region was found in DYF399S1. RM Y-STRs had more diverse sequences than conventional Y-STRs. Furthermore, null alleles were observed in DYS576 due to primer-binding site mutation, and allele drop-outs in DYS449 resulted from low marker coverage of less than the threshold. CONCLUSION The results suggest that the expanded and discriminative MPS assay could provide more genetic information for Y-STRs, especially for RM Y-STRs, and could advance male individualization. Compiling sequence-based Y-STR data for worldwide populations would facilitate the application of MPS in the field of forensic genetics and could be applicable in solving male-related forensic cases.
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Affiliation(s)
- Mi Hyeon Moon
- Department of Forensic Medicine, Yonsei University College of Medicine, Seoul, Korea
- Graduate School of Medical Science and Brain Korea 21 Project, Yonsei University, Seoul, Korea
| | - Sae Rom Hong
- Department of Forensic Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Kyoung-Jin Shin
- Department of Forensic Medicine, Yonsei University College of Medicine, Seoul, Korea
- Graduate School of Medical Science and Brain Korea 21 Project, Yonsei University, Seoul, Korea.
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29
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Wang F, Song F, Song M, Luo H, Hou Y. Genetic structure and paternal admixture of the modern Chinese Zhuang population based on 37 Y-STRs and 233 Y-SNPs. Forensic Sci Int Genet 2022; 58:102681. [DOI: 10.1016/j.fsigen.2022.102681] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 01/05/2022] [Accepted: 02/20/2022] [Indexed: 11/25/2022]
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30
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Fan GY, Song DL, Jin HY, Zheng XK. Gene flow and phylogenetic analyses of paternal lineages in the Yi-Luo valley using Y-STR genetic markers. Ann Hum Biol 2022; 48:627-634. [DOI: 10.1080/03014460.2021.2017480] [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]
Affiliation(s)
- Guang-Yao Fan
- Forensic Center, College of Medicine, Shaoxing University, Shaoxing, China
| | - Dan-Lu Song
- Ningbo Health Gene Technologies Co. Ltd., Ningbo, China
| | - Hai-Ying Jin
- Ningbo Health Gene Technologies Co. Ltd., Ningbo, China
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Improving the regional Y-STR haplotype resolution utilizing haplogroup-determining Y-SNPs and the application of machine learning in Y-SNP haplogroup prediction in a forensic Y-STR database: A pilot study on male Chinese Yunnan Zhaoyang Han population. Forensic Sci Int Genet 2021; 57:102659. [PMID: 35007855 DOI: 10.1016/j.fsigen.2021.102659] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 12/14/2021] [Accepted: 12/27/2021] [Indexed: 11/23/2022]
Abstract
Improving the resolution of the current widely used Y-chromosomal short tandem repeat (Y-STR) dataset is of great importance for forensic investigators, and the current approach is limited, except for the addition of more Y-STR loci. In this research, a regional Y-DNA database was investigated to improve the Y-STR haplotype resolution utilizing a Y-SNP Pedigree Tagging System that includes 24 Y-chromosomal single nucleotide polymorphism (Y-SNP) loci. This pilot study was conducted in the Chinese Yunnan Zhaoyang Han population, and 3473 unrelated male individuals were enrolled. Based on data on the male haplogroups under different panels, the matched or near-matching (NM) Y-STR haplotype pairs from different haplogroups indicated the critical roles of haplogroups in improving the regional Y-STR haplotype resolution. A classic median-joining network analysis was performed using Y-STR or Y-STR/Y-SNP data to reconstruct population substructures, which revealed the ability of Y-SNPs to correct misclassifications from Y-STRs. Additionally, population substructures were reconstructed using multiple unsupervised or supervised dimensionality reduction methods, which indicated the potential of Y-STR haplotypes in predicting Y-SNP haplogroups. Haplogroup prediction models were built based on nine publicly accessible machine-learning (ML) approaches. The results showed that the best prediction accuracy score could reach 99.71% for major haplogroups and 98.54% for detailed haplogroups. Potential influences on prediction accuracy were assessed by adjusting the Y-STR locus numbers, selecting Y-STR loci with various mutabilities, and performing data processing. ML-based predictors generally presented a better prediction accuracy than two available predictors (Nevgen and EA-YPredictor). Three tree models were developed based on the Yfiler Plus panel with unprocessed input data, which showed their strong generalization ability in classifying various Chinese Han subgroups (validation dataset). In conclusion, this study revealed the significance and application prospects of Y-SNP haplogroups in improving regional Y-STR databases. Y-SNP haplogroups can be used to discriminate NM Y-STR haplotype pairs, and it is important for forensic Y-STR databases to develop haplogroup prediction tools to improve the accuracy of biogeographic ancestry inferences.
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何 传锦, 张 荣芳, 邹 磊, 郑 冰洁, 宋 丹璐, 黄 景峰, 兰 江维. [Not Available]. FA YI XUE ZA ZHI 2021; 37:699-703. [PMID: 35191237 DOI: 10.12116/j.issn.1004-5619.2020.500901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
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Wang M, Yuan D, Zou X, Wang Z, Yeh HY, Liu J, Wei LH, Wang CC, Zhu B, Liu C, He G. Fine-Scale Genetic Structure and Natural Selection Signatures of Southwestern Hans Inferred From Patterns of Genome-Wide Allele, Haplotype, and Haplogroup Lineages. Front Genet 2021; 12:727821. [PMID: 34504517 PMCID: PMC8421688 DOI: 10.3389/fgene.2021.727821] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 07/29/2021] [Indexed: 12/15/2022] Open
Abstract
The evolutionary and admixture history of Han Chinese have been widely discussed via traditional autosomal and uniparental genetic markers [e.g., short tandem repeats, low-density single nucleotide polymorphisms). However, their fine-scale genetic landscapes (admixture scenarios and natural selection signatures) based on the high-density allele/haplotype sharing patterns have not been deeply characterized. Here, we collected and generated genome-wide data of 50 Han Chinese individuals from four populations in Guizhou Province, one of the most ethnolinguistically diverse regions, and merged it with over 3,000 publicly available modern and ancient Eurasians to describe the genetic origin and population admixture history of Guizhou Hans and their neighbors. PCA and ADMIXTURE results showed that the studied four populations were homogeneous and grouped closely to central East Asians. Genetic homogeneity within Guizhou populations was further confirmed via the observed strong genetic affinity with inland Hmong-Mien people through the observed genetic clade in Fst and outgroup f3/f4-statistics. qpGraph-based phylogenies and f4-based demographic models illuminated that Guizhou Hans were well fitted via the admixture of ancient Yellow River Millet farmers related to Lajia people and southern Yangtze River farmers related to Hanben people. Further ChromoPainter-based chromosome painting profiles and GLOBETROTTER-based admixture signatures confirmed the two best source matches for southwestern Hans, respectively, from northern Shaanxi Hans and southern indigenes with variable mixture proportions in the historical period. Further three-way admixture models revealed larger genetic contributions from coastal southern East Asians into Guizhou Hans compared with the proposed inland ancient source from mainland Southeast Asia. We also identified candidate loci (e.g., MTUS2, NOTCH4, EDAR, ADH1B, and ABCG2) with strong natural selection signatures in Guizhou Hans via iHS, nSL, and ihh, which were associated with the susceptibility of the multiple complex diseases, morphology formation, alcohol and lipid metabolism. Generally, we provided a case and ideal strategy to reconstruct the detailed demographic evolutionary history of Guizhou Hans, which provided new insights into the fine-scale genomic formation of one ethnolinguistically specific targeted population from the comprehensive perspectives of the shared unlinked alleles, linked haplotypes, and paternal and maternal lineages.
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Affiliation(s)
- Mengge Wang
- Guangzhou Forensic Science Institute, Guangzhou, China.,Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Didi Yuan
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Xing Zou
- College of Basic Medicine, Chongqing University, Chongqing, China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, China
| | - Hui-Yuan Yeh
- School of Humanities, Nanyang Technological University, Singapore, Singapore
| | - Jing Liu
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, China
| | - Lan-Hai Wei
- State Key Laboratory of Marine Environmental Science, State Key Laboratory of Cellular Stress Biology, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, Xiamen, China
| | - Chuan-Chao Wang
- State Key Laboratory of Marine Environmental Science, State Key Laboratory of Cellular Stress Biology, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, Xiamen, China
| | - Bofeng Zhu
- Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, China.,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
| | - Chao Liu
- Guangzhou Forensic Science Institute, Guangzhou, China.,Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Guanglin He
- School of Humanities, Nanyang Technological University, Singapore, Singapore.,State Key Laboratory of Marine Environmental Science, State Key Laboratory of Cellular Stress Biology, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, Xiamen, China
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Li L, Yao L, Gong H, Luo L, Liang H, Zhang J, Wang Y, He G, Jia F, Chen P. Genetic characterisation for Yan'an Han population in Northern Shaanxi Province, China, via 38Y-STRs using Yfiler™ Platinum. Ann Hum Biol 2021; 48:327-334. [PMID: 34308740 DOI: 10.1080/03014460.2021.1951350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
BACKGROUND Haplotype/allele frequency data of Y-chromosomal STR loci in ethnically diverse populations are essential for forensics, anthropology and genealogy. However, genetic structure and forensic characterisation of the Chinese Han population residing in Yan'an, in the Northern Shaanxi Province, remain unclear. AIM To assess forensic efficiency for 38 Y-Chromosomal STR loci in Yan'an Han population and reveal the population genetic relationships between Yan'an Han and other populations at a nationwide and worldwide level. SUBJECTS AND METHODS 719 healthy unrelated males were genotyped using the Yfiler™ Platinum system. Haplotype/allele frequencies and forensic parameters were calculated. Multi-dimensional scaling plots (MDS) and neighbor-joining (N-J) tree were used to explore the population structure based on the pairwise gene distances (Rst). RESULTS A total of 707 haplotypes were identified, among which 697 unique haplotypes were observed (98.59%). The overall haplotype diversity (HD) and discrimination capacity (DC) were 0.9999 and 0.9833, respectively. Comprehensive population comparisons showed Yan'an Han is genetically closer to linguistically similar populations in China, and more related to East Asian populations around the world. CONCLUSION The present results give a unique insight into the Yan'an Han population via the set of 38 Y-STRs, which can be used for forensic practice and human genetics research.
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Affiliation(s)
- Luyao Li
- Department of Pathology, The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, China
| | - Lilan Yao
- Key Laboratory of Cell Engineering in Guizhou Province, Affiliated Hospital of Zunyi Medical University, Guizhou, China.,Center of Forensic Expertise, Affiliated hospital of Zunyi Medical University, Guizhou, China
| | - Huilin Gong
- Department of Pathology, The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, China
| | - Li Luo
- Key Laboratory of Cell Engineering in Guizhou Province, Affiliated Hospital of Zunyi Medical University, Guizhou, China.,Center of Forensic Expertise, Affiliated hospital of Zunyi Medical University, Guizhou, China
| | - Hau Liang
- Department of Pathology, The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, China
| | - Jiaojiao Zhang
- Department of Pathology, The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, China
| | - Yuanyuan Wang
- Department of Pathology, The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, China
| | - Guanglin He
- Institute of Forensic medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Sichuan, China
| | - Fuquan Jia
- Department of Forensic Medicine, Inner Mongolia Medical University, Inner Mongolia Autonomous Region, Hohhot, China
| | - Pengyu Chen
- Key Laboratory of Cell Engineering in Guizhou Province, Affiliated Hospital of Zunyi Medical University, Guizhou, China.,Center of Forensic Expertise, Affiliated hospital of Zunyi Medical University, Guizhou, China
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Genetic insights into the paternal admixture history of Chinese Mongolians via high-resolution customized Y-SNP SNaPshot panels. Forensic Sci Int Genet 2021; 54:102565. [PMID: 34332322 DOI: 10.1016/j.fsigen.2021.102565] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 07/10/2021] [Accepted: 07/15/2021] [Indexed: 12/12/2022]
Abstract
The Mongolian people, one of the Mongolic-speaking populations, are native to the Mongolian Plateau in North China and southern Siberia. Many ancient DNA studies recently reported extensive population transformations during the Paleolithic to historic periods in this region, while little is known about the paternal genetic legacy of modern geographically different Mongolians. Here, we genotyped 215 Y-chromosomal single nucleotide polymorphisms (Y-SNPs) and 37 Y-chromosomal short tandem repeats (Y-STRs) among 679 Mongolian individuals from Hohhot, Hulunbuir, and Ordos in North China using the AGCU Y37 kit and our developed eight Y-SNP SNaPshot panels (including two panels first reported herein). The C-M130 Y-SNP SNaPshot panel defines 28 subhaplogroups, and the N/O/Q complementary Y-SNP SNaPshot panel defines 30 subhaplogroups of N1b-F2930, N1a1a1a1a3-B197, Q-M242, and O2a2b1a1a1a4a-CTS4658, which improved the resolution our developed Y-SNP SNaPshot panel set and could be applied for dissecting the finer-scale paternal lineages of Mongolic speakers. We found a strong association between Mongolian-prevailing haplogroups and some observed microvariants among the newly generated Y-STR haplotype data, suggesting the possibility of haplogroup prediction based on the distribution of Y-STR haplotypes. We identified three main ancestral sources of the observed Mongolian-dominant haplogroups, including the local lineage of C2*-M217 and incoming lineages from other regions of southern East Asia (O2*-M122, O1b*-P31, and N1*-CTS3750) and western Eurasia (R1*-M173). We also observed DE-M145, D1*-M174, C1*-F3393, G*-M201, I-M170, J*-M304, L-M20, O1a*-M119, and Q*-M242 at relatively low frequencies (< 5.00%), suggesting a complex admixture history between Mongolians and other incoming Eurasians from surrounding regions. Genetic clustering analyses indicated that the studied Mongolians showed close genetic affinities with other Altaic-speaking populations and Sinitic-speaking Hui people. The Y-SNP haplotype/haplogroup-based genetic legacy not only revealed that the stratification among geographically/linguistically/ethnically different Chinese populations was highly consistent with the geographical division and language classification, but also demonstrated that patrilineal genetic materials could provide fine-scale genetic structures among geographically different Mongolian people, suggesting that our developed high-resolution Y-SNP SNaPshot panels have the potential for forensic pedigree searches and biogeographical ancestry inference.
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Luo L, Yao L, Chai S, Zhang H, Li M, Yu J, Hu X, Li C, Bian Y, Chen P. Forensic characteristics and population construction of two major minorities from southwest China revealed by a novel 37 Y-STR loci system. ROYAL SOCIETY OPEN SCIENCE 2021; 8:210447. [PMID: 34350019 PMCID: PMC8316789 DOI: 10.1098/rsos.210447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 07/06/2021] [Indexed: 06/13/2023]
Abstract
Y-chromosome short tandem repeats (Y-STRs) have become important supplementary evidence in forensic science. Nowadays, the Y-chromosome STR haplotype reference database (YHRD) contains abundant Y-STR haplotype data from all over the world, while haplotype data of Guizhou Miao and Tujia are scarce. Hence, genetic polymorphisms of 37 Y-STRs were investigated in 446 unrelated males (206 Miao males and 246 Tujia males) residing in Guizhou Province. A total of 206 and 242 unique haplotypes with the highest diversity value of 0.9665 and 0.9470 were obtained. The heatmap, multidimensional scaling (MDS), the unweighted pair-group method with arithmetic means (UPGMA) tree and principal component analysis (PCA) based on the genetic distance (Rst) value within our studied populations and other 26 populations indicated that population structures follow the boundary of the continent. Guizhou Miao and Guizhou Tujia populations have intimate relationships with East Asian populations, especially the geographically close, similar history and the same language family populations.
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Affiliation(s)
- Li Luo
- Key Laboratory of Cell Engineering in Guizhou Province, Affiliated Hospital of Zunyi Medical University, Zunyi 563099, Guizhou, People's Republic of China
- School of Forensic Medicine, Zunyi Medical University, Zunyi 563099, Guizhou, People's Republic of China
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Shanghai 200063, People's Republic of China
| | - Lilan Yao
- Key Laboratory of Cell Engineering in Guizhou Province, Affiliated Hospital of Zunyi Medical University, Zunyi 563099, Guizhou, People's Republic of China
- School of Forensic Medicine, Zunyi Medical University, Zunyi 563099, Guizhou, People's Republic of China
| | - Siyu Chai
- Key Laboratory of Cell Engineering in Guizhou Province, Affiliated Hospital of Zunyi Medical University, Zunyi 563099, Guizhou, People's Republic of China
- School of Forensic Medicine, Zunyi Medical University, Zunyi 563099, Guizhou, People's Republic of China
| | - Hao Zhang
- Key Laboratory of Cell Engineering in Guizhou Province, Affiliated Hospital of Zunyi Medical University, Zunyi 563099, Guizhou, People's Republic of China
- School of Forensic Medicine, Zunyi Medical University, Zunyi 563099, Guizhou, People's Republic of China
| | - Min Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Shanghai 200063, People's Republic of China
- Institute of Forensic Medicine, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu 610000, Sichuan, People's Republic of China
| | - Jian Yu
- School of Forensic Medicine, Zunyi Medical University, Zunyi 563099, Guizhou, People's Republic of China
| | - Xijie Hu
- Key Laboratory of Cell Engineering in Guizhou Province, Affiliated Hospital of Zunyi Medical University, Zunyi 563099, Guizhou, People's Republic of China
- School of Forensic Medicine, Zunyi Medical University, Zunyi 563099, Guizhou, People's Republic of China
| | - Chengtao Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Shanghai 200063, People's Republic of China
- Institute of Forensic Medicine, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu 610000, Sichuan, People's Republic of China
| | - Yingnan Bian
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Shanghai 200063, People's Republic of China
| | - Pengyu Chen
- Key Laboratory of Cell Engineering in Guizhou Province, Affiliated Hospital of Zunyi Medical University, Zunyi 563099, Guizhou, People's Republic of China
- School of Forensic Medicine, Zunyi Medical University, Zunyi 563099, Guizhou, People's Republic of China
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Fan H, Xie Q, Li Y, Wang L, Wen SQ, Qiu P. Insights Into Forensic Features and Genetic Structures of Guangdong Maoming Han Based on 27 Y-STRs. Front Genet 2021; 12:690504. [PMID: 34220963 PMCID: PMC8253533 DOI: 10.3389/fgene.2021.690504] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 05/14/2021] [Indexed: 11/13/2022] Open
Abstract
Maoming is located in the southwest region of Guangdong Province and is the cradle of Gaoliang culture, which is the representative branch of Lingnan cultures. Historical records showed that the amalgamations between Gaoliang aborigines and distinct ethnic minorities had some influences on the shaping of Gaoliang culture, especially for the local Tai-kadai language-speaking Baiyue and Han Chinese from Central China. However, there is still no exact genetic evidence for the influences on the genetic pool of Maoming Han, and the genetic relationships between Maoming Han and other Chinese populations are still unclear. Hence, in order to get a better understanding of the paternal genetic structures and characterize the forensic features of 27 Y-chromosomal short tandem repeats (Y-STRs) in Han Chinese from Guangdong Maoming, we firstly applied the AmpFLSTR® Yfiler® Plus PCR Amplification Kit (Thermo Fisher Scientific, Waltham, MA, United States) to genotype the haplotypes in 431 Han males residing in Maoming. A total of 263 different alleles were determined across all 27 Y-STRs with the corresponding allelic frequencies from 0.0004 to 0.7401, and the range of genetic diversity (GD) was 0.4027 (DYS391) to 0.9596 (DYS385a/b). In the first batch of 27 Yfiler data in Maoming Han, 417 distinct haplotypes were discovered, and nine off-ladder alleles were identified at six Y-STRs; in addition, no copy number variant or null allele was detected. The overall haplotype diversity (HD) and discrimination capacity (DC) of 27 Yfiler were 0.9997 and 0.9675, respectively, which demonstrated that the 6-dye and 27-plex system has sufficient system effectiveness for forensic applications in Maoming Han. What is more, the phylogenetic analyses indicated that Maoming Han, which is a Southern Han Chinese population, has a close relationship with Meizhou Kejia, which uncovered that the role of the gene flows from surrounding Han populations in shaping the genetic pool of Maoming Han cannot be ignored. From the perspectives of genetics, linguistics, and geographies, the genetic structures of Han populations correspond to the patterns of the geographical-scale spatial distributions and the relationships of language families. Nevertheless, no exact genetic evidence supports the intimate relationships between Maoming Han and Tai-Kadai language-speaking populations and Han populations of Central Plains in the present study.
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Affiliation(s)
- Haoliang Fan
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
- Institute of Archaeological Science, Fudan University, Shanghai, China
- School of Basic Medicine and Life Science, Hainan Medical University, Haikou, China
| | - Qiqian Xie
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Yanning Li
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
- School of Basic Medicine, Gannan Medical University, Ganzhou, China
| | - Lingxiang Wang
- Institute of Archaeological Science, Fudan University, Shanghai, China
| | - Shao-Qing Wen
- Institute of Archaeological Science, Fudan University, Shanghai, China
| | - Pingming Qiu
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
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Fan H, Zeng Y, Wu W, Liu H, Xu Q, Du W, Hao H, Liu C, Ren W, Wu W, Chen L, Liu C. The Y-STR landscape of coastal southeastern Han: Forensic characteristics, haplotype analyses, mutation rates, and population genetics. Electrophoresis 2021; 42:1578-1593. [PMID: 34018209 DOI: 10.1002/elps.202100037] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 04/16/2021] [Accepted: 05/15/2021] [Indexed: 11/09/2022]
Abstract
The Y-STR landscape of Coastal Southeastern Han (CSEH) living in Chinese southeast areas (including Guangdong, Fujian, and Zhejiang provinces) is still unclear. We investigated 62 Y-STR markers in a reasonably large number of 1021 unrelated males and 1027 DNA-confirmed father-son pairs to broaden the genetic backgrounds of CSEH. In total, 85 null alleles, 121 off-ladder alleles, and 95 copy number variants were observed, and 1012 distinct haplotypes were determined with the overall HD and DC values of 0.999974 and 0.9912. We observed 369 mutations in 76 099 meiotic transfers, and the average estimated Y-STR mutation rate was 4.85 × 10-3 (95% CI, 4.4 × 10-3 -5.4 × 10-3 ). The Spearman correlation analyses indicated that GD values (R2 = 0.6548) and average allele sizes (R2 = 0.5989) have positive correlations with Y-STR mutation rates. Our RM Y-STR set including 8 candidate RM Y-STRs, of which DYS534, DYS630, and DYS713 are new candidates in CSEH, distinguished 18.52% of father-son pairs. This study also clarified the population structures of CSEH which isolated in population-mixed South China relatively. The strategy, SM Y-STRs for familial searching and RM Y-STRs for individual identification regionally, could be applicable based on enough knowledge of the Y-STR mutability of different populations.
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Affiliation(s)
- Haoliang Fan
- School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Ying Zeng
- School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Weiwei Wu
- Zhejiang Key Laboratory of Forensic Science and Technology, Institute of Forensic Science of Zhejiang Provincial Public Security Bureau, Hangzhou, P. R. China
| | - Hong Liu
- Guangzhou Forensic Science Institute, Guangzhou, P. R. China
| | - Quyi Xu
- Guangzhou Forensic Science Institute, Guangzhou, P. R. China
| | - Weian Du
- School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Honglei Hao
- Zhejiang Key Laboratory of Forensic Science and Technology, Institute of Forensic Science of Zhejiang Provincial Public Security Bureau, Hangzhou, P. R. China
| | - Changhui Liu
- Guangzhou Forensic Science Institute, Guangzhou, P. R. China
| | - Wenyan Ren
- Zhejiang Key Laboratory of Forensic Science and Technology, Institute of Forensic Science of Zhejiang Provincial Public Security Bureau, Hangzhou, P. R. China
| | - Weibin Wu
- School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Ling Chen
- School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Chao Liu
- School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China.,Guangzhou Forensic Science Institute, Guangzhou, P. R. China
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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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40
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Wang F, Song F, Song M, Li J, Xie M, Hou Y. Genetic reconstruction and phylogenetic analysis by 193 Y-SNPs and 27 Y-STRs in a Chinese Yi ethnic group. Electrophoresis 2021; 42:1480-1487. [PMID: 33909307 DOI: 10.1002/elps.202100003] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 04/12/2021] [Accepted: 04/20/2021] [Indexed: 01/06/2023]
Abstract
Yi is the seventh-largest ethnic group in China and features mountainous regional characteristics. The Liangshan Yi Autonomous Prefecture is the largest Yi agglomeration with isolated geographical conditions, profoundly impeding genetic communication. Here, we investigated 427 unrelated males of Liangshan from 193 Y-chromosome single nucleotide polymorphisms (Y-SNPs) and 27 Y-chromosome short tandem repeats (Y-STRs) to reveal the genetic structure and paternal phylogeny of the group. The haplogroup diversity reached 0.9169 with 46 different subhaplogroups by 193 Y-SNPs, and the haplotype diversity reached 0.9999 by 27 Y-STR loci. Multidimensional scaling (MDS), N-J tree, and Network were constructed to decipher and visualize the genetic relations between Yi and worldwide groups. Our results revealed: (1) the Network by Y-STRs and Y-SNPs showed the haplogroup D1a1a-M15 in the Liangshan Yi population was a ramification of Tibetan groups' expansion from west to east on the plateau; (2) the haplogroup distribution and the mismatch mutation analysis indicated the haplogroup O2a2b1a1a1a4a2-Z25929 of Liangshan Yi derived from manifold Southeast Asian immigrants; (3) a high-resolution Y-SNPs panel is vital to depict accurate paternal derivations and build an integrated and refining genetic structure of ethnic groups.
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Affiliation(s)
- Fei Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan Province, P. R. China
| | - Feng Song
- Institute of Forensic Medicine, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan Province, P. R. China
| | - Mengyuan Song
- Institute of Forensic Medicine, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan Province, P. R. China
| | - Jienan Li
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan Province, P. R. China
| | - Mingkun Xie
- Department of Obstetrics, Xiangya Hospital, Central South University, Changsha, P. R. China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan Province, P. R. China
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41
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The forensic landscape and the population genetic analyses of Hainan Li based on massively parallel sequencing DNA profiling. Int J Legal Med 2021; 135:1295-1317. [PMID: 33847803 DOI: 10.1007/s00414-021-02590-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 03/26/2021] [Indexed: 12/30/2022]
Abstract
Due to the formation of the Qiongzhou Strait by climate change and marine transition, Hainan island was isolated from the mainland southern China during the Last Glacial Maximum. Hainan island, located at the southernmost part of China and separated from the Leizhou Peninsula by the Qiongzhou Strait, laid on one of the modern human northward migration routes from Southeast Asia to East Asia. The Hlai language-speaking Li minority, the second largest population after Han Chinese in Hainan island, is the direct descendants of the initial migrants in Hainan island and has unique ethnic properties and derived characteristics; however, the forensic-associated studies on Hainan Li population are still insufficient. Hence, 136 Hainan Li individuals were genotyped in this study using the MPS-based ForenSeq™ DNA Signature Prep Kit (DNA Primer Set A, DPMA) to characterize the forensic genetic polymorphism landscape, and DNA profiles were obtained from 152 different molecular genetic markers (27 autosomal STRs, 24 Y-STRs, 7 X-STRs, and 94 iiSNPs). A total of 419 distinct length variants and 586 repeat sequence sub-variants, with 31 novel alleles (at 17 loci), were identified across the 58 STR loci from the DNA profiles of Hainan Li population. We evaluated the forensic characteristics and efficiencies of DPMA, demonstrating that the STRs and iiSNPs in DPMA were highly polymorphic in Hainan Li population and could be employed in forensic applications. In addition, we set up three datasets, which included the genetic data of (i) iiSNPs (27 populations, 2640 individuals), (ii) Y-STRs (42 populations, 8281 individuals), and (iii) Y haplogroups (123 populations, 4837 individuals) along with the population ancestries and language families, to perform population genetic analyses separately from different perspectives. In conclusion, the phylogenetic analyses indicated that Hainan Li, with a southern East Asia origin and Tai-Kadai language-speaking language, is an isolated population relatively. But the genetic pool of Hainan Li influenced by the limited gene flows from other Tai-Kadai populations and Hainan populations. Furthermore, the establishment of isolated population models will be beneficial to clarify the exquisite population structures and develop specific genetic markers for subpopulations in forensic genetic fields.
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42
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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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43
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Liu J, Ming T, Lang M, Liu H, Xie M, Li J, Wang M, Song F, He G, Wang S, Wang Z, Hou Y. Exploitation of a novel slowly mutating Y-STRs set and evaluation of slowly mutating Y-STRs plus Y-SNPs typing strategy in forensic genetics and evolutionary research. Electrophoresis 2021; 42:774-785. [PMID: 33434344 DOI: 10.1002/elps.202000302] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 11/17/2020] [Accepted: 12/12/2020] [Indexed: 11/09/2022]
Abstract
The Y-chromosome short tandem repeats (Y-STRs) loci with different mutation rates existing in the Y chromosome non-recombination region (NRY) allow to be applied in human forensics, genealogical researches, historical investigations and evolutionary studies. Currently, there is a high demand for pedigree search to narrow the scope of crime investigations. However, the commonly used Y-STRs kits generally contain Y-STRs with high mutation rates that could cause individuals from the same pedigree to display different haplotypes. Herein, we put forward a new strategy of Slowly Mutating (SM) Y-STRs plus Y-SNPs typing, which could not only improve the resolution and accuracy of pedigree search, but also be applicable to evolutionary research. First, we developed a nine SM Y-STRs assay by evaluating their mutation rates in 210 pedigrees. Then the gene diversity and efficiency of the SM Y-STRs and 172 Y-SNPs sets were investigated by 2304 unrelated males from 24 populations. Furthermore, network and time estimation analyses were performed to evaluate the new strategy's capability to reconstruct phylogenetic tree and reliability to infer the time to the most recent common ancestor (TMRCA). The nine SM Y-STRs assay even had a higher resolution and a comparable capacity of revealing population genetic differentiation compared to 172 Y-SNPs system. This new strategy could optimize the phylogenetic tree generated by commonly used Y-STR panels and obtain a quite consistent time estimations with the published dating.
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Affiliation(s)
- Jing Liu
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Tianyue Ming
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Min Lang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China.,Law School, Sichuan University, Chengdu, P. R. China
| | - Hai Liu
- The Institute of Forensic Science and Technology, Henan Provincial Public Security Bureau, Zhengzhou, P. R. China
| | - Minkun Xie
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China.,Department of Obstetrics, Xiangya Hospital, Central South University, Changsha, P. R. China
| | - Jienan Li
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China.,Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, P. R. China
| | - Mengge Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Feng Song
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Guanglin He
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China.,Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, P. R. China
| | - Shouyu Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China
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44
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27 Y-chromosomal STR haplotypic structure for the Chinese Han population from Changchun, Northeastern China. Leg Med (Tokyo) 2020; 48:101813. [PMID: 33264698 DOI: 10.1016/j.legalmed.2020.101813] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 10/11/2020] [Accepted: 11/12/2020] [Indexed: 11/23/2022]
Abstract
Y- Changchun is the capital and largest city of Jilin Province in the northeast China. In this study, we genotyped and investigated haplotypes of 27 Y-STR loci in 1037 Changchun Han male individuals using commercially available AmpFlSTR Yfiler® Plus kit. We calculated the Gene diversity (GD) values and haplotype diversity (HD) as important forensic parameters. Furthermore, we observed genetic affinities between Changchun Han with other Northern Han Chinese populations and also Korans in Yanbian in the Multidimensional scaling and phylogenetic tree analysis.
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45
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Li M, Zhang Y, Luo L, Bian Y, Li C. Development and validation of a custom panel including 183 Y-SNPs for Chinese Y-chromosomal haplogroups dissection using a MALDI-TOF MS system. Electrophoresis 2020; 41:2047-2054. [PMID: 32854146 DOI: 10.1002/elps.202000145] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 08/21/2020] [Accepted: 08/25/2020] [Indexed: 11/12/2022]
Abstract
Y-chromosome SNP haplogroups exhibit geographic structuring in many populations around the world. Therefore, Y-chromosome haplogroups have been widely used to infer paternal biogeographical ancestry and high-resolution paternal lineage classification. In the present study, we designed a customized panel containing 183 Y-SNPs based on previous studies and evaluated the genotyping performance and repeatability, concordance, sensitivity, and ability of analysing case-type samples using a MALDI-TOF MS platform. The average call rate for duplicate typing of any one SNP in the panel was 97.0%. In the concordance and accuracy study, the results of haplogroup designation obtained from MALDI-TOF MS platform were fully consistent with those obtained from the next-generation sequencing (NGS) platform. The optimal amount of template DNA in the PCR seemed to be 10 ng. However, if less DNA (≥156.25 pg) was available, it was still possible to obtain meaningful haplogroup information. For the application part, this panel could be applied for the detection of blood, semen, and buccal swabs samples. Particularly, blood stain on FTA card samples could be dissected by direct PCR amplification on the MALDI-TOF MS platform. Besides, 371 unrelated male individuals from four Chinese ethnic groups (Han, Hui, Mongolian, and Kazak) were detected using this panel. Total 78 terminal haplogroups were found and the haplogroup diversity was 0.933576. The results demonstrate that this panel could be an accurate, fast, and cost-effective method for database construction where the amount of sample material is less of a concern and when the cost of the assay is taken into consideration.
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Affiliation(s)
- Min Li
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China.,Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, P.R. China, Ministry of Justice, Shanghai, P. R. China
| | - Yilun Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, P.R. China, Ministry of Justice, Shanghai, P. R. China.,School of Basic Medicine, Inner Mongolia Autonomous Region, Baotou Medical College, Baotou, P. R. China
| | - Li Luo
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, P.R. China, Ministry of Justice, Shanghai, P. R. China.,Department of Forensic Medicine, Zunyi Medical University, Zunyi, Guizhou, P. R. China
| | - Yingnan Bian
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, P.R. China, Ministry of Justice, Shanghai, P. R. China
| | - Chengtao Li
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China.,Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, P.R. China, Ministry of Justice, Shanghai, P. R. China
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46
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Della Rocca C, Cannone F, D'Atanasio E, Bonito M, Anagnostou P, Russo G, Barni F, Alladio E, Destro-Bisol G, Trombetta B, Berti A, Cruciani F. Ethnic fragmentation and degree of urbanization strongly affect the discrimination power of Y-STR haplotypes in central Sahel. Forensic Sci Int Genet 2020; 49:102374. [PMID: 32890883 DOI: 10.1016/j.fsigen.2020.102374] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 07/06/2020] [Accepted: 08/16/2020] [Indexed: 10/23/2022]
Abstract
Y chromosome short tandem repeats (Y-STRs) are commonly used to identify male lineages for investigative and judicial purposes and could represent the only source of male-specific genetic information from unbalanced female-male mixtures. The Yfiler Plus multiplex, which includes twenty conventional and seven rapidly-mutating Y-STRs, represents the most discriminating patrilineal system commercially available to date. Over the past five years, this multiplex has been used to analyze several Eurasian populations, with a reported discrimination capacity (DC) approaching or corresponding to the highest possible value. However, despite the inclusion of rapidly mutating Y-STRs, extensive haplotype sharing was still reported for some African populations due to a number of different factors affecting the effective population size. In the present study, we analyzed 27 Y-STRs included in the Yfiler Plus multiplex and 82 Y-SNPs in central Sahel (northern Cameroon and western Chad), an African region characterized by a strong ethnic fragmentation and linguistic diversity. We evaluated the effects of population sub-structuring on genetic diversity by stratifying a sample composed of 431 males according to their ethnicity (44 different ethnic groups) and urbanization degree (four villages and four towns). Overall, we observed a low discrimination capacity (DC = 0.90), with 71 subjects (16.5 %) sharing 27 Y-STR haplotypes. Haplotype sharing was essentially limited to subjects with the same binary haplogroup, coming from the same location and belonging to the same ethnic group. Haplotype sharing was much higher in rural areas (average DC = 0.83) than urban settlements (average DC = 0.96) with a significant correlation between DC and census size (r = 0.89; p = 0.003). Notably, we found that genetic differentiation between villages from the same country (ΦST = 0.14) largely exceeded that found among countries (ΦST = 0.02). These findings have important implications for the choice of the appropriate reference population database to evaluate the statistical relevance of forensic Y-haplotype matches.
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Affiliation(s)
- Chiara Della Rocca
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Francesco Cannone
- Reparto Carabinieri Investigazioni Scientifiche di Roma - Sezione di Biologia, Viale Tor di Quinto 119, 00191, Rome, Italy
| | | | - Maria Bonito
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Paolo Anagnostou
- Dipartimento di Biologia Ambientale, Sapienza Università di Roma, P.le Aldo Moro 5, 00185 - Rome, Italy; Istituto Italiano di Antropologia, Rome, Italy
| | - Gianluca Russo
- Dipartimento di Sanità Pubblica e Malattie Infettive, Sapienza Università di Roma, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Filippo Barni
- Reparto Carabinieri Investigazioni Scientifiche di Roma - Sezione di Biologia, Viale Tor di Quinto 119, 00191, Rome, Italy
| | - Eugenio Alladio
- Reparto Carabinieri Investigazioni Scientifiche di Roma - Sezione di Biologia, Viale Tor di Quinto 119, 00191, Rome, Italy
| | - Giovanni Destro-Bisol
- Dipartimento di Biologia Ambientale, Sapienza Università di Roma, P.le Aldo Moro 5, 00185 - Rome, Italy; Istituto Italiano di Antropologia, Rome, Italy
| | - Beniamino Trombetta
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Andrea Berti
- Reparto Carabinieri Investigazioni Scientifiche di Roma - Sezione di Biologia, Viale Tor di Quinto 119, 00191, Rome, Italy
| | - Fulvio Cruciani
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, P.le Aldo Moro 5, 00185 Rome, Italy; Istituto di Biologia e Patologia Molecolari, CNR, Rome, Italy.
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47
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Genetic Reconstruction and Forensic Analysis of Chinese Shandong and Yunnan Han Populations by Co-Analyzing Y Chromosomal STRs and SNPs. Genes (Basel) 2020; 11:genes11070743. [PMID: 32635262 PMCID: PMC7397191 DOI: 10.3390/genes11070743] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 06/30/2020] [Accepted: 07/02/2020] [Indexed: 12/27/2022] Open
Abstract
Y chromosomal short tandem repeats (Y-STRs) have been widely harnessed for forensic applications, such as pedigree source searching from public security databases and male identification from male–female mixed samples. For various populations, databases composed of Y-STR haplotypes have been built to provide investigating leads for solving difficult or cold cases. Recently, the supplementary application of Y chromosomal haplogroup-determining single-nucleotide polymorphisms (SNPs) for forensic purposes was under heated debate. This study provides Y-STR haplotypes for 27 markers typed by the Yfiler™ Plus kit and Y-SNP haplogroups defined by 24 loci within the Y-SNP Pedigree Tagging System for Shandong Han (n = 305) and Yunnan Han (n = 565) populations. The genetic backgrounds of these two populations were explicitly characterized by the analysis of molecular variance (AMOVA) and multi-dimensional scaling (MDS) plots based on 27 Y-STRs. Then, population comparisons were conducted by observing Y-SNP allelic frequencies and Y-SNP haplogroups distribution, estimating forensic parameters, and depicting distribution spectrums of Y-STR alleles in sub-haplogroups. The Y-STR variants, including null alleles, intermedia alleles, and copy number variations (CNVs), were co-listed, and a strong correlation between Y-STR allele variants (“DYS518~.2” alleles) and the Y-SNP haplogroup QR-M45 was observed. A network was reconstructed to illustrate the evolutionary pathway and to figure out the ancestral mutation event. Also, a phylogenetic tree on the individual level was constructed to observe the relevance of the Y-STR haplotypes to the Y-SNP haplogroups. This study provides the evidence that basic genetic backgrounds, which were revealed by both Y-STR and Y-SNP loci, would be useful for uncovering detailed population differences and, more importantly, demonstrates the contributing role of Y-SNPs in population differentiation and male pedigree discrimination.
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48
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Zhang Y, Zhang R, Li M, Luo L, Zhang J, Ding J, Zhang S, Li C, Bian Y, Zhou C. Genetic polymorphism of both 29 Y-STRs and 213 Y-SNPs in Han populations from Shandong Province, China. Leg Med (Tokyo) 2020; 47:101738. [PMID: 32818903 DOI: 10.1016/j.legalmed.2020.101738] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 06/11/2020] [Accepted: 06/14/2020] [Indexed: 11/27/2022]
Abstract
Genetic markers on the Y chromosome, including short tandem repeats (Y-STRs) and single nucleotide polymorphisms (Y-SNPs), are used widely in forensic genetics. Both Y-STR-based haplotypes and Y-SNP-based haplogroups provide information on a population's genetic structure, which is useful for the identification of individuals. However, there are few studies on these two types of genetic markers in the various Chinese populations. In this study, 284 Han individuals from four prefecture-level cities in Shandong Province (Binzhou, Dezhou, Heze, and Weihai) were genotyped by 29 Y-STRs (from our previous study) and 213 Y-SNPs (self-designed for the Haplogroup O2 Y-SNP panel). Haplogroup O was the most predominant among the four cities. The highest haplogroup diversity (0.9745) was observed in the Heze population, with a discrimination capacity (DC) value of 0.5625. The haplotype diversity and DC values of the Binzhou and Heze populations were 1.0000. Furthermore, genetic differences were observed between the coastal and inland cities; the results of their statistical analysis are presented herein.
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Affiliation(s)
- Yilun Zhang
- Baotou Medical College, School of Basic Medicine, Baotou 014060, Inner Mongolia Autonomous Region, China; Academy of Forensic Science-Ministry of Justice-China, Forensic Genetic, Shanghai 200063, China
| | - Rong Zhang
- Baotou Medical College, School of Basic Medicine, Baotou 014060, Inner Mongolia Autonomous Region, China
| | - Min Li
- Academy of Forensic Science-Ministry of Justice-China, Forensic Genetic, Shanghai 200063, China; Sichuan University, Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Chengdu 610064, Sichuan Province, China
| | - Li Luo
- Academy of Forensic Science-Ministry of Justice-China, Forensic Genetic, Shanghai 200063, China; Department of Forensic Medicine, Zunyi Medical University, Zunyi 563099, Guizhou, China
| | - Jiayi Zhang
- Academy of Forensic Science-Ministry of Justice-China, Forensic Genetic, Shanghai 200063, China; Department of Forensic Medicine, Inner Mongolia Medical University, Hohhot 010030, Inner Mongolia Autonomous Region, China
| | - Jidong Ding
- Baotou Medical College, School of Basic Medicine, Baotou 014060, Inner Mongolia Autonomous Region, China
| | - Suhua Zhang
- Academy of Forensic Science-Ministry of Justice-China, Forensic Genetic, Shanghai 200063, China
| | - Chengtao Li
- Academy of Forensic Science-Ministry of Justice-China, Forensic Genetic, Shanghai 200063, China
| | - Yingnan Bian
- Academy of Forensic Science-Ministry of Justice-China, Forensic Genetic, Shanghai 200063, China.
| | - Chengjiang Zhou
- Baotou Medical College, School of Basic Medicine, Baotou 014060, Inner Mongolia Autonomous Region, China.
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49
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Zhou Z, Zhou Y, Yao Y, Qian J, Liu B, Yang Q, Shao C, Li H, Sun K, Tang Q, Xie J. A 16-plex Y-SNP typing system based on allele-specific PCR for the genotyping of Chinese Y-chromosomal haplogroups. Leg Med (Tokyo) 2020; 46:101720. [PMID: 32505804 DOI: 10.1016/j.legalmed.2020.101720] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 05/17/2020] [Accepted: 05/25/2020] [Indexed: 02/06/2023]
Abstract
Y-chromosomal SNP (Y-SNP), with its stable inheritance and low mutation, can provide Supplementary information in forensic investigation. While commonly used Y-chromosomal STR haplotypes show their limitations, typing of Y-SNP would become a powerful complement. In this study, a 16-plex Y-SNP typing system based on allele-specific PCR (AS-PCR) was developed to discriminate four dominant Y-chromosomal haplogroups (C-M130, D-CTS3946, N-M231, and O-M175) and 12 predominant sub-haplogroups of O-M175 (O1a-M119, O1a1a1a-CTS3265, O1b-M268, O1b1a2-Page59, O2-M122, O2a1-L127.1, O2a1b-F240, O2a1b1a1-CTS5820, O2a2-P201, O2a2b1a1-M177, O2a2b1a1a1a-Y17728, O2a2b1a2-F114). A series of experimental validation studies including sensitivity, species specificity, male-female mixture and inhibition were performed. The discrimination of the typing system was preliminarily proved with a haplogroup diversity of 0.9239. Altogether, the Y-SNP typing system based on AS-PCR should be capable of distinguishing China's dominant Y-chromosomal haplogroups in a rapid and reliable manner, thus can be employed as a useful complement in forensic casework.
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Affiliation(s)
- Zhihan Zhou
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Yuxiang Zhou
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Yining Yao
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Jinglei Qian
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Baonian Liu
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Qinrui Yang
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Chengchen Shao
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Hui Li
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China; Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Research Institute of Criminal Science and Technology, Shanghai 200083, China
| | - Kuan Sun
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Qiqun Tang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Jianhui Xie
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, 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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