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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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Chen C, Guo Y, Fang Y, Shi J, Meng H, Qu L, Zhang X, Zhu B. The maternal phylogenetic insights of Yunnan Miao group revealed by complete mitogenomes. Gene 2024; 901:148046. [PMID: 38081335 DOI: 10.1016/j.gene.2023.148046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 11/28/2023] [Indexed: 01/21/2024]
Abstract
The Miao group is one of the representative Hmong-Mien-speaking populations and primarily scattered in southern China and Southeast Asia, which has experienced massive migrations in history and thus forms distinctive evolutionary genetics. Yet, the genetic explorations of Miao group are relatively limited based on complete mitochondrial genome (mitogenome), especially for the Miao group from Yunnan Province (YNM). Here, we sequenced complete mitogenomes of 132 Miao individuals from Yunnan Province using massively parallel sequencing method. Total 132 Miao individuals could be allocated to 119 various haplotypes, which were mainly dominated by haplogroups prevalent in southern East Asia (B, F, M7 and R9), and rarely occupied by northern lineages (A, D, G and M8). In order to dissect the genetic background of YNM more comprehensively, we introduced 99 published population data with 7135 complete mitochondrial sequences for population genetic comparisons. YNM exhibited closer genetic relationships with Hmong-Mien, Tai-Kadai, Sino-Tibetan and Austroasiatic populations, especially for Hmong-Mien populations; we further speculated that Miao group might have certain direct or indirect gene exchanges with ancient Baiyue groups. Several maternal lineages, such as B5a1c1a, F1g1, B4a5 and D4e1a3, were found to be specifically shared by YNM and other Hmong-Mien populations, and these matrilineal expansions occurred roughly during the Neolithic period. Eventually, according to the population dynamic analyses of YNM, the population size began to emerge recovery ∼1-0.5 kya after a long-term population reduction ∼1-5 kya, during which the B5a1c1a haplogroup manifested relatively apparent lineage expansion.
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Affiliation(s)
- Chong Chen
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an 710004, China; Department of Forensic Medicine, Faculty of Basic Medical Science, Chongqing Medical University, Chongqing 400016, China
| | - Yuxin Guo
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an 710004, China
| | - Yating Fang
- School of Basic Medical Sciences, Anhui Medical University, Anhui 230031, China
| | - Jianfeng Shi
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an 710004, China
| | - Haotian Meng
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an 710004, China
| | - Li Qu
- Department of Rheumatology and Immunology, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710004, China
| | - Xingru Zhang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an 710004, China; College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China
| | - Bofeng Zhu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an 710004, China; College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China; Multi-Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China.
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Xie S, Ma Y, Liu Y, Tao D, Wang Z, Yang Y. Primary azoospermia factor C duplication associated with spermatogenic impariment: a case-control study based on Y-chromosome haplogrouping in a Han Chinese population. Andrology 2024; 12:561-569. [PMID: 37594248 DOI: 10.1111/andr.13510] [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: 03/24/2023] [Revised: 06/22/2023] [Accepted: 08/06/2023] [Indexed: 08/19/2023]
Abstract
BACKGROUND Azoospermia factor C (AZFc) in the male-specific region of Y-chromosome (MSY) presents wide structure variation mainly due to frequent non-allele homologous recombination, leading to significant copy number variation of the AZFc-linked coding sequences involving in spermatogenesis. A large number of studies had been conducted to investigate the association between AZFc deletions and male infertility in certain Y chromosome genetic backgrounds, however, the influence of primary AZFc duplication on spermatogenesis remained controversial and the cause of the discrepant outcomes is unknown. METHODS In the present study, a total of 1,102 unrelated Han Chinese males without any detectable AZF deletions were recruited from 2014 to 2019, including 411 controls with normozoospermia and 691 patients with idiopathic spermatogenic failure. Using multiple paralog ratio tests (PRTs), the structure duplications were classified by the copy number of the AZFc-linked amplicons and genes. The Y-chromosome haplogroup (Y-hg) was categorized by genetyping of MSY-linked polymorphism loci. The association of primary AZFc duplication with spermatogenic phenotype was investigated in males with the same Y-hg. RESULTS Within Y-hg O3* group, the frequency of the gr/gr duplication in patients is significantly higher than that of controls (P = 1.29×10-3 , odds ratio (OR) 7.64, 95% confidence interval (CI) 1.79-32.57). Moreover, Y-hg O3* males with the gr/gr duplication presented a significantly lower sperm production compared with non-AZFc duplicated ones (sperm concentration: P = 1.46×10-3 ; total sperm count: P = 1.82 ×10-3 ). The b2/b3 duplication were identified clustered in Y-hg Cα2*, and the significant difference in the distribution was not observed between patients with spermatogenic failure and controls. CONCLUSION The results suggest that, in the Han Chinese population, the gr/gr duplication is a predisposing genetic factor for spermatogenic impairment in males harboring Y-hg O3* . Meanwhile, the b2/b3 duplication may be fixed on a yet-unidentified subbranch of Y-hg Cα2* without significantly deleterious effect on spermatogenesis. Our findings provide evidence that the difference in the Y-hg composition may cause the discrepancy on the association of AZFc duplication with spermatogenic failure among the studied populations.
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Affiliation(s)
- Shengyu Xie
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, West China School of medicine, Sichuan University, Chengdu, China
| | - Yongyi Ma
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, West China School of medicine, Sichuan University, Chengdu, China
- Precision Medicine Center, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, China
| | - Yunqiang Liu
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, West China School of medicine, Sichuan University, Chengdu, China
| | - Dachang Tao
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, West China School of medicine, Sichuan University, Chengdu, China
| | - Zhaokun Wang
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, West China School of medicine, Sichuan University, Chengdu, China
| | - Yuan Yang
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, West China School of medicine, Sichuan University, Chengdu, China
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Aoki K, Takahata N, Oota H, Wakano JY, Feldman MW. Infectious diseases may have arrested the southward advance of microblades in Upper Palaeolithic East Asia. Proc Biol Sci 2023; 290:20231262. [PMID: 37644833 PMCID: PMC10465978 DOI: 10.1098/rspb.2023.1262] [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: 06/06/2023] [Accepted: 08/01/2023] [Indexed: 08/31/2023] Open
Abstract
An unsolved archaeological puzzle of the East Asian Upper Palaeolithic is why the southward expansion of an innovative lithic technology represented by microblades stalled at the Qinling-Huaihe Line. It has been suggested that the southward migration of foragers with microblades stopped there, which is consistent with ancient DNA studies showing that populations to the north and south of this line had differentiated genetically by 19 000 years ago. Many infectious pathogens are believed to have been associated with hominins since the Palaeolithic, and zoonotic pathogens in particular are prevalent at lower latitudes, which may have produced a disease barrier. We propose a mathematical model to argue that mortality due to infectious diseases may have arrested the wave-of-advance of the technologically advantaged foragers from the north.
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Affiliation(s)
- Kenichi Aoki
- Graduate School of Science, University of Tokyo, Hongo, Tokyo 113-0033, Japan
| | - Naoyuki Takahata
- Graduate University for Advanced Studies, Hayama, Kanagawa 240-0116, Japan
| | - Hiroki Oota
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo, Tokyo 113-0033, Japan
| | - Joe Yuichiro Wakano
- School of Interdisciplinary Mathematical Sciences, Meiji University, Nakano, Tokyo 164-8525, Japan
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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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Zhang X, Ji X, Li C, Yang T, Huang J, Zhao Y, Wu Y, Ma S, Pang Y, Huang Y, He Y, Su B. A Late Pleistocene human genome from Southwest China. Curr Biol 2022; 32:3095-3109.e5. [PMID: 35839766 DOI: 10.1016/j.cub.2022.06.016] [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: 12/24/2021] [Revised: 05/27/2022] [Accepted: 06/08/2022] [Indexed: 11/25/2022]
Abstract
Southern East Asia is the dispersal center regarding the prehistoric settlement and migrations of modern humans in Asia-Pacific regions. However, the settlement pattern and population structure of paleolithic humans in this region remain elusive, and ancient DNA can provide direct information. Here, we sequenced the genome of a Late Pleistocene hominin (MZR), dated ∼14.0 thousand years ago from Red Deer Cave located in Southwest China, which was previously reported possessing mosaic features of modern and archaic hominins. MZR is the first Late Pleistocene genome from southern East Asia. Our results indicate that MZR is a modern human who represents an early diversified lineage in East Asia. The mtDNA of MZR belongs to an extinct basal lineage of the M9 haplogroup, reflecting a rich matrilineal diversity in southern East Asia during the Late Pleistocene. Combined with the published data, we detected clear genetic stratification in ancient southern populations of East/Southeast Asia and some degree of south-versus-north divergency during the Late Pleistocene, and MZR was identified as a southern East Asian who exhibits genetic continuity to present day populations. Markedly, MZR is linked deeply to the East Asian ancestry that contributed to First Americans.
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Affiliation(s)
- Xiaoming Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650201, China
| | - Xueping Ji
- Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Department of Paleoanthropology, Yunnan Institute of Cultural Relics and Archaeology, Kunming 650118, China.
| | - Chunmei Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650201, China
| | - Tingyu Yang
- Biomedical Pioneering Innovation Center (BIOPIC) and Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing 100871, China
| | - Jiahui Huang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yinhui Zhao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yun Wu
- Department of Paleoanthropology, Yunnan Institute of Cultural Relics and Archaeology, Kunming 650118, China; School of History, Wuhan University, Wuhan 430072, China; Archaeological Institute for Yangtze Civilization, Wuhan University, Wuhan 430072, China
| | - Shiwu Ma
- Mengzi Institute of Cultural Relics, Mengzi, Yunnan Province 661100, China
| | - Yuhong Pang
- Biomedical Pioneering Innovation Center (BIOPIC) and Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing 100871, China
| | - Yanyi Huang
- Biomedical Pioneering Innovation Center (BIOPIC) and Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing 100871, China
| | - Yaoxi He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650201, China.
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650201, China.
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Yang Z, Chen H, Lu Y, Gao Y, Sun H, Wang J, Jin L, Chu J, Xu S. Genetic evidence of tri-genealogy hypothesis on the origin of ethnic minorities in Yunnan. BMC Biol 2022; 20:166. [PMID: 35864541 PMCID: PMC9306206 DOI: 10.1186/s12915-022-01367-3] [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] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 07/05/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Yunnan is located in Southwest China and consists of great cultural, linguistic, and genetic diversity. However, the genomic diversity of ethnic minorities in Yunnan is largely under-investigated. To gain insights into population history and local adaptation of Yunnan minorities, we analyzed 242 whole-exome sequencing data with high coverage (~ 100-150 ×) of Yunnan minorities representing Achang, Jingpo, Dai, and Deang, who were linguistically assumed to be derived from three ancient lineages (the tri-genealogy hypothesis), i.e., Di-Qiang, Bai-Yue, and Bai-Pu. RESULTS Yunnan minorities show considerable genetic differences. Di-Qiang populations likely migrated from the Tibetan area about 6700 years ago. Genetic divergence between Bai-Yue and Di-Qiang was estimated to be 7000 years, and that between Bai-Yue and Bai-Pu was estimated to be 5500 years. Bai-Pu is relatively isolated, but gene flow from surrounding Di-Qiang and Bai-Yue populations was also found. Furthermore, we identified genetic variants that are differentiated within Yunnan minorities possibly due to the living circumstances and habits. Notably, we found that adaptive variants related to malaria and glucose metabolism suggest the adaptation to thalassemia and G6PD deficiency resulting from malaria resistance in the Dai population. CONCLUSIONS We provided genetic evidence of the tri-genealogy hypothesis as well as new insights into the genetic history and local adaptation of the Yunnan minorities.
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Affiliation(s)
- Zhaoqing Yang
- Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences, Kunming, 650118, China
| | - Hao Chen
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yan Lu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yang Gao
- Human Phenome Institute, Zhangjiang Fudan International Innovation Center, and Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai, 201203, China
| | - Hao Sun
- Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences, Kunming, 650118, China
| | - Jiucun Wang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Human Phenome Institute, Zhangjiang Fudan International Innovation Center, and Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai, 201203, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Human Phenome Institute, Zhangjiang Fudan International Innovation Center, and Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai, 201203, China
| | - Jiayou Chu
- Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences, Kunming, 650118, China.
| | - Shuhua Xu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China.
- Human Phenome Institute, Zhangjiang Fudan International Innovation Center, and Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai, 201203, China.
- Department of Liver Surgery and Transplantation Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
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Microhaplotype and Y-SNP/STR (MY): A novel MPS-based system for genotype pattern recognition in two-person DNA mixtures. Forensic Sci Int Genet 2022; 59:102705. [DOI: 10.1016/j.fsigen.2022.102705] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 03/10/2022] [Accepted: 04/10/2022] [Indexed: 12/13/2022]
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Guo J, Wang W, Zhao K, Li G, He G, Zhao J, Yang X, Chen J, Zhu K, Wang R, Ma H, Xu B, Wang C. Genomic insights into
Neolithic
farming‐related migrations in the junction of east and southeast
Asia. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2021. [DOI: 10.1002/ajpa.24434] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Jianxin Guo
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, State Key Laboratory of Marine Environmental Science Xiamen University Xiamen China
| | - Weitao Wang
- Yunnan Modern Forensic Institute Kunming China
| | - Kai Zhao
- Yunnan Modern Forensic Institute Kunming China
| | | | - Guanglin He
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, State Key Laboratory of Marine Environmental Science Xiamen University Xiamen China
| | - Jing Zhao
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, State Key Laboratory of Marine Environmental Science Xiamen University Xiamen China
| | - Xiaomin Yang
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, State Key Laboratory of Marine Environmental Science Xiamen University Xiamen China
| | - Jinwen Chen
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, State Key Laboratory of Marine Environmental Science Xiamen University Xiamen China
| | - Kongyang Zhu
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, State Key Laboratory of Marine Environmental Science Xiamen University Xiamen China
| | - Rui Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, State Key Laboratory of Marine Environmental Science Xiamen University Xiamen China
| | - Hao Ma
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, State Key Laboratory of Marine Environmental Science Xiamen University Xiamen China
| | - Bingying Xu
- Research Center of Biomedical Engineering Kunming Medical University Kunming China
| | - Chuan‐Chao Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, State Key Laboratory of Marine Environmental Science Xiamen University Xiamen China
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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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Luo X, Zhang XM, Wu LS, Chen J, Chen Y. Prevalence and clinical phenotype of the triplicated α-globin genes and its ethnic and geographical distribution in Guizhou of China. BMC Med Genomics 2021; 14:97. [PMID: 33827577 PMCID: PMC8025570 DOI: 10.1186/s12920-021-00944-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/22/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND α-thalassemia is relatively endemic in Guizhou province of southwestern China. To predict the clinical manifestations of α-globin gene aberration for genetic counseling, we examined the prevalence of the α-globin triplication and the genotype-phenotype correlation in this subpopulation METHODS: A cohort of 7644 subjects was selected from nine ethnicities covering four regions in Guizhou province of China. Peripheral blood was collected from each participant for routine blood testing and hemoglobin electrophoresis. PCR-DNA sequencing and Gap-PCR were used to identify the thalassemia gene mutations. Chi-square tests and one-way analysis of variance (ANOVA) were used to statistically analyze the data. RESULTS We found that the frequency of α-globin triplication in Guizhou province was 0.772% (59/7644). Genotypically, the αααanti4.2/αα accounted for 0.523% (40/7644), the αααanti3.7/αα for 0.235% (18/7644), and the αααanti3.7/-SEA for 0.013% (1/7644). The αααanti4.2/αα is more prevalent than the αααanti3.7/αα in Guizhou. In addition, the frequency of the HKαα/αα (that by GAP-PCR is like αααanti4.2/-α3.7) was 0.235% (18/7644). Ethnically, the Tujia group presented the highest prevalence (2.47%) of α-globin triplication. Geographically, the highest frequency of the α-globin triplication was identified in Qiannan region (2.23%). Of the triplicated α-globin cases, 5 coinherited with heterozygote β-thalassemia and presented various clinical manifestations of anemia. CONCLUSIONS These data will be used to update the Chinese triplicated α-globin thalassemia database and provide insights into the pathogenesis of thalassemia. These findings will be helpful for the diagnosis of thalassemia and future genetic counseling in those regions.
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Affiliation(s)
- Xi Luo
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, Guizhou, China
| | - Xiang-Mei Zhang
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, Guizhou, China
| | - Liu-Song Wu
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, Guizhou, China
| | - Jindong Chen
- Department of Medical Genetics, Zunyi Medical University, Zunyi, 563000, Guizhou, China
- Exploring Health LLC, Guangzhou, 510663, Guangdong, China
- Department of Urology, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Yan Chen
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, Guizhou, China.
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12
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Peng W, Huang X, Storozum MJ, Fan Y, Zhang H. An updated chronology and paleoenvironmental background for the Paleolithic Loufangzi site, North China. J Hum Evol 2021; 152:102948. [PMID: 33529839 DOI: 10.1016/j.jhevol.2020.102948] [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: 03/02/2020] [Revised: 12/27/2020] [Accepted: 12/27/2020] [Indexed: 10/22/2022]
Abstract
The relationship between the environment and human activities during Marine Isotope Stage (MIS) 4 is important for understanding the origins of modern humans (Homo sapiens) in East Asia, an area where various hypotheses of human origins have been vigorously debated over the past three decades. Unfortunately, only a handful of Paleolithic sites date to MIS 4 in East Asia, hampering our understanding of how environmental changes affected human activities during this time period. Here, we used stratigraphic correlation analysis and optically stimulated luminescence to date the Loufangzi site, an important Paleolithic site in North China that has had an unreliable chronology. Pollen analysis, grain size, and magnetic susceptibility were also used to reconstruct environmental conditions at the Loufangzi site area. Our results show that (1) the age of the upper culture layer of the Loufangzi site is bracketed between ∼70 ka and ∼60 ka and dates to MIS 4 and (2) the regional vegetation from MIS 5 to MIS 4 to MIS 3 was mainly dominated by forest steppe, desert steppe/desert, and steppe, respectively, indicating harsh environmental conditions during MIS 4. Combined with the discovery of Mousterian-like scrapers in the upper culture layer of MIS 4, our results challenge the view that the area was unsuitable for human survival during the Last Glacial period and instead suggest that humans used new technologies to increase their resilience to the cooling climate.
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Affiliation(s)
- Wei Peng
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming Yunnan, 650504, China; Key Laboratory of Western China's Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou Gansu, 730000, China
| | - Xiaozhong Huang
- Key Laboratory of Western China's Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou Gansu, 730000, China.
| | - Michael J Storozum
- Institute of Archaeological Science, Fudan University, 220 Handan Road, Yangpu District, Shanghai, 200433, China; Department of Cultural Heritage and Museology, Fudan University, 220 Handan Road, Yangpu District, Shanghai, 200433, China
| | - Yuxin Fan
- School of Earth Sciences & Key Laboratory of Mineral Resources in Western China (Gansu Province), Lanzhou University, Lanzhou 730000, China
| | - Hucai Zhang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming Yunnan, 650504, China.
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13
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Li W, Wang X, Wang X, Wang F, Du Z, Fu F, Wu W, Wang S, Mu Z, Chen C, Hu X, Ding J, Meng Y, Qiu P, Fan H. Forensic characteristics and phylogenetic analyses of one branch of Tai-Kadai language-speaking Hainan Hlai (Ha Hlai) via 23 autosomal STRs included in the Huaxia ™ Platinum System. Mol Genet Genomic Med 2020; 8:e1462. [PMID: 32862500 PMCID: PMC7549582 DOI: 10.1002/mgg3.1462] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/20/2020] [Accepted: 08/04/2020] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Hainan Island, located in the South China Sea and separated from the Leizhou Peninsula by Qiongzhou Strait, is the second largest island after Taiwan in China. With the expansion of Han Chinese and the gradual formation of "South Hlai and North Han", nowadays, Hainan Hlai is the second largest population after Han Chinese in Hainan Island. Ha Hlai, distributed in southwest and southern Hainan Island, is the dominant branch of Hlai and speaks Ha localism. METHODS We utilized the Huaxia™ Platinum PCR Amplification System (including 23 autosomal STRs and 2 sex-linked markers) to obtain the first STR profiling batch of 657 Ha Hlai individuals (497 males and 160 females). In order to explore the genetic relationships between the studied Ha Hlai and other reference populations with different language families, population genetic analyses, including PCA, MDS, STRUCTURE, and phylogenetic analysis, were conducted based upon the raw data and allelic frequencies of the polymorphic autosomal STR markers. RESULTS In total, 271 distinct alleles were observed at the 23 STR loci. The number of diverse alleles ranged from 7 at TPOX locus to 23 at FGA locus, and the allelic frequencies varied from 0.0008 to 0.5533. In addition, the CPE and CPD were 1-7.39 × 10-10 and 1-3.13 × 10-28 , respectively. The phylogenetic analyses indicated that Ha Hlai is a Tai-Kadai language-speaking and relatively isolated population which has a close genetic and geographical relationship with Hainan Hlai, and M95 is the dominant haplogroup in Ha Hlai (56.18%). CONCLUSION The 23 autosomal STR genetic markers were highly polymorphic as well as potentially useful for forensic applications in Hainan Ha Hlai population. The phylogenetic analyses demonstrated that small geographic scale gene flows could not be ignored and the shaping of the unique gene pool for each population was the combination effects of geographic, language, and cultural isolations.
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Affiliation(s)
- Wenhui Li
- School of Basic Medicine and Life ScienceHainan Medical UniversityHaikouChina
- Forensic Science Center of Hainan Medical UniversityHainan Medical UniversityHaikouChina
| | - Xianwen Wang
- Criminal Technical DetachmentHaikou City Public Security BureauHaikouChina
| | - Xiehong Wang
- Criminal Technical DetachmentHaikou City Public Security BureauHaikouChina
| | - Fenfen Wang
- First Clinical Medical CollegeHainan Medical UniversityHaikouChina
| | - Zhengming Du
- First Clinical Medical CollegeHainan Medical UniversityHaikouChina
| | - Fangshu Fu
- School of Biomedical Information and EngineeringHainan Medical UniversityHaikouChina
| | - Wenlong Wu
- First Clinical Medical CollegeHainan Medical UniversityHaikouChina
| | - Shuya Wang
- School of Public HealthHainan Medical UniversityHaikouChina
| | - Ziqing Mu
- School of ManagementHainan Medical UniversityHaikouChina
| | - Chunwei Chen
- Public Security and Judicial Appraisal Center of Sanya CitySanyaChina
| | - Xiaomin Hu
- Hainan Zhujian Center for Molecular Cytogenetic Clinical TestingHaikouChina
| | - Jiuyang Ding
- School of Forensic MedicineGuizhou Medical UniversityGuiyangChina
| | - Yunle Meng
- School of Forensic MedicineSouthern Medical UniversityGuangzhouChina
| | - Pingming Qiu
- School of Forensic MedicineSouthern Medical UniversityGuangzhouChina
- Multi‐Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics, School of Forensic MedicineSouthern Medical UniversityGuangzhouChina
| | - Haoliang Fan
- School of Basic Medicine and Life ScienceHainan Medical UniversityHaikouChina
- Forensic Science Center of Hainan Medical UniversityHainan Medical UniversityHaikouChina
- School of Forensic MedicineSouthern Medical UniversityGuangzhouChina
- Multi‐Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics, School of Forensic MedicineSouthern Medical UniversityGuangzhouChina
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14
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Paleolithic genetic link between Southern China and Mainland Southeast Asia revealed by ancient mitochondrial genomes. J Hum Genet 2020; 65:1125-1128. [DOI: 10.1038/s10038-020-0796-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 06/21/2020] [Accepted: 06/27/2020] [Indexed: 12/26/2022]
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15
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Li F, Kuhn SL, Chen FY, Gao X. Intra-assemblage variation in the macro-blade assemblage from the 1963 excavation at Shuidonggou locality 1, northern China, in the context of regional variation. PLoS One 2020; 15:e0234576. [PMID: 32542019 PMCID: PMC7295238 DOI: 10.1371/journal.pone.0234576] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 05/27/2020] [Indexed: 11/25/2022] Open
Abstract
The emergence of the Upper Paleolithic and regional variability in early Upper Paleolithic industries are prominent topics in Paleolithic archaeology, with special relevance to the dispersal and differentiation of early modern human cultures across Eurasia. The so-called Initial Upper Paleolithic (IUP) has been considered a key element in the emergence of the Upper Paleolithic in northern Asia. Here, we examine the intra-assemblage variation in the collection from the 1963 excavation at Shuidonggou locality 1, a major IUP site in northern China. We combine technological and quantitative attribute analyses to investigate the variety of core reduction sequences and tool manufacture behaviors at the site. A range of core reduction sequences have been documented at Shuidonggou locality 1, including both simple core reduction and prepared core reduction yielding laminar (blade-like) products. The simple core reduction component may due to mixed non-IUP assemblages from different archaeological layers. Among the laminar core reduction sequences, the main strategy involves asymmetrical exploitation of the broad face of core blank, producing blades and elongate flakes, and resembling a recurrent Levallois blade method sensu lato. We compare Shuidonggou laminar blank production with that of IUP assemblages in the Siberian Altai, northern Mongolia, and the Transbaikal region. The comparison demonstrates a general consistency to the basic blank production in IUP assemblages across northern Asia, with some regional variation. The results suggest a multi-directional model of diffusion of the IUP in northeast Asia.
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Affiliation(s)
- Feng Li
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Life and Paleoenvironment, Beijing, China
- * E-mail:
| | - Steven L. Kuhn
- School of Anthropology, University of Arizona, Tucson, AZ, United States of America
| | - Fu-you Chen
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Life and Paleoenvironment, Beijing, China
| | - Xing Gao
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Life and Paleoenvironment, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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16
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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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17
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Yin C, Ren Y, Adnan A, Tian J, Guo K, Xia M, He Z, Zhai D, Chen X, Wang L, Li X, Qin X, Li S, Jin L. Title: Developmental validation of Y-SNP pedigree tagging system: A panel via quick ARMS PCR. Forensic Sci Int Genet 2020; 46:102271. [DOI: 10.1016/j.fsigen.2020.102271] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 03/01/2020] [Accepted: 03/02/2020] [Indexed: 11/26/2022]
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18
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Lu Q, Cheng HZ, Li L, Yao HB, Ru K, Wen SQ, Shi MS, Zeng ZS, Wei LH. Paternal heritage of the Han Chinese in Henan province (Central China): high diversity and evidence of in situ Neolithic expansions. Ann Hum Biol 2020; 47:294-299. [PMID: 32281408 DOI: 10.1080/03014460.2020.1748226] [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: 10/24/2022]
Abstract
Background: Due to their long history, complex admixture processes and large population sizes, more research is required to explore the fine genetic structure of Han populations from different geographic locations of China.Aim: To characterise the paternal genetic structure of the Han Chinese in Henan province, which was once the central living region of the ancient Huaxia population, the precursors of the Han Chinese.Subjects and methods: We sequenced Y chromosomes of 60 males from Zhengzhou, Henan Province, and reconstructed a phylogenetic tree for these samples with age estimation.Results: We observed high diversity of paternal lineages in our collection. We found that the in situ Neolithic expansion of the "Major lineages" contributed to a large portion of the paternal gene pool of the Han population in Henan Province. We also detected a large number of "Minor lineages" that diverged in the Palaeolithic Age.Conclusion: We suggest that the high genetic diversity in the paternal gene pool of modern Han populations is mainly attributed to the reservation of a larger number of lineages that diverged in the Palaeolithic Age, while the recent expansion of limited lineages contributed to the majority of the gene pool of modern Han populations. We propose that such a structure is a basal characteristic for the genetic structure of modern Han populations.
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Affiliation(s)
- Qi Lu
- Department of Forensic Medicine, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Hui-Zhen Cheng
- Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, China
| | - Li Li
- Department of Obstetrics & Gynecology, Zhengzhou Central Hospital, Zhengzhou University, Zhengzhou, China
| | - Hong-Bin Yao
- Key Laboratory of Evidence Science of Gansu Province, Gansu University of Political Science and Law, Lanzhou, China
| | - Kai Ru
- Institute of Archaeological Science, Fudan University, Shanghai, China
| | - Shao-Qing Wen
- Institute of Archaeological Science, Fudan University, Shanghai, China.,B&R International Joint Laboratory for Eurasian Anthropology, Fudan University, Shanghai, China
| | - Mei-Sen Shi
- Institute of the Investigation, School of Criminal Justice, China University of Political Science and Law, Beijing, China
| | - Zhao-Shu Zeng
- Department of Forensic Medicine, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Lan-Hai Wei
- Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, China.,B&R International Joint Laboratory for Eurasian Anthropology, Fudan University, Shanghai, China
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Guo J, Xu B, Li L, He G, Zhang H, Cheng HZ, Ba J, Yang X, Wei L, Hu R, Wang CC. Paternal Y chromosomal genotyping reveals multiple large-scale admixtures in the formation of Lolo-Burmese-speaking populations in southwest China. Ann Hum Biol 2019; 46:581-588. [PMID: 31825250 DOI: 10.1080/03014460.2019.1698655] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Background: Bai and Yi people are two Tibeto-Burman speaking ethnic groups in Yunnan, southwest China. The genetic structure and history of these two groups are largely unknown due to a lack of available genetic data.Aim: To investigate the paternal genetic structure and population relationship of the Yi and Bai people.Subjects and methods: We collected samples from 278 Bai individuals and 283 Yi individuals from Yunnan and subsequently genotyped 43 phylogenetically relevant Y-SNPs in those samples. We estimated haplogroup frequencies and merged our data with a reference database including 46 representative worldwide populations to infer genetic relationships.Results: Y chromosomal haplogroup O-M175 is the dominant lineage in both Bai and Yi people. The Bai and Yi show a close genetic relationship with other Tibeto-Burman-speaking populations with high frequencies of haplogroup O2a2b1a1-Page23, which is also confirmed by PCA. The frequencies of the Tai-Kadai specific lineage O1a-M119, the southern China widespread lineage O1b-P31 and the eastern China enriched lineage O2a1b-002611, are also relatively high in our studied populations.Conclusions: The paternal Y chromosomal affinity of the Bai and Yi with Tibeto-Burman groups is consistent with the language classification. During the formation of the Bai and Yi populations, there were multiple large-scale admixtures, including the expansion of Neolithic farming populations from northern China, the assimilation of Tai-Kadai-speaking populations in southwest China, the demographic expansion driven by Neolithic agricultural revolution from southern China, and the admixture with populations of military immigration from northern and eastern China.
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Affiliation(s)
- Jianxin Guo
- Department of History, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Bingying Xu
- Research Center of Biomedical Engineering, Kunming Medical University, Kunming, China
| | - Lanjiang Li
- Research Center of Biomedical Engineering, Kunming Medical University, Kunming, China
| | - Guanglin He
- Department of History, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, China
| | - Han Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Hui-Zhen Cheng
- Department of History, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Jinxing Ba
- Department of History, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Xiaomin Yang
- Department of History, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Lanhai Wei
- Department of History, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Rong Hu
- Department of History, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Chuan-Chao Wang
- Department of History, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
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20
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Xiang L, Tao J, Deng K, Li X, Li Q, Yuan X, Liang J, Yu E, Wang M, Wang H, Liu H, Zhu J. Phenylketonuria incidence in China between 2013 and 2017 based on data from the Chinese newborn screening information system: a descriptive study. BMJ Open 2019; 9:e031474. [PMID: 31444193 PMCID: PMC6707664 DOI: 10.1136/bmjopen-2019-031474] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 07/02/2019] [Accepted: 07/17/2019] [Indexed: 11/25/2022] Open
Abstract
OBJECTIVE This study examines the incidence and spatial clustering of phenylketonuria (PKU) in China between 2013 and 2017. METHODS Data from the Chinese Newborn Screening Information System were analysed to assess PKU incidence with 95% CIs by province, region and disease severity. Spatial clustering of PKU cases was analysed using global and local spatial autocorrelation analysis in the geographic information system. RESULTS The database contained 4925 neonates with confirmed PKU during the study period, corresponding to an incidence of 6.28 (95% CI: 6.11 to 6.46) per 100 000 neonates screened. Incidence was highest in the provinces of Gansu, Ningxia and Qinghai, where it ranged from 19.00 to 28.63 per 100 000 neonates screened. Overall incidence was higher in the northern part of the country, where classical disease predominated, than in the southern part, where mild disease predominated. PKU cases clustered spatially (global Moran's I=0.3603, Z=5.3097, p<0.001), and local spatial autocorrelation identified four northern provinces as high-high clusters (Gansu, Qinghai, Ningxia and Shanxi). CONCLUSIONS China shows an intermediate PKU incidence among countries, and incidence differs substantially among Chinese provinces and between northern and southern regions. Our results suggest the need to focus efforts on screening, diagnosing and treating PKU in high-incidence provinces.
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Affiliation(s)
- Liangcheng Xiang
- National Office for Maternal and Child Health Surveillance of China, Sichuan University West China Second University Hospital, Chengdu, China
| | - Jing Tao
- National Office for Maternal and Child Health Surveillance of China, Sichuan University West China Second University Hospital, Chengdu, China
| | - Kui Deng
- National Office for Maternal and Child Health Surveillance of China, Sichuan University West China Second University Hospital, Chengdu, China
| | - Xiaohong Li
- National Office for Maternal and Child Health Surveillance of China, Sichuan University West China Second University Hospital, Chengdu, China
| | - Qi Li
- National Office for Maternal and Child Health Surveillance of China, Sichuan University West China Second University Hospital, Chengdu, China
| | - Xuelian Yuan
- National Office for Maternal and Child Health Surveillance of China, Sichuan University West China Second University Hospital, Chengdu, China
| | - Juan Liang
- National Office for Maternal and Child Health Surveillance of China, Sichuan University West China Second University Hospital, Chengdu, China
| | - Erling Yu
- National Office for Maternal and Child Health Surveillance of China, Sichuan University West China Second University Hospital, Chengdu, China
| | - Meixian Wang
- National Office for Maternal and Child Health Surveillance of China, Sichuan University West China Second University Hospital, Chengdu, China
| | - Huiqing Wang
- Department of Pediatrics, Sichuan University West China Second University Hospital, Chengdu, China
| | - Hanmin Liu
- Department of Pediatrics, Sichuan University West China Second University Hospital, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Sichuan University West China Second University Hospital, Chengdu, China
| | - Jun Zhu
- National Office for Maternal and Child Health Surveillance of China, Sichuan University West China Second University Hospital, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Sichuan University West China Second University Hospital, Chengdu, China
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21
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Xu B, Guo J, Huang Y, Chen X, Deng X, Wang CC. The paternal genetic structure of Jingpo and Dai in southwest China. Ann Hum Biol 2019; 46:279-283. [PMID: 31179767 DOI: 10.1080/03014460.2019.1624821] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Yunnan province harbours substantial genetic, cultural and linguistic diversity, with the largest number of Aborigines in China, but the relationship among these Aborigines remains enigmatic. This study genotyped 45 Y chromosomal single nucleotide polymorphisms (SNPs) of 500 males from two aboriginal cross-border populations, Jingpo and Dai, from Dehong, Yunnan. It is reported that Haplogroup O2a2b1a1-M117 is the dominant lineage in both Jingpo and Dai. The Jingpo people show affinity with Tibeto-Burman speaking populations with a relatively high frequency of Haplogroup D-M174, and the Dai people are generally genetically similar with Tai-Kadai speaking populations with high frequencies of Haplogroup O1a-M119 and O1b1a1a-M95, which is consistent with their language classification.
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Affiliation(s)
- Bingying Xu
- Research Center of Biomedical Engineering, Kunming Medical University, Kunming, PR China
| | - Jianxin Guo
- Department of History, Xiamen University, Xiamen, PR China.,Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, PR China
| | - Ying Huang
- Research Center of Biomedical Engineering, Kunming Medical University, Kunming, PR China
| | - Xueyun Chen
- Research Center of Biomedical Engineering, Kunming Medical University, Kunming, PR China
| | - Xiaohua Deng
- Fujian University of Technology, Fuzhou, PR China
| | - Chuan-Chao Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, PR China
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22
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Li F, Vanwezer N, Boivin N, Gao X, Ott F, Petraglia M, Roberts P. Heading north: Late Pleistocene environments and human dispersals in central and eastern Asia. PLoS One 2019; 14:e0216433. [PMID: 31141504 PMCID: PMC6541242 DOI: 10.1371/journal.pone.0216433] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 04/20/2019] [Indexed: 11/18/2022] Open
Abstract
The adaptability of our species, as revealed by the geographic routes and palaeoenvironmental contexts of human dispersal beyond Africa, is a prominent topic in archaeology and palaeoanthropology. Northern and Central Asia have largely been neglected as it has been assumed that the deserts and mountain ranges of these regions acted as 'barriers', forcing human populations to arc north into temperate and arctic Siberia. Here, we test this proposition by constructing Least Cost Path models of human dispersal under glacial and interstadial conditions between prominent archaeological sites in Central and East Asia. Incorporating information from palaeoclimatic, palaeolake, and archaeological data, we demonstrate that regions such as the Gobi Desert and the Altai Mountain chains could have periodically acted as corridors and routes for human dispersals and framing biological interactions between hominin populations. Review of the archaeological datasets in these regions indicates the necessity of wide-scale archaeological survey and excavations in many poorly documented parts of Eurasia. We argue that such work is likely to highlight the 'northern routes' of human dispersal as variable, yet crucial, foci for understanding the extreme adaptive plasticity characteristic of the emergence of Homo sapiens as a global species, as well as the cultural and biological hybridization of the diverse hominin species present in Asia during the Late Pleistocene.
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Affiliation(s)
- Feng Li
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Life and Paleoenvironment, Beijing, China
| | - Nils Vanwezer
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Nicole Boivin
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Xing Gao
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Life and Paleoenvironment, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Florian Ott
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Michael Petraglia
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- Human Origins Program, National Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America
| | - Patrick Roberts
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- School of Social Science, The University of Queensland, St Lucia, Brisbane, Australia
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Forensic characteristics and phylogenetic analysis of both Y-STR and Y-SNP in the Li and Han ethnic groups from Hainan Island of China. Forensic Sci Int Genet 2019; 39:e14-e20. [DOI: 10.1016/j.fsigen.2018.11.016] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 10/24/2018] [Accepted: 11/26/2018] [Indexed: 11/21/2022]
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24
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Liu X, Yang S, Meng L, Chen C, Hui X, Jiang Y, Jiao X, Lv K, Song T. Association between PTCH1 and RAD54B single‐nucleotide polymorphisms and non‐syndromic orofacial clefts in a northern Chinese population. J Gene Med 2018; 20:e3055. [PMID: 30172247 DOI: 10.1002/jgm.3055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 08/24/2018] [Accepted: 08/27/2018] [Indexed: 12/11/2022] Open
Affiliation(s)
- Xiaotong Liu
- Department of Oral and Maxillofacial Surgerythe First Affiliated Hospital of Harbin Medical University Heilongjiang China
| | | | - Lingwei Meng
- Department of Xiang Ya School of StamatologyCentral South University Hunan China
| | - Chunyu Chen
- Department of Oral and Maxillofacial Surgerythe First Affiliated Hospital of Harbin Medical University Heilongjiang China
| | - Xiang Hui
- Department of Oral and Maxillofacial Surgerythe First Affiliated Hospital of Harbin Medical University Heilongjiang China
| | - Yuxin Jiang
- Department of Oral and Maxillofacial Surgerythe First Affiliated Hospital of Harbin Medical University Heilongjiang China
| | - Xiaohui Jiao
- Department of Oral and Maxillofacial Surgerythe First Affiliated Hospital of Harbin Medical University Heilongjiang China
| | - Kewen Lv
- Department of Oral and Maxillofacial Surgerythe First Affiliated Hospital of Harbin Medical University Heilongjiang China
| | - Tao Song
- Department of Oral and Maxillofacial Surgerythe First Affiliated Hospital of Harbin Medical University Heilongjiang China
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25
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Re-dating Zhoukoudian Upper Cave, northern China and its regional significance. J Hum Evol 2018; 121:170-177. [DOI: 10.1016/j.jhevol.2018.02.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 02/19/2018] [Accepted: 02/20/2018] [Indexed: 01/29/2023]
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26
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Fujito NT, Satta Y, Hane M, Matsui A, Yashima K, Kitajima K, Sato C, Takahata N, Hayakawa T. Positive selection on schizophrenia-associated ST8SIA2 gene in post-glacial Asia. PLoS One 2018; 13:e0200278. [PMID: 30044798 PMCID: PMC6059407 DOI: 10.1371/journal.pone.0200278] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 06/23/2018] [Indexed: 11/19/2022] Open
Abstract
A number of loci are associated with highly heritable schizophrenia and the prevalence of this mental illness has had considerable negative fitness effects on human populations. Here we focused on one particular schizophrenia-associated gene that encodes a sialyltransferase (ST8SIA2) and is expressed preferentially in the brain with the level being largely determined by three SNPs in the promoter region. It is suggested that the expression level of the ST8SIA2 gene is a genetic determinant of schizophrenia risk, and we found that a geographically differentiated non-risk SNP type (CGC-type) has significantly reduced promoter activity. A newly developed method for detecting ongoing positive selection was applied to the ST8SIA2 genomic region with the identification of an unambiguous sweep signal in a rather restricted region of 18 kb length surrounding the promoter. We also found that while the CGC-type emerged in anatomically modern humans in Africa over 100 thousand years ago, it has increased its frequency in Asia only during the past 20-30 thousand years. These findings support that the positive selection is driven by psychosocial stress due to changing social environments since around the last glacial maximum, and raise a possibility that schizophrenia extensively emerged during the Upper Paleolithic and Neolithic era.
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Affiliation(s)
- Naoko T. Fujito
- School of Advanced Sciences, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Kanagawa, Japan
| | - Yoko Satta
- School of Advanced Sciences, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Kanagawa, Japan
| | - Masaya Hane
- Bioscience and Biotechnology Center, Nagoya University, Aichi, Japan
| | - Atsushi Matsui
- Primate Research Institute, Kyoto University, Aichi, Japan
| | - Kenta Yashima
- School of Advanced Sciences, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Kanagawa, Japan
| | - Ken Kitajima
- Bioscience and Biotechnology Center, Nagoya University, Aichi, Japan
| | - Chihiro Sato
- Bioscience and Biotechnology Center, Nagoya University, Aichi, Japan
| | - Naoyuki Takahata
- School of Advanced Sciences, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Kanagawa, Japan
| | - Toshiyuki Hayakawa
- Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan
- Faculty of Arts and Science, Kyushu University, Fukuoka, Japan
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A founder homozygous DSG2 variant in East Asia results in ARVC with full penetrance and heart failure phenotype. Int J Cardiol 2018; 274:263-270. [PMID: 30454721 DOI: 10.1016/j.ijcard.2018.06.105] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 06/17/2018] [Accepted: 06/27/2018] [Indexed: 12/31/2022]
Abstract
BACKGROUND Variants in the desmoglein-2 (DSG2) gene account for a significant proportion of patients with Arrhythmogenic Right Ventricular Cardiomyopathy (ARVC). The aim of this study was to evaluate the genetic epidemiology of DSG2 and the impact of a frequent homozygous DSG2 variant in East Asia. METHODS Genetic screening of 14 ARVC related genes was performed in 118 unrelated index patients using next-generation sequencing. Following that, family screening, clinical evaluation and haplotype analysis were performed among eight probands who carry the same homozygous DSG2 variant. We also examined the histopathology and protein expression using immunofluorescence staining on the myocardial tissue of two probands undergoing heart transplant. RESULTS Eighteen (15.2%) patients bear rare putatively deleterious variants in DSG2, among which 8 patients shared the homozygous DSG2 p.Phe531Cys variant. Family screening demonstrated that only homozygous variant carriers exhibited definite ARVC phenotype with 100% penetrance, while heterozygous variant carriers were either unaffected or only presented mild ARVC related symptoms in 25% relatives. Left ventricular involvement and bi-ventricular failure were common among homozygous p. Phe531Cys variant patients even at early age. Haplotype analysis demonstrated p. Phe531Cys was a founder variant in East Asia population with an allele frequency of 0.12%. CONCLUSIONS We identified, for the first time, a homozygous founder variant of DSG2 in East Asia, which was at surprisingly high frequency of 8.47% among Chinese ARVC patients with a full penetrance. This result suggested an urgent demand of genetic counseling for the probands and their relatives with heterozygous variant.
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Yan Y, Yang X, Liu Y, Shen Y, Tu W, Dong Q, Yang D, Ma Y, Yang Y. Copy number variation of functional RBMY1 is associated with sperm motility: an azoospermia factor-linked candidate for asthenozoospermia. Hum Reprod 2018; 32:1521-1531. [PMID: 28498920 DOI: 10.1093/humrep/dex100] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 04/28/2017] [Indexed: 02/05/2023] Open
Abstract
STUDY QUESTION What is the influence of copy number variation (CNV) in functional RNA binding motif protein Y-linked family 1 (RBMY1) on spermatogenic phenotypes? SUMMARY ANSWER The RBMY1 functional copy dosage is positively correlated with sperm motility, and dosage insufficiency is an independent risk factor for asthenozoospermia. WHAT IS KNOWN ALREADY RBMY1, a multi-copy gene expressed exclusively in the adult testis, is one of the most important candidates for male infertility in the azoospermia factor (AZF) region of the Y-chromosome. RBMY1 encodes an RNA-binding protein that serves as a pre-mRNA splicing regulator during spermatogenesis, and male mice deficient in Rbmy are sterile. STUDY DESIGN, SIZE, DURATION A total of 3127 adult males were recruited from 2009 to 2016; of this group, the dosage of RBMY1 functional copy were investigated in 486 fertile males. In the remaining 2641 males with known spermatogenesis status, 1070 Y-chromosome haplogroup (Y-hg) O3* or O3e carriers without chromosomal aberration or known AZF structure mutations responsible for spermatogenic impairment, including 506 men with normozoospermia and 564 men with oligozoospermia or/and asthenozoospermia, were screened, and the RBMY1 functional copy dosage and copy conversion were determined to explore their associations with sperm phenotypes. The correlation between RBMY1 dosage and its mRNA level or RBMY1 protein level and the correlation between sperm RBMY1 level and motility were analysed in 15 testis tissue samples and eight semen samples. Ten additional semen samples were used to confirm the subcellular localization of RBMY1 in individual sperm. PARTICIPANTS/MATERIALS, SETTING, METHODS All the Han volunteers donating whole blood, semen and testis tissue were from southwest China. RBMY1 copy number, copy conversion, mRNA/protein amount and protein location in sperm were detected using the AccuCopy® assay method, paralog ratio test, quantitative PCR, western blotting and immunofluorescence staining methods, respectively. MAIN RESULTS AND THE ROLE OF CHANCE This study identified Y-hg-independent CNV of functional RBMY1 in the enrolled population. A difference in the distribution of RBMY1 copy number was observed between the group with normal sperm motility and the group with asthenozoospermia. A positive correlation between the RBMY1 copy dosage and sperm motility was identified, and the males with fewer than six copies of RBMY1 showed an elevated risk for asthenozoospermia relative to those with six RBMY1 copies, the most common dosage in the population. The RBMY1 copy dosage was positively correlated with its mRNA and protein level in the testis. Sperm with high motility were found to carry more RBMY1 protein than those with relatively low motility. The RBMY1 protein was confirmed to predominantly localize in the neck and mid-piece region of sperm as well as the principal piece of the sperm tail. Our population study completes a chain of evidence suggesting that RBMY1 influences the susceptibility of males to asthenozoospermia by modulating sperm motility. LIMITATIONS REASONS FOR CAUTION High sequence similarity between the RBMY1 functional copies and a large number of pseudogenes potentially reduces the accuracy of the copy number detection. The mechanism underlying the CNV in RBMY1 is still unclear, and the effect of the structural variations in the RBMY1 copy cluster on the copy dosage of other protein-coding genes located in the region cannot be excluded, which may potentially bias our observations. WIDER IMPLICATIONS OF THE FINDINGS Asthenozoospermia is a multi-factor complex disease with a limited number of proven susceptibility genes. This study identified a novel genomic candidate independently contributing to the condition, enriching our understanding of the role of AZF-linked genes in male reproduction. Our finding provides insight into the physiological and pathological characteristics of RBMY1 in terms of sperm motility, supplies persuasive evidence of the significance of RBMY1 copy number analysis in the clinical counselling of male infertility resulting from asthenozoospermia. STUDY FUNDING/COMPETING INTEREST(S) This work was funded by the National Natural Science Foundation of China (Nos. 81370748 and 30971598). The authors have no conflicts of interest.
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Affiliation(s)
- Yuanlong Yan
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, No. 1, Keyuan Road 4, Gaopeng Street, Chengdu, Sichuan 610041, China
| | - Xiling Yang
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, No. 1, Keyuan Road 4, Gaopeng Street, Chengdu, Sichuan 610041, China
| | - Yunqiang Liu
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, No. 1, Keyuan Road 4, Gaopeng Street, Chengdu, Sichuan 610041, China
| | - Ying Shen
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, No. 1, Keyuan Road 4, Gaopeng Street, Chengdu, Sichuan 610041, China
| | - Wenling Tu
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, No. 1, Keyuan Road 4, Gaopeng Street, Chengdu, Sichuan 610041, China
| | - Qiang Dong
- Department of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Dong Yang
- Reproductive Medicine Institute, Chengdu Women's and Children's Central Hospital, Chengdu, Sichuan 610031, China
| | - Yongyi Ma
- Jinjiang Maternal and Child Health Hospital, Chengdu, Sichuan 610016, China
| | - Yuan Yang
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, No. 1, Keyuan Road 4, Gaopeng Street, Chengdu, Sichuan 610041, China
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Sun LL, Zhang SJ, Chen MJ, Elena K, Qiao H. Relationship between Modulator Recognition Factor 2/AT-rich Interaction Domain 5B Gene Variations and Type 2 Diabetes Mellitus or Lipid Metabolism in a Northern Chinese Population. Chin Med J (Engl) 2018; 130:1055-1061. [PMID: 28469100 PMCID: PMC5421175 DOI: 10.4103/0366-6999.204926] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Background: Four single nucleotide polymorphisms (SNPs) in the modulator recognition factor 2/AT-rich interaction domain 5B (MRF2/ARID5B) gene located at chromosome 10q21.2 have been shown to be associated with both type 2 diabetes mellitus (T2DM) and coronary artery disease in a Japanese cohort. This study aimed to investigate the relationship between these SNPs (rs2893880, rs10740055, rs7087507, rs10761600) and new-onset T2DM and lipid metabolism in a Northern Chinese population. Methods: This was a case-control study. The rs2893880, rs10740055, rs7087507, and rs10761600 genetic variants were genotyped by SNPscan and analyzed in relation to T2DM susceptibility in 2000 individuals (999 with newly diagnosed T2DM and 1001 controls without diabetes mellitus). Associations between the MRF2/ARID5B genetic models and T2DM were determined by multivariate logistic regression. Results: Regarding the rs10740055 SNP, AA was associated with a higher risk of T2DM compared with codominant-type CC (adjusted by sex, age, and body mass index [BMI], P = 0.041, odds ratio [OR] = 1.421, 95% confidence interval [CI] 1.014–1.991). Meanwhile, AA individuals were at increased risk of presenting with T2DM compared with individuals with CC or a single C (adjusted by sex, age, and BMI, P = 0.034, OR = 1.366, 95% CI 1.023–1.824). With respect to rs10761600, AT contributed to a higher risk of T2DM compared with AA (adjusted by sex, age, and BMI, P = 0.013, OR = 1.585, 95% CI 1.101–2.282), while TT also increased the risk of presenting with T2DM compared with AA or A (adjusted by sex, age, and BMI, P = 0.004, OR = 1.632, 95% CI 1.166–2.284). High-density lipoprotein cholesterol (HDL-C) levels were significantly different among the three genotypes of rs7087507 in the controls (P = 0.048) (GG>GA). Conclusions: The present results identified MRF2/ARID5B as a potential susceptibility gene for new-onset T2DM in a Northern Chinese population, while the rs7087507 SNP was associated with HDL-C levels. Further larger studies are required to validate these findings.
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Affiliation(s)
- Lu-Lu Sun
- Department of Endocrinology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150000, China
| | - Si-Jia Zhang
- Department of Endocrinology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150000, China
| | - Mei-Jun Chen
- Department of Endocrinology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150000, China
| | - Kazakova Elena
- Department of Endocrinology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150000, China
| | - Hong Qiao
- Department of Endocrinology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150000, China
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30
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Ji J, Qin Y, Wang R, Huang Z, Zhang Y, Zhou R, Song L, Ling X, Hu Z, Miao D, Shen H, Xia Y, Wang X, Lu C. Copy number gain of VCX, X-linked multi-copy gene, leads to cell proliferation and apoptosis during spermatogenesis. Oncotarget 2018; 7:78532-78540. [PMID: 27705943 PMCID: PMC5340235 DOI: 10.18632/oncotarget.12397] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 09/25/2016] [Indexed: 11/25/2022] Open
Abstract
Male factor infertility affects one-sixth of couples worldwide, and non-obstructive azoospermia (NOA) is one of the most severe forms. In recent years there has been increasing evidence to implicate the participation of X chromosome in the process of spermatogenesis. To uncover the roles of X-linked multi-copy genes in spermatogenesis, we performed systematic analysis of X-linked gene copy number variations (CNVs) and Y chromosome haplogrouping in 447 idiopathic NOA patients and 485 healthy controls. Interestingly, the frequency of individuals with abnormal level copy of Variable charge, X-linked (VCX) was significantly different between cases and controls after multiple test correction (p = 5.10 × 10−5). To discriminate the effect of gain/loss copies in these genes, we analyzed the frequency of X-linked multi-copy genes in subjects among subdivided groups. Our results demonstrated that individuals with increased copy numbers of Nuclear RNA export factor 2 (NXF2) (p = 9.21 × 10−8) and VCX (p = 1.97 × 10−4) conferred the risk of NOA. In vitro analysis demonstrated that increasing copy number of VCX could upregulate the gene expression and regulate cell proliferation and apoptosis. Our study establishes a robust association between the VCX CNVs and NOA risk.
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Affiliation(s)
- Juan Ji
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China.,Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China.,Department of Children Health Care, Nanjing Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Yufeng Qin
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Rong Wang
- Research Center for Bone and Stem Cells, Department of Anatomy, Histology, and Embryology, Nanjing Medical University, Nanjing, China
| | - Zhenyao Huang
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China.,Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yan Zhang
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China.,Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Ran Zhou
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China.,Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Ling Song
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China.,Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xiufeng Ling
- Department of Children Health Care, Nanjing Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Zhibin Hu
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China.,Department of Epidemiology and Biostatistics and Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Dengshun Miao
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China.,Research Center for Bone and Stem Cells, Department of Anatomy, Histology, and Embryology, Nanjing Medical University, Nanjing, China
| | - Hongbing Shen
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China.,Department of Epidemiology and Biostatistics and Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yankai Xia
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China.,Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xinru Wang
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China.,Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Chuncheng Lu
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China.,Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
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32
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Bae CJ, Douka K, Petraglia MD. Human Colonization of Asia in the Late Pleistocene. CURRENT ANTHROPOLOGY 2017. [DOI: 10.1086/694420] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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33
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Hu W, Chen M, Ji J, Qin Y, Zhang F, Xu M, Wu W, Du G, Wu D, Han X, Jin L, Xia Y, Lu C, Wang X. Interaction between Y chromosome haplogroup O3 * and 4-n-octylphenol exposure reduces the susceptibility to spermatogenic impairment in Han Chinese. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2017; 144:450-455. [PMID: 28667856 DOI: 10.1016/j.ecoenv.2017.06.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 06/09/2017] [Accepted: 06/12/2017] [Indexed: 06/07/2023]
Abstract
Certain genetic background (mainly Y chromosome haplogroups, Y-hg) may modify the susceptibility of certain environmental exposure to some diseases. Compared with respective main effects of genetic background or environmental exposure, interactions between them reflect more realistic combined effects on the susceptibility to a disease. To identify the interactions on spermatogenic impairment, we performed Y chromosome haplotyping and measurement of 9 urinary phenols concentrations in 774 infertile males and 520 healthy controls in a Han Chinese population, and likelihood ratio tests were used to examine the interactions between Y-hgs and phenols. Originally, we observed that Y-hg C and Y-hg F* might modify the susceptibility to male infertility with urinary 4-n-octylphenol (4-n-OP) level (Pinter = 0.005 and 0.019, respectively). Subsequently, based on our results, two panels were tested to identify the possible protective sub-branches of Y-hg F* to 4-n-OP exposure, and Y-hg O3* was uncovered to interact with 4-n-OP (Pinter = 0.019). In conclusion, while 4-n-OP shows an adverse effect on spermatogenesis, Y-hg O3* makes individuals more adaptive to such an effect for maintaining basic reproductive capacity.
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Affiliation(s)
- Weiyue Hu
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Minjian Chen
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Juan Ji
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yufeng Qin
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Feng Zhang
- MOE Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Miaofei Xu
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Wei Wu
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Guizhen Du
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Di Wu
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xiumei Han
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Li Jin
- MOE Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China; Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yankai Xia
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Chuncheng Lu
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China.
| | - Xinru Wang
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China.
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Wang H, Ba H, Yang C, Zhang J, Tai Y. Inner and inter population structure construction of Chinese Jiangsu Han population based on Y23 STR system. PLoS One 2017; 12:e0180921. [PMID: 28704439 PMCID: PMC5509181 DOI: 10.1371/journal.pone.0180921] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 06/25/2017] [Indexed: 01/22/2023] Open
Abstract
In this study, we analyzed the genetic polymorphisms of 23 Y-STR loci from PowerPlex® Y23 system in 916 unrelated healthy male individuals from Chinese Jiangsu Han, and observed 912 different haplotypes including 908 unique haplotypes and 4 duplicate haplotypes. The haplotype diversity reached 0.99999 and the discrimination capacity and match probability were 0.9956 and 0.0011, respectively. The gene diversity values ranged from 0.3942 at DYS438 to 0.9607 at DYS385a/b. Population differentiation within 10 Jiangsu Han subpopulations were evaluated by RST values and visualized in Neighbor-Joining trees and Multi-Dimensional Scaling plots as well as population relationships between the Jiangsu Han population and other 18 Eastern Asian populations. Such results indicated that the 23 Y-STR loci were highly polymorphic in Jiangsu Han population and played crucial roles in forensic application as well as population genetics. For the first time, we reported the genetic diversity of male lineages in Jiangsu Han population at a high-resolution level of 23 Y-STR set and consequently contributed to familial searching, offender tracking, and anthropology analysis of Jiangsu Han population.
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Affiliation(s)
- Huipin Wang
- Zhongshan City People's Hospital, Zhongshan, Guangdong, P. R., China
| | - Huajie Ba
- DNA Laboratory, Public Security Bureau of Changzhou, Changzhou, Jiangsu, P. R., China
| | - Chun Yang
- Department of Psychiatry, Psychiatry Center of Chinese People’s Liberation Army, No. 102 Hospital of People’s Liberation Army, Changzhou, Jiangsu, P. R., China
| | - Jianqiu Zhang
- DNA Laboratory, Public Security Bureau of Yangzhou, Yangzhou, Jiangsu, P. R., China
| | - Yunchun Tai
- School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, P. R., China
- * E-mail:
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35
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Nothnagel M, Fan G, Guo F, He Y, Hou Y, Hu S, Huang J, Jiang X, Kim W, Kim K, Li C, Li H, Li L, Li S, Li Z, Liang W, Liu C, Lu D, Luo H, Nie S, Shi M, Sun H, Tang J, Wang L, Wang CC, Wang D, Wen SQ, Wu H, Wu W, Xing J, Yan J, Yan S, Yao H, Ye Y, Yun L, Zeng Z, Zha L, Zhang S, Zheng X, Willuweit S, Roewer L. Revisiting the male genetic landscape of China: a multi-center study of almost 38,000 Y-STR haplotypes. Hum Genet 2017; 136:485-497. [PMID: 28138773 DOI: 10.1007/s00439-017-1759-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 01/13/2017] [Indexed: 02/05/2023]
Abstract
China has repeatedly been the subject of genetic studies to elucidate its prehistoric and historic demography. While some studies reported a genetic distinction between Northern and Southern Han Chinese, others showed a more clinal picture of small differences within China. Here, we investigated the distribution of Y chromosome variation along administrative as well as ethnic divisions in the mainland territory of the People's Republic of China, including 28 administrative regions and 19 recognized Chinese nationalities, to assess the impact of recent demographic processes. To this end, we analyzed 37,994 Y chromosomal 17-marker haplotype profiles from the YHRD database with respect to forensic diversity measures and genetic distance between groups defined by administrative boundaries and ethnic origin. We observed high diversity throughout all Chinese provinces and ethnicities. Some ethnicities, including most prominently Kazakhs and Tibetans, showed significant genetic differentiation from the Han and other groups. However, differences between provinces were, except for those located on the Tibetan plateau, less pronounced. This discrepancy is explicable by the sizeable presence of Han speakers, who showed high genetic homogeneity all across China, in nearly all studied provinces. Furthermore, we observed a continuous genetic North-South gradient in the Han, confirming previous reports of a clinal distribution of Y chromosome variation and being in notable concordance with the previously observed spatial distribution of autosomal variation. Our findings shed light on the demographic changes in China accrued by a fast-growing and increasingly mobile population.
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Affiliation(s)
- Michael Nothnagel
- Department of Statistical Genetics and Bioinformatics, Cologne Center for Genomics (CCG), University of Cologne, Weyertal 115b, 50931, Cologne, Germany.
| | - Guangyao Fan
- Department of Public Security Technology, The Center for Forensic Science Research, Railway Police College, Zhengzhou, 450053, People's Republic of China
| | - Fei Guo
- Department of Forensic Medicine, National Police University of China, Shenyang, 110854, People's Republic of China
| | - Yongfeng He
- Department of Criminal Investigation, Shaanxi Provincial Public Security Bureau, Xi'an, 710016, People's Republic of China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Shengping Hu
- Molecular Biology and Forensic Genetics Laboratory, Shantou University Medical College, Shantou, People's Republic of China
| | - Jiang Huang
- Department of Forensic Medicine, Guizhou Medical University, Beijing Road, 9th, Guiyang, 550004, People's Republic of China
| | - Xianhua Jiang
- Liaoning Criminal and Science Technology Research Institute, Shenyang, 110032, People's Republic of China
| | - Wook Kim
- Department of Biological Sciences, Dankook University, Cheonan, 330-714, Republic of Korea
| | - Kicheol Kim
- Department of Neurology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Chengtao Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Institute of Forensic Sciences, Ministry of Justice, P.R. China, Shanghai, 200063, People's Republic of China
| | - Hui Li
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, People's Republic of China
| | - Liming Li
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, People's Republic of China
| | - Shilin Li
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, People's Republic of China
| | - Zhao Li
- Department of Criminal Investigation, Hebei Provincial Public Security Bureau, Shijiazhuang City, 050000, People's Republic of China
| | - Weibo Liang
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Chao Liu
- Guangzhou Forensic Science Institute, Guangzhou, 510030, People's Republic of China
| | - Di Lu
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, People's Republic of China
| | - Haibo Luo
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Shengjie Nie
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, People's Republic of China
| | - Meisen Shi
- Center of Cooperative Innovation for Judicial Civilization, Institute of Evidence Law and Forensic Science, China University of Political Science and Law, Ministry of Education, Beijing, 100088, People's Republic of China
| | - Hongyu Sun
- Department of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510089, People's Republic of China
| | - Jianpin Tang
- Department of Forensic Medicine, Guangdong Medical University, Dongguan, 523808, People's Republic of China
| | - Lei Wang
- Department of Forensic Sciences, Police Station of Zhengzhou, Zhengzhou, Henan, 450008, People's Republic of China
| | - Chuan-Chao Wang
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Dan Wang
- Institute of Forensic Medicine and Laboratory Medicine, Jining Medical University, Jining, Shandong, People's Republic of China
| | - Shao-Qing Wen
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, People's Republic of China
| | - Hongyan Wu
- Xinxiang Medical University School of Basic Medical, Xinxiang, Henan, 453003, People's Republic of China
| | - Weiwei Wu
- Institute of Forensic Science, Zhejiang Provincial Public Security Bureau, Hangzhou, 310009, People's Republic of China
| | - Jiaxin Xing
- School of Forensic Medicine, China Medical University, Shenyang, People's Republic of China
| | - Jiangwei Yan
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Shi Yan
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, People's Republic of China
| | - Hongbing Yao
- Key Laboratory of Evidence Science of Gansu Province, Gansu Institute of Political Science and Law, Lanzhou, 730070, People's Republic of China
| | - Yi Ye
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Libing Yun
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Zhaoshu Zeng
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450052, People's Republic of China
| | - Lagabaiyila Zha
- Forensic Science Department, School of Basic Medical Sciences, Central South University, Changsha, 410013, People's Republic of China
| | - Suhua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Institute of Forensic Sciences, Ministry of Justice, P.R. China, Shanghai, 200063, People's Republic of China
| | - Xiufen Zheng
- Department of Pathology, Department of Surgery, Department of Oncology, University of Western Ontario, Lawson Health Research Institute, London, Canada
| | - Sascha Willuweit
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Lutz Roewer
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin Berlin, Berlin, Germany
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Improved phylogenetic resolution for Y-chromosome Haplogroup O2a1c-002611. Sci Rep 2017; 7:1146. [PMID: 28442769 PMCID: PMC5430735 DOI: 10.1038/s41598-017-01340-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 03/28/2017] [Indexed: 11/25/2022] Open
Abstract
Y-chromosome Haplogroup O2a1c-002611 is one of the dominant lineages of East Asians and Southeast Asians. However, its internal phylogeny remains insufficiently investigated. In this study, we genotyped 89 new highly informative single nucleotide polymorphisms (SNPs) in 305 individuals with Haplogroup O2a1c-002611 identified from 2139 Han Chinese males. Two major branches were identified, O2a1c1-F18 and O2a1c2-L133.2 and the first was further divided into two main subclades, O2a1c1a-F11 and O2a1c1b-F449, accounting for 11.13% and 2.20% of Han Chinese, respectively. In Haplogroup O2a1c1a-F11, we also determined seven sublineages with quite different frequency distributions in Han Chinese ranging from 0.187% to 3.553%, implying they might have different demographic history. The reconstructed haplogroup tree for all the major clades within Haplogroup O2a1c-002611 permits better resolution of male lineages in population studies of East Asia and Southeast Asia. The dataset generated in the present study are also valuable for forensic identification and paternity tests in China.
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Wei LH, Li H. Fuyan human of 120-80kya cannot challenge the Out-of-Africa theory for modern human dispersal. Sci Bull (Beijing) 2017; 62:316-318. [PMID: 36659414 DOI: 10.1016/j.scib.2017.01.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Lan-Hai Wei
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Hui Li
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200438, China.
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Variability of 128 schizophrenia-associated gene variants across distinct ethnic populations. Transl Psychiatry 2017; 7:e988. [PMID: 28045464 PMCID: PMC5545726 DOI: 10.1038/tp.2016.260] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 10/06/2016] [Accepted: 10/31/2016] [Indexed: 12/20/2022] Open
Abstract
Schizophrenia is a common polygenetic disease affecting 0.5-1% of individuals across distinct ethnic populations. PGC-II, the largest genome-wide association study investigating genetic risk factors for schizophrenia, previously identified 128 independent schizophrenia-associated genetic variants (GVs). The current study examined the genetic variability of GVs across ethnic populations. To assess the genetic variability across populations, the 'variability indices' (VIs) of the 128 schizophrenia-associated GVs were calculated. We used 2504 genomes from the 1000 Genomes Project taken from 26 worldwide healthy samples comprising five major ethnicities: East Asian (EAS: n=504), European (EUR: n=503), African (AFR: n=661), American (AMR: n=347) and South Asian (SAS: n=489). The GV with the lowest variability was rs36068923 (VI=1.07). The minor allele frequencies (MAFs) were 0.189, 0.192, 0.256, 0.183 and 0.194 for EAS, EUR, AFR, AMR and SAS, respectively. The GV with the highest variability was rs7432375 (VI=9.46). The MAFs were 0.791, 0.435, 0.041, 0.594 and 0.508 for EAS, EUR, AFR, AMR and SAS, respectively. When we focused on the EAS and EUR population, the allele frequencies of 86 GVs significantly differed between the EAS and EUR (P<3.91 × 10-4). The GV with the highest variability was rs4330281 (P=1.55 × 10-138). The MAFs were 0.023 and 0.519 for the EAS and EUR, respectively. The GV with the lowest variability was rs2332700 (P=9.80 × 10-1). The MAFs were similar between these populations (that is, 0.246 and 0.247 for the EAS and EUR, respectively). Interestingly, the mean allele frequencies of the GVs did not significantly differ between these populations (P>0.05). Although genetic heterogeneities were observed in the schizophrenia-associated GVs across ethnic groups, the combination of these GVs might increase the risk of schizophrenia.
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39
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Ko KH. Hominin interbreeding and the evolution of human variation. JOURNAL OF BIOLOGICAL RESEARCH-THESSALONIKI 2016; 23:17. [PMID: 27429943 PMCID: PMC4947341 DOI: 10.1186/s40709-016-0054-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Accepted: 06/30/2016] [Indexed: 11/29/2022]
Abstract
Mitochondrial Eve confirms the “out of Africa” theory, but the evidence also supports interbreeding between Homo sapiens and other hominins: Neanderthals, Denisovans, and Homo heidelbergensis. This article explains how interbreeding between early H. sapiens and archaic hominins occurred. The availability of edible insects in East Asia aided the spread of the unaggressive, highly cooperative Neanderthals, who interbred with H. sapiens in Asia, resulting in a higher admixture of Neanderthal DNA in East Asian populations. Geographical variation in degree of interbreeding between H. sapiens and Neanderthals likely contributed to neurological and behavioral differences in modern humans. Similarly, people with Denisovan genetic admixture were better able to dwell in mountainous regions, allowing their genetic legacy to cross the Himalayas and persist in Southeast Asian and Oceanian H. sapiens. In the Sub-Saharan region, unaffected by Denisovan or Neanderthal interbreeding, H. sapiens interbred with H. heidelbergensis, because high humidity militated against fire-making and allowed the survival of these non-fire-making hominins.
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40
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Wong HM, Wen YF, Jayaraman J, Li J, Sun L, King NM, Roberts GJ. Northern Chinese dental ages estimated from southern Chinese reference datasets closely correlate with chronological age. Heliyon 2016; 2:e00216. [PMID: 28018985 PMCID: PMC5176030 DOI: 10.1016/j.heliyon.2016.e00216] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Revised: 11/25/2016] [Accepted: 12/09/2016] [Indexed: 11/17/2022] Open
Abstract
While northern and southern Chinese are genetically correlated, there exists notable environmental differences in their living conditions. This study aimed to evaluate validity of the southern Chinese reference dataset for dental age estimation applied to northern Chinese. Dental panoramic tomographs of 437 northern Chinese aged 3 to 21 years were analysed. All the left maxillary and mandibular permanent teeth plus the 2 third molars on the right side were scored based on Demirjian's classification of tooth development stages. Mean and standard error of dental age were obtained for each tooth development stage, followed by random effect meta-analysis for mean dental age estimation. Validity of the method was examined through measures of agreement (95% limits of agreement, standard error of measurement, and Lin's concordance correlation coefficient) and measure of reliability (Intraclass correlation coefficient). On average, the estimated dental age overestimated chronological age by only around 1 month in both females and males. The Intraclass correlation coefficient values were 0.99 for both sexes, suggesting excellent reliability of the method. Reference dataset for dental age estimation developed on the basis of southern Chinese was applicable for use among the northern Chinese.
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Affiliation(s)
- Hai Ming Wong
- Paediatric Dentistry, Faculty of Dentistry, The University of Hong Kong, Prince Philip Dental Hospital, 34 Hospital Road, Sai Ying Pun, Hong Kong
| | - Yi Feng Wen
- Paediatric Dentistry, Faculty of Dentistry, The University of Hong Kong, Prince Philip Dental Hospital, 34 Hospital Road, Sai Ying Pun, Hong Kong
| | - Jayakumar Jayaraman
- School of Dentistry, International Medical University, Kuala Lumpur, Malaysia
| | - Jing Li
- Department of Pediatric Dentistry, Peking University School and Hospital of Stomatology, Beijing, China
| | - Ling Sun
- Paediatric Dentistry, Faculty of Dentistry, The University of Hong Kong, Prince Philip Dental Hospital, 34 Hospital Road, Sai Ying Pun, Hong Kong
| | - Nigel Martyn King
- Paediatric Dentistry, School of Dentistry, University of Western Australia, Oral Health Centre of WA, Australia
| | - Graham J. Roberts
- Paediatric Dentistry, King’s College London Dental Institute, London, United Kingdom
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41
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Sikdar M. Hemoglobin E in Northeast India: A review on its origin, distribution, migration and health implication. ANTHROPOLOGICAL REVIEW 2016. [DOI: 10.1515/anre-2016-0019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
A systematic review of the studies on hemoglobin E in Northeast India has been carried out to understand the magnitude of research undertaken on this aspect during the last seven decades. Owing to the high prevalence of hemoglobin E in this part of India different authors have studied this hemoglobin from different perspectives and found conflicting results. However a systematic review of such studies is lacking from a holistic point of view. Most of the epidemiological, in vitro as well as in vivo studies show signatures of selection with this hemoglobin locus. However, how this polymorphism is maintained at different rates at different geographical region is still a matter of contention. This review will fill the gap from all perspectives starting from the frequency distribution of hemoglobin E and its spread in different parts of Northeast India, its relationship with malaria hypothesis, the population migration, population affinity and most importantly the health implication arising out of it. A probable origin of hemoglobin E among an Austroasiatic population of Northeast India has been postulated with the help of advance molecular anthropological knowledge like the deep rooted markers of mt DNA and Y-chromosome haplotypes.
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42
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Lu C, Wen Y, Hu W, Lu F, Qin Y, Wang Y, Li S, Yang S, Lin Y, Wang C, Jin L, Shen H, Sha J, Wang X, Hu Z, Xia Y. Y chromosome haplogroups based genome-wide association study pinpoints revelation for interactions on non-obstructive azoospermia. Sci Rep 2016; 6:33363. [PMID: 27628680 PMCID: PMC5024297 DOI: 10.1038/srep33363] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 08/25/2016] [Indexed: 01/02/2023] Open
Abstract
The Y chromosome has high genetic variability with low rates of parallel and back mutations, which make up the most informative haplotyping system. To examine whether Y chromosome haplogroups (Y-hgs) could modify the effects of autosomal variants on non-obstructive azoospermia (NOA), based on our previous genome-wide association study (GWAS), we conducted a genetic interaction analysis in GWAS subjects. Logistic regression analysis demonstrated a protective effect of Y-hg O3e* on NOA. Then, we explored the potential interaction between Y-hg O3e* and autosomal variants. Our results demonstrated that there was a suggestively significant interaction between Y-hg O3e* and rs11135484 on NOA (Pinter = 9.89 × 10−5). Bioinformatic analysis revealed that genes annotated by significant single nucleotide polymorphisms (SNPs) were mainly enriched in immunological pathways. This is the first study of interactions between Y-hgs and autosomal variants on a genome-wide scale, which addresses the missing heritability in spermatogenic impairment and sheds new light on the pathogenesis of male infertility.
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Affiliation(s)
- Chuncheng Lu
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing 210029, China.,Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 210029, China
| | - Yang Wen
- Department of Epidemiology and Biostatistics and Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Weiyue Hu
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 210029, China
| | - Feng Lu
- Department of Epidemiology and Biostatistics and Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yufeng Qin
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 210029, China
| | - Ying Wang
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 210029, China
| | - Shilin Li
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Shuping Yang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Yuan Lin
- Department of Epidemiology and Biostatistics and Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Cheng Wang
- Department of Epidemiology and Biostatistics and Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China.,Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Hongbing Shen
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing 210029, China.,Department of Epidemiology and Biostatistics and Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Jiahao Sha
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing 210029, China
| | - Xinru Wang
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing 210029, China.,Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 210029, China
| | - Zhibin Hu
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing 210029, China.,Department of Epidemiology and Biostatistics and Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yankai Xia
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing 210029, China.,Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 210029, China
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43
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Fan GY, Ye Y, Hou YP. Detecting a hierarchical genetic population structure via Multi-InDel markers on the X chromosome. Sci Rep 2016; 6:32178. [PMID: 27535707 PMCID: PMC4989243 DOI: 10.1038/srep32178] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 08/03/2016] [Indexed: 01/15/2023] Open
Abstract
Detecting population structure and estimating individual biogeographical ancestry are very important in population genetics studies, biomedical research and forensics. Single-nucleotide polymorphism (SNP) has long been considered to be a primary ancestry-informative marker (AIM), but it is constrained by complex and time-consuming genotyping protocols. Following up on our previous study, we propose that a multi-insertion-deletion polymorphism (Multi-InDel) with multiple haplotypes can be useful in ancestry inference and hierarchical genetic population structures. A validation study for the X chromosome Multi-InDel marker (X-Multi-InDel) as a novel AIM was conducted. Genetic polymorphisms and genetic distances among three Chinese populations and 14 worldwide populations obtained from the 1000 Genomes database were analyzed. A Bayesian clustering method (STRUCTURE) was used to discern the continental origins of Europe, East Asia, and Africa. A minimal panel of ten X-Multi-InDels was verified to be sufficient to distinguish human ancestries from three major continental regions with nearly the same efficiency of the earlier panel with 21 insertion-deletion AIMs. Along with the development of more X-Multi-InDels, an approach using this novel marker has the potential for broad applicability as a cost-effective tool toward more accurate determinations of individual biogeographical ancestry and population stratification.
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Affiliation(s)
- Guang Yao Fan
- Department of Forensic Genetics, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China
- The Center for Forensic Science Research, Department of Public Security Technology, Railway Police College, Zhengzhou 450053, China
| | - Yi Ye
- The Center for Forensic Science Research, Department of Public Security Technology, Railway Police College, Zhengzhou 450053, China
- Department of Forensic Analytical Toxicology, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China
| | - Yi Ping Hou
- Department of Forensic Genetics, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China
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Yao M, Wu Y, Fang Q, Sun L, Li T, Qiao H. Association of ADIPOQ variants with type 2 diabetes mellitus susceptibility in ethnic Han Chinese from northeast China. J Diabetes Investig 2016; 7:853-859. [PMID: 27181706 PMCID: PMC5089947 DOI: 10.1111/jdi.12535] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 03/30/2016] [Accepted: 04/28/2016] [Indexed: 01/08/2023] Open
Abstract
AIMS/INTRODUCTION To investigate the association between two single nucleotide polymorphisms (SNPs; rs3774261 and rs822393) in the ADIPOQ gene and type 2 diabetes mellitus in Han Chinese from northeast China. MATERIALS AND METHODS The present study comprised 993 type 2 diabetes mellitus patients and 966 unrelated controls from northeastern China. Two SNPs were sequenced using SNPscan. The distribution of genotype frequencies of the two SNPs in ADIPOQ between cases and controls, and in subgroups stratified based on body mass index, were compared using logistic regression analysis. Linear regression was used to analyze the association between each SNP and clinical indicators. RESULTS The GG genotype of rs3774261 increased the risk of type 2 diabetes mellitus compared with the AA genotype in participants with a body mass index <24 (P = 0.021; odds ratio 1.636, 95% CI 1.708-2.484). Rs822393 was correlated with glycosylated hemoglobin (P = 0.043) in controls. Rs3774261 had an association with diastolic blood pressure (P = 0.017) in controls, and in controls with a body mass index <24; rs3774261 also had an association with both systolic blood pressure (P = 0.025) and diastolic blood pressure (P = 0.043). CONCLUSIONS The present results confirm the association between ADIPOQ variants and type 2 diabetes mellitus in northeastern China. However, additional larger replication studies are required to validate these findings.
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Affiliation(s)
- Meidong Yao
- Department of Endocrinology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang, China
| | - Yanhui Wu
- Department of Endocrinology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang, China
| | - Qingxiao Fang
- Department of Endocrinology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang, China
| | - Lulu Sun
- Department of Endocrinology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang, China
| | - Tingting Li
- Department of Endocrinology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang, China
| | - Hong Qiao
- Department of Endocrinology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang, China.
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Yang Z, Zhong H, Chen J, Zhang X, Zhang H, Luo X, Xu S, Chen H, Lu D, Han Y, Li J, Fu L, Qi X, Peng Y, Xiang K, Lin Q, Guo Y, Li M, Cao X, Zhang Y, Liao S, Peng Y, Zhang L, Guo X, Dong S, Liang F, Wang J, Willden A, Seang Aun H, Serey B, Sovannary T, Bunnath L, Samnom H, Mardon G, Li Q, Meng A, Shi H, Su B. A Genetic Mechanism for Convergent Skin Lightening during Recent Human Evolution. Mol Biol Evol 2016; 33:1177-87. [PMID: 26744415 PMCID: PMC4839214 DOI: 10.1093/molbev/msw003] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Skin lightening among Eurasians is thought to have been a convergence occurring independently in Europe and East Asia as an adaptation to high latitude environments. Among Europeans, several genes responsible for such lightening have been found, but the information available for East Asians is much more limited. Here, a genome-wide comparison between dark-skinned Africans and Austro-Asiatic speaking aborigines and light-skinned northern Han Chinese identified the pigmentation gene OCA2, showing unusually deep allelic divergence between these groups. An amino acid substitution (His615Arg) of OCA2 prevalent in most East Asian populations—but absent in Africans and Europeans—was significantly associated with skin lightening among northern Han Chinese. Further transgenic and targeted gene modification analyses of zebrafish and mouse both exhibited the phenotypic effect of the OCA2 variant manifesting decreased melanin production. These results indicate that OCA2 plays an important role in the convergent skin lightening of East Asians during recent human evolution.
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Affiliation(s)
- Zhaohui Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Hua Zhong
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX
| | - Jing Chen
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Xiaoming Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Hui Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Xin Luo
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Shuhua Xu
- Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society (CAS-MPG) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Hua Chen
- Center for Computational Genomics, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Dongsheng Lu
- Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society (CAS-MPG) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yinglun Han
- College of Life Science, Liaoning Normal University, Dalian, China
| | - Jinkun Li
- Department of Urology, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Lijie Fu
- Department of Urology, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Xuebin Qi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yi Peng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Kun Xiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Qiang Lin
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Yan Guo
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Ming Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Xiangyu Cao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yanfeng Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Shiyu Liao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yingmei Peng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Lin Zhang
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Xiaosen Guo
- BGI-Shenzhen, Shenzhen, China Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Jun Wang
- BGI-Shenzhen, Shenzhen, China Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Andrew Willden
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Hong Seang Aun
- Geography and Land Management, Royal University of Phnom Penh, Phnom Penh, Kingdom of Cambodia
| | - Bun Serey
- Geography and Land Management, Royal University of Phnom Penh, Phnom Penh, Kingdom of Cambodia
| | - Tuot Sovannary
- Geography and Land Management, Royal University of Phnom Penh, Phnom Penh, Kingdom of Cambodia
| | - Long Bunnath
- Geography and Land Management, Royal University of Phnom Penh, Phnom Penh, Kingdom of Cambodia
| | - Ham Samnom
- Capacity Development Facilitator for Handicap International Federation and Freelance Researcher, Battambang, Kingdom of Cambodia
| | - Graeme Mardon
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX
| | - Qingwei Li
- College of Life Science, Liaoning Normal University, Dalian, China
| | - Anming Meng
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Hong Shi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
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Abstract
The causative agent of human tuberculosis (TB), Mycobacterium tuberculosis, is an obligate pathogen that evolved to exclusively persist in human populations. For M. tuberculosis to transmit from person to person, it has to cause pulmonary disease. Therefore, M. tuberculosis virulence has likely been a significant determinant of the association between M. tuberculosis and humans. Indeed, the evolutionary success of some M. tuberculosis genotypes seems at least partially attributable to their increased virulence. The latter possibly evolved as a consequence of human demographic expansions. If co-evolution occurred, humans would have counteracted to minimize the deleterious effects of M. tuberculosis virulence. The fact that human resistance to infection has a strong genetic basis is a likely consequence of such a counter-response. The genetic architecture underlying human resistance to M. tuberculosis remains largely elusive. However, interactions between human genetic polymorphisms and M. tuberculosis genotypes have been reported. Such interactions are consistent with local adaptation and allow for a better understanding of protective immunity in TB. Future 'genome-to-genome' studies, in which locally associated human and M. tuberculosis genotypes are interrogated in conjunction, will help identify new protective antigens for the development of better TB vaccines.
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Affiliation(s)
- Daniela Brites
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute and University of Basel, Basel, Switzerland
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Y-chromosome diversity suggests southern origin and Paleolithic backwave migration of Austro-Asiatic speakers from eastern Asia to the Indian subcontinent. Sci Rep 2015; 5:15486. [PMID: 26482917 PMCID: PMC4611482 DOI: 10.1038/srep15486] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 09/28/2015] [Indexed: 01/01/2023] Open
Abstract
Analyses of an Asian-specific Y-chromosome lineage (O2a1-M95)—the dominant paternal lineage in Austro-Asiatic (AA) speaking populations, who are found on both sides of the Bay of Bengal—led to two competing hypothesis of this group’s geographic origin and migratory routes. One hypothesis posits the origin of the AA speakers in India and an eastward dispersal to Southeast Asia, while the other places an origin in Southeast Asia with westward dispersal to India. Here, we collected samples of AA-speaking populations from mainland Southeast Asia (MSEA) and southern China, and genotyped 16 Y-STRs of 343 males who belong to the O2a1-M95 lineage. Combining our samples with previous data, we analyzed both the Y-chromosome and mtDNA diversities. We generated a comprehensive picture of the O2a1-M95 lineage in Asia. We demonstrated that the O2a1-M95 lineage originated in the southern East Asia among the Daic-speaking populations ~20–40 thousand years ago and then dispersed southward to Southeast Asia after the Last Glacial Maximum before moving westward to the Indian subcontinent. This migration resulted in the current distribution of this Y-chromosome lineage in the AA-speaking populations. Further analysis of mtDNA diversity showed a different pattern, supporting a previously proposed sex-biased admixture of the AA-speaking populations in India.
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Li T, Ren Z, Deng Y, Wang Y, Zhou H. Lack of association between RAD50-IL13 polymorphisms and pediatric asthma susceptibility in Northeastern Han Chinese. J Asthma 2015; 53:114-8. [PMID: 26365633 DOI: 10.3109/02770903.2015.1067322] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
OBJECTIVE RAD50-IL13 region has been recently identified as one of critical asthma susceptibility loci in genome-wide association studies, yet the role of these genetic variants or single-nucleotide polymorphisms (SNPs) in the risk of developing asthma in Northeastern Han Chinese remains largely unknown. METHODS We conducted an association study by genotyping four SNPs (rs2244012 and rs6871536 in RAD50 as well as rs1295686 and rs1800925 in IL13) in 652 asthmatic children and age-matched 752 healthy controls from Northeastern Han Chinese to evaluate the asthma susceptibility with each individual SNP using SNaPshot genotyping method. RESULTS We did not find the allele or genotype frequency distribution of four SNPs in RAD50-IL13 region which was significantly different between asthmatic children and controls (p > 0.05). CONCLUSIONS Our findings first suggested that the variants in RAD50-IL13 region were not associated with asthma risk in Northeastern Han Chinese children.
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Affiliation(s)
- Tianxiao Li
- a Department of Biochemistry and Molecular Biology , Harbin Medical University , Harbin , China
| | | | - Ying Deng
- c Department of Emergency , The Second Affiliated Hospital, Harbin Medical University , Harbin , China , and
| | - Yi Wang
- d Biotechnology Experimental Teaching Center, Harbin Medical University , Harbin , China
| | - Hongbo Zhou
- a Department of Biochemistry and Molecular Biology , Harbin Medical University , Harbin , China
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Ning C, Yan S, Hu K, Cui YQ, Jin L. Refined phylogenetic structure of an abundant East Asian Y-chromosomal haplogroup O*-M134. Eur J Hum Genet 2015; 24:307-9. [PMID: 26306641 DOI: 10.1038/ejhg.2015.183] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 07/02/2015] [Accepted: 07/05/2015] [Indexed: 11/09/2022] Open
Abstract
The human Y-chromosome haplogroup O-M134 is one of the most abundant paternal lineages in East Asian populations, comprising ~13% of Han Chinese males, and also common in Kazakh, Korean, Japanese, Thai and so on. Despite its considerable prevalence, its current substructure is poorly resolved with only one downstream marker (M117) previously investigated. Here we address this deficiency by investigating some single-nucleotide polymorphisms (SNPs) previously reported being potentially associated with O-M134 based on high-throughput DNA-sequencing data. Using a panel of 1301 Chinese males we first identified 154 haplogroup O-M134 subjects. We then investigated the phylogenetic structure within this haplogroup using 10 SNPs (F444, F629, F3451, F46, F48, F209, F2887, F3386, F1739 and F152). Two major branches were identified, O-M117 and O-F444 and the latter was further divided into two main subclades, O-F629 and O-F3451, accounting for 10.84 and 0.92% of the Han Chinese, respectively. This update of O-M134 diversification permits better resolution of male lineages in population studies of East Asia.
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Affiliation(s)
- Chao Ning
- School of Life Sciences, Jilin University, Changchun, China
| | - Shi Yan
- Ministry of Education, Key Laboratory of Contemporary Anthropology and Center for Evolutionary Biology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Kang Hu
- Key Laboratory of High Altitude Environment and Gene Related to Disease of Tibet Ministry of Education, Tibet University for Nationalities, Xianyang, China
| | - Yin-Qiu Cui
- School of Life Sciences, Jilin University, Changchun, China
| | - Li Jin
- Ministry of Education, Key Laboratory of Contemporary Anthropology and Center for Evolutionary Biology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Chinese Academy of Sciences Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, SIBS, CAS, Shanghai, China
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50
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Sun H, Yang Z, Lin K, Liu S, Huang K, Wang X, Chu J, Huang X. The Adaptive Change of HLA-DRB1 Allele Frequencies Caused by Natural Selection in a Mongolian Population That Migrated to the South of China. PLoS One 2015; 10:e0134334. [PMID: 26230582 PMCID: PMC4521750 DOI: 10.1371/journal.pone.0134334] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 07/08/2015] [Indexed: 01/18/2023] Open
Abstract
Pathogen-driven balancing selection determines the richness of human leukocyte antigen (HLA) alleles. Changes in the pathogen spectrum may cause corresponding changes in HLA loci. Approximately 700 years ago, a Mongolian population moved from the north of China to the Yunnan region in the south of China. The pathogen spectrum in the south of China differs from that in the north. In this study, changes in the HLA genes in the Yunnan Mongolian population, as well as the underlying mechanism, were investigated. A sequence-based typing method (SBT) was used to genotype HLA-DRB1 in 470 individuals from two Mongolian populations and another five ethnic groups. Meanwhile, 10 autosomal short tandem repeats (STRs) were genotyped to assess the influence of genetic background on HLA-DRB1 frequencies. The frequencies of certain alleles changed significantly in the Mongolian population that migrated to Yunnan. For example, DRB1*12:02:01 increased from 6.1% to 35.4%. STR analysis excluded the possibility of a recent bottleneck and indicated that 50% of the genetic consistency between northern and southern Mongolians; Tajima's D value for HLA-DRB1 exon2 and dN/dS analysis showed that the HLA-DRB1 genes in both Mongolian populations were under balancing selection. However, the sites under natural selection changed. We proposed that the dramatically change of HLA frequencies in southern Mongolian was caused by a combination of inter-population gene flow and natural selection. Certain diseases specific to the south of China, such as malaria, may be the driving force behind the enhanced DRB1*12:02:01 frequency.
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Affiliation(s)
- Hao Sun
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China
| | - Zhaoqing Yang
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China
| | - Keqin Lin
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China
| | - Shuyuan Liu
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China
| | - Kai Huang
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China
| | - Xiuyun Wang
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China
| | - Jiayou Chu
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China
| | - Xiaoqin Huang
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China
- * E-mail:
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