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Lee J, Lee J, Jeon S, Lee J, Jang I, Yang JO, Park S, Lee B, Choi J, Choi BO, Gee HY, Oh J, Jang IJ, Lee S, Baek D, Koh Y, Yoon SS, Kim YJ, Chae JH, Park WY, Bhak JH, Choi M. A database of 5305 healthy Korean individuals reveals genetic and clinical implications for an East Asian population. Exp Mol Med 2022; 54:1862-1871. [PMID: 36323850 PMCID: PMC9628380 DOI: 10.1038/s12276-022-00871-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/21/2022] [Accepted: 08/08/2022] [Indexed: 11/29/2022] Open
Abstract
Despite substantial advances in disease genetics, studies to date have largely focused on individuals of European descent. This limits further discoveries of novel functional genetic variants in other ethnic groups. To alleviate the paucity of East Asian population genome resources, we established the Korean Variant Archive 2 (KOVA 2), which is composed of 1896 whole-genome sequences and 3409 whole-exome sequences from healthy individuals of Korean ethnicity. This is the largest genome database from the ethnic Korean population to date, surpassing the 1909 Korean individuals deposited in gnomAD. The variants in KOVA 2 displayed all the known genetic features of those from previous genome databases, and we compiled data from Korean-specific runs of homozygosity, positively selected intervals, and structural variants. In doing so, we found loci, such as the loci of ADH1A/1B and UHRF1BP1, that are strongly selected in the Korean population relative to other East Asian populations. Our analysis of allele ages revealed a correlation between variant functionality and evolutionary age. The data can be browsed and downloaded from a public website ( https://www.kobic.re.kr/kova/ ). We anticipate that KOVA 2 will serve as a valuable resource for genetic studies involving East Asian populations.
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Affiliation(s)
- Jeongeun Lee
- grid.31501.360000 0004 0470 5905Interdisciplinary Program in Bioengineering, Graduate School, Seoul National University, Seoul, 03080 Republic of Korea
| | - Jean Lee
- grid.31501.360000 0004 0470 5905Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080 Republic of Korea
| | - Sungwon Jeon
- grid.42687.3f0000 0004 0381 814XDepartment of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
| | - Jeongha Lee
- grid.31501.360000 0004 0470 5905Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080 Republic of Korea
| | - Insu Jang
- grid.249967.70000 0004 0636 3099Korea BioInformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141 Republic of Korea
| | - Jin Ok Yang
- grid.249967.70000 0004 0636 3099Korea BioInformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141 Republic of Korea ,grid.37172.300000 0001 2292 0500Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141 Republic of Korea
| | - Soojin Park
- grid.31501.360000 0004 0470 5905Department of Pediatrics, Seoul National University College of Medicine, Seoul, 03080 Republic of Korea
| | - Byungwook Lee
- grid.249967.70000 0004 0636 3099Korea BioInformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141 Republic of Korea
| | - Jinwook Choi
- grid.31501.360000 0004 0470 5905Interdisciplinary Program in Bioengineering, Graduate School, Seoul National University, Seoul, 03080 Republic of Korea ,grid.31501.360000 0004 0470 5905Department of Biomedical Engineering, Seoul National University College of Medicine, Seoul, 03080 Republic of Korea
| | - Byung-Ok Choi
- grid.264381.a0000 0001 2181 989XDepartment of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351 Republic of Korea
| | - Heon Yung Gee
- grid.15444.300000 0004 0470 5454Department of Pharmacology, Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, Seoul, 03722 Republic of Korea
| | - Jaeseong Oh
- grid.31501.360000 0004 0470 5905Department of Clinical Pharmacology and Therapeutics, Seoul National University College of Medicine and Hospital, Seoul, 03080 Republic of Korea
| | - In-Jin Jang
- grid.31501.360000 0004 0470 5905Department of Clinical Pharmacology and Therapeutics, Seoul National University College of Medicine and Hospital, Seoul, 03080 Republic of Korea
| | - Sanghyuk Lee
- grid.255649.90000 0001 2171 7754Department of Bio-Information Science, Ewha Womans University, Seoul, 03760 Republic of Korea
| | - Daehyun Baek
- grid.31501.360000 0004 0470 5905School of Biological Sciences, Seoul National University, Seoul, 08826 Republic of Korea
| | - Youngil Koh
- grid.412484.f0000 0001 0302 820XDepartment of Internal Medicine, Seoul National University Hospital, Seoul, 03080 Republic of Korea
| | - Sung-Soo Yoon
- grid.412484.f0000 0001 0302 820XDepartment of Internal Medicine, Seoul National University Hospital, Seoul, 03080 Republic of Korea
| | - Young-Joon Kim
- grid.15444.300000 0004 0470 5454Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722 Republic of Korea
| | - Jong-Hee Chae
- grid.31501.360000 0004 0470 5905Department of Pediatrics, Seoul National University College of Medicine, Seoul, 03080 Republic of Korea ,grid.412484.f0000 0001 0302 820XDepartment of Genomic Medicine, Seoul National University Hospital, Seoul, 03080 Republic of Korea
| | - Woong-Yang Park
- grid.414964.a0000 0001 0640 5613Samsung Genome Institute, Samsung Medical Center, Seoul, 06351 Republic of Korea
| | - Jong Hwa Bhak
- grid.42687.3f0000 0004 0381 814XDepartment of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
| | - Murim Choi
- grid.31501.360000 0004 0470 5905Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080 Republic of Korea
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2
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Zhang X, Sun A, Ge J. Origin and Spread of the ALDH2 Glu504Lys Allele. PHENOMICS (CHAM, SWITZERLAND) 2021; 1:222-228. [PMID: 36939783 PMCID: PMC9590465 DOI: 10.1007/s43657-021-00017-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/28/2021] [Accepted: 05/19/2021] [Indexed: 01/14/2023]
Abstract
Gene polymorphism of acetaldehyde dehydrogenase 2 (ALDH2), a key enzyme for alcohol metabolism in humans, can affect catalytic activity. The ALDH2 Glu504Lys mutant allele has a high-frequency distribution in East Asian populations and has been demonstrated to be associated with an increased risk of cardiovascular disease, stroke, and tumors. Available evidence suggests that the evolution of the ALDH2 gene has been influenced by multiple factors. Random mutations produce Glu504Lys, and genetic drift alters the frequency of this allele; additionally, environmental factors such as hepatitis B virus infection and high-elevation hypoxia affect its frequency through selective effects, ultimately resulting in a high frequency of this allele in East Asian populations. Here, the origin, selection, and spread of the ALDH2 Glu504Lys allele are discussed, and an outlook for further research is proposed to realize a precision medical strategy based on the genetic and environmental variations in ALDH2.
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Affiliation(s)
- Xiaokai Zhang
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai 200032, China
| | - Aijun Sun
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai 200032, China
- Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Junbo Ge
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai 200032, China
- Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China
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Abstract
East Asia constitutes one-fifth of the global population and exhibits substantial genetic diversity. However, genetic investigations on populations in this region have been largely under-represented compared with European populations. Nonetheless, the last decade has seen considerable efforts and progress in genome-wide genotyping and whole-genome sequencing of the East-Asian ethnic groups. Here, we review the recent studies in terms of ancestral origin, population relationship, genetic differentiation, and admixture of major East- Asian groups, such as the Chinese, Korean, and Japanese populations. We mainly focus on insights from the whole-genome sequence data and also include the recent progress based on mitochondrial DNA (mtDNA) and Y chromosome data. We further discuss the evolutionary forces driving genetic diversity in East-Asian populations, and provide our perspectives for future directions on population genetics studies, particularly on underrepresented indigenous groups in East Asia.
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Affiliation(s)
- Ziqing Pan
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Shuhua Xu
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
- School of Life Science and Technology, ShanghaiTech Universit, Shanghai, 201210, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
- Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200438, China.
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4
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Jeon S, Bhak Y, Choi Y, Jeon Y, Kim S, Jang J, Jang J, Blazyte A, Kim C, Kim Y, Shim J, Kim N, Kim YJ, Park SG, Kim J, Cho YS, Park Y, Kim HM, Kim BC, Park NH, Shin ES, Kim BC, Bolser D, Manica A, Edwards JS, Church G, Lee S, Bhak J. Korean Genome Project: 1094 Korean personal genomes with clinical information. SCIENCE ADVANCES 2020; 6:eaaz7835. [PMID: 32766443 PMCID: PMC7385432 DOI: 10.1126/sciadv.aaz7835] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 03/19/2020] [Indexed: 05/30/2023]
Abstract
We present the initial phase of the Korean Genome Project (Korea1K), including 1094 whole genomes (sequenced at an average depth of 31×), along with data of 79 quantitative clinical traits. We identified 39 million single-nucleotide variants and indels of which half were singleton or doubleton and detected Korean-specific patterns based on several types of genomic variations. A genome-wide association study illustrated the power of whole-genome sequences for analyzing clinical traits, identifying nine more significant candidate alleles than previously reported from the same linkage disequilibrium blocks. Also, Korea1K, as a reference, showed better imputation accuracy for Koreans than the 1KGP panel. As proof of utility, germline variants in cancer samples could be filtered out more effectively when the Korea1K variome was used as a panel of normals compared to non-Korean variome sets. Overall, this study shows that Korea1K can be a useful genotypic and phenotypic resource for clinical and ethnogenetic studies.
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Affiliation(s)
- Sungwon Jeon
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, UNIST, Ulsan 44919, Republic of Korea
| | - Youngjune Bhak
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, UNIST, Ulsan 44919, Republic of Korea
- Clinomics Inc., Ulsan 44919, Republic of Korea
| | - Yeonsong Choi
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, UNIST, Ulsan 44919, Republic of Korea
| | - Yeonsu Jeon
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, UNIST, Ulsan 44919, Republic of Korea
| | - Seunghoon Kim
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, UNIST, Ulsan 44919, Republic of Korea
| | - Jaeyoung Jang
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Jinho Jang
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, UNIST, Ulsan 44919, Republic of Korea
| | - Asta Blazyte
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Changjae Kim
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Clinomics Inc., Ulsan 44919, Republic of Korea
| | - Yeonkyung Kim
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Jungae Shim
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Nayeong Kim
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Yeo Jin Kim
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Seung Gu Park
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Jungeun Kim
- Personal Genomics Institute (PGI), Genome Research Foundation (GRF), Osong 28160, Republic of Korea
| | | | - Yeshin Park
- Clinomics Inc., Ulsan 44919, Republic of Korea
| | - Hak-Min Kim
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, UNIST, Ulsan 44919, Republic of Korea
- Clinomics Inc., Ulsan 44919, Republic of Korea
| | | | - Neung-Hwa Park
- Department of Internal Medicine, University of Ulsan College of Medicine, Ulsan University Hospital, Ulsan 44033, Republic of Korea
- Biomedical Research Center, University of Ulsan College of Medicine, Ulsan University Hospital, Ulsan 44033, Republic of Korea
| | - Eun-Seok Shin
- Division of Cardiology, Department of Internal Medicine, Ulsan Medical Center, Ulsan 44686, Republic of Korea
| | | | - Dan Bolser
- Clinomics Inc., Ulsan 44919, Republic of Korea
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Jeremy S. Edwards
- Department of Chemistry and Chemical Biology, University of New Mexico and University of New Mexico Comprehensive Cancer Center, Albuquerque, NM 87106, USA
| | - George Church
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Semin Lee
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, UNIST, Ulsan 44919, Republic of Korea
| | - Jong Bhak
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, UNIST, Ulsan 44919, Republic of Korea
- Clinomics Inc., Ulsan 44919, Republic of Korea
- Personal Genomics Institute (PGI), Genome Research Foundation (GRF), Osong 28160, Republic of Korea
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5
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Genetic characteristics of Y-chromosome short tandem repeat haplotypes from cigarette butt samples presumed to be smoked by North Korean men. Genes Genomics 2018; 40:819-824. [PMID: 30047114 DOI: 10.1007/s13258-018-0701-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 03/11/2018] [Indexed: 10/17/2022]
Abstract
Korea has been divided into South Korea and North Korea for over 70 years. DNA profiles of the North Korean population have never been reported in the Y-chromosome STR Haplotype Reference Database (YHRD; https://yhrd.org ). To investigate genetic features of Y-chromosome STR haplotypes of the North Korean population for the first time. Genomic DNA was isolated from 838 cigarette butts assumed to have been smoked by North Korean men and amplified with PowerPlex Y23 (PPY23) kit. Statistical parameters were calculated using Nei's formula and analysis of molecular variance (AMOVA). Multidimensional scaling (MDS) plot was constructed by the AMOVA tool and neighbor-joining (NJ) tree was constructed by MEGA 6.06. A total of 121 haplotypes were analyzed for PPY23 loci from a sample population. Haplotype diversity and discrimination capacity were 0.9992 and 0.9837, respectively. Genetic diversities ranged from 0.2981 to 0.9716. For the 16 Y-filer loci and eight minimal loci, respectively 90.9 and 82.6% of the matched haplotypes were estimated to belong to haplogroup O, representing the Southeast and East Asian type. The MDS plot and NJ tree indicated that the samples are most closely related to South Korean. In addition, p-value in the pairwise comparison to the South Korean was slightly above statistical significance (p = 0.0534). The Y-STR haplotypes of the samples were unique and highly genetically polymorphic. Despite the separation between North and South Korea for 70 years, they can still be considered a single genetic population, based on Y-STR haplotypes.
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6
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Huang X, Zhou Q, Bin X, Lai S, Lin C, Hu R, Xiao J, Luo D, Li Y, Wei LH, Yeh HY, Chen G, Wang CC. The genetic assimilation in language borrowing inferred from Jing People. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2018; 166:638-648. [DOI: 10.1002/ajpa.23449] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 01/10/2018] [Accepted: 02/15/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Xiufeng Huang
- College of Basic Medical Sciences; Youjiang Medical University for Nationalities; Baise Guangxi 533000 China
| | - Qinghui Zhou
- College of Basic Medical Sciences; Youjiang Medical University for Nationalities; Baise Guangxi 533000 China
| | - Xiaoyun Bin
- College of Basic Medical Sciences; Youjiang Medical University for Nationalities; Baise Guangxi 533000 China
| | - Shu Lai
- College of Basic Medical Sciences; Youjiang Medical University for Nationalities; Baise Guangxi 533000 China
| | - Chaowen Lin
- College of Basic Medical Sciences; Youjiang Medical University for Nationalities; Baise Guangxi 533000 China
| | - Rong Hu
- Department of Anthropology and Ethnology; Xiamen University; Xiamen 361005 China
- International Medical Anthropology Team; Xiamen University; Xiamen 361005 China
| | | | | | | | - Lan-Hai Wei
- Institut National des Langues et Civilisations Orientales; Paris 75214 France
| | - Hui-Yuan Yeh
- School of Humanities; Nanyang Technological University; Nanyang 639798 Singapore
| | | | - Chuan-Chao Wang
- Department of Anthropology and Ethnology; Xiamen University; Xiamen 361005 China
- International Medical Anthropology Team; Xiamen University; Xiamen 361005 China
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Erzurumluoglu AM, Baird D, Richardson TG, Timpson NJ, Rodriguez S. Using Y-Chromosomal Haplogroups in Genetic Association Studies and Suggested Implications. Genes (Basel) 2018; 9:E45. [PMID: 29361760 PMCID: PMC5793196 DOI: 10.3390/genes9010045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 01/16/2018] [Accepted: 01/16/2018] [Indexed: 11/16/2022] Open
Abstract
Y-chromosomal (Y-DNA) haplogroups are more widely used in population genetics than in genetic epidemiology, although associations between Y-DNA haplogroups and several traits, including cardiometabolic traits, have been reported. In apparently homogeneous populations defined by principal component analyses, there is still Y-DNA haplogroup variation which will result from population history. Therefore, hidden stratification and/or differential phenotypic effects by Y-DNA haplogroups could exist. To test this, we hypothesised that stratifying individuals according to their Y-DNA haplogroups before testing for associations between autosomal single nucleotide polymorphisms (SNPs) and phenotypes will yield difference in association. For proof of concept, we derived Y-DNA haplogroups from 6537 males from two epidemiological cohorts, Avon Longitudinal Study of Parents and Children (ALSPAC) (n = 5080; 816 Y-DNA SNPs) and the 1958 Birth Cohort (n = 1457; 1849 Y-DNA SNPs), and studied the robust associations between 32 SNPs and body mass index (BMI), including SNPs in or near Fat Mass and Obesity-associated protein (FTO) which yield the strongest effects. Overall, no association was replicated in both cohorts when Y-DNA haplogroups were considered and this suggests that, for BMI at least, there is little evidence of differences in phenotype or SNP association by Y-DNA structure. Further studies using other traits, phenome-wide association studies (PheWAS), other haplogroups and/or autosomal SNPs are required to test the generalisability and utility of this approach.
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Affiliation(s)
- A Mesut Erzurumluoglu
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester LE1 7RH, UK.
| | - Denis Baird
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.
| | - Tom G Richardson
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.
| | - Nicholas J Timpson
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.
| | - Santiago Rodriguez
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.
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8
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Siska V, Jones ER, Jeon S, Bhak Y, Kim HM, Cho YS, Kim H, Lee K, Veselovskaya E, Balueva T, Gallego-Llorente M, Hofreiter M, Bradley DG, Eriksson A, Pinhasi R, Bhak J, Manica A. Genome-wide data from two early Neolithic East Asian individuals dating to 7700 years ago. SCIENCE ADVANCES 2017; 3:e1601877. [PMID: 28164156 PMCID: PMC5287702 DOI: 10.1126/sciadv.1601877] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 12/21/2016] [Indexed: 05/06/2023]
Abstract
Ancient genomes have revolutionized our understanding of Holocene prehistory and, particularly, the Neolithic transition in western Eurasia. In contrast, East Asia has so far received little attention, despite representing a core region at which the Neolithic transition took place independently ~3 millennia after its onset in the Near East. We report genome-wide data from two hunter-gatherers from Devil's Gate, an early Neolithic cave site (dated to ~7.7 thousand years ago) located in East Asia, on the border between Russia and Korea. Both of these individuals are genetically most similar to geographically close modern populations from the Amur Basin, all speaking Tungusic languages, and, in particular, to the Ulchi. The similarity to nearby modern populations and the low levels of additional genetic material in the Ulchi imply a high level of genetic continuity in this region during the Holocene, a pattern that markedly contrasts with that reported for Europe.
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Affiliation(s)
- Veronika Siska
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB23EJ, U.K
- Corresponding author. (V.S.); (R.P.); (J.B.); (A.M.)
| | - Eppie Ruth Jones
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB23EJ, U.K
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Sungwon Jeon
- The Genomics Institute, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Youngjune Bhak
- The Genomics Institute, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Hak-Min Kim
- The Genomics Institute, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Yun Sung Cho
- The Genomics Institute, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Hyunho Kim
- Geromics, Ulsan 44919, Republic of Korea
| | - Kyusang Lee
- Clinomics Inc., Ulsan 4919, Republic of Korea
| | | | - Tatiana Balueva
- Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, Russia
| | | | - Michael Hofreiter
- Institute for Biochemistry and Biology, Faculty for Mathematics and Natural Sciences, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam-Golm, Germany
| | - Daniel G. Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Anders Eriksson
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB23EJ, U.K
| | - Ron Pinhasi
- School of Archaeology and Earth Institute, University College Dublin, Dublin, Ireland
- Corresponding author. (V.S.); (R.P.); (J.B.); (A.M.)
| | - Jong Bhak
- The Genomics Institute, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
- Geromics, Ulsan 44919, Republic of Korea
- Corresponding author. (V.S.); (R.P.); (J.B.); (A.M.)
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB23EJ, U.K
- Corresponding author. (V.S.); (R.P.); (J.B.); (A.M.)
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9
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Zheng W, Yang Q, Peng K, Yu F. What's in the Chinese Babyface? Cultural Differences in Understanding the Babyface. Front Psychol 2016; 7:819. [PMID: 27303360 PMCID: PMC4886646 DOI: 10.3389/fpsyg.2016.00819] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 05/17/2016] [Indexed: 11/13/2022] Open
Abstract
We investigated the cultural differences in understanding and reacting to the babyface in an effort to identify both cultural and gender biases in the universal hypothesis that the babyfaced individuals are perceived as naïve, cute, innocent, and more trustworthy. Sixty-six Chinese and Sixty-six American participants were required to evaluate Chinese faces selected from the Chinese Academy of Sciences (CAS)—Pose, Expression, Accessories, and Lighting (PEAL) Large-Scale Chinese Face Database. In our study, we applied Active Shape Models, a modern technique of machine learning to measure facial features. We found some cultural similarities and also found that a Chinese babyface has bigger eyes, higher eyebrows, a smaller chin, and greater WHR (Facial width-to-height ratio), and looks more attractive and warmer. New findings demonstrate that Chinese babyfaces have a lower forehead and closer pupil distance (PD). We found that when evaluating the babyfacedness of a face, Chinese are more concerned with the combination of all facial features and American are more sensitive to specific highlighted babyfaced features. The Chinese babyface tended to be perceived as more babyfaced for American participants, but not less competent for Chinese participants.
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Affiliation(s)
- Wenwen Zheng
- Department of Psychology, Tsinghua University Beijing, China
| | - Qian Yang
- Department of Public Health, Zhejiang University Hangzhou, China
| | - Kaiping Peng
- Department of Psychology, Tsinghua University Beijing, China
| | - Feng Yu
- Department of Leadership and Organization Management, School of Economics and Management, Tsinghua University Beijing, China
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10
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Population and forensic genetic analyses of mitochondrial DNA control region variation from six major provinces in the Korean population. Forensic Sci Int Genet 2015; 17:99-103. [DOI: 10.1016/j.fsigen.2015.03.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 03/19/2015] [Accepted: 03/27/2015] [Indexed: 11/23/2022]
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11
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Phylogenetic analysis of two haploid markers of 500-years-old human remains found in a central region of Korea. Genes Genomics 2015. [DOI: 10.1007/s13258-014-0226-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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12
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CHOI JEEHYE, MIN NAYOUNG, PARK SANGKIL, GAVAACHIMED LKHAGVASUREN, KO YOUNGJONG, HAN SUNGHOON, KIM KYUNGYONG, KIM KIJUNG, LEE KWANGHO, PARK AEJA. Dual matrilineal geographic distribution of Korean type 2 diabetes mellitus-associated -11,377 G adiponectin allele. Mol Med Rep 2014; 10:2993-3002. [DOI: 10.3892/mmr.2014.2639] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Accepted: 06/26/2014] [Indexed: 11/05/2022] Open
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Trejaut JA, Poloni ES, Yen JC, Lai YH, Loo JH, Lee CL, He CL, Lin M. Taiwan Y-chromosomal DNA variation and its relationship with Island Southeast Asia. BMC Genet 2014; 15:77. [PMID: 24965575 PMCID: PMC4083334 DOI: 10.1186/1471-2156-15-77] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 06/10/2014] [Indexed: 01/12/2023] Open
Abstract
Background Much of the data resolution of the haploid non-recombining Y chromosome (NRY) haplogroup O in East Asia are still rudimentary and could be an explanatory factor for current debates on the settlement history of Island Southeast Asia (ISEA). Here, 81 slowly evolving markers (mostly SNPs) and 17 Y-chromosomal short tandem repeats were used to achieve higher level molecular resolution. Our aim is to investigate if the distribution of NRY DNA variation in Taiwan and ISEA is consistent with a single pre-Neolithic expansion scenario from Southeast China to all ISEA, or if it better fits an expansion model from Taiwan (the OOT model), or whether a more complex history of settlement and dispersals throughout ISEA should be envisioned. Results We examined DNA samples from 1658 individuals from Vietnam, Thailand, Fujian, Taiwan (Han, plain tribes and 14 indigenous groups), the Philippines and Indonesia. While haplogroups O1a*-M119, O1a1*-P203, O1a2-M50 and O3a2-P201 follow a decreasing cline from Taiwan towards Western Indonesia, O2a1-M95/M88, O3a*-M324, O3a1c-IMS-JST002611 and O3a2c1a-M133 decline northward from Western Indonesia towards Taiwan. Compared to the Taiwan plain tribe minority groups the Taiwanese Austronesian speaking groups show little genetic paternal contribution from Han. They are also characterized by low Y-chromosome diversity, thus testifying for fast drift in these populations. However, in contrast to data provided from other regions of the genome, Y-chromosome gene diversity in Taiwan mountain tribes significantly increases from North to South. Conclusion The geographic distribution and the diversity accumulated in the O1a*-M119, O1a1*-P203, O1a2-M50 and O3a2-P201 haplogroups on one hand, and in the O2a1-M95/M88, O3a*-M324, O3a1c-IMS-JST002611 and O3a2c1a-M133 haplogroups on the other, support a pincer model of dispersals and gene flow from the mainland to the islands which likely started during the late upper Paleolithic, 18,000 to 15,000 years ago. The branches of the pincer contributed separately to the paternal gene pool of the Philippines and conjointly to the gene pools of Madagascar and the Solomon Islands. The North to South increase in diversity found for Taiwanese Austronesian speaking groups contrasts with observations based on mitochondrial DNA, thus hinting to a differentiated demographic history of men and women in these populations.
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Affiliation(s)
- Jean A Trejaut
- Mackay Memorial Hospital, Taipei, Molecular Anthropology Laboratory, 45 Min-Sheng Road,225115 Tamsui, New Taipei city, Taiwan.
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Hong SB, Kim KC, Kim W. Mitochondrial DNA haplogroups and homogeneity in the Korean population. Genes Genomics 2014. [DOI: 10.1007/s13258-014-0194-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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15
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16
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Y-SNP miniplexes for East Asian Y-chromosomal haplogroup determination in degraded DNA. Forensic Sci Int Genet 2013; 7:75-81. [DOI: 10.1016/j.fsigen.2012.06.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2011] [Revised: 05/14/2012] [Accepted: 06/26/2012] [Indexed: 11/18/2022]
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Choi J, Song SH, Bak CW, Sung SR, Yoon TK, Lee DR, Shim SH. Impaired spermatogenesis and gr/gr deletions related to Y chromosome haplogroups in Korean men. PLoS One 2012; 7:e43550. [PMID: 22927988 PMCID: PMC3426531 DOI: 10.1371/journal.pone.0043550] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Accepted: 07/23/2012] [Indexed: 11/18/2022] Open
Abstract
Microdeletion of the Azoospermia Factor (AZF) regions in Y chromosome is a well-known genetic cause of male infertility resulting from spermatogenetic impairment. However, the partial deletions of AZFc region related to spermatogenetic impairment are controversial. In this study, we characterized partial deletion of AZFc region in Korean patients with spermatogenetic impairment and assessed whether the DAZ and CDY1 contributes to the phenotype in patients with gr/gr deletions. Total of 377 patients with azoo-/oligozoospermia and 217 controls were analyzed using multiplex polymerase chain reaction (PCR), analysis of DAZ-CDY1 sequence family variants (SFVs), and quantitative fluorescent (QF)-PCR. Of the 377 men with impaired spermatogenesis, 59 cases (15.6%) had partial AZFc deletions, including 32 gr/gr (8.5%), 22 b2/b3 (5.8%), four b1/b3 (1.1%) and one b3/b4 (0.3%) deletion. In comparison, 14 of 217 normozoospermic controls (6.5%) had partial AZFc deletions, including five gr/gr (2.3%) and nine b2/b3 (4.1%) deletions. The frequency of gr/gr deletions was significantly higher in the azoo-/oligozoospermic group than in the normozoospermic control group (p = 0.003; OR = 3.933; 95% CI = 1.509-10.250). Concerning Y haplogroup, we observed no significant differences in the frequency of gr/gr deletions between the case and the control groups in the YAP+ lineages, while gr/gr deletion were significantly higher in azoo-/oligozoospermia than normozoospermia in the YAP- lineage (p = 0.004; OR = 6.341; 95% CI = 1.472-27.312). Our data suggested that gr/gr deletion is associated with impaired spermatogenesis in Koreans with YAP- lineage, regardless of the gr/gr subtypes.
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Affiliation(s)
- Jin Choi
- Genetics Laboratory, Fertility Center of CHA Gangnam Medical Center, Seoul, South Korea
| | - Seung-Hun Song
- Department of Urology, Fertility Center of CHA Gangnam Medical Center, CHA University, Seoul, South Korea
| | - Chong Won Bak
- Department of Urology, Fertility Center of CHA Gangnam Medical Center, CHA University, Seoul, South Korea
| | - Se Ra Sung
- Genetics Laboratory, Fertility Center of CHA Gangnam Medical Center, Seoul, South Korea
| | - Tae Ki Yoon
- Department of Obstetrics and Gynecology, Fertility Center of CHA Gangnam Medical Center, CHA University, Seoul, South Korea
| | - Dong Ryul Lee
- Department of Biomedical Science, CHA University, Seoul, South Korea
| | - Sung Han Shim
- Genetics Laboratory, Fertility Center of CHA Gangnam Medical Center, Seoul, South Korea
- Department of Biomedical Science, CHA University, Seoul, South Korea
- * E-mail:
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Nakahori Y, Sato Y, Ewis AA, Iwamoto T, Shinka T, Nozawa S, Yoshiike M, Yang XJ, Sei M, Namiki M, Kou E, Ito N, Komatsu K, Matsumiya K, Nakagome Y. Climatic influence on the reproductive characteristics of Japanese males. J Hum Genet 2012; 57:375-8. [PMID: 22534769 DOI: 10.1038/jhg.2012.38] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We previously performed a survey of the sperm characteristics of the partners of pregnant women in four cities in Japan. In the present study, we analyzed the sperm characteristics of these subjects and the correlations between these sperm characteristics and climatic changes or Y chromosome haplogroups. Our results showed that more haplogroup D2a1 males than O2b1 males were born in the first half of the year (January to June), whereas more O2b1 males were born in the last half of the year (July to December) (P<0.05). This was agreed and correlated with the seasonal variations in their mean sperm concentrations. The haplogroup C, D* and D2a1 males displayed lower sperm concentrations from March to May, followed by an increase in their sperm concentrations starting in June or July, while the O2b1 males displayed higher sperm concentrations in the first half of the year followed by a sudden decrease from July to August (P<0.05). We hypothesize that the Japanese climate has different effects on the sperm characteristics and reproductive seasonality of males from different lineages; and therefore, has influenced the modern population of Japan.
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Affiliation(s)
- Yutaka Nakahori
- Department of Human Genetics and Public Health, Graduate School of Medical Science, University of Tokushima, Tokushima, Japan
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Yang JH, Sohn YH, Ko SY, Choi SE, Kim MH, Oh HB. Anthropological analysis of Koreans using HLA class II diversity among East Asians. ACTA ACUST UNITED AC 2011; 76:282-8. [PMID: 20522202 DOI: 10.1111/j.1399-0039.2010.01511.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Human leukocyte antigens (HLAs) are useful markers for anthropological investigations because the allele and haplotype distributions at these loci vary widely among ethnic groups. HLA frequencies in Koreans, however, have not previously been analyzed on a phylogenetic basis. We determined the allele frequencies of four HLA class II (HLA-DRB1, -DQA1, -DQB1, and -DPB1) loci in 149 unrelated Korean individuals using a sequence-based typing method. A total of 29 HLA-DRB1, 17 HLA-DQA1, 16 HLA-DQB1, and 15 HLA-DPB1 alleles were identified. The most common allele at each locus was DRB1*0901, DQA1*0102, DQB1*0301, and DPB1*0501, respectively. Four-locus allelic association analysis showed the existence of 25 DRB1-DQA1-DQB1-DPB1 haplotypes with a frequency greater than 0.010. A dataset comprising ethnicity-specific information from published literature and the dbMHC database, as well as the allele frequencies determined in this study, was subjected to phylogenetic analysis. The analysis showed that Koreans are most closely related to Japanese and Han Chinese from Shandong province. Correspondence analyses showed that the current Korean population is located in a position intermediate between the northern and southern East Asian groups, supporting the theory of a bi- and/or multidirectional route of migration of early Korean settlers. This report can be used for anthropological studies, and may also be of use in the International Hematopoietic Stem Cell Sharing program.
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Affiliation(s)
- J H Yang
- Department of Laboratory Medicine, Korea University Medical College, Seoul, Korea
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Kim SH, Kim KC, Shin DJ, Jin HJ, Kwak KD, Han MS, Song JM, Kim W, Kim W. High frequencies of Y-chromosome haplogroup O2b-SRY465 lineages in Korea: a genetic perspective on the peopling of Korea. INVESTIGATIVE GENETICS 2011; 2:10. [PMID: 21463511 PMCID: PMC3087676 DOI: 10.1186/2041-2223-2-10] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2011] [Accepted: 04/04/2011] [Indexed: 11/11/2022]
Abstract
Background Koreans are generally considered a Northeast Asian group, thought to be related to Altaic-language-speaking populations. However, recent findings have indicated that the peopling of Korea might have been more complex, involving dual origins from both southern and northern parts of East Asia. To understand the male lineage history of Korea, more data from informative genetic markers from Korea and its surrounding regions are necessary. In this study, 25 Y-chromosome single nucleotide polymorphism markers and 17 Y-chromosome short tandem repeat (Y-STR) loci were genotyped in 1,108 males from several populations in East Asia. Results In general, we found East Asian populations to be characterized by male haplogroup homogeneity, showing major Y-chromosomal expansions of haplogroup O-M175 lineages. Interestingly, a high frequency (31.4%) of haplogroup O2b-SRY465 (and its sublineage) is characteristic of male Koreans, whereas the haplogroup distribution elsewhere in East Asian populations is patchy. The ages of the haplogroup O2b-SRY465 lineages (~9,900 years) and the pattern of variation within the lineages suggested an ancient origin in a nearby part of northeastern Asia, followed by an expansion in the vicinity of the Korean Peninsula. In addition, the coalescence time (~4,400 years) for the age of haplogroup O2b1-47z, and its Y-STR diversity, suggest that this lineage probably originated in Korea. Further studies with sufficiently large sample sizes to cover the vast East Asian region and using genomewide genotyping should provide further insights. Conclusions These findings are consistent with linguistic, archaeological and historical evidence, which suggest that the direct ancestors of Koreans were proto-Koreans who inhabited the northeastern region of China and the Korean Peninsula during the Neolithic (8,000-1,000 BC) and Bronze (1,500-400 BC) Ages.
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Affiliation(s)
- Soon-Hee Kim
- School of Biological Sciences, Seoul National University, Seoul 151-747, Korea.,Eastern District Office, National Forensic Service, Gangwon-do 220-805, Korea
| | - Ki-Cheol Kim
- Department of Biological Sciences, Dankook University, Cheonan 330-714, Korea
| | - Dong-Jik Shin
- Cardiovascular Genome Center, Yonsei University College of Medicine, Seoul 120-749, Korea
| | - Han-Jun Jin
- Center for Genome Science, Korea National Institute of Health, Seoul 122-701, Korea
| | - Kyoung-Don Kwak
- DNA Analysis Division, National Forensic Service, Seoul 158-707, Korea
| | - Myun-Soo Han
- DNA Analysis Division, National Forensic Service, Seoul 158-707, Korea
| | - Joon-Myong Song
- Research Institute of Pharmaceutical Sciences and College of Pharmacy, Seoul National University, Seoul 151-742, Korea
| | - Won Kim
- School of Biological Sciences, Seoul National University, Seoul 151-747, Korea
| | - Wook Kim
- Department of Biological Sciences, Dankook University, Cheonan 330-714, Korea
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Kim JH, Gansukh O, Amarsaikhan B, Lee SJ, Kim TW. Comparison of cephalometric norms between Mongolian and Korean adults with normal occlusions and well-balanced profiles. ACTA ACUST UNITED AC 2011. [DOI: 10.4041/kjod.2011.41.1.42] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Ji-Hwan Kim
- Graduate Student, Department of Orthodontics, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, Korea
| | - Odontuya Gansukh
- Graduate Student, Department of Orthodontics, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, Korea
| | - Bazar Amarsaikhan
- Professor, Department of Prosthodontics and Orthodontics, School of Dentistry, Health Science University of Mongolia, Ulaanbaatar, Mongolia
| | - Shin-Jae Lee
- Associate Professor, Department of Orthodontics, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, Korea
| | - Tae-Woo Kim
- Professor, Department of Orthodontics, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, Korea
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Kim K, Brenner CH, Mair VH, Lee KH, Kim JH, Gelegdorj E, Batbold N, Song YC, Yun HW, Chang EJ, Lkhagvasuren G, Bazarragchaa M, Park AJ, Lim I, Hong YP, Kim W, Chung SI, Kim DJ, Chung YH, Kim SS, Lee WB, Kim KY. A western Eurasian male is found in 2000-year-old elite Xiongnu cemetery in Northeast Mongolia. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2010; 142:429-40. [PMID: 20091844 DOI: 10.1002/ajpa.21242] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We analyzed mitochondrial DNA (mtDNA), Y-chromosome single nucleotide polymorphisms (Y-SNP), and autosomal short tandem repeats (STR) of three skeletons found in a 2,000-year-old Xiongnu elite cemetery in Duurlig Nars of Northeast Mongolia. This study is one of the first reports of the detailed genetic analysis of ancient human remains using the three types of genetic markers. The DNA analyses revealed that one subject was an ancient male skeleton with maternal U2e1 and paternal R1a1 haplogroups. This is the first genetic evidence that a male of distinctive Indo-European lineages (R1a1) was present in the Xiongnu of Mongolia. This might indicate an Indo-European migration into Northeast Asia 2,000 years ago. Other specimens are a female with mtDNA haplogroup D4 and a male with Y-SNP haplogroup C3 and mtDNA haplogroup D4. Those haplogroups are common in Northeast Asia. There was no close kinship among them. The genetic evidence of U2e1 and R1a1 may help to clarify the migration patterns of Indo-Europeans and ancient East-West contacts of the Xiongnu Empire. Artifacts in the tombs suggested that the Xiongnu had a system of the social stratification. The West Eurasian male might show the racial tolerance of the Xiongnu Empire and some insight into the Xiongnu society.
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Affiliation(s)
- Kijeong Kim
- Institute for Medical Sciences, College of Medicine, Chung-Ang University, Seoul, South Korea, Republic of Korea
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Jin HJ, Kim KC, Kim W. Genetic diversity of two haploid markers in the Udegey population from southeastern Siberia. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2010; 142:303-13. [PMID: 19953529 DOI: 10.1002/ajpa.21232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The Udegeys are a small ethnic group who live along the tributaries of the Amur River Basin of southeastern Siberia in Russia. They are thought to speak a language belonging to a subdivision of the Tungusic-Manchu branch of the Altaic family. To understand the genetic features and genetic history of the Udegeys, we analyzed two haploid markers, mitochondrial DNA (mtDNA), and Y-chromosomal variation, in 51 individuals (including 21 males) from the Udegey population. In general, the Udegeys' mtDNA profiles revealed similarities to Siberians and other northeastern Asian populations, although a moderate European contribution was also detected. Interestingly, pairwise values of F(ST) and the MDS plots based on the mtDNA variation showed that the Orok and Nivkh inhabiting the very same region of the Udegey were significantly different from the Udegey, implying that they may have been isolated and undergone substantial genetic drift. The Udegeys were characterized by a high frequency (66.7%) of Y chromosome haplogroup C, indicating a close genetic relationship with Mongolians and Siberians. On the paternal side, however, very little admixture was observed between the Udegeys and Europeans. Thus, the combined haploid genetic markers of both mtDNA and the Y chromosome imply that the Udegeys are overall closest to Siberians and northeast Asians of the Altaic linguistic family, with a minor maternal contribution from the European part of the continent.
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Affiliation(s)
- Han-Jun Jin
- Department of Biological Sciences, Dankook University, Cheonan 330-714, Korea
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Kim SH, Chun BW, Jung J, Kemp BM, Kwak KD, Cho NS, Kim JJ, Han MS, Kim W. A preliminary study on the origin of Koreans based on Y-STR variation. Genes Genomics 2010. [DOI: 10.1007/s13258-010-0030-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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25
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Jung J, Kang H, Cho YS, Oh JH, Ryu MH, Chung HW, Seo JS, Lee JE, Oh B, Bhak J, Kim HL. Gene flow between the Korean peninsula and its neighboring countries. PLoS One 2010; 5:e11855. [PMID: 20686617 PMCID: PMC2912326 DOI: 10.1371/journal.pone.0011855] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2010] [Accepted: 07/05/2010] [Indexed: 01/15/2023] Open
Abstract
SNP markers provide the primary data for population structure analysis. In this study, we employed whole-genome autosomal SNPs as a marker set (54,836 SNP markers) and tested their possible effects on genetic ancestry using 320 subjects covering 24 regional groups including Northern (=16) and Southern (=3) Asians, Amerindians (=1), and four HapMap populations (YRI, CEU, JPT, and CHB). Additionally, we evaluated the effectiveness and robustness of 50K autosomal SNPs with various clustering methods, along with their dependencies on recombination hotspots (RH), linkage disequilibrium (LD), missing calls and regional specific markers. The RH- and LD-free multi-dimensional scaling (MDS) method showed a broad picture of human migration from Africa to North-East Asia on our genome map, supporting results from previous haploid DNA studies. Of the Asian groups, the East Asian group showed greater differentiation than the Northern and Southern Asian groups with respect to Fst statistics. By extension, the analysis of monomorphic markers implied that nine out of ten historical regions in South Korea, and Tokyo in Japan, showed signs of genetic drift caused by the later settlement of East Asia (South Korea, Japan and China), while Gyeongju in South East Korea showed signs of the earliest settlement in East Asia. In the genome map, the gene flow to the Korean Peninsula from its neighboring countries indicated that some genetic signals from Northern populations such as the Siberians and Mongolians still remain in the South East and West regions, while few signals remain from the early Southern lineages.
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Affiliation(s)
- Jongsun Jung
- Syntekabio Inc., Seoul, Korea
- DNA link Inc., Seoul, Korea
- Division of Structural and Functional Genomics, Center for Genome Science, Korea National Institute of Health, Seoul, Korea
| | - Hoyoung Kang
- Korean Bioinformation Center, KRIBB, Daejeon, Korea
- University of Science and Technology, Daejeon, Korea
| | - Yoon Shin Cho
- Division of Structural and Functional Genomics, Center for Genome Science, Korea National Institute of Health, Seoul, Korea
| | - Ji Hee Oh
- Division of Structural and Functional Genomics, Center for Genome Science, Korea National Institute of Health, Seoul, Korea
| | - Min Hyung Ryu
- Division of Structural and Functional Genomics, Center for Genome Science, Korea National Institute of Health, Seoul, Korea
| | - Hye Won Chung
- Department of Obstetrics and Gynecology, College of Medicine, Ewha Womans University, Seoul, Korea
| | - Jeong-Sun Seo
- Department of Biochemistry and Molecular Biology, Seoul National University of Medicine, Seoul, Korea
| | | | - Bermseok Oh
- Department of Biomedical Engineering, Kyung Hee University College of Medicine, Seoul, Korea
| | - Jong Bhak
- Korean Bioinformation Center, KRIBB, Daejeon, Korea
| | - Hyung-Lae Kim
- Division of Structural and Functional Genomics, Center for Genome Science, Korea National Institute of Health, Seoul, Korea
- * E-mail:
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Global distribution of Y-chromosome haplogroup C reveals the prehistoric migration routes of African exodus and early settlement in East Asia. J Hum Genet 2010; 55:428-35. [PMID: 20448651 DOI: 10.1038/jhg.2010.40] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Yi CH, Lee SK, Cheong JY, Cho SW, Kwack K. Single nucleotide polymorphisms and the linkage disequilibrium at the LDL receptor gene in Koreans. Genes Genomics 2010. [DOI: 10.1007/s13258-010-0365-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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28
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Mizuno N, Kitayama T, Fujii K, Nakahara H, Yoshida K, Sekiguchi K, Yonezawa N, Nakano M, Kasai K. A forensic method for the simultaneous analysis of biallelic markers identifying Y chromosome haplogroups inferred as having originated in Asia and the Japanese archipelago. Forensic Sci Int Genet 2009; 4:73-9. [PMID: 20129464 DOI: 10.1016/j.fsigen.2009.06.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2008] [Revised: 04/24/2009] [Accepted: 06/02/2009] [Indexed: 11/25/2022]
Abstract
Information regarding the ancestral and geographical origins of biological evidence samples may be useful for crime investigators as they narrow down the possible donors of the sample. A method for simultaneous analysis of seven biallelic markers (M130, M131, M57, M125, M175, M122 and M134) was developed for forensic application. M57, M125 and M131 are included to identify haplogroups inferred as having originated in the Japanese archipelago. Our method employs allele-specific PCR and fragment analysis using fluorescently labeled primers and capillary electrophoresis. This method can be used to assign a haplogroup from both of degraded male DNA samples and DNA samples containing a mixture of female and male DNA by designing PCR primers that generate small amplicons and are highly specific for targets on the Y chromosome. A total of 1346 samples from Japanese males collected from the four major islands and Okinawa island were classified into seven Y binary haplogroups i.e., C-M130, C-M131, D-M57, D-M125, O-M175, O-M122 and O-M134, and a "no-mutation detected" group and their frequencies were 0.0617, 0.0565, 0.1441, 0.182, 0.3418, 0.11, 0.0847 and 0.0193, respectively. Samples of "no-mutation detected" were further analyzed by direct sequencing for identification of the major haplogroup to which they belong. Along with the haplogroup data, we report haplotype data for the 16 Y-STR markers included in the AmpFlSTR Yfiler PCR amplification kit (Applied Biosystems). These data will be useful in the prediction of haplogroups based on Y-STR haplotypes.
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Affiliation(s)
- Natsuko Mizuno
- National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, 277-0882, Japan.
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Kim SH, Jung J, Cho NS, Hwang JH, Yoo SY, Seong KM, Han MS, Kim W. Y-STR genetic structure of the most common surnames in Korea. Genes Genomics 2009. [DOI: 10.1007/bf03191196] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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30
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The first Korean genome sequence and analysis: full genome sequencing for a socio-ethnic group. Genome Res 2009; 19:1622-9. [PMID: 19470904 DOI: 10.1101/gr.092197.109] [Citation(s) in RCA: 265] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We present the first Korean individual genome sequence (SJK) and analysis results. The diploid genome of a Korean male was sequenced to 28.95-fold redundancy using the Illumina paired-end sequencing method. SJK covered 99.9% of the NCBI human reference genome. We identified 420,083 novel single nucleotide polymorphisms (SNPs) that are not in the dbSNP database. Despite a close similarity, significant differences were observed between the Chinese genome (YH), the only other Asian genome available, and SJK: (1) 39.87% (1,371,239 out of 3,439,107) SNPs were SJK-specific (49.51% against Venter's, 46.94% against Watson's, and 44.17% against the Yoruba genomes); (2) 99.5% (22,495 out of 22,605) of short indels (< 4 bp) discovered on the same loci had the same size and type as YH; and (3) 11.3% (331 out of 2920) deletion structural variants were SJK-specific. Even after attempting to map unmapped reads of SJK to unanchored NCBI scaffolds, HGSV, and available personal genomes, there were still 5.77% SJK reads that could not be mapped. All these findings indicate that the overall genetic differences among individuals from closely related ethnic groups may be significant. Hence, constructing reference genomes for minor socio-ethnic groups will be useful for massive individual genome sequencing.
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Abstract
The first inhabitants of Japan, the Jomon hunter-gatherers, had their culture significantly modified by that of the Yayoi farmers, who arrived at a later stage from mainland Asia. How this change took place is still debated, but it has been suggested that modern Japanese are the product of an admixture between these two populations. Here, we applied for the first time an admixture approach to study the Jomon-Yayoi transition, using Y-chromosomal data published earlier. Our results suggest that the Neolithic transition, in this part of the world, probably took place by a process of demic diffusion. We also show that for two populations that could not have contributed to this process, our approach is able to detect inconsistencies when they are used as parental populations. However, despite these promising results, we could not locate precisely the geographical origin of the Yayoi in mainland Asia, as different potential sources gave similarly good results. This suggests that more loci would be required for a better understanding of the peopling of Japan.
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Luo HR, Wu GS, Pakstis AJ, Tong L, Oota H, Kidd KK, Zhang YP. Origin and dispersal of atypical aldehyde dehydrogenase ALDH2487Lys. Gene 2009; 435:96-103. [PMID: 19393179 DOI: 10.1016/j.gene.2008.12.021] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2008] [Revised: 12/18/2008] [Accepted: 12/24/2008] [Indexed: 10/21/2022]
Abstract
The East Asian respond with a marked facial flushing and mild to moderate symptoms of intoxication after drinking the amounts of alcohol that has no detectable effect on European. The alcohol sensitivity in Orientals is due to a delayed oxidation of acetaldehyde by an atypical aldehyde dehydrogenase ALDH2487Lys, which is resulted from a structural mutation in gene ALDH2. The atypical ALDH2487Lys allele has been associated with various phenotypic statuses, such as protective against alcohol dependence and the risk of alcohol-related digestive tract cancers. Here, we have examined this SNP, adjacent four non-coding SNPs, and one downstream STRP on ALDH2 gene, in total of 1072 unrelated healthy individuals from 14 Chinese populations and 130 Indian individuals. Five major haplotypes based on five SNPs across the ALDH2 gene 40 kb were found in all East Asian populations. The frequencies of the ancestral haplotype GCCTG and the East Asian special haplotype GCCTA containing the atypical ALDH2487Lys allele were 44.8% and 14.9%, respectively. The frequency of the atypical ALDH2487Lys allele or the East Asian specific haplotype GCCTA is high in Yunnan, South coastal, east coastal of China, and decreased gradually toward inland China, West, Northwest and North China. Combined with demographic history in East Asian, our results showed that the presence of ALDH2487Lys allele in peripheral regions of China might be the results of historical migration events from China to these regions. The origin of ALDH2487Lys could be possibly traced back to ancient Pai-Yuei tribe in South China.
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Affiliation(s)
- Huai-Rong Luo
- Kunming Institute of Zoology, The Chinese Academy of Sciences, Yunnan, China
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Jin HJ, Tyler-Smith C, Kim W. The peopling of Korea revealed by analyses of mitochondrial DNA and Y-chromosomal markers. PLoS One 2009; 4:e4210. [PMID: 19148289 PMCID: PMC2615218 DOI: 10.1371/journal.pone.0004210] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2008] [Accepted: 12/08/2008] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The Koreans are generally considered a northeast Asian group because of their geographical location. However, recent findings from Y chromosome studies showed that the Korean population contains lineages from both southern and northern parts of East Asia. To understand the genetic history and relationships of Korea more fully, additional data and analyses are necessary. METHODOLOGY AND RESULTS We analyzed mitochondrial DNA (mtDNA) sequence variation in the hypervariable segments I and II (HVS-I and HVS-II) and haplogroup-specific mutations in coding regions in 445 individuals from seven east Asian populations (Korean, Korean-Chinese, Mongolian, Manchurian, Han (Beijing), Vietnamese and Thais). In addition, published mtDNA haplogroup data (N = 3307), mtDNA HVS-I sequences (N = 2313), Y chromosome haplogroup data (N = 1697) and Y chromosome STR data (N = 2713) were analyzed to elucidate the genetic structure of East Asian populations. All the mtDNA profiles studied here were classified into subsets of haplogroups common in East Asia, with just two exceptions. In general, the Korean mtDNA profiles revealed similarities to other northeastern Asian populations through analysis of individual haplogroup distributions, genetic distances between populations or an analysis of molecular variance, although a minor southern contribution was also suggested. Reanalysis of Y-chromosomal data confirmed both the overall similarity to other northeastern populations, and also a larger paternal contribution from southeastern populations. CONCLUSION The present work provides evidence that peopling of Korea can be seen as a complex process, interpreted as an early northern Asian settlement with at least one subsequent male-biased southern-to-northern migration, possibly associated with the spread of rice agriculture.
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Affiliation(s)
- Han-Jun Jin
- Department of Biological Sciences, Dankook University, Cheonan, Korea
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Chris Tyler-Smith
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Wook Kim
- Department of Biological Sciences, Dankook University, Cheonan, Korea
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Hiura Y, Fukushima Y, Kokubo Y, Okamura T, Goto Y, Nonogi H, Takahashi R, Iwai N. Effects of the Y chromosome on cardiovascular risk factors in Japanese men. Hypertens Res 2009; 31:1687-94. [PMID: 18971546 DOI: 10.1291/hypres.31.1687] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Excess cardiovascular risk in men compared with women has been suggested to be partly explained by effects of the Y chromosome. However, inconsistent results have been reported on the Y chromosome's genetic influence on blood pressure and lipid levels. The purpose of the present study was to settle the question whether genetic variants of the Y chromosome influence cardiovascular risk factors using a large epidemiological cohort, the Suita study. Possible influences of the Y chromosome polymorphisms (Y chromosome Alu insertion polymorphism [YAP], M175 and SRY+465) on cardiovascular risk factors were assessed in 974 Japanese men. The frequency of the YAP(+) allele in our study sample was 0.31. The prevalence of hypertension tended to be higher in YAP(+) than in YAP(-) men, and this tendency was found to be stronger among men aged 65 years or older. Men with the YAP(+) genotype had higher levels of high density lipoprotein (HDL) cholesterol compared with those with the YAP(-) genotype, even after adjustment for age, body mass index, and daily ethanol and cigarette consumption (57.0+/-14.6 mg/dL vs. 54.2+/-14.2 mg/dL, nominal p=0.011, adjusted p=0.0062). However, these observed nominal associations disappeared after adjusting for multiple testing (Bonferroni). No association was detected between the YAP genotype and myocardial infarction. Similarly, none of the associations with M175 and SRY+465 attained significance when multiple testing was taken into account. In conclusion, Y chromosome polymorphisms (YAP, M175 and SRY+465) do not appear to be associated with cardiovascular risk factors in Japanese men. Studies using much larger sample sizes and/or additional independent samples will be required for definitive conclusions.
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Affiliation(s)
- Yumiko Hiura
- Department of Epidemiology, Research Institute, National Cardiovascular Center, 5-7-1 Fujishirodai, Suita, Japan
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Shi H, Zhong H, Peng Y, Dong YL, Qi XB, Zhang F, Liu LF, Tan SJ, Ma RZ, Xiao CJ, Wells RS, Jin L, Su B. Y chromosome evidence of earliest modern human settlement in East Asia and multiple origins of Tibetan and Japanese populations. BMC Biol 2008; 6:45. [PMID: 18959782 PMCID: PMC2605740 DOI: 10.1186/1741-7007-6-45] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2008] [Accepted: 10/29/2008] [Indexed: 12/27/2022] Open
Abstract
Background The phylogeography of the Y chromosome in Asia previously suggested that modern humans of African origin initially settled in mainland southern East Asia, and about 25,000–30,000 years ago, migrated northward, spreading throughout East Asia. However, the fragmented distribution of one East Asian specific Y chromosome lineage (D-M174), which is found at high frequencies only in Tibet, Japan and the Andaman Islands, is inconsistent with this scenario. Results In this study, we collected more than 5,000 male samples from 73 East Asian populations and reconstructed the phylogeography of the D-M174 lineage. Our results suggest that D-M174 represents an extremely ancient lineage of modern humans in East Asia, and a deep divergence was observed between northern and southern populations. Conclusion We proposed that D-M174 has a southern origin and its northward expansion occurred about 60,000 years ago, predating the northward migration of other major East Asian lineages. The Neolithic expansion of Han culture and the last glacial maximum are likely the key factors leading to the current relic distribution of D-M174 in East Asia. The Tibetan and Japanese populations are the admixture of two ancient populations represented by two major East Asian specific Y chromosome lineages, the O and D haplogroups.
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Affiliation(s)
- Hong Shi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology and Kunming Primate Research Centre, Chinese Academy of Sciences, Kunming, PR China.
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Lindström S, Adami HO, Adolfsson J, Wiklund F. Y Chromosome Haplotypes and Prostate Cancer in Sweden. Clin Cancer Res 2008; 14:6712-6. [DOI: 10.1158/1078-0432.ccr-08-0658] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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37
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Kim W, Yoo TK, Shin DJ, Rho HW, Jin HJ, Kim ET, Bae YS. Mitochondrial DNA haplogroup analysis reveals no association between the common genetic lineages and prostate cancer in the Korean population. PLoS One 2008; 3:e2211. [PMID: 18493608 PMCID: PMC2376063 DOI: 10.1371/journal.pone.0002211] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2008] [Accepted: 04/08/2008] [Indexed: 01/29/2023] Open
Abstract
Mitochondrial DNA (mtDNA) variation has recently been suggested to have an association with various cancers, including prostate cancer risk, in human populations. Since mtDNA is haploid and lacks recombination, specific mutations in the mtDNA genome associated with human diseases arise and remain in particular genetic backgrounds referred to as haplogroups. To assess the possible contribution of mtDNA haplogroup-specific mutations to the occurrence of prostate cancer, we have therefore performed a population-based study of a prostate cancer cases and corresponding controls from the Korean population. No statistically significant difference in the distribution of mtDNA haplogroup frequencies was observed between the case and control groups of Koreans. Thus, our data imply that specific mtDNA mutations/lineages did not appear to have a significant effect on a predisposition to prostate cancer in the Korean population, although larger sample sizes are necessary to validate our results.
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Affiliation(s)
- Wook Kim
- Department of Biological Sciences, Dankook University, Cheonan, Korea.
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38
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Zhang F, Su B, Zhang YP, Jin L. Genetic studies of human diversity in East Asia. Philos Trans R Soc Lond B Biol Sci 2007; 362:987-95. [PMID: 17317646 PMCID: PMC2435565 DOI: 10.1098/rstb.2007.2028] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
East Asia is one of the most important regions for studying evolution and genetic diversity of human populations. Recognizing the relevance of characterizing the genetic diversity and structure of East Asian populations for understanding their genetic history and designing and interpreting genetic studies of human diseases, in recent years researchers in China have made substantial efforts to collect samples and generate data especially for markers on Y chromosomes and mtDNA. The hallmark of these efforts is the discovery and confirmation of consistent distinction between northern and southern East Asian populations at genetic markers across the genome. With the confirmation of an African origin for East Asian populations and the observation of a dominating impact of the gene flow entering East Asia from the south in early human settlement, interpretation of the north-south division in this context poses the challenge to the field. Other areas of interest that have been studied include the gene flow between East Asia and its neighbouring regions (i.e. Central Asia, the Sub-continent, America and the Pacific Islands), the origin of Sino-Tibetan populations and expansion of the Chinese.
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Affiliation(s)
- Feng Zhang
- Institute of Genetics, School of Life Sciences, Fudan UniversityShanghai 200433, People's Republic of China
| | - Bing Su
- Laboratory of Cellular and Molecular Evolution, Kunming Institute of Zoology, Chinese Academy of SciencesKunming 650223, People's Republic of China
| | - Ya-ping Zhang
- Laboratory of Cellular and Molecular Evolution, Kunming Institute of Zoology, Chinese Academy of SciencesKunming 650223, People's Republic of China
- Laboratory for Conservation and Utilization of Bio-resource, Yunnan UniversityKunming 650091, People's Republic of China
| | - Li Jin
- Institute of Genetics, School of Life Sciences, Fudan UniversityShanghai 200433, People's Republic of China
- CAS-MPG Partner Institute of Computational Biology, Chinese Academy of SciencesShanghai 200031, People's Republic of China
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Garcia-Gonzalez CL, Montoya-Fuentes H, Padilla-Rosas M, Sanchez-Corona J. Amylin S20G mutation in Mexican population. Diabetes Res Clin Pract 2007; 76:146-8. [PMID: 16950544 DOI: 10.1016/j.diabres.2006.07.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2006] [Accepted: 07/31/2006] [Indexed: 10/24/2022]
Abstract
Diabetes Mellitus type 2 (DM2) is a group of metabolic disorders characterized by defective insulin action or secretion or both with a 10.6% incidence in Mexican Mestizo population, DM2 is also classified within the localized misfolding diseases due to the amyloid pancreatic deposits found in 90% of the DM2 necropsies. The pancreatic amyloid main component is a protein known as human islet amyloid polypeptide (hIAPP) or amylin, the most common mutation is the S20G in Asian population with a polymorphic frequency in DM2 Asian patients. The aim of this study was to search this mutation in Mexican Mestizo general population (104) and DM2 patients (100). This is the first molecular study of hIAPP gene in Mexican population and in which we developed an alternative more effective antisense primer for the analysis of the NFGAILSS region in hIAPP exon 3 critical for the amyloid beta structure formation. We did not find the mutation in any of the 204 analyzed samples, thus the findings show that S20G is not a common mutation in Mexican Mestizo population.
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Affiliation(s)
- Claudia Lorena Garcia-Gonzalez
- Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social Guadalajara, Sierra Mojada No. 800, Colonia Independencia, S.L. CP. 44340, Guadalajara, Jalisco, México.
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40
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Nonaka I, Minaguchi K, Takezaki N. Y-chromosomal binary haplogroups in the Japanese population and their relationship to 16 Y-STR polymorphisms. Ann Hum Genet 2007; 71:480-95. [PMID: 17274803 DOI: 10.1111/j.1469-1809.2006.00343.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We investigated Y chromosomal binary and STR polymorphisms in 263 unrelated male individuals from the Japanese population and further examined the relationships between the two separate types of data. Using 47 biallelic markers we distinguished 20 haplogroups, four of which (D2b1/-022457, O3/-002611*, O3/-LINE1 del, and O3/-021354*) were newly defined in this study. Most haplogroups in the Japanese population are found in one of the three major clades, C, D, or O. Among these, two major lineages, D2b and O2b, account for 66% of Japanese Y chromosomes. Haplotype diversity of binary markers was calculated at 86.3%. The addition of 16 Y-STR markers increased the number of haplotypes to 225, yielding a haplotype diversity of 99.40%. A comparison of binary haplogroups and Y-STR type revealed a close association between certain binary haplogroups and Y-STR allelic or conformational differences, such as those at the DXYS156Y, DYS390m, DYS392, DYS437, DYS438 and DYS388 loci. Based on our data on the relationships between binary and STR polymorphisms, we estimated the binary haplogroups of individuals from STR haplotypes and frequencies of binary haplogroups in other Japanese, Korean and Taiwanese Han populations. The present data will enable researchers to connect data from binary haplogrouping in anthropological studies and Y-STR typing in forensic studies in East Asian populations, especially those in and around Japan.
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Affiliation(s)
- I Nonaka
- Department of Forensic Odontology, Tokyo Dental College, 1-2-2 Masago, Mihama-ku, Chiba City, 261-0011, Japan
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Kim W, Yoo TK, Kim SJ, Shin DJ, Tyler-Smith C, Jin HJ, Kwak KD, Kim ET, Bae YS. Lack of association between Y-chromosomal haplogroups and prostate cancer in the Korean population. PLoS One 2007; 2:e172. [PMID: 17245448 PMCID: PMC1766463 DOI: 10.1371/journal.pone.0000172] [Citation(s) in RCA: 17] [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: 11/07/2006] [Accepted: 12/21/2006] [Indexed: 11/30/2022] Open
Abstract
The Y chromosome has recently been suggested to have an association with prostate cancer risk in human populations. Since this chromosome is haploid and lacks recombination over most of its length, haplotypes constructed from binary markers throughout the chromosome can be used for association studies. To assess the possible Y-chromosomal contribution to prostate cancer risk, we have therefore analyzed 14 Y-chromosomal binary markers in 106 prostate cancer cases and 110 controls from the Korean population. In contrast to previous findings in the Japanese population, no statistically significant difference in the distribution of Y-chromosomal haplogroup frequencies was observed between the case and control groups of Koreans. Thus, our data imply that the previously reported associations between Y-chromosomal lineages and a predisposition to, or protection against, prostate cancer might be explained by statistical fluctuations, or by genetic effects that are seen only in some environments.
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Affiliation(s)
- Wook Kim
- Department of Biological Sciences, Dankook University, Cheonan, Korea.
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42
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de Carvalho CMB, Zuccherato LW, Fujisawa M, Shirakawa T, Ribeiro-Dos-Santos AKC, Santos SEB, Pena SDJ, Santos FR. Study of AZFc partial deletion gr/gr in fertile and infertile Japanese males. J Hum Genet 2006; 51:794-799. [PMID: 16900294 DOI: 10.1007/s10038-006-0024-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2006] [Accepted: 05/26/2006] [Indexed: 11/27/2022]
Abstract
A recurrent partial azoospermia factor C (AZFc) deletion, called gr/gr, has been reported to be a male infertility risk factor. A specific type of Y chromosome observed in approximately 30% of Japanese males (haplogroup D derived at YAP+) is believed to have a fixed gr/gr deletion. A recent study claimed that spermatogenic failure is more likely in males with D Y chromosomes, because of the gr/gr deletion, the presence of which is not well characterized among D haplogroup chromosomes. We therefore decided to perform a systematic study of the frequency of the gr/gr deletion in the Japanese. We studied fertile and infertile males to investigate the possibility of different gr/gr frequencies. The deletions were detected by use of single tagged-sequences (STSs) and the D haplogroup sub-lineages typing were done by use of the biallelic markers M174, M64, M116.1, 12f2.2, M15, M151, and M125. Analysis of gr/gr deleted Y chromosomes showed that all are classified as haplogroup D2, suggesting a lineage association. The subtype D2b1 was most frequent among the Japanese, in control and infertile samples. The haplogroups D2b2, D*, and D1 were not found in any population group. Remarkably, we observed no statistical difference between haplogroup D sub-lineages of the infertile and control groups, although the statistical power of this study is low. This study suggests lack of significant evidence of increased infertility risk in haplogroup D Japanese males. We were also able to establish the ancestral chromosome that suffered a gr/gr deletion, and propose a new Y chromosome phylogeny for haplogroup D and its derivatives. In summary, we were able to define the frequency of gr/gr deletion in Japanese males and show that the gr/gr deletion was probably present in the ancestral Y chromosome that entered Japan at least 12,000 years ago.
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Affiliation(s)
| | - Luciana Werneck Zuccherato
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | | | | | | | | | - Sérgio Danilo Junho Pena
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Fabrício Rodrigues Santos
- Departamento de Biologia Geral, ICB, UFMG, Universidade Federal de Minas Gerais, C.P. 486, Av. Antônio Carlos 6627, 31270-010, Belo Horizonte, MG, Brazil.
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Jin HJ, Kwak KD, Hong SB, Shin DJ, Han MS, Tyler-Smith C, Kim W. Forensic genetic analysis of mitochondrial DNA hypervariable region I/II sequences: An expanded Korean population database. Forensic Sci Int 2006; 158:125-30. [PMID: 15990264 DOI: 10.1016/j.forsciint.2005.03.026] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2005] [Revised: 03/25/2005] [Accepted: 03/28/2005] [Indexed: 11/20/2022]
Abstract
We have analyzed variation of the mitochondrial DNA (mtDNA) hypervariable segments I and II (HVS-I and HVS-II) in 185 randomly chosen individuals from Korea to provide an expanded and reliable Korean database. Combined sequence comparison of HVS-I and HVS-II led to the identification of 167 different haplotypes characterized by 154 variable sites. One hundred and fifty-one of the haplotypes were individual-specific, 14 were found in two individuals and 2 were found in three individuals. A pairwise comparison of the 185 HVS-I/II sequences found an average of 10.11 +/- 4.63 differences between individuals. The random match probability and gene diversity for the combined hypervariable regions were estimated at 0.66% and 0.9988, respectively. Analyzing the expanded database including three previously reported data sets and the present data using haplogroup-based comparisons and comparison with closely related sequences allowed errors to be detected and eliminated, thus considerably improving data quality. Sample division comparisons based on PhiST genetic distance measures revealed no significant population differentiation in the distribution of mtDNA sequence variations between the present data set and a database in The Scientific Working Group on DNA Analysis Methods (SWGDAM), but did indicate differences from other sets of data. Based on the results of mtDNA profiles, almost all of the mtDNA types studied here could be classified into subsets of haplogroups common in east Asia, and show that the Koreans possess lineages from both the southern and the northern haplogroup complexes of east Asian populations. The new data, combined with other mtDNA sequences, demonstrate how useful comparison with closely related mtDNA sequences can be for improving database quality, as well as providing haplotype information for forensic and population genetic analyses in the Korean population.
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Affiliation(s)
- Han Jun Jin
- Department of Biological Sciences, Dankook University, San 29, Anseo-dong, Cheonan, Choong-nam 330-714, Republic of Korea
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Shi H, Dong YL, Wen B, Xiao CJ, Underhill PA, Shen PD, Chakraborty R, Jin L, Su B. Y-chromosome evidence of southern origin of the East Asian-specific haplogroup O3-M122. Am J Hum Genet 2005; 77:408-19. [PMID: 16080116 PMCID: PMC1226206 DOI: 10.1086/444436] [Citation(s) in RCA: 126] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2005] [Accepted: 06/29/2005] [Indexed: 11/03/2022] Open
Abstract
The prehistoric peopling of East Asia by modern humans remains controversial with respect to early population migrations. Here, we present a systematic sampling and genetic screening of an East Asian-specific Y-chromosome haplogroup (O3-M122) in 2,332 individuals from diverse East Asian populations. Our results indicate that the O3-M122 lineage is dominant in East Asian populations, with an average frequency of 44.3%. The microsatellite data show that the O3-M122 haplotypes in southern East Asia are more diverse than those in northern East Asia, suggesting a southern origin of the O3-M122 mutation. It was estimated that the early northward migration of the O3-M122 lineages in East Asia occurred approximately 25,000-30,000 years ago, consistent with the fossil records of modern humans in East Asia.
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Affiliation(s)
- Hong Shi
- Key Laboratory of Cellular and Molecular Evolution, Kunming Institute of Zoology, Kunming, China.
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45
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Lu YB, Kobayashi K, Ushikai M, Tabata A, Iijima M, Li MX, Lei L, Kawabe K, Taura S, Yang Y, Liu TT, Chiang SH, Hsiao KJ, Lau YL, Tsui LC, Lee DH, Saheki T. Frequency and distribution in East Asia of 12 mutations identified in the SLC25A13 gene of Japanese patients with citrin deficiency. J Hum Genet 2005; 50:338-346. [PMID: 16059747 DOI: 10.1007/s10038-005-0262-8] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2005] [Accepted: 05/26/2005] [Indexed: 02/07/2023]
Abstract
Deficiency of citrin, a liver-type mitochondrial aspartate-glutamate carrier (AGC), encoded by the SLC25A13 gene on chromosome 7q21.3, causes autosomal recessive disorders: adult-onset type II citrullinemia (CTLN2) and neonatal hepatitis associated with intrahepatic cholestasis (NICCD). So far, we have described 12 SLC25A13 mutations: 11 were from Japan and one from Israel. Three mutations found in Chinese and Vietnamese patients were the same as those in Japanese patients. In the present study, we identified a novel mutation IVS6+1G>C in a Japanese CTLN2 patient and widely screened 12 SLC25A13 mutations found in Japanese patients in control individuals from East Asia to confirm our preliminary results that the carrier frequency was high in Asian populations. Mutations 851-854del and 1638-1660dup were found in all Asian countries tested, and 851-854del associated with 290-haplotype in microsatellite marker D7S1812 was especially frequent. Other mutations frequently detected were IVS11+1G>A in Japanese and Korean, S225X in Japanese, and IVS6+5G>A in Chinese populations. We found a remarkable difference in carrier rates in China (including Taiwan) between north (1/940) and south (1/48) of the Yangtze River. We detected many carriers in Chinese (64/4169 = 1/65), Japanese (20/1372 = 1/69) and Korean (22/2455 = 1/112) populations, suggesting that over 80,000 East Asians are homozygotes with two mutated SLC25A13 alleles.
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Affiliation(s)
- Yao Bang Lu
- Department of Molecular Metabolism and Biochemical Genetics, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima 890-8544, Japan
| | - Keiko Kobayashi
- Department of Molecular Metabolism and Biochemical Genetics, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima 890-8544, Japan.
| | - Miharu Ushikai
- Department of Molecular Metabolism and Biochemical Genetics, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima 890-8544, Japan
| | - Ayako Tabata
- Department of Molecular Metabolism and Biochemical Genetics, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima 890-8544, Japan
| | - Mikio Iijima
- Department of Molecular Metabolism and Biochemical Genetics, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima 890-8544, Japan
| | - Meng Xian Li
- Department of Molecular Metabolism and Biochemical Genetics, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima 890-8544, Japan
| | - Lei Lei
- Department of Molecular Metabolism and Biochemical Genetics, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima 890-8544, Japan
| | - Kotaro Kawabe
- Division of Gene Research, Research Centre for Life Science Resources, Kagoshima University, Kagoshima, Japan
| | - Satoru Taura
- Division of Gene Research, Research Centre for Life Science Resources, Kagoshima University, Kagoshima, Japan
| | - Yanling Yang
- Department of Pediatrics, The First Hospital of Peking University, Beijing, China
| | - Tze-Tze Liu
- Genome Research Center, National Yang-Ming University, Taipei, Taiwan, ROC
| | | | | | - Yu-Lung Lau
- Department of Pediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Lap-Chee Tsui
- Vice Chancellor's Office, The University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Dong Hwan Lee
- Department of Pediatrics, Soonchunhyang University Hospital, Seoul, Korea
| | - Takeyori Saheki
- Department of Molecular Metabolism and Biochemical Genetics, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima 890-8544, Japan
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Kim JJ, Verdu P, Pakstis AJ, Speed WC, Kidd JR, Kidd KK. Use of autosomal loci for clustering individuals and populations of East Asian origin. Hum Genet 2005; 117:511-9. [PMID: 16028061 DOI: 10.1007/s00439-005-1334-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2004] [Accepted: 04/14/2005] [Indexed: 10/25/2022]
Abstract
We studied the genetic relationships among East Asian populations based on allele frequency differences to clarify the relative similarities of East Asian populations with a specific focus on the relationships among the Koreans, the Japanese, and the Chinese populations known to be genetically similar. The goal is to find markers appropriate for differentiating among the specific populations. In this study, no prior data existed for Koreans and the markers were selected to differentiate Chinese and Japanese. We typed, using AB TaqMan assays, single-nucleotide polymorphisms (SNPs) at 43 highly selected mostly independent diallelic sites, on 386 individuals from eight East Asian populations (Han Chinese from San Francisco, Han Chinese from Taiwan, Hakka, Koreans, Japanese, Ami, Atayal, and Cambodians) and one Siberian population (Yakut). We inferred group membership of individuals using a model-based clustering method implemented by the STRUCTURE program and population clustering by using computer programs DISTANCE, NEIGHBOR, LSSEARCH, and DRAWTREE, respectively, calculating genetic distances among populations, calculating neighbor-joining and least-squares trees, and drawing the calculated trees. On average 52% of individuals in the three Chinese groups were assigned into one cluster, and, respectively, 78 and 69% of Koreans and Japanese into a different cluster. Koreans differentiated from the Chinese groups and clustered with the Japanese in the principal component analysis (PCA) and in the best least-squares tree. The majority of Koreans were difficult to distinguish from the Japanese. This study shows that a relatively few highly selected markers can, within limits, differentiate between closely related populations.
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Affiliation(s)
- Jong-Jin Kim
- National Institute of Scientific Investigation, DNA Analysis Division, Seoul, Korea
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Kwak KD, Jin HJ, Shin DJ, Kim JM, Roewer L, Krawczak M, Tyler-Smith C, Kim W. Y-chromosomal STR haplotypes and their applications to forensic and population studies in east Asia. Int J Legal Med 2005; 119:195-201. [PMID: 15856270 DOI: 10.1007/s00414-004-0518-4] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2004] [Accepted: 12/08/2004] [Indexed: 11/26/2022]
Abstract
We have analyzed 11 Y-STR loci (DYS19, the two DYS385 loci, DYS388, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DXYS156Y) in 700 males from ten ethnic groups in east Asia in order to evaluate their usefulness for forensic and population genetic studies. A total of 644 different haplotypes were identified, among which 603 (86.14%) were individual-specific. The haplotype diversity averaged over all populations was 0.9997; using only the nine Y-STRs comprising the "minimal haplotype" (excluding DYS388 and DXYS156Y) it was 0.9996, a value similar to that found in 1924 samples from other Asian populations (0.9996; Lessig et al. Legal Medicine 5(2003) 160-163), and slightly higher than in European populations (0.9976; n=11,610; Roewer et al. For Sci International (2001) 118:103-111). All of the individual east Asian populations examined here had high haplotype diversity (> or =0.997), except for the Mongolians (0.992) and Manchurians (0.960). The most frequent haplotype identified by the nine markers was present at only 1% (7/700). Population comparisons based on Phi(ST) or rho genetic distance measures revealed clustering according to the traditional northeast-southeast distinction, but with exceptions. For example, the Yunnan population from southern China lay among the northern populations, possibly reflecting recent migration, while the Korean population, traditionally considered northern, lay at the boundary between northern and southern populations. An admixture estimate suggested 55(51-59)% northern, 45(41-49)% southern contribution to the Koreans, illustrating the complexity of the genetic history of this region.
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Affiliation(s)
- Kyoung Don Kwak
- Department of Biological Sciences, Dankook University, Cheonan, 330-714, South Korea
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