1
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Kasai F, Fukushima M, Miyagi Y, Nakamura Y. Genetic diversity among the present Japanese population: evidence from genotyping of human cell lines established in Japan. Hum Cell 2024; 37:944-950. [PMID: 38639832 PMCID: PMC11194210 DOI: 10.1007/s13577-024-01055-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 03/12/2024] [Indexed: 04/20/2024]
Abstract
Japan is often assumed to have a highly homogeneous ethnic population, because it is an island country. This is evident in human cell lines collected from cell banks; however, these genotypes have not been thoroughly characterized. To examine the population genotypes of human cell lines established in Japan, we conducted SNP genotyping on 57 noncancerous cell lines and 43 lung cancer cell lines. Analysis of biogeographic ancestry revealed that 58 cell lines had non-admixed Japanese genotypes, 21 cell lines had an admixture of Japanese and East Asian genotypes, and the remaining 21 cell lines had East Asian genotypes. The proportion of non-admixed Japanese genotypes was similar between lung cancer and noncancerous cell lines, suggesting that patients in Japan may not exclusively have Japanese genotypes. This could influence the incidence of inherited diseases and should be taken into account in personalized medicine tailored to genetic background. The genetic makeup of the present-day Japanese population cannot be fully explained by the ancestral Jomon and Yayoi lineages. Instead, it is necessary to consider a certain level of genetic admixture between Japanese and neighboring Asian populations. Our study revealed genetic variation among human cell lines derived from Japanese individuals, reflecting the diversity present within the Japanese population.
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Affiliation(s)
- Fumio Kasai
- Cell Engineering Division, BioResource Research Center, RIKEN Cell Bank, Tsukuba, Japan.
| | - Makoto Fukushima
- Cell Engineering Division, BioResource Research Center, RIKEN Cell Bank, Tsukuba, Japan
| | - Yohei Miyagi
- Molecular Pathology and Genetics Division, Kanagawa Cancer Center Research Institute, Yokohama, Japan
| | - Yukio Nakamura
- Cell Engineering Division, BioResource Research Center, RIKEN Cell Bank, Tsukuba, Japan
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2
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Wang Z, Wang M, Hu L, He G, Nie S. Evolutionary profiles and complex admixture landscape in East Asia: New insights from modern and ancient Y chromosome variation perspectives. Heliyon 2024; 10:e30067. [PMID: 38756579 PMCID: PMC11096704 DOI: 10.1016/j.heliyon.2024.e30067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 04/08/2024] [Accepted: 04/18/2024] [Indexed: 05/18/2024] Open
Abstract
Human Y-chromosomes are characterized by nonrecombination and uniparental inheritance, carrying traces of human history evolution and admixture. Large-scale population-specific genomic sources based on advanced sequencing technologies have revolutionized our understanding of human Y chromosome diversity and its anthropological and forensic applications. Here, we reviewed and meta-analyzed the Y chromosome genetic diversity of modern and ancient people from China and summarized the patterns of founding lineages of spatiotemporally different populations associated with their origin, expansion, and admixture. We emphasized the strong association between our identified founding lineages and language-related human dispersal events correlated with the Sino-Tibetan, Altaic, and southern Chinese multiple-language families related to the Hmong-Mien, Tai-Kadai, Austronesian, and Austro-Asiatic languages. We subsequently summarize the recent advances in translational applications in forensic and anthropological science, including paternal biogeographical ancestry inference (PBGAI), surname investigation, and paternal history reconstruction. Whole-Y sequencing or high-resolution panels with high coverage of terminal Y chromosome lineages are essential for capturing the genomic diversity of ethnolinguistically diverse East Asians. Generally, we emphasized the importance of including more ethnolinguistically diverse, underrepresented modern and spatiotemporally different ancient East Asians in human genetic research for a comprehensive understanding of the paternal genetic landscape of East Asians with a detailed time series and for the reconstruction of a reference database in the PBGAI, even including new technology innovations of Telomere-to-Telomere (T2T) for new genetic variation discovery.
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Affiliation(s)
- Zhiyong Wang
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China
| | - Mengge Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510275, China
| | - Liping Hu
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Guanglin He
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China
| | - Shengjie Nie
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
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3
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Feng Y, Zhao Y, Lu X, Li H, Zhao K, Shi M, Wen S. Forensic analysis and sequence variation of 133 STRs in the Hakka population. Front Genet 2024; 15:1347868. [PMID: 38317659 PMCID: PMC10839782 DOI: 10.3389/fgene.2024.1347868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 01/05/2024] [Indexed: 02/07/2024] Open
Abstract
Introduction: Short Tandem Repeats (STRs) are highly valuable genetic markers in forensic science. However, the conventional PCR-CE technique has limitations, and the emergence of massively parallel sequencing (MPS) technology presents new opportunities for STR analysis. Yet, there is limited research on Chinese population diversity using MPS. Methods: In this study, we obtained genotype data for 52 A-STRs and 81 Y-STRs from the Hakka population in Meizhou, Guangdong, China, using the Forensic Analysis System Multiplecues SetB Kit on the MGISEQ-2000 platform. Results: Our findings demonstrate that these 133 STRs are highly efficient for forensic applications within the Meizhou Hakka population. Statistical analysis revealed Hobs values ranging from 0.61306 to 0.91083 and Hexp values ranging from 0.59156 to 0.91497 for A-STRs based on length polymorphism. For sequence polymorphism, Hobs values ranged from 0.61306 to 0.94586, and Hexp values fluctuated between 0.59156 and 0.94487. The CPE values were 1-5.0779620E-21 and 1-3.257436E-24 for length and sequence polymorphism, respectively, while the CPD values were 1-1.727007E-59 and 1-5.517015E-66, respectively. Among the 80 Y-STR loci, the HD values for length and sequence polymorphism were 0.99764282 and 0.99894195, respectively. The HMP values stood at 0.00418102 and 0.00288427, respectively, and the DC values were 0.75502742 and 0.83363803, respectively. For the 52 A-STR loci, we identified 554 and 989 distinct alleles based on length and sequence polymorphisms, respectively. For the 81 Y-STR loci, 464 and 652 unique alleles were detected at the length and sequence level, respectively. Population genetic analysis revealed that the Meizhou Hakka population has a close kinship relationship with the Asian populations THI and KOR based on length polymorphism data of A-STRs. Conversely, based on length polymorphism data of Y-STRs, the Meizhou Hakka population has the closest kinship relationship with the Henan Han population. Discussion: Overall, the variation information of repeat region sequences significantly enhances the forensic identification efficacy of STR genetic markers, providing an essential database for forensic individual and paternity testing in this region. Additionally, the data generated by our study will serve as a vital resource for research into the genetic structure and historical origins of the Meizhou Hakka population.
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Affiliation(s)
- Yuhang Feng
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yutao Zhao
- Public Security Bureau of Zhaoqing Municipality, Zhaoqing, China
| | - Xiaoyu Lu
- Deepreads Biotech Company Limited, Guangzhou, China
| | - Haiyan Li
- Criminal Technology Center of Guangdong Provincial Public Security Department, Guangzhou, China
| | - Kai Zhao
- Criminal Technology Center of Guangdong Provincial Public Security Department, Guangzhou, China
| | - Meisen Shi
- Criminal Justice College of China University of Political Science and Law, Beijing, China
| | - Shaoqing Wen
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
- Institute of Archaeological Science, Fudan University, Shanghai, China
- MOE Laboratory for National Development and Intelligent Governance, Fudan University, Shanghai, China
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4
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Chao KH, Zimin AV, Pertea M, Salzberg SL. The first gapless, reference-quality, fully annotated genome from a Southern Han Chinese individual. G3 (BETHESDA, MD.) 2023; 13:jkac321. [PMID: 36630290 PMCID: PMC9997556 DOI: 10.1093/g3journal/jkac321] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/27/2022] [Accepted: 11/03/2022] [Indexed: 01/12/2023]
Abstract
We used long-read DNA sequencing to assemble the genome of a Southern Han Chinese male. We organized the sequence into chromosomes and filled in gaps using the recently completed T2T-CHM13 genome as a guide, yielding a gap-free genome, Han1, containing 3,099,707,698 bases. Using the T2T-CHM13 annotation as a reference, we mapped all genes onto the Han1 genome and identified additional gene copies, generating a total of 60,708 putative genes, of which 20,003 are protein-coding. A comprehensive comparison between the genes revealed that 235 protein-coding genes were substantially different between the individuals, with frameshifts or truncations affecting the protein-coding sequence. Most of these were heterozygous variants in which one gene copy was unaffected. This represents the first gene-level comparison between two finished, annotated individual human genomes.
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Affiliation(s)
- Kuan-Hao Chao
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Aleksey V Zimin
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Mihaela Pertea
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Steven L Salzberg
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21211, USA
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5
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Lo YH, Cheng HC, Hsiung CN, Yang SL, Wang HY, Peng CW, Chen CY, Lin KP, Kang ML, Chen CH, Chu HW, Lin CF, Lee MH, Liu Q, Satta Y, Lin CJ, Lin M, Chaw SM, Loo JH, Shen CY, Ko WY. Detecting Genetic Ancestry and Adaptation in the Taiwanese Han People. Mol Biol Evol 2021; 38:4149-4165. [PMID: 33170928 PMCID: PMC8476137 DOI: 10.1093/molbev/msaa276] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The Taiwanese people are composed of diverse indigenous populations and the Taiwanese Han. About 95% of the Taiwanese identify themselves as Taiwanese Han, but this may not be a homogeneous population because they migrated to the island from various regions of continental East Asia over a period of 400 years. Little is known about the underlying patterns of genetic ancestry, population admixture, and evolutionary adaptation in the Taiwanese Han people. Here, we analyzed the whole-genome single-nucleotide polymorphism genotyping data from 14,401 individuals of Taiwanese Han collected by the Taiwan Biobank and the whole-genome sequencing data for a subset of 772 people. We detected four major genetic ancestries with distinct geographic distributions (i.e., Northern, Southeastern, Japonic, and Island Southeast Asian ancestries) and signatures of population mixture contributing to the genomes of Taiwanese Han. We further scanned for signatures of positive natural selection that caused unusually long-range haplotypes and elevations of hitchhiked variants. As a result, we identified 16 candidate loci in which selection signals can be unambiguously localized at five single genes: CTNNA2, LRP1B, CSNK1G3, ASTN2, and NEO1. Statistical associations were examined in 16 metabolic-related traits to further elucidate the functional effects of each candidate gene. All five genes appear to have pleiotropic connections to various types of disease susceptibility and significant associations with at least one metabolic-related trait. Together, our results provide critical insights for understanding the evolutionary history and adaption of the Taiwanese Han population.
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Affiliation(s)
- Yun-Hua Lo
- Faculty of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Hsueh-Chien Cheng
- Faculty of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Chia-Ni Hsiung
- Institute of Biomedical Sciences, Academia Sinica, Taipei City, Taiwan
| | - Show-Ling Yang
- Institute of Biomedical Sciences, Academia Sinica, Taipei City, Taiwan
| | - Han-Yu Wang
- Faculty of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Chia-Wei Peng
- Faculty of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Chun-Yu Chen
- Faculty of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Kung-Ping Lin
- Faculty of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Mei-Ling Kang
- Faculty of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Chien-Hsiun Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei City, Taiwan
| | - Hou-Wei Chu
- Institute of Biomedical Sciences, Academia Sinica, Taipei City, Taiwan
| | | | - Mei-Hsuan Lee
- Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Quintin Liu
- Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Japan
| | - Yoko Satta
- Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Japan
| | - Cheng-Jui Lin
- Molecular Anthropology and Transfusion Medicine Research Laboratory, Mackay Memorial Hospital, Taipei, Taiwan
| | - Marie Lin
- Molecular Anthropology and Transfusion Medicine Research Laboratory, Mackay Memorial Hospital, Taipei, Taiwan
| | - Shu-Miaw Chaw
- Biodiversity Research Center, Academia Sinica, Taipei City, Taiwan
| | - Jun-Hun Loo
- Molecular Anthropology and Transfusion Medicine Research Laboratory, Mackay Memorial Hospital, Taipei, Taiwan
| | - Chen-Yang Shen
- Institute of Biomedical Sciences, Academia Sinica, Taipei City, Taiwan
| | - Wen-Ya Ko
- Faculty of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
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6
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Lin WX, Yaqub MR, Zhang ZH, Mao M, Zeng HS, Chen FP, Li WM, Cai WZ, Li YQ, Tan ZY, Sheng W, Li ZM, Tao XL, Li YX, Zhang JP, Han YB, Li Y, Duan WQ, Ye BN, Li YR, Song YZ. Molecular epidemiologic study of citrin deficiency by screening for four reported pathogenic SLC25A13 variants in the Shaanxi and Guangdong provinces, China. Transl Pediatr 2021; 10:1658-1667. [PMID: 34295780 PMCID: PMC8261583 DOI: 10.21037/tp-21-58] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 04/19/2021] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Citrin deficiency (CD) is an autosomal recessive disease resulting from biallelic mutations of the SLC25A13 gene. This study aimed to investigate the molecular epidemiological features of CD in the Guangdong and Shaanxi provinces of China. METHODS A total of 3,409 peripheral blood samples from Guangdong and 2,746 such samples from Shaanxi province were collected. Four prevalent SLC25A13 mutations NG_012247.2 (NM_014251.3): c.852_855del, c.1638_1660dup, c.615+5G>A, and c.1751-5_1751-4ins(2684) were screened by using the conventional polymerase chain reaction (PCR)/PCR-restriction fragment length polymorphism and newly-developed multiplex PCR methods, respectively. The mutated SLC25A13 allele frequencies, carrier frequencies, and CD morbidity rates were calculated and then compared with the Chi-square and Fisher's exact tests. RESULTS The mutations were detected in 68 out of 6,818 SLC25A13 alleles in Guangdong and 29 out of 5,492 alleles in the Shaanxi population. The carrier frequencies were subsequently calculated to be 1/51 and 1/95, while the CD morbidity rates were 1/10,053 and 1/35,865, in the 2 populations, respectively. When compared with the Shaanxi population, Guangdong exhibited a higher frequency of mutated SLC25A13 allele (68/6,818 vs. 29/5,492, χ2=8.570, P=0.003) in general, with higher c.852_855del (54/6,818 vs. 13/5,492, χ2=17.328, P=0.000) but lower c.1751-5_1751 -4ins(2684) (2/6,818 vs. 9/5,492, P=0.015) allele frequencies. The distribution of c.615+5G>A and c.1638_1660dup between the 2 provinces, as well as all 4 prevalent mutations among different geographic regions within the 2 provinces, did not differed significantly. CONCLUSIONS Our findings depicted the CD molecular epidemiological features in Guangdong and Shaanxi populations, providing preliminary but significant laboratory evidences for the subsequent CD diagnosis and management in the 2 provinces of mainland China.
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Affiliation(s)
- Wei-Xia Lin
- Department of Pediatrics, the First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Muhammad Rauf Yaqub
- Department of Pediatrics, the First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Zhan-Hui Zhang
- Clinical Medicine Research Institute, the First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Man Mao
- Department of Pediatrics, the First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Han-Shi Zeng
- Department of Pediatrics, the First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Feng-Ping Chen
- Department of Laboratory Science, the First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Wei-Ming Li
- Department of Pediatrics, Maternal and Child Health Hospital of Qingyuan City, Qingyuan, China
| | - Wen-Zhe Cai
- Department of Internal Medicine, Central Hospital of Shantou City, Shantou, China
| | - Ying-Qiang Li
- Department of Internal Medicine, Maternal and Child Health Hospital of Yunfu City, Yunfu, China
| | - Zhi-Yong Tan
- Department of Pediatrics, Maternal and Child Health Hospital of Shaoguan City, Shaoguan, China
| | - Wei Sheng
- Department of Pediatrics, Weinan First Hospital, Weinan, China
| | - Zhi-Min Li
- Department of Pediatrics, San Er Ling Yi Hospital, Hanzhong, China
| | - Xiao-Ling Tao
- Department of Pediatrics, Xianyang Rainbow Hospital (Xianyang Children's Hospital), Xianyang, China
| | - Yuan-Xia Li
- Department of Pediatrics, Yan'an University Hospital, Yan'an, China
| | - Jun-Ping Zhang
- Clinical laboratory, Qishan County Hospital, Qishan, China
| | - Yao-Bin Han
- Department of Infectious Diseases, Shenmu Hospital of Northwestern University, Shenmu, China
| | - Yan Li
- Department of Pediatrics, Zhashui County Hospital, Zhashui, China
| | - Wu-Qiong Duan
- Department of Pediatrics, Ankang Central Hospital, Ankang, China
| | - Bao-Ni Ye
- Department of Pediatrics, Southern Campus of Tongchuan People's Hospital, Tongchuan, China
| | - Ya-Rong Li
- The Third Department of Infectious Diseases, Xi'an Children's Hospital, Xi'an, China
| | - Yuan-Zong Song
- Department of Pediatrics, the First Affiliated Hospital, Jinan University, Guangzhou, China
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7
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Moore KJ, Hubbard AK, Williams LA, Spector LG. Childhood cancer incidence among specific Asian and Pacific Islander populations in the United States. Int J Cancer 2020; 147:3339-3348. [PMID: 32535909 PMCID: PMC7736474 DOI: 10.1002/ijc.33153] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 05/21/2020] [Accepted: 05/30/2020] [Indexed: 12/19/2022]
Abstract
Despite the vast genetic and environmental diversity in Asia, individuals of Asian and Pacific Islander (API) descent are often combined into a single group for epidemiologic analyses within the U.S. We used the Surveillance, Epidemiology and End Results (SEER) Detailed Asian/Pacific Islander Database to calculate incidence rates for discrete groups among children aged 0 to 19 years. Due to sample size constraints we pooled incidence among regional groups based on countries of origin: East Asians (Chinese, Japanese, Korean), Southeast (SE) Asians (Vietnamese, Laotian, Cambodian), Asian Indian/Pakistani, Oceanians (Guamanian, Samoan, Tongan) and Filipinos. Incidence rate ratios (IRR) and 95% confidence intervals (CI) were calculated comparing each API regional group to Non-Hispanic Whites (NHW) and East Asians. Finally, we calculated the correlation between incidence of cancer in specific API ethnicities in SEER and in originating countries in the Cancer Incidence in Five Continents. Incidence rates among API regional groups varied. Acute lymphoblastic leukemia (ALL) was lower in children of SE Asian descent (IRR 0.65, 95% CI 0.44, 0.96) compared to NHW. Acute myeloid leukemia (AML) was more common among children from Oceania compared to NHW (IRR 3.88, 95% CI 1.83, 8.22). East Asians had higher incidence rates than SE Asians but lower rates compared to children from Oceania. Correlation of some incidence rates between US-based API ethnicities and originating countries were similar. The variation observed in childhood cancer incidence patterns among API groups may indicate differences in underlying genetics and/or patterns of exposure.
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Affiliation(s)
- Kristin J. Moore
- Program in Health Disparities Research, University of Minnesota Medical School, University of Minnesota
| | - Aubrey K. Hubbard
- Division of Epidemiology and Clinical Research, Department of Pediatrics, University of Minnesota
| | - Lindsay A. Williams
- Division of Epidemiology and Clinical Research, Department of Pediatrics, University of Minnesota
- Masonic Cancer Center, University of Minnesota
| | - Logan G. Spector
- Division of Epidemiology and Clinical Research, Department of Pediatrics, University of Minnesota
- Masonic Cancer Center, University of Minnesota
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8
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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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9
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Bhaskaran SP, Huang T, Rajendran BK, Guo M, Luo J, Qin Z, Zhao B, Chian J, Li S, Wang SM. Ethnic-specific BRCA1/2 variation within Asia population: evidence from over 78 000 cancer and 40 000 non-cancer cases of Indian, Chinese, Korean and Japanese populations. J Med Genet 2020; 58:752-759. [PMID: 32963034 DOI: 10.1136/jmedgenet-2020-107299] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 08/06/2020] [Accepted: 08/13/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Germline mutation in BRCA1 and BRCA2 (BRCA) is genetic predisposition for breast and ovarian cancer. Identification of mutation carriers is a critical step to prevent and treat the cancer in the mutation carriers. Human BRCA variation has been well determined as ethnic-specific by studies in Ashkenazi Jewish, Polish and Icelandic populations in the 1990s. However, sufficient evidence is lacking to determine if ethnic-specific BRCA variation is also present in Asia population, which is the largest and the most diversified in modern humans. Our current study aims to investigate ethnic-specific BRCA variation in Asian population. METHODS We performed a comprehensive data mining to collect BRCA variation data in Indian, Chinese, Korean and Japanese populations derived from over 78 000 cancer and 40 000 non-cancer cases. We standardised all BRCA variation data following the international standard. We made a systematic comparison between the datasets including variant composition, variation spectrum, variant type, clinical class, founder mutation and high-frequent variants. RESULTS Our analysis showed that over half of the Asian BRCA variants were Asian-specific, and significant differences were present between the four Asia populations in each category analysed. CONCLUSION Data from our study reveal that ethnic-specific BRCA variation is commonly present in Asia population as existing in non-Asian populations. Our study indicates that ethnicity should be an important factor to consider in prevention and treatment of BRCA mutation-related cancer in the Asia population. We recommend that the current BRCA variation databases should include ethnic variation information in order to function as true global BRCA references.
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Affiliation(s)
| | - Teng Huang
- Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | | | - Maoni Guo
- Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Jiangtao Luo
- Healthcare Analytics Institute, Eastern Virginia Medical School, Norfolk, VA, USA
| | - Zixin Qin
- Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Bojin Zhao
- Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Jiasheng Chian
- Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Suicheng Li
- Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - San Ming Wang
- Faculty of Health Sciences, University of Macau, Taipa, Macau, China
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10
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Branco C, Ray N, Currat M, Arenas M. Influence of Paleolithic range contraction, admixture and long-distance dispersal on genetic gradients of modern humans in Asia. Mol Ecol 2020; 29:2150-2159. [PMID: 32436243 DOI: 10.1111/mec.15479] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 05/08/2020] [Accepted: 05/11/2020] [Indexed: 12/29/2022]
Abstract
Cavalli-Sforza and coauthors originally explored the genetic variation of modern humans throughout the world and observed an overall east-west genetic gradient in Asia. However, the specific environmental and population genetics processes causing this gradient were not formally investigated and promoted discussion in recent studies. Here we studied the influence of diverse environmental and population genetics processes on Asian genetic gradients and identified which could have produced the observed gradient. To do so, we performed extensive spatially-explicit computer simulations of genetic data under the following scenarios: (a) variable levels of admixture between Paleolithic and Neolithic populations, (b) migration through long-distance dispersal (LDD), (c) Paleolithic range contraction induced by the last glacial maximum (LGM), and (d) Neolithic range expansions from one or two geographic origins (the Fertile Crescent and the Yangzi and Yellow River Basins). Next, we estimated genetic gradients from the simulated data and we found that they were sensible to the analysed processes, especially to the range contraction induced by LGM and to the number of Neolithic expansions. Some scenarios were compatible with the observed east-west genetic gradient, such as the Paleolithic expansion with a range contraction induced by the LGM or two Neolithic range expansions from both the east and the west. In general, LDD increased the variance of genetic gradients among simulations. We interpreted the obtained gradients as a consequence of both allele surfing caused by range expansions and isolation by distance along the vast east-west geographic axis of this continent.
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Affiliation(s)
- Catarina Branco
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain.,Biomedical Research Center (CINBIO), University of Vigo, Vigo, Spain
| | - Nicolas Ray
- GeoHealth Group, Institute of Global Health, University of Geneva, Geneva, Switzerland.,Institute for Environmental Sciences, University of Geneva, Geneva, Switzerland
| | - Mathias Currat
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva, Geneva, Switzerland
| | - Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain.,Biomedical Research Center (CINBIO), University of Vigo, Vigo, Spain
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11
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Li YC, Ye WJ, Jiang CG, Zeng Z, Tian JY, Yang LQ, Liu KJ, Kong QP. River Valleys Shaped the Maternal Genetic Landscape of Han Chinese. Mol Biol Evol 2020; 36:1643-1652. [PMID: 31112995 DOI: 10.1093/molbev/msz072] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
A general south-north genetic divergence has been observed among Han Chinese in previous studies. However, these studies, especially those on mitochondrial DNA (mtDNA), are based either on partial mtDNA sequences or on limited samples. Given that Han Chinese comprise the world's largest population and reside around the whole China, whether the north-south divergence can be observed after all regional populations are considered remains unknown. Moreover, factors involved in shaping the genetic landscape of Han Chinese need further investigation. In this study, we dissected the matrilineal landscape of Han Chinese by studying 4,004 mtDNA haplogroup-defining variants in 21,668 Han samples from virtually all provinces in China. Our results confirmed the genetic divergence between southern and northern Han populations. However, we found a significant genetic divergence among populations from the three main river systems, that is, the Yangtze, the Yellow, and the Zhujiang (Pearl) rivers, which largely attributed to the prevalent distribution of haplogroups D4, B4, and M7 in these river valleys. Further analyses based on 4,986 mitogenomes, including 218 newly generated sequences, indicated that this divergence was already established during the early Holocene and may have resulted from population expansion facilitated by ancient agricultures along these rivers. These results imply that the maternal gene pools of the contemporary Han populations have retained the genetic imprint of early Neolithic farmers from different river basins, or that river valleys represented relative migration barriers that facilitated genetic differentiation, thus highlighting the importance of the three ancient agricultures in shaping the genetic landscape of the Han Chinese.
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Affiliation(s)
- Yu-Chun Li
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.,Kunming Key Laboratory of Healthy Aging Study, Kunming, China
| | - Wei-Jian Ye
- Chengdu 23 Mofang Biotechnology Co., Ltd, Chengdu, China
| | | | - Zhen Zeng
- Chengdu 23 Mofang Biotechnology Co., Ltd, Chengdu, China
| | - Jiao-Yang Tian
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.,Kunming Key Laboratory of Healthy Aging Study, Kunming, China
| | - Li-Qin Yang
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.,Kunming Key Laboratory of Healthy Aging Study, Kunming, China
| | - Kai-Jun Liu
- Chengdu 23 Mofang Biotechnology Co., Ltd, Chengdu, China
| | - Qing-Peng Kong
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.,Kunming Key Laboratory of Healthy Aging Study, Kunming, China.,KIZ-SU Joint Laboratory of Animal Model and Drug Development, College of Pharmaceutical Sciences, Soochow University, Suzhou, China.,KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, China
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12
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Tan-Koi WC, Limenta M, Mohamed EHM, Lee EJD. The Importance of Ethnicity Definitions and Pharmacogenomics in Ethnobridging and Pharmacovigilance. Pharmacogenomics 2019. [DOI: 10.1016/b978-0-12-812626-4.00011-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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13
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Pei Y, Huang H, Li H, Chen J, Wu G. Allelic and haplotype diversity of HLA-A, HLA-B and HLA-DRB1 gene at high resolution in the Nanning Han population. Int J Immunogenet 2018; 45:201-209. [DOI: 10.1111/iji.12379] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 03/26/2018] [Accepted: 04/13/2018] [Indexed: 12/22/2022]
Affiliation(s)
- YongFeng Pei
- Nanning Blood Center; Nanning Institute of Transfusion Medicine; Nanning China
| | - HuiNi Huang
- Nanning Blood Center; Nanning Institute of Transfusion Medicine; Nanning China
| | - HengCong Li
- Nanning Blood Center; Nanning Institute of Transfusion Medicine; Nanning China
| | - JieRun Chen
- Nanning Blood Center; Nanning Institute of Transfusion Medicine; Nanning China
| | - GuoGuang Wu
- Nanning Blood Center; Nanning Institute of Transfusion Medicine; Nanning China
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14
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Zhu C, Zhang X, Zhao Q, Chen Q. Hybrid marriages and phenotypic heterosis in offspring: Evidence from China. ECONOMICS AND HUMAN BIOLOGY 2018; 29:102-114. [PMID: 29547802 DOI: 10.1016/j.ehb.2018.02.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 12/21/2017] [Accepted: 02/16/2018] [Indexed: 06/08/2023]
Abstract
In genetics, heterosis refers to the phenomenon that cross-breeding within species leads to offspring that are genetically fitter than their parents and exhibit improved phenotypic characteristics. Based on the theory of heterosis and existing genetic evidence, offspring of "hybrid" marriages (spouses originating from different states/provinces/countries/areas), though relatively rare due to physical boundaries, may exhibit greater genetic fitness in terms of intelligence, height, or physical attractiveness (the "distance-performance" hypothesis). This study explores whether heterosis is a contributing factor to offspring's educational attainment in China by applying a high-dimensional fixed effects (HDFE) modelling framework to the unique 0.1% micro-sample of the 2000 Chinese Population Census data. Concerning potential endogeneity of hybrid marriages, we conduct a series of robustness checks. Reassuringly, the estimated heterosis effect remains significantly positive across various measurements, after controlling for parental educational attainments/height, environmental influences, and over a thousand region and region-by-year fixed effects. The effects in male and higher-educated offspring are found to be stronger. Results are replicated when analyzing body height using data from the China Health and Nutrition Survey. Although endogeneity of "hybrid marriages" may not be completely ruled out, the current study sheds light on the potentially beneficial effects of interprovincial migration on population-level human capital accumulation, and we hope that this paper can intrigue future studies that further address endogeneity. The implied heterosis effect could, therefore, be profound for Homo sapiens as a species from an evolutionary point of view. An additional important implication is that the overall genetic influences of parents on offspring's performance may be further decomposed into a conventional heredity effect and a heterosis effect that has been neglected previously.
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Affiliation(s)
- Chen Zhu
- College of Economics and Management, China Agricultural University, Beijing 100083, China; Institute for Population and Labor Economics, Chinese Academy of Social Sciences, Beijing, China
| | - Xiaohui Zhang
- School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Qiran Zhao
- College of Economics and Management, China Agricultural University, Beijing 100083, China
| | - Qihui Chen
- Center for Food and Health Economic Research, College of Economics and Management, China Agricultural University, Beijing 100083, China.
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15
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Association between PARK16 and Parkinson's disease: A meta-analysis. Neurosci Lett 2017; 657:179-188. [PMID: 28807727 DOI: 10.1016/j.neulet.2017.08.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 06/21/2017] [Accepted: 08/08/2017] [Indexed: 12/14/2022]
Abstract
Recent years, several case-control studies reported that two polymorphisms (rs947211 and 1572913) within the PARK16 locus were associated with the Parkinson's disease (PD). However, the results were still controversial. Herein, we conducted a comprehensive meta-analysis to estimate the associations between two polymorphisms and PD. Seven databases (PubMed, Google Scholar, EMBASE, Web of Science, CNKI (China National Knowledge Infrastructure), VIP and Wanfang) were searched to identify the eligible studies. Odds ratios (ORs) with 95% confidence intervals (CIs) were calculated to evaluate the associations of two polymorphisms with PD susceptibility. Totally, 15 studies with 6637 cases and 6774 controls were included in our meta-analysis. The results showed that rs947211 variants were associated with a decreased risk of PD in overall population. Stratified analysis found that rs947211 variants were associated with a significantly decreased risk of PD in Northeast Asian population, but a slightly decreased risk of PD in Southeast Asian and Caucasian population. With regard to rs1572913 polymorphism, the results suggested that rs1572913 variants contribute to decrease the risk of PD. Therefore, our meta-analysis suggested that rs947211 variants (A allele, AG and GG genotypes) may decrease the risk of PD in overall population, particularly in Northeast Asian population; and T allele, TC and TT genotypes of rs1572913 variants contributed to decrease the risk of PD.
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16
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A panel of 74 AISNPs: Improved ancestry inference within Eastern Asia. Forensic Sci Int Genet 2016; 23:101-110. [DOI: 10.1016/j.fsigen.2016.04.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 02/17/2016] [Accepted: 04/01/2016] [Indexed: 02/04/2023]
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17
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Genetic analysis of the aquaporin-4 gene for anti-AQP4 antibody-positive neuromyelitis optica in a Japanese population. Jpn J Ophthalmol 2016; 60:198-205. [DOI: 10.1007/s10384-016-0441-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 02/29/2016] [Indexed: 11/25/2022]
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18
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Algee-Hewitt BF. Population inference from contemporary American craniometrics. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2016; 160:604-24. [DOI: 10.1002/ajpa.22959] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 12/06/2015] [Accepted: 01/20/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Bridget F.B. Algee-Hewitt
- Department of Biology; Stanford University; Stanford CA 94305
- Departments of Anthropology and Scientific Computing; Florida State University; Tallahassee FL 32306
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19
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Analysis of genetic admixture in Uyghur using the 26 Y-STR loci system. Sci Rep 2016; 6:19998. [PMID: 26842947 PMCID: PMC4740765 DOI: 10.1038/srep19998] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 12/22/2015] [Indexed: 11/24/2022] Open
Abstract
The Uyghur population has experienced extensive interaction with European and Eastern Asian populations historically. A set of high-resolution genetic markers could be useful to infer the genetic relationships between the Uyghur population and European and Asian populations. In this study we typed 100 unrelated Uyghur males living in southern Xinjiang at 26 Y-STR loci. Using the high-resolution 26 Y-STR loci system, we investigated genetic and phylogenetic relationship between the Uyghur population and 23 reference European or Asian populations. We found that the Uyghur population exhibited a genetic admixture of Eastern Asian and European populations, and had a slightly closer relationship with the selected European populations than the Eastern Asian populations. We also demonstrated that the 26 Y-STR loci system was potentially useful in forensic sciences because it has a large power of discrimination and rarely exhibits common haplotypes. However, ancestry inference of Uyghur samples could be challenging due to the admixed nature of the population.
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20
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Inferring the Dynamics of Effective Population Size Using Autosomal Genomes. Sci Rep 2016; 6:20079. [PMID: 26832887 PMCID: PMC4735516 DOI: 10.1038/srep20079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 08/20/2015] [Indexed: 01/25/2023] Open
Abstract
Next-generation sequencing technology has provided a great opportunity for inferring human demographic history by investigating changes in the effective population size (Ne). In this report, we introduce a strategy for estimating Ne dynamics, allowing the exploration of large multi-locus SNP datasets. We applied this strategy to the Phase 1 Han Chinese samples from the 1000 Genomes Project. The Han Chinese population has undergone a continuous expansion since 25,000 years ago, at first slowly from about 7,300 to 9,800 (at the end of the last glacial maximum about 15,000 YBP), then more quickly to about 46,000 (at the beginning of the Neolithic about 8,000 YBP), and then even more quickly to reach a population size of about 140,000 (recently).
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21
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Di D, Sanchez-Mazas A, Currat M. Computer simulation of human leukocyte antigen genes supports two main routes of colonization by human populations in East Asia. BMC Evol Biol 2015; 15:240. [PMID: 26530905 PMCID: PMC4632674 DOI: 10.1186/s12862-015-0512-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 10/19/2015] [Indexed: 11/10/2022] Open
Abstract
Background Recent genetic studies have suggested that the colonization of East Asia by modern humans was more complex than a single origin from the South, and that a genetic contribution via a Northern route was probably quite substantial. Results Here we use a spatially-explicit computer simulation approach to investigate the human migration hypotheses of this region based on one-route or two-route models. We test the likelihood of each scenario by using Human Leukocyte Antigen (HLA) − A, −B, and − DRB1 genetic data of East Asian populations, with both selective and demographic parameters considered. The posterior distribution of each parameter is estimated by an Approximate Bayesian Computation (ABC) approach. Conclusions Our results strongly support a model with two main routes of colonization of East Asia on both sides of the Himalayas, with distinct demographic histories in Northern and Southern populations, characterized by more isolation in the South. In East Asia, gene flow between populations originating from the two routes probably existed until a remote prehistoric period, explaining the continuous pattern of genetic variation currently observed along the latitude. A significant although dissimilar level of balancing selection acting on the three HLA loci is detected, but its effect on the local genetic patterns appears to be minor compared to those of past demographic events. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0512-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Da Di
- Department of Genetics and Evolution - Anthropology Unit, Laboratory of Anthropology, Genetics and Peopling history (AGP lab), University of Geneva, 12 rue Gustave-Revilliod, Geneva, CH-1211, Geneva 4, Switzerland.
| | - Alicia Sanchez-Mazas
- Department of Genetics and Evolution - Anthropology Unit, Laboratory of Anthropology, Genetics and Peopling history (AGP lab), University of Geneva, 12 rue Gustave-Revilliod, Geneva, CH-1211, Geneva 4, Switzerland. .,Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva Medical Centre (CMU), 1 rue Michel-Servet, Geneva, CH-1211, Geneva 4, Switzerland.
| | - Mathias Currat
- Department of Genetics and Evolution - Anthropology Unit, Laboratory of Anthropology, Genetics and Peopling history (AGP lab), University of Geneva, 12 rue Gustave-Revilliod, Geneva, CH-1211, Geneva 4, Switzerland.
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22
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Inherited metabolic diseases in the Southern Chinese population: spectrum of diseases and estimated incidence from recurrent mutations. Pathology 2015; 46:375-82. [PMID: 24992243 DOI: 10.1097/pat.0000000000000140] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Inherited metabolic diseases (IMDs) are a large group of rare genetic diseases. The spectrum and incidences of IMDs differ among populations, which has been well characterised in Caucasians but much less so in Chinese. In a setting of a University Hospital Metabolic Clinic in Hong Kong, over 100 patients with IMDs have been seen during a period of 13 years (from 1997 to 2010). The data were used to define the spectrum of diseases in the Southern Chinese population. Comparison with other populations revealed a unique spectrum of common IMDs. Furthermore, the incidence of the common IMDs was estimated by using population carrier frequencies of known recurrent mutations. Locally common diseases (their estimated incidence) include (1) glutaric aciduria type 1 (∼1/60,000), (2) multiple carboxylase deficiency (∼1/60,000), (3) primary carnitine deficiency (∼1/60,000), (4) carnitine-acylcarnitine translocase deficiency (∼1/60,000), (5) glutaric aciduria type 2 (∼1/22,500), (6) citrin deficiency (∼1/17,000), (7) tetrahydrobiopterin-deficient hyperphenylalaninaemia due to 6-pyruvoyl-tetrahydropterin synthase deficiency (∼1/60,000), (8) glycogen storage disease type 1 (∼1/150,000). In addition, ornithine carbamoyltransferase deficiency and X-linked adrenoleukodystrophy are common X-linked diseases. Findings of the disease spectrum and treatment outcome are summarised here which may be useful for clinical practice. In addition, data will also be useful for policy makers in planning of newborn screening programs and resource allocation.
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23
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Klitz W. Whitey crumbles. Trends Genet 2014; 30:516-8. [PMID: 25443044 DOI: 10.1016/j.tig.2014.10.004] [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: 10/04/2014] [Accepted: 10/07/2014] [Indexed: 12/01/2022]
Abstract
Despite scientific evidence to the contrary, cultural notions that incorrectly aggrandize genetic differences between ethnicities persist. New work on the genetic makeup of Europeans now shows even more definitively how false those notions are.
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Affiliation(s)
- William Klitz
- Department of Integrative Biology, University of California, Berkeley, CA 94720-3140, USA.
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24
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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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25
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He Y, Ren LY, Shan KR, Zhang T, Wang CJ, Guan ZZ. Characterization of polymorphisms in the mitochondrial DNA of twelve ethnic groups in the Guizhou province of China. ACTA ACUST UNITED AC 2014; 27:365-70. [PMID: 24660920 DOI: 10.3109/19401736.2014.895990] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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26
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Di D, Sanchez-Mazas A. HLA variation reveals genetic continuity rather than population group structure in East Asia. Immunogenetics 2014; 66:153-60. [PMID: 24449274 DOI: 10.1007/s00251-014-0757-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 01/07/2014] [Indexed: 01/15/2023]
Abstract
Genetic differences between Northeast Asian (NEA) and Southeast Asian (SEA) populations have been observed in numerous studies. At the among-population level, despite a clear north-south differentiation observed for many genetic markers, debates were led between abrupt differences and a continuous pattern. At the within-population level, whether NEA or SEA populations have higher genetic diversity is also highly controversial. In this study, we analyzed a large set of HLA data from East Asia in order to map the genetic variation among and within populations in this continent and to clarify the distribution pattern of HLA lineages and alleles. We observed a genetic differentiation between NEA and SEA populations following a continuous pattern from north to south, and we show a significant and continuous decrease of HLA diversity by the same direction. This continuity is shaped by clinal distributions of many HLA lineages and alleles with increasing or decreasing frequencies along the latitude. These results bring new evidence in favor of the "overlapping model" proposed previously for East Asian peopling history, whereby modern humans migrated eastward from western Eurasia via two independent routes along each side of the Himalayas and, later, overlapped in East Asia across open land areas. Our study strongly suggests that intensive gene flow between NEA and SEA populations occurred and shaped the latitude-related continuous pattern of genetic variation and the peculiar HLA lineage and allele distributions observed in this continent. Probably for a very long period, the exact duration of these events remains to be estimated.
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Affiliation(s)
- Da Di
- Laboratory of Anthropology, Genetics and Peopling History (AGP lab), Anthropology Unit, Department of Genetics and Evolution, University of Geneva, 12 rue Gustave-Revilliod, CH-1211, Geneva, Switzerland,
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27
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28
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Magalhães TR, Casey JP, Conroy J, Regan R, Fitzpatrick DJ, Shah N, Sobral J, Ennis S. HGDP and HapMap analysis by Ancestry Mapper reveals local and global population relationships. PLoS One 2012; 7:e49438. [PMID: 23189146 PMCID: PMC3506643 DOI: 10.1371/journal.pone.0049438] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Accepted: 10/09/2012] [Indexed: 11/18/2022] Open
Abstract
Knowledge of human origins, migrations, and expansions is greatly enhanced by the availability of large datasets of genetic information from different populations and by the development of bioinformatic tools used to analyze the data. We present Ancestry Mapper, which we believe improves on existing methods, for the assignment of genetic ancestry to an individual and to study the relationships between local and global populations. The principle function of the method, named Ancestry Mapper, is to give each individual analyzed a genetic identifier, made up of just 51 genetic coordinates, that corresponds to its relationship to the HGDP reference population. As a consequence, the Ancestry Mapper Id (AMid) has intrinsic biological meaning and provides a tool to measure similarity between world populations. We applied Ancestry Mapper to a dataset comprised of the HGDP and HapMap data. The results show distinctions at the continental level, while simultaneously giving details at the population level. We clustered AMids of HGDP/HapMap and observe a recapitulation of human migrations: for a small number of clusters, individuals are grouped according to continental origins; for a larger number of clusters, regional and population distinctions are evident. Calculating distances between AMids allows us to infer ancestry. The number of coordinates is expandable, increasing the power of Ancestry Mapper. An R package called Ancestry Mapper is available to apply this method to any high density genomic data set.
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Affiliation(s)
- Tiago R. Magalhães
- School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
| | - Jillian P. Casey
- School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
- National Children’s Research Centre, Our Lady’s Childrens Hospital Crumlin, Dublin, Ireland
| | - Judith Conroy
- School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
| | - Regina Regan
- School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
- National Children’s Research Centre, Our Lady’s Childrens Hospital Crumlin, Dublin, Ireland
| | - Darren J. Fitzpatrick
- School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
- Clique Research Cluster, School of Computer Science and Informatics, University College Dublin, Dublin, Ireland
| | - Naisha Shah
- School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
- Complex and Adaptive Systems Laboratory, and Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - João Sobral
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Sean Ennis
- School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
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29
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Badano I, Schurr TG, Stietz SM, Dulik MC, Mampaey M, Quintero IM, Zinovich JB, Campos RH, Liotta DJ. TNF promoter SNP variation in Amerindians and white-admixed women from Misiones, Argentina. Int J Immunogenet 2012; 40:216-21. [DOI: 10.1111/iji.12002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Revised: 07/12/2012] [Accepted: 09/12/2012] [Indexed: 01/05/2023]
Affiliation(s)
- I. Badano
- Laboratorio de Biología Molecular Aplicada; Facultad de Ciencias Exactas; Quimicas y Naturales; Universidad Nacional de Misiones; Misiones; Argentina
| | - T. G. Schurr
- Laboratory of Molecular Anthropology; Department of Anthropology; University of Pennsylvania; Philadelphia; PA; USA
| | - S. M. Stietz
- Laboratorio de Biología Molecular Aplicada; Facultad de Ciencias Exactas; Quimicas y Naturales; Universidad Nacional de Misiones; Misiones; Argentina
| | - M. C. Dulik
- Laboratory of Molecular Anthropology; Department of Anthropology; University of Pennsylvania; Philadelphia; PA; USA
| | - M. Mampaey
- Ministerio de Salud Pública de la Provincia de Misiones; Misiones; Argentina
| | - I. M. Quintero
- Laboratorio de Biología Molecular Aplicada; Facultad de Ciencias Exactas; Quimicas y Naturales; Universidad Nacional de Misiones; Misiones; Argentina
| | - J. B. Zinovich
- Ministerio de Salud Pública de la Provincia de Misiones; Misiones; Argentina
| | - R. H. Campos
- Cátedra de Virología; Facultad de Farmacia y Bioquímica; Universidad de Buenos Aires; Buenos Aires; Argentina
| | - D. J. Liotta
- Laboratorio de Biología Molecular Aplicada; Facultad de Ciencias Exactas; Quimicas y Naturales; Universidad Nacional de Misiones; Misiones; Argentina
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Associations of HLA-DP variants with hepatitis B virus infection in southern and northern Han Chinese populations: a multicenter case-control study. PLoS One 2011; 6:e24221. [PMID: 21904616 PMCID: PMC3164164 DOI: 10.1371/journal.pone.0024221] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Accepted: 08/05/2011] [Indexed: 12/15/2022] Open
Abstract
Background Human leukocyte antigen DP (HLA-DP) locus has been reported to be associated with hepatitis B virus (HBV) infection in populations of Japan and Thailand. We aimed to examine whether the association can be replicated in Han Chinese populations. Methodology/Principal Findings Two HLA-DP variants rs2395309 and rs9277535 (the most strongly associated SNPs from each HLA-DP locus) were genotyped in three independent Han cohorts consisting of 2 805 cases and 1 796 controls. By using logistic regression analysis, these two SNPs in the HLA-DPA1 and HLA-DPB1 genes were significantly associated with HBV infection in Han Chinese populations (P = 0.021∼3.36×10−8 at rs2395309; P = 8.37×10−3∼2.68×10−10 at rs9277535). In addition, the genotype distributions of both sites (rs2395309 and rs9277535) were clearly different between southern and northern Chinese population (P = 8.95×10−5 at rs2395309; P = 1.64×10−9 at rs9277535). By using asymptomatic HBV carrier as control group, our study showed that there were no associations of two HLA-DP variants with HBV progression (P = 0.305∼0.822 and 0.163∼0.881 in southern Chinese population, respectively; P = 0.097∼0.697 and 0.198∼0.615 in northern Chinese population, respectively). Conclusions Our results confirmed that two SNPs (rs2395309 and rs9277535) in the HLA-DP loci were strongly associated with HBV infection in southern and northern Han Chinese populations, but not with HBV progression.
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Cai X, Qin Z, Wen B, Xu S, Wang Y, Lu Y, Wei L, Wang C, Li S, Huang X, Jin L, Li H. Human migration through bottlenecks from Southeast Asia into East Asia during Last Glacial Maximum revealed by Y chromosomes. PLoS One 2011; 6:e24282. [PMID: 21904623 PMCID: PMC3164178 DOI: 10.1371/journal.pone.0024282] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Accepted: 08/09/2011] [Indexed: 11/18/2022] Open
Abstract
Molecular anthropological studies of the populations in and around East Asia have resulted in the discovery that most of the Y-chromosome lineages of East Asians came from Southeast Asia. However, very few Southeast Asian populations had been investigated, and therefore, little was known about the purported migrations from Southeast Asia into East Asia and their roles in shaping the genetic structure of East Asian populations. Here, we present the Y-chromosome data from 1,652 individuals belonging to 47 Mon-Khmer (MK) and Hmong-Mien (HM) speaking populations that are distributed primarily across Southeast Asia and extend into East Asia. Haplogroup O3a3b-M7, which appears mainly in MK and HM, indicates a strong tie between the two groups. The short tandem repeat network of O3a3b-M7 displayed a hierarchical expansion structure (annual ring shape), with MK haplotypes being located at the original point, and the HM and the Tibeto-Burman haplotypes distributed further away from core of the network. Moreover, the East Asian dominant haplogroup O3a3c1-M117 shows a network structure similar to that of O3a3b-M7. These patterns indicate an early unidirectional diffusion from Southeast Asia into East Asia, which might have resulted from the genetic drift of East Asian ancestors carrying these two haplogroups through many small bottle-necks formed by the complicated landscape between Southeast Asia and East Asia. The ages of O3a3b-M7 and O3a3c1-M117 were estimated to be approximately 19 thousand years, followed by the emergence of the ancestors of HM lineages out of MK and the unidirectional northward migrations into East Asia.
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Affiliation(s)
- Xiaoyun Cai
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Zhendong Qin
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Bo Wen
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Shuhua Xu
- Chinese Academy of Sciences and Max Planck Society Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yi Wang
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yan Lu
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Lanhai Wei
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Chuanchao Wang
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Shilin Li
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Xingqiu Huang
- Institute of Ethnology and Anthropology, Guangxi University for Nationalities, Nanning, Guangxi, China
| | - Li Jin
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- Chinese Academy of Sciences and Max Planck Society Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Institute of Health Sciences, China Medical City, Taizhou, Jiangsu, China
| | - Hui Li
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- * E-mail:
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Suo C, Xu H, Khor CC, Ong RT, Sim X, Chen J, Tay WT, Sim KS, Zeng YX, Zhang X, Liu J, Tai ES, Wong TY, Chia KS, Teo YY. Natural positive selection and north-south genetic diversity in East Asia. Eur J Hum Genet 2011; 20:102-10. [PMID: 21792231 DOI: 10.1038/ejhg.2011.139] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Recent reports have identified a north-south cline in genetic variation in East and South-East Asia, but these studies have not formally explored the basis of these clinical differences. Understanding the origins of these variations may provide valuable insights in tracking down the functional variants in genomic regions identified by genetic association studies. Here we investigate the genetic basis of these differences with genome-wide data from the HapMap, the Human Genome Diversity Project and the Singapore Genome Variation Project. We implemented four bioinformatic measures to discover genomic regions that are considerably differentiated either between two Han Chinese populations in the north and south of China, or across 22 populations in East and South-East Asia. These measures prioritized genomic stretches with: (i) regional differences in the allelic spectrum for SNPs common to the two Han Chinese populations; (ii) differential evidence of positive selection between the two populations as quantified by integrated haplotype score (iHS) and cross-population extended haplotype homozygosity (XP-EHH); (iii) significant correlation between allele frequencies and geographical latitudes of the 22 populations. We also explored the extent of linkage disequilibrium variations in these regions, which is important in combining genetic association studies from North and South Chinese. Two of the regions that emerged are found in HLA class I and II, suggesting that the HLA imputation panel from the HapMap may not be directly applicable to every Chinese sample. This has important implications to autoimmune studies that plan to impute the classical HLA alleles to fine map the SNP association signals.
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Affiliation(s)
- Chen Suo
- Centre for Molecular Epidemiology, National University of Singapore, Singapore, Singapore
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Li H, Gu S, Han Y, Xu Z, Pakstis AJ, Jin L, Kidd JR, Kidd KK. Diversification of the ADH1B gene during expansion of modern humans. Ann Hum Genet 2011; 75:497-507. [PMID: 21592108 PMCID: PMC3722864 DOI: 10.1111/j.1469-1809.2011.00651.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A variant allele, ADH1B*48His, also known as ADH1B*2, at the human Alcohol Dehydrogenase 1B gene (ADH1B) is strongly associated with alcoholism in some populations and has an unusual geographic distribution. Strong evidence implies selection has increased the frequency of this allele in some East Asian populations but does not fully explain its geographic pattern. We have studied haplotypes of 10 single nucleotide polymorphisms (SNPs) and two short tandem repeat polymorphisms (STRPs) in the ADH1B region in 2,206 individuals from a worldwide set of populations. These SNPs and STRPs define nine common haplogroups most of which have distinct geographic patterns. The haplogroups H5 and H6, both with the derived ADH1B*48His allele, appear restricted to the Middle East and East Asia, respectively. The positively selected H7 is derived from H6 by a new regulatory region variant defining SNP rs3811801 restricted to East Asia. Age estimates of the haplogroups based on the STRPs also agree with the time of the migration events estimated by other studies. H7 is estimated to have expanded recently, around 2,800 years ago, and ancient DNA samples from North China confirm its presence about that time. The dating of the H7 expansion may help understand the selective force on the ADH1B gene.
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Affiliation(s)
- Hui Li
- Department of Genetics, School of Medicine, Yale University, New Haven, CT 06520 USA
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Sheng Gu
- Department of Genetics, School of Medicine, Yale University, New Haven, CT 06520 USA
| | - Yi Han
- Department of Genetics, School of Medicine, Yale University, New Haven, CT 06520 USA
| | - Zhi Xu
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Andrew J. Pakstis
- Department of Genetics, School of Medicine, Yale University, New Haven, CT 06520 USA
| | - Li Jin
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Judith R. Kidd
- Department of Genetics, School of Medicine, Yale University, New Haven, CT 06520 USA
| | - Kenneth K. Kidd
- Department of Genetics, School of Medicine, Yale University, New Haven, CT 06520 USA
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Zhou DX, Huang XC, Wang XF, Zhang J, Wang H, Tian Z. Association study of human leucocyte antigen-A gene with idiopathic male infertility in Han population of China. Andrologia 2011; 44 Suppl 1:213-8. [DOI: 10.1111/j.1439-0272.2011.01166.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
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Di D, Sanchez-Mazas A. Challenging views on the peopling history of East Asia: the story according to HLA markers. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2011; 145:81-96. [PMID: 21484761 DOI: 10.1002/ajpa.21470] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Accepted: 11/15/2010] [Indexed: 12/31/2022]
Abstract
The peopling of East Asia by the first modern humans is strongly debated from a genetic point of view. A north-south genetic differentiation observed in this geographic area suggests different hypotheses on the origin of Northern East Asian (NEA) and Southern East Asian (SEA) populations. In this study, the highly polymorphic HLA markers were used to investigate East Asian genetic diversity. Our database covers a total of about 127,000 individuals belonging to 84 distinct Asian populations tested for HLA-A, -B, -C, -DPB1, and/or -DRB1 alleles. Many Chinese populations are represented, which have been sampled in the last 30 years but rarely taken into account in international research due to their data published in Chinese. By using different statistical methods, we found a significant correlation between genetics and geography and relevant genetic clines in East Asia. Additionally, HLA alleles appear to be unevenly distributed: some alleles observed in NEA populations are widespread at the global level, while some alleles observed in SEA populations are virtually unique in Asia. The HLA genetic variation in East Asia is also characterized by a decrease of diversity from north to south, although a reverse pattern appears when one only focuses on alleles restricted to Asia. These results reflect a more complex migration history than that illustrated by the "southern-origin" hypothesis, as genetic contribution of ancient human migrations through a northern route has probably been quite substantial. We thus suggest a new overlapping model where northward and southward opposite migrations occurring at different periods overlapped.
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Affiliation(s)
- Da Di
- Department of Anthropology, Laboratory of Anthropology, Genetics and Peopling History, University of Geneva, Switzerland.
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Ding QL, Wang CC, Farina SE, Li H. Mapping Human Genetic Diversity on the Japanese Archipelago. ACTA ACUST UNITED AC 2011. [DOI: 10.4236/aa.2011.12004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Qin Z, Yang Y, Kang L, Yan S, Cho K, Cai X, Lu Y, Zheng H, Zhu D, Fei D, Li S, Jin L, Li H. A mitochondrial revelation of early human migrations to the Tibetan Plateau before and after the last glacial maximum. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2010; 143:555-69. [DOI: 10.1002/ajpa.21350] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Zhong H, Shi H, Qi XB, Duan ZY, Tan PP, Jin L, Su B, Ma RZ. Extended Y chromosome investigation suggests postglacial migrations of modern humans into East Asia via the northern route. Mol Biol Evol 2010; 28:717-27. [PMID: 20837606 DOI: 10.1093/molbev/msq247] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Genetic diversity data, from Y chromosome and mitochondrial DNA as well as recent genome-wide autosomal single nucleotide polymorphisms, suggested that mainland Southeast Asia was the major geographic source of East Asian populations. However, these studies also detected Central-South Asia (CSA)- and/or West Eurasia (WE)-related genetic components in East Asia, implying either recent population admixture or ancient migrations via the proposed northern route. To trace the time period and geographic source of these CSA- and WE-related genetic components, we sampled 3,826 males (116 populations from China and 1 population from North Korea) and performed high-resolution genotyping according to the well-resolved Y chromosome phylogeny. Our data, in combination with the published East Asian Y-haplogroup data, show that there are four dominant haplogroups (accounting for 92.87% of the East Asian Y chromosomes), O-M175, D-M174, C-M130 (not including C5-M356), and N-M231, in both southern and northern East Asian populations, which is consistent with the proposed southern route of modern human origin in East Asia. However, there are other haplogroups (6.79% in total) (E-SRY4064, C5-M356, G-M201, H-M69, I-M170, J-P209, L-M20, Q-M242, R-M207, and T-M70) detected primarily in northern East Asian populations and were identified as Central-South Asian and/or West Eurasian origin based on the phylogeographic analysis. In particular, evidence of geographic distribution and Y chromosome short tandem repeat (Y-STR) diversity indicates that haplogroup Q-M242 (the ancestral haplogroup of the native American-specific haplogroup Q1a3a-M3) and R-M207 probably migrated into East Asia via the northern route. The age estimation of Y-STR variation within haplogroups suggests the existence of postglacial (∼18 Ka) migrations via the northern route as well as recent (∼3 Ka) population admixture. We propose that although the Paleolithic migrations via the southern route played a major role in modern human settlement in East Asia, there are ancient contributions, though limited, from WE, which partly explain the genetic divergence between current southern and northern East Asian populations.
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Affiliation(s)
- Hua Zhong
- Center for Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
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Yuasa I, Umetsu K, Matsusue A, Nishimukai H, Harihara S, Fukumori Y, Saitou N, Jin F, Chattopadhyay PK, Henke L, Henke J. A Japanese-specific allele in the GALNT11 gene. Leg Med (Tokyo) 2010; 12:208-11. [DOI: 10.1016/j.legalmed.2010.04.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2010] [Revised: 03/29/2010] [Accepted: 04/04/2010] [Indexed: 10/19/2022]
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Kang L, Li S, Gupta S, Zhang Y, Liu K, Zhao J, Jin L, Li H. Genetic structures of the Tibetans and the Deng people in the Himalayas viewed from autosomal STRs. J Hum Genet 2010; 55:270-7. [DOI: 10.1038/jhg.2010.21] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Yang G, Deng YJ, Qin H, Zhu BF, Chen F, Shen CM, Sun ZM, Chen LP, Wu J, Mu HF, Lucas R. HLA-B*15 subtypes distribution in Han population in Beijing, China, as compared with those of other populations. Int J Immunogenet 2010; 37:205-12. [DOI: 10.1111/j.1744-313x.2010.00910.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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López Herráez D, Bauchet M, Tang K, Theunert C, Pugach I, Li J, Nandineni MR, Gross A, Scholz M, Stoneking M. Genetic variation and recent positive selection in worldwide human populations: evidence from nearly 1 million SNPs. PLoS One 2009; 4:e7888. [PMID: 19924308 PMCID: PMC2775638 DOI: 10.1371/journal.pone.0007888] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2009] [Accepted: 10/20/2009] [Indexed: 01/21/2023] Open
Abstract
Background Genome-wide scans of hundreds of thousands of single-nucleotide polymorphisms (SNPs) have resulted in the identification of new susceptibility variants to common diseases and are providing new insights into the genetic structure and relationships of human populations. Moreover, genome-wide data can be used to search for signals of recent positive selection, thereby providing new insights into the genetic adaptations that occurred as modern humans spread out of Africa and around the world. Methodology We genotyped approximately 500,000 SNPs in 255 individuals (5 individuals from each of 51 worldwide populations) from the Human Genome Diversity Panel (HGDP-CEPH). When merged with non-overlapping SNPs typed previously in 250 of these same individuals, the resulting data consist of over 950,000 SNPs. We then analyzed the genetic relationships and ancestry of individuals without assigning them to populations, and we also identified candidate regions of recent positive selection at both the population and regional (continental) level. Conclusions Our analyses both confirm and extend previous studies; in particular, we highlight the impact of various dispersals, and the role of substructure in Africa, on human genetic diversity. We also identified several novel candidate regions for recent positive selection, and a gene ontology (GO) analysis identified several GO groups that were significantly enriched for such candidate genes, including immunity and defense related genes, sensory perception genes, membrane proteins, signal receptors, lipid binding/metabolism genes, and genes involved in the nervous system. Among the novel candidate genes identified are two genes involved in the thyroid hormone pathway that show signals of selection in African Pygmies that may be related to their short stature.
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Affiliation(s)
| | - Marc Bauchet
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Kun Tang
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | | | - Irina Pugach
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Jing Li
- National Drug Screening Laboratory, China Pharmaceutical University, Nanjing City, China
| | - Madhusudan R. Nandineni
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Laboratory of DNA Fingerprinting, Centre for DNA Fingerprinting and Diagnostics, Nampally, Hyderabad, India
| | - Arnd Gross
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Markus Scholz
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Mark Stoneking
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- * E-mail:
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Tian C, Kosoy R, Lee A, Ransom M, Belmont JW, Gregersen PK, Seldin MF. Analysis of East Asia genetic substructure using genome-wide SNP arrays. PLoS One 2008; 3:e3862. [PMID: 19057645 PMCID: PMC2587696 DOI: 10.1371/journal.pone.0003862] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2008] [Accepted: 11/10/2008] [Indexed: 11/19/2022] Open
Abstract
Accounting for population genetic substructure is important in reducing type 1 errors in genetic studies of complex disease. As efforts to understand complex genetic disease are expanded to different continental populations the understanding of genetic substructure within these continents will be useful in design and execution of association tests. In this study, population differentiation (Fst) and Principal Components Analyses (PCA) are examined using >200 K genotypes from multiple populations of East Asian ancestry. The population groups included those from the Human Genome Diversity Panel [Cambodian, Yi, Daur, Mongolian, Lahu, Dai, Hezhen, Miaozu, Naxi, Oroqen, She, Tu, Tujia, Naxi, Xibo, and Yakut], HapMap [ Han Chinese (CHB) and Japanese (JPT)], and East Asian or East Asian American subjects of Vietnamese, Korean, Filipino and Chinese ancestry. Paired Fst (Wei and Cockerham) showed close relationships between CHB and several large East Asian population groups (CHB/Korean, 0.0019; CHB/JPT, 00651; CHB/Vietnamese, 0.0065) with larger separation with Filipino (CHB/Filipino, 0.014). Low levels of differentiation were also observed between Dai and Vietnamese (0.0045) and between Vietnamese and Cambodian (0.0062). Similarly, small Fst's were observed among different presumed Han Chinese populations originating in different regions of mainland of China and Taiwan (Fst's <0.0025 with CHB). For PCA, the first two PC's showed a pattern of relationships that closely followed the geographic distribution of the different East Asian populations. PCA showed substructure both between different East Asian groups and within the Han Chinese population. These studies have also identified a subset of East Asian substructure ancestry informative markers (EASTASAIMS) that may be useful for future complex genetic disease association studies in reducing type 1 errors and in identifying homogeneous groups that may increase the power of such studies.
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Affiliation(s)
- Chao Tian
- Rowe Program in Human Genetics, Departments of Biochemistry and Medicine, University of California Davis, Davis, California, United States of America
| | - Roman Kosoy
- Rowe Program in Human Genetics, Departments of Biochemistry and Medicine, University of California Davis, Davis, California, United States of America
| | - Annette Lee
- The Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institute for Medical Research, North Shore LIJ Health System, Manhasset, New York, United States of America
| | - Michael Ransom
- Rowe Program in Human Genetics, Departments of Biochemistry and Medicine, University of California Davis, Davis, California, United States of America
| | - John W. Belmont
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Peter K. Gregersen
- The Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institute for Medical Research, North Shore LIJ Health System, Manhasset, New York, United States of America
| | - Michael F. Seldin
- Rowe Program in Human Genetics, Departments of Biochemistry and Medicine, University of California Davis, Davis, California, United States of America
- * E-mail:
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Li D, Li H, Ou C, Lu Y, Sun Y, Yang B, Qin Z, Zhou Z, Li S, Jin L. Paternal genetic structure of Hainan aborigines isolated at the entrance to East Asia. PLoS One 2008; 3:e2168. [PMID: 18478090 PMCID: PMC2374892 DOI: 10.1371/journal.pone.0002168] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2008] [Accepted: 04/01/2008] [Indexed: 11/25/2022] Open
Abstract
Background At the southern entrance to East Asia, early population migration has affected most of the Y-chromosome variations of East Asians. Methodology/Principal Findings To assess the isolated genetic structure of Hainan Island and the original genetic structure at the southern entrance, we studied the Y chromosome diversity of 405 Hainan Island aborigines from all the six populations, who have little influence of the recent mainland population relocations and admixtures. Here we report that haplogroups O1a* and O2a* are dominant among Hainan aborigines. In addition, the frequency of the mainland dominant haplogroup O3 is quite low among these aborigines, indicating that they have lived rather isolated. Clustering analyses suggests that the Hainan aborigines have been segregated since about 20 thousand years ago, after two dominant haplogroups entered East Asia (31 to 36 thousand years ago). Conclusions/Significance Our results suggest that Hainan aborigines have been isolated at the entrance to East Asia for about 20 thousand years, whose distinctive genetic characteristics could be used as important controls in many population genetic studies.
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Affiliation(s)
- Dongna Li
- Department of Biology, Hainan Medical College, Haikou, Hainan, China
| | - Hui Li
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
- Department of Genetics, School of Medicine, Yale University, New Haven, Connecticut, United States of America
- * E-mail:
| | - Caiying Ou
- Department of Biology, Hainan Medical College, Haikou, Hainan, China
| | - Yan Lu
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yuantian Sun
- Department of Biology, Hainan Medical College, Haikou, Hainan, China
| | - Bo Yang
- Department of Anatomy, Third Military Medical University, Chongqing, China
| | - Zhendong Qin
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Zhenjian Zhou
- Department of Biology, Hainan Medical College, Haikou, Hainan, China
| | - Shilin Li
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Li Jin
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
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Li H, Mukherjee N, Soundararajan U, Tarnok Z, Barta C, Khaliq S, Mohyuddin A, Kajuna SLB, Mehdi SQ, Kidd JR, Kidd KK. Geographically separate increases in the frequency of the derived ADH1B*47His allele in eastern and western Asia. Am J Hum Genet 2007; 81:842-6. [PMID: 17847010 PMCID: PMC2227934 DOI: 10.1086/521201] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2007] [Accepted: 06/18/2007] [Indexed: 11/03/2022] Open
Abstract
The ADH1B Arg47His polymorphism has been convincingly associated with alcoholism in numerous studies of several populations in Asia and Europe. In a review of literature from the past 30 years, we have identified studies that report allele frequencies of this polymorphism for 131 population samples from many different parts of the world. The derived ADH1B*47His allele reaches high frequencies only in western and eastern Asia. To pursue this pattern, we report here new frequency data for 37 populations. Most of our data are from South and Southeast Asia and confirm that there is a low frequency of this allele in the region between eastern and western Asia. The distribution suggests that the derived allele increased in frequency independently in western and eastern Asia after humans had spread across Eurasia.
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Affiliation(s)
- Hui Li
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
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47
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Li H, Huang Y, Mustavich LF, Zhang F, Tan JZ, Wang LE, Qian J, Gao MH, Jin L. Y chromosomes of prehistoric people along the Yangtze River. Hum Genet 2007; 122:383-8. [PMID: 17657509 DOI: 10.1007/s00439-007-0407-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2007] [Accepted: 07/16/2007] [Indexed: 10/23/2022]
Abstract
The ability to extract mitochondrial and nuclear DNA from ancient remains has enabled the study of ancient DNA, a legitimate field for over 20 years now. Recently, Y chromosome genotyping has begun to be applied to ancient DNA. The Y chromosome haplogroup in East Asia has since caught the attention of molecular anthropologists, as it is one of the most ethnic-related genetic markers of the region. In this paper, the Y chromosome haplogroup of DNA from ancient East Asians was examined, in order to genetically link them to modern populations. Fifty-six human remains were sampled from five archaeological sites, primarily along the Yangtze River. Strict criteria were followed to eliminate potential contamination. Five SNPs from the Y chromosome were successfully amplified from most of the samples, with at least 62.5% of the samples belonging to the O haplogroup, similar to the frequency for modern East Asian populations. A high frequency of O1 was found in Liangzhu Culture sites around the mouth of the Yangtze River, linking this culture to modern Austronesian and Daic populations. A rare haplogroup, O3d, was found at the Daxi site in the middle reaches of the Yangtze River, indicating that the Daxi people might be the ancestors of modern Hmong-Mien populations, which show only small traces of O3d today. Noticeable genetic segregation was observed among the prehistoric cultures, demonstrating the genetic foundation of the multiple origins of the Chinese Civilization.
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Affiliation(s)
- Hui Li
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China.
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Chen Z. Introduction. China in the era of life science and biotechnology. Philos Trans R Soc Lond B Biol Sci 2007. [DOI: 10.1098/rstb.2007.2024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Zhu Chen
- Chinese Academy of Sciences52 Sanlihe Road, 100864 Beijing, People's Republic of China
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