1
|
Cooke NP, Murray M, Cassidy LM, Mattiangeli V, Okazaki K, Kasai K, Gakuhari T, Bradley DG, Nakagome S. Genomic imputation of ancient Asian populations contrasts local adaptation in pre- and post-agricultural Japan. iScience 2024; 27:110050. [PMID: 38883821 PMCID: PMC11176660 DOI: 10.1016/j.isci.2024.110050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 03/25/2024] [Accepted: 05/17/2024] [Indexed: 06/18/2024] Open
Abstract
Early modern humans lived as hunter-gatherers for millennia before agriculture, yet the genetic adaptations of these populations remain a mystery. Here, we investigate selection in the ancient hunter-gatherer-fisher Jomon and contrast pre- and post-agricultural adaptation in the Japanese archipelago. Building on the successful validation of imputation with ancient Asian genomes, we identify selection signatures in the Jomon, particularly robust signals from KITLG variants, which may have influenced dark pigmentation evolution. The Jomon lacks well-known adaptive variants (EDAR, ADH1B, and ALDH2), marking their emergence after the advent of farming in the archipelago. Notably, the EDAR and ADH1B variants were prevalent in the archipelago 1,300 years ago, whereas the ALDH2 variant could have emerged later due to its absence in other ancient genomes. Overall, our study underpins local adaptation unique to the Jomon population, which in turn sheds light on post-farming selection that continues to shape contemporary Asian populations.
Collapse
Affiliation(s)
- Niall P Cooke
- School of Medicine, Trinity College Dublin, Dublin, Ireland
| | | | - Lara M Cassidy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | | | - Kenji Okazaki
- Department of Anatomy, Faculty of Medicine, Tottori University, Yonago, Japan
| | - Kenji Kasai
- Toyama Prefectural Center for Archaeological Operations, Toyama, Japan
| | - Takashi Gakuhari
- Institute for the Study of Ancient Civilizations and Cultural Resources, Kanazawa University, Kanazawa, Japan
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Shigeki Nakagome
- School of Medicine, Trinity College Dublin, Dublin, Ireland
- Institute for the Study of Ancient Civilizations and Cultural Resources, Kanazawa University, Kanazawa, Japan
| |
Collapse
|
2
|
Kawai Y, Watanabe Y, Omae Y, Miyahara R, Khor SS, Noiri E, Kitajima K, Shimanuki H, Gatanaga H, Hata K, Hattori K, Iida A, Ishibashi-Ueda H, Kaname T, Kanto T, Matsumura R, Miyo K, Noguchi M, Ozaki K, Sugiyama M, Takahashi A, Tokuda H, Tomita T, Umezawa A, Watanabe H, Yoshida S, Goto YI, Maruoka Y, Matsubara Y, Niida S, Mizokami M, Tokunaga K. Exploring the genetic diversity of the Japanese population: Insights from a large-scale whole genome sequencing analysis. PLoS Genet 2023; 19:e1010625. [PMID: 38060463 PMCID: PMC10703243 DOI: 10.1371/journal.pgen.1010625] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 10/24/2023] [Indexed: 12/18/2023] Open
Abstract
The Japanese archipelago is a terminal location for human migration, and the contemporary Japanese people represent a unique population whose genomic diversity has been shaped by multiple migrations from Eurasia. We analyzed the genomic characteristics that define the genetic makeup of the modern Japanese population from a population genetics perspective from the genomic data of 9,287 samples obtained by high-coverage whole-genome sequencing (WGS) by the National Center Biobank Network. The dataset comprised populations from the Ryukyu Islands and other parts of the Japanese archipelago (Hondo). The Hondo population underwent two episodes of population decline during the Jomon period, corresponding to the Late Neolithic, and the Edo period, corresponding to the Early Modern era, while the Ryukyu population experienced a population decline during the shell midden period of the Late Neolithic in this region. Haplotype analysis suggested increased allele frequencies for genes related to alcohol and fatty acid metabolism, which were reported as loci that had experienced positive natural selection. Two genes related to alcohol metabolism were found to be 12,500 years out of phase with the time when they began to increase in the allele frequency; this finding indicates that the genomic diversity of Japanese people has been shaped by events closely related to agriculture and food production.
Collapse
Affiliation(s)
- Yosuke Kawai
- Genome Medical Science Project, Research Institute, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, Japan
| | - Yusuke Watanabe
- Genome Medical Science Project, Research Institute, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, Japan
| | - Yosuke Omae
- Genome Medical Science Project, Research Institute, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, Japan
- Central Biobank, National Center Biobank Network, Shinjuku-ku, Tokyo, Japan
| | - Reiko Miyahara
- Central Biobank, National Center Biobank Network, Shinjuku-ku, Tokyo, Japan
| | - Seik-Soon Khor
- Genome Medical Science Project, Research Institute, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, Japan
| | - Eisei Noiri
- Central Biobank, National Center Biobank Network, Shinjuku-ku, Tokyo, Japan
| | - Koji Kitajima
- Central Biobank, National Center Biobank Network, Shinjuku-ku, Tokyo, Japan
- Department of Data Science Center for Clinical Sciences, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, Japan
| | - Hideyuki Shimanuki
- Central Biobank, National Center Biobank Network, Shinjuku-ku, Tokyo, Japan
- Department of Data Science Center for Clinical Sciences, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, Japan
| | - Hiroyuki Gatanaga
- AIDS Clinical Center, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Center for Child Health and Development, Setagaya-ku, Tokyo, Japan
| | - Kotaro Hattori
- Department of Bioresources, Medical Genome Center, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
| | - Aritoshi Iida
- Department of Clinical Genome Analysis, Medical Genome Center, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
| | | | - Tadashi Kaname
- Department of Genome Medicine, National Center for Child Health and Development, Setagaya-ku, Tokyo, Japan
| | - Tatsuya Kanto
- Department of Liver Disease, Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Ichikawa, Chiba, Japan
| | - Ryo Matsumura
- Department of Bioresources, Medical Genome Center, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
| | - Kengo Miyo
- Center for Medical Informatics Intelligence, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, Japan
| | - Michio Noguchi
- NCVC Biobank, National Cerebral and Cardiovascular Center, Suita, Osaka, Japan
| | - Kouichi Ozaki
- Medical Genome Center, Research Institute, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Masaya Sugiyama
- Department of Viral Pathogenesis and Controls, Research Institute, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, Japan
| | - Ayako Takahashi
- NCVC Biobank, National Cerebral and Cardiovascular Center, Suita, Osaka, Japan
| | - Haruhiko Tokuda
- Core Facility Administration, Research Institute, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan
- Department of Metabolic Research, Research Institute, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan
- Department of Clinical Laboratory, Hospital, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan
| | - Tsutomu Tomita
- NCVC Biobank, National Cerebral and Cardiovascular Center, Suita, Osaka, Japan
| | - Akihiro Umezawa
- Center for Regenerative Medicine, Research Institute, National Center for Child Health and Development, Setagaya-ku, Tokyo, Japan
| | - Hiroshi Watanabe
- Core Facility Administration, Research Institute, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan
- Innovation Center for Translational Research, Hospital, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan
| | - Sumiko Yoshida
- Department of Bioresources, Medical Genome Center, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
| | - Yu-ichi Goto
- Medical Genome Center, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
| | - Yutaka Maruoka
- Department of Oral and Maxillofacial Surgery, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, Japan
| | - Yoichi Matsubara
- National Center for Child Health and Development, Setagaya-ku, Tokyo, Japan
| | - Shumpei Niida
- Core Facility Administration, Research Institute, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan
| | - Masashi Mizokami
- Genome Medical Science Project, Research Institute, National Center for Global Health and Medicine, Ichikawa, Chiba, Japan
| | - Katsushi Tokunaga
- Genome Medical Science Project, Research Institute, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, Japan
- Central Biobank, National Center Biobank Network, Shinjuku-ku, Tokyo, Japan
| |
Collapse
|
3
|
Luo H, Zhang P, Zhang W, Zheng Y, Hao D, Shi Y, Niu Y, Song T, Li Y, Zhao S, Chen H, Xu T, He S. Recent positive selection signatures reveal phenotypic evolution in the Han Chinese population. Sci Bull (Beijing) 2023; 68:2391-2404. [PMID: 37661541 DOI: 10.1016/j.scib.2023.08.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/08/2023] [Accepted: 08/10/2023] [Indexed: 09/05/2023]
Abstract
Characterizing natural selection signatures and relationships with phenotype spectra is important for understanding human evolution and both biological and pathological mechanisms. Here, we identified 24 genetic loci under recent selection by analyzing rare singletons in 3946 high-depth whole-genome sequencing data of Han Chinese. The loci include immune-related gene regions (MHC cluster, IGH cluster, STING1, and PSG), alcohol metabolism-related gene regions (ADH1B, ALDH2, and ALDH3B2), and the olfactory perception gene OR4C16, in which the MHC cluster, ADH1B, and ALDH2 were also identified by TOPMed and WestLake Biobank. Among the signals, the IGH cluster is particularly interesting, in which the favored allele of variant 14_105737776_C_T (rs117518546, IgG1-G396R) promotes immune response, but also increases the risk of an autoimmune disease systemic lupus erythematosus (SLE). It is also surprising that our newly discovered ALDH3B2 evolved in the opposite direction to ALDH2 for alcohol metabolism. Besides monogenic traits, we found that multiple complex traits experienced polygenic adaptation. Particularly, multi-methods consistently revealed that lower blood pressure was favored in natural selection. Finally, we built a database named RePoS (recent positive selection, http://bigdata.ibp.ac.cn/RePoS/) to integrate and display multi-population selection signals. Our study extended our understanding of natural evolution and phenotype adaptation in Han Chinese as well as other populations.
Collapse
Affiliation(s)
- Huaxia Luo
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Department of Pediatrics, Peking University First Hospital, Beijing 100034, China
| | - Peng Zhang
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Wanyu Zhang
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yu Zheng
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Di Hao
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yirong Shi
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yiwei Niu
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tingrui Song
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanyan Li
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Shilei Zhao
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; China National Center for Bioinformation, Beijing 100101, China
| | - Hua Chen
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; China National Center for Bioinformation, Beijing 100101, China.
| | - Tao Xu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Shandong First Medical University & Shandong Academy of Medical Sciences, Taian 271016, China.
| | - Shunmin He
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
| |
Collapse
|
4
|
Lee J, Lee J, Jeon S, Lee J, Jang I, Yang JO, Park S, Lee B, Choi J, Choi BO, Gee HY, Oh J, Jang IJ, Lee S, Baek D, Koh Y, Yoon SS, Kim YJ, Chae JH, Park WY, Bhak JH, Choi M. A database of 5305 healthy Korean individuals reveals genetic and clinical implications for an East Asian population. Exp Mol Med 2022; 54:1862-1871. [PMID: 36323850 PMCID: PMC9628380 DOI: 10.1038/s12276-022-00871-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/21/2022] [Accepted: 08/08/2022] [Indexed: 11/29/2022] Open
Abstract
Despite substantial advances in disease genetics, studies to date have largely focused on individuals of European descent. This limits further discoveries of novel functional genetic variants in other ethnic groups. To alleviate the paucity of East Asian population genome resources, we established the Korean Variant Archive 2 (KOVA 2), which is composed of 1896 whole-genome sequences and 3409 whole-exome sequences from healthy individuals of Korean ethnicity. This is the largest genome database from the ethnic Korean population to date, surpassing the 1909 Korean individuals deposited in gnomAD. The variants in KOVA 2 displayed all the known genetic features of those from previous genome databases, and we compiled data from Korean-specific runs of homozygosity, positively selected intervals, and structural variants. In doing so, we found loci, such as the loci of ADH1A/1B and UHRF1BP1, that are strongly selected in the Korean population relative to other East Asian populations. Our analysis of allele ages revealed a correlation between variant functionality and evolutionary age. The data can be browsed and downloaded from a public website ( https://www.kobic.re.kr/kova/ ). We anticipate that KOVA 2 will serve as a valuable resource for genetic studies involving East Asian populations.
Collapse
Affiliation(s)
- Jeongeun Lee
- grid.31501.360000 0004 0470 5905Interdisciplinary Program in Bioengineering, Graduate School, Seoul National University, Seoul, 03080 Republic of Korea
| | - Jean Lee
- grid.31501.360000 0004 0470 5905Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080 Republic of Korea
| | - Sungwon Jeon
- grid.42687.3f0000 0004 0381 814XDepartment of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
| | - Jeongha Lee
- grid.31501.360000 0004 0470 5905Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080 Republic of Korea
| | - Insu Jang
- grid.249967.70000 0004 0636 3099Korea BioInformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141 Republic of Korea
| | - Jin Ok Yang
- grid.249967.70000 0004 0636 3099Korea BioInformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141 Republic of Korea ,grid.37172.300000 0001 2292 0500Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141 Republic of Korea
| | - Soojin Park
- grid.31501.360000 0004 0470 5905Department of Pediatrics, Seoul National University College of Medicine, Seoul, 03080 Republic of Korea
| | - Byungwook Lee
- grid.249967.70000 0004 0636 3099Korea BioInformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141 Republic of Korea
| | - Jinwook Choi
- grid.31501.360000 0004 0470 5905Interdisciplinary Program in Bioengineering, Graduate School, Seoul National University, Seoul, 03080 Republic of Korea ,grid.31501.360000 0004 0470 5905Department of Biomedical Engineering, Seoul National University College of Medicine, Seoul, 03080 Republic of Korea
| | - Byung-Ok Choi
- grid.264381.a0000 0001 2181 989XDepartment of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351 Republic of Korea
| | - Heon Yung Gee
- grid.15444.300000 0004 0470 5454Department of Pharmacology, Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, Seoul, 03722 Republic of Korea
| | - Jaeseong Oh
- grid.31501.360000 0004 0470 5905Department of Clinical Pharmacology and Therapeutics, Seoul National University College of Medicine and Hospital, Seoul, 03080 Republic of Korea
| | - In-Jin Jang
- grid.31501.360000 0004 0470 5905Department of Clinical Pharmacology and Therapeutics, Seoul National University College of Medicine and Hospital, Seoul, 03080 Republic of Korea
| | - Sanghyuk Lee
- grid.255649.90000 0001 2171 7754Department of Bio-Information Science, Ewha Womans University, Seoul, 03760 Republic of Korea
| | - Daehyun Baek
- grid.31501.360000 0004 0470 5905School of Biological Sciences, Seoul National University, Seoul, 08826 Republic of Korea
| | - Youngil Koh
- grid.412484.f0000 0001 0302 820XDepartment of Internal Medicine, Seoul National University Hospital, Seoul, 03080 Republic of Korea
| | - Sung-Soo Yoon
- grid.412484.f0000 0001 0302 820XDepartment of Internal Medicine, Seoul National University Hospital, Seoul, 03080 Republic of Korea
| | - Young-Joon Kim
- grid.15444.300000 0004 0470 5454Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722 Republic of Korea
| | - Jong-Hee Chae
- grid.31501.360000 0004 0470 5905Department of Pediatrics, Seoul National University College of Medicine, Seoul, 03080 Republic of Korea ,grid.412484.f0000 0001 0302 820XDepartment of Genomic Medicine, Seoul National University Hospital, Seoul, 03080 Republic of Korea
| | - Woong-Yang Park
- grid.414964.a0000 0001 0640 5613Samsung Genome Institute, Samsung Medical Center, Seoul, 06351 Republic of Korea
| | - Jong Hwa Bhak
- grid.42687.3f0000 0004 0381 814XDepartment of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
| | - Murim Choi
- grid.31501.360000 0004 0470 5905Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080 Republic of Korea
| |
Collapse
|
5
|
McQuillan MA, Ranciaro A, Hansen MEB, Fan S, Beggs W, Belay G, Woldemeskel D, Tishkoff SA. Signatures of Convergent Evolution and Natural Selection at the Alcohol Dehydrogenase Gene Region are Correlated with Agriculture in Ethnically Diverse Africans. Mol Biol Evol 2022; 39:msac183. [PMID: 36026493 PMCID: PMC9547508 DOI: 10.1093/molbev/msac183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The alcohol dehydrogenase (ADH) family of genes encodes enzymes that catalyze the metabolism of ethanol into acetaldehyde. Nucleotide variation in ADH genes can affect the catalytic properties of these enzymes and is associated with a variety of traits, including alcoholism and cancer. Some ADH variants, including the ADH1B*48His (rs1229984) mutation in the ADH1B gene, reduce the risk of alcoholism and are under positive selection in multiple human populations. The advent of Neolithic agriculture and associated increase in fermented foods and beverages is hypothesized to have been a selective force acting on such variants. However, this hypothesis has not been tested in populations outside of Asia. Here, we use genome-wide selection scans to show that the ADH gene region is enriched for variants showing strong signals of positive selection in multiple Afroasiatic-speaking, agriculturalist populations from Ethiopia, and that this signal is unique among sub-Saharan Africans. We also observe strong selection signals at putatively functional variants in nearby lipid metabolism genes, which may influence evolutionary dynamics at the ADH region. Finally, we show that haplotypes carrying these selected variants were introduced into Northeast Africa from a West-Eurasian source within the last ∼2,000 years and experienced positive selection following admixture. These selection signals are not evident in nearby, genetically similar populations that practice hunting/gathering or pastoralist subsistence lifestyles, supporting the hypothesis that the emergence of agriculture shapes patterns of selection at ADH genes. Together, these results enhance our understanding of how adaptations to diverse environments and diets have influenced the African genomic landscape.
Collapse
Affiliation(s)
| | - Alessia Ranciaro
- Department of Genetics, University of Pennsylvania, Philadelphia, PA
| | | | - Shaohua Fan
- Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai, China
| | - William Beggs
- Department of Genetics, University of Pennsylvania, Philadelphia, PA
| | - Gurja Belay
- Department of Microbial Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Dawit Woldemeskel
- Department of Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Sarah A Tishkoff
- Department of Genetics, University of Pennsylvania, Philadelphia, PA
| |
Collapse
|
6
|
Cong PK, Bai WY, Li JC, Yang MY, Khederzadeh S, Gai SR, Li N, Liu YH, Yu SH, Zhao WW, Liu JQ, Sun Y, Zhu XW, Zhao PP, Xia JW, Guan PL, Qian Y, Tao JG, Xu L, Tian G, Wang PY, Xie SY, Qiu MC, Liu KQ, Tang BS, Zheng HF. Genomic analyses of 10,376 individuals in the Westlake BioBank for Chinese (WBBC) pilot project. Nat Commun 2022; 13:2939. [PMID: 35618720 PMCID: PMC9135724 DOI: 10.1038/s41467-022-30526-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 05/05/2022] [Indexed: 01/04/2023] Open
Abstract
We initiate the Westlake BioBank for Chinese (WBBC) pilot project with 4,535 whole-genome sequencing (WGS) individuals and 5,841 high-density genotyping individuals, and identify 81.5 million SNPs and INDELs, of which 38.5% are absent in dbSNP Build 151. We provide a population-specific reference panel and an online imputation server ( https://wbbc.westlake.edu.cn/ ) which could yield substantial improvement of imputation performance in Chinese population, especially for low-frequency and rare variants. By analyzing the singleton density of the WGS data, we find selection signatures in SNX29, DNAH1 and WDR1 genes, and the derived alleles of the alcohol metabolism genes (ADH1A and ADH1B) emerge around 7,000 years ago and tend to be more common from 4,000 years ago in East Asia. Genetic evidence supports the corresponding geographical boundaries of the Qinling-Huaihe Line and Nanling Mountains, which separate the Han Chinese into subgroups, and we reveal that North Han was more homogeneous than South Han.
Collapse
Affiliation(s)
- Pei-Kuan Cong
- Diseases & Population (DaP) Geninfo Lab, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Wei-Yang Bai
- Diseases & Population (DaP) Geninfo Lab, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Jin-Chen Li
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Center for Medical Genetics & Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Meng-Yuan Yang
- Diseases & Population (DaP) Geninfo Lab, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Saber Khederzadeh
- Diseases & Population (DaP) Geninfo Lab, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Si-Rui Gai
- Diseases & Population (DaP) Geninfo Lab, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Nan Li
- The High-Performance Computing Center, Westlake University, Hangzhou, Zhejiang, China
| | - Yu-Heng Liu
- The High-Performance Computing Center, Westlake University, Hangzhou, Zhejiang, China
| | - Shi-Hui Yu
- Clinical Genome Center, KingMed Diagnostics, Co., Ltd., Guangzhou, Guangdong, China
| | - Wei-Wei Zhao
- Clinical Genome Center, KingMed Diagnostics, Co., Ltd., Guangzhou, Guangdong, China
| | - Jun-Quan Liu
- Clinical Genome Center, KingMed Diagnostics, Co., Ltd., Guangzhou, Guangdong, China
| | - Yi Sun
- Clinical Genome Center, KingMed Diagnostics, Co., Ltd., Guangzhou, Guangdong, China
| | - Xiao-Wei Zhu
- Diseases & Population (DaP) Geninfo Lab, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Pian-Pian Zhao
- Diseases & Population (DaP) Geninfo Lab, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Jiang-Wei Xia
- Diseases & Population (DaP) Geninfo Lab, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Peng-Lin Guan
- Diseases & Population (DaP) Geninfo Lab, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Yu Qian
- Diseases & Population (DaP) Geninfo Lab, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Jian-Guo Tao
- Diseases & Population (DaP) Geninfo Lab, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Lin Xu
- WBBC Shandong Center, Binzhou Medical University, Yantai, Shandong, China
| | - Geng Tian
- WBBC Shandong Center, Binzhou Medical University, Yantai, Shandong, China
| | - Ping-Yu Wang
- WBBC Shandong Center, Binzhou Medical University, Yantai, Shandong, China
| | - Shu-Yang Xie
- WBBC Shandong Center, Binzhou Medical University, Yantai, Shandong, China
| | - Mo-Chang Qiu
- WBBC Jiangxi Center, Jiangxi Medical College, Shangrao, Jiangxi, China
| | - Ke-Qi Liu
- WBBC Jiangxi Center, Jiangxi Medical College, Shangrao, Jiangxi, China
| | - Bei-Sha Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China.
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China.
| | - Hou-Feng Zheng
- Diseases & Population (DaP) Geninfo Lab, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China.
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China.
| |
Collapse
|
7
|
Pan Y, Zhang C, Lu Y, Ning Z, Lu D, Gao Y, Zhao X, Yang Y, Guan Y, Mamatyusupu D, Xu S. Genomic diversity and post-admixture adaptation in the Uyghurs. Natl Sci Rev 2022; 9:nwab124. [PMID: 35350227 PMCID: PMC8953455 DOI: 10.1093/nsr/nwab124] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 05/30/2021] [Accepted: 06/07/2021] [Indexed: 11/17/2022] Open
Abstract
Population admixture results in genome-wide combinations of genetic variants derived from different ancestral populations of distinct ancestry, thus providing a unique opportunity for understanding the genetic determinants of phenotypic variation in humans. Here, we used whole-genome sequencing of 92 individuals with high coverage (30–60×) to systematically investigate genomic diversity in the Uyghurs living in Xinjiang, China (XJU), an admixed population of both European-like and East-Asian-like ancestry. The XJU population shows greater genetic diversity, especially a higher proportion of rare variants, compared with their ancestral source populations, corresponding to greater phenotypic diversity of XJU. Admixture-induced functional variants in EDAR were associated with the diversity of facial morphology in XJU. Interestingly, the interaction of functional variants between SLC24A5 and OCA2 likely influences the diversity of skin pigmentation. Notably, selection has seemingly been relaxed or canceled in several genes with significantly biased ancestry, such as HERC2–OCA2. Moreover, signatures of post-admixture adaptation in XJU were identified, including genes related to metabolism (e.g. CYP2D6), digestion (e.g. COL11A1), olfactory perception (e.g. ANO2) and immunity (e.g. HLA). Our results demonstrated population admixture as a driving force, locally or globally, in shaping human genetic and phenotypic diversity as well as in adaptive evolution.
Collapse
Affiliation(s)
- Yuwen Pan
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences , Shanghai 200031, China
| | - Chao Zhang
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences , Shanghai 200031, China
| | - Yan Lu
- State Key Laboratory of Genetic Engineering and Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University , Shanghai 200438, China
| | - Zhilin Ning
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences , Shanghai 200031, China
| | - Dongsheng Lu
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences , Shanghai 200031, China
| | - Yang Gao
- Key Laboratory of 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 University , Shanghai 201210, China
| | - Xiaohan Zhao
- Human Phenome Institute, Fudan University , Shanghai 201203, China
| | - Yajun Yang
- State Key Laboratory of Genetic Engineering and Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University , Shanghai 200438, China
| | - Yaqun Guan
- Department of Biochemistry and Molecular Biology, Preclinical Medicine College, Xinjiang Medical University , Urumqi 830011, China
| | - Dolikun Mamatyusupu
- College of the Life Sciences and Technology, Xinjiang University , Urumqi 830046, China
| | - Shuhua Xu
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences , Shanghai 200031, China
- State Key Laboratory of Genetic Engineering and Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University , Shanghai 200438, China
- School of Life Science and Technology, ShanghaiTech University , Shanghai 201210, China
- Human Phenome Institute, Fudan University , Shanghai 201203, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences , Kunming 650223, China
- Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University , Zhengzhou 450052, China
| |
Collapse
|
8
|
Schaschl H, Göllner T, Morris DL. Positive selection acts on regulatory genetic variants in populations of European ancestry that affect ALDH2 gene expression. Sci Rep 2022; 12:4563. [PMID: 35296751 PMCID: PMC8927298 DOI: 10.1038/s41598-022-08588-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 03/09/2022] [Indexed: 11/09/2022] Open
Abstract
ALDH2 is a key enzyme in alcohol metabolism that protects cells from acetaldehyde toxicity. Using iHS, iSAFE and FST statistics, we identified regulatory acting variants affecting ALDH2 gene expression under positive selection in populations of European ancestry. Several SNPs (rs3184504, rs4766578, rs10774625, rs597808, rs653178, rs847892, rs2013002) that function as eQTLs for ALDH2 in various tissues showed evidence of strong positive selection. Very large pairwise FST values indicated high genetic differentiation at these loci between populations of European ancestry and populations of other global ancestries. Estimating the timing of positive selection on the beneficial alleles suggests that these variants were recently adapted approximately 3000-3700 years ago. The derived beneficial alleles are in complete linkage disequilibrium with the derived ALDH2 promoter variant rs886205, which is associated with higher transcriptional activity. The SNPs rs4766578 and rs847892 are located in binding sequences for the transcription factor HNF4A, which is an important regulatory element of ALDH2 gene expression. In contrast to the missense variant ALDH2 rs671 (ALDH2*2), which is common only in East Asian populations and is associated with greatly reduced enzyme activity and alcohol intolerance, the beneficial alleles of the regulatory variants identified in this study are associated with increased expression of ALDH2. This suggests adaptation of Europeans to higher alcohol consumption.
Collapse
Affiliation(s)
- Helmut Schaschl
- Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria.
| | - Tobias Göllner
- Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - David L Morris
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, Great Maze Pond, London, SE1 9RT, UK
| |
Collapse
|
9
|
Dilber E, Terhorst J. Robust detection of natural selection using a probabilistic model of tree imbalance. Genetics 2022; 220:6511494. [PMID: 35100408 PMCID: PMC8893258 DOI: 10.1093/genetics/iyac009] [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: 10/06/2021] [Accepted: 12/16/2021] [Indexed: 01/21/2023] Open
Abstract
Neutrality tests such as Tajima's D and Fay and Wu's H are standard implements in the population genetics toolbox. One of their most common uses is to scan the genome for signals of natural selection. However, it is well understood that D and H are confounded by other evolutionary forces-in particular, population expansion-that may be unrelated to selection. Because they are not model-based, it is not clear how to deconfound these tests in a principled way. In this article, we derive new likelihood-based methods for detecting natural selection, which are robust to fluctuations in effective population size. At the core of our method is a novel probabilistic model of tree imbalance, which generalizes Kingman's coalescent to allow certain aberrant tree topologies to arise more frequently than is expected under neutrality. We derive a frequency spectrum-based estimator that can be used in place of D, and also extend to the case where genealogies are first estimated. We benchmark our methods on real and simulated data, and provide an open source software implementation.
Collapse
Affiliation(s)
- Enes Dilber
- Department of Statistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jonathan Terhorst
- Department of Statistics, University of Michigan, Ann Arbor, MI 48109, USA,Corresponding author: Department of Statistics, University of Michigan, Ann Arbor, MI 48109, USA.
| |
Collapse
|
10
|
Abstract
As human populations spread across the world, they adapted genetically to local conditions. So too did the resident microorganism communities that everyone carries with them. However, the collective influence of the diverse and dynamic community of resident microbes on host evolution is poorly understood. The taxonomic composition of the microbiota varies among individuals and displays a range of sometimes redundant functions that modify the physicochemical environment of the host and may alter selection pressures. Here we review known human traits and genes for which the microbiota may have contributed or responded to changes in host diet, climate, or pathogen exposure. Integrating host–microbiota interactions in human adaptation could offer new approaches to improve our understanding of human health and evolution.
Collapse
Affiliation(s)
- Taichi A. Suzuki
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Ruth E. Ley
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| |
Collapse
|
11
|
Peng M, Zhang J, Zeng T, Hu X, Min J, Tian S, Wang Y, Liu G, Wan L, Huang Q, Hu S, Chen L. Alcohol consumption and diabetes risk in a Chinese population: a Mendelian randomization analysis. Addiction 2019; 114:436-449. [PMID: 30326548 DOI: 10.1111/add.14475] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 08/03/2018] [Accepted: 10/05/2018] [Indexed: 01/06/2023]
Abstract
AIM To assess the causality between alcohol intake, diabetes risk and related traits. DESIGN Mendelian randomization (MR) study. Subgroup analysis, standard instrumental variable analysis and local average treatment effect (LATE) methods were applied to assess linear and non-linear causality. SETTING China. PARTICIPANTS A total of 4536 participants, including 721 diabetes cases. FINDINGS Carriage of an ALDH2 rs671 A allele reduced alcohol consumption by 44.63% [95% confidence interval (CI) = -49.44%, -39.37%]. In males, additional carriage of an A allele was significantly connected to decreased diabetes risk for the overall population [odds ratio (OR) = 0.716, 95% CI = 0.567-0.904, P = 0.005] or moderate drinkers (OR = 0.564, 95% CI = 0.355-0.894, P = 0.015). In instrumental variable (IV) analysis, increasing alcohol consumption by 1.7-fold was associated with an incidence-rate ratio of 1.32 (95% CI = 1.06-1.67, P = 0.014) for diabetes risk, and elevated alcohol intake was causally connected to natural log-transformed fasting, 2-hour post-load plasma glucose (β = 0.036, 95% CI = 0.018-0.054; β = 0.072, 95% CI = 0.035-0.108) and insulin resistance [homeostatic model assessment for IR (HOMA-IR] (β = 0.104, 95% CI = 0.039-0.169), but was not associated with beta-cell function (HOMA-beta). In addition, the LATE method did not identify significant U-shaped causality between alcohol consumption and diabetes-related traits. In females, the effects of alcohol intake on all the outcomes were non-significant. CONCLUSION Among men in China, higher alcohol intake appears to be causally associated with increased diabetes risk and worsened related traits, even for moderate drinkers. This study found no significant U-shaped causality between alcohol consumption and diabetes-related traits.
Collapse
Affiliation(s)
- Miaomiao Peng
- Department of Endocrinology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiaoyue Zhang
- Department of Endocrinology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tianshu Zeng
- Department of Endocrinology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiang Hu
- Department of Endocrinology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jie Min
- Department of Endocrinology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shenghua Tian
- Department of Endocrinology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ying Wang
- Department of Endocrinology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Geng Liu
- Department of Endocrinology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Limin Wan
- Department of Endocrinology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Department of Rheumatology and Immunology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qiulan Huang
- Department of Endocrinology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Department of Endocrinology, Bao'an People's Hospital, Shenzhen, China
| | - Shengqing Hu
- Department of Endocrinology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lulu Chen
- Department of Endocrinology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| |
Collapse
|
12
|
Chiang CWK, Mangul S, Robles C, Sankararaman S. A Comprehensive Map of Genetic Variation in the World's Largest Ethnic Group-Han Chinese. Mol Biol Evol 2018; 35:2736-2750. [PMID: 30169787 PMCID: PMC6693441 DOI: 10.1093/molbev/msy170] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
As are most non-European populations, the Han Chinese are relatively understudied in population and medical genetics studies. From low-coverage whole-genome sequencing of 11,670 Han Chinese women we present a catalog of 25,057,223 variants, including 548,401 novel variants that are seen at least 10 times in our data set. Individuals from this data set came from 24 out of 33 administrative divisions across China (including 19 provinces, 4 municipalities, and 1 autonomous region), thus allowing us to study population structure, genetic ancestry, and local adaptation in Han Chinese. We identified previously unrecognized population structure along the East-West axis of China, demonstrated a general pattern of isolation-by-distance among Han Chinese, and reported unique regional signals of admixture, such as European influences among the Northwestern provinces of China. Furthermore, we identified a number of highly differentiated, putatively adaptive, loci (e.g., MTHFR, ADH7, and FADS, among others) that may be driven by immune response, climate, and diet in the Han Chinese. Finally, we have made available allele frequency estimates stratified by administrative divisions across China in the Geography of Genetic Variant browser for the broader community. By leveraging the largest currently available genetic data set for Han Chinese, we have gained insights into the history and population structure of the world's largest ethnic group.
Collapse
Affiliation(s)
- Charleston W K Chiang
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA
| | - Serghei Mangul
- Department of Computer Science, University of California Los Angeles, Los Angeles, CA
- Institute for Quantitative and Computational Bioscience, University of California Los Angeles, Los Angeles, CA
| | - Christopher Robles
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
| | - Sriram Sankararaman
- Department of Computer Science, University of California Los Angeles, Los Angeles, CA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
| |
Collapse
|
13
|
Saifullah, Tsukahara T. Genotyping of single nucleotide polymorphisms using the SNP-RFLP method. Biosci Trends 2018; 12:240-246. [PMID: 30012914 DOI: 10.5582/bst.2018.01102] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Genetic polymorphisms, including single nucleotide polymorphisms (SNPs), are responsible for inter-individual variability in susceptibility to cancer and other disorders. Both environmental factors (e.g., smoking or carcinogen exposure) and genetic variation underlie the development of cancer; however, studies of twins suggest that genetic variation is more important. Hence, the identification of SNPs makes an important contribution to cancer research. In this study, 13 SNPs in 12 genes were genotyped in HEK 293 and HeLa cells using the simple and inexpensive SNP-RFLP method. Sanger sequencing was performed for one SNP to validate the SNP-RFLP results. Of the 13 SNPs, 10 were homozygous and three were heterozygous (rs10937405, rs12296850, and rs3814113) in HEK 293 cells, while 12 were homozygous and one was heterozygous (rs995030) in HeLa cells. The cells carried eight disease-associated risk alleles (32% of typed alleles), including rs2853677, rs995030, rs2736100, and rs6010620 in HEK 293 cells, and rs10937405, rs3814113, rs4767364, and rs6010620 in HeLa cells. Four SNP loci were homozygous for different alleles in each cell line, with HEK 293 cells having a CC genotype at rs2853677, GG at rs2736100 and rs4767364, and TT at rs3819197, while HeLa cells had TT genotypes at rs2853677 and rs2736100, AA at rs4767364, and CC at rs3819197. In conclusion, these results are potentially applicable for testing of novel gene therapeutic approaches in future experiments where the non-risk alleles of the eight identified risk alleles are substituted into HEK 293 or HeLa cells.
Collapse
Affiliation(s)
- Saifullah
- Area of Bioscience and Biotechnology, School of Materials Science, Japan Advanced Institute of Science and Technology (JAIST)
| | - Toshifumi Tsukahara
- Area of Bioscience and Biotechnology, School of Materials Science, Japan Advanced Institute of Science and Technology (JAIST)
| |
Collapse
|
14
|
Gu S, Li H, Pakstis AJ, Speed WC, Gurwitz D, Kidd JR, Kidd KK. Recent Selection on a Class I ADH Locus Distinguishes Southwest Asian Populations Including Ashkenazi Jews. Genes (Basel) 2018; 9:genes9090452. [PMID: 30205534 PMCID: PMC6162407 DOI: 10.3390/genes9090452] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 08/21/2018] [Accepted: 08/21/2018] [Indexed: 12/29/2022] Open
Abstract
The derived human alcohol dehydrogenase (ADH)1B*48His allele of the ADH1B Arg48His polymorphism (rs1229984) has been identified as one component of an East Asian specific core haplotype that underwent recent positive selection. Our study has been extended to Southwest Asia and additional markers in East Asia. Fst values (Sewall Wright’s fixation index) and long-range haplotype analyses identify a strong signature of selection not only in East Asian but also in Southwest Asian populations. However, except for the ADH2B*48His allele, different core haplotypes occur in Southwest Asia compared to East Asia and the extended haplotypes also differ. Thus, the ADH1B*48His allele, as part of a core haplotype of 10 kb, has undergone recent rapid increases in frequency independently in the two regions after divergence of the respective populations. Emergence of agriculture may be the common factor underlying the evident selection.
Collapse
Affiliation(s)
- Sheng Gu
- Department of Genetics, School of Medicine, Yale University, New Haven, CT 06520, USA.
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China.
| | - Hui Li
- Ministry of Education 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.
| | - William C Speed
- Department of Genetics, School of Medicine, Yale University, New Haven, CT 06520, USA.
| | - David Gurwitz
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
| | - 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.
| |
Collapse
|
15
|
Johnson KE, Voight BF. Patterns of shared signatures of recent positive selection across human populations. Nat Ecol Evol 2018; 2:713-720. [PMID: 29459708 PMCID: PMC5866773 DOI: 10.1038/s41559-018-0478-6] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 01/11/2018] [Indexed: 12/28/2022]
Abstract
Signatures of recent positive selection often overlap across human populations, but the question of how often these overlaps represent a single ancestral event remains unresolved. If a single selective event spread across many populations, the same sweeping haplotype should appear in each population and the selective pressure could be common across populations and environments. Identifying such shared selective events could identify genomic loci and human traits important in recent history across the globe. In addition, genomic annotations that recently became available could help attach these signatures to a potential gene and molecular phenotype selected across populations. Here, we present a catalogue of selective sweeps in humans, and identify those that overlap and share a sweeping haplotype. We connect these sweep overlaps with potential biological mechanisms at several loci, including potential new sites of adaptive introgression, the glycophorin locus associated with malarial resistance and the alcohol dehydrogenase cluster associated with alcohol dependency.
Collapse
Affiliation(s)
- Kelsey Elizabeth Johnson
- Genetics and Gene Regulation Program, Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Benjamin F Voight
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|
16
|
Polimanti R, Gelernter J. ADH1B: From alcoholism, natural selection, and cancer to the human phenome. Am J Med Genet B Neuropsychiatr Genet 2018; 177:113-125. [PMID: 28349588 PMCID: PMC5617762 DOI: 10.1002/ajmg.b.32523] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 12/19/2016] [Indexed: 12/18/2022]
Abstract
The ADH1B (Alcohol Dehydrogenase 1B (class I), Beta Polypeptide) gene and its best-known functional alleles, Arg48His (rs1229984, ADH1B*2) and Arg370Cys (rs2066702, ADH1B*3), have been investigated in relation to many phenotypic traits; most frequently including alcohol metabolism and alcohol drinking behaviors, but also human evolution, liver function, cancer, and, recently, the comprehensive human phenome. To understand ADH1B functions and consequences, we provide here a bioinformatic analysis of its gene regulation and molecular functions, literature review of studies focused on this gene, and a discussion regarding future research perspectives. Certain ADH1B alleles have large effects on alcohol metabolism, and this relationship particularly encourages further investigations in relation to alcoholism and alcohol-associated cancer to understand better the mechanisms by which alcohol metabolism contributes to alcohol abuse and carcinogenesis. We also observed that ADH1B has complex mechanisms that regulate its expression across multiple human tissues, and these may be involved in cardiac and metabolic traits. Evolutionary data strongly suggest that the selection signatures at the ADH1B locus are primarily related to effects other than those on alcohol metabolism. This is also supported by the involvement of ADH1B in multiple molecular pathways and by the findings of our recent phenome-wide association study. Accordingly, future studies should also investigate other functions of ADH1B potentially relevant for the human phenome. © 2017 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Renato Polimanti
- Department of Psychiatry, Yale School of Medicine and VA CT Healthcare Center, West Haven, CT, USA
| | - Joel Gelernter
- Department of Psychiatry, Yale School of Medicine and VA CT Healthcare Center, West Haven, CT, USA
- Department of Genetics, Yale School of Medicine, West Haven, CT, USA
- Department of Neuroscience, Yale School of Medicine, West Haven, CT, USA
| |
Collapse
|
17
|
Szpak M, Mezzavilla M, Ayub Q, Chen Y, Xue Y, Tyler-Smith C. FineMAV: prioritizing candidate genetic variants driving local adaptations in human populations. Genome Biol 2018; 19:5. [PMID: 29343290 PMCID: PMC5771147 DOI: 10.1186/s13059-017-1380-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 12/12/2017] [Indexed: 12/30/2022] Open
Abstract
We present a new method, Fine-Mapping of Adaptive Variation (FineMAV), which combines population differentiation, derived allele frequency, and molecular functionality to prioritize positively selected candidate variants for functional follow-up. We calibrate and test FineMAV using eight experimentally validated "gold standard" positively selected variants and simulations. FineMAV has good sensitivity and a low false discovery rate. Applying FineMAV to the 1000 Genomes Project Phase 3 SNP dataset, we report many novel selected variants, including ones in TGM3 and PRSS53 associated with hair phenotypes that we validate using available independent data. FineMAV is widely applicable to sequence data from both human and other species.
Collapse
Affiliation(s)
- Michał Szpak
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA UK
| | - Massimo Mezzavilla
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA UK
- Division of Experimental Genetics, Sidra Medical and Research Center, Doha, Qatar
| | - Qasim Ayub
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA UK
- Present Address: Genomics Facility, School of Science, Monash University Malaysia, Bandar Sunway, Selangor, Darul Ehsan Malaysia
| | - Yuan Chen
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA UK
| | - Yali Xue
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA UK
| | - Chris Tyler-Smith
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA UK
| |
Collapse
|
18
|
Takeuchi F, Katsuya T, Kimura R, Nabika T, Isomura M, Ohkubo T, Tabara Y, Yamamoto K, Yokota M, Liu X, Saw WY, Mamatyusupu D, Yang W, Xu S, Teo YY, Kato N. The fine-scale genetic structure and evolution of the Japanese population. PLoS One 2017; 12:e0185487. [PMID: 29091727 PMCID: PMC5665431 DOI: 10.1371/journal.pone.0185487] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 09/13/2017] [Indexed: 11/21/2022] Open
Abstract
The contemporary Japanese populations largely consist of three genetically distinct groups—Hondo, Ryukyu and Ainu. By principal-component analysis, while the three groups can be clearly separated, the Hondo people, comprising 99% of the Japanese, form one almost indistinguishable cluster. To understand fine-scale genetic structure, we applied powerful haplotype-based statistical methods to genome-wide single nucleotide polymorphism data from 1600 Japanese individuals, sampled from eight distinct regions in Japan. We then combined the Japanese data with 26 other Asian populations data to analyze the shared ancestry and genetic differentiation. We found that the Japanese could be separated into nine genetic clusters in our dataset, showing a marked concordance with geography; and that major components of ancestry profile of Japanese were from the Korean and Han Chinese clusters. We also detected and dated admixture in the Japanese. While genetic differentiation between Ryukyu and Hondo was suggested to be caused in part by positive selection, genetic differentiation among the Hondo clusters appeared to result principally from genetic drift. Notably, in Asians, we found the possibility that positive selection accentuated genetic differentiation among distant populations but attenuated genetic differentiation among close populations. These findings are significant for studies of human evolution and medical genetics.
Collapse
Affiliation(s)
- Fumihiko Takeuchi
- Department of Gene Diagnostics and Therapeutics, National Center for Global Health and Medicine, Tokyo, Japan
- * E-mail: (FT); (NK)
| | - Tomohiro Katsuya
- Department of Clinical Gene Therapy, Osaka University Graduate School of Medicine, Suita, Japan
| | - Ryosuke Kimura
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara-cho, Japan
| | - Toru Nabika
- Department of Functional Pathology, Shimane University School of Medicine, Izumo, Japan
| | - Minoru Isomura
- Department of Functional Pathology, Shimane University School of Medicine, Izumo, Japan
| | - Takayoshi Ohkubo
- Department of Hygiene and Public Health, Teikyo University School of Medicine, Tokyo, Japan
| | - Yasuharu Tabara
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Ken Yamamoto
- Department of Medical Chemistry, Kurume University School of Medicine, Kurume, Japan
| | - Mitsuhiro Yokota
- Department of Genome Science, School of Dentistry, Aichi Gakuin University, Nagoya, Japan
| | - Xuanyao Liu
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
- NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore, Singapore
| | - Woei-Yuh Saw
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
- Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Dolikun Mamatyusupu
- College of the Life Sciences and Technology, Xinjiang University, Urumqi, China
| | - Wenjun Yang
- Key Laboratory of Reproduction and Heredity of Ningxia Region, Ningxia Medical University, Yinchuan, Ningxia, China
| | - Shuhua Xu
- Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences Shanghai, China
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China
- Collaborative Innovation Center of Genetics and Development, Shanghai, China
| | | | - Yik-Ying Teo
- Department of Gene Diagnostics and Therapeutics, National Center for Global Health and Medicine, Tokyo, Japan
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
- NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore, Singapore
- Life Sciences Institute, National University of Singapore, Singapore, Singapore
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
- Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore
| | - Norihiro Kato
- Department of Gene Diagnostics and Therapeutics, National Center for Global Health and Medicine, Tokyo, Japan
- * E-mail: (FT); (NK)
| |
Collapse
|
19
|
Genome-wide association study identifies 112 new loci for body mass index in the Japanese population. Nat Genet 2017; 49:1458-1467. [DOI: 10.1038/ng.3951] [Citation(s) in RCA: 267] [Impact Index Per Article: 38.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 08/14/2017] [Indexed: 12/15/2022]
|
20
|
Akiyama T, Katsumura T, Nakagome S, Lee SI, Joh K, Soejima H, Fujimoto K, Kimura R, Ishida H, Hanihara T, Yasukouchi A, Satta Y, Higuchi S, Oota H. An ancestral haplotype of the human PERIOD2 gene associates with reduced sensitivity to light-induced melatonin suppression. PLoS One 2017. [PMID: 28650999 PMCID: PMC5484468 DOI: 10.1371/journal.pone.0178373] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Humans show various responses to the environmental stimulus in individual levels as “physiological variations.” However, it has been unclear if these are caused by genetic variations. In this study, we examined the association between the physiological variation of response to light-stimulus and genetic polymorphisms. We collected physiological data from 43 subjects, including light-induced melatonin suppression, and performed haplotype analyses on the clock genes, PER2 and PER3, exhibiting geographical differentiation of allele frequencies. Among the haplotypes of PER3, no significant difference in light sensitivity was found. However, three common haplotypes of PER2 accounted for more than 96% of the chromosomes in subjects, and 1 of those 3 had a significantly low-sensitive response to light-stimulus (P < 0.05). The homozygote of the low-sensitive PER2 haplotype showed significantly lower percentages of melatonin suppression (P < 0.05), and the heterozygotes of the haplotypes varied their ratios, indicating that the physiological variation for light-sensitivity is evidently related to the PER2 polymorphism. Compared with global haplotype frequencies, the haplotype with a low-sensitive response was more frequent in Africans than in non-Africans, and came to the root in the phylogenetic tree, suggesting that the low light-sensitive haplotype is the ancestral type, whereas the other haplotypes with high sensitivity to light are the derived types. Hence, we speculate that the high light-sensitive haplotypes have spread throughout the world after the Out-of-Africa migration of modern humans.
Collapse
Affiliation(s)
- Tokiho Akiyama
- Department of Anatomy, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
- Department of Biosciences, School of Science, Kitasato University, Sagamihara, Kanagawa, Japan
- Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Kanagawa, Japan
| | - Takafumi Katsumura
- Department of Anatomy, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Shigeki Nakagome
- Department of Mathematical Analysis and Statistical Inference, The Institute of Statistical Mathematics, Tachikawa, Tokyo, Japan
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Sang-il Lee
- Department of Human Science, Faculty of Design, Kyushu University, Minami-ku Fukuoka, Japan
| | - Keiichiro Joh
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Science, Faculty of Medicine, Saga University, Nabeshima, Saga, Japan
| | - Hidenobu Soejima
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Science, Faculty of Medicine, Saga University, Nabeshima, Saga, Japan
| | - Kazuma Fujimoto
- Department of Internal Medicine, Faculty of Medicine, Saga University, Nabeshima, Saga, Japan
| | - Ryosuke Kimura
- Department of Human Biology and Anatomy, Faculty of Medicine, University of the Ryukyus, Nishihara-cho, Okinawa, Japan
| | - Hajime Ishida
- Department of Human Biology and Anatomy, Faculty of Medicine, University of the Ryukyus, Nishihara-cho, Okinawa, Japan
| | - Tsunehiko Hanihara
- Department of Anatomy, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
- Department of Biological Structure, Kitasato University Graduate School of Medical Sciences, Sagamihara, Kanagawa, Japan
| | - Akira Yasukouchi
- Department of Human Science, Faculty of Design, Kyushu University, Minami-ku Fukuoka, Japan
| | - Yoko Satta
- Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Kanagawa, Japan
| | - Shigekazu Higuchi
- Department of Human Science, Faculty of Design, Kyushu University, Minami-ku Fukuoka, Japan
- * E-mail: (SH); (HO)
| | - Hiroki Oota
- Department of Anatomy, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
- Department of Biological Structure, Kitasato University Graduate School of Medical Sciences, Sagamihara, Kanagawa, Japan
- * E-mail: (SH); (HO)
| |
Collapse
|
21
|
Unterländer M, Palstra F, Lazaridis I, Pilipenko A, Hofmanová Z, Groß M, Sell C, Blöcher J, Kirsanow K, Rohland N, Rieger B, Kaiser E, Schier W, Pozdniakov D, Khokhlov A, Georges M, Wilde S, Powell A, Heyer E, Currat M, Reich D, Samashev Z, Parzinger H, Molodin VI, Burger J. Ancestry and demography and descendants of Iron Age nomads of the Eurasian Steppe. Nat Commun 2017; 8:14615. [PMID: 28256537 PMCID: PMC5337992 DOI: 10.1038/ncomms14615] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 01/13/2017] [Indexed: 01/10/2023] Open
Abstract
During the 1st millennium before the Common Era (BCE), nomadic tribes associated with the Iron Age Scythian culture spread over the Eurasian Steppe, covering a territory of more than 3,500 km in breadth. To understand the demographic processes behind the spread of the Scythian culture, we analysed genomic data from eight individuals and a mitochondrial dataset of 96 individuals originating in eastern and western parts of the Eurasian Steppe. Genomic inference reveals that Scythians in the east and the west of the steppe zone can best be described as a mixture of Yamnaya-related ancestry and an East Asian component. Demographic modelling suggests independent origins for eastern and western groups with ongoing gene-flow between them, plausibly explaining the striking uniformity of their material culture. We also find evidence that significant gene-flow from east to west Eurasia must have occurred early during the Iron Age.
Collapse
Affiliation(s)
- Martina Unterländer
- Palaeogenetics Group, Institute of Evolutionary Biology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Friso Palstra
- CNRS UMR 7206 Eco-anthropologie, Muséum National d'Histoire Naturelle, 75016 Paris, France
| | - Iosif Lazaridis
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Aleksandr Pilipenko
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Science, Akademika Lavrentieva 10, Novosibirsk 630090, Russia
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Science, Akademika Lavrentieva 17, Novosibirsk 630090, Russia
- Novosibirsk State University, Pirogova str. 2, Novosibirsk 630090, Russia
| | - Zuzana Hofmanová
- Palaeogenetics Group, Institute of Evolutionary Biology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Melanie Groß
- Palaeogenetics Group, Institute of Evolutionary Biology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Christian Sell
- Palaeogenetics Group, Institute of Evolutionary Biology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Jens Blöcher
- Palaeogenetics Group, Institute of Evolutionary Biology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Karola Kirsanow
- Palaeogenetics Group, Institute of Evolutionary Biology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Benjamin Rieger
- Molecular Genetics and Genome Analysis Group, Institute of Evolutionary Biology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Elke Kaiser
- Department of History and Cultural Studies, Freie Universität Berlin, 14195 Berlin, Germany
| | - Wolfram Schier
- Department of History and Cultural Studies, Freie Universität Berlin, 14195 Berlin, Germany
| | - Dimitri Pozdniakov
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Science, Akademika Lavrentieva 10, Novosibirsk 630090, Russia
| | - Aleksandr Khokhlov
- Samara State University of Social Sciences and Education, Samara 443099, Russian Federation
| | - Myriam Georges
- CNRS UMR 7206 Eco-anthropologie, Muséum National d'Histoire Naturelle, 75016 Paris, France
| | - Sandra Wilde
- Palaeogenetics Group, Institute of Evolutionary Biology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Adam Powell
- Palaeogenetics Group, Institute of Evolutionary Biology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
- Max Planck Institute for the Science of Human History, Kahlaische Straße 10, 07745 Jena, Germany
| | - Evelyne Heyer
- CNRS UMR 7206 Eco-anthropologie, Muséum National d'Histoire Naturelle, 75016 Paris, France
| | - Mathias Currat
- Dépt. de Génétique & Evolution, Unité d'anthropologie, Université de Genève, 1205 Genève, Suisse
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Zainolla Samashev
- Branch of Margulan Institute of Archaeology, Astana 010000, Kazakhstan
| | | | - Vyacheslav I. Molodin
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Science, Akademika Lavrentieva 10, Novosibirsk 630090, Russia
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Science, Akademika Lavrentieva 17, Novosibirsk 630090, Russia
| | - Joachim Burger
- Palaeogenetics Group, Institute of Evolutionary Biology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| |
Collapse
|
22
|
Koganebuchi K, Haneji K, Toma T, Joh K, Soejima H, Fujimoto K, Ishida H, Ogawa M, Hanihara T, Harada S, Kawamura S, Oota H. The allele frequency of ALDH2*Glu504Lys and ADH1B*Arg47His for the Ryukyu islanders and their history of expansion among East Asians. Am J Hum Biol 2016; 29. [PMID: 27801545 DOI: 10.1002/ajhb.22933] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 09/09/2016] [Accepted: 10/04/2016] [Indexed: 11/08/2022] Open
Abstract
OBJECTIVES A cline of frequencies of the derived allele of the ALDH2 gene, which causes a deficiency of an enzyme and "facial flushing" in humans who drink alcohol, has been known among the people of the Japanese archipelago. This cline is conventionally explained by admixture with immigrants from the Asian continent occurring during the Yayoi period. Previous studies lack sufficient data from the peripheral regions of the indigenous Jomon people, and those data the ADH1B gene that is involved in the Class I ADH gene cluster and contains another variant leading to a functional change. METHODS We focused on the southwestern-most people from the Ryukyu Islands (n = 218) and those from northern Kyushu (n = 21) where the Yayoi immigrants likely arrived. We investigated both the Class I ADH and ALDH2 loci, as well as neutral genetic markers. RESULTS In the Ryukyu Islands, the frequencies of the ancestral alleles in both loci were always higher than those in mainland Japan, while the frequencies of ADH1B were less than those of the derived allele. A haplotype block was not observed in ALDH2 but was in Class I ADH. DISCUSSION Our data suggest that the derived allele of ALDH2 came with the Yayoi immigrants from the Asian continent to the Japanese archipelago. However, the derived allele of ADH1B is unlikely to be related to the Yayoi migration. Therefore, we postulate that the expansion of the derived allele of ADHIB in East Asia could be traced back to the last glacial period.
Collapse
Affiliation(s)
- Kae Koganebuchi
- Department of Biological Structure, Kitasato University Graduate School of Medical Sciences, Kanagawa, 252-0373, Japan.,Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Kuniaki Haneji
- Haneji Oral Surgery Clinic, Medical Corporation Hayamakai, Okinawa, 906-0015, Japan.,Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara, Okinawa, 903-0215, Japan
| | - Takashi Toma
- Department of Oral and Maxillofacial Surgery, Adventist Medical Center, Okinawa, 903-0201, Japan.,Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara, Okinawa, 903-0215, Japan
| | - Keiichiro Joh
- Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, 849-8501, Japan
| | - Hidenobu Soejima
- Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, 849-8501, Japan
| | - Kazuma Fujimoto
- Department of Internal Medicine, Faculty of Medicine, Saga University, Saga, 849-8501, Japan
| | - Hajime Ishida
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara, Okinawa, 903-0215, Japan
| | - Motoyuki Ogawa
- Department of Biological Structure, Kitasato University Graduate School of Medical Sciences, Kanagawa, 252-0373, Japan.,Department of Anatomy, Kitasato University School of Medicine, Kanagawa, 252-0374, Japan
| | - Tsunehiko Hanihara
- Department of Biological Structure, Kitasato University Graduate School of Medical Sciences, Kanagawa, 252-0373, Japan.,Department of Anatomy, Kitasato University School of Medicine, Kanagawa, 252-0374, Japan.,The University Museum, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Shoji Harada
- Ex-Institute of Community Medicine, University of Tsukuba, Ibaraki, 305-8575, Japan
| | - Shoji Kawamura
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Hiroki Oota
- Department of Biological Structure, Kitasato University Graduate School of Medical Sciences, Kanagawa, 252-0373, Japan.,Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan.,Department of Anatomy, Kitasato University School of Medicine, Kanagawa, 252-0374, Japan
| |
Collapse
|
23
|
Martins H, Caye K, Luu K, Blum MGB, François O. Identifying outlier loci in admixed and in continuous populations using ancestral population differentiation statistics. Mol Ecol 2016; 25:5029-5042. [DOI: 10.1111/mec.13822] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Accepted: 08/18/2016] [Indexed: 01/05/2023]
Affiliation(s)
- Helena Martins
- Centre National de la Recherche Scientifique; TIMC-IMAG UMR 5525; Université Grenoble-Alpes; Grenoble 38042 France
| | - Kevin Caye
- Centre National de la Recherche Scientifique; TIMC-IMAG UMR 5525; Université Grenoble-Alpes; Grenoble 38042 France
| | - Keurcien Luu
- Centre National de la Recherche Scientifique; TIMC-IMAG UMR 5525; Université Grenoble-Alpes; Grenoble 38042 France
| | - Michael G. B. Blum
- Centre National de la Recherche Scientifique; TIMC-IMAG UMR 5525; Université Grenoble-Alpes; Grenoble 38042 France
| | - Olivier François
- Centre National de la Recherche Scientifique; TIMC-IMAG UMR 5525; Université Grenoble-Alpes; Grenoble 38042 France
| |
Collapse
|
24
|
Duforet-Frebourg N, Luu K, Laval G, Bazin E, Blum MGB. Detecting Genomic Signatures of Natural Selection with Principal Component Analysis: Application to the 1000 Genomes Data. Mol Biol Evol 2016; 33:1082-93. [PMID: 26715629 PMCID: PMC4776707 DOI: 10.1093/molbev/msv334] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
To characterize natural selection, various analytical methods for detecting candidate genomic regions have been developed. We propose to perform genome-wide scans of natural selection using principal component analysis (PCA). We show that the common FST index of genetic differentiation between populations can be viewed as the proportion of variance explained by the principal components. Considering the correlations between genetic variants and each principal component provides a conceptual framework to detect genetic variants involved in local adaptation without any prior definition of populations. To validate the PCA-based approach, we consider the 1000 Genomes data (phase 1) considering 850 individuals coming from Africa, Asia, and Europe. The number of genetic variants is of the order of 36 millions obtained with a low-coverage sequencing depth (3×). The correlations between genetic variation and each principal component provide well-known targets for positive selection (EDAR, SLC24A5, SLC45A2, DARC), and also new candidate genes (APPBPP2, TP1A1, RTTN, KCNMA, MYO5C) and noncoding RNAs. In addition to identifying genes involved in biological adaptation, we identify two biological pathways involved in polygenic adaptation that are related to the innate immune system (beta defensins) and to lipid metabolism (fatty acid omega oxidation). An additional analysis of European data shows that a genome scan based on PCA retrieves classical examples of local adaptation even when there are no well-defined populations. PCA-based statistics, implemented in the PCAdapt R package and the PCAdapt fast open-source software, retrieve well-known signals of human adaptation, which is encouraging for future whole-genome sequencing project, especially when defining populations is difficult.
Collapse
Affiliation(s)
- Nicolas Duforet-Frebourg
- TIMC-IMAG UMR 5525, Univ. Grenoble Alpes, Grenoble, France CNRS, TIMC-IMAG, Grenoble, France Department of Integrative Biology, University of California, Berkeley
| | - Keurcien Luu
- TIMC-IMAG UMR 5525, Univ. Grenoble Alpes, Grenoble, France CNRS, TIMC-IMAG, Grenoble, France
| | - Guillaume Laval
- Department of Genomes and Genetics, Institut Pasteur, Human Evolutionary Genetics, Paris, France Centre National De La Recherche Scientifique, URA3012, Paris, France
| | - Eric Bazin
- CNRS, Laboratoire D'ecologie Alpine UMR 5553, Univ. Grenoble Alpes, Grenoble, France
| | - Michael G B Blum
- TIMC-IMAG UMR 5525, Univ. Grenoble Alpes, Grenoble, France CNRS, TIMC-IMAG, Grenoble, France
| |
Collapse
|
25
|
Galinsky KJ, Bhatia G, Loh PR, Georgiev S, Mukherjee S, Patterson NJ, Price AL. Fast Principal-Component Analysis Reveals Convergent Evolution of ADH1B in Europe and East Asia. Am J Hum Genet 2016; 98:456-472. [PMID: 26924531 PMCID: PMC4827102 DOI: 10.1016/j.ajhg.2015.12.022] [Citation(s) in RCA: 226] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 12/31/2015] [Indexed: 01/13/2023] Open
Abstract
Searching for genetic variants with unusual differentiation between subpopulations is an established approach for identifying signals of natural selection. However, existing methods generally require discrete subpopulations. We introduce a method that infers selection using principal components (PCs) by identifying variants whose differentiation along top PCs is significantly greater than the null distribution of genetic drift. To enable the application of this method to large datasets, we developed the FastPCA software, which employs recent advances in random matrix theory to accurately approximate top PCs while reducing time and memory cost from quadratic to linear in the number of individuals, a computational improvement of many orders of magnitude. We apply FastPCA to a cohort of 54,734 European Americans, identifying 5 distinct subpopulations spanning the top 4 PCs. Using the PC-based test for natural selection, we replicate previously known selected loci and identify three new genome-wide significant signals of selection, including selection in Europeans at ADH1B. The coding variant rs1229984(∗)T has previously been associated to a decreased risk of alcoholism and shown to be under selection in East Asians; we show that it is a rare example of independent evolution on two continents. We also detect selection signals at IGFBP3 and IGH, which have also previously been associated to human disease.
Collapse
Affiliation(s)
- Kevin J Galinsky
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Gaurav Bhatia
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Po-Ru Loh
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | | | - Sayan Mukherjee
- Departments of Statistical Science, Computer Science, and Mathematics, Duke University, Durham, NC 27708, USA
| | - Nick J Patterson
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alkes L Price
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.
| |
Collapse
|
26
|
Evsyukov A, Ivanov D. Selection variability for Arg48His in alcohol dehydrogenase ADH1B among Asian populations. Hum Biol 2015; 85:569-77. [PMID: 25019189 DOI: 10.3378/027.085.0404] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/29/2013] [Indexed: 11/05/2022]
Abstract
The variant His at codon 48 of the alcohol dehydrogenase gene (ADH1B) results in more efficient ethanol metabolism than with the "typical" codon 48Arg. In this study we introduced selection properties of Arg48His genotypes of ADH1B and estimated fitness in four ethnic-geographical clusters in Asia. Population genetics models were employed that derive observed gene frequencies from fitness relationships among genotypes, to infer the selection pattern of polymorphisms in an indirect manner. The data were analyzed using the model of "complete stationary distribution" by Wright that takes into account random genetic drift, pressure of migrations, mutations, and selection as influential factors of gene frequency. We found that the different population groups showed some variation in the types of selection for Arg48His. Han Chinese from eastern and southeastern China and the Japanese and Korean populations showed stabilizing selection, while the groups from Central Asian and Indochina showed divergent selection. However, all the groups demonstrated a strong positive selection for Arg48His.
Collapse
Affiliation(s)
- Alexey Evsyukov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Denis Ivanov
- Faculty of Geography, Lomonosov Moscow State Unibersity, Vorob'evy Gory, Moscow, Russia
| |
Collapse
|
27
|
Bühler KM, Giné E, Echeverry-Alzate V, Calleja-Conde J, de Fonseca FR, López-Moreno JA. Common single nucleotide variants underlying drug addiction: more than a decade of research. Addict Biol 2015; 20:845-71. [PMID: 25603899 DOI: 10.1111/adb.12204] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Drug-related phenotypes are common complex and highly heritable traits. In the last few years, candidate gene (CGAS) and genome-wide association studies (GWAS) have identified a huge number of single nucleotide polymorphisms (SNPs) associated with drug use, abuse or dependence, mainly related to alcohol or nicotine. Nevertheless, few of these associations have been replicated in independent studies. The aim of this study was to provide a review of the SNPs that have been most significantly associated with alcohol-, nicotine-, cannabis- and cocaine-related phenotypes in humans between the years of 2000 and 2012. To this end, we selected CGAS, GWAS, family-based association and case-only studies published in peer-reviewed international scientific journals (using the PubMed/MEDLINE and Addiction GWAS Resource databases) in which a significant association was reported. A total of 371 studies fit the search criteria. We then filtered SNPs with at least one replication study and performed meta-analysis of the significance of the associations. SNPs in the alcohol metabolizing genes, in the cholinergic gene cluster CHRNA5-CHRNA3-CHRNB4, and in the DRD2 and ANNK1 genes, are, to date, the most replicated and significant gene variants associated with alcohol- and nicotine-related phenotypes. In the case of cannabis and cocaine, a far fewer number of studies and replications have been reported, indicating either a need for further investigation or that the genetics of cannabis/cocaine addiction are more elusive. This review brings a global state-of-the-art vision of the behavioral genetics of addiction and collaborates on formulation of new hypothesis to guide future work.
Collapse
Affiliation(s)
- Kora-Mareen Bühler
- Department of Psychobiology; School of Psychology; Complutense University of Madrid; Málaga Spain
| | - Elena Giné
- Department of Cellular Biology; School of Medicine; Complutense University of Madrid; Málaga Spain
| | - Victor Echeverry-Alzate
- Department of Psychobiology; School of Psychology; Complutense University of Madrid; Málaga Spain
| | - Javier Calleja-Conde
- Department of Psychobiology; School of Psychology; Complutense University of Madrid; Málaga Spain
| | | | | |
Collapse
|
28
|
Lyon KF, Strong CL, Schooler SG, Young RJ, Roy N, Ozar B, Bachmeier M, Rajasekaran S, Schiller MR. Natural variability of minimotifs in 1092 people indicates that minimotifs are targets of evolution. Nucleic Acids Res 2015; 43:6399-412. [PMID: 26068475 PMCID: PMC4513861 DOI: 10.1093/nar/gkv580] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 04/17/2015] [Accepted: 05/21/2015] [Indexed: 01/05/2023] Open
Abstract
Since the function of a short contiguous peptide minimotif can be introduced or eliminated by a single point mutation, these functional elements may be a source of human variation and a target of selection. We analyzed the variability of ∼300 000 minimotifs in 1092 human genomes from the 1000 Genomes Project. Most minimotifs have been purified by selection, with a 94% invariance, which supports important functional roles for minimotifs. Minimotifs are generally under negative selection, possessing high genomic evolutionary rate profiling (GERP) and sitewise likelihood-ratio (SLR) scores. Some are subject to neutral drift or positive selection, similar to coding regions. Most SNPs in minimotif were common variants, but with minor allele frequencies generally <10%. This was supported by low substation rates and few newly derived minimotifs. Several minimotif alleles showed different intercontinental and regional geographic distributions, strongly suggesting a role for minimotifs in adaptive evolution. We also note that 4% of PTM minimotif sites in histone tails were common variants, which has the potential to differentially affect DNA packaging among individuals. In conclusion, minimotifs are a source of functional genetic variation in the human population; thus, they are likely to be an important target of selection and evolution.
Collapse
Affiliation(s)
- Kenneth F Lyon
- Nevada Institute of Personalized Medicine and School of Life Sciences, University of Nevada Las Vegas, 4505 Maryland Parkway, Las Vegas, NV 89154-4004, USA
| | - Christy L Strong
- Nevada Institute of Personalized Medicine and School of Life Sciences, University of Nevada Las Vegas, 4505 Maryland Parkway, Las Vegas, NV 89154-4004, USA
| | - Steve G Schooler
- Nevada Institute of Personalized Medicine and School of Life Sciences, University of Nevada Las Vegas, 4505 Maryland Parkway, Las Vegas, NV 89154-4004, USA
| | - Richard J Young
- Nevada Institute of Personalized Medicine and School of Life Sciences, University of Nevada Las Vegas, 4505 Maryland Parkway, Las Vegas, NV 89154-4004, USA Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269-2155, USA
| | - Nervik Roy
- Nevada Institute of Personalized Medicine and School of Life Sciences, University of Nevada Las Vegas, 4505 Maryland Parkway, Las Vegas, NV 89154-4004, USA
| | - Brittany Ozar
- Nevada Institute of Personalized Medicine and School of Life Sciences, University of Nevada Las Vegas, 4505 Maryland Parkway, Las Vegas, NV 89154-4004, USA
| | - Mark Bachmeier
- Nevada Institute of Personalized Medicine and School of Life Sciences, University of Nevada Las Vegas, 4505 Maryland Parkway, Las Vegas, NV 89154-4004, USA
| | - Sanguthevar Rajasekaran
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269-2155, USA
| | - Martin R Schiller
- Nevada Institute of Personalized Medicine and School of Life Sciences, University of Nevada Las Vegas, 4505 Maryland Parkway, Las Vegas, NV 89154-4004, USA
| |
Collapse
|
29
|
An J, Zhao J, Zhang X, Ding R, Geng T, Feng T, Jin T. Impact of multiple Alcohol Dehydrogenase gene polymorphisms on risk of laryngeal, esophageal, gastric and colorectal cancers in Chinese Han population. Am J Cancer Res 2015; 5:2508-2515. [PMID: 26396927 PMCID: PMC4568787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 07/01/2015] [Indexed: 06/05/2023] Open
Abstract
Alcohol intake is positively associated with the risk of upper aerodigestive tract (UADT) cancers; but its effect on gastric or colorectal cancer is controversial. Previous study had identified several single nucleotide polymorphisms (SNPs) of Alcohol Dehydrogenase (ADH) genes associated with UADT cancers in European and Japanese populations. We sought to determine if these SNPs associated with laryngeal, esophageal, gastric or colorectal cancer in Chinese population. We conducted a case-control study among 1577 cases and 1013 healthy controls from northwest China. Five SNPs associated with UADT cancers risk were selected from previous genome-wide association studies and genotyped using Sequenom Mass-ARRAY technology. Odds ratios and 95% confidence intervals (CIs) were calculated by unconditional logistic regression adjusting for age and gender. We identified that the minor alleles of rs1789924 and rs971074 were associated with decreased risk of laryngeal cancer (OR = 0.311; 95% CI = 0.161-0.602; P < 0.001) and esophagus cancer (OR = 0.711; 95% CI = 0.526-0.962; P = 0.027) in allelic model analysis, respectively. In the genetic model analysis, we found the "C/T" genotype of rs1789924 was associated with decreased laryngeal cancer risk in codominant model (P = 0.046) and overdominant model (P = 0.013); the "C/T-T/T" genotype of rs1789924 was associated with reduced risk of laryngeal cancer under dominant model (P = 0.013). Additionally, none of the SNPs was associated with gastric or colorectal cancer in our study. Our data shed new light on the association between ADH SNPs and respiratory and digestive tract cancers susceptibility in the Han Chinese population.
Collapse
Affiliation(s)
- Jiaze An
- Department of Hepatobiliary and Pancreaticosplenic Surgery, Xijing Hospital, The Fourth Military Medical UniversityXi’an 710032, Shaanxi, China
| | - Junsheng Zhao
- Department of Pain Medicine, No. 324 Hospital of PLAChongqing 404000, China
| | - Xiyang Zhang
- School of Life Sciences, Northwest UniversityXi’an 710069, Shaanxi, China
| | - Rui Ding
- Department of Hepatobiliary and Pancreaticosplenic Surgery, Xijing Hospital, The Fourth Military Medical UniversityXi’an 710032, Shaanxi, China
| | - Tingting Geng
- National Engineering Research Center for Miniaturized Detection SystemsXi’an 710069, China
| | - Tian Feng
- National Engineering Research Center for Miniaturized Detection SystemsXi’an 710069, China
| | - Tianbo Jin
- School of Life Sciences, Northwest UniversityXi’an 710069, Shaanxi, China
- National Engineering Research Center for Miniaturized Detection SystemsXi’an 710069, China
- Key Laboratory of High Altitude Environment and Genes Related to Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu UniversityXianyang 712082, Shaanxi, China
| |
Collapse
|
30
|
Norden-Krichmar TM, Gizer IR, Wilhelmsen KC, Schork NJ, Ehlers CL. Protective variant associated with alcohol dependence in a Mexican American cohort. BMC MEDICAL GENETICS 2014; 15:136. [PMID: 25527893 PMCID: PMC4337107 DOI: 10.1186/s12881-014-0136-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 12/08/2014] [Indexed: 01/11/2023]
Abstract
Background Mexican Americans, particularly those born in the United States, are at greater risk for alcohol associated morbidity and mortality. The present study sought to investigate whether specific genetic variants may be associated with alcohol use disorder phenotypes in a select population of Mexican American young adults. Methods The study evaluated a cohort of 427 (age 18 – 30 years) Mexican American men (n = 171) and women (n = 256). Information on alcohol dependence was obtained through interview using the Semi-Structured Assessment for the Genetics of Alcoholism (SSAGA). For all subjects, DNA was extracted from blood samples, followed by genotyping using an Affymetrix Axiom Exome1A chip. Results A protective variant (rs991316) located downstream from the ADH7 (alcohol dehydrogenase 7) gene showed suggestive significance in association with alcohol dependence symptom counts derived from DSM-III-R and DSM-IV criteria, as well as to clustered alcohol dependence symptoms. Additional linkage analysis suggested that nearby variants in linkage disequilibrium with rs991316 were not responsible for the observed association with the alcohol dependence phenotypes in this study. Conclusions ADH7 has been shown to have a protective role against alcohol dependence in previous studies involving other ethnicities, but has not been reported for Mexican Americans. These results suggest that variants near ADH7 may play a role in protection from alcohol dependence in this Mexican American cohort.
Collapse
|
31
|
Brinkworth JF, Barreiro LB. The contribution of natural selection to present-day susceptibility to chronic inflammatory and autoimmune disease. Curr Opin Immunol 2014; 31:66-78. [PMID: 25458997 DOI: 10.1016/j.coi.2014.09.008] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 09/08/2014] [Accepted: 09/29/2014] [Indexed: 12/20/2022]
Abstract
Chronic inflammatory and autoimmune diseases have been the focus of many genome-wide association studies (GWAS) because they represent a significant cause of illness and morbidity, and many are heritable. Almost a decade of GWAS studies suggests that the pathological inflammation associated with these diseases is controlled by a limited number of networked immune system genes. Chronic inflammatory and autoimmune diseases are enigmatic from an evolutionary perspective because they exert a negative affect on reproductive fitness. The persistence of these conditions may be partially explained by the important roles the implicated immune genes play in pathogen defense and other functions thought to be under strong natural selection in humans. The evolutionary reasons for chronic inflammatory and autoimmune disease persistence and uneven distribution across populations are the focus of this review.
Collapse
Affiliation(s)
- Jessica F Brinkworth
- Sainte-Justine Hospital Research Centre, Montréal, Quebec H3T 1C5, Canada; Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal, Quebec H3T 1J4, Canada
| | - Luis B Barreiro
- Sainte-Justine Hospital Research Centre, Montréal, Quebec H3T 1C5, Canada; Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal, Quebec H3T 1J4, Canada.
| |
Collapse
|
32
|
Extended genetic effects of ADH cluster genes on the risk of alcohol dependence: from GWAS to replication. Hum Genet 2013; 132:657-68. [PMID: 23456092 DOI: 10.1007/s00439-013-1281-8] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 02/19/2013] [Indexed: 10/27/2022]
Abstract
Alcohol dependence (AD) is a multifactorial and polygenic disorder involving complex gene-to-gene and gene-to-environment interactions. Several genome-wide association studies have reported numerous risk factors for AD, but replication results following these studies have been controversial. To identify new candidate genes, the present study used GWAS and replication studies in a Korean cohort with AD. Genome-wide association analysis revealed that two chromosome regions on Chr. 4q22-q23 (ADH gene cluster, including ADH5, ADH4, ADH6, ADH1A, ADH1B, and ADH7) and Chr. 12q24 (ALDH2) showed multiple association signals for the risk of AD. To investigate detailed genetic effects of these ADH genes on AD, a follow-up study of the ADH gene cluster on 4q22-q23 was performed. A total of 90 SNPs, including ADH1B rs1229984 (H47R), were genotyped in an additional 975 Korean subjects. In case-control analysis, ADH1B rs1229984 (H47R) showed the most significant association with the risk of AD (p = 2.63 × 10(-21), OR = 2.35). Moreover, subsequent conditional analyses revealed that all positive associations of other ADH genes in the cluster disappeared, which suggested that ADH1B rs1229984 (H47R) might be the sole functional genetic marker across the ADH gene cluster. Our findings could provide additional information on the ADH gene cluster regarding the risk of AD, as well as a new and important insight into the genetic factors associated with AD.
Collapse
|
33
|
Muñoz X, Amiano P, Celorrio D, Dorronsoro M, Sánchez MJ, Huerta JM, Barricarte A, Arriola L, Navarro C, Molina-Montes E, Chirlaque MD, Ardanaz E, Rodriguez L, Duell EJ, Hijona E, Herreros-Villanueva M, Sala N, Bujanda L. Association of alcohol dehydrogenase polymorphisms and life-style factors with excessive alcohol intake within the Spanish population (EPIC-Spain). Addiction 2012; 107:2117-27. [PMID: 22690706 DOI: 10.1111/j.1360-0443.2012.03970.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Revised: 03/20/2012] [Accepted: 05/29/2012] [Indexed: 01/10/2023]
Abstract
AIMS To analyse associations between alcohol dehydrogenase (ADH) polymorphisms and alcohol intake in Spanish men and women. DESIGN AND SETTINGS We analysed the relationship between 21 genetic variants in ADH genes and excessive alcohol intake in both men and women. Single nucleotide polymorphisms (SNPs) were genotyped using a customized array and a sex-stratified analysis was performed. MEASUREMENTS Ethanol intake was calculated using a validated dietary history questionnaire. PARTICIPANTS Heavy consumers of alcohol (≥70 g/day in men, ≥42 g/day in women) (653 cases) and very low or non-consumers (<2 g/day) (880 controls) from the Spanish cohort of the European Prospective Investigation into Cancer (EPIC). FINDINGS We found statistically significant associations between alcohol intake and known life-style factors; namely, smoking and food energy intake (meat and fruit/seeds) in both men and women, as well as with physical activity in women and educational level in men. Additionally, we found that a non-synonymous coding SNP in ADH1B (rs1229984) is associated inversely with excessive alcohol intake in men [odds ratio (OR) = 0.19, 95% confidence interval (CI) = 0.11-0.33; P = 4.77E(-10) ) and women (OR = 0.48, 95% CI = 0.27-0.83; P = 0.0067). Furthermore, ADH6 rs3857224 was found associated with heavy alcohol intake in women (OR = 1.61, 95% CI = 1.21-2.14; P = 1.01E(-3) ), but not in men. CONCLUSIONS In the Spanish population, the single nucleotide polymorphism of alcohol dehydrogenase ADH1B, rs1229984, is associated inversely with alcohol intake in both men and women. Another polymorphism of ADH6, rs3857224, is associated with heavy alcohol intake in women.
Collapse
Affiliation(s)
- Xavier Muñoz
- Molecular Epidemiology Group, Translational Research Laboratory, Catalan Institute of Oncology (ICO-IDIBELL), Barcelona, Spain
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
34
|
Lu Y, Kang L, Hu K, Wang C, Sun X, Chen F, Kidd JR, Kidd KK, Li H. High diversity and no significant selection signal of human ADH1B gene in Tibet. INVESTIGATIVE GENETICS 2012; 3:23. [PMID: 23176670 PMCID: PMC3528464 DOI: 10.1186/2041-2223-3-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 11/14/2012] [Indexed: 01/09/2023]
Abstract
UNLABELLED BACKGROUND ADH1B is one of the most studied human genes with many polymorphic sites. One of the single nucleotide polymorphism (SNP), rs1229984, coding for the Arg48His substitution, have been associated with many serious diseases including alcoholism and cancers of the digestive system. The derived allele, ADH1B*48His, reaches high frequency only in East Asia and Southwest Asia, and is highly associated with agriculture. Micro-evolutionary study has defined seven haplogroups for ADH1B based on seven SNPs encompassing the gene. Three of those haplogroups, H5, H6, and H7, contain the ADH1B*48His allele. H5 occurs in Southwest Asia and the other two are found in East Asia. H7 is derived from H6 by the derived allele of rs3811801. The H7 haplotype has been shown to have undergone significant positive selection in Han Chinese, Hmong, Koreans, Japanese, Khazak, Mongols, and so on. METHODS In the present study, we tested whether Tibetans also showed evidence for selection by typing 23 SNPs in the region covering the ADH1B gene in 1,175 individuals from 12 Tibetan populations representing all districts of the Tibet Autonomous Region. Multiple statistics were estimated to examine the gene diversities and positive selection signals among the Tibetans and other populations in East Asia. RESULTS The larger Tibetan populations (Qamdo, Lhasa, Nagqu, Nyingchi, Shannan, and Shigatse) comprised mostly farmers, have around 12% of H7, and 2% of H6. The smaller populations, living on hunting or recently switched to farming, have lower H7 frequencies (Tingri 9%, Gongbo 8%, Monba and Sherpa 6%). Luoba (2%) and Deng (0%) have even lower frequencies. Long-range haplotype analyses revealed very weak signals of positive selection for H7 among Tibetans. Interestingly, the haplotype diversity of H7 is higher in Tibetans than in any other populations studied, indicating a longer diversification history for that haplogroup in Tibetans. Network analysis on the long-range haplotypes revealed that H7 in the Han Chinese did not come from the Tibetans but from a common ancestor of the two populations. CONCLUSIONS We argue that H7 of ADH1B originated in the ancestors of Sino-Tibetan populations and flowed to Tibetans very early. However, as Tibetans depend less on crops, and therefore were not significantly affected by selection. Thus, H7 has not risen to a high frequency, whereas the diversity of the haplogroup has accumulated to a very high level.
Collapse
Affiliation(s)
- Yan Lu
- State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Longli Kang
- State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
- Tibet University for Nationalities, Xianyang, Shaanxi, China
| | - Kang Hu
- Tibet University for Nationalities, Xianyang, Shaanxi, China
| | - Chuanchao Wang
- State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Xiaoji Sun
- State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Feng Chen
- Tibet University for Nationalities, Xianyang, Shaanxi, China
| | - Judith R Kidd
- Department of Genetics, School of Medicine, Yale University, New Haven, CT, USA
| | - Kenneth K Kidd
- Department of Genetics, School of Medicine, Yale University, New Haven, CT, USA
| | - Hui Li
- State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
- Tibet University for Nationalities, Xianyang, Shaanxi, China
- Department of Genetics, School of Medicine, Yale University, New Haven, CT, USA
| |
Collapse
|
35
|
Abstract
We propose that haplotyped loci with high heterozygosity can be useful in human identification, especially within families, if recombination is very low among the sites. Three or more SNPs extending over small molecular intervals (<10 KB) can be identified in the human genome to define miniature haplotypes with moderate levels of linkage disequilibrium. Properly selected, these mini-haplotypes (or minihaps) consist of multiple haplotype lineages (alleles) that have evolved from the ancestral human haplotype but show no evidence of recurring recombination, allowing each distinct haplotype to be equated with an allele, all copies of which are essentially identical by descent. Historic recombinants, representing rare events that have drifted to common frequencies over many generations, can be identified in some cases, they do not equate to frequently recurring recombination. We have identified examples in our data collected on various projects and present eight such mini-haplotypes comprised of informative SNPs. We also discuss the ideal characteristics and advantages of minihaps for human familial identification and ancestry inference, and compare them to other types of forensic markers in use and/or that have been proposed. We expect that it is possible to carry out a systematic search and identify a useful panel of mini-haplotypes, with even better properties than the examples presented here.
Collapse
|
36
|
Agrawal A, Freedman ND, Cheng YC, Lin P, Shaffer JR, Sun Q, Taylor K, Yaspan B, Cole JW, Cornelis MC, DeSensi RS, Fitzpatrick A, Heiss G, Kang JH, O'Connell J, Bennett S, Bookman E, Bucholz KK, Caporaso N, Crout R, Dick DM, Edenberg HJ, Goate A, Hesselbrock V, Kittner S, Kramer J, Nurnberger JI, Qi L, Rice JP, Schuckit M, van Dam RM, Boerwinkle E, Hu F, Levy S, Marazita M, Mitchell BD, Pasquale LR, Bierut LJ. Measuring alcohol consumption for genomic meta-analyses of alcohol intake: opportunities and challenges. Am J Clin Nutr 2012; 95:539-47. [PMID: 22301922 PMCID: PMC3278237 DOI: 10.3945/ajcn.111.015545] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Accepted: 12/21/2011] [Indexed: 01/09/2023] Open
Abstract
Whereas moderate drinking may have health benefits, excessive alcohol consumption causes many important acute and chronic diseases and is the third leading contributor to preventable death in the United States. Twin studies suggest that alcohol-consumption patterns are heritable (50%); however, multiple genetic variants of modest effect size are likely to contribute to this heritable variation. Genome-wide association studies provide a tool for discovering genetic loci that contribute to variations in alcohol consumption. Opportunities exist to identify susceptibility loci with modest effect by meta-analyzing together multiple studies. However, existing studies assessed many different aspects of alcohol use, such as typical compared with heavy drinking, and these different assessments can be difficult to reconcile. In addition, many studies lack the ability to distinguish between lifetime and recent abstention or to assess the pattern of drinking during the week, and a variety of such concerns surround the appropriateness of developing a common summary measure of alcohol intake. Combining such measures of alcohol intake can cause heterogeneity and exposure misclassification, cause a reduction in power, and affect the magnitude of genetic association signals. In this review, we discuss the challenges associated with harmonizing alcohol-consumption data from studies with widely different assessment instruments, with a particular focus on large-scale genetic studies.
Collapse
Affiliation(s)
- Arpana Agrawal
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO 63110, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Nakagome S, Mano S, Kozlowski L, Bujnicki JM, Shibata H, Fukumaki Y, Kidd JR, Kidd KK, Kawamura S, Oota H. Crohn's disease risk alleles on the NOD2 locus have been maintained by natural selection on standing variation. Mol Biol Evol 2012; 29:1569-85. [PMID: 22319155 DOI: 10.1093/molbev/mss006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Risk alleles for complex diseases are widely spread throughout human populations. However, little is known about the geographic distribution and frequencies of risk alleles, which may contribute to differences in disease susceptibility and prevalence among populations. Here, we focus on Crohn's disease (CD) as a model for the evolutionary study of complex disease alleles. Recent genome-wide association studies and classical linkage analyses have identified more than 70 susceptible genomic regions for CD in Europeans, but only a few have been confirmed in non-European populations. Our analysis of eight European-specific susceptibility genes using HapMap data shows that at the NOD2 locus the CD-risk alleles are linked with a haplotype specific to CEU at a frequency that is significantly higher compared with the entire genome. We subsequently examined nine global populations and found that the CD-risk alleles spread through hitchhiking with a high-frequency haplotype (H1) exclusive to Europeans. To examine the neutrality of NOD2, we performed phylogenetic network analyses, coalescent simulation, protein structural prediction, characterization of mutation patterns, and estimations of population growth and time to most recent common ancestor (TMRCA). We found that while H1 was significantly prevalent in European populations, the H1 TMRCA predated human migration out of Africa. H1 is likely to have undergone negative selection because 1) the root of H1 genealogy is defined by a preexisting amino acid substitution that causes serious conformational changes to the NOD2 protein, 2) the haplotype has almost become extinct in Africa, and 3) the haplotype has not been affected by the recent European expansion reflected in the other haplotypes. Nevertheless, H1 has survived in European populations, suggesting that the haplotype is advantageous to this group. We propose that several CD-risk alleles, which destabilize and disrupt the NOD2 protein, have been maintained by natural selection on standing variation because the deleterious haplotype of NOD2 is advantageous in diploid individuals due to heterozygote advantage and/or intergenic interactions.
Collapse
Affiliation(s)
- Shigeki Nakagome
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwanoha, Kashiwa, Chiba, Japan
| | | | | | | | | | | | | | | | | | | |
Collapse
|
38
|
Somel M, Tang L, Khaitovich P. The Role of Neoteny in Human Evolution: From Genes to the Phenotype. POST-GENOME BIOLOGY OF PRIMATES 2012. [DOI: 10.1007/978-4-431-54011-3_3] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
39
|
Agrawal A. Identifying genetic variation for alcohol dependence. Alcohol Res 2012; 34:274-81. [PMID: 23134043 PMCID: PMC3662475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Researchers are using various strategies to identify the genes that may be associated with alcoholism. The initial efforts primarily relied on candidate gene and linkage studies; more recently, however, modern advances in genotyping have resulted in widespread use of genome-wide association studies for alcohol dependence. The key findings of the earlier studies were that variations (i.e., polymorphisms) in the DNA sequences of the genes encoding alcohol dehydrogenase 1B (i.e., the ADH1B gene), aldehyde dehydrogenase 2 (i.e., the ALDH2 gene), and other alcohol-metabolizing enzymes mediate the risk for alcoholism; moreover, these polymorphisms also have an impact on the risk of alcohol-related cancers, such as esophageal cancer. In addition, a gene encoding one of the receptors for the neurotransmitter γ-aminobutyric acid (GABA) known as GABRA2 seems to have a role in the development of alcohol dependence. Genome-wide association studies now offer a host of emerging opportunities, as well as challenges, for discovering the genetic etiology of alcohol dependence and for unveiling new treatment strategies.
Collapse
|
40
|
Lai CQ. Adaptive genetic variation and population differences. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2012; 108:461-89. [PMID: 22656388 DOI: 10.1016/b978-0-12-398397-8.00018-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Since the expansion of modern humans (Homo sapiens) from Africa to the rest of the world between 50,000 and 100,000 years ago, the human genome has been shaped not only by demographic history but also by adaptation to local environments, including regional climate, landscape, food sources, culture, and pathogens. Genetic differences among populations interact with environmental factors, such as diet and lifestyle, leading to differences in nutrient metabolism, which translate into differences in susceptibility to a variety of diseases. Individuals from different populations sharing the same environments can exhibit differences in disease risk, as do individuals from the same population living in various regions of the globe. Therefore, it is important to understand how adaptive genetic variations interact with environments to influence health. This knowledge will provide a broad foundation for designing experiments and approaches in nutrigenomics research and strengthening the knowledge base for dietary recommendations for disease prevention. The objectives of this chapter are to (1) understand the methodology employed in examining adaptive genetic variation across populations, (2) establish the importance of adaptive genetic variation to human health, and (3) discuss the implications for nutrigenomics research and disease prevention.
Collapse
Affiliation(s)
- Chao-Qiang Lai
- Nutrition and Genomics Laboratory, Jean Meyer USDA Human Nutrition Research Center on Aging, Tufts University, Boston, Massachusetts, USA
| |
Collapse
|
41
|
Abstract
Mutations in the gene OCA2 are responsible for oculocutaneous albinism type 2, but polymorphisms in and around OCA2 have also been associated with normal pigment variation. In Europeans, three haplotypes in the region have been shown to be associated with eye pigmentation and a missense SNP (rs1800407) has been associated with green/hazel eyes (Branicki et al. in Ann Hum Genet 73:160–170, 2009). In addition, a missense mutation (rs1800414) is a candidate for light skin pigmentation in East Asia (Yuasa et al. in Biochem Genet 45:535–542, 2007; Anno et al. in Int J Biol Sci 4, 2008). We have genotyped 3,432 individuals from 72 populations for 21 SNPs in the OCA2-HERC2 region including those previously associated with eye or skin pigmentation. We report that the blue-eye associated alleles at all three haplotypes were found at high frequencies in Europe; however, one is restricted to Europe and surrounding regions, while the other two are found at moderate to high frequencies throughout the world. We also observed that the derived allele of rs1800414 is essentially limited to East Asia where it is found at high frequencies. Long-range haplotype tests provide evidence of selection for the blue-eye allele at the three haplotyped systems but not for the green/hazel eye SNP allele. We also saw evidence of selection at the derived allele of rs1800414 in East Asia. Our data suggest that the haplotype restricted to Europe is the strongest marker for blue eyes globally and add further inferential evidence that the derived allele of rs1800414 is an East Asian skin pigmentation allele.
Collapse
|
42
|
Ye K, Gu Z. Recent advances in understanding the role of nutrition in human genome evolution. Adv Nutr 2011; 2:486-96. [PMID: 22332091 PMCID: PMC3226386 DOI: 10.3945/an.111.001024] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Dietary transitions in human history have been suggested to play important roles in the evolution of mankind. Genetic variations caused by adaptation to diet during human evolution could have important health consequences in current society. The advance of sequencing technologies and the rapid accumulation of genome information provide an unprecedented opportunity to comprehensively characterize genetic variations in human populations and unravel the genetic basis of human evolution. Series of selection detection methods, based on various theoretical models and exploiting different aspects of selection signatures, have been developed. Their applications at the species and population levels have respectively led to the identification of human specific selection events that distinguish human from nonhuman primates and local adaptation events that contribute to human diversity. Scrutiny of candidate genes has revealed paradigms of adaptations to specific nutritional components and genome-wide selection scans have verified the prevalence of diet-related selection events and provided many more candidates awaiting further investigation. Understanding the role of diet in human evolution is fundamental for the development of evidence-based, genome-informed nutritional practices in the era of personal genomics.
Collapse
Affiliation(s)
| | - Zhenglong Gu
- To whom correspondence should be addressed. E-mail:
| |
Collapse
|
43
|
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.
Collapse
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
| |
Collapse
|
44
|
Gizer IR, Edenberg HJ, Gilder DA, Wilhelmsen KC, Ehlers CL. Association of alcohol dehydrogenase genes with alcohol-related phenotypes in a Native American community sample. Alcohol Clin Exp Res 2011; 35:2008-18. [PMID: 21635275 DOI: 10.1111/j.1530-0277.2011.01552.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BACKGROUND Previous linkage studies, including a study of the Native American population described in the present report, have provided evidence for linkage of alcohol dependence and related traits to chromosome 4q near a cluster of alcohol dehydrogenase (ADH) genes, which encode enzymes of alcohol metabolism. METHODS The present study tested for associations between alcohol dependence and related traits and 22 single-nucleotide polymorphisms (SNPs) spanning the 7 ADH genes. Participants included 586 adult men and women recruited from 8 contiguous Native American reservations. A structured interview was used to assess DSM-III-R alcohol dependence criteria as well as a set of severe alcohol misuse symptoms and alcohol withdrawal symptoms. RESULTS No evidence for association with the alcohol dependence diagnosis was observed, but an SNP in exon 9 of ADH1B (rs2066702; ADH1B*3) and an SNP at the 5' end of ADH4 (rs3762894) showed significant evidence of association with the presence of withdrawal symptoms (p = 0.0018 and 0.0012, respectively). Further, a haplotype analysis of these 2 SNPs suggested that the haplotypes containing either of the minor alleles were protective against alcohol withdrawal relative to the ancestral haplotype (p = 0.000006). CONCLUSIONS These results suggest that variants in the ADH1B and ADH4 genes may be protective against the development of some symptoms associated with alcohol dependence.
Collapse
Affiliation(s)
- Ian R Gizer
- Department of Psychological Sciences, University of Missouri, Columbia, Missouri, USA
| | | | | | | | | |
Collapse
|
45
|
Celorrio D, Bujanda L, Chbel F, Sánchez D, Martinez-Jarreta B, de Pancorbo MM. Alcohol-metabolizing enzyme gene polymorphisms in the Basque Country, Morocco, and Ecuador. Alcohol Clin Exp Res 2011; 35:879-84. [PMID: 21303386 DOI: 10.1111/j.1530-0277.2010.01418.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND Genes ADH1B and ADH1C have certain functional SNPs that are related to alcoholism. The frequencies of these polymorphisms vary between populations, so studying them in populations made up of groups with different phylogeographic origins requires an individualized analysis of each group. In the Basque Country, various recently arrived foreign groups live side by side with the original Southern European population, particularly North Africans from Morocco and Hispanics from Ecuador. This study sets out to examine the distribution of the frequencies of alleles that encode alcohol dehydrogenase with different metabolization rates, as higher rates make for greater susceptibility to alcoholism. METHODS Four SNPs: rs1229984, rs2066702, rs698, and rs1693482 using Taqman technology with a Rt-PCR were studied in a sample of 114 European individuals originating from the Basque Country, 100 North Africans from Morocco, and 109 Hispanics from Ecuador. The allele and genotype frequencies were calculated using Genepop v4.0. The most frequent haplotypes were estimated using the ELB algorithm with Arlequin v3.01. A breakdown of the complete disequilibrium commonly observed between the 2 missense polymorphisms that distinguish the common ADH1C alleles rs698 and rs1693482 was observed and confirmed by sequencing in 2 individuals from the Basque Country. RESULTS A higher frequency of protective allele ADH1C*1 was found in the North African population group. Haplotype combinations are also studied, and the rare association of alleles ADH1B*2-ADH1C*2 was observed in the Southern European group in the Basque Country, along with an allele not hitherto described in the ADH1C locus. CONCLUSIONS This study provides the first data published on the allele and genotype frequencies of the ADH1C locus in the Moroccan population and on the ADH1B and ADH1C loci in the Ecuadorian population. The study shows differences in the distribution of the frequency of allele ADH1C*1 between the Basque Country and Moroccan populations, and a new allele not described to date.
Collapse
Affiliation(s)
- David Celorrio
- BIOMICs Research Group, Department of Z. and Cell Biology, DNA Bank, University of Basque Country, Spain
| | | | | | | | | | | |
Collapse
|
46
|
Shi H, Su B. Molecular adaptation of modern human populations. INTERNATIONAL JOURNAL OF EVOLUTIONARY BIOLOGY 2010; 2011:484769. [PMID: 21350631 PMCID: PMC3039432 DOI: 10.4061/2011/484769] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Accepted: 12/14/2010] [Indexed: 12/19/2022]
Abstract
Modern humans have gone through varied processes of genetic adaptations when their ancestors left Africa about 100,000 years ago. The environmental stresses and the social transitions (e.g., emergence of the Neolithic culture) have been acting as the major selective forces reshaping the genetic make-up of human populations. Genetic adaptations have occurred in many aspects of human life, including the adaptation to cold climate and high-altitude hypoxia, the improved ability of defending infectious diseases, and the polished strategy of utilizing new diet with the advent of agriculture. At the same time, the adaptations once developed during evolution may sometimes generate deleterious effects (e.g., susceptibility to diseases) when facing new environmental and social changes. The molecular (especially the genome-wide screening of genetic variations) studies in recent years have detected many genetic variants that show signals of Darwinian positive selection in modern human populations, which will not only provide a better understanding of human evolutionary history, but also help dissecting the genetic basis of human complex diseases.
Collapse
Affiliation(s)
- Hong Shi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology and Kunming Primate Research Centre, Chinese Academy of Sciences, Kunming 650223, China
| | | |
Collapse
|
47
|
Stearns SC, Byars SG, Govindaraju DR, Ewbank D. Measuring selection in contemporary human populations. Nat Rev Genet 2010; 11:611-22. [PMID: 20680024 DOI: 10.1038/nrg2831] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Are humans currently evolving? This question can be answered using data on lifetime reproductive success, multiple traits and genetic variation and covariation in those traits. Such data are available in existing long-term, multigeneration studies - both clinical and epidemiological - but they have not yet been widely used to address contemporary human evolution. Here we review methods to predict evolutionary change and attempts to measure selection and inheritance in humans. We also assemble examples of long-term studies in which additional measurements of evolution could be made. The evidence strongly suggests that we are evolving and that our nature is dynamic, not static.
Collapse
Affiliation(s)
- Stephen C Stearns
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520-8102, USA.
| | | | | | | |
Collapse
|
48
|
Laland KN, Odling-Smee J, Myles S. How culture shaped the human genome: bringing genetics and the human sciences together. Nat Rev Genet 2010; 11:137-48. [PMID: 20084086 DOI: 10.1038/nrg2734] [Citation(s) in RCA: 366] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Researchers from diverse backgrounds are converging on the view that human evolution has been shaped by gene-culture interactions. Theoretical biologists have used population genetic models to demonstrate that cultural processes can have a profound effect on human evolution, and anthropologists are investigating cultural practices that modify current selection. These findings are supported by recent analyses of human genetic variation, which reveal that hundreds of genes have been subject to recent positive selection, often in response to human activities. Here, we collate these data, highlighting the considerable potential for cross-disciplinary exchange to provide novel insights into how culture has shaped the human genome.
Collapse
Affiliation(s)
- Kevin N Laland
- School of Biology, University of St Andrews, Bute Building, Westburn Lane, St Andrews, Fife KY16 9TS, UK.
| | | | | |
Collapse
|
49
|
Mukherjee N, Kidd KK, Pakstis AJ, Speed WC, Li H, Tarnok Z, Barta C, Kajuna SLB, Kidd JR. The complex global pattern of genetic variation and linkage disequilibrium at catechol-O-methyltransferase. Mol Psychiatry 2010; 15:216-25. [PMID: 18574484 PMCID: PMC2811226 DOI: 10.1038/mp.2008.64] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genetic variation at the catechol-O-methyltransferase (COMT) gene has been significantly associated with risk for various neuropsychiatric conditions such as schizophrenia, panic disorder, bipolar disorders, anorexia nervosa and others. It has also been associated with nicotine dependence, sensitivity to pain and cognitive dysfunctions especially in schizophrenia. The non-synonymous single nucleotide polymorphism (SNP) in exon 4--Val108/158Met--is the most studied SNP at COMT and is the basis for most associations. It is not, however, the only variation in the gene; several haplotypes exist across the gene. Some studies indicate that the haplotypic combinations of alleles at the Val108/158Met SNP with those in the promoter region and in the 3'-untranslated region are responsible for the associations with disorders and not the non-synonymous SNP by itself. We have now studied DNA samples from 45 populations for 63 SNPs in a region of 172 kb across the region of 22q11.2 encompassing the COMT gene. We focused on 28 SNPs spanning the COMT-coding region and immediately flanking DNA, and found that the haplotypes are from diverse evolutionary lineages that could harbor as yet undetected variants with functional consequences. Future association studies should be based on SNPs that define the common haplotypes in the population(s) being studied.
Collapse
Affiliation(s)
- N Mukherjee
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA - 06511
| | - KK Kidd
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA - 06511
| | - AJ Pakstis
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA - 06511
| | - WC Speed
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA - 06511
| | - H Li
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA - 06511
| | - Z Tarnok
- Vadaskert Child and Adolescent Psychiatric clinic, Budapest, Hungary
| | - C Barta
- Institute of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest,Hungary
| | - SLB Kajuna
- Hubert Kairuki Memorial University, Dar es Salaam, Tanzania
| | - JR Kidd
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA - 06511,Correspondence to: Judith Kidd. Ph.D Department of Genetics, Yale University School of Medicine, P.O. Box 208005, 333 Cedar Street, New Haven, CT-06520-8005. E-mail:
| |
Collapse
|
50
|
Peng Y, Shi H, Qi XB, Xiao CJ, Zhong H, Ma RLZ, Su B. The ADH1B Arg47His polymorphism in east Asian populations and expansion of rice domestication in history. BMC Evol Biol 2010; 10:15. [PMID: 20089146 PMCID: PMC2823730 DOI: 10.1186/1471-2148-10-15] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2009] [Accepted: 01/20/2010] [Indexed: 11/25/2022] Open
Abstract
Background The emergence of agriculture about 10,000 years ago marks a dramatic change in human evolutionary history. The diet shift in agriculture societies might have a great impact on the genetic makeup of Neolithic human populations. The regionally restricted enrichment of the class I alcohol dehydrogenase sequence polymorphism (ADH1BArg47His) in southern China and the adjacent areas suggests Darwinian positive selection on this genetic locus during Neolithic time though the driving force is yet to be disclosed. Results We studied a total of 38 populations (2,275 individuals) including Han Chinese, Tibetan and other ethnic populations across China. The geographic distribution of the ADH1B*47His allele in these populations indicates a clear east-to-west cline, and it is dominant in south-eastern populations but rare in Tibetan populations. The molecular dating suggests that the emergence of the ADH1B*47His allele occurred about 10,000~7,000 years ago. Conclusion We present genetic evidence of selection on the ADH1BArg47His polymorphism caused by the emergence and expansion of rice domestication in East Asia. The geographic distribution of the ADH1B*47His allele in East Asia is consistent with the unearthed culture relic sites of rice domestication in China. The estimated origin time of ADH1B*47His allele in those populations coincides with the time of origin and expansion of Neolithic agriculture in southern China.
Collapse
Affiliation(s)
- Yi Peng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology and Kunming Primate Research Centre, Chinese Academy of Sciences, Kunming, China
| | | | | | | | | | | | | |
Collapse
|