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Bhak Y, Tenesa A. Mendelian randomization study of whole blood viscosity and cardiovascular diseases. PLoS One 2024; 19:e0294095. [PMID: 38669241 PMCID: PMC11051600 DOI: 10.1371/journal.pone.0294095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 02/04/2024] [Indexed: 04/28/2024] Open
Abstract
AIMS Association between whole blood viscosity (WBV) and an increased risk of cardiovascular disease (CVD) has been reported. However, the causal relationship between WBV and CVD remains not thoroughly investigated. The aim of this study was to investigate the causal relation between WBV and CVD. METHODS Two-sample Mendelian randomization (MR) was employed, with inverse variance weighting (IVW) as the primary method, to investigate the casual relationship between WBV and CVD. The calculated WBV and medical records of 378,210 individuals participating in the UK Biobank study were divided into halves and analyzed. RESULTS The means of calculated WBVs were 16.9 (standard deviation: 0.8) and 55.1 (standard deviation: 17.2) for high shear rate (HSR) and low shear rate (LSR), respectively. 37,859 (10.0%) major cardiovascular events (MACE) consisted of 23,894 (6.3%) cases of myocardial infarction (MI), 9,245 (2.4%) cases of ischemic stroke, 10,377 (2.7%) cases of revascularization, and 5,703 (1.5%) cases of coronary heart disease-related death. In the MR analysis, no evidence was found indicating a causal effect of WBV on MACE (IVW p-value for HSR = 0.81, IVW p-value for LSR = 0.47), MI (0.92, 0.83), ischemic stroke (0.52, 0.74), revascularization (0.71, 0.54), and coronary heart disease-related death (0.83, 0.70). The lack of sufficient evidence for causality persisted in other MR methods, including weighted median and MR-egger. CONCLUSIONS The Mendelian randomization analysis conducted in this study does not support a causal relationship between calculated WBV and CVD.
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Affiliation(s)
- Youngjune Bhak
- MRC Human Genetics Unit at the MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Albert Tenesa
- MRC Human Genetics Unit at the MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
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2
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Teng J, Gao Y, Yin H, Bai Z, Liu S, Zeng H, Bai L, Cai Z, Zhao B, Li X, Xu Z, Lin Q, Pan Z, Yang W, Yu X, Guan D, Hou Y, Keel BN, Rohrer GA, Lindholm-Perry AK, Oliver WT, Ballester M, Crespo-Piazuelo D, Quintanilla R, Canela-Xandri O, Rawlik K, Xia C, Yao Y, Zhao Q, Yao W, Yang L, Li H, Zhang H, Liao W, Chen T, Karlskov-Mortensen P, Fredholm M, Amills M, Clop A, Giuffra E, Wu J, Cai X, Diao S, Pan X, Wei C, Li J, Cheng H, Wang S, Su G, Sahana G, Lund MS, Dekkers JCM, Kramer L, Tuggle CK, Corbett R, Groenen MAM, Madsen O, Gòdia M, Rocha D, Charles M, Li CJ, Pausch H, Hu X, Frantz L, Luo Y, Lin L, Zhou Z, Zhang Z, Chen Z, Cui L, Xiang R, Shen X, Li P, Huang R, Tang G, Li M, Zhao Y, Yi G, Tang Z, Jiang J, Zhao F, Yuan X, Liu X, Chen Y, Xu X, Zhao S, Zhao P, Haley C, Zhou H, Wang Q, Pan Y, Ding X, Ma L, Li J, Navarro P, Zhang Q, Li B, Tenesa A, Li K, Liu GE, Zhang Z, Fang L. A compendium of genetic regulatory effects across pig tissues. Nat Genet 2024; 56:112-123. [PMID: 38177344 PMCID: PMC10786720 DOI: 10.1038/s41588-023-01585-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 10/13/2023] [Indexed: 01/06/2024]
Abstract
The Farm Animal Genotype-Tissue Expression (FarmGTEx) project has been established to develop a public resource of genetic regulatory variants in livestock, which is essential for linking genetic polymorphisms to variation in phenotypes, helping fundamental biological discovery and exploitation in animal breeding and human biomedicine. Here we show results from the pilot phase of PigGTEx by processing 5,457 RNA-sequencing and 1,602 whole-genome sequencing samples passing quality control from pigs. We build a pig genotype imputation panel and associate millions of genetic variants with five types of transcriptomic phenotypes in 34 tissues. We evaluate tissue specificity of regulatory effects and elucidate molecular mechanisms of their action using multi-omics data. Leveraging this resource, we decipher regulatory mechanisms underlying 207 pig complex phenotypes and demonstrate the similarity of pigs to humans in gene expression and the genetic regulation behind complex phenotypes, supporting the importance of pigs as a human biomedical model.
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Affiliation(s)
- Jinyan Teng
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University (SCAU), Guangzhou, China
| | - Yahui Gao
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University (SCAU), Guangzhou, China
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service (ARS), U.S. Department of Agriculture (USDA), Beltsville, MD, USA
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, USA
| | - Hongwei Yin
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhonghao Bai
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark
- MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Shuli Liu
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service (ARS), U.S. Department of Agriculture (USDA), Beltsville, MD, USA
- School of Life Sciences, Westlake University, Hangzhou, China
| | - Haonan Zeng
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University (SCAU), Guangzhou, China
| | - Lijing Bai
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zexi Cai
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark
| | - Bingru Zhao
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xiujin Li
- Guangdong Provincial Key Laboratory of Waterfowl Healthy Breeding, College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Zhiting Xu
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University (SCAU), Guangzhou, China
| | - Qing Lin
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University (SCAU), Guangzhou, China
| | - Zhangyuan Pan
- Department of Animal Science, University of California, Davis, Davis, CA, USA
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wenjing Yang
- College of Animal Science and Technology, China Agricultural University, Beijing, China
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | - Xiaoshan Yu
- MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Dailu Guan
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | - Yali Hou
- Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | - Brittney N Keel
- ARS, USDA, U.S. Meat Animal Research Center, Clay Center, NE, USA
| | - Gary A Rohrer
- ARS, USDA, U.S. Meat Animal Research Center, Clay Center, NE, USA
| | | | - William T Oliver
- ARS, USDA, U.S. Meat Animal Research Center, Clay Center, NE, USA
| | - Maria Ballester
- Animal Breeding and Genetics Programme, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Torre Marimon, Caldes de Montbui, Spain
| | - Daniel Crespo-Piazuelo
- Animal Breeding and Genetics Programme, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Torre Marimon, Caldes de Montbui, Spain
| | - Raquel Quintanilla
- Animal Breeding and Genetics Programme, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Torre Marimon, Caldes de Montbui, Spain
| | - Oriol Canela-Xandri
- MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Konrad Rawlik
- Baillie Gifford Pandemic Science Hub, University of Edinburgh, Edinburgh, UK
| | - Charley Xia
- Lothian Birth Cohort studies, University of Edinburgh, Edinburgh, UK
- Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Yuelin Yao
- MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
- School of Informatics, The University of Edinburgh, Edinburgh, UK
| | - Qianyi Zhao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Wenye Yao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands
| | - Liu Yang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Houcheng Li
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark
| | - Huicong Zhang
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark
| | - Wang Liao
- MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Tianshuo Chen
- MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Peter Karlskov-Mortensen
- Animal Genetics, Bioinformatics and Breeding, Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Merete Fredholm
- Animal Genetics, Bioinformatics and Breeding, Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Marcel Amills
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Spain
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Alex Clop
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Spain
- Consejo Superior de Investigaciones Científicas, Barcelona, Spain
| | - Elisabetta Giuffra
- Paris-Saclay University, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Jun Wu
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University (SCAU), Guangzhou, China
| | - Xiaodian Cai
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University (SCAU), Guangzhou, China
| | - Shuqi Diao
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University (SCAU), Guangzhou, China
| | - Xiangchun Pan
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University (SCAU), Guangzhou, China
| | - Chen Wei
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University (SCAU), Guangzhou, China
| | - Jinghui Li
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | - Hao Cheng
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | - Sheng Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Guosheng Su
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark
| | - Goutam Sahana
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark
| | - Mogens Sandø Lund
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark
| | - Jack C M Dekkers
- Department of Animal Science, Iowa State University, Ames, IA, USA
| | - Luke Kramer
- Department of Animal Science, Iowa State University, Ames, IA, USA
| | | | - Ryan Corbett
- Department of Animal Science, Iowa State University, Ames, IA, USA
| | - Martien A M Groenen
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands
| | - Ole Madsen
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands
| | - Marta Gòdia
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Dominique Rocha
- Paris-Saclay University, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Mathieu Charles
- Paris-Saclay University, INRAE, AgroParisTech, GABI, SIGENAE, Jouy-en-Josas, France
| | - Cong-Jun Li
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service (ARS), U.S. Department of Agriculture (USDA), Beltsville, MD, USA
| | - Hubert Pausch
- Animal Genomics, ETH Zurich, Universitaetstrasse 2, Zurich, Switzerland
| | - Xiaoxiang Hu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Laurent Frantz
- Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Yonglun Luo
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Research, Qingdao, China
| | - Lin Lin
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark
| | - Zhongyin Zhou
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Zhe Zhang
- Department of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Zitao Chen
- Department of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Leilei Cui
- School of Life Sciences, Nanchang University, Nanchang, China
- Human Aging Research Institute and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Jiangxi, China
- UCL Genetics Institute, University College London, London, UK
| | - Ruidong Xiang
- Faculty of Veterinary and Agricultural Science, The University of Melbourne, Parkville, Victoria, Australia
- Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, Victoria, Australia
| | - Xia Shen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Center for Intelligent Medicine Research, Greater Bay Area Institute of Precision Medicine, Fudan University, Guangzhou, China
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Pinghua Li
- Institute of Swine Science, Nanjing Agricultural University, Nanjing, China
| | - Ruihua Huang
- Institute of Swine Science, Nanjing Agricultural University, Nanjing, China
| | - Guoqing Tang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Mingzhou Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yunxiang Zhao
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Guoqiang Yi
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhonglin Tang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jicai Jiang
- Department of Animal Science, North Carolina State University, Raleigh, NC, USA
| | - Fuping Zhao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaolong Yuan
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University (SCAU), Guangzhou, China
| | - Xiaohong Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yaosheng Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xuewen Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Pengju Zhao
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, China
| | - Chris Haley
- MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK
| | - Huaijun Zhou
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | - Qishan Wang
- Department of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Yuchun Pan
- Department of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Xiangdong Ding
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Li Ma
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, USA
| | - Jiaqi Li
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University (SCAU), Guangzhou, China
| | - Pau Navarro
- MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK
| | - Qin Zhang
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an, China
| | - Bingjie Li
- Scotland's Rural College (SRUC), Roslin Institute Building, Midlothian, UK
| | - Albert Tenesa
- MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK.
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK.
| | - Kui Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service (ARS), U.S. Department of Agriculture (USDA), Beltsville, MD, USA.
| | - Zhe Zhang
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University (SCAU), Guangzhou, China.
| | - Lingzhao Fang
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark.
- MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK.
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Xiang R, Fang L, Liu S, Macleod IM, Liu Z, Breen EJ, Gao Y, Liu GE, Tenesa A, Mason BA, Chamberlain AJ, Wray NR, Goddard ME. Gene expression and RNA splicing explain large proportions of the heritability for complex traits in cattle. Cell Genom 2023; 3:100385. [PMID: 37868035 PMCID: PMC10589627 DOI: 10.1016/j.xgen.2023.100385] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 08/10/2022] [Accepted: 07/26/2023] [Indexed: 10/24/2023]
Abstract
Many quantitative trait loci (QTLs) are in non-coding regions. Therefore, QTLs are assumed to affect gene regulation. Gene expression and RNA splicing are primary steps of transcription, so DNA variants changing gene expression (eVariants) or RNA splicing (sVariants) are expected to significantly affect phenotypes. We quantify the contribution of eVariants and sVariants detected from 16 tissues (n = 4,725) to 37 traits of ∼120,000 cattle (average magnitude of genetic correlation between traits = 0.13). Analyzed in Bayesian mixture models, averaged across 37 traits, cis and trans eVariants and sVariants detected from 16 tissues jointly explain 69.2% (SE = 0.5%) of heritability, 44% more than expected from the same number of random variants. This 69.2% includes an average of 24% from trans e-/sVariants (14% more than expected). Averaged across 56 lipidomic traits, multi-tissue cis and trans e-/sVariants also explain 71.5% (SE = 0.3%) of heritability, demonstrating the essential role of proximal and distal regulatory variants in shaping mammalian phenotypes.
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Affiliation(s)
- Ruidong Xiang
- Faculty of Veterinary & Agricultural Science, the University of Melbourne, Parkville, VIC 3052, Australia
- Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, VIC 3083, Australia
- Cambridge-Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC 3004, Australia
| | - Lingzhao Fang
- MRC Human Genetics Unit at the Institute of Genetics and Cancer, the University of Edinburgh, Edinburgh, UK
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark
| | - Shuli Liu
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China
| | - Iona M. Macleod
- Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, VIC 3083, Australia
| | - Zhiqian Liu
- Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, VIC 3083, Australia
| | - Edmond J. Breen
- Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, VIC 3083, Australia
| | - Yahui Gao
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - George E. Liu
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Albert Tenesa
- MRC Human Genetics Unit at the Institute of Genetics and Cancer, the University of Edinburgh, Edinburgh, UK
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, the University of Edinburgh, Midlothian EH25 9RG, UK
| | - CattleGTEx Consortium
- Faculty of Veterinary & Agricultural Science, the University of Melbourne, Parkville, VIC 3052, Australia
- Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, VIC 3083, Australia
- Cambridge-Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC 3004, Australia
- MRC Human Genetics Unit at the Institute of Genetics and Cancer, the University of Edinburgh, Edinburgh, UK
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, the University of Edinburgh, Midlothian EH25 9RG, UK
- Institute for Molecular Bioscience, the University of Queensland, Brisbane, QLD 4072, Australia
- Queensland Brain Institute, the University of Queensland, Brisbane, QLD 4072, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083, Australia
| | - Brett A. Mason
- Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, VIC 3083, Australia
| | - Amanda J. Chamberlain
- Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, VIC 3083, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083, Australia
| | - Naomi R. Wray
- Institute for Molecular Bioscience, the University of Queensland, Brisbane, QLD 4072, Australia
- Queensland Brain Institute, the University of Queensland, Brisbane, QLD 4072, Australia
| | - Michael E. Goddard
- Faculty of Veterinary & Agricultural Science, the University of Melbourne, Parkville, VIC 3052, Australia
- Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, VIC 3083, Australia
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4
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Pairo-Castineira E, Rawlik K, Bretherick AD, Qi T, Wu Y, Nassiri I, McConkey GA, Zechner M, Klaric L, Griffiths F, Oosthuyzen W, Kousathanas A, Richmond A, Millar J, Russell CD, Malinauskas T, Thwaites R, Morrice K, Keating S, Maslove D, Nichol A, Semple MG, Knight J, Shankar-Hari M, Summers C, Hinds C, Horby P, Ling L, McAuley D, Montgomery H, Openshaw PJM, Begg C, Walsh T, Tenesa A, Flores C, Riancho JA, Rojas-Martinez A, Lapunzina P, Yang J, Ponting CP, Wilson JF, Vitart V, Abedalthagafi M, Luchessi AD, Parra EJ, Cruz R, Carracedo A, Fawkes A, Murphy L, Rowan K, Pereira AC, Law A, Fairfax B, Hendry SC, Baillie JK. Author Correction: GWAS and meta-analysis identifies 49 genetic variants underlying critical COVID-19. Nature 2023; 619:E61. [PMID: 37433877 PMCID: PMC10371859 DOI: 10.1038/s41586-023-06383-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2023]
Affiliation(s)
- Erola Pairo-Castineira
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Konrad Rawlik
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Andrew D Bretherick
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Pain Service, NHS Tayside, Ninewells Hospital and Medical School, Dundee, UK
| | - Ting Qi
- School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
| | - Yang Wu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Isar Nassiri
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Marie Zechner
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Lucija Klaric
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Fiona Griffiths
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Wilna Oosthuyzen
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | - Anne Richmond
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Jonathan Millar
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Clark D Russell
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Tomas Malinauskas
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Ryan Thwaites
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Kirstie Morrice
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Sean Keating
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - David Maslove
- Department of Critical Care Medicine, Queen's University and Kingston Health Sciences Centre, Kingston, Ontario, Canada
| | - Alistair Nichol
- Clinical Research Centre at St Vincent's University Hospital, University College Dublin, Dublin, Ireland
| | - Malcolm G Semple
- NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences University of Liverpool, Liverpool, UK
- Respiratory Medicine, Alder Hey Children's Hospital, Institute in The Park, University of Liverpool, Alder Hey Children's Hospital, Liverpool, UK
| | - Julian Knight
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Manu Shankar-Hari
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
- Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | | | - Charles Hinds
- William Harvey Research Institute Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Peter Horby
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Lowell Ling
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | - Danny McAuley
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
- Department of Intensive Care Medicine, Royal Victoria Hospital, Belfast, UK
| | | | - Peter J M Openshaw
- National Heart and Lung Institute, Imperial College London, London, UK
- Imperial College Healthcare NHS Trust, London, UK
| | - Colin Begg
- Royal Hospital for Children, Glasgow, UK
| | - Timothy Walsh
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Albert Tenesa
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - Carlos Flores
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
- Research Unit, Hospital Universitario N.S. de Candelaria, Santa Cruz de Tenerife, Spain
- Centre for Biomedical Network Research on Respiratory Diseases (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
- Department of Clinical Sciences, University Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - José A Riancho
- IDIVAL, Santander, Spain
- Universidad de Cantabria, Santander, Spain
- Hospital U M Valdecilla, Santander, Spain
| | - Augusto Rojas-Martinez
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud and Hospital San Jose TecSalud, Monterrey, Mexico
| | - Pablo Lapunzina
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz-IDIPAZ, Madrid, Spain
- ERN-ITHACA-European Reference Network, Paris, France
| | - Jian Yang
- School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
| | - Chris P Ponting
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - James F Wilson
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - Veronique Vitart
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Malak Abedalthagafi
- Genomic Research Department, King Fahad Medical City, Riyadh, Saudi Arabia
- Department of Pathology & Laboratory Medicine, Emory University Hospital, Atlanta, GA, USA
| | - Andre D Luchessi
- Department of Clinical Analysis and Toxicology, Federal University of Rio Grande do Norte, Natal, Brazil
- Department of Anthropology, University of Toronto at Mississauga, Mississauga, Ontario, Canada
| | - Esteban J Parra
- Department of Anthropology, University of Toronto at Mississauga, Mississauga, Ontario, Canada
| | - Raquel Cruz
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Angel Carracedo
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain
- Fundación Pública Galega de Medicina Xenómica, Sistema Galego de Saúde (SERGAS) Santiago de Compostela, Santiago de Compostela, Spain
| | - Angie Fawkes
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Lee Murphy
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Kathy Rowan
- Intensive Care National Audit & Research Centre, London, UK
| | | | - Andy Law
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Benjamin Fairfax
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Sara Clohisey Hendry
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - J Kenneth Baillie
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK.
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK.
- Roslin Institute, University of Edinburgh, Edinburgh, UK.
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK.
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5
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Villaplana-Velasco A, Pigeyre M, Engelmann J, Rawlik K, Canela-Xandri O, Tochel C, Lona-Durazo F, Mookiah MRK, Doney A, Parra EJ, Trucco E, MacGillivray T, Rannikmae K, Tenesa A, Pairo-Castineira E, Bernabeu MO. Fine-mapping of retinal vascular complexity loci identifies Notch regulation as a shared mechanism with myocardial infarction outcomes. Commun Biol 2023; 6:523. [PMID: 37188768 DOI: 10.1038/s42003-023-04836-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 04/12/2023] [Indexed: 05/17/2023] Open
Abstract
There is increasing evidence that the complexity of the retinal vasculature measured as fractal dimension, Df, might offer earlier insights into the progression of coronary artery disease (CAD) before traditional biomarkers can be detected. This association could be partly explained by a common genetic basis; however, the genetic component of Df is poorly understood. We present a genome-wide association study (GWAS) of 38,000 individuals with white British ancestry from the UK Biobank aimed to comprehensively study the genetic component of Df and analyse its relationship with CAD. We replicated 5 Df loci and found 4 additional loci with suggestive significance (P < 1e-05) to contribute to Df variation, which previously were reported in retinal tortuosity and complexity, hypertension, and CAD studies. Significant negative genetic correlation estimates support the inverse relationship between Df and CAD, and between Df and myocardial infarction (MI), one of CAD's fatal outcomes. Fine-mapping of Df loci revealed Notch signalling regulatory variants supporting a shared mechanism with MI outcomes. We developed a predictive model for MI incident cases, recorded over a 10-year period following clinical and ophthalmic evaluation, combining clinical information, Df, and a CAD polygenic risk score. Internal cross-validation demonstrated a considerable improvement in the area under the curve (AUC) of our predictive model (AUC = 0.770 ± 0.001) when comparing with an established risk model, SCORE, (AUC = 0.741 ± 0.002) and extensions thereof leveraging the PRS (AUC = 0.728 ± 0.001). This evidences that Df provides risk information beyond demographic, lifestyle, and genetic risk factors. Our findings shed new light on the genetic basis of Df, unveiling a common control with MI, and highlighting the benefits of its application in individualised MI risk prediction.
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Affiliation(s)
- Ana Villaplana-Velasco
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh, Scotland, UK
- Centre for Medical Informatics, Usher Institute, The University of Edinburgh, Edinburgh, Scotland, UK
| | - Marie Pigeyre
- Population Health Research Institute (PHRI), Department of Medicine, Faculty of Health Sciences, McMaster University, McMaster University, Hamilton, Ontario, Canada
| | - Justin Engelmann
- Centre for Medical Informatics, Usher Institute, The University of Edinburgh, Edinburgh, Scotland, UK
| | - Konrad Rawlik
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh, Scotland, UK
| | - Oriol Canela-Xandri
- MRC Human Genetics Unit, IGC, The University of Edinburgh, Edinburgh, Scotland, UK
| | - Claire Tochel
- Centre for Medical Informatics, Usher Institute, The University of Edinburgh, Edinburgh, Scotland, UK
| | | | | | - Alex Doney
- VAMPIRE project, Computing, School of Science and Engineering, University of Dundee, Dundee, Scotland, UK
| | - Esteban J Parra
- University of Toronto at Mississauga, Mississauga, Ontario, Canada
| | - Emanuele Trucco
- VAMPIRE project, Computing, School of Science and Engineering, University of Dundee, Dundee, Scotland, UK
| | - Tom MacGillivray
- VAMPIRE project, Centre for Clinical Brain Sciences, The University of Edinburgh, Edinburgh, Scotland, UK
| | - Kristiina Rannikmae
- Centre for Medical Informatics, Usher Institute, The University of Edinburgh, Edinburgh, Scotland, UK
| | - Albert Tenesa
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh, Scotland, UK
- Centre for Medical Informatics, Usher Institute, The University of Edinburgh, Edinburgh, Scotland, UK
- MRC Human Genetics Unit, IGC, The University of Edinburgh, Edinburgh, Scotland, UK
| | - Erola Pairo-Castineira
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh, Scotland, UK
| | - Miguel O Bernabeu
- Centre for Medical Informatics, Usher Institute, The University of Edinburgh, Edinburgh, Scotland, UK.
- The Bayes Centre, The University of Edinburgh, Edinburgh, Scotland, UK.
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6
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Pairo-Castineira E, Rawlik K, Bretherick AD, Qi T, Wu Y, Nassiri I, McConkey GA, Zechner M, Klaric L, Griffiths F, Oosthuyzen W, Kousathanas A, Richmond A, Millar J, Russell CD, Malinauskas T, Thwaites R, Morrice K, Keating S, Maslove D, Nichol A, Semple MG, Knight J, Shankar-Hari M, Summers C, Hinds C, Horby P, Ling L, McAuley D, Montgomery H, Openshaw PJM, Begg C, Walsh T, Tenesa A, Flores C, Riancho JA, Rojas-Martinez A, Lapunzina P, Yang J, Ponting CP, Wilson JF, Vitart V, Abedalthagafi M, Luchessi AD, Parra EJ, Cruz R, Carracedo A, Fawkes A, Murphy L, Rowan K, Pereira AC, Law A, Fairfax B, Hendry SC, Baillie JK. GWAS and meta-analysis identifies 49 genetic variants underlying critical COVID-19. Nature 2023; 617:764-768. [PMID: 37198478 PMCID: PMC10208981 DOI: 10.1038/s41586-023-06034-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 03/27/2023] [Indexed: 05/19/2023]
Abstract
Critical illness in COVID-19 is an extreme and clinically homogeneous disease phenotype that we have previously shown1 to be highly efficient for discovery of genetic associations2. Despite the advanced stage of illness at presentation, we have shown that host genetics in patients who are critically ill with COVID-19 can identify immunomodulatory therapies with strong beneficial effects in this group3. Here we analyse 24,202 cases of COVID-19 with critical illness comprising a combination of microarray genotype and whole-genome sequencing data from cases of critical illness in the international GenOMICC (11,440 cases) study, combined with other studies recruiting hospitalized patients with a strong focus on severe and critical disease: ISARIC4C (676 cases) and the SCOURGE consortium (5,934 cases). To put these results in the context of existing work, we conduct a meta-analysis of the new GenOMICC genome-wide association study (GWAS) results with previously published data. We find 49 genome-wide significant associations, of which 16 have not been reported previously. To investigate the therapeutic implications of these findings, we infer the structural consequences of protein-coding variants, and combine our GWAS results with gene expression data using a monocyte transcriptome-wide association study (TWAS) model, as well as gene and protein expression using Mendelian randomization. We identify potentially druggable targets in multiple systems, including inflammatory signalling (JAK1), monocyte-macrophage activation and endothelial permeability (PDE4A), immunometabolism (SLC2A5 and AK5), and host factors required for viral entry and replication (TMPRSS2 and RAB2A).
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Affiliation(s)
- Erola Pairo-Castineira
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Konrad Rawlik
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Andrew D Bretherick
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Pain Service, NHS Tayside, Ninewells Hospital and Medical School, Dundee, UK
| | - Ting Qi
- School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
| | - Yang Wu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Isar Nassiri
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Marie Zechner
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Lucija Klaric
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Fiona Griffiths
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Wilna Oosthuyzen
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | - Anne Richmond
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Jonathan Millar
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Clark D Russell
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Tomas Malinauskas
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Ryan Thwaites
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Kirstie Morrice
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Sean Keating
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - David Maslove
- Department of Critical Care Medicine, Queen's University and Kingston Health Sciences Centre, Kingston, Ontario, Canada
| | - Alistair Nichol
- Clinical Research Centre at St Vincent's University Hospital, University College Dublin, Dublin, Ireland
| | - Malcolm G Semple
- NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences University of Liverpool, Liverpool, UK
- Respiratory Medicine, Alder Hey Children's Hospital, Institute in The Park, University of Liverpool, Alder Hey Children's Hospital, Liverpool, UK
| | - Julian Knight
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Manu Shankar-Hari
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
- Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | | | - Charles Hinds
- William Harvey Research Institute Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Peter Horby
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Lowell Ling
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | - Danny McAuley
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
- Department of Intensive Care Medicine, Royal Victoria Hospital, Belfast, UK
| | | | - Peter J M Openshaw
- National Heart and Lung Institute, Imperial College London, London, UK
- Imperial College Healthcare NHS Trust, London, UK
| | - Colin Begg
- Royal Hospital for Children, Glasgow, UK
| | - Timothy Walsh
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Albert Tenesa
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - Carlos Flores
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
- Research Unit, Hospital Universitario N.S. de Candelaria, Santa Cruz de Tenerife, Spain
- Centre for Biomedical Network Research on Respiratory Diseases (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
- Department of Clinical Sciences, University Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - José A Riancho
- IDIVAL, Santander, Spain
- Universidad de Cantabria, Santander, Spain
- Hospital U M Valdecilla, Santander, Spain
| | - Augusto Rojas-Martinez
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud and Hospital San Jose TecSalud, Monterrey, Mexico
| | - Pablo Lapunzina
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz-IDIPAZ, Madrid, Spain
- ERN-ITHACA-European Reference Network, Paris, France
| | - Jian Yang
- School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
| | - Chris P Ponting
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - James F Wilson
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - Veronique Vitart
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Malak Abedalthagafi
- Genomic Research Department, King Fahad Medical City, Riyadh, Saudi Arabia
- Department of Pathology & Laboratory Medicine, Emory University Hospital, Atlanta, GA, USA
| | - Andre D Luchessi
- Department of Clinical Analysis and Toxicology, Federal University of Rio Grande do Norte, Natal, Brazil
- Department of Anthropology, University of Toronto at Mississauga, Mississauga, Ontario, Canada
| | - Esteban J Parra
- Department of Anthropology, University of Toronto at Mississauga, Mississauga, Ontario, Canada
| | - Raquel Cruz
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Angel Carracedo
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain
- Fundación Pública Galega de Medicina Xenómica, Sistema Galego de Saúde (SERGAS) Santiago de Compostela, Santiago de Compostela, Spain
| | - Angie Fawkes
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Lee Murphy
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Kathy Rowan
- Intensive Care National Audit & Research Centre, London, UK
| | | | - Andy Law
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Benjamin Fairfax
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Sara Clohisey Hendry
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - J Kenneth Baillie
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK.
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK.
- Roslin Institute, University of Edinburgh, Edinburgh, UK.
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK.
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7
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Ferguson AC, Thrippleton S, Henshall D, Whittaker E, Conway B, MacLeod M, Malik R, Rawlik K, Tenesa A, Sudlow C, Rannikmae K. Frequency and Phenotype Associations of Rare Variants in 5 Monogenic Cerebral Small Vessel Disease Genes in 200,000 UK Biobank Participants. Neurol Genet 2022; 8:e200015. [PMID: 36035235 PMCID: PMC9403885 DOI: 10.1212/nxg.0000000000200015] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 06/17/2022] [Indexed: 04/14/2023]
Abstract
BACKGROUND AND OBJECTIVES Based on previous case reports and disease-based cohorts, a minority of patients with cerebral small vessel disease (cSVD) have a monogenic cause, with many also manifesting extracerebral phenotypes. We investigated the frequency, penetrance, and phenotype associations of putative pathogenic variants in cSVD genes in the UK Biobank (UKB), a large population-based study. METHODS We used a systematic review of previous literature and ClinVar to identify putative pathogenic rare variants in CTSA, TREX1, HTRA1, and COL4A1/2. We mapped phenotypes previously attributed to these variants (phenotypes-of-interest) to disease coding systems used in the UKB's linked health data from UK hospital admissions, death records, and primary care. Among 199,313 exome-sequenced UKB participants, we assessed the following: the proportion of participants carrying ≥1 variant(s); phenotype-of-interest penetrance; and the association between variant carrier status and phenotypes-of-interest using a binary (any phenotype present/absent) and phenotype burden (linear score of the number of phenotypes a participant possessed) approach. RESULTS Among UKB participants, 0.5% had ≥1 variant(s) in studied genes. Using hospital admission and death records, 4%-20% of variant carriers per gene had an associated phenotype. This increased to 7%-55% when including primary care records. Only COL4A1 variant carrier status was significantly associated with having ≥1 phenotype-of-interest and a higher phenotype score (OR = 1.29, p = 0.006). DISCUSSION While putative pathogenic rare variants in monogenic cSVD genes occur in 1:200 people in the UKB population, only approximately half of variant carriers have a relevant disease phenotype recorded in their linked health data. We could not replicate most previously reported gene-phenotype associations, suggesting lower penetrance rates, overestimated pathogenicity, and/or limited statistical power.
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8
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Zhao R, Talenti A, Fang L, Liu S, Liu G, Chue Hong NP, Tenesa A, Hassan M, Prendergast JGD. The conservation of human functional variants and their effects across livestock species. Commun Biol 2022; 5:1003. [PMID: 36131008 PMCID: PMC9492664 DOI: 10.1038/s42003-022-03961-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 09/07/2022] [Indexed: 11/24/2022] Open
Abstract
Despite the clear potential of livestock models of human functional variants to provide important insights into the biological mechanisms driving human diseases and traits, their use to date has been limited. Generating such models via genome editing is costly and time consuming, and it is unclear which variants will have conserved effects across species. In this study we address these issues by studying naturally occurring livestock models of human functional variants. We show that orthologues of over 1.6 million human variants are already segregating in domesticated mammalian species, including several hundred previously directly linked to human traits and diseases. Models of variants linked to particular phenotypes, including metabolomic disorders and height, are preferentially shared across species, meaning studying the genetic basis of these phenotypes is particularly tractable in livestock. Using machine learning we demonstrate it is possible to identify human variants that are more likely to have an existing livestock orthologue, and, importantly, we show that the effects of functional variants are often conserved in livestock, acting on orthologous genes with the same direction of effect. Consequently, this work demonstrates the substantial potential of naturally occurring livestock carriers of orthologues of human functional variants to disentangle their functional impacts. An investigation of genetic variants that exist across human and livestock species supports the clear potential of livestock models in providing insights into the mechanisms driving human diseases and traits.
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Affiliation(s)
- Rongrong Zhao
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Andrea Talenti
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Lingzhao Fang
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Shuli Liu
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, 310024, China
| | - George Liu
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, Agricultural Research Service, USDA, Beltsville, Maryland, 20705, USA
| | | | - Albert Tenesa
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Musa Hassan
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - James G D Prendergast
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK.
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9
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Yao Y, Liu S, Xia C, Gao Y, Pan Z, Canela-Xandri O, Khamseh A, Rawlik K, Wang S, Li B, Zhang Y, Pairo-Castineira E, D’Mellow K, Li X, Yan Z, Li CJ, Yu Y, Zhang S, Ma L, Cole JB, Ross PJ, Zhou H, Haley C, Liu GE, Fang L, Tenesa A. Comparative transcriptome in large-scale human and cattle populations. Genome Biol 2022; 23:176. [PMID: 35996157 PMCID: PMC9394047 DOI: 10.1186/s13059-022-02745-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 08/09/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cross-species comparison of transcriptomes is important for elucidating evolutionary molecular mechanisms underpinning phenotypic variation between and within species, yet to date it has been essentially limited to model organisms with relatively small sample sizes. RESULTS Here, we systematically analyze and compare 10,830 and 4866 publicly available RNA-seq samples in humans and cattle, respectively, representing 20 common tissues. Focusing on 17,315 orthologous genes, we demonstrate that mean/median gene expression, inter-individual variation of expression, expression quantitative trait loci, and gene co-expression networks are generally conserved between humans and cattle. By examining large-scale genome-wide association studies for 46 human traits (average n = 327,973) and 45 cattle traits (average n = 24,635), we reveal that the heritability of complex traits in both species is significantly more enriched in transcriptionally conserved than diverged genes across tissues. CONCLUSIONS In summary, our study provides a comprehensive comparison of transcriptomes between humans and cattle, which might help decipher the genetic and evolutionary basis of complex traits in both species.
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Affiliation(s)
- Yuelin Yao
- MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, EH4 2XU Edinburgh, UK
- School of Informatics, The University of Edinburgh, Edinburgh, EH8 9AB UK
| | - Shuli Liu
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland 20705 USA
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Charley Xia
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG UK
- Department of Psychology, 7 George Square, The University of Edinburgh, Edinburgh, EH8 9JZ UK
| | - Yahui Gao
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland 20705 USA
- Department of Animal and Avian Sciences, University of Maryland, College Park, MA 20742 USA
| | - Zhangyuan Pan
- Department of Animal Science, University of California, Davis, CA 95616 USA
- Present address: Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Oriol Canela-Xandri
- MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, EH4 2XU Edinburgh, UK
| | - Ava Khamseh
- MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, EH4 2XU Edinburgh, UK
- School of Informatics, The University of Edinburgh, Edinburgh, EH8 9AB UK
| | - Konrad Rawlik
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG UK
| | - Sheng Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223 Yunnan China
| | - Bingjie Li
- Scotland’s Rural College (SRUC), Roslin Institute Building, Midlothian, EH25 9RG UK
| | - Yi Zhang
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Erola Pairo-Castineira
- MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, EH4 2XU Edinburgh, UK
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG UK
| | - Kenton D’Mellow
- MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, EH4 2XU Edinburgh, UK
| | - Xiujin Li
- Guangdong Provincial Key Laboratory of Waterfowl Healthy Breeding, College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225 Guangdong China
| | - Ze Yan
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Cong-jun Li
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland 20705 USA
| | - Ying Yu
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Shengli Zhang
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Li Ma
- Department of Animal and Avian Sciences, University of Maryland, College Park, MA 20742 USA
| | - John B. Cole
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland 20705 USA
| | - Pablo J. Ross
- Department of Animal Science, University of California, Davis, CA 95616 USA
| | - Huaijun Zhou
- Department of Animal Science, University of California, Davis, CA 95616 USA
| | - Chris Haley
- MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, EH4 2XU Edinburgh, UK
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG UK
| | - George E. Liu
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland 20705 USA
| | - Lingzhao Fang
- MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, EH4 2XU Edinburgh, UK
- Present address: Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark
| | - Albert Tenesa
- MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, EH4 2XU Edinburgh, UK
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG UK
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10
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Liu S, Gao Y, Canela-Xandri O, Wang S, Yu Y, Cai W, Li B, Xiang R, Chamberlain AJ, Pairo-Castineira E, D'Mellow K, Rawlik K, Xia C, Yao Y, Navarro P, Rocha D, Li X, Yan Z, Li C, Rosen BD, Van Tassell CP, Vanraden PM, Zhang S, Ma L, Cole JB, Liu GE, Tenesa A, Fang L. A multi-tissue atlas of regulatory variants in cattle. Nat Genet 2022; 54:1438-1447. [PMID: 35953587 PMCID: PMC7613894 DOI: 10.1038/s41588-022-01153-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 07/07/2022] [Indexed: 12/12/2022]
Abstract
Characterization of genetic regulatory variants acting on livestock gene expression is essential for interpreting the molecular mechanisms underlying traits of economic value and for increasing the rate of genetic gain through artificial selection. Here we build a Cattle Genotype-Tissue Expression atlas (CattleGTEx) as part of the pilot phase of the Farm animal GTEx (FarmGTEx) project for the research community based on 7,180 publicly available RNA-sequencing (RNA-seq) samples. We describe the transcriptomic landscape of more than 100 tissues/cell types and report hundreds of thousands of genetic associations with gene expression and alternative splicing for 23 distinct tissues. We evaluate the tissue-sharing patterns of these genetic regulatory effects, and functionally annotate them using multiomics data. Finally, we link gene expression in different tissues to 43 economically important traits using both transcriptome-wide association and colocalization analyses to decipher the molecular regulatory mechanisms underpinning such agronomic traits in cattle.
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Affiliation(s)
- Shuli Liu
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, USA.,National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.,School of Life Sciences, Westlake University, Hangzhou, China
| | - Yahui Gao
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, USA.,Department of Animal and Avian Sciences, University of Maryland, College Park, MD, USA
| | - Oriol Canela-Xandri
- MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Sheng Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Ying Yu
- National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Wentao Cai
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China
| | - Bingjie Li
- Scotland's Rural College (SRUC), Roslin Institute Building, Midlothian, UK
| | - Ruidong Xiang
- Faculty of Veterinary & Agricultural Science, The University of Melbourne, Parkville, Victoria, Australia.,Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, Victoria, Australia
| | - Amanda J Chamberlain
- Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, Victoria, Australia
| | - Erola Pairo-Castineira
- MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK.,The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK
| | - Kenton D'Mellow
- MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Konrad Rawlik
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK
| | - Charley Xia
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK
| | - Yuelin Yao
- MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Pau Navarro
- MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Dominique Rocha
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, Jouy-en-Josas, France
| | - Xiujin Li
- Guangdong Provincial Key Laboratory of Waterfowl Healthy Breeding, College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Ze Yan
- National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Congjun Li
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, USA
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, USA
| | - Curtis P Van Tassell
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, USA
| | - Paul M Vanraden
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, USA
| | - Shengli Zhang
- National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Li Ma
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, USA
| | - John B Cole
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, USA
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, USA.
| | - Albert Tenesa
- MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK. .,The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK.
| | - Lingzhao Fang
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, USA. .,MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK. .,Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark.
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11
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Pathak GA, Karjalainen J, Stevens C, Neale BM, Daly M, Ganna A, Andrews SJ, Kanai M, Cordioli M, Polimanti R, Harerimana N, Pirinen M, Liao RG, Chwialkowska K, Trankiem A, Balaconis MK, Nguyen H, Solomonson M, Veerapen K, Wolford B, Roberts G, Park D, Ball CA, Coignet M, McCurdy S, Knight S, Partha R, Rhead B, Zhang M, Berkowitz N, Gaddis M, Noto K, Ruiz L, Pavlovic M, Hong EL, Rand K, Girshick A, Guturu H, Baltzell AH, Niemi MEK, Rahmouni S, Guntz J, Beguin Y, Cordioli M, Pigazzini S, Nkambule L, Georges M, Moutschen M, Misset B, Darcis G, Guiot J, Azarzar S, Gofflot S, Claassen S, Malaise O, Huynen P, Meuris C, Thys M, Jacques J, Léonard P, Frippiat F, Giot JB, Sauvage AS, Frenckell CV, Belhaj Y, Lambermont B, Nakanishi T, Morrison DR, Mooser V, Richards JB, Butler-Laporte G, Forgetta V, Li R, Ghosh B, Laurent L, Belisle A, Henry D, Abdullah T, Adeleye O, Mamlouk N, Kimchi N, Afrasiabi Z, Rezk N, Vulesevic B, Bouab M, Guzman C, Petitjean L, Tselios C, Xue X, Afilalo J, Afilalo M, Oliveira M, Brenner B, Brassard N, Durand M, Schurr E, Lepage P, Ragoussis J, Auld D, Chassé M, Kaufmann DE, Lathrop GM, Adra D, Hayward C, Glessner JT, Shaw DM, Campbell A, Morris M, Hakonarson H, Porteous DJ, Below J, Richmond A, Chang X, Polikowski H, Lauren PE, Chen HH, Wanying Z, Fawns-Ritchie C, North K, McCormick JB, Chang X, Glessner JR, Hakonarson H, Gignoux CR, Wicks SJ, Crooks K, Barnes KC, Daya M, Shortt J, Rafaels N, Chavan S, Timmers PRHJ, Wilson JF, Tenesa A, Kerr SM, D’Mellow K, Shahin D, El-Sherbiny YM, von Hohenstaufen KA, Sobh A, Eltoukhy MM, Nkambul L, Elhadidy TA, Abd Elghafar MS, El-Jawhari JJ, Mohamed AAS, Elnagdy MH, Samir A, Abdel-Aziz M, Khafaga WT, El-Lawaty WM, Torky MS, El-shanshory MR, Yassen AM, Hegazy MAF, Okasha K, Eid MA, Moahmed HS, Medina-Gomez C, Ikram MA, Uitterlinden AG, Mägi R, Milani L, Metspalu A, Laisk T, Läll K, Lepamets M, Esko T, Reimann E, Naaber P, Laane E, Pesukova J, Peterson P, Kisand K, Tabri J, Allos R, Hensen K, Starkopf J, Ringmets I, Tamm A, Kallaste A, Alavere H, Metsalu K, Puusepp M, Batini C, Tobin MD, Venn LD, Lee PH, Shrine N, Williams AT, Guyatt AL, John C, Packer RJ, Ali A, Free RC, Wang X, Wain LV, Hollox EJ, Bee CE, Adams EL, Palotie A, Ripatti S, Ruotsalainen S, Kristiansson K, Koskelainen S, Perola M, Donner K, Kivinen K, Palotie A, Kaunisto M, Rivolta C, Bochud PY, Bibert S, Boillat N, Nussle SG, Albrich W, Quinodoz M, Kamdar D, Suh N, Neofytos D, Erard V, Voide C, Bochud PY, Rivolta C, Bibert S, Quinodoz M, Kamdar D, Neofytos D, Erard V, Voide C, Friolet R, Vollenweider P, Pagani JL, Oddo M, zu Bentrup FM, Conen A, Clerc O, Marchetti O, Guillet A, Guyat-Jacques C, Foucras S, Rime M, Chassot J, Jaquet M, Viollet RM, Lannepoudenx Y, Portopena L, Bochud PY, Vollenweider P, Pagani JL, Desgranges F, Filippidis P, Guéry B, Haefliger D, Kampouri EE, Manuel O, Munting A, Papadimitriou-Olivgeris M, Regina J, Rochat-Stettler L, Suttels V, Tadini E, Tschopp J, Van Singer M, Viala B, Boillat-Blanco N, Brahier T, Hügli O, Meuwly JY, Pantet O, Gonseth Nussle S, Bochud M, D’Acremont V, Estoppey Younes S, Albrich WC, Suh N, Cerny A, O’Mahony L, von Mering C, Bochud PY, Frischknecht M, Kleger GR, Filipovic M, Kahlert CR, Wozniak H, Negro TR, Pugin J, Bouras K, Knapp C, Egger T, Perret A, Montillier P, di Bartolomeo C, Barda B, de Cid R, Carreras A, Moreno V, Kogevinas M, Galván-Femenía I, Blay N, Farré X, Sumoy L, Cortés B, Mercader JM, Guindo-Martinez M, Torrents D, Garcia-Aymerich J, Castaño-Vinyals G, Dobaño C, Gori M, Renieri A, Mari F, Mondelli MU, Castelli F, Vaghi M, Rusconi S, Montagnani F, Bargagli E, Franchi F, Mazzei MA, Cantarini L, Tacconi D, Feri M, Scala R, Spargi G, Nencioni C, Bandini M, Caldarelli GP, Canaccini A, Ognibene A, D’Arminio Monforte A, Girardis M, Antinori A, Francisci D, Schiaroli E, Scotton PG, Panese S, Scaggiante R, Monica MD, Capasso M, Fiorentino G, Castori M, Aucella F, Biagio AD, Masucci L, Valente S, Mandalà M, Zucchi P, Giannattasio F, Coviello DA, Mussini C, Tavecchia L, Crotti L, Rizzi M, Rovere MTL, Sarzi-Braga S, Bussotti M, Ravaglia S, Artuso R, Perrella A, Romani D, Bergomi P, Catena E, Vincenti A, Ferri C, Grassi D, Pessina G, Tumbarello M, Pietro MD, Sabrina R, Luchi S, Furini S, Dei S, Benetti E, Picchiotti N, Sanarico M, Ceri S, Pinoli P, Raimondi F, Biscarini F, Stella A, Zguro K, Capitani K, Nkambule L, Tanfoni M, Fallerini C, Daga S, Baldassarri M, Fava F, Frullanti E, Valentino F, Doddato G, Giliberti A, Tita R, Amitrano S, Bruttini M, Croci S, Meloni I, Mencarelli MA, Rizzo CL, Pinto AM, Beligni G, Tommasi A, Sarno LD, Palmieri M, Carriero ML, Alaverdian D, Busani S, Bruno R, Vecchia M, Belli MA, Mantovani S, Ludovisi S, Quiros-Roldan E, Antoni MD, Zanella I, Siano M, Emiliozzi A, Fabbiani M, Rossetti B, Bergantini L, D’Alessandro M, Cameli P, Bennett D, Anedda F, Marcantonio S, Scolletta S, Guerrini S, Conticini E, Frediani B, Spertilli C, Donati A, Guidelli L, Corridi M, Croci L, Piacentini P, Desanctis E, Cappelli S, Verzuri A, Anemoli V, Pancrazzi A, Lorubbio M, Miraglia FG, Venturelli S, Cossarizza A, Vergori A, Gabrieli A, Riva A, Paciosi F, Andretta F, Gatti F, Parisi SG, Baratti S, Piscopo C, Russo R, Andolfo I, Iolascon A, Carella M, Merla G, Squeo GM, Raggi P, Marciano C, Perna R, Bassetti M, Sanguinetti M, Giorli A, Salerni L, Parravicini P, Menatti E, Trotta T, Coiro G, Lena F, Martinelli E, Mancarella S, Gabbi C, Maggiolo F, Ripamonti D, Bachetti T, Suardi C, Parati G, Bottà G, Domenico PD, Rancan I, Bianchi F, Colombo R, Barbieri C, Acquilini D, Andreucci E, Segala FV, Tiseo G, Falcone M, Lista M, Poscente M, Vivo OD, Petrocelli P, Guarnaccia A, Baroni S, Hayward C, Porteous DJ, Fawns-Ritchie C, Richmond A, Campbell A, van Heel DA, Hunt KA, Trembath RC, Huang QQ, Martin HC, Mason D, Trivedi B, Wright J, Finer S, Akhtar S, Anwar M, Arciero E, Ashraf S, Breen G, Chung R, Curtis CJ, Chowdhury M, Colligan G, Deloukas P, Durham C, Finer S, Griffiths C, Huang QQ, Hurles M, Hunt KA, Hussain S, Islam K, Khan A, Khan A, Lavery C, Lee SH, Lerner R, MacArthur D, MacLaughlin B, Martin H, Mason D, Miah S, Newman B, Safa N, Tahmasebi F, Trembath RC, Trivedi B, van Heel DA, Wright J, Griffiths CJ, Smith AV, Boughton AP, Li KW, LeFaive J, Annis A, Niavarani A, Aliannejad R, Sharififard B, Amirsavadkouhi A, Naderpour Z, Tadi HA, Aleagha AE, Ahmadi S, Moghaddam SBM, Adamsara A, Saeedi M, Abdollahi H, Hosseini A, Chariyavilaskul P, Jantarabenjakul W, Hirankarn N, Chamnanphon M, Suttichet TB, Shotelersuk V, Pongpanich M, Phokaew C, Chetruengchai W, Putchareon O, Torvorapanit P, Puthanakit T, Suchartlikitwong P, Nilaratanakul V, Sodsai P, Brumpton BM, Hveem K, Willer C, Wolford B, Zhou W, Rogne T, Solligard E, Åsvold BO, Franke L, Boezen M, Deelen P, Claringbould A, Lopera E, Warmerdam R, Vonk JM, van Blokland I, Lanting P, Ori APS, Feng YCA, Mercader J, Weiss ST, Karlson EW, Smoller JW, Murphy SN, Meigs JB, Woolley AE, Green RC, Perez EF, Wolford B, Zöllner S, Wang J, Beck A, Sloofman LG, Ascolillo S, Sebra RP, Collins BL, Levy T, Buxbaum JD, Sealfon SC, Jordan DM, Thompson RC, Gettler K, Chaudhary K, Belbin GM, Preuss M, Hoggart C, Choi S, Underwood SJ, Salib I, Britvan B, Keller K, Tang L, Peruggia M, Hiester LL, Niblo K, Aksentijevich A, Labkowsky A, Karp A, Zlatopolsky M, Zyndorf M, Charney AW, Beckmann ND, Schadt EE, Abul-Husn NS, Cho JH, Itan Y, Kenny EE, Loos RJF, Nadkarni GN, Do R, O’Reilly P, Huckins LM, Ferreira MAR, Abecasis GR, Leader JB, Cantor MN, Justice AE, Carey DJ, Chittoor G, Josyula NS, Kosmicki JA, Horowitz JE, Baras A, Gass MC, Yadav A, Mirshahi T, Hottenga JJ, Bartels M, de geus EEJC, Nivard MMG, Verma A, Ritchie MD, Rader D, Li B, Verma SS, Lucas A, Bradford Y, Abedalthagafi M, Alaamery M, Alshareef A, Sawaji M, Massadeh S, AlMalik A, Alqahtani S, Baraka D, Harthi FA, Alsolm E, Safieh LA, Alowayn AM, Alqubaishi F, Mutairi AA, Mangul S, Almutairi M, Aljawini N, Albesher N, Arabi YM, Mahmoud ES, Khattab AK, Halawani RT, Alahmadey ZZ, Albakri JK, Felemban WA, Suliman BA, Hasanato R, Al-Awdah L, Alghamdi J, AlZahrani D, AlJohani S, Al-Afghani H, AlDhawi N, AlBardis H, Alkwai S, Alswailm M, Almalki F, Albeladi M, Almohammed I, Barhoush E, Albader A, Alotaibi S, Alghamdi B, Jung J, fawzy MS, Alrashed M, Zeberg H, Nkambul L, Frithiof R, Hultström M, Lipcsey M, Tardif N, Rooyackers O, Grip J, Maricic T, Helgeland Ø, Magnus P, Trogstad LIS, Lee Y, Harris JR, Mangino M, Spector TD, Emma D, Moutsianas L, Caulfield MJ, Scott RH, Kousathanas A, Pasko D, Walker S, Stuckey A, Odhams CA, Rhodes D, Fowler T, Rendon A, Chan G, Arumugam P, Karczewski KJ, Martin AR, Wilson DJ, Spencer CCA, Crook DW, Wyllie DH, O’Connell AM, Atkinson EG, Kanai M, Tsuo K, Baya N, Turley P, Gupta R, Walters RK, Palmer DS, Sarma G, Solomonson M, Cheng N, Lu W, Churchhouse C, Goldstein JI, King D, Zhou W, Seed C, Daly MJ, Neale BM, Finucane H, Bryant S, Satterstrom FK, Band G, Earle SG, Lin SK, Arning N, Koelling N, Armstrong J, Rudkin JK, Callier S, Bryant S, Cusick C, Soranzo N, Zhao JH, Danesh J, Angelantonio ED, Butterworth AS, Sun YV, Huffman JE, Cho K, O’Donnell CJ, Tsao P, Gaziano JM, Peloso G, Ho YL, Smieszek SP, Polymeropoulos C, Polymeropoulos V, Polymeropoulos MH, Przychodzen BP, Fernandez-Cadenas I, Planas AM, Perez-Tur J, Llucià-Carol L, Cullell N, Muiño E, Cárcel-Márquez J, DeDiego ML, Iglesias LL, Soriano A, Rico V, Agüero D, Bedini JL, Lozano F, Domingo C, Robles V, Ruiz-Jaén F, Márquez L, Gomez J, Coto E, Albaiceta GM, García-Clemente M, Dalmau D, Arranz MJ, Dietl B, Serra-Llovich A, Soler P, Colobrán R, Martín-Nalda A, Martínez AP, Bernardo D, Rojo S, Fiz-López A, Arribas E, de la Cal-Sabater P, Segura T, González-Villa E, Serrano-Heras G, Martí-Fàbregas J, Jiménez-Xarrié E, de Felipe Mimbrera A, Masjuan J, García-Madrona S, Domínguez-Mayoral A, Villalonga JM, Menéndez-Valladares P, Chasman DI, Sesso HD, Manson JE, Buring JE, Ridker PM, Franco G, Davis L, Lee S, Priest J, Sankaran VG, van Heel D, Biesecker L, Kerchberger VE, Baillie JK. A first update on mapping the human genetic architecture of COVID-19. Nature 2022; 608:E1-E10. [PMID: 35922517 PMCID: PMC9352569 DOI: 10.1038/s41586-022-04826-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 04/29/2022] [Indexed: 01/04/2023]
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Kousathanas A, Pairo-Castineira E, Rawlik K, Stuckey A, Odhams CA, Walker S, Russell CD, Malinauskas T, Wu Y, Millar J, Shen X, Elliott KS, Griffiths F, Oosthuyzen W, Morrice K, Keating S, Wang B, Rhodes D, Klaric L, Zechner M, Parkinson N, Siddiq A, Goddard P, Donovan S, Maslove D, Nichol A, Semple MG, Zainy T, Maleady-Crowe F, Todd L, Salehi S, Knight J, Elgar G, Chan G, Arumugam P, Patch C, Rendon A, Bentley D, Kingsley C, Kosmicki JA, Horowitz JE, Baras A, Abecasis GR, Ferreira MAR, Justice A, Mirshahi T, Oetjens M, Rader DJ, Ritchie MD, Verma A, Fowler TA, Shankar-Hari M, Summers C, Hinds C, Horby P, Ling L, McAuley D, Montgomery H, Openshaw PJM, Elliott P, Walsh T, Tenesa A, Fawkes A, Murphy L, Rowan K, Ponting CP, Vitart V, Wilson JF, Yang J, Bretherick AD, Scott RH, Hendry SC, Moutsianas L, Law A, Caulfield MJ, Baillie JK. Whole-genome sequencing reveals host factors underlying critical COVID-19. Nature 2022; 607:97-103. [PMID: 35255492 PMCID: PMC9259496 DOI: 10.1038/s41586-022-04576-6] [Citation(s) in RCA: 132] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 02/23/2022] [Indexed: 12/15/2022]
Abstract
Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2-4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes-including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)-in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease.
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Affiliation(s)
| | - Erola Pairo-Castineira
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Konrad Rawlik
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | | | | | - Clark D Russell
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Tomas Malinauskas
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Yang Wu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | | | - Xia Shen
- Biostatistics Group, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou, China
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | | | | | | | - Kirstie Morrice
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Sean Keating
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Bo Wang
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | - Lucija Klaric
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Marie Zechner
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Nick Parkinson
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | | | | | - David Maslove
- Department of Critical Care Medicine, Queen's University and Kingston Health Sciences Centre, Kingston, Ontario, Canada
| | - Alistair Nichol
- Clinical Research Centre at St Vincent's University Hospital, University College Dublin, Dublin, Ireland
| | - Malcolm G Semple
- NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Respiratory Medicine and Institute in the Park, Alder Hey Children's Hospital and University of Liverpool, Liverpool, UK
| | | | | | | | | | - Julian Knight
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | | | | | | | | | | | | | | | | | - Aris Baras
- Regeneron Genetics Center, Tarrytown, NY, USA
| | | | | | | | | | | | - Daniel J Rader
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Marylyn D Ritchie
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Anurag Verma
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Tom A Fowler
- Genomics England, London, UK
- Test and Trace, the Health Security Agency, Department of Health and Social Care, London, UK
| | - Manu Shankar-Hari
- Department of Intensive Care Medicine, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | | | - Charles Hinds
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Peter Horby
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Lowell Ling
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | - Danny McAuley
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
- Department of Intensive Care Medicine, Royal Victoria Hospital, Belfast, UK
| | | | - Peter J M Openshaw
- National Heart and Lung Institute, Imperial College London, London, UK
- Imperial College Healthcare NHS Trust: London, London, UK
| | | | - Timothy Walsh
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Albert Tenesa
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - Angie Fawkes
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Lee Murphy
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Kathy Rowan
- Intensive Care National Audit and Research Centre, London, UK
| | - Chris P Ponting
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Veronique Vitart
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - James F Wilson
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - Jian Yang
- School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
| | - Andrew D Bretherick
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Richard H Scott
- Genomics England, London, UK
- Great Ormond Street Hospital, London, UK
| | | | | | - Andy Law
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Mark J Caulfield
- Genomics England, London, UK.
- William Harvey Research Institute, Queen Mary University of London, London, UK.
| | - J Kenneth Baillie
- Roslin Institute, University of Edinburgh, Edinburgh, UK.
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK.
- Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK.
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK.
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13
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David A, Parkinson N, Peacock TP, Pairo-Castineira E, Khanna T, Cobat A, Tenesa A, Sancho-Shimizu V, Casanova JL, Abel L, Barclay WS, Baillie JK, Sternberg MJ. A common TMPRSS2 variant has a protective effect against severe COVID-19. Curr Res Transl Med 2022; 70:103333. [PMID: 35104687 PMCID: PMC8743599 DOI: 10.1016/j.retram.2022.103333] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/22/2021] [Accepted: 01/06/2022] [Indexed: 12/30/2022]
Abstract
BACKGROUND The human protein transmembrane protease serine type 2 (TMPRSS2) plays a key role in SARS-CoV-2 infection, as it is required to activate the virus' spike protein, facilitating entry into target cells. We hypothesized that naturally-occurring TMPRSS2 human genetic variants affecting the structure and function of the TMPRSS2 protein may modulate the severity of SARS-CoV-2 infection. METHODS We focused on the only common TMPRSS2 non-synonymous variant predicted to be damaging (rs12329760 C>T, p.V160M), which has a minor allele frequency ranging from 0.14 in Ashkenazi Jewish to 0.38 in East Asians. We analysed the association between the rs12329760 and COVID-19 severity in 2,244 critically ill patients with COVID-19 from 208 UK intensive care units recruited as part of the GenOMICC (Genetics Of Mortality In Critical Care) study. Logistic regression analyses were adjusted for sex, age and deprivation index. For in vitro studies, HEK293 cells were co-transfected with ACE2 and either TMPRSS2 wild type or mutant (TMPRSS2V160M). A SARS-CoV-2 pseudovirus entry assay was used to investigate the ability of TMPRSS2V160M to promote viral entry. RESULTS We show that the T allele of rs12329760 is associated with a reduced likelihood of developing severe COVID-19 (OR 0.87, 95%CI:0.79-0.97, p = 0.01). This association was stronger in homozygous individuals when compared to the general population (OR 0.65, 95%CI:0.50-0.84, p = 1.3 × 10-3). We demonstrate in vitro that this variant, which causes the amino acid substitution valine to methionine, affects the catalytic activity of TMPRSS2 and is less able to support SARS-CoV-2 spike-mediated entry into cells. CONCLUSION TMPRSS2 rs12329760 is a common variant associated with a significantly decreased risk of severe COVID-19. Further studies are needed to assess the expression of TMPRSS2 across different age groups. Moreover, our results identify TMPRSS2 as a promising drug target, with a potential role for camostat mesilate, a drug approved for the treatment of chronic pancreatitis and postoperative reflux esophagitis, in the treatment of COVID-19. Clinical trials are needed to confirm this.
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Affiliation(s)
- Alessia David
- Centre for Integrative System Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK.
| | - Nicholas Parkinson
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK
| | - Thomas P Peacock
- Department of Infectious Diseases, Imperial College London, London, W2 1PG, UK
| | | | - Tarun Khanna
- Centre for Integrative System Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Aurelie Cobat
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, EU France; University of Paris, Imagine Institute, Paris, EU France
| | - Albert Tenesa
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK
| | - Vanessa Sancho-Shimizu
- Department of Paediatric Infectious Diseases & Virology, Imperial College London, London, UK; Centre for Paediatrics and Child Health, Faculty of Medicine, Imperial College London, London, UK
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, EU France; University of Paris, Imagine Institute, Paris, EU France; Howard Hughes Medical Institute, New York, NY, USA
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, EU France; University of Paris, Imagine Institute, Paris, EU France
| | - Wendy S Barclay
- Department of Infectious Diseases, Imperial College London, London, W2 1PG, UK
| | - J Kenneth Baillie
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK; Intenstive Care Unit, Royal Infirmary of Edinburgh, 54 Little France Drive, Edinburgh, EH16 5SA, UK
| | - Michael Je Sternberg
- Centre for Integrative System Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
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Rannikmäe K, Rawlik K, Ferguson AC, Avramidis N, Jiang M, Pirastu N, Shen X, Davidson E, Woodfield R, Malik R, Dichgans M, Tenesa A, Sudlow C. Physician-Confirmed and Administrative Definitions of Stroke in UK Biobank Reflect the Same Underlying Genetic Trait. Front Neurol 2022; 12:787107. [PMID: 35185750 PMCID: PMC8847736 DOI: 10.3389/fneur.2021.787107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 12/13/2021] [Indexed: 11/15/2022] Open
Abstract
Background Stroke in UK Biobank (UKB) is ascertained via linkages to coded administrative datasets and self-report. We studied the accuracy of these codes using genetic validation. Methods We compiled stroke-specific and broad cerebrovascular disease (CVD) code lists (Read V2/V3, ICD-9/-10) for medical settings (hospital, death record, primary care) and self-report. Among 408,210 UKB participants, we identified all with a relevant code, creating 12 stroke definitions based on the code type and source. We performed genome-wide association studies (GWASs) for each definition, comparing summary results against the largest published stroke GWAS (MEGASTROKE), assessing genetic correlations, and replicating 32 stroke-associated loci. Results The stroke case numbers identified varied widely from 3,976 (primary care stroke-specific codes) to 19,449 (all codes, all sources). All 12 UKB stroke definitions were significantly correlated with the MEGASTROKE summary GWAS results (rg.81-1) and each other (rg.4-1). However, Bonferroni-corrected confidence intervals were wide, suggesting limited precision of some results. Six previously reported stroke-associated loci were replicated using ≥1 UKB stroke definition. Conclusions Stroke case numbers in UKB depend on the code source and type used, with a 5-fold difference in the maximum case-sample size. All stroke definitions are significantly genetically correlated with the largest stroke GWAS to date.
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Affiliation(s)
- Kristiina Rannikmäe
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
- *Correspondence: Kristiina Rannikmäe
| | - Konrad Rawlik
- Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Amy C. Ferguson
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Nikos Avramidis
- School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Muchen Jiang
- Medical School, University of Edinburgh, Edinburgh, United Kingdom
| | - Nicola Pirastu
- Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Xia Shen
- Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
- Biostatistics Group, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou, China
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Emma Davidson
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Rebecca Woodfield
- Department of Medicine for the Elderly, Western General Hospital, Edinburgh, United Kingdom
| | - Rainer Malik
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
| | - Martin Dichgans
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
- Munich Cluster for Systems Neurology, Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Albert Tenesa
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
- Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Cathie Sudlow
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
- BHF Data Science Centre, Health Data Research UK, London, United Kingdom
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15
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Grosche S, Marenholz I, Esparza-Gordillo J, Arnau-Soler A, Pairo-Castineira E, Rüschendorf F, Ahluwalia TS, Almqvist C, Arnold A, Baurecht H, Bisgaard H, Bønnelykke K, Brown SJ, Bustamante M, Curtin JA, Custovic A, Dharmage SC, Esplugues A, Falchi M, Fernandez-Orth D, Ferreira MAR, Franke A, Gerdes S, Gieger C, Hakonarson H, Holt PG, Homuth G, Hubner N, Hysi PG, Jarvelin MR, Karlsson R, Koppelman GH, Lau S, Lutz M, Magnusson PKE, Marks GB, Müller-Nurasyid M, Nöthen MM, Paternoster L, Pennell CE, Peters A, Rawlik K, Robertson CF, Rodriguez E, Sebert S, Simpson A, Sleiman PMA, Standl M, Stölzl D, Strauch K, Szwajda A, Tenesa A, Thompson PJ, Ullemar V, Visconti A, Vonk JM, Wang CA, Weidinger S, Wielscher M, Worth CL, Xu CJ, Lee YA. Rare variant analysis in eczema identifies exonic variants in DUSP1, NOTCH4 and SLC9A4. Nat Commun 2021; 12:6618. [PMID: 34785669 PMCID: PMC8595373 DOI: 10.1038/s41467-021-26783-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 10/21/2021] [Indexed: 11/10/2022] Open
Abstract
Previous genome-wide association studies revealed multiple common variants involved in eczema but the role of rare variants remains to be elucidated. Here, we investigate the role of rare variants in eczema susceptibility. We meta-analyze 21 study populations including 20,016 eczema cases and 380,433 controls. Rare variants are imputed with high accuracy using large population-based reference panels. We identify rare exonic variants in DUSP1, NOTCH4, and SLC9A4 to be associated with eczema. In DUSP1 and NOTCH4 missense variants are predicted to impact conserved functional domains. In addition, five novel common variants at SATB1-AS1/KCNH8, TRIB1/LINC00861, ZBTB1, TBX21/OSBPL7, and CSF2RB are discovered. While genes prioritized based on rare variants are significantly up-regulated in the skin, common variants point to immune cell function. Over 20% of the single nucleotide variant-based heritability is attributable to rare and low-frequency variants. The identified rare/low-frequency variants located in functional protein domains point to promising targets for novel therapeutic approaches to eczema. Genetic studies of eczema to date have mostly explored common genetic variation. Here, the authors perform a large meta-analysis for common and rare variants and discover 8 loci associated with eczema. Over 20% of the heritability of the condition is attributable to rare variants.
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Affiliation(s)
- Sarah Grosche
- Max-Delbrück-Center (MDC) for Molecular Medicine, Berlin, Germany.,Clinic for Pediatric Allergy, Experimental and Clinical Research Center, Charité University Medical Center, Berlin, Germany.,CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Ingo Marenholz
- Max-Delbrück-Center (MDC) for Molecular Medicine, Berlin, Germany.,Clinic for Pediatric Allergy, Experimental and Clinical Research Center, Charité University Medical Center, Berlin, Germany
| | - Jorge Esparza-Gordillo
- Max-Delbrück-Center (MDC) for Molecular Medicine, Berlin, Germany.,Clinic for Pediatric Allergy, Experimental and Clinical Research Center, Charité University Medical Center, Berlin, Germany.,GlaxoSmithKline, Stevenage, UK
| | - Aleix Arnau-Soler
- Max-Delbrück-Center (MDC) for Molecular Medicine, Berlin, Germany.,Clinic for Pediatric Allergy, Experimental and Clinical Research Center, Charité University Medical Center, Berlin, Germany
| | - Erola Pairo-Castineira
- Roslin Institute, University of Edinburgh, Edinburgh, UK.,MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | | | - Tarunveer S Ahluwalia
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark.,Steno Diabetes Center Copenhagen, Gentofte, Denmark
| | - Catarina Almqvist
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden.,Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Andreas Arnold
- Clinic and Polyclinic of Dermatology, University Medicine Greifswald, Greifswald, Germany
| | | | - Hansjörg Baurecht
- Department of Dermatology, Allergology and Venereology, University Hospital Schleswig-Holstein, Kiel, Germany.,Department of Epidemiology and Preventive Medicine, University Regensburg, Regensburg, Germany
| | - Hans Bisgaard
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Klaus Bønnelykke
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Sara J Brown
- Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Mariona Bustamante
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
| | - John A Curtin
- Division of Infection Immunity and Respiratory Medicine, School of Biological Sciences, The University of Manchester, Manchester Academic Health Science Centre and Manchester University NHS Foundation Trust, Manchester, UK
| | - Adnan Custovic
- National Lung and Heart Institute, Imperial College London, London, UK
| | - Shyamali C Dharmage
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
| | - Ana Esplugues
- Nursing School, University of Valencia, FISABIO-University Jaume I-University of Valencia Joint Research Unit of Epidemiology and Environmental Health, CIBERESP, Valencia, Spain
| | - Mario Falchi
- Department of Twins Research and Genetic Epidemiology, King's College London, London, UK
| | | | - Manuel A R Ferreira
- Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Sascha Gerdes
- Department of Dermatology, Allergology and Venereology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Christian Gieger
- Research Unit Molecular Epidemiology, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Germany
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, and Division of Human Genetics, Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Patrick G Holt
- Telethon Kids Institute, The University of Western Australia, Perth, Australia
| | - Georg Homuth
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Norbert Hubner
- Max-Delbrück-Center (MDC) for Molecular Medicine, Berlin, Germany
| | - Pirro G Hysi
- Department of Twins Research and Genetic Epidemiology, King's College London, London, UK
| | - Marjo-Riitta Jarvelin
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, UK.,Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Robert Karlsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Gerard H Koppelman
- Department of Pediatric Pulmonology and Pediatric Allergology, University of Groningen, University Medical Center Groningen, GRIAC Research Institute, Groningen, the Netherlands
| | - Susanne Lau
- Department of Pediatric Pulmonology, Immunology and Intensive Care Medicine, Charité University Medical Center, Berlin, Germany
| | - Manuel Lutz
- Institute of Genetic Epidemiology, Helmholtz Center Munich-German Research Center for Environmental Health, Neuherberg, Germany
| | - Patrik K E Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Guy B Marks
- Woolcock Institute of Medical Research, University of Sydney, Sydney, Australia
| | - Martina Müller-Nurasyid
- Institute of Genetic Epidemiology, Helmholtz Center Munich-German Research Center for Environmental Health, Neuherberg, Germany.,Institute for Medical Information Processing, Biometry, and Epidemiology (IBE), Faculty of Medicine, LMU Munich, Munich, Germany.,Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Lavinia Paternoster
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Craig E Pennell
- School of Medicine and Public Health, Faculty of Medicine and Health, The University of Newcastle, Newcastle, Australia
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Center Munich-German Research Center for Environmental Health, Neuherberg, Germany
| | - Konrad Rawlik
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Colin F Robertson
- Respiratory Research, Murdoch Children's Research Institute, Melbourne, Australia
| | - Elke Rodriguez
- Department of Dermatology, Allergology and Venereology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Sylvain Sebert
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, UK.,Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Angela Simpson
- Division of Infection Immunity and Respiratory Medicine, School of Biological Sciences, The University of Manchester, Manchester Academic Health Science Centre and Manchester University NHS Foundation Trust, Manchester, UK
| | - Patrick M A Sleiman
- Center for Applied Genomics, Children's Hospital of Philadelphia, and Division of Human Genetics, Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Marie Standl
- Institute of Epidemiology, Helmholtz Center Munich-German Research Center for Environmental Health, Neuherberg, Germany
| | - Dora Stölzl
- Department of Dermatology, Allergology and Venereology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Center Munich-German Research Center for Environmental Health, Neuherberg, Germany.,Institute for Medical Information Processing, Biometry, and Epidemiology (IBE), Faculty of Medicine, LMU Munich, Munich, Germany.,Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Agnieszka Szwajda
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Albert Tenesa
- Roslin Institute, University of Edinburgh, Edinburgh, UK.,MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK.,Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - Philip J Thompson
- Institute for Respiratory Health and Centre for Respiratory Health, School of Biomedical Sciences, University of Western Australia, Nedlands, Australia
| | - Vilhelmina Ullemar
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Alessia Visconti
- Department of Twins Research and Genetic Epidemiology, King's College London, London, UK
| | - Judith M Vonk
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, GRIAC Research Institute, Groningen, the Netherlands
| | - Carol A Wang
- School of Medicine and Public Health, Faculty of Medicine and Health, The University of Newcastle, Newcastle, Australia
| | - Stephan Weidinger
- Department of Dermatology, Allergology and Venereology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Matthias Wielscher
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, UK
| | | | - Chen-Jian Xu
- Department of Pediatric Pulmonology and Pediatric Allergology, University of Groningen, University Medical Center Groningen, GRIAC Research Institute, Groningen, the Netherlands.,Department of Gastroenterology, Hepatology and Endocrinology, Centre for individualized infection medicine (CIIM), Hannover Medical School, Hannover, Germany
| | - Young-Ae Lee
- Max-Delbrück-Center (MDC) for Molecular Medicine, Berlin, Germany. .,Clinic for Pediatric Allergy, Experimental and Clinical Research Center, Charité University Medical Center, Berlin, Germany.
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16
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Bernabeu E, Canela-Xandri O, Rawlik K, Talenti A, Prendergast J, Tenesa A. Sex differences in genetic architecture in the UK Biobank. Nat Genet 2021; 53:1283-1289. [PMID: 34493869 DOI: 10.1038/s41588-021-00912-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 07/12/2021] [Indexed: 01/05/2023]
Abstract
Males and females present differences in complex traits and in the risk of a wide array of diseases. Genotype by sex (GxS) interactions are thought to account for some of these differences. However, the extent and basis of GxS are poorly understood. In the present study, we provide insights into both the scope and the mechanism of GxS across the genome of about 450,000 individuals of European ancestry and 530 complex traits in the UK Biobank. We found small yet widespread differences in genetic architecture across traits. We also found that, in some cases, sex-agnostic analyses may be missing trait-associated loci and looked into possible improvements in the prediction of high-level phenotypes. Finally, we studied the potential functional role of the differences observed through sex-biased gene expression and gene-level analyses. Our results suggest the need to consider sex-aware analyses for future studies to shed light onto possible sex-specific molecular mechanisms.
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Affiliation(s)
- Elena Bernabeu
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian, UK
| | - Oriol Canela-Xandri
- Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Konrad Rawlik
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian, UK
| | - Andrea Talenti
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian, UK
| | - James Prendergast
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian, UK
| | - Albert Tenesa
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian, UK.
- Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK.
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17
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Kosmicki JA, Horowitz JE, Banerjee N, Lanche R, Marcketta A, Maxwell E, Bai X, Sun D, Backman JD, Sharma D, Kury FSP, Kang HM, O'Dushlaine C, Yadav A, Mansfield AJ, Li AH, Watanabe K, Gurski L, McCarthy SE, Locke AE, Khalid S, O'Keeffe S, Mbatchou J, Chazara O, Huang Y, Kvikstad E, O'Neill A, Nioi P, Parker MM, Petrovski S, Runz H, Szustakowski JD, Wang Q, Wong E, Cordova-Palomera A, Smith EN, Szalma S, Zheng X, Esmaeeli S, Davis JW, Lai YP, Chen X, Justice AE, Leader JB, Mirshahi T, Carey DJ, Verma A, Sirugo G, Ritchie MD, Rader DJ, Povysil G, Goldstein DB, Kiryluk K, Pairo-Castineira E, Rawlik K, Pasko D, Walker S, Meynert A, Kousathanas A, Moutsianas L, Tenesa A, Caulfield M, Scott R, Wilson JF, Baillie JK, Butler-Laporte G, Nakanishi T, Lathrop M, Richards JB, Jones M, Balasubramanian S, Salerno W, Shuldiner AR, Marchini J, Overton JD, Habegger L, Cantor MN, Reid JG, Baras A, Abecasis GR, Ferreira MAR. Pan-ancestry exome-wide association analyses of COVID-19 outcomes in 586,157 individuals. Am J Hum Genet 2021; 108:1350-1355. [PMID: 34115965 PMCID: PMC8173480 DOI: 10.1016/j.ajhg.2021.05.017] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 05/24/2021] [Indexed: 01/08/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19), a respiratory illness that can result in hospitalization or death. We used exome sequence data to investigate associations between rare genetic variants and seven COVID-19 outcomes in 586,157 individuals, including 20,952 with COVID-19. After accounting for multiple testing, we did not identify any clear associations with rare variants either exome wide or when specifically focusing on (1) 13 interferon pathway genes in which rare deleterious variants have been reported in individuals with severe COVID-19, (2) 281 genes located in susceptibility loci identified by the COVID-19 Host Genetics Initiative, or (3) 32 additional genes of immunologic relevance and/or therapeutic potential. Our analyses indicate there are no significant associations with rare protein-coding variants with detectable effect sizes at our current sample sizes. Analyses will be updated as additional data become available, and results are publicly available through the Regeneron Genetics Center COVID-19 Results Browser.
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Affiliation(s)
- Jack A Kosmicki
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Julie E Horowitz
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Nilanjana Banerjee
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Rouel Lanche
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Anthony Marcketta
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Evan Maxwell
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Xiaodong Bai
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Dylan Sun
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Joshua D Backman
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Deepika Sharma
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Fabricio S P Kury
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Hyun M Kang
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Colm O'Dushlaine
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Ashish Yadav
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Adam J Mansfield
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Alexander H Li
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Kyoko Watanabe
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Lauren Gurski
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Shane E McCarthy
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Adam E Locke
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Shareef Khalid
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Sean O'Keeffe
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Joelle Mbatchou
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Olympe Chazara
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | | | - Erika Kvikstad
- Bristol Myers Squibb, Route 206 and Province Line Road, Princeton, NJ 08543, USA
| | - Amanda O'Neill
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - Paul Nioi
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, MA 02142, USA
| | - Meg M Parker
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, MA 02142, USA
| | - Slavé Petrovski
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - Heiko Runz
- Biogen, 300 Binney Street, Cambridge, MA 02142, USA
| | | | - Quanli Wang
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - Emily Wong
- Takeda California, Inc., 9625 Towne Centre Drive, San Diego, CA 92121, USA
| | | | - Erin N Smith
- Takeda California, Inc., 9625 Towne Centre Drive, San Diego, CA 92121, USA
| | - Sandor Szalma
- Takeda California, Inc., 9625 Towne Centre Drive, San Diego, CA 92121, USA
| | - Xiuwen Zheng
- AbbVie, Inc., 1 N. Waukegan Road, North Chicago, IL 60064, USA
| | - Sahar Esmaeeli
- AbbVie, Inc., 1 N. Waukegan Road, North Chicago, IL 60064, USA
| | - Justin W Davis
- AbbVie, Inc., 1 N. Waukegan Road, North Chicago, IL 60064, USA
| | - Yi-Pin Lai
- Pfizer, Inc., 1 Portland Street, Cambridge, MA 02139, USA
| | - Xing Chen
- Pfizer, Inc., 1 Portland Street, Cambridge, MA 02139, USA
| | | | | | | | | | - Anurag Verma
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Giorgio Sirugo
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Marylyn D Ritchie
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Daniel J Rader
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gundula Povysil
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Genetics and Development, Columbia University, New York, NY 10032, USA
| | - Krzysztof Kiryluk
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA; Division of Nephrology, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Erola Pairo-Castineira
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK; MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Konrad Rawlik
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK
| | | | | | - Alison Meynert
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | | | | | - Albert Tenesa
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK; MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK; Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Teviot Place, Edinburgh EH8 9AG, UK
| | - Mark Caulfield
- Genomics England, London EC1M 6BQ, UK; William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Richard Scott
- Genomics England, London EC1M 6BQ, UK; Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - James F Wilson
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK; Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Teviot Place, Edinburgh EH8 9AG, UK
| | - J Kenneth Baillie
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK; MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK; Intensive Care Unit, Royal Infirmary of Edinburgh, 54 Little France Drive, Edinburgh EH16 5SA, UK
| | - Guillaume Butler-Laporte
- Lady Davis Institute, Jewish General Hospital, Montréal, QC H3T 1E2, Canada; Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, QC H3A 0G4, Canada
| | - Tomoko Nakanishi
- Lady Davis Institute, Jewish General Hospital, Montréal, QC H3T 1E2, Canada; Department of Human Genetics, McGill University, Montréal, QC H3A 0G4, Canada; Kyoto-McGill International Collaborative School in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Mark Lathrop
- Department of Human Genetics, McGill University, Montréal, QC H3A 0G4, Canada; Canadian Centre for Computational Genomics, McGill University, Montréal, QC H3A 0G4, Canada
| | - J Brent Richards
- Lady Davis Institute, Jewish General Hospital, Montréal, QC H3T 1E2, Canada; Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, QC H3A 0G4, Canada; Department of Human Genetics, McGill University, Montréal, QC H3A 0G4, Canada; Department of Twins Research, King's College London, London WC2R 2LS, UK
| | - Marcus Jones
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | | | - William Salerno
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Alan R Shuldiner
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Jonathan Marchini
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - John D Overton
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Lukas Habegger
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Michael N Cantor
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Jeffrey G Reid
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Aris Baras
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Goncalo R Abecasis
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA.
| | - Manuel A R Ferreira
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA.
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18
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Pairo-Castineira E, Clohisey S, Klaric L, Bretherick AD, Rawlik K, Pasko D, Walker S, Parkinson N, Fourman MH, Russell CD, Furniss J, Richmond A, Gountouna E, Wrobel N, Harrison D, Wang B, Wu Y, Meynert A, Griffiths F, Oosthuyzen W, Kousathanas A, Moutsianas L, Yang Z, Zhai R, Zheng C, Grimes G, Beale R, Millar J, Shih B, Keating S, Zechner M, Haley C, Porteous DJ, Hayward C, Yang J, Knight J, Summers C, Shankar-Hari M, Klenerman P, Turtle L, Ho A, Moore SC, Hinds C, Horby P, Nichol A, Maslove D, Ling L, McAuley D, Montgomery H, Walsh T, Pereira AC, Renieri A, Shen X, Ponting CP, Fawkes A, Tenesa A, Caulfield M, Scott R, Rowan K, Murphy L, Openshaw PJM, Semple MG, Law A, Vitart V, Wilson JF, Baillie JK. Genetic mechanisms of critical illness in COVID-19. Nature 2021; 591:92-98. [PMID: 33307546 DOI: 10.1038/s41586-020-03065-y] [Citation(s) in RCA: 790] [Impact Index Per Article: 263.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 11/30/2020] [Indexed: 02/06/2023]
Abstract
Host-mediated lung inflammation is present1, and drives mortality2, in the critical illness caused by coronavirus disease 2019 (COVID-19). Host genetic variants associated with critical illness may identify mechanistic targets for therapeutic development3. Here we report the results of the GenOMICC (Genetics Of Mortality In Critical Care) genome-wide association study in 2,244 critically ill patients with COVID-19 from 208 UK intensive care units. We have identified and replicated the following new genome-wide significant associations: on chromosome 12q24.13 (rs10735079, P = 1.65 × 10-8) in a gene cluster that encodes antiviral restriction enzyme activators (OAS1, OAS2 and OAS3); on chromosome 19p13.2 (rs74956615, P = 2.3 × 10-8) near the gene that encodes tyrosine kinase 2 (TYK2); on chromosome 19p13.3 (rs2109069, P = 3.98 × 10-12) within the gene that encodes dipeptidyl peptidase 9 (DPP9); and on chromosome 21q22.1 (rs2236757, P = 4.99 × 10-8) in the interferon receptor gene IFNAR2. We identified potential targets for repurposing of licensed medications: using Mendelian randomization, we found evidence that low expression of IFNAR2, or high expression of TYK2, are associated with life-threatening disease; and transcriptome-wide association in lung tissue revealed that high expression of the monocyte-macrophage chemotactic receptor CCR2 is associated with severe COVID-19. Our results identify robust genetic signals relating to key host antiviral defence mechanisms and mediators of inflammatory organ damage in COVID-19. Both mechanisms may be amenable to targeted treatment with existing drugs. However, large-scale randomized clinical trials will be essential before any change to clinical practice.
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Affiliation(s)
- Erola Pairo-Castineira
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Sara Clohisey
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Lucija Klaric
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Andrew D Bretherick
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Konrad Rawlik
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | | | - Nick Parkinson
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | - Clark D Russell
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - James Furniss
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Anne Richmond
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Elvina Gountouna
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Nicola Wrobel
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - David Harrison
- Intensive Care National Audit & Research Centre, London, UK
| | - Bo Wang
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Yang Wu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Alison Meynert
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | | | | | | | | | - Zhijian Yang
- Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ranran Zhai
- Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Chenqing Zheng
- Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Graeme Grimes
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | | | | | - Barbara Shih
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Sean Keating
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Marie Zechner
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Chris Haley
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - David J Porteous
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Jian Yang
- School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
| | - Julian Knight
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Manu Shankar-Hari
- Department of Intensive Care Medicine, Guy's and St Thomas' NHS Foundation Trust, London, UK
- School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Paul Klenerman
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Lance Turtle
- NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Antonia Ho
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Shona C Moore
- NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Charles Hinds
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Peter Horby
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Alistair Nichol
- Clinical Research Centre at St Vincent's University Hospital, University College Dublin, Dublin, Ireland
- Australian and New Zealand Intensive Care Research Centre, Monash University, Melbourne, Victoria, Australia
- Intensive Care Unit, Alfred Hospital, Melbourne, Victoria, Australia
| | - David Maslove
- Department of Critical Care Medicine, Queen's University and Kingston Health Sciences Centre, Kingston, Ontario, Canada
| | - Lowell Ling
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | - Danny McAuley
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
- Department of Intensive Care Medicine, Royal Victoria Hospital, Belfast, UK
| | - Hugh Montgomery
- UCL Centre for Human Health and Performance, University College London, London, UK
| | - Timothy Walsh
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Alexandre C Pereira
- Faculty of Medicine, University of São Paulo, São Paulo, Brazil
- Heart Institute, University of São Paulo, São Paulo, Brazil
| | - Alessandra Renieri
- Medical Genetics, University of Siena, Siena, Italy
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
| | - Xia Shen
- Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Chris P Ponting
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Angie Fawkes
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Albert Tenesa
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - Mark Caulfield
- Genomics England, London, UK
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Richard Scott
- Genomics England, London, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Kathy Rowan
- Intensive Care National Audit & Research Centre, London, UK
| | - Lee Murphy
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Peter J M Openshaw
- National Heart and Lung Institute, Imperial College London, London, UK
- Imperial College Healthcare NHS Trust London, London, UK
| | - Malcolm G Semple
- NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Respiratory Medicine, Alder Hey Children's Hospital, Institute in The Park, University of Liverpool, Liverpool, UK
| | - Andrew Law
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Veronique Vitart
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - James F Wilson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - J Kenneth Baillie
- Roslin Institute, University of Edinburgh, Edinburgh, UK.
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK.
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK.
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19
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Abstract
Indirect genetic effects, the effects of the genotype of one individual on the phenotype of other individuals, are environmental factors associated with human disease and complex trait variation that could help to expand our understanding of the environment linked to complex traits. Here, we study indirect genetic effects in 80,889 human couples of European ancestry for 105 complex traits. Using a linear mixed model approach, we estimate partner indirect heritability and find evidence of partner heritability on ~50% of the analysed traits. Follow-up analysis suggests that in at least ~25% of these traits, the partner heritability is consistent with the existence of indirect genetic effects including a wide variety of traits such as dietary traits, mental health and disease. This shows that the environment linked to complex traits is partially explained by the genotype of other individuals and motivates the need to find new ways of studying the environment.
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Affiliation(s)
- Charley Xia
- The Roslin Institute, The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Oriol Canela-Xandri
- The Roslin Institute, The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
- MRC IGMM, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Konrad Rawlik
- The Roslin Institute, The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Albert Tenesa
- The Roslin Institute, The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK.
- MRC IGMM, Western General Hospital, University of Edinburgh, Edinburgh, UK.
- Usher Institute, Edinburgh bioQuarter, University of Edinburgh, Edinburgh, UK.
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20
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Kosmicki JA, Horowitz JE, Banerjee N, Lanche R, Marcketta A, Maxwell E, Bai X, Sun D, Backman JD, Sharma D, Kang HM, O'Dushlaine C, Yadav A, Mansfield AJ, Li AH, Watanabe K, Gurski L, McCarthy SE, Locke AE, Khalid S, O'Keeffe S, Mbatchou J, Chazara O, Huang Y, Kvikstad E, O'Neill A, Nioi P, Parker MM, Petrovski S, Runz H, Szustakowski JD, Wang Q, Wong E, Cordova-Palomera A, Smith EN, Szalma S, Zheng X, Esmaeeli S, Davis JW, Lai YP, Chen X, Justice AE, Leader JB, Mirshahi T, Carey DJ, Verma A, Sirugo G, Ritchie MD, Rader DJ, Povysil G, Goldstein DB, Kiryluk K, Pairo-Castineira E, Rawlik K, Pasko D, Walker S, Meynert A, Kousathanas A, Moutsianas L, Tenesa A, Caulfield M, Scott R, Wilson JF, Baillie JK, Butler-Laporte G, Nakanishi T, Lathrop M, Richards JB, Jones M, Balasubramanian S, Salerno W, Shuldiner AR, Marchini J, Overton JD, Habegger L, Cantor MN, Reid JG, Baras A, Abecasis GR, Ferreira MA. A catalog of associations between rare coding variants and COVID-19 outcomes. medRxiv 2021:2020.10.28.20221804. [PMID: 33655273 PMCID: PMC7924298 DOI: 10.1101/2020.10.28.20221804] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causes coronavirus disease-19 (COVID-19), a respiratory illness that can result in hospitalization or death. We investigated associations between rare genetic variants and seven COVID-19 outcomes in 543,213 individuals, including 8,248 with COVID-19. After accounting for multiple testing, we did not identify any clear associations with rare variants either exome-wide or when specifically focusing on (i) 14 interferon pathway genes in which rare deleterious variants have been reported in severe COVID-19 patients; (ii) 167 genes located in COVID-19 GWAS risk loci; or (iii) 32 additional genes of immunologic relevance and/or therapeutic potential. Our analyses indicate there are no significant associations with rare protein-coding variants with detectable effect sizes at our current sample sizes. Analyses will be updated as additional data become available, with results publicly browsable at https://rgc-covid19.regeneron.com.
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Affiliation(s)
- J A Kosmicki
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - J E Horowitz
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - N Banerjee
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - R Lanche
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - A Marcketta
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - E Maxwell
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - X Bai
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - D Sun
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - J D Backman
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - D Sharma
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - H M Kang
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - C O'Dushlaine
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - A Yadav
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - A J Mansfield
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - A H Li
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - K Watanabe
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - L Gurski
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - S E McCarthy
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - A E Locke
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - S Khalid
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - S O'Keeffe
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - J Mbatchou
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - O Chazara
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - Y Huang
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - E Kvikstad
- Bristol Myers Squibb, Route 206 and Province Line Road, Princeton, NJ 08543, USA
| | - A O'Neill
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - P Nioi
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - M M Parker
- Alnylam Pharmaceuticals, 675 West Kendall St, Cambridge, MA 02142, USA
| | - S Petrovski
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - H Runz
- Biogen, 300 Binney St, Cambridge, MA 02142, USA
| | - J D Szustakowski
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - Q Wang
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - E Wong
- Biogen, 300 Binney St, Cambridge, MA 02142, USA
| | | | - E N Smith
- Takeda California Inc., 9625 Towne Centre Dr, San Diego, CA 92121, USA
| | - S Szalma
- Takeda California Inc., 9625 Towne Centre Dr, San Diego, CA 92121, USA
| | - X Zheng
- AbbVie, Inc., 1 N. Waukegan Rd, North Chicago, IL 60064, USA
| | - S Esmaeeli
- AbbVie, Inc., 1 N. Waukegan Rd, North Chicago, IL 60064, USA
| | - J W Davis
- AbbVie, Inc., 1 N. Waukegan Rd, North Chicago, IL 60064, USA
| | - Y-P Lai
- Pfizer, Inc., 1 Portland Street, Cambridge MA 02139, USA
| | - X Chen
- Pfizer, Inc., 1 Portland Street, Cambridge MA 02139, USA
| | | | | | | | | | - A Verma
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - G Sirugo
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - M D Ritchie
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - D J Rader
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - G Povysil
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - D B Goldstein
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Genetics & Development, Columbia University, New York, NY 10032, USA
| | - K Kiryluk
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY 10032, USA
| | - E Pairo-Castineira
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
| | - K Rawlik
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK
| | - D Pasko
- Genomics England, London EC1M 6BQ, UK
| | - S Walker
- Genomics England, London EC1M 6BQ, UK
| | - A Meynert
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
| | | | | | - A Tenesa
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Teviot Place, Edinburgh EH8 9AG, UK
| | - M Caulfield
- Genomics England, London EC1M 6BQ, UK
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - R Scott
- Genomics England, London EC1M 6BQ, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - J F Wilson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Teviot Place, Edinburgh EH8 9AG, UK
| | - J K Baillie
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
- Intensive Care Unit, Royal Infirmary of Edinburgh, 54 Little France Drive, Edinburgh, EH16 5SA, UK
| | - G Butler-Laporte
- Lady Davis Institute, Jewish General Hospital, Montréal, Québec H3T 1E2, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec H3A 0G4, Canada
| | - T Nakanishi
- Lady Davis Institute, Jewish General Hospital, Montréal, Québec H3T 1E2, Canada
- Department of Human Genetics, McGill University, Montréal, Québec H3A 0G4, Canada
- Kyoto-McGill International Collaborative School in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
- Research Fellow, Japan Society for the Promotion of Science
| | - M Lathrop
- Department of Human Genetics, McGill University, Montréal, Québec H3A 0G4, Canada
- Canadian Centre for Computational Genomics, McGill University, Montréal, Québec H3A 0G4, Canada
| | - J B Richards
- Lady Davis Institute, Jewish General Hospital, Montréal, Québec H3T 1E2, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec H3A 0G4, Canada
- Department of Human Genetics, McGill University, Montréal, Québec H3A 0G4, Canada
- Department of Twins Research, King's College London, London WC2R 2LS, UK
| | - M Jones
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - S Balasubramanian
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - W Salerno
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - A R Shuldiner
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - J Marchini
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - J D Overton
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - L Habegger
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - M N Cantor
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - J G Reid
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - A Baras
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - G R Abecasis
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - M A Ferreira
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
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21
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Liu S, Yu Y, Zhang S, Cole JB, Tenesa A, Wang T, McDaneld TG, Ma L, Liu GE, Fang L. Epigenomics and genotype-phenotype association analyses reveal conserved genetic architecture of complex traits in cattle and human. BMC Biol 2020; 18:80. [PMID: 32620158 PMCID: PMC7334855 DOI: 10.1186/s12915-020-00792-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 05/12/2020] [Indexed: 02/01/2023] Open
Abstract
Background Lack of comprehensive functional annotations across a wide range of tissues and cell types severely hinders the biological interpretations of phenotypic variation, adaptive evolution, and domestication in livestock. Here we used a combination of comparative epigenomics, genome-wide association study (GWAS), and selection signature analysis, to shed light on potential adaptive evolution in cattle. Results We cross-mapped 8 histone marks of 1300 samples from human to cattle, covering 178 unique tissues/cell types. By uniformly analyzing 723 RNA-seq and 40 whole genome bisulfite sequencing (WGBS) datasets in cattle, we validated that cross-mapped histone marks captured tissue-specific expression and methylation, reflecting tissue-relevant biology. Through integrating cross-mapped tissue-specific histone marks with large-scale GWAS and selection signature results, we for the first time detected relevant tissues and cell types for 45 economically important traits and artificial selection in cattle. For instance, immune tissues are significantly associated with health and reproduction traits, multiple tissues for milk production and body conformation traits (reflecting their highly polygenic architecture), and thyroid for the different selection between beef and dairy cattle. Similarly, we detected relevant tissues for 58 complex traits and diseases in humans and observed that immune and fertility traits in humans significantly correlated with those in cattle in terms of relevant tissues, which facilitated the identification of causal genes for such traits. For instance, PIK3CG, a gene highly specifically expressed in mononuclear cells, was significantly associated with both age-at-menopause in human and daughter-still-birth in cattle. ICAM, a T cell-specific gene, was significantly associated with both allergic diseases in human and metritis in cattle. Conclusion Collectively, our results highlighted that comparative epigenomics in conjunction with GWAS and selection signature analyses could provide biological insights into the phenotypic variation and adaptive evolution. Cattle may serve as a model for human complex traits, by providing additional information beyond laboratory model organisms, particularly when more novel phenotypes become available in the near future.
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Affiliation(s)
- Shuli Liu
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, BARC-East, Beltsville, MD, 20705, USA.,College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Ying Yu
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Shengli Zhang
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - John B Cole
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, BARC-East, Beltsville, MD, 20705, USA
| | - Albert Tenesa
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK.,The Roslin Institute, University of Edinburgh, Edinburgh, EH25 9RG, UK
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Tara G McDaneld
- US Meat Animal Research Center, Agricultural Research Service, USDA, Clay Center, NE, 68933, USA
| | - Li Ma
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA.
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, BARC-East, Beltsville, MD, 20705, USA.
| | - Lingzhao Fang
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, BARC-East, Beltsville, MD, 20705, USA. .,MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK. .,Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA.
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22
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Bretherick AD, Canela-Xandri O, Joshi PK, Clark DW, Rawlik K, Boutin TS, Zeng Y, Amador C, Navarro P, Rudan I, Wright AF, Campbell H, Vitart V, Hayward C, Wilson JF, Tenesa A, Ponting CP, Baillie JK, Haley C. Linking protein to phenotype with Mendelian Randomization detects 38 proteins with causal roles in human diseases and traits. PLoS Genet 2020; 16:e1008785. [PMID: 32628676 PMCID: PMC7337286 DOI: 10.1371/journal.pgen.1008785] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 04/21/2020] [Indexed: 01/25/2023] Open
Abstract
To efficiently transform genetic associations into drug targets requires evidence that a particular gene, and its encoded protein, contribute causally to a disease. To achieve this, we employ a three-step proteome-by-phenome Mendelian Randomization (MR) approach. In step one, 154 protein quantitative trait loci (pQTLs) were identified and independently replicated. From these pQTLs, 64 replicated locally-acting variants were used as instrumental variables for proteome-by-phenome MR across 846 traits (step two). When its assumptions are met, proteome-by-phenome MR, is equivalent to simultaneously running many randomized controlled trials. Step 2 yielded 38 proteins that significantly predicted variation in traits and diseases in 509 instances. Step 3 revealed that amongst the 271 instances from GeneAtlas (UK Biobank), 77 showed little evidence of pleiotropy (HEIDI), and 92 evidence of colocalization (eCAVIAR). Results were wide ranging: including, for example, new evidence for a causal role of tyrosine-protein phosphatase non-receptor type substrate 1 (SHPS1; SIRPA) in schizophrenia, and a new finding that intestinal fatty acid binding protein (FABP2) abundance contributes to the pathogenesis of cardiovascular disease. We also demonstrated confirmatory evidence for the causal role of four further proteins (FGF5, IL6R, LPL, LTA) in cardiovascular disease risk.
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Affiliation(s)
- Andrew D. Bretherick
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, Scotland, United Kingdom
| | - Oriol Canela-Xandri
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, Scotland, United Kingdom
- The Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, Scotland, United Kingdom
| | - Peter K. Joshi
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh, Scotland, United Kingdom
| | - David W. Clark
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh, Scotland, United Kingdom
| | - Konrad Rawlik
- The Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, Scotland, United Kingdom
| | - Thibaud S. Boutin
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, Scotland, United Kingdom
| | - Yanni Zeng
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, Scotland, United Kingdom
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
- Guangdong Province Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Carmen Amador
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, Scotland, United Kingdom
| | - Pau Navarro
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, Scotland, United Kingdom
| | - Igor Rudan
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh, Scotland, United Kingdom
| | - Alan F. Wright
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, Scotland, United Kingdom
| | - Harry Campbell
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh, Scotland, United Kingdom
| | - Veronique Vitart
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, Scotland, United Kingdom
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, Scotland, United Kingdom
| | - James F. Wilson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, Scotland, United Kingdom
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh, Scotland, United Kingdom
| | - Albert Tenesa
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, Scotland, United Kingdom
- The Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, Scotland, United Kingdom
| | - Chris P. Ponting
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, Scotland, United Kingdom
| | - J. Kenneth Baillie
- The Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, Scotland, United Kingdom
| | - Chris Haley
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, Scotland, United Kingdom
- The Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, Scotland, United Kingdom
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23
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Fang L, Cai W, Liu S, Canela-Xandri O, Gao Y, Jiang J, Rawlik K, Li B, Schroeder SG, Rosen BD, Li CJ, Sonstegard TS, Alexander LJ, Van Tassell CP, VanRaden PM, Cole JB, Yu Y, Zhang S, Tenesa A, Ma L, Liu GE. Comprehensive analyses of 723 transcriptomes enhance genetic and biological interpretations for complex traits in cattle. Genome Res 2020; 30:790-801. [PMID: 32424068 PMCID: PMC7263193 DOI: 10.1101/gr.250704.119] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 05/01/2020] [Indexed: 12/13/2022]
Abstract
By uniformly analyzing 723 RNA-seq data from 91 tissues and cell types, we built a comprehensive gene atlas and studied tissue specificity of genes in cattle. We demonstrated that tissue-specific genes significantly reflected the tissue-relevant biology, showing distinct promoter methylation and evolution patterns (e.g., brain-specific genes evolve slowest, whereas testis-specific genes evolve fastest). Through integrative analyses of those tissue-specific genes with large-scale genome-wide association studies, we detected relevant tissues/cell types and candidate genes for 45 economically important traits in cattle, including blood/immune system (e.g., CCDC88C) for male fertility, brain (e.g., TRIM46 and RAB6A) for milk production, and multiple growth-related tissues (e.g., FGF6 and CCND2) for body conformation. We validated these findings by using epigenomic data across major somatic tissues and sperm. Collectively, our findings provided novel insights into the genetic and biological mechanisms underlying complex traits in cattle, and our transcriptome atlas can serve as a primary source for biological interpretation, functional validation, studies of adaptive evolution, and genomic improvement in livestock.
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Affiliation(s)
- Lingzhao Fang
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland 20705, USA
- Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland 20742, USA
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian EH25 9RG, United Kingdom
- Medical Research Council Human Genetics Unit at the Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Wentao Cai
- Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland 20742, USA
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Shuli Liu
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland 20705, USA
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Oriol Canela-Xandri
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian EH25 9RG, United Kingdom
- Medical Research Council Human Genetics Unit at the Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Yahui Gao
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland 20705, USA
- Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland 20742, USA
| | - Jicai Jiang
- Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland 20742, USA
| | - Konrad Rawlik
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian EH25 9RG, United Kingdom
| | - Bingjie Li
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland 20705, USA
| | - Steven G Schroeder
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland 20705, USA
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland 20705, USA
| | - Cong-Jun Li
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland 20705, USA
| | | | - Leeson J Alexander
- Fort Keogh Livestock and Range Research Laboratory, Agricultural Research Service, USDA, Miles City, Montana 59301, USA
| | - Curtis P Van Tassell
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland 20705, USA
| | - Paul M VanRaden
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland 20705, USA
| | - John B Cole
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland 20705, USA
| | - Ying Yu
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Shengli Zhang
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Albert Tenesa
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian EH25 9RG, United Kingdom
- Medical Research Council Human Genetics Unit at the Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Li Ma
- Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland 20742, USA
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland 20705, USA
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24
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Li Y, Cho H, Wang F, Canela-Xandri O, Luo C, Rawlik K, Archacki S, Xu C, Tenesa A, Chen Q, Wang QK. Statistical and Functional Studies Identify Epistasis of Cardiovascular Risk Genomic Variants From Genome-Wide Association Studies. J Am Heart Assoc 2020; 9:e014146. [PMID: 32237974 PMCID: PMC7428625 DOI: 10.1161/jaha.119.014146] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Background Epistasis describes how gene‐gene interactions affect phenotypes, and could have a profound impact on human diseases such as coronary artery disease (CAD). The goal of this study was to identify gene‐gene interactions in CAD using an easily generalizable multi‐stage approach. Methods and Results Our forward genetic approach consists of multiple steps that combine statistical and functional approaches, and analyze information from global gene expression profiling, functional interactions, and genetic interactions to robustly identify gene‐gene interactions. Global gene expression profiling shows that knockdown of ANRIL (DQ485454) at 9p21.3 GWAS (genome‐wide association studies) CAD locus upregulates TMEM100 and TMEM106B. Functional studies indicate that the increased monocyte adhesion to endothelial cells and transendothelial migration of monocytes, 2 critical processes in the initiation of CAD, by ANRIL knockdown are reversed by knockdown of TMEM106B, but not of TMEM100. Furthermore, the decreased monocyte adhesion to endothelial cells and transendothelial migration of monocytes induced by ANRIL overexpression was reversed by overexpressing TMEM106B. TMEM106B expression was upregulated by >2‐fold in CAD coronary arteries. A significant association was found between variants in TMEM106B (but not in TMEM100) and CAD (P=1.9×10−8). Significant gene‐gene interaction was detected between ANRIL variant rs2383207 and TMEM106B variant rs3807865 (P=0.009). A similar approach also identifies significant interaction between rs6903956 in ADTRP and rs17465637 in MIA3 (P=0.005). Conclusions We demonstrate 2 pairs of epistatic interactions between GWAS loci for CAD and offer important insights into the genetic architecture and molecular mechanisms for the pathogenesis of CAD. Our strategy has broad applicability to the identification of epistasis in other human diseases.
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Affiliation(s)
- Yabo Li
- College of Life Sciences Lanzhou University Lanzhou Gansu Province P. R. China.,Department of Cardiovascular and Metabolic Sciences Lerner Research Institute Cleveland Clinic Cleveland OH.,Department of Molecular Medicine Cleveland Clinic Lerner College of Medicine of Case Western Reserve University Cleveland OH
| | - Hyosuk Cho
- Department of Cardiovascular and Metabolic Sciences Lerner Research Institute Cleveland Clinic Cleveland OH.,Department of Molecular Medicine Cleveland Clinic Lerner College of Medicine of Case Western Reserve University Cleveland OH.,Department of Genetics and Genome Sciences Case Western Reserve University School of Medicine Cleveland OH
| | - Fan Wang
- Department of Cardiovascular and Metabolic Sciences Lerner Research Institute Cleveland Clinic Cleveland OH.,Department of Molecular Medicine Cleveland Clinic Lerner College of Medicine of Case Western Reserve University Cleveland OH
| | - Oriol Canela-Xandri
- MRC Human Genetics Unit at the MRC IGMM Western General Hospital University of Edinburgh United Kingdom.,The Roslin Institute Royal (Dick) School of Veterinary Studies The University of Edinburgh, Easter Bush Campus Midlothian Edinburgh Scotland
| | - Chunyan Luo
- Key Laboratory of Molecular Biophysics College of Life Science and Technology Huazhong University of Science and Technology Wuhan Hubei China
| | - Konrad Rawlik
- The Roslin Institute Royal (Dick) School of Veterinary Studies The University of Edinburgh, Easter Bush Campus Midlothian Edinburgh Scotland
| | - Stephen Archacki
- Department of Cardiovascular and Metabolic Sciences Lerner Research Institute Cleveland Clinic Cleveland OH.,Department of Molecular Medicine Cleveland Clinic Lerner College of Medicine of Case Western Reserve University Cleveland OH
| | - Chengqi Xu
- Key Laboratory of Molecular Biophysics College of Life Science and Technology Huazhong University of Science and Technology Wuhan Hubei China
| | - Albert Tenesa
- MRC Human Genetics Unit at the MRC IGMM Western General Hospital University of Edinburgh United Kingdom.,The Roslin Institute Royal (Dick) School of Veterinary Studies The University of Edinburgh, Easter Bush Campus Midlothian Edinburgh Scotland
| | - Qiuyun Chen
- Department of Cardiovascular and Metabolic Sciences Lerner Research Institute Cleveland Clinic Cleveland OH.,Department of Molecular Medicine Cleveland Clinic Lerner College of Medicine of Case Western Reserve University Cleveland OH
| | - Qing Kenneth Wang
- Department of Cardiovascular and Metabolic Sciences Lerner Research Institute Cleveland Clinic Cleveland OH.,Department of Molecular Medicine Cleveland Clinic Lerner College of Medicine of Case Western Reserve University Cleveland OH.,Department of Genetics and Genome Sciences Case Western Reserve University School of Medicine Cleveland OH
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25
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Wragg D, Liu Q, Lin Z, Riggio V, Pugh CA, Beveridge AJ, Brown H, Hume DA, Harris SE, Deary IJ, Tenesa A, Prendergast JGD. Using regulatory variants to detect gene-gene interactions identifies networks of genes linked to cell immortalisation. Nat Commun 2020; 11:343. [PMID: 31953380 PMCID: PMC6969137 DOI: 10.1038/s41467-019-13762-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 11/19/2019] [Indexed: 12/30/2022] Open
Abstract
The extent to which the impact of regulatory genetic variants may depend on other factors, such as the expression levels of upstream transcription factors, remains poorly understood. Here we report a framework in which regulatory variants are first aggregated into sets, and using these as estimates of the total cis-genetic effects on a gene we model their non-additive interactions with the expression of other genes in the genome. Using 1220 lymphoblastoid cell lines across platforms and independent datasets we identify 74 genes where the impact of their regulatory variant-set is linked to the expression levels of networks of distal genes. We show that these networks are predominantly associated with tumourigenesis pathways, through which immortalised cells are able to rapidly proliferate. We consequently present an approach to define gene interaction networks underlying important cellular pathways such as cell immortalisation.
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Affiliation(s)
- D. Wragg
- 0000 0004 1936 7988grid.4305.2The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG UK
| | - Q. Liu
- 0000 0004 1936 7988grid.4305.2The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG UK
| | - Z. Lin
- 0000 0004 1936 7988grid.4305.2The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG UK
| | - V. Riggio
- 0000 0004 1936 7988grid.4305.2The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG UK
| | - C. A. Pugh
- 0000 0004 1936 7988grid.4305.2The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG UK
| | - A. J. Beveridge
- 0000 0001 2193 314Xgrid.8756.cGlasgow Polyomics, College of Medical, Veterinary and Life Science, University of Glasgow, Glasgow, UK
| | - H. Brown
- 0000 0004 1936 7988grid.4305.2The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG UK
| | - D. A. Hume
- 0000000406180938grid.489335.0Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, QLD 4102 Australia
| | - S. E. Harris
- 0000 0004 1936 7988grid.4305.2Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ UK
| | - I. J. Deary
- 0000 0004 1936 7988grid.4305.2Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ UK
| | - A. Tenesa
- 0000 0004 1936 7988grid.4305.2The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG UK
| | - J. G. D. Prendergast
- 0000 0004 1936 7988grid.4305.2The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG UK
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26
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Fang L, Liu S, Liu M, Kang X, Lin S, Li B, Connor EE, Baldwin RL, Tenesa A, Ma L, Liu GE, Li CJ. Functional annotation of the cattle genome through systematic discovery and characterization of chromatin states and butyrate-induced variations. BMC Biol 2019; 17:68. [PMID: 31419979 PMCID: PMC6698049 DOI: 10.1186/s12915-019-0687-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 08/05/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The functional annotation of genomes, including chromatin accessibility and modifications, is important for understanding and effectively utilizing the increased amount of genome sequences reported. However, while such annotation has been well explored in a diverse set of tissues and cell types in human and model organisms, relatively little data are available for livestock genomes, hindering our understanding of complex trait variation, domestication, and adaptive evolution. Here, we present the first complete global landscape of regulatory elements in cattle and explore the dynamics of chromatin states in rumen epithelial cells induced by the rumen developmental regulator-butyrate. RESULTS We established the first global map of regulatory elements (15 chromatin states) and defined their coordinated activities in cattle, through genome-wide profiling for six histone modifications, RNA polymerase II, CTCF-binding sites, DNA accessibility, DNA methylation, and transcriptome in rumen epithelial primary cells (REPC), rumen tissues, and Madin-Darby bovine kidney epithelial cells (MDBK). We demonstrated that each chromatin state exhibited specific enrichment for sequence ontology, transcription, methylation, trait-associated variants, gene expression-associated variants, selection signatures, and evolutionarily conserved elements, implying distinct biological functions. After butyrate treatments, we observed that the weak enhancers and flanking active transcriptional start sites (TSS) were the most dynamic chromatin states, occurred concomitantly with significant alterations in gene expression and DNA methylation, which was significantly associated with heifer conception rate and stature economic traits. CONCLUSION Our results demonstrate the crucial role of functional genome annotation for understanding genome regulation, complex trait variation, and adaptive evolution in livestock. Using butyrate to induce the dynamics of the epigenomic landscape, we were able to establish the correlation among nutritional elements, chromatin states, gene activities, and phenotypic outcomes.
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Affiliation(s)
- Lingzhao Fang
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742 USA
| | - Shuli Liu
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Mei Liu
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
- College of Animal Science and Technology, Shaanxi Key Laboratory of Agricultural Molecular Biology, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Xiaolong Kang
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
- College of Agriculture, Ningxia University, Yinchuan, 750021 China
| | - Shudai Lin
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science of South China Agricultural University, Guangzhou, 510642 China
| | - Bingjie Li
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Erin E. Connor
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Ransom L. Baldwin
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Albert Tenesa
- The Roslin Institute, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Li Ma
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742 USA
| | - George E. Liu
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Cong-jun Li
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
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27
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Zeng Y, Amador C, Xia C, Marioni R, Sproul D, Walker RM, Morris SW, Bretherick A, Canela-Xandri O, Boutin TS, Clark DW, Campbell A, Rawlik K, Hayward C, Nagy R, Tenesa A, Porteous DJ, Wilson JF, Deary IJ, Evans KL, McIntosh AM, Navarro P, Haley CS. Publisher Correction: Parent of origin genetic effects on methylation in humans are common and influence complex trait variation. Nat Commun 2019; 10:2069. [PMID: 31043600 PMCID: PMC6494888 DOI: 10.1038/s41467-019-10155-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
In the original version of this Article, the legend in the upper panel of Figure 2 incorrectly read 'paternal imprinting' and should have read 'maternal imprinting'. This has been corrected in both the PDF and HTML versions of the Article.
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Affiliation(s)
- Yanni Zeng
- MRC Human Genetic Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Carmen Amador
- MRC Human Genetic Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Charley Xia
- MRC Human Genetic Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
- The Roslin Institute and Royal (Dick) School of Veterinary Sciences, University of Edinburgh, Edinburgh, EH25 9RG, UK
| | - Riccardo Marioni
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Centre for Genomic and Experimental Medicine, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Duncan Sproul
- MRC Human Genetic Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
- Edinburgh Cancer Research Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - Rosie M Walker
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Centre for Genomic and Experimental Medicine, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Stewart W Morris
- Centre for Genomic and Experimental Medicine, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Andrew Bretherick
- MRC Human Genetic Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Oriol Canela-Xandri
- MRC Human Genetic Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
- The Roslin Institute and Royal (Dick) School of Veterinary Sciences, University of Edinburgh, Edinburgh, EH25 9RG, UK
| | - Thibaud S Boutin
- MRC Human Genetic Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - David W Clark
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, EH8 9AG, UK
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Konrad Rawlik
- The Roslin Institute and Royal (Dick) School of Veterinary Sciences, University of Edinburgh, Edinburgh, EH25 9RG, UK
| | - Caroline Hayward
- MRC Human Genetic Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Reka Nagy
- MRC Human Genetic Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Albert Tenesa
- MRC Human Genetic Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
- The Roslin Institute and Royal (Dick) School of Veterinary Sciences, University of Edinburgh, Edinburgh, EH25 9RG, UK
| | - David J Porteous
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Centre for Genomic and Experimental Medicine, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - James F Wilson
- MRC Human Genetic Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, EH8 9AG, UK
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Kathryn L Evans
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Centre for Genomic and Experimental Medicine, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Andrew M McIntosh
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Division of Psychiatry, University of Edinburgh, Edinburgh, EH10 5HF, UK
| | - Pau Navarro
- MRC Human Genetic Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Chris S Haley
- MRC Human Genetic Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK.
- The Roslin Institute and Royal (Dick) School of Veterinary Sciences, University of Edinburgh, Edinburgh, EH25 9RG, UK.
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28
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Zeng Y, Amador C, Xia C, Marioni R, Sproul D, Walker RM, Morris SW, Bretherick A, Canela-Xandri O, Boutin TS, Clark DW, Campbell A, Rawlik K, Hayward C, Nagy R, Tenesa A, Porteous DJ, Wilson JF, Deary IJ, Evans KL, McIntosh AM, Navarro P, Haley CS. Parent of origin genetic effects on methylation in humans are common and influence complex trait variation. Nat Commun 2019; 10:1383. [PMID: 30918249 PMCID: PMC6437195 DOI: 10.1038/s41467-019-09301-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 02/28/2019] [Indexed: 01/11/2023] Open
Abstract
Parent-of-origin effects (POE) exist when there is differential expression of alleles inherited from the two parents. A genome-wide scan for POE on DNA methylation at 639,238 CpGs in 5,101 individuals identifies 733 independent methylation CpGs potentially influenced by POE at a false discovery rate ≤ 0.05 of which 331 had not previously been identified. Cis and trans methylation quantitative trait loci (mQTL) regulate methylation variation through POE at 54% (399/733) of the identified POE-influenced CpGs. The combined results provide strong evidence for previously unidentified POE-influenced CpGs at 171 independent loci. Methylation variation at 14 of the POE-influenced CpGs is associated with multiple metabolic traits. A phenome-wide association analysis using the POE mQTL SNPs identifies a previously unidentified imprinted locus associated with waist circumference. These results provide a high resolution population-level map for POE on DNA methylation sites, their local and distant regulators and potential consequences for complex traits.
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Affiliation(s)
- Yanni Zeng
- MRC Human Genetic Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Carmen Amador
- MRC Human Genetic Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Charley Xia
- MRC Human Genetic Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
- The Roslin Institute and Royal (Dick) School of Veterinary Sciences, University of Edinburgh, Edinburgh, EH25 9RG, UK
| | - Riccardo Marioni
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Centre for Genomic and Experimental Medicine, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Duncan Sproul
- MRC Human Genetic Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
- Edinburgh Cancer Research Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - Rosie M Walker
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Centre for Genomic and Experimental Medicine, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Stewart W Morris
- Centre for Genomic and Experimental Medicine, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Andrew Bretherick
- MRC Human Genetic Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Oriol Canela-Xandri
- MRC Human Genetic Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
- The Roslin Institute and Royal (Dick) School of Veterinary Sciences, University of Edinburgh, Edinburgh, EH25 9RG, UK
| | - Thibaud S Boutin
- MRC Human Genetic Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - David W Clark
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, EH8 9AG, UK
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Konrad Rawlik
- The Roslin Institute and Royal (Dick) School of Veterinary Sciences, University of Edinburgh, Edinburgh, EH25 9RG, UK
| | - Caroline Hayward
- MRC Human Genetic Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Reka Nagy
- MRC Human Genetic Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Albert Tenesa
- MRC Human Genetic Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
- The Roslin Institute and Royal (Dick) School of Veterinary Sciences, University of Edinburgh, Edinburgh, EH25 9RG, UK
| | - David J Porteous
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Centre for Genomic and Experimental Medicine, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - James F Wilson
- MRC Human Genetic Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, EH8 9AG, UK
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Kathryn L Evans
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Centre for Genomic and Experimental Medicine, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Andrew M McIntosh
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Division of Psychiatry, University of Edinburgh, Edinburgh, EH10 5HF, UK
| | - Pau Navarro
- MRC Human Genetic Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Chris S Haley
- MRC Human Genetic Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK.
- The Roslin Institute and Royal (Dick) School of Veterinary Sciences, University of Edinburgh, Edinburgh, EH25 9RG, UK.
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Theodoratou E, Farrington SM, Timofeeva M, Din FV, Svinti V, Tenesa A, Liu T, Lindblom A, Gallinger S, Campbell H, Dunlop MG. Genome-wide scan of the effect of common nsSNPs on colorectal cancer survival outcome. Br J Cancer 2018; 119:988-993. [PMID: 30135471 PMCID: PMC6203849 DOI: 10.1038/s41416-018-0117-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 04/16/2018] [Accepted: 04/20/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND We conducted a genome-wide scan to identify non-synonymous SNPs (nsSNPs) that might influence survival after a diagnosis of colorectal cancer (CRC). METHODS We genotyped 7679 nsSNPs in 1939 Scottish patients from the Scottish Colorectal Cancer Study recruited soon after a CRC diagnosis and prospectively followed for survival outcomes. All-cause and CRC-specific survival analyses were conducted using Cox proportional hazard models adjusted for stage, age and sex for all cancer cases, after cancer type stratification and assuming additive and recessive models of inheritance. For all the SNPs that had a p-value < 0.10 a meta-analysis was performed combining the results of the discovery set and a replication set of 899 Scottish CRC patients. The p-value threshold of significance was set as at p < 10-8. RESULTS 897 and 894 nsSNPs were associated with all-cause and CRC-specific mortality, respectively, at a p-value level < 0.10 in the discovery set. Meta-analysis of the results from the discovery and replication sets was performed overall and for cancers of colon and rectum separately and none of the variants reached a p-value < 10-8. CONCLUSIONS This large scale well-powered analysis demonstrates that common nsSNPs are not associated with CRC prognosis overall.
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Affiliation(s)
- Evropi Theodoratou
- Centre of Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, UK
- Colon Cancer Genetics Group and Academic Coloproctology, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit Western General Hospital Edinburgh, Edinburgh, EH4 2XU, UK
| | - Susan M Farrington
- Colon Cancer Genetics Group and Academic Coloproctology, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit Western General Hospital Edinburgh, Edinburgh, EH4 2XU, UK
| | - Maria Timofeeva
- Colon Cancer Genetics Group and Academic Coloproctology, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit Western General Hospital Edinburgh, Edinburgh, EH4 2XU, UK
| | - Farhat Vn Din
- Colon Cancer Genetics Group and Academic Coloproctology, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit Western General Hospital Edinburgh, Edinburgh, EH4 2XU, UK
| | - Victoria Svinti
- Colon Cancer Genetics Group and Academic Coloproctology, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit Western General Hospital Edinburgh, Edinburgh, EH4 2XU, UK
| | - Albert Tenesa
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, EH25 9RG, UK
| | - Tao Liu
- Department of Molecular Medicine and Surgery, Karolinska Institute and Department of Clinical Genetics, Karolinska University Hospital, Solna, SE-17176, Stockholm, Sweden
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institute and Department of Clinical Genetics, Karolinska University Hospital, Solna, SE-17176, Stockholm, Sweden
| | - Steven Gallinger
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Harry Campbell
- Centre of Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, UK
- Colon Cancer Genetics Group and Academic Coloproctology, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit Western General Hospital Edinburgh, Edinburgh, EH4 2XU, UK
| | - Malcolm G Dunlop
- Colon Cancer Genetics Group and Academic Coloproctology, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit Western General Hospital Edinburgh, Edinburgh, EH4 2XU, UK.
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Sanabria-Salas MC, Fejerman L, Rawlik K, Tenesa A, Serrano-Lopez ML, Zabaleta J, Hernandez-Suarez GA. Abstract A37: Genome-wide association study of colorectal tumors in Latin American individuals from Colombia. Cancer Epidemiol Biomarkers Prev 2018. [DOI: 10.1158/1538-7755.disp17-a37] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Abstract
Introduction: Colorectal cancer (CRC) is one of the most common cancers worldwide, with higher incidence among more developed countries. However, mortality rates are higher and increasing in less-developed regions, including Colombia. Incidence and mortality rates of CRC vary across the country, with the lowest rates among populations with increased concentration of Native Americans. Our group previously reported that increased European and African ancestry was associated with higher adenomatous polyps (AP) and CRC risk in Colombians. Based on this observation we hypothesize that genetic contribution to the observed regional variation on CRC development in Colombia might be partly explained by the influence of genetic variants with different frequency distribution in the European, Amerindian, and African ancestral components.
Objective: To test our hypothesis we performed a genome-wide association study (GWAS) of colorectal tumors in Colombian CRC and AP cases and controls.
Materials and Methods: We conducted a GWAS of Colombians from different regions of the country that included 162 CRC cases, 122 AP cases, and 131 controls. Only SNPs with MAF ≥ 0.05 were included. The role of these common variants was assessed by logistic regression models adjusted for age, sex, and the first 10 principal components (PCs) of the genetic variation. Analyses were performed for a total of 606410 SNPs. The P value threshold for genome-wide significant SNPs was set at the traditional value of ≤ 5 × 10−8.
Results: We replicated some of the previously reported associations (8 out of 44 SNPs, P ≤ 0.05) of which 7 had directionally concordant ORs. Regarding the remaining 36 published risk variants, 25 had directionally concordant ORs, even though neither of them was significant at nominal P ≤ 0.05. None of the SNPs analyzed passed the threshold for genome-wide significance. However, we found multiple suggestive associations. One novel SNP within the region 2q11.2-q12 near the gene MAP4K4 was associated with the risk of AP (rs4280476-G; OR 0.36; 95% CI 0.23-0.56; P = 8.7 x 10-6). We also found four novel SNPs across three regions with suggestive CRC risk associations: rs10514122-A located in the locus 5q14 near the TBCA gene (OR 0.30; 95% CI 0.18-0.49; P = 3.6 x 10-6), rs10746883-G (OR 0.37; 95% CI 0.25-0.56; P = 3.2 x 10-6) and the rs10781032-A (OR 0.35; 95% CI 0.22-0.53; P = 1.7 x 10-6), in high LD with each other (R2 = 0.81), located in the locus 9q21.1-q21.2 near the genes TRPM3 and TMEM2 and the SNP rs2800641-G located in the region 6q25.2 near the MYCT1 gene (OR 2.96; 95% CI 1.83-4.77; P = 8.9 x 10-6). The inflation factors (λ), when comparing AP or CRC cases vs controls, were 1.05 and 1.04, respectively, indicating appropriate control for population stratification. Finally, it is of note that the MAF reported for the 5 novel SNPs identified in our study shows important differences between European, Asian, and African reference populations from the public database 1,000 genomes.
Conclusions: In this GWAS of AP and CRC in individuals from Colombia, we replicated some of the previously reported associations and identified suggestive signals for 5 novel risk alleles located at four loci (2q11.2-q12, 5q14, 9q21.1-q21.2, and 6q25.2). Further work is needed to replicate our findings in other Latin American populations.
Citation Format: Maria Carolina Sanabria-Salas, Laura Fejerman, Konrad Rawlik, Albert Tenesa, Martha L. Serrano-Lopez, Jovanny Zabaleta, Gustavo A. Hernandez-Suarez. Genome-wide association study of colorectal tumors in Latin American individuals from Colombia [abstract]. In: Proceedings of the Tenth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2017 Sep 25-28; Atlanta, GA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2018;27(7 Suppl):Abstract nr A37.
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Affiliation(s)
| | - Laura Fejerman
- 2Institute of Human Genetics, University of California San Francisco, San Francisco, CA,
| | - Konrad Rawlik
- 3Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom,
| | - Albert Tenesa
- 3Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom,
| | | | - Jovanny Zabaleta
- 5Stanley S Scott Cancer Center, Louisiana State University, New Orleans, LA
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Baillie JK, Bretherick A, Haley CS, Clohisey S, Gray A, Neyton LPA, Barrett J, Stahl EA, Tenesa A, Andersson R, Brown JB, Faulkner GJ, Lizio M, Schaefer U, Daub C, Itoh M, Kondo N, Lassmann T, Kawai J, Mole D, Bajic VB, Heutink P, Rehli M, Kawaji H, Sandelin A, Suzuki H, Satsangi J, Wells CA, Hacohen N, Freeman TC, Hayashizaki Y, Carninci P, Forrest ARR, Hume DA. Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease. PLoS Comput Biol 2018; 14:e1005934. [PMID: 29494619 PMCID: PMC5849332 DOI: 10.1371/journal.pcbi.1005934] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 03/13/2018] [Accepted: 12/18/2017] [Indexed: 12/13/2022] Open
Abstract
Genetic variants underlying complex traits, including disease susceptibility, are enriched within the transcriptional regulatory elements, promoters and enhancers. There is emerging evidence that regulatory elements associated with particular traits or diseases share similar patterns of transcriptional activity. Accordingly, shared transcriptional activity (coexpression) may help prioritise loci associated with a given trait, and help to identify underlying biological processes. Using cap analysis of gene expression (CAGE) profiles of promoter- and enhancer-derived RNAs across 1824 human samples, we have analysed coexpression of RNAs originating from trait-associated regulatory regions using a novel quantitative method (network density analysis; NDA). For most traits studied, phenotype-associated variants in regulatory regions were linked to tightly-coexpressed networks that are likely to share important functional characteristics. Coexpression provides a new signal, independent of phenotype association, to enable fine mapping of causative variants. The NDA coexpression approach identifies new genetic variants associated with specific traits, including an association between the regulation of the OCT1 cation transporter and genetic variants underlying circulating cholesterol levels. NDA strongly implicates particular cell types and tissues in disease pathogenesis. For example, distinct groupings of disease-associated regulatory regions implicate two distinct biological processes in the pathogenesis of ulcerative colitis; a further two separate processes are implicated in Crohn's disease. Thus, our functional analysis of genetic predisposition to disease defines new distinct disease endotypes. We predict that patients with a preponderance of susceptibility variants in each group are likely to respond differently to pharmacological therapy. Together, these findings enable a deeper biological understanding of the causal basis of complex traits.
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Affiliation(s)
- J. Kenneth Baillie
- Division of Genetics and Genomics, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Inflammation Research, University of Edinburgh, Edinburgh, United Kingdom
- Intensive Care Unit, Royal Infirmary Edinburgh, Edinburgh, United Kingdom
| | - Andrew Bretherick
- Division of Genetics and Genomics, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Christopher S. Haley
- Division of Genetics and Genomics, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
- Institute for Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Sara Clohisey
- Division of Genetics and Genomics, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Alan Gray
- Edinburgh Parallel Computing Centre, The University of Edinburgh, Edinburgh, United Kingdom
| | - Lucile P. A. Neyton
- Division of Genetics and Genomics, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Jeffrey Barrett
- Statistical Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Eli A. Stahl
- Center for Statistical Genetics, Icahn School of Medicine at Mount Sinai, New York, United States of America
| | - Albert Tenesa
- Division of Genetics and Genomics, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Robin Andersson
- The Bioinformatics Centre, Department of Biology & Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - J. Ben Brown
- Department of Statistics, University of California, Berkeley, United States of America
| | - Geoffrey J. Faulkner
- Mater Research Institute, University of Queensland, University of Queensland, Brisbane, Australia
| | - Marina Lizio
- RIKEN Omics Science Center, Yokohama, Japan, Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Ulf Schaefer
- Department for Infectious Disease Informatics, Public Health England, Colindale, United Kingdom
| | - Carsten Daub
- RIKEN Omics Science Center, Yokohama, Japan, Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Masayoshi Itoh
- RIKEN Omics Science Center, Yokohama, Japan, Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Japan
| | - Naoto Kondo
- RIKEN Omics Science Center, Yokohama, Japan, Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Timo Lassmann
- RIKEN Omics Science Center, Yokohama, Japan, Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Jun Kawai
- RIKEN Omics Science Center, Yokohama, Japan, Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - IIBDGC Consortium
- Harry Perkins Institute of Medical Research, and the Centre for Medical Research, University of Western Australia, QEII Medical Centre, Nedlands, Perth, Western Australia, Australia
| | - Damian Mole
- Centre for Inflammation Research, University of Edinburgh, Edinburgh, United Kingdom
| | - Vladimir B. Bajic
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center, Thuwal, Kingdom of Saudi Arabia
| | - Peter Heutink
- German Center for Neurodegenerative Diseases, Tübingen, Germany
| | - Michael Rehli
- Dept. Hematology, University Hospital Regensburg, Regensburg, Germany
| | - Hideya Kawaji
- RIKEN Omics Science Center, Yokohama, Japan, Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Japan
| | - Albin Sandelin
- The Bioinformatics Centre, Department of Biology & Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Harukazu Suzuki
- RIKEN Omics Science Center, Yokohama, Japan, Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Jack Satsangi
- Institute for Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Christine A. Wells
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, St Lucia, Brisbane Australia
| | - Nir Hacohen
- Broad Institute of Harvard and MIT, Cambridge, United States of America
| | - Thomas C. Freeman
- Division of Genetics and Genomics, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Yoshihide Hayashizaki
- RIKEN Omics Science Center, Yokohama, Japan, Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Piero Carninci
- RIKEN Omics Science Center, Yokohama, Japan, Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Alistair R. R. Forrest
- Harry Perkins Institute of Medical Research, and the Centre for Medical Research, University of Western Australia, QEII Medical Centre, Nedlands, Perth, Western Australia, Australia
| | - David A. Hume
- Division of Genetics and Genomics, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
- Mater Research Institute, University of Queensland, University of Queensland, Brisbane, Australia
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Tanskanen T, van den Berg L, Välimäki N, Aavikko M, Ness-Jensen E, Hveem K, Wettergren Y, Bexe Lindskog E, Tõnisson N, Metspalu A, Silander K, Orlando G, Law PJ, Tuupanen S, Gylfe AE, Hänninen UA, Cajuso T, Kondelin J, Sarin AP, Pukkala E, Jousilahti P, Salomaa V, Ripatti S, Palotie A, Järvinen H, Renkonen-Sinisalo L, Lepistö A, Böhm J, Mecklin JP, Al-Tassan NA, Palles C, Martin L, Barclay E, Tenesa A, Farrington S, Timofeeva MN, Meyer BF, Wakil SM, Campbell H, Smith CG, Idziaszczyk S, Maughan TS, Kaplan R, Kerr R, Kerr D, Buchanan DD, Win AK, Hopper J, Jenkins M, Newcomb PA, Gallinger S, Conti D, Schumacher FR, Casey G, Cheadle JP, Dunlop MG, Tomlinson IP, Houlston RS, Palin K, Aaltonen LA. Genome-wide association study and meta-analysis in Northern European populations replicate multiple colorectal cancer risk loci. Int J Cancer 2018; 142:540-546. [PMID: 28960316 PMCID: PMC6383773 DOI: 10.1002/ijc.31076] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 08/04/2017] [Accepted: 09/01/2017] [Indexed: 12/14/2022]
Abstract
Genome-wide association studies have been successful in elucidating the genetic basis of colorectal cancer (CRC), but there remains unexplained variability in genetic risk. To identify new risk variants and to confirm reported associations, we conducted a genome-wide association study in 1,701 CRC cases and 14,082 cancer-free controls from the Finnish population. A total of 9,068,015 genetic variants were imputed and tested, and 30 promising variants were studied in additional 11,647 cases and 12,356 controls of European ancestry. The previously reported association between the single-nucleotide polymorphism (SNP) rs992157 (2q35) and CRC was independently replicated (p = 2.08 × 10-4 ; OR, 1.14; 95% CI, 1.06-1.23), and it was genome-wide significant in combined analysis (p = 1.50 × 10-9 ; OR, 1.12; 95% CI, 1.08-1.16). Variants at 2q35, 6p21.2, 8q23.3, 8q24.21, 10q22.3, 10q24.2, 11q13.4, 11q23.1, 14q22.2, 15q13.3, 18q21.1, 20p12.3 and 20q13.33 were associated with CRC in the Finnish population (false discovery rate < 0.1), but new risk loci were not found. These results replicate the effects of multiple loci on the risk of CRC and identify shared risk alleles between the Finnish population isolate and outbred populations.
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Affiliation(s)
- Tomas Tanskanen
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Linda van den Berg
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Niko Välimäki
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Mervi Aavikko
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Eivind Ness-Jensen
- HUNT Research Centre, Department of Public Health, NTNU, Norwegian University of Science and Technology, Levanger, Norway
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Department of Medicine, Levanger Hospital, Nord-Trøndelag Hospital Trust, Levanger, Norway
| | - Kristian Hveem
- HUNT Research Centre, Department of Public Health, NTNU, Norwegian University of Science and Technology, Levanger, Norway
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Yvonne Wettergren
- Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Sweden
| | - Elinor Bexe Lindskog
- Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Sweden
| | - Neeme Tõnisson
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | | | - Kaisa Silander
- National Institute for Health and Welfare, Helsinki, Finland
| | - Giulia Orlando
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Philip J. Law
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Sari Tuupanen
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Alexandra E. Gylfe
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Ulrika A. Hänninen
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Tatiana Cajuso
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Johanna Kondelin
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Antti-Pekka Sarin
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Eero Pukkala
- Finnish Cancer Registry, Institute for Statistical and Epidemiological Cancer Research, Helsinki, Finland
- Faculty of Social Sciences, University of Tampere, Tampere, Finland
| | | | - Veikko Salomaa
- National Institute for Health and Welfare, Helsinki, Finland
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Heikki Järvinen
- Department of Surgery, Abdominal Center, Helsinki University Hospital, Helsinki, Finland
| | | | - Anna Lepistö
- Department of Surgery, Abdominal Center, Helsinki University Hospital, Helsinki, Finland
| | - Jan Böhm
- Department of Pathology, Central Finland Central Hospital, Jyväskylä, Finland
| | - Jukka-Pekka Mecklin
- Department of Surgery, Jyväskylä Central Hospital, University of Eastern Finland, Jyväskylä, Finland
| | - Nada A. Al-Tassan
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Claire Palles
- Wellcome Trust Centre for Human Genetics and NIHR Comprehensive Biomedical Research Centre, Oxford, UK
| | - Lynn Martin
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Ella Barclay
- Wellcome Trust Centre for Human Genetics and NIHR Comprehensive Biomedical Research Centre, Oxford, UK
| | - Albert Tenesa
- Colon Cancer Genetics Group, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital, Edinburgh, UK
- The Roslin Institute, University of Edinburgh, Easter Bush, Roslin, UK
| | - Susan Farrington
- Colon Cancer Genetics Group, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital, Edinburgh, UK
| | - Maria N. Timofeeva
- Colon Cancer Genetics Group, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital, Edinburgh, UK
| | - Brian F. Meyer
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Salma M. Wakil
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Harry Campbell
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, UK
| | - Christopher G. Smith
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Shelley Idziaszczyk
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Tim S. Maughan
- CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | | | - Rachel Kerr
- Oxford Cancer Centre, Department of Oncology, University of Oxford, Churchill Hospital, Oxford, UK
| | - David Kerr
- Nuffield Department of Clinical Laboratory Sciences, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Daniel D. Buchanan
- Colorectal Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne, VIC, Australia
| | - Aung K. Win
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne, VIC, Australia
| | - John Hopper
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne, VIC, Australia
| | - Mark Jenkins
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne, VIC, Australia
| | - Polly A. Newcomb
- Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Steve Gallinger
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - David Conti
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Fredrick R. Schumacher
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA
| | - Graham Casey
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Jeremy P. Cheadle
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Malcolm G. Dunlop
- Colon Cancer Genetics Group, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital, Edinburgh, UK
| | - Ian P. Tomlinson
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Richard S. Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Kimmo Palin
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Lauri A. Aaltonen
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
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Rawlik K, Rowlatt A, Sanabria-Salas MC, Hernández-Suárez G, Serrano López ML, Zabaleta J, Tenesa A. Evidence of epigenetic admixture in the Colombian population. Hum Mol Genet 2017; 26:501-508. [PMID: 28073928 PMCID: PMC5409088 DOI: 10.1093/hmg/ddw407] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 11/23/2016] [Indexed: 01/10/2023] Open
Abstract
DNA methylation (DNAm) measured in lymphoblastoid cell lines has been repeatedly demonstrated to differ between various human populations. Due to the role that DNAm plays in controlling gene expression, these differences could significantly contribute to ethnic phenotypic differences. However, because previous studies have compared distinct ethnic groups where genetic and environmental context are confounded, their relative contribution to phenotypic differences between ethnicities remains unclear. Using DNAm assayed in whole blood and colorectal tissue of 132 admixed individuals from Colombia, we identified sites where differential DNAm levels were associated with the local ancestral genetic context. Our results are consistent with population specific DNAm being primarily driven by between population genetic differences in cis, with little environmental contribution, and with consistent effects across tissues. The findings offer new insights into a possible mechanism driving phenotypic differences among different ethnic groups, and could help explain ethnic differences in colorectal cancer incidence.
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Affiliation(s)
- Konrad Rawlik
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian, Scotland, UK
| | - Amy Rowlatt
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian, Scotland, UK
| | - María Carolina Sanabria-Salas
- Subdirección de Investigaciones, Instituto Nacional de Cancerología, Bogotá D.C., Colombia.,Departamento de Química, Universidad Nacional de Colombia, Bogotá D.C., Colombia
| | | | - Martha Lucía Serrano López
- Subdirección de Investigaciones, Instituto Nacional de Cancerología, Bogotá D.C., Colombia.,Departamento de Química, Universidad Nacional de Colombia, Bogotá D.C., Colombia
| | - Jovanny Zabaleta
- Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA, USA.,Department of Pediatrics, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Albert Tenesa
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian, Scotland, UK.,MRC HGU at the MRC IGMM, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh, UK
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Sanabria-Salas MC, Rawlik K, Tenesa A, Umaña-Pérez A, Serrano-López ML, Gómez MSD, Zabaleta J, Hernández-Suárez G. Abstract LB-162: Common genetic variants within TEP1 gene (14q11.2 locus) and TK1 gene (17q25.3 locus) are associated with the risk of colorectal tumors in Latinos. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-lb-162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: Around 63 common risk variants have been associated with colorectal cancer (CRC) through genome-wide association studies (GWAS) in European and Asian populations; these variants, together with the high penetrance genes responsible for 5% of the cases, do not completely explain the CRC heritability estimated at ~ 35%.
Objective: To discover new common variants associated with the risk of colorectal tumors, taking advantage of the high level of admixture in Latino populations.
Materials and methods: We performed a candidate gene association (CG) and GWAS analyses, in a multicenter case-control study that included 313 cases of CRC, 200 cases of adenomatous polyps (AP) and 506 controls from six Colombian cities. The role of these common variants was assessed by basic SNP association analyses (X2) and logistic regressions adjusted for age, sex and ancestry proportions. Selected SNPs were genotyped by TaqMan in additional samples.
Results: European ancestry was associated with the risk of AP while African ancestry was associated with the risk of both, AP and CCR, (P ≤ 0.01). In the adjusted logistic regression analyses of the CG study, we found that the minor allele (A) of the SNP 14q11.2:rs1760898 (C>A) was associated with the risk of CRC (OR 0.48; 95% CI 0.33-0.69; UNADJ P = 6.8 x 10-5; 100,000 Pperm = 0.03). This association persisted in the adjusted logistic regressions analyses with additional samples genotyped by TaqMan (P = 0.03). In the basic SNP association analyses (X2) of the GWAS study, we found that the minor allele (A) of the SNP 17q25.3:rs1065768 (G>A) was associated with the risk of AP (OR 0.35; 95% CI 0.24 -0.51; UNADJ P = 3.4 x 10-8; Bonferroni corrected P = 0.02). This association persisted after including additional samples genotyped by TaqMan, both, in the basic SNP analysis (P = 1.7 x 10-7) and in the adjusted logistic regressions analysis (P = 9.7 x 10-5). Moreover, the association remained when other variables were also included in the model, such as the first 10 major principal components of genetic variability, ancestry proportions along chromosome 17 and locus-specific ancestry (P = 1.7 x 10-4).
Conclusions: The SNP rs1760898 (TEP1, Telomerase Associated Protein 1 gene) confers a change of Asparagine (Asn) to Lysine (Lys) within the RNA binding domain, TROVE. This change could affect the activity of telomerase enzyme that has an important role in cancer development. The SNP rs1065768 (3'UTR TK1, Thymidine kinase 1 gene) could affect mRNA stability and protein production of TK1, which is essential in DNA synthesis. Although, functional analyses are required to confirm their potential role in colorectal tumorogenesis, our findings help increase our understanding about the biological basis for the development of colorectal tumors, as well as will contribute to the overall knowledge on the heritability of CRC.
Citation Format: María Carolina Sanabria-Salas, Konrad Rawlik, Albert Tenesa, Adriana Umaña-Pérez, Martha Lucía Serrano-López, Myriam Sánchez de Gómez, Jovanny Zabaleta, Gustavo Hernández-Suárez. Common genetic variants within TEP1 gene (14q11.2 locus) and TK1 gene (17q25.3 locus) are associated with the risk of colorectal tumors in Latinos [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-162. doi:10.1158/1538-7445.AM2017-LB-162
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Sanabria-Salas MC, Hernández-Suárez G, Umaña-Pérez A, Rawlik K, Tenesa A, Serrano-López ML, Sánchez de Gómez M, Rojas MP, Bravo LE, Albis R, Plata JL, Green H, Borgovan T, Li L, Majumdar S, Garai J, Lee E, Ashktorab H, Brim H, Li L, Margolin D, Fejerman L, Zabaleta J. IL1B-CGTC haplotype is associated with colorectal cancer in admixed individuals with increased African ancestry. Sci Rep 2017; 7:41920. [PMID: 28157220 PMCID: PMC5291207 DOI: 10.1038/srep41920] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 01/03/2017] [Indexed: 02/07/2023] Open
Abstract
Single-nucleotide polymorphisms (SNPs) in cytokine genes can affect gene expression and thereby modulate inflammation and carcinogenesis. However, the data on the association between SNPs in the interleukin 1 beta gene (IL1B) and colorectal cancer (CRC) are conflicting. We found an association between a 4-SNP haplotype block of the IL1B (-3737C/-1464G/-511T/-31C) and CRC risk, and this association was exclusively observed in individuals with a higher proportion of African ancestry, such as individuals from the Coastal Colombian region (odds ratio, OR 2.06; 95% CI 1.31–3.25; p < 0.01). Moreover, a significant interaction between this CRC risk haplotype and local African ancestry dosage was identified in locus 2q14 (p = 0.03). We conclude that Colombian individuals with high African ancestry proportions at locus 2q14 harbour more IL1B-CGTC copies and are consequently at an increased risk of CRC. This haplotype has been previously found to increase the IL1B promoter activity and is the most frequent haplotype in African Americans. Despite of limitations in the number of samples and the lack of functional analysis to examine the effect of these haplotypes on CRC cell lines, our results suggest that inflammation and ethnicity play a major role in the modulation of CRC risk.
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Affiliation(s)
- María Carolina Sanabria-Salas
- Subdirección de Investigaciones, Instituto Nacional de Cancerología de Colombia, Bogotá D.C., Colombia.,Departamento de Química, Universidad Nacional de Colombia, Bogotá D.C., Colombia
| | - Gustavo Hernández-Suárez
- Subdirección de Investigaciones, Instituto Nacional de Cancerología de Colombia, Bogotá D.C., Colombia
| | - Adriana Umaña-Pérez
- Departamento de Química, Universidad Nacional de Colombia, Bogotá D.C., Colombia
| | - Konrad Rawlik
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, UK
| | - Albert Tenesa
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, UK.,MRC-Human Genetics Unit, University of Edinburgh, UK
| | - Martha Lucía Serrano-López
- Subdirección de Investigaciones, Instituto Nacional de Cancerología de Colombia, Bogotá D.C., Colombia.,Departamento de Química, Universidad Nacional de Colombia, Bogotá D.C., Colombia
| | | | - Martha Patricia Rojas
- Subdirección de Investigaciones, Instituto Nacional de Cancerología de Colombia, Bogotá D.C., Colombia
| | | | - Rosario Albis
- Servicio de Gastroenterología, Instituto Nacional de Cancerología de Colombia, Bogotá D.C., Colombia
| | | | | | | | - Li Li
- Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA, US
| | - Sumana Majumdar
- Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA, US
| | - Jone Garai
- Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA, US
| | - Edward Lee
- Department of Pathology &Cancer Center, Howard University College of Medicine, Washington, D.C., US
| | - Hassan Ashktorab
- Department of Pathology &Cancer Center, Howard University College of Medicine, Washington, D.C., US
| | - Hassan Brim
- Department of Pathology &Cancer Center, Howard University College of Medicine, Washington, D.C., US
| | - Li Li
- Ochsner Clinic Foundation, New Orleans, LA, US
| | | | - Laura Fejerman
- Department of Medicine, Division of General Internal Medicine, Institute for Human Genetics and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, US
| | - Jovanny Zabaleta
- Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA, US.,Department of Pediatrics, Louisiana State University Health Sciences Center, New Orleans, LA, US
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Tenesa A, Rawlik K, Navarro P, Canela-Xandri O. Erratum to: Genetic determination of height-mediated mate choice. Genome Biol 2016; 17:26. [PMID: 26868669 PMCID: PMC4751647 DOI: 10.1186/s13059-016-0894-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Accepted: 02/07/2016] [Indexed: 05/29/2023] Open
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Muñoz M, Pong-Wong R, Canela-Xandri O, Rawlik K, Haley CS, Tenesa A. Evaluating the contribution of genetics and familial shared environment to common disease using the UK Biobank. Nat Genet 2016; 48:980-3. [PMID: 27428752 PMCID: PMC5989924 DOI: 10.1038/ng.3618] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 06/14/2016] [Indexed: 12/15/2022]
Abstract
Genome-wide association studies have detected many loci underlying susceptibility to disease, but most of the genetic factors that contribute to disease susceptibility remain unknown. Here we provide evidence that part of the 'missing heritability' can be explained by an overestimation of heritability. We estimated the heritability of 12 complex human diseases using family history of disease in 1,555,906 individuals of white ancestry from the UK Biobank. Estimates using simple family-based statistical models were inflated on average by ∼47% when compared with those from structural equation modeling (SEM), which specifically accounted for shared familial environmental factors. In addition, heritabilities estimated using SNP data explained an average of 44.2% of the simple family-based estimates across diseases and an average of 57.3% of the SEM-estimated heritabilities, accounting for almost all of the SEM heritability for hypertension. Our results show that both genetics and familial environment make substantial contributions to familial clustering of disease.
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Affiliation(s)
- María Muñoz
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The
University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Ricardo Pong-Wong
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The
University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Oriol Canela-Xandri
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The
University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Konrad Rawlik
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The
University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Chris S. Haley
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The
University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
- MRC Human Genetics Unit at the MRC Institute of Genetics and
Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road
South, Edinburgh, EH4 2XU, UK
| | - Albert Tenesa
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The
University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
- MRC Human Genetics Unit at the MRC Institute of Genetics and
Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road
South, Edinburgh, EH4 2XU, UK
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Rawlik K, Canela-Xandri O, Tenesa A. Evidence for sex-specific genetic architectures across a spectrum of human complex traits. Genome Biol 2016; 17:166. [PMID: 27473438 PMCID: PMC4965887 DOI: 10.1186/s13059-016-1025-x] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 07/12/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sex differences are a common feature of human traits; however, the role sex determination plays in human genetic variation remains unclear. The presence of gene-by-sex (GxS) interactions implies that trait genetic architecture differs between men and women. Here, we show that GxS interactions and genetic heterogeneity among sexes are small but common features of a range of high-level complex traits. RESULTS We analyzed 19 complex traits measured in 54,040 unrelated men and 59,820 unrelated women from the UK Biobank cohort to estimate autosomal genetic correlations and heritability differences between men and women. For 13 of the 19 traits examined, there is evidence that the trait measured is genetically different between males and females. We find that estimates of genetic correlations, based on ~114,000 unrelated individuals and ~19,000 related individuals from the same cohort, are largely consistent. Genetic predictors using a sex-specific model that incorporated GxS interactions led to a relative improvement of up to 4 % (mean 1.4 % across all relevant phenotypes) over those provided by a sex-agnostic model. This further supports the hypothesis of the presence of sexual genetic heterogeneity across high-level phenotypes. CONCLUSIONS The sex-specific environment seems to play a role in changing genotype expression across a range of human complex traits. Further studies of GxS interactions for high-level human traits may shed light on the molecular mechanisms that lead to biological differences between men and women. However, this may be a challenging endeavour due to the likely small effects of the interactions at individual loci.
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Affiliation(s)
- Konrad Rawlik
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, Scotland, UK
| | - Oriol Canela-Xandri
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, Scotland, UK
| | - Albert Tenesa
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, Scotland, UK. .,MRC Human Genetics Unit at the MRC IGMM, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh, EH4 2XU, UK.
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Howrigan DP, Simonson MA, Davies G, Harris SE, Tenesa A, Starr JM, Liewald DC, Deary IJ, McRae A, Wright MJ, Montgomery GW, Hansell N, Martin NG, Payton A, Horan M, Ollier WE, Abdellaoui A, Boomsma DI, DeRosse P, Knowles EEM, Glahn DC, Djurovic S, Melle I, Andreassen OA, Christoforou A, Steen VM, Hellard SL, Sundet K, Reinvang I, Espeseth T, Lundervold AJ, Giegling I, Konte B, Hartmann AM, Rujescu D, Roussos P, Giakoumaki S, Burdick KE, Bitsios P, Donohoe G, Corley RP, Visscher PM, Pendleton N, Malhotra AK, Neale BM, Lencz T, Keller MC. Genome-wide autozygosity is associated with lower general cognitive ability. Mol Psychiatry 2016; 21:837-43. [PMID: 26390830 PMCID: PMC4803638 DOI: 10.1038/mp.2015.120] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 05/23/2015] [Accepted: 07/13/2015] [Indexed: 01/12/2023]
Abstract
Inbreeding depression refers to lower fitness among offspring of genetic relatives. This reduced fitness is caused by the inheritance of two identical chromosomal segments (autozygosity) across the genome, which may expose the effects of (partially) recessive deleterious mutations. Even among outbred populations, autozygosity can occur to varying degrees due to cryptic relatedness between parents. Using dense genome-wide single-nucleotide polymorphism (SNP) data, we examined the degree to which autozygosity associated with measured cognitive ability in an unselected sample of 4854 participants of European ancestry. We used runs of homozygosity-multiple homozygous SNPs in a row-to estimate autozygous tracts across the genome. We found that increased levels of autozygosity predicted lower general cognitive ability, and estimate a drop of 0.6 s.d. among the offspring of first cousins (P=0.003-0.02 depending on the model). This effect came predominantly from long and rare autozygous tracts, which theory predicts as more likely to be deleterious than short and common tracts. Association mapping of autozygous tracts did not reveal any specific regions that were predictive beyond chance after correcting for multiple testing genome wide. The observed effect size is consistent with studies of cognitive decline among offspring of known consanguineous relationships. These findings suggest a role for multiple recessive or partially recessive alleles in general cognitive ability, and that alleles decreasing general cognitive ability have been selected against over evolutionary time.
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Affiliation(s)
- D P Howrigan
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Genetics, Broad Institute of Harvard and MIT, Cambridge Center, Cambridge, MA, USA
| | - M A Simonson
- Division of Data Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - G Davies
- Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - S E Harris
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Medical Genetics Section, University of Edinburgh Centre for Genomic and Experimental Medicine and MRC Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, UK
| | - A Tenesa
- Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit, Western General Hospital, University of Edinburgh, Edinburgh, UK
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin, UK
| | - J M Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Alzheimer Scotland Dementia Research Centre, University of Edinburgh, Edinburgh, UK
| | - D C Liewald
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - I J Deary
- Department of Psychology, University of Edinburgh, Edinburgh, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - A McRae
- Queensland Institute of Medical Research Berghofer, Brisbane, QLD, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - M J Wright
- Queensland Institute of Medical Research Berghofer, Brisbane, QLD, Australia
| | - G W Montgomery
- Queensland Institute of Medical Research Berghofer, Brisbane, QLD, Australia
| | - N Hansell
- Queensland Institute of Medical Research Berghofer, Brisbane, QLD, Australia
| | - N G Martin
- Queensland Institute of Medical Research Berghofer, Brisbane, QLD, Australia
| | - A Payton
- Centre for Integrated Genomic Medical Research, Institute of Population Health, University of Manchester, Manchester, UK
| | - M Horan
- Centre for Clinical and Cognitive Neurosciences, Institute of Brain Behaviour and Mental Health, University of Manchester, Salford Royal NHS Foundation Trust, Salford, UK
| | - W E Ollier
- Centre for Integrated Genomic Medical Research, Institute of Population Health, University of Manchester, Manchester, UK
| | - A Abdellaoui
- Department of Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands
- Neuroscience Campus Amsterdam, Amsterdam, The Netherlands
| | - D I Boomsma
- Department of Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands
- Neuroscience Campus Amsterdam, Amsterdam, The Netherlands
- EMGO+ Institute for Health and Care Research, Amsterdam, The Netherlands
| | - P DeRosse
- Division of Psychiatry Research, Zucker Hillside Hospital, Glen Oaks, NY, USA
- Center for Psychiatric Neuroscience, Feinstein Institute for Medical Research, Manhasset, NY, USA
- Hofstra North Shore - LIJ School of Medicine, Departments of Psychiatry and Molecular Medicine, Hempstead, NY, USA
| | - E E M Knowles
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - D C Glahn
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - S Djurovic
- NORMENT, KG Jebsen Centre, Oslo, Norway
- Oslo University Hospital, Oslo, Norway
| | - I Melle
- NORMENT, KG Jebsen Centre, Oslo, Norway
- Oslo University Hospital, Oslo, Norway
- University of Oslo, Oslo, Norway
| | - O A Andreassen
- NORMENT, KG Jebsen Centre, Oslo, Norway
- Oslo University Hospital, Oslo, Norway
- University of Oslo, Oslo, Norway
| | - A Christoforou
- K.G. Jebsen Centre for Psychosis Research, Dr. Einar Martens Research Group for Biological Psychiatry, Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - V M Steen
- K.G. Jebsen Centre for Psychosis Research, Dr. Einar Martens Research Group for Biological Psychiatry, Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - S L Hellard
- K.G. Jebsen Centre for Psychosis Research, Dr. Einar Martens Research Group for Biological Psychiatry, Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - K Sundet
- NORMENT, KG Jebsen Centre, Oslo, Norway
- Department of Psychology, University of Oslo, Oslo, Norway
| | - I Reinvang
- Department of Psychology, University of Oslo, Oslo, Norway
| | - T Espeseth
- Department of Psychology, University of Oslo, Oslo, Norway
- Norwegian Center for Mental Disorders Research, KG Jebsen Centre for Psychosis Research, Oslo University Hospital, Oslo, Norway
| | - A J Lundervold
- K.G. Jebsen Centre for Research on Neuropsychiatric Disorders, University of Bergen, Bergen, Norway
- Department of Biological and Medical Psychology, University of Bergen, Bergen, Norway
- Kavli Research Centre for Aging and Dementia, Haraldsplass Deaconess Hospital, Bergen, Norway
| | - I Giegling
- Department of Psychiatry, University of Halle, Halle, Germany
| | - B Konte
- Department of Psychiatry, University of Halle, Halle, Germany
| | - A M Hartmann
- Department of Psychiatry, University of Halle, Halle, Germany
| | - D Rujescu
- Department of Psychiatry, University of Halle, Halle, Germany
| | - P Roussos
- Department of Psychiatry, Friedman Brain Institute, Department of Genetics and Genomic Sciences, and Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- James J. Peters VA Medical Center, Mental Illness Research Education and Clinical Center (MIRECC), Bronx, NY, USA
| | - S Giakoumaki
- Department of Psychology, University of Crete, Rethymno, Crete, Greece
| | - K E Burdick
- Department of Psychiatry, Friedman Brain Institute, Department of Genetics and Genomic Sciences, and Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - P Bitsios
- Department of Psychiatry, Faculty of Medicine, University of Crete, Heraklion, Crete, Greece
- Computational Medicine Laboratory, Institute of Computer Science at FORTH, Heraklion, Greece
| | - G Donohoe
- School of Psychology, National University of Ireland Galway, Galway, Ireland
| | - R P Corley
- Institute for Behavioral Genetics, University of Colorado at Boulder, Boulder, CO, USA
| | - P M Visscher
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Queensland Institute of Medical Research Berghofer, Brisbane, QLD, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
- University of Queensland Diamantina Institute, The University of Queensland, Princess Alexandra Hospital, Brisbane, QLD, Australia
| | - N Pendleton
- Centre for Integrated Genomic Medical Research, Institute of Population Health, University of Manchester, Manchester, UK
| | - A K Malhotra
- Division of Psychiatry Research, Zucker Hillside Hospital, Glen Oaks, NY, USA
- Center for Psychiatric Neuroscience, Feinstein Institute for Medical Research, Manhasset, NY, USA
- Hofstra North Shore - LIJ School of Medicine, Departments of Psychiatry and Molecular Medicine, Hempstead, NY, USA
| | - B M Neale
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Genetics, Broad Institute of Harvard and MIT, Cambridge Center, Cambridge, MA, USA
| | - T Lencz
- Division of Psychiatry Research, Zucker Hillside Hospital, Glen Oaks, NY, USA
- Center for Psychiatric Neuroscience, Feinstein Institute for Medical Research, Manhasset, NY, USA
- Hofstra North Shore - LIJ School of Medicine, Departments of Psychiatry and Molecular Medicine, Hempstead, NY, USA
| | - M C Keller
- Institute for Behavioral Genetics, University of Colorado at Boulder, Boulder, CO, USA
- Department of Psychology, University of Colorado at Boulder, Boulder, CO, USA
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Orlando G, Law PJ, Palin K, Tuupanen S, Gylfe A, Hänninen UA, Cajuso T, Tanskanen T, Kondelin J, Kaasinen E, Sarin AP, Kaprio J, Eriksson JG, Rissanen H, Knekt P, Pukkala E, Jousilahti P, Salomaa V, Ripatti S, Palotie A, Järvinen H, Renkonen-Sinisalo L, Lepistö A, Böhm J, Mecklin JP, Al-Tassan NA, Palles C, Martin L, Barclay E, Tenesa A, Farrington S, Timofeeva MN, Meyer BF, Wakil SM, Campbell H, Smith CG, Idziaszczyk S, Maughan TS, Kaplan R, Kerr R, Kerr D, Buchanan DD, Win AK, Hopper J, Jenkins M, Lindor NM, Newcomb PA, Gallinger S, Conti D, Schumacher F, Casey G, Taipale J, Cheadle JP, Dunlop MG, Tomlinson IP, Aaltonen LA, Houlston RS. Variation at 2q35 (PNKD and TMBIM1) influences colorectal cancer risk and identifies a pleiotropic effect with inflammatory bowel disease. Hum Mol Genet 2016; 25:2349-2359. [PMID: 27005424 PMCID: PMC5081051 DOI: 10.1093/hmg/ddw087] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 02/05/2016] [Accepted: 03/14/2016] [Indexed: 01/07/2023] Open
Abstract
To identify new risk loci for colorectal cancer (CRC), we conducted a meta-analysis of seven genome-wide association studies (GWAS) with independent replication, totalling 13 656 CRC cases and 21 667 controls of European ancestry. The combined analysis identified a new risk association for CRC at 2q35 marked by rs992157 (P = 3.15 × 10-8, odds ratio = 1.10, 95% confidence interval = 1.06-1.13), which is intronic to PNKD (paroxysmal non-kinesigenic dyskinesia) and TMBIM1 (transmembrane BAX inhibitor motif containing 1). Intriguingly this susceptibility single-nucleotide polymorphism (SNP) is in strong linkage disequilibrium (r2 = 0.90, D' = 0.96) with the previously discovered GWAS SNP rs2382817 for inflammatory bowel disease (IBD). Following on from this observation we examined for pleiotropy, or shared genetic susceptibility, between CRC and the 200 established IBD risk loci, identifying an additional 11 significant associations (false discovery rate [FDR]) < 0.05). Our findings provide further insight into the biological basis of inherited genetic susceptibility to CRC, and identify risk factors that may influence the development of both CRC and IBD.
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Affiliation(s)
- Giulia Orlando
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Philip J Law
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Kimmo Palin
- Genome-Scale Biology Research Program, Research Programs Unit Department of Medical and Clinical Genetics, Medicum
| | - Sari Tuupanen
- Genome-Scale Biology Research Program, Research Programs Unit Department of Medical and Clinical Genetics, Medicum
| | - Alexandra Gylfe
- Genome-Scale Biology Research Program, Research Programs Unit Department of Medical and Clinical Genetics, Medicum
| | - Ulrika A Hänninen
- Genome-Scale Biology Research Program, Research Programs Unit Department of Medical and Clinical Genetics, Medicum
| | - Tatiana Cajuso
- Genome-Scale Biology Research Program, Research Programs Unit Department of Medical and Clinical Genetics, Medicum
| | - Tomas Tanskanen
- Genome-Scale Biology Research Program, Research Programs Unit Department of Medical and Clinical Genetics, Medicum
| | - Johanna Kondelin
- Genome-Scale Biology Research Program, Research Programs Unit Department of Medical and Clinical Genetics, Medicum
| | - Eevi Kaasinen
- Genome-Scale Biology Research Program, Research Programs Unit Department of Medical and Clinical Genetics, Medicum
| | - Antti-Pekka Sarin
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki 00014, Finland
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki 00014, Finland National Institute for Health and Welfare, Helsinki 00271, Finland
| | - Johan G Eriksson
- Folkhälsan Research Centre, Helsinki 00250, Finland Unit of General Practice and Primary Health Care, University of Helsinki and Helsinki University Hospital, Helsinki 00014, Finland
| | - Harri Rissanen
- National Institute for Health and Welfare, Helsinki 00271, Finland
| | - Paul Knekt
- National Institute for Health and Welfare, Helsinki 00271, Finland
| | - Eero Pukkala
- Finnish Cancer Registry, Institute for Statistical and Epidemiological Cancer Research, Helsinki 00130, Finland School of Health Sciences, University of Tampere, Tampere 33014, Finland
| | - Pekka Jousilahti
- National Institute for Health and Welfare, Helsinki 00271, Finland
| | - Veikko Salomaa
- National Institute for Health and Welfare, Helsinki 00271, Finland
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki 00014, Finland
| | - Aarno Palotie
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki 00014, Finland Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Heikki Järvinen
- Department of Surgery, Helsinki University Central Hospital, Hospital District of Helsinki and Uusimaa, Helsinki 00029, Finland
| | - Laura Renkonen-Sinisalo
- Department of Surgery, Abdominal Center, Helsinki University Hospital, Helsinki 00029, Finland
| | - Anna Lepistö
- Department of Surgery, Abdominal Center, Helsinki University Hospital, Helsinki 00029, Finland
| | - Jan Böhm
- Department of Pathology, Central Finland Central Hospital, Jyväskylä 40620, Finland
| | - Jukka-Pekka Mecklin
- Department of Surgery, Jyväskylä Central Hospital, University of Eastern Finland, Jyväskylä 40620, Finland
| | - Nada A Al-Tassan
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 12713, Saudi Arabia
| | - Claire Palles
- Wellcome Trust Centre for Human Genetics and NIHR Comprehensive Biomedical Research Centre, Oxford OX3 7BN, UK
| | - Lynn Martin
- Wellcome Trust Centre for Human Genetics and NIHR Comprehensive Biomedical Research Centre, Oxford OX3 7BN, UK
| | - Ella Barclay
- Wellcome Trust Centre for Human Genetics and NIHR Comprehensive Biomedical Research Centre, Oxford OX3 7BN, UK
| | - Albert Tenesa
- Colon Cancer Genetics Group, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital, Edinburgh EH4 2XU, UK The Roslin Institute, University of Edinburgh, Easter Bush, Roslin EH25 9RG, UK
| | - Susan Farrington
- Colon Cancer Genetics Group, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Maria N Timofeeva
- Colon Cancer Genetics Group, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Brian F Meyer
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 12713, Saudi Arabia
| | - Salma M Wakil
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 12713, Saudi Arabia
| | - Harry Campbell
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Christopher G Smith
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Shelley Idziaszczyk
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Timothy S Maughan
- CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Richard Kaplan
- MRC Clinical Trials Unit, Aviation House, London WC2B 6NH, UK
| | - Rachel Kerr
- Department of Oncology, Oxford Cancer Centre, Churchill Hospital
| | - David Kerr
- Nuffield Department of Clinical Laboratory Sciences, John Radcliffe Hospital, University of Oxford, Oxford OX3 7LE, UK
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne, Vic. 3010, Australia
| | - Aung Ko Win
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne, Vic. 3010, Australia
| | - John Hopper
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne, Vic. 3010, Australia
| | - Mark Jenkins
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne, Vic. 3010, Australia
| | - Noralane M Lindor
- Department of Health Sciences Research, Mayo Clinic, Scottsdale, AZ 85259, USA
| | - Polly A Newcomb
- Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Steve Gallinger
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - David Conti
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Fred Schumacher
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Graham Casey
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Jussi Taipale
- Genome-Scale Biology Research Program, Research Programs Unit Department of Medical and Clinical Genetics, Medicum Department of Biosciences and Nutrition, SciLife Center, Karolinska Institute, Stockholm, SE 141 83, Sweden
| | - Jeremy P Cheadle
- Genome-Scale Biology Research Program, Research Programs Unit Genome-Scale Biology Research Program, Research Programs Unit
| | - Malcolm G Dunlop
- Colon Cancer Genetics Group, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Ian P Tomlinson
- Wellcome Trust Centre for Human Genetics and NIHR Comprehensive Biomedical Research Centre, Oxford OX3 7BN, UK
| | - Lauri A Aaltonen
- Genome-Scale Biology Research Program, Research Programs Unit Department of Medical and Clinical Genetics, Medicum
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SW7 3RP, UK
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Rowlatt A, Hernández-Suárez G, Sanabria-Salas MC, Serrano-López M, Rawlik K, Hernandez-Illan E, Alenda C, Castillejo A, Soto JL, Haley CS, Tenesa A. The heritability and patterns of DNA methylation in normal human colorectum. Hum Mol Genet 2016; 25:2600-2611. [PMID: 26936820 PMCID: PMC5181623 DOI: 10.1093/hmg/ddw072] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 01/15/2016] [Accepted: 02/26/2016] [Indexed: 12/30/2022] Open
Abstract
DNA methylation (DNAm) has been linked to changes in chromatin structure, gene expression and disease. The DNAm level can be affected by genetic variation; although, how this differs by CpG dinucleotide density and genic location of the DNAm site is not well understood. Moreover, the effect of disease causing variants on the DNAm level in a tissue relevant to disease has yet to be fully elucidated. To this end, we investigated the phenotypic profiles, genetic effects and regional genomic heritability for 196080 DNAm sites in healthy colorectum tissue from 132 unrelated Colombian individuals. DNAm sites in regions of low-CpG density were more variable, on average more methylated and were more likely to be significantly heritable when compared with DNAm sites in regions of high-CpG density. DNAm sites located in intergenic regions had a higher mean DNAm level and were more likely to be heritable when compared with DNAm sites in the transcription start site (TSS) of a gene expressed in colon tissue. Within CpG-dense regions, the propensity of the DNAm level to be heritable was lower in the TSS of genes expressed in colon tissue than in the TSS of genes not expressed in colon tissue. In addition, regional genetic variation was associated with variation in local DNAm level no more frequently for DNAm sites within colorectal cancer risk regions than it was for DNAm sites outside such regions. Overall, DNAm sites located in different genomic contexts exhibited distinguishable profiles and may have a different biological function.
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Affiliation(s)
- Amy Rowlatt
- The Roslin Institute, The University of Edinburgh, Edinburgh, EH25 9RG, UK
| | | | - María Carolina Sanabria-Salas
- Grupo de Investigación en Biología del Cáncer, Instituto Nacional de Cancerología, Bogotá, Colombia.,Departamento de Química, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Martha Serrano-López
- Grupo de Investigación en Biología del Cáncer, Instituto Nacional de Cancerología, Bogotá, Colombia.,Departamento de Química, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Konrad Rawlik
- The Roslin Institute, The University of Edinburgh, Edinburgh, EH25 9RG, UK
| | - Eva Hernandez-Illan
- Laboratorio Genética Molecular, Hospital General Universitario de Elche, 03203 Elche, Alicante, Spain
| | - Cristina Alenda
- Pathology, Alicante University Hospital, Alicante, Spain and
| | - Adela Castillejo
- Laboratorio Genética Molecular, Hospital General Universitario de Elche, 03203 Elche, Alicante, Spain
| | - Jose Luis Soto
- Laboratorio Genética Molecular, Hospital General Universitario de Elche, 03203 Elche, Alicante, Spain
| | - Chris S Haley
- The Roslin Institute, The University of Edinburgh, Edinburgh, EH25 9RG, UK.,MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Albert Tenesa
- The Roslin Institute, The University of Edinburgh, Edinburgh, EH25 9RG, UK, .,MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, EH4 2XU, UK
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Sanabria-Salas MC, Hernández-Suárez GA, Umaña-Pérez A, Serrano-Pérez ML, Gómez MSD, Rojas MP, Zabaleta J, Rawlik K, Tenesa A. Abstract PR08: The role of genetic structure in Colombian coastal and Andean populations on disparities in colorectal adenomas and cancer risk. Cancer Epidemiol Biomarkers Prev 2016. [DOI: 10.1158/1538-7755.disp15-pr08] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Abstract
Background: Latin-Americans have different proportions of Amerindian, African and European genetic ancestry. Particularly, in Colombia the degree of admixture varies across the country as a result of very complex demographic events taken place since 16th century (colonization) and sex-bias gene flow effects. Colorectal cancer (CRC) mortality rates are heterogeneous across Colombian territory and this variation could be explained by regional differences in Colombian genetic background.
Methods: To evaluate the association of genetic ancestry and colorectal adenomas and cancer risk, we genotyped 813 samples from Colombian coastal and andean regions, including 349 controls, 292 CRC cases and 172 adenomatous polyps (AP). Autosomal and X-chromosome individual ancestries were estimated using ADMIXTURE software with 556 AIMS (Fst > 0.5 among HAPMAP reference populations; k=3) and differences in ancestry proportions were assessed using a t-test. Multinomial logit model analysis between phenotype and ancestry proportions (covariates: sex, age, NSAIDs consumption, city of provenance and educational level) were conducted in R.
Results: We found statistical differences (p < 0.05) between African, European and Asian (as a measure of Amerindian) ancestry means of autosomes versus X-chromosome (sex bias). As expected, ancestry means were different between the coast versus andean regions (African 0.27 vs 0.09; European 0.44 vs 0.57 and Asian/Amerindian 0.29 vs 0.35, respectively), reflecting differences among cities. For controls, AP and CRC the respective ancestry means were: African (0.17, 0.18 and 0,20), European (0.50, 0.53 and 0.48) and Asian/Ameridian (0.33, 0.29, 0.32). Univariate analysis showed that European ancestry was associated with an increased risk of AP (p < 0.05) and that African ancestry was associated with an increased risk of CRC (p < 0.05); no differences were found for phenotype among cities. After running full multinomial model, the association between European ancestry and the risk of AP remained (OR 8.50; 95%CI 1.65-43.78; p = 0.011); on the other hand, the association between African ancestry and CRC risk had the same direction but was not significant (OR 1.06; 95%CI 1.00-1.13, p = 0.065). On the full model, we also found that Colombians with no education have more CRC than those with at least high school degree, and this was consistent with univariate analysis. No differences were seeing between educational level and AP, neither in the univariate nor in the multivariate analysis, even though multinomial model of education by ancestry (corrected by city), showed that Colombians with high European ancestry are more likely to hold advance education degree.
Conclusions: Colombian regions have differences in the degree of admixture as a consequence of the highly asymmetric pattern of mating of European men with Native American women and the African slavery trade in the coasts since the colonization period, according to this study and others on Y-chromosome and mtDNA. There was no signal of sampling bias in our study (no differences in phenotypes by city). The association of CRC risk and African ancestry did not remain in the full model, probably due to a small effect, small sample size or the fact that people without education (low socioeconomical status) have less access to health system. The association of AP risk with European ancestry remained after controlling with covariates (including educational level); this probably indicates that there are European genetic factors (ej: SNPs) modifying the risk of AP in Colombians. Our results highlight the importance of performing Local Admixture Inference analysis in order to estimate the ancestry of specific chromosomal regions in admixed individuals in the study of human evolutionary history and genetic association studies.
This abstract is also presented as Poster C37.
Citation Format: Maria Carolina Sanabria-Salas, Gustavo Adolfo Hernández-Suárez, Adriana Umaña-Pérez, Martha Lucía Serrano-Pérez, Myriam Sánchez de Gómez, Martha Patricia Rojas, Jovanny Zabaleta, Konrad Rawlik, Albert Tenesa. The role of genetic structure in Colombian coastal and Andean populations on disparities in colorectal adenomas and cancer risk. [abstract]. In: Proceedings of the Eighth AACR Conference on The Science of Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; Nov 13-16, 2015; Atlanta, GA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2016;25(3 Suppl):Abstract nr PR08.
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Affiliation(s)
| | | | | | | | | | | | | | - Konrad Rawlik
- 4The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Albert Tenesa
- 4The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
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Abstract
BACKGROUND Numerous studies have reported positive correlations among couples for height. This suggests that humans find individuals of similar height attractive. However, the answer to whether the choice of a mate with a similar phenotype is genetically or environmentally determined has been elusive. RESULTS Here we provide an estimate of the genetic contribution to height choice in mates in 13,068 genotyped couples. Using a mixed linear model we show that 4.1% of the variation in the mate height choice is determined by a person's own genotype, as expected in a model where one's height determines the choice of mate height. Furthermore, the genotype of an individual predicts their partners' height in an independent dataset of 15,437 individuals with 13% accuracy, which is 64% of the theoretical maximum achievable with a heritability of 0.041. Theoretical predictions suggest that approximately 5% of the heritability of height is due to the positive covariance between allelic effects at different loci, which is caused by assortative mating. Hence, the coupling of alleles with similar effects could substantially contribute to the missing heritability of height. CONCLUSIONS These estimates provide new insight into the mechanisms that govern mate choice in humans and warrant the search for the genetic causes of choice of mate height. They have important methodological implications and contribute to the missing heritability debate.
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Affiliation(s)
- Albert Tenesa
- The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, Scotland, UK. .,MRC HGU at the MRC IGMM, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh, EH4 2XU, Scotland, UK. .,Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, Scotland, UK.
| | - Konrad Rawlik
- The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, Scotland, UK.,Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, Scotland, UK
| | - Pau Navarro
- MRC HGU at the MRC IGMM, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh, EH4 2XU, Scotland, UK
| | - Oriol Canela-Xandri
- The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, Scotland, UK.,Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, Scotland, UK
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Canela-Xandri O, Law A, Gray A, Woolliams JA, Tenesa A. A new tool called DISSECT for analysing large genomic data sets using a Big Data approach. Nat Commun 2015; 6:10162. [PMID: 26657010 PMCID: PMC4682108 DOI: 10.1038/ncomms10162] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 11/10/2015] [Indexed: 12/03/2022] Open
Abstract
Large-scale genetic and genomic data are increasingly available and the major bottleneck in their analysis is a lack of sufficiently scalable computational tools. To address this problem in the context of complex traits analysis, we present DISSECT. DISSECT is a new and freely available software that is able to exploit the distributed-memory parallel computational architectures of compute clusters, to perform a wide range of genomic and epidemiologic analyses, which currently can only be carried out on reduced sample sizes or under restricted conditions. We demonstrate the usefulness of our new tool by addressing the challenge of predicting phenotypes from genotype data in human populations using mixed-linear model analysis. We analyse simulated traits from 470,000 individuals genotyped for 590,004 SNPs in ∼4 h using the combined computational power of 8,400 processor cores. We find that prediction accuracies in excess of 80% of the theoretical maximum could be achieved with large sample sizes. Availability of computing power can limit computational analysis of large genetic and genomic datasets. Here, Canela-Xandri, et al. describe a software called DISSECT that is capable of analyzing large-scale genetic data by distributing the work across thousands of networked computers.
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Affiliation(s)
- Oriol Canela-Xandri
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Edinburgh EH25 9RG, UK
| | - Andy Law
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Edinburgh EH25 9RG, UK
| | - Alan Gray
- EPCC, The University of Edinburgh, Edinburgh EH9 3FD, UK
| | - John A Woolliams
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Edinburgh EH25 9RG, UK
| | - Albert Tenesa
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Edinburgh EH25 9RG, UK.,MRC HGU at the MRC IGMM, University of Edinburgh, Edinburgh EH4 2XU, UK
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45
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Cheng THT, Thompson D, Painter J, O’Mara T, Gorman M, Martin L, Palles C, Jones A, Buchanan DD, Ko Win A, Hopper J, Jenkins M, Lindor NM, Newcomb PA, Gallinger S, Conti D, Schumacher F, Casey G, Giles GG, Pharoah P, Peto J, Cox A, Swerdlow A, Couch F, Cunningham JM, Goode EL, Winham SJ, Lambrechts D, Fasching P, Burwinkel B, Brenner H, Brauch H, Chang-Claude J, Salvesen HB, Kristensen V, Darabi H, Li J, Liu T, Lindblom A, Hall P, de Polanco ME, Sans M, Carracedo A, Castellvi-Bel S, Rojas-Martinez A, Aguiar Jnr S, Teixeira MR, Dunning AM, Dennis J, Otton G, Proietto T, Holliday E, Attia J, Ashton K, Scott RJ, McEvoy M, Dowdy SC, Fridley BL, Werner HMJ, Trovik J, Njolstad TS, Tham E, Mints M, Runnebaum I, Hillemanns P, Dörk T, Amant F, Schrauwen S, Hein A, Beckmann MW, Ekici A, Czene K, Meindl A, Bolla MK, Michailidou K, Tyrer JP, Wang Q, Ahmed S, Healey CS, Shah M, Annibali D, Depreeuw J, Al-Tassan NA, Harris R, Meyer BF, Whiffin N, Hosking FJ, Kinnersley B, Farrington SM, Timofeeva M, Tenesa A, Campbell H, Haile RW, Hodgson S, Carvajal-Carmona L, Cheadle JP, Easton D, Dunlop M, Houlston R, Spurdle A, Tomlinson I. Meta-analysis of genome-wide association studies identifies common susceptibility polymorphisms for colorectal and endometrial cancer near SH2B3 and TSHZ1. Sci Rep 2015; 5:17369. [PMID: 26621817 PMCID: PMC4664893 DOI: 10.1038/srep17369] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 10/28/2015] [Indexed: 11/17/2022] Open
Abstract
High-risk mutations in several genes predispose to both colorectal cancer (CRC) and endometrial cancer (EC). We therefore hypothesised that some lower-risk genetic variants might also predispose to both CRC and EC. Using CRC and EC genome-wide association series, totalling 13,265 cancer cases and 40,245 controls, we found that the protective allele [G] at one previously-identified CRC polymorphism, rs2736100 near TERT, was associated with EC risk (odds ratio (OR) = 1.08, P = 0.000167); this polymorphism influences the risk of several other cancers. A further CRC polymorphism near TERC also showed evidence of association with EC (OR = 0.92; P = 0.03). Overall, however, there was no good evidence that the set of CRC polymorphisms was associated with EC risk, and neither of two previously-reported EC polymorphisms was associated with CRC risk. A combined analysis revealed one genome-wide significant polymorphism, rs3184504, on chromosome 12q24 (OR = 1.10, P = 7.23 × 10(-9)) with shared effects on CRC and EC risk. This polymorphism, a missense variant in the gene SH2B3, is also associated with haematological and autoimmune disorders, suggesting that it influences cancer risk through the immune response. Another polymorphism, rs12970291 near gene TSHZ1, was associated with both CRC and EC (OR = 1.26, P = 4.82 × 10(-8)), with the alleles showing opposite effects on the risks of the two cancers.
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Affiliation(s)
- Timothy HT Cheng
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Deborah Thompson
- Centre for Cancer Genetic Epidemiology, Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Jodie Painter
- The Molecular Cancer Epidemiology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane 4006, Australia
| | - Tracy O’Mara
- The Molecular Cancer Epidemiology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane 4006, Australia
| | - Maggie Gorman
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Lynn Martin
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Claire Palles
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Angela Jones
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Daniel D. Buchanan
- Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Victoria, Australia
| | - Aung Ko Win
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Victoria, Australia
| | - John Hopper
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Victoria, Australia
| | - Mark Jenkins
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Victoria, Australia
| | - Noralane M. Lindor
- Department of Health Sciences Research, Mayo Clinic, Scottsdale, AZ, USA
| | - Polly A. Newcomb
- Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Steve Gallinger
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - David Conti
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Fred Schumacher
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Graham Casey
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Graham G Giles
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Victoria, Australia
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Australia
| | - Paul Pharoah
- Centre for Cancer Genetic Epidemiology, Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Julian Peto
- London School of Hygiene and Tropical Medicine, London, UK
| | - Angela Cox
- Sheffield Cancer Research Centre, Department of Oncology, University of Sheffield, Sheffield, UK
| | - Anthony Swerdlow
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK and 17 Division of Breast Cancer Research, Institute of Cancer Research, London, UK
| | - Fergus Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Julie M Cunningham
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Ellen L Goode
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Stacey J Winham
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | | | - Peter Fasching
- University of California at Los Angeles, Department of Medicine, Division of Hematology/Oncology, David Geffen School of Medicine, Los Angeles, CA, USA
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Barbara Burwinkel
- Division of Cancer Epidemiology, German Cancer Research Center, Heidelberg, Germany
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology Stuttgart, University of Tuebingen, Germany
| | - Hermann Brenner
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology Stuttgart, University of Tuebingen, Germany
- Division of Cancer Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Hiltrud Brauch
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology Stuttgart, University of Tuebingen, Germany
- Division of Cancer Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Helga B. Salvesen
- Department of Clinical Science, Center for Cancer Biomarkers, University of Bergen, Norway
| | - Vessela Kristensen
- Department of Genetics, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo, Norway; The K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway; Department of Clinical Molecular Oncology, Division of Medicine, Akershus University Hospital, Ahus, Norway
| | - Hatef Darabi
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Jingmei Li
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Tao Liu
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Magdalena Echeverry de Polanco
- Grupo de investigación Citogenética, Filogenia y Evolución de Poblaciones, Universidad del Tolima, Ibagué, Tolima, Colombia
| | - Monica Sans
- Departamento de Antropologia Biologica, Facultad de Humanidades, UDELAR, Magallanes 1577, CP 11200, Montevideo, Uruguay
| | - Angel Carracedo
- Universidade de Santiago de Compostel, R/ San Francisco s/n 15782, Santiago de Compostela, Spain
| | - Sergi Castellvi-Bel
- Genetic Predisposition to Colorectal Cancer Group, Gastrointestinal & Pancreatic Oncology Team, IDIBAPS/CIBERehd/Hospital Clínic, Centre Esther Koplowitz (CEK), Rosselló 153 planta 4, 08036 Barcelona, Spain
| | - Augusto Rojas-Martinez
- Universidad Autónoma De Nuevo León, Pedro de Alba s/n, San Nicolás de Los Garza, Nuevo León, Mexico
| | | | - Manuel R. Teixeira
- Department of Genetics and IPO-Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal, and Biomedical Sciences Institute (ICBAS), University of Porto, Porto, Portugal
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Geoffrey Otton
- School of Medicine and Public Health, University of Newcastle, NSW, Australia
| | - Tony Proietto
- School of Medicine and Public Health, University of Newcastle, NSW, Australia
| | - Elizabeth Holliday
- Hunter Medical Research Institute, John Hunter Hospital, Newcastle, NSW, Australia
| | - John Attia
- Hunter Medical Research Institute, John Hunter Hospital, Newcastle, NSW, Australia
| | - Katie Ashton
- Hunter Medical Research Institute, John Hunter Hospital, Newcastle, NSW, Australia
| | - Rodney J Scott
- Hunter Medical Research Institute, John Hunter Hospital, Newcastle, NSW, Australia
| | - Mark McEvoy
- Centre for Clinical Epidemiology and Biostatistics, School of Medicine and Public Health, University of Newcastle, NSW, Australia
| | - Sean C Dowdy
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, Mayo Clinic, Rochester, MN, USA
| | - Brooke L Fridley
- Department of Biostatistics, University of Kansas Medical Center, Kansas City, KS, USA
| | - Henrica MJ Werner
- Centre for Cancer Biomarkers, Department of Clinical Science, The University of Bergen, Norway
| | - Jone Trovik
- Centre for Cancer Biomarkers, Department of Clinical Science, The University of Bergen, Norway
| | - Tormund S Njolstad
- Centre for Cancer Biomarkers, Department of Clinical Science, The University of Bergen, Norway
| | - Emma Tham
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Miriam Mints
- Department of Women’s and Children’s Health, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Ingo Runnebaum
- Department of Gynaecology, Jena University Hospital - Friedrich Schiller University, Jena, Germany
| | - Peter Hillemanns
- Hannover Medical School, Clinics of Gynaecology and Obstetrics, Hannover, Germany
| | - Thilo Dörk
- Hannover Medical School, Gynaecology Research Unit, Hannover, Germany
| | - Frederic Amant
- Division of Gynaecological Oncology, University Hospital Leuven, Leuven, Belgium
| | | | - Alexander Hein
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Matthias W Beckmann
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Arif Ekici
- Institute of Human Genetics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Alfons Meindl
- Department of Obstetrics and Gynecology, Division of Tumor Genetics, Technical University of Munich, Munich, Germany
| | - Manjeet K Bolla
- Centre for Cancer Genetic Epidemiology, Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Kyriaki Michailidou
- Centre for Cancer Genetic Epidemiology, Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Jonathan P Tyrer
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Shahana Ahmed
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Catherine S Healey
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Mitul Shah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Daniela Annibali
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, University Hospitals, KU Leuven, University of Leuven, 3000, Belgium
| | - Jeroen Depreeuw
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, University Hospitals, KU Leuven, University of Leuven, 3000, Belgium
| | - Nada A. Al-Tassan
- Department of Genetics, King Faisal Specialist Hospital and Research Center, P.O.Box 3354, Riyadh11211, Saudi Arabia
| | - Rebecca Harris
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Brian F. Meyer
- Department of Genetics, King Faisal Specialist Hospital and Research Center, P.O.Box 3354, Riyadh11211, Saudi Arabia
| | - Nicola Whiffin
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
| | - Fay J Hosking
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
| | - Ben Kinnersley
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
| | - Susan M. Farrington
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Maria Timofeeva
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Albert Tenesa
- The Roslin Institute, University of Edinburgh, Easter Bush, Roslin, EH25 9RG, UK
| | - Harry Campbell
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, EH8 9AG, UK
| | - Robert W. Haile
- Stanford Cancer Institute, Lorry Lokey Building/SIM 1, 265 Campus Drive, Ste G2103, Stanford, CA 94305-5456, USA
| | - Shirley Hodgson
- Department of Cancer Genetics, St. George’s University of London, London SW17 0RE, UK
| | - Luis Carvajal-Carmona
- Genome Center and Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, USA
| | - Jeremy P. Cheadle
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Douglas Easton
- Centre for Cancer Genetic Epidemiology, Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Malcolm Dunlop
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Richard Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
| | - Amanda Spurdle
- The Molecular Cancer Epidemiology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane 4006, Australia
| | - Ian Tomlinson
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
- Oxford NIHR Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
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Saura M, Tenesa A, Woolliams JA, Fernández A, Villanueva B. Evaluation of the linkage-disequilibrium method for the estimation of effective population size when generations overlap: an empirical case. BMC Genomics 2015; 16:922. [PMID: 26559809 PMCID: PMC4642667 DOI: 10.1186/s12864-015-2167-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 10/29/2015] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Within the genetic methods for estimating effective population size (N e ), the method based on linkage disequilibrium (LD) has advantages over other methods, although its accuracy when applied to populations with overlapping generations is a matter of controversy. It is also unclear the best way to account for mutation and sample size when this method is implemented. Here we have addressed the applicability of this method using genome-wide information when generations overlap by profiting from having available a complete and accurate pedigree from an experimental population of Iberian pigs. Precise pedigree-based estimates of N e were considered as a baseline against which to compare LD-based estimates. METHODS We assumed six different statistical models that varied in the adjustments made for mutation and sample size. The approach allowed us to determine the most suitable statistical model of adjustment when the LD method is used for species with overlapping generations. A novel approach used here was to treat different generations as replicates of the same population in order to assess the error of the LD-based N e estimates. RESULTS LD-based N e estimates obtained by estimating the mutation parameter from the data and by correcting sample size using the 1/2n term were the closest to pedigree-based estimates. The N e at the time of the foundation of the herd (26 generations ago) was 20.8 ± 3.7 (average and SD across replicates), while the pedigree-based estimate was 21. From that time on, this trend was in good agreement with that followed by pedigree-based N e. CONCLUSIONS Our results showed that when using genome-wide information, the LD method is accurate and broadly applicable to small populations even when generations overlap. This supports the use of the method for estimating N e when pedigree information is unavailable in order to effectively monitor and manage populations and to early detect population declines. To our knowledge this is the first study using replicates of empirical data to evaluate the applicability of the LD method by comparing results with accurate pedigree-based estimates.
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Affiliation(s)
- María Saura
- Departamento de Mejora Genética Animal, INIA, Carretera de la Coruña km 7.5, 28040, Madrid, Spain.
| | - Albert Tenesa
- The Roslin Institute and R(D)SVS, University of Edinburgh, EH25 9RG, Midlothian, UK.
| | - John A Woolliams
- The Roslin Institute and R(D)SVS, University of Edinburgh, EH25 9RG, Midlothian, UK.
| | - Almudena Fernández
- Departamento de Mejora Genética Animal, INIA, Carretera de la Coruña km 7.5, 28040, Madrid, Spain.
| | - Beatriz Villanueva
- Departamento de Mejora Genética Animal, INIA, Carretera de la Coruña km 7.5, 28040, Madrid, Spain.
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Timofeeva MN, Kinnersley B, Farrington SM, Whiffin N, Palles C, Svinti V, Lloyd A, Gorman M, Ooi LY, Hosking F, Barclay E, Zgaga L, Dobbins S, Martin L, Theodoratou E, Broderick P, Tenesa A, Smillie C, Grimes G, Hayward C, Campbell A, Porteous D, Deary IJ, Harris SE, Northwood EL, Barrett JH, Smith G, Wolf R, Forman D, Morreau H, Ruano D, Tops C, Wijnen J, Schrumpf M, Boot A, Vasen HFA, Hes FJ, van Wezel T, Franke A, Lieb W, Schafmayer C, Hampe J, Buch S, Propping P, Hemminki K, Försti A, Westers H, Hofstra R, Pinheiro M, Pinto C, Teixeira M, Ruiz-Ponte C, Fernández-Rozadilla C, Carracedo A, Castells A, Castellví-Bel S, Campbell H, Bishop DT, Tomlinson IPM, Dunlop MG, Houlston RS. Recurrent Coding Sequence Variation Explains Only A Small Fraction of the Genetic Architecture of Colorectal Cancer. Sci Rep 2015; 5:16286. [PMID: 26553438 PMCID: PMC4639776 DOI: 10.1038/srep16286] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 09/21/2015] [Indexed: 12/21/2022] Open
Abstract
Whilst common genetic variation in many non-coding genomic regulatory regions are known to impart risk of colorectal cancer (CRC), much of the heritability of CRC remains unexplained. To examine the role of recurrent coding sequence variation in CRC aetiology, we genotyped 12,638 CRCs cases and 29,045 controls from six European populations. Single-variant analysis identified a coding variant (rs3184504) in SH2B3 (12q24) associated with CRC risk (OR = 1.08, P = 3.9 × 10(-7)), and novel damaging coding variants in 3 genes previously tagged by GWAS efforts; rs16888728 (8q24) in UTP23 (OR = 1.15, P = 1.4 × 10(-7)); rs6580742 and rs12303082 (12q13) in FAM186A (OR = 1.11, P = 1.2 × 10(-7) and OR = 1.09, P = 7.4 × 10(-8)); rs1129406 (12q13) in ATF1 (OR = 1.11, P = 8.3 × 10(-9)), all reaching exome-wide significance levels. Gene based tests identified associations between CRC and PCDHGA genes (P < 2.90 × 10(-6)). We found an excess of rare, damaging variants in base-excision (P = 2.4 × 10(-4)) and DNA mismatch repair genes (P = 6.1 × 10(-4)) consistent with a recessive mode of inheritance. This study comprehensively explores the contribution of coding sequence variation to CRC risk, identifying associations with coding variation in 4 genes and PCDHG gene cluster and several candidate recessive alleles. However, these findings suggest that recurrent, low-frequency coding variants account for a minority of the unexplained heritability of CRC.
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Affiliation(s)
- Maria N. Timofeeva
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, United Kingdom
| | - Ben Kinnersley
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, United Kingdom
| | - Susan M. Farrington
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, United Kingdom
| | - Nicola Whiffin
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, United Kingdom
| | - Claire Palles
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Victoria Svinti
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, United Kingdom
| | - Amy Lloyd
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, United Kingdom
| | - Maggie Gorman
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Li-Yin Ooi
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, United Kingdom
| | - Fay Hosking
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, United Kingdom
| | - Ella Barclay
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Lina Zgaga
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, United Kingdom
| | - Sara Dobbins
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, United Kingdom
| | - Lynn Martin
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Evropi Theodoratou
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, United Kingdom
- Centre for Population Health Sciences, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, United Kingdom
| | - Peter Broderick
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, United Kingdom
| | - Albert Tenesa
- Roslin Institute, University of Edinburgh, Easter Bush, Roslin EH25 9RG, United Kingdom
- Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, United Kingdom
| | - Claire Smillie
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, United Kingdom
| | - Graeme Grimes
- Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, United Kingdom
| | - Caroline Hayward
- Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, United Kingdom
| | - Archie Campbell
- Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, United Kingdom
- Generation Scotland, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, United Kingdom
| | - David Porteous
- Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, United Kingdom
- Generation Scotland, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, United Kingdom
| | - Ian J. Deary
- University of Edinburgh Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh EH8 9JZ, United Kingdom
| | - Sarah E. Harris
- Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, United Kingdom
- University of Edinburgh Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh EH8 9JZ, United Kingdom
| | - Emma L. Northwood
- Section of Epidemiology & Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, St James’s University Hospital, Leeds, UK
| | - Jennifer H. Barrett
- Section of Epidemiology & Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, St James’s University Hospital, Leeds, UK
| | - Gillian Smith
- Medical Research Institute, University of Dundee, Dundee, UK
| | - Roland Wolf
- Medical Research Institute, University of Dundee, Dundee, UK
| | | | - Hans Morreau
- Department of Pathology, Leiden University Medical Center, The Netherlands
| | - Dina Ruano
- Department of Pathology, Leiden University Medical Center, The Netherlands
| | - Carli Tops
- Department of Clinical Genetics, Leiden University Medical Center, The Netherlands
| | - Juul Wijnen
- Department of Human Genetics, Leiden University Medical Center, The Netherlands
| | - Melanie Schrumpf
- Department of Pathology, Leiden University Medical Center, The Netherlands
| | - Arnoud Boot
- Department of Pathology, Leiden University Medical Center, The Netherlands
| | - Hans F A Vasen
- Department of Gastroenterology, Leiden University Medical Center, The Netherlands
| | - Frederik J. Hes
- Department of Clinical Genetics, Leiden University Medical Center, The Netherlands
| | - Tom van Wezel
- Department of Pathology, Leiden University Medical Center, The Netherlands
| | - Andre Franke
- Institute of Clinical Molecular Biology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Wolgang Lieb
- Institute of Epidemiology, Christian-Albrechts-University Kiel, Kiel
| | - Clemens Schafmayer
- Department of General and Thoracic Surgery, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Jochen Hampe
- Medical Department 1, University Hospital Dresden, TU Dresden, Dresden, Germany
| | - Stephan Buch
- Medical Department 1, University Hospital Dresden, TU Dresden, Dresden, Germany
| | - Peter Propping
- Institute of Human Genetics, University Hospital Bonn, Bonn, Germany
| | - Kari Hemminki
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany
- Center for Primary Health Care Research, Lund University, 205 02 Malmö, Sweden
| | - Asta Försti
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany
- Center for Primary Health Care Research, Lund University, 205 02 Malmö, Sweden
| | - Helga Westers
- University of Groningen, University Medical Centre Groningen, Department of Genetics, PO Box 30001, 9700 RB Groningen, the Netherlands
| | - Robert Hofstra
- University of Groningen, University Medical Centre Groningen, Department of Genetics, PO Box 30001, 9700 RB Groningen, the Netherlands
- Department of Clinical Genetics, Erasmus Medical Center, Dr. Molewaterplein 50, 3015 GE Rotterdam, the Netherlands
| | - Manuela Pinheiro
- Department of Genetics, Portuguese Oncology Institute and Biomedical Sciences Institute (ICBAS), University of Porto, Porto, Portugal
| | - Carla Pinto
- Department of Genetics, Portuguese Oncology Institute and Biomedical Sciences Institute (ICBAS), University of Porto, Porto, Portugal
| | - Manuel Teixeira
- Department of Genetics, Portuguese Oncology Institute and Biomedical Sciences Institute (ICBAS), University of Porto, Porto, Portugal
| | - Clara Ruiz-Ponte
- Fundación Pública Galega de Medicina Xenómica (FPGMX), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Genomics Medicine Group, Hospital Clínico, 15706 Santiago de Compostela, University of Santiago de Compostela, Galicia, Spain
| | - Ceres Fernández-Rozadilla
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
- Fundación Pública Galega de Medicina Xenómica (FPGMX), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Genomics Medicine Group, Hospital Clínico, 15706 Santiago de Compostela, University of Santiago de Compostela, Galicia, Spain
| | - Angel Carracedo
- Fundación Pública Galega de Medicina Xenómica (FPGMX), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Genomics Medicine Group, Hospital Clínico, 15706 Santiago de Compostela, University of Santiago de Compostela, Galicia, Spain
| | - Antoni Castells
- Servei de Gastroenterologia, Hospital Clínic, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, 08036 Barcelona, Catalonia, Spain
| | - Sergi Castellví-Bel
- Servei de Gastroenterologia, Hospital Clínic, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, 08036 Barcelona, Catalonia, Spain
| | - Harry Campbell
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, United Kingdom
- Centre for Population Health Sciences, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, United Kingdom
| | - D. Timothy Bishop
- Section of Epidemiology & Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, St James’s University Hospital, Leeds, UK
| | - Ian P M Tomlinson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Malcolm G. Dunlop
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, United Kingdom
| | - Richard S. Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, United Kingdom
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48
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Al-Tassan NA, Whiffin N, Hosking FJ, Palles C, Farrington SM, Dobbins SE, Harris R, Gorman M, Tenesa A, Meyer BF, Wakil SM, Kinnersley B, Campbell H, Martin L, Smith CG, Idziaszczyk S, Barclay E, Maughan TS, Kaplan R, Kerr R, Kerr D, Buchanan DD, Win AK, Hopper J, Jenkins M, Lindor NM, Newcomb PA, Gallinger S, Conti D, Schumacher F, Casey G, Dunlop MG, Tomlinson IP, Cheadle JP, Houlston RS. Erratum: A new GWAS and meta-analysis with 1000Genomes imputation identifies novel risk variants for colorectal cancer. Sci Rep 2015; 5:12372. [PMID: 26237130 PMCID: PMC4523102 DOI: 10.1038/srep12372] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Al-Tassan NA, Whiffin N, Hosking FJ, Palles C, Farrington SM, Dobbins SE, Harris R, Gorman M, Tenesa A, Meyer BF, Wakil SM, Kinnersley B, Campbell H, Martin L, Smith CG, Idziaszczyk S, Barclay E, Maughan TS, Kaplan R, Kerr R, Kerr D, Buchannan DD, Ko Win A, Hopper J, Jenkins M, Lindor NM, Newcomb PA, Gallinger S, Conti D, Schumacher F, Casey G, Dunlop MG, Tomlinson IP, Cheadle JP, Houlston RS. A new GWAS and meta-analysis with 1000Genomes imputation identifies novel risk variants for colorectal cancer. Sci Rep 2015; 5:10442. [PMID: 25990418 PMCID: PMC4438486 DOI: 10.1038/srep10442] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 04/13/2015] [Indexed: 12/17/2022] Open
Abstract
Genome-wide association studies (GWAS) of colorectal cancer (CRC) have identified 23 susceptibility loci thus far. Analyses of previously conducted GWAS indicate additional risk loci are yet to be discovered. To identify novel CRC susceptibility loci, we conducted a new GWAS and performed a meta-analysis with five published GWAS (totalling 7,577 cases and 9,979 controls of European ancestry), imputing genotypes utilising the 1000 Genomes Project. The combined analysis identified new, significant associations with CRC at 1p36.2 marked by rs72647484 (minor allele frequency [MAF] = 0.09) near CDC42 and WNT4 (P = 1.21 × 10(-8), odds ratio [OR] = 1.21 ) and at 16q24.1 marked by rs16941835 (MAF = 0.21, P = 5.06 × 10(-8); OR = 1.15) within the long non-coding RNA (lncRNA) RP11-58A18.1 and ~500 kb from the nearest coding gene FOXL1. Additionally we identified a promising association at 10p13 with rs10904849 intronic to CUBN (MAF = 0.32, P = 7.01 × 10(-8); OR = 1.14). These findings provide further insights into the genetic and biological basis of inherited genetic susceptibility to CRC. Additionally, our analysis further demonstrates that imputation can be used to exploit GWAS data to identify novel disease-causing variants.
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Affiliation(s)
- Nada A. Al-Tassan
- Department of Genetics, King Faisal Specialist Hospital and Research Center, P.O.Box 3354, Riyadh 11211, Saudi Arabia
| | - Nicola Whiffin
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Fay J. Hosking
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Claire Palles
- Wellcome Trust Centre for Human Genetics and NIHR Comprehensive Biomedical Research Centre, Oxford, UK
| | - Susan M. Farrington
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Sara E. Dobbins
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Rebecca Harris
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Maggie Gorman
- Wellcome Trust Centre for Human Genetics and NIHR Comprehensive Biomedical Research Centre, Oxford, UK
| | - Albert Tenesa
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
- The Roslin Institute, University of Edinburgh, Easter Bush, Roslin, EH25 9RG, UK
| | - Brian F. Meyer
- Department of Genetics, King Faisal Specialist Hospital and Research Center, P.O.Box 3354, Riyadh 11211, Saudi Arabia
| | - Salma M. Wakil
- Department of Genetics, King Faisal Specialist Hospital and Research Center, P.O.Box 3354, Riyadh 11211, Saudi Arabia
| | - Ben Kinnersley
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Harry Campbell
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, EH8 9AG, UK
| | - Lynn Martin
- Wellcome Trust Centre for Human Genetics and NIHR Comprehensive Biomedical Research Centre, Oxford, UK
| | - Christopher G. Smith
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Shelley Idziaszczyk
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Ella Barclay
- Wellcome Trust Centre for Human Genetics and NIHR Comprehensive Biomedical Research Centre, Oxford, UK
| | - Timothy S. Maughan
- CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Richard Kaplan
- MRC Clinical Trials Unit, Aviation House, 125 Kingsway, London, WC2B 6NH, UK
| | - Rachel Kerr
- Oxford Cancer Centre, Department of Oncology, University of Oxford, Churchill Hospital, Old Road, Headington, Oxford, OX3 7LE, UK
| | - David Kerr
- Nuffield Department of Clinical Laboratory Sciences, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK
| | - Daniel D. Buchannan
- Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology, The Univers‡ity of Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Victoria, Australia
| | - Aung Ko Win
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Victoria, Australia
| | - John Hopper
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Victoria, Australia
| | - Mark Jenkins
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Victoria, Australia
| | - Noralane M. Lindor
- Department of Health Sciences Research, Mayo Clinic, Scottsdale, AZ, USA
| | - Polly A. Newcomb
- Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Steve Gallinger
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - David Conti
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Fred Schumacher
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Graham Casey
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Malcolm G. Dunlop
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Ian P. Tomlinson
- Wellcome Trust Centre for Human Genetics and NIHR Comprehensive Biomedical Research Centre, Oxford, UK
| | - Jeremy P. Cheadle
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Richard S. Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
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50
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Huffman JE, Albrecht E, Teumer A, Mangino M, Kapur K, Johnson T, Kutalik Z, Pirastu N, Pistis G, Lopez LM, Haller T, Salo P, Goel A, Li M, Tanaka T, Dehghan A, Ruggiero D, Malerba G, Smith AV, Nolte IM, Portas L, Phipps-Green A, Boteva L, Navarro P, Johansson A, Hicks AA, Polasek O, Esko T, Peden JF, Harris SE, Murgia F, Wild SH, Tenesa A, Tin A, Mihailov E, Grotevendt A, Gislason GK, Coresh J, D'Adamo P, Ulivi S, Vollenweider P, Waeber G, Campbell S, Kolcic I, Fisher K, Viigimaa M, Metter JE, Masciullo C, Trabetti E, Bombieri C, Sorice R, Döring A, Reischl E, Strauch K, Hofman A, Uitterlinden AG, Waldenberger M, Wichmann HE, Davies G, Gow AJ, Dalbeth N, Stamp L, Smit JH, Kirin M, Nagaraja R, Nauck M, Schurmann C, Budde K, Farrington SM, Theodoratou E, Jula A, Salomaa V, Sala C, Hengstenberg C, Burnier M, Mägi R, Klopp N, Kloiber S, Schipf S, Ripatti S, Cabras S, Soranzo N, Homuth G, Nutile T, Munroe PB, Hastie N, Campbell H, Rudan I, Cabrera C, Haley C, Franco OH, Merriman TR, Gudnason V, Pirastu M, Penninx BW, Snieder H, Metspalu A, Ciullo M, Pramstaller PP, van Duijn CM, Ferrucci L, Gambaro G, Deary IJ, Dunlop MG, Wilson JF, Gasparini P, Gyllensten U, Spector TD, Wright AF, Hayward C, Watkins H, Perola M, Bochud M, Kao WHL, Caulfield M, Toniolo D, Völzke H, Gieger C, Köttgen A, Vitart V. Modulation of genetic associations with serum urate levels by body-mass-index in humans. PLoS One 2015; 10:e0119752. [PMID: 25811787 PMCID: PMC4374966 DOI: 10.1371/journal.pone.0119752] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 02/03/2015] [Indexed: 11/17/2022] Open
Abstract
We tested for interactions between body mass index (BMI) and common genetic variants affecting serum urate levels, genome-wide, in up to 42569 participants. Both stratified genome-wide association (GWAS) analyses, in lean, overweight and obese individuals, and regression-type analyses in a non BMI-stratified overall sample were performed. The former did not uncover any novel locus with a major main effect, but supported modulation of effects for some known and potentially new urate loci. The latter highlighted a SNP at RBFOX3 reaching genome-wide significant level (effect size 0.014, 95% CI 0.008-0.02, Pinter= 2.6 x 10-8). Two top loci in interaction term analyses, RBFOX3 and ERO1LB-EDARADD, also displayed suggestive differences in main effect size between the lean and obese strata. All top ranking loci for urate effect differences between BMI categories were novel and most had small magnitude but opposite direction effects between strata. They include the locus RBMS1-TANK (men, Pdifflean-overweight= 4.7 x 10-8), a region that has been associated with several obesity related traits, and TSPYL5 (men, Pdifflean-overweight= 9.1 x 10-8), regulating adipocytes-produced estradiol. The top-ranking known urate loci was ABCG2, the strongest known gout risk locus, with an effect halved in obese compared to lean men (Pdifflean-obese= 2 x 10-4). Finally, pathway analysis suggested a role for N-glycan biosynthesis as a prominent urate-associated pathway in the lean stratum. These results illustrate a potentially powerful way to monitor changes occurring in obesogenic environment.
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Affiliation(s)
- Jennifer E Huffman
- Medical Research Council (MRC) Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Edinburgh, United Kingdom
| | - Eva Albrecht
- Institute of Genetic Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Alexander Teumer
- Interfaculty Institute for Genetics and Functional Genomics, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
| | - Massimo Mangino
- King's College London, St. Thomas' Hospital Campus, London, United Kingdom
| | - Karen Kapur
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Toby Johnson
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Zoltán Kutalik
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Nicola Pirastu
- Institute for Maternal and Child Health-Istituto Di Ricovero e Cura a Carattere Scientifico (IRCCS) "Burlo Garofolo", Trieste, Italy; University of Trieste, Trieste, Italy
| | - Giorgio Pistis
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milano, Italy
| | - Lorna M Lopez
- Department of Psychology, The University of Edinburgh, Edinburgh, United Kingdom; Centre for Cognitive Ageing and Cognitive Epidemiology, The University of Edinburgh, Edinburgh, United Kingdom
| | - Toomas Haller
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Perttu Salo
- Department of Chronic Disease Prevention, National Institute for Health and Welfare (THL), Helsinki, Finland
| | - Anuj Goel
- Department of Cardiovascular Medicine, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Man Li
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States of America
| | - Toshiko Tanaka
- Clinical Research Branch, National Institute on Aging, Baltimore, MD, United States of America
| | - Abbas Dehghan
- Member of Netherlands Consortium for Healthy Aging (NCHA) sponsored by Netherlands Genomics Initiative (NGI), Leiden, The Netherlands; Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Daniela Ruggiero
- Institute of Genetics and Biophysics "A. Buzzati-Traverso"-Consiglio Nazionale delle Ricerche (CNR), Naples, Italy
| | - Giovanni Malerba
- Biology and Genetics section, Department of Life and Reproduction Sciences, University of Verona, Verona, Italy
| | - Albert V Smith
- Icelandic Heart Association Research Institute, Kopavogur, Iceland; University of Iceland, Reykjavik, Iceland
| | - Ilja M Nolte
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Laura Portas
- Institute of Population Genetics, National Research Council of Italy, Sassari, Italy
| | | | - Lora Boteva
- Medical Research Council (MRC) Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Edinburgh, United Kingdom
| | - Pau Navarro
- Medical Research Council (MRC) Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Edinburgh, United Kingdom
| | - Asa Johansson
- Uppsala Clinical Research Center, Uppsala University Hospital, Upsalla, Sweden; Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, 751 85, Sweden
| | - Andrew A Hicks
- Center for Biomedicine, European Academy Bozen/Bolzano (EURAC), Bolzano, Italy; Affiliated Institute of the University of Lübeck, Lübeck, Germany
| | - Ozren Polasek
- Faculty of Medicine, University of Split, Croatia, Soltanska 2, Split, 21000, Croatia
| | - Tõnu Esko
- Estonian Genome Center, University of Tartu, Tartu, Estonia; Broad Institute, Cambridge, MA, United States of America; Children's Hospital Boston, Boston, MA, United States of America
| | - John F Peden
- Department of Cardiovascular Medicine, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Sarah E Harris
- Centre for Cognitive Ageing and Cognitive Epidemiology, The University of Edinburgh, Edinburgh, United Kingdom; Medical Genetics Section, University of Edinburgh Centre for Genomics and Experimental Medicine and MRC Institute of Genetics and Molecular Medicine, Edinburgh, United Kingdom
| | - Federico Murgia
- Institute of Population Genetics, National Research Council of Italy, Sassari, Italy
| | - Sarah H Wild
- Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Albert Tenesa
- Medical Research Council (MRC) Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Edinburgh, United Kingdom; Roslin Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Adrienne Tin
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States of America
| | | | - Anne Grotevendt
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Ernst-Moritz-Arndt University Greifswald, Greifswald, Germany
| | - Gauti K Gislason
- Icelandic Heart Association Research Institute, Kopavogur, Iceland
| | - Josef Coresh
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States of America; Welch Center for Prevention, Epidemiology and Clinical Research, John Hopkins University, Baltimore, MD, United States of America
| | - Pio D'Adamo
- Institute for Maternal and Child Health-Istituto Di Ricovero e Cura a Carattere Scientifico (IRCCS) "Burlo Garofolo", Trieste, Italy; University of Trieste, Trieste, Italy
| | - Sheila Ulivi
- Institute for Maternal and Child Health-Istituto Di Ricovero e Cura a Carattere Scientifico (IRCCS) "Burlo Garofolo", Trieste, Italy
| | - Peter Vollenweider
- Department of Medicine, Internal Medicine, Lausanne University Hospital, Lausanne, Switzerland
| | - Gerard Waeber
- Department of Medicine, Internal Medicine, Lausanne University Hospital, Lausanne, Switzerland
| | - Susan Campbell
- Medical Research Council (MRC) Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Edinburgh, United Kingdom
| | - Ivana Kolcic
- Faculty of Medicine, University of Split, Croatia, Soltanska 2, Split, 21000, Croatia
| | - Krista Fisher
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Margus Viigimaa
- Tallinn University of Technology, Department of Biomedical Engineering, Chair of Medical Physics, Tallinn, Estonia; Centre of Cardiology, North Estonia Medical Centre, Tallinn, Estonia
| | - Jeffrey E Metter
- Clinical Research Branch, National Institute on Aging, Baltimore, MD, United States of America
| | - Corrado Masciullo
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milano, Italy
| | - Elisabetta Trabetti
- Biology and Genetics section, Department of Life and Reproduction Sciences, University of Verona, Verona, Italy
| | - Cristina Bombieri
- Biology and Genetics section, Department of Life and Reproduction Sciences, University of Verona, Verona, Italy
| | - Rossella Sorice
- Institute of Genetics and Biophysics "A. Buzzati-Traverso"-Consiglio Nazionale delle Ricerche (CNR), Naples, Italy
| | - Angela Döring
- Institute of Epidemiology II, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany; Institute of Epidemiology I, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Eva Reischl
- Institute of Epidemiology II, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany; Research Unit of Molecular Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany; Institute of Medical Informatics, Biometry and Epidemiology, Chair of Genetic Epidemiology, Ludwig-Maximilians-University, Munich, Germany
| | - Albert Hofman
- Member of Netherlands Consortium for Healthy Aging (NCHA) sponsored by Netherlands Genomics Initiative (NGI), Leiden, The Netherlands; Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Andre G Uitterlinden
- Member of Netherlands Consortium for Healthy Aging (NCHA) sponsored by Netherlands Genomics Initiative (NGI), Leiden, The Netherlands; Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Melanie Waldenberger
- Institute of Epidemiology II, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany; Research Unit of Molecular Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - H-Erich Wichmann
- Institute of Epidemiology I, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany; Institute of Medical Informatics, Biometry and Epidemiology, Chair of Genetic Epidemiology, Ludwig-Maximilians-University, Munich, Germany; Klinikum Grosshadern, Munich, Germany
| | - Gail Davies
- Department of Psychology, The University of Edinburgh, Edinburgh, United Kingdom; Centre for Cognitive Ageing and Cognitive Epidemiology, The University of Edinburgh, Edinburgh, United Kingdom
| | - Alan J Gow
- Department of Psychology, The University of Edinburgh, Edinburgh, United Kingdom; Centre for Cognitive Ageing and Cognitive Epidemiology, The University of Edinburgh, Edinburgh, United Kingdom
| | - Nicola Dalbeth
- Bone and Joint Research Group, Department of Medicine, University of Auckland, Auckland, New Zealand
| | - Lisa Stamp
- Department of Medicine, University of Otago, Christchurch, New Zealand
| | - Johannes H Smit
- Department of Psychiatry/EMGO Institute, VU University Medical Centre, Amsterdam, the Netherlands
| | - Mirna Kirin
- Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Ramaiah Nagaraja
- Laboratory of Genetics, National Institute on Aging (NIA), Baltimore, MD, United States of America
| | - Matthias Nauck
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Ernst-Moritz-Arndt University Greifswald, Greifswald, Germany
| | - Claudia Schurmann
- Interfaculty Institute for Genetics and Functional Genomics, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
| | - Kathrin Budde
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Ernst-Moritz-Arndt University Greifswald, Greifswald, Germany
| | - Susan M Farrington
- Medical Research Council (MRC) Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Edinburgh, United Kingdom
| | - Evropi Theodoratou
- Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Antti Jula
- Department of Chronic Disease Prevention, National Institute for Health and Welfare (THL), Turku, Finland
| | - Veikko Salomaa
- Department of Chronic Disease Prevention, National Institute for Health and Welfare (THL), Helsinki, Finland
| | - Cinzia Sala
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milano, Italy
| | | | - Michel Burnier
- Department of Medicine, Nephrology Division, Lausanne University Hospital, Lausanne, Switzerland
| | - Reedik Mägi
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Norman Klopp
- Institute of Medical Informatics, Biometry and Epidemiology, Chair of Genetic Epidemiology, Ludwig-Maximilians-University, Munich, Germany
| | | | - Sabine Schipf
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Samuli Ripatti
- Department of Chronic Disease Prevention, National Institute for Health and Welfare (THL), Turku, Finland; Human Genetics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom; University of Helsinki, Institute of Molecular Medicine, Helsinki, Finland
| | - Stefano Cabras
- Department of Mathematics and Informatics, Università di Cagliari, Cagliari, Italy; Department of Statistics, Universidad Carlos III de Madrid, Madrid, Spain
| | - Nicole Soranzo
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Georg Homuth
- Interfaculty Institute for Genetics and Functional Genomics, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
| | - Teresa Nutile
- Institute of Genetics and Biophysics "A. Buzzati-Traverso"-Consiglio Nazionale delle Ricerche (CNR), Naples, Italy
| | - Patricia B Munroe
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Nicholas Hastie
- Medical Research Council (MRC) Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Edinburgh, United Kingdom
| | - Harry Campbell
- Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Igor Rudan
- Faculty of Medicine, University of Split, Croatia, Soltanska 2, Split, 21000, Croatia; Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | | | - Chris Haley
- Medical Research Council (MRC) Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Edinburgh, United Kingdom; Roslin Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Oscar H Franco
- Member of Netherlands Consortium for Healthy Aging (NCHA) sponsored by Netherlands Genomics Initiative (NGI), Leiden, The Netherlands; Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Tony R Merriman
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Vilmundur Gudnason
- Icelandic Heart Association Research Institute, Kopavogur, Iceland; University of Iceland, Reykjavik, Iceland
| | - Mario Pirastu
- Institute of Population Genetics, National Research Council of Italy, Sassari, Italy
| | - Brenda W Penninx
- Department of Psychiatry, Leiden University Medical Center, Leiden, The Netherlands; Department of Epidemiology, Subdivision Genetic Epidemiology, Erasmus MC, Rotterdam, The Netherlands; Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - Harold Snieder
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | | | - Marina Ciullo
- Institute of Genetics and Biophysics "A. Buzzati-Traverso"-Consiglio Nazionale delle Ricerche (CNR), Naples, Italy
| | - Peter P Pramstaller
- Center for Biomedicine, European Academy Bozen/Bolzano (EURAC), Bolzano, Italy; Affiliated Institute of the University of Lübeck, Lübeck, Germany
| | - Cornelia M van Duijn
- Department of Epidemiology, Subdivision Genetic Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | - Luigi Ferrucci
- Clinical Research Branch, National Institute on Aging, Baltimore, MD, United States of America
| | - Giovanni Gambaro
- Institute of Internal Medicine, Renal Program, Columbus-Gemelli University Hospital, Catholic University, Rome, Italy
| | - Ian J Deary
- Department of Psychology, The University of Edinburgh, Edinburgh, United Kingdom; Centre for Cognitive Ageing and Cognitive Epidemiology, The University of Edinburgh, Edinburgh, United Kingdom
| | - Malcolm G Dunlop
- Medical Research Council (MRC) Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Edinburgh, United Kingdom
| | - James F Wilson
- Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Paolo Gasparini
- Institute for Maternal and Child Health-Istituto Di Ricovero e Cura a Carattere Scientifico (IRCCS) "Burlo Garofolo", Trieste, Italy; University of Trieste, Trieste, Italy
| | - Ulf Gyllensten
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, 751 85, Sweden
| | - Tim D Spector
- King's College London, St. Thomas' Hospital Campus, London, United Kingdom
| | - Alan F Wright
- Medical Research Council (MRC) Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Edinburgh, United Kingdom
| | - Caroline Hayward
- Medical Research Council (MRC) Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Edinburgh, United Kingdom
| | - Hugh Watkins
- on behalf of PROCARDIS; Department of Cardiovascular Medicine, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Markus Perola
- Estonian Genome Center, University of Tartu, Tartu, Estonia; Department of Chronic Disease Prevention, National Institute for Health and Welfare (THL), Helsinki, Finland; University of Helsinki, Institute of Molecular Medicine, Helsinki, Finland
| | - Murielle Bochud
- University Institute of Social and Preventive Medicine, Lausanne, Switzerland
| | - W H Linda Kao
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States of America; Welch Center for Prevention, Epidemiology and Clinical Research, John Hopkins University, Baltimore, MD, United States of America
| | - Mark Caulfield
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Daniela Toniolo
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milano, Italy
| | - Henry Völzke
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Christian Gieger
- Institute of Genetic Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Anna Köttgen
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States of America; Renal Division, Freiburg University Hospital, Freiburg, Germany
| | - Veronique Vitart
- Medical Research Council (MRC) Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Edinburgh, United Kingdom
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