1
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Fan Q, Li H, Wang X, Tham YC, Teo KYC, Yasuda M, Lim WK, Kwan YP, Teo JX, Chen CJ, Chen LJ, Ahn J, Davila S, Miyake M, Tan P, Park KH, Pang CP, Khor CC, Wong TY, Yanagi Y, Cheung CMG, Cheng CY. Contribution of common and rare variants to Asian neovascular age-related macular degeneration subtypes. Nat Commun 2023; 14:5574. [PMID: 37696869 PMCID: PMC10495468 DOI: 10.1038/s41467-023-41256-z] [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: 05/29/2022] [Accepted: 08/28/2023] [Indexed: 09/13/2023] Open
Abstract
Neovascular age-related macular degeneration (nAMD), along with its clinical subtype known as polypoidal choroidal vasculopathy (PCV), are among the leading causes of vision loss in elderly Asians. In a genome-wide association study (GWAS) comprising 3,128 nAMD (1,555 PCV and 1,573 typical nAMD), and 5,493 controls of East Asian ancestry, we identify twelve loci, of which four are novel ([Formula: see text]). Substantial genetic sharing between PCV and typical nAMD is noted (rg = 0.666), whereas collagen extracellular matrix and fibrosis-related pathways are more pronounced for PCV. Whole-exome sequencing in 259 PCV patients revealed functional rare variants burden in collagen type I alpha 1 chain gene (COL1A1; [Formula: see text]) and potential enrichment of functional rare mutations at AMD-associated loci. At the GATA binding protein 5 (GATA5) locus, the most significant GWAS novel loci, the expressions of genes including laminin subunit alpha 5 (Lama5), mitochondrial ribosome associated GTPase 2 (Mtg2), and collagen type IX alpha 3 chain (Col9A3), are significantly induced during retinal angiogenesis and subretinal fibrosis in murine models. Furthermore, retinoic acid increased the expression of LAMA5 and MTG2 in vitro. Taken together, our data provide insights into the genetic basis of AMD pathogenesis in the Asian population.
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Affiliation(s)
- Qiao Fan
- Center for Quantitative Medicine, Duke-NUS Medical School, National University of Singapore, Singapore, Singapore.
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore.
| | - Hengtong Li
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Centre for Innovation and Precision Eye Health, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Xiaomeng Wang
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
- Center for Vision Research, Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Yih-Chung Tham
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Centre for Innovation and Precision Eye Health, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Kelvin Yi Chong Teo
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Masayuki Yasuda
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Weng Khong Lim
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore, Singapore
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore, Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
- Laboratory of Genome Variation Analytics, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Yuet Ping Kwan
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
| | - Jing Xian Teo
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore, Singapore
| | - Ching-Jou Chen
- Center for Vision Research, Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Li Jia Chen
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Jeeyun Ahn
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul Metropolitan Government Seoul National University Boramae Medical Center, Seoul, Korea
| | - Sonia Davila
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore, Singapore
| | - Masahiro Miyake
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Patrick Tan
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore, Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
- Human Genetics, Genome Institute of Singapore, Singapore, Singapore
| | - Kyu Hyung Park
- Department of Ophthalmology, Seoul National University Hospital, Seoul, Korea
| | - Chi Pui Pang
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Chiea Chuan Khor
- Human Genetics, Genome Institute of Singapore, Singapore, Singapore
| | - Tien Yin Wong
- Tsinghua Medicine, Tsinghua University, Beijing, China
| | - Yasuo Yanagi
- Department of Ophthalmology and Microtechnology, Yokohama City University, Yokohama, Japan
| | - Chui Ming Gemmy Cheung
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Ching-Yu Cheng
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore.
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore.
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Centre for Innovation and Precision Eye Health, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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2
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Bulut M, Alseekh S, Fernie AR. Natural variation of respiration-related traits in plants. Plant Physiol 2023; 191:2120-2132. [PMID: 36546766 PMCID: PMC10069898 DOI: 10.1093/plphys/kiac593] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
Plant respiration is one of the greatest global metabolic fluxes, but rates of respiration vary massively both within different cell types as well as between different individuals and different species. Whilst this is well known, few studies have detailed population-level variation of respiration until recently. The last 20 years have seen a renaissance in studies of natural variance. In this review, we describe how experimental breeding populations and collections of large populations of accessions can be used to determine the genetic architecture of plant traits. We further detail how these approaches have been used to study the rate of respiration per se as well as traits that are intimately associated with respiration. The review highlights specific breakthroughs in these areas but also concludes that the approach should be more widely adopted in the study of respiration per se as opposed to the more frequently studied respiration-related traits.
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Affiliation(s)
- Mustafa Bulut
- Department of Root Biology and Symbiosis, Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
| | - Saleh Alseekh
- Department of Root Biology and Symbiosis, Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
- Center for Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria
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3
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Appadurai V, Bybjerg-Grauholm J, Krebs MD, Rosengren A, Buil A, Ingason A, Mors O, Børglum AD, Hougaard DM, Nordentoft M, Mortensen PB, Delaneau O, Werge T, Schork AJ. Accuracy of haplotype estimation and whole genome imputation affects complex trait analyses in complex biobanks. Commun Biol 2023; 6:101. [PMID: 36697501 PMCID: PMC9876938 DOI: 10.1038/s42003-023-04477-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 01/12/2023] [Indexed: 01/27/2023] Open
Abstract
Sample recruitment for research consortia, biobanks, and personal genomics companies span years, necessitating genotyping in batches, using different technologies. As marker content on genotyping arrays varies, integrating such datasets is non-trivial and its impact on haplotype estimation (phasing) and whole genome imputation, necessary steps for complex trait analysis, remains under-evaluated. Using the iPSYCH dataset, comprising 130,438 individuals, genotyped in two stages, on different arrays, we evaluated phasing and imputation performance across multiple phasing methods and data integration protocols. While phasing accuracy varied by choice of method and data integration protocol, imputation accuracy varied mostly between data integration protocols. We demonstrate an attenuation in imputation accuracy within samples of non-European origin, highlighting challenges to studying complex traits in diverse populations. Finally, imputation errors can bias association tests, reduce predictive utility of polygenic scores. Carefully optimized data integration strategies enhance accuracy and replicability of complex trait analyses in complex biobanks.
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Affiliation(s)
- Vivek Appadurai
- Institute of Biological Psychiatry, Mental Health Center Sankt Hans, Roskilde, 4000 Denmark ,grid.452548.a0000 0000 9817 5300The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
| | - Jonas Bybjerg-Grauholm
- grid.452548.a0000 0000 9817 5300The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark ,grid.6203.70000 0004 0417 4147Danish Center for Neonatal Screening, Statens Serum Institut, Copenhagen, Denmark
| | - Morten Dybdahl Krebs
- Institute of Biological Psychiatry, Mental Health Center Sankt Hans, Roskilde, 4000 Denmark ,grid.452548.a0000 0000 9817 5300The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
| | - Anders Rosengren
- Institute of Biological Psychiatry, Mental Health Center Sankt Hans, Roskilde, 4000 Denmark ,grid.452548.a0000 0000 9817 5300The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
| | - Alfonso Buil
- Institute of Biological Psychiatry, Mental Health Center Sankt Hans, Roskilde, 4000 Denmark ,grid.452548.a0000 0000 9817 5300The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
| | - Andrés Ingason
- Institute of Biological Psychiatry, Mental Health Center Sankt Hans, Roskilde, 4000 Denmark ,grid.452548.a0000 0000 9817 5300The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
| | - Ole Mors
- grid.452548.a0000 0000 9817 5300The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark ,grid.154185.c0000 0004 0512 597XPsychosis Research Unit, Aarhus University Hospital - Psychiatry, Aarhus, Denmark
| | - Anders D. Børglum
- grid.452548.a0000 0000 9817 5300The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark ,grid.7048.b0000 0001 1956 2722Department of Biomedicine and Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark ,grid.7048.b0000 0001 1956 2722Center for Genomics and Personalized Medicine, CGPM, Aarhus University, Aarhus, Denmark
| | - David M. Hougaard
- grid.452548.a0000 0000 9817 5300The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark ,grid.6203.70000 0004 0417 4147Danish Center for Neonatal Screening, Statens Serum Institut, Copenhagen, Denmark
| | - Merete Nordentoft
- grid.452548.a0000 0000 9817 5300The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark ,grid.466916.a0000 0004 0631 4836Mental Health Services in the Capital Region of Denmark, Copenhagen, Denmark ,grid.5254.60000 0001 0674 042XDepartment of Clinical Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Preben B. Mortensen
- grid.452548.a0000 0000 9817 5300The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark ,grid.7048.b0000 0001 1956 2722NCRR - National Center for Register-Based Research, Business and Social Sciences, Aarhus University, Aarhus, Denmark ,grid.7048.b0000 0001 1956 2722CIRRAU - Centre for Integrated Register-Based Research, Aarhus University, Aarhus, Denmark
| | - Olivier Delaneau
- grid.9851.50000 0001 2165 4204Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Thomas Werge
- Institute of Biological Psychiatry, Mental Health Center Sankt Hans, Roskilde, 4000 Denmark ,grid.452548.a0000 0000 9817 5300The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
| | - Andrew J. Schork
- Institute of Biological Psychiatry, Mental Health Center Sankt Hans, Roskilde, 4000 Denmark ,grid.452548.a0000 0000 9817 5300The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark ,grid.250942.80000 0004 0507 3225The Translational Genomics Research Institute, Phoenix, AZ USA
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4
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Mathur R, Fang F, Gaddis N, Hancock DB, Cho MH, Hokanson JE, Bierut LJ, Lutz SM, Young K, Smith AV, Silverman EK, Page GP, Johnson EO. GAWMerge expands GWAS sample size and diversity by combining array-based genotyping and whole-genome sequencing. Commun Biol 2022; 5:806. [PMID: 35953715 PMCID: PMC9372058 DOI: 10.1038/s42003-022-03738-6] [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: 12/21/2021] [Accepted: 07/18/2022] [Indexed: 11/09/2022] Open
Abstract
Genome-wide association studies (GWAS) have made impactful discoveries for complex diseases, often by amassing very large sample sizes. Yet, GWAS of many diseases remain underpowered, especially for non-European ancestries. One cost-effective approach to increase sample size is to combine existing cohorts, which may have limited sample size or be case-only, with public controls, but this approach is limited by the need for a large overlap in variants across genotyping arrays and the scarcity of non-European controls. We developed and validated a protocol, Genotyping Array-WGS Merge (GAWMerge), for combining genotypes from arrays and whole-genome sequencing, ensuring complete variant overlap, and allowing for diverse samples like Trans-Omics for Precision Medicine to be used. Our protocol involves phasing, imputation, and filtering. We illustrated its ability to control technology driven artifacts and type-I error, as well as recover known disease-associated signals across technologies, independent datasets, and ancestries in smoking-related cohorts. GAWMerge enables genetic studies to leverage existing cohorts to validly increase sample size and enhance discovery for understudied traits and ancestries.
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Affiliation(s)
- Ravi Mathur
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, Research Triangle Park, NC, USA
| | - Fang Fang
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, Research Triangle Park, NC, USA
| | - Nathan Gaddis
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, Research Triangle Park, NC, USA
| | - Dana B Hancock
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, Research Triangle Park, NC, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - John E Hokanson
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Denver, Aurora, CO, USA
| | - Laura J Bierut
- Department of Psychiatry, Washington University, St. Louis, MO, USA
| | - Sharon M Lutz
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care, Boston, MA, USA
| | - Kendra Young
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Denver, Aurora, CO, USA
| | - Albert V Smith
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Grier P Page
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, Research Triangle Park, NC, USA
- Fellow Program, RTI International, Research Triangle Park, NC, USA
| | - Eric O Johnson
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, Research Triangle Park, NC, USA.
- Fellow Program, RTI International, Research Triangle Park, NC, USA.
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5
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Zeng Q, Zhao B, Wang H, Wang M, Teng M, Hu J, Bao Z, Wang Y. Aquaculture Molecular Breeding Platform (AMBP): a comprehensive web server for genotype imputation and genetic analysis in aquaculture. Nucleic Acids Res 2022; 50:W66-W74. [PMID: 35639514 PMCID: PMC9252723 DOI: 10.1093/nar/gkac424] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 03/21/2022] [Revised: 04/19/2022] [Accepted: 05/09/2022] [Indexed: 12/26/2022] Open
Abstract
It is of vital importance to understand the population structure, dissect the genetic bases of performance traits, and make proper strategies for selection in breeding programs. However, there is no single webserver covering the specific needs in aquaculture. We present Aquaculture Molecular Breeding Platform (AMBP), the first web server for genetic data analysis in aquatic species of farming interest. AMBP integrates the haplotype reference panels of 18 aquaculture species, which greatly improves the accuracy of genotype imputation. It also supports multiple tools to infer genetic structures, dissect the genetic architecture of performance traits, estimate breeding values, and predict optimum contribution. All the tools are coherently linked in a web-interface for users to generate interpretable results and evaluate statistical appropriateness. The webserver supports standard VCF and PLINK (PED, MAP) files, and implements automated pipelines for format transformation and visualization to simplify the process of analysis. As a demonstration, we applied the webserver to Pacific white shrimp and Atlantic salmon datasets. In summary, AMBP constitutes comprehensive resources and analytical tools for exploring genetic data and guiding practical breeding programs. AMBP is available at http://mgb.qnlm.ac.
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Affiliation(s)
- Qifan Zeng
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.,Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanog Inst, Ocean Univ China, Sanya 572000, Peoples R China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Baojun Zhao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Hao Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Mengqiu Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Mingxuan Teng
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Jingjie Hu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.,Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanog Inst, Ocean Univ China, Sanya 572000, Peoples R China
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.,Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanog Inst, Ocean Univ China, Sanya 572000, Peoples R China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Yangfan Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
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6
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Chen W, Wu Y, Zheng Z, Qi T, Visscher PM, Zhu Z, Yang J. Improved analyses of GWAS summary statistics by reducing data heterogeneity and errors. Nat Commun 2021; 12:7117. [PMID: 34880243 PMCID: PMC8654883 DOI: 10.1038/s41467-021-27438-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 11/17/2021] [Indexed: 01/08/2023] Open
Abstract
statistics from genome-wide association studies (GWAS) have facilitated the development of various summary data-based methods, which typically require a reference sample for linkage disequilibrium (LD) estimation. Analyses using these methods may be biased by errors in GWAS summary data or LD reference or heterogeneity between GWAS and LD reference. Here we propose a quality control method, DENTIST, that leverages LD among genetic variants to detect and eliminate errors in GWAS or LD reference and heterogeneity between the two. Through simulations, we demonstrate that DENTIST substantially reduces false-positive rate in detecting secondary signals in the summary-data-based conditional and joint association analysis, especially for imputed rare variants (false-positive rate reduced from >28% to <2% in the presence of heterogeneity between GWAS and LD reference). We further show that DENTIST can improve other summary-data-based analyses such as fine-mapping analysis.
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Affiliation(s)
- Wenhan Chen
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- Epigenetics Research Laboratory, Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Yang Wu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Zhili Zheng
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ting Qi
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, 310024, China
| | - Peter M Visscher
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Zhihong Zhu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jian Yang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China.
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, 310024, China.
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7
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Kim M, Harmanci AO, Bossuat JP, Carpov S, Cheon JH, Chillotti I, Cho W, Froelicher D, Gama N, Georgieva M, Hong S, Hubaux JP, Kim D, Lauter K, Ma Y, Ohno-Machado L, Sofia H, Son Y, Song Y, Troncoso-Pastoriza J, Jiang X. Ultrafast homomorphic encryption models enable secure outsourcing of genotype imputation. Cell Syst 2021; 12:1108-1120.e4. [PMID: 34464590 PMCID: PMC9898842 DOI: 10.1016/j.cels.2021.07.010] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 04/21/2021] [Accepted: 07/29/2021] [Indexed: 02/06/2023]
Abstract
Genotype imputation is a fundamental step in genomic data analysis, where missing variant genotypes are predicted using the existing genotypes of nearby "tag" variants. Although researchers can outsource genotype imputation, privacy concerns may prohibit genetic data sharing with an untrusted imputation service. Here, we developed secure genotype imputation using efficient homomorphic encryption (HE) techniques. In HE-based methods, the genotype data are secure while it is in transit, at rest, and in analysis. It can only be decrypted by the owner. We compared secure imputation with three state-of-the-art non-secure methods and found that HE-based methods provide genetic data security with comparable accuracy for common variants. HE-based methods have time and memory requirements that are comparable or lower than those for the non-secure methods. Our results provide evidence that HE-based methods can practically perform resource-intensive computations for high-throughput genetic data analysis. The source code is freely available for download at https://github.com/K-miran/secure-imputation.
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Affiliation(s)
- Miran Kim
- Department of Computer Science and Engineering and Graduate School of Artificial Intelligence, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Arif Ozgun Harmanci
- Center for Precision Health, School of Biomedical Informatics, University of Texas Health Science Center, Houston, TX, 77030, USA.,Corresponding authors: ,
| | | | - Sergiu Carpov
- Inpher, EPFL Innovation Park Bàtiment A, 3rd Fl, 1015 Lausanne, Switzerland.,CEA, LIST, 91191 Gif-sur-Yvette Cedex, France
| | - Jung Hee Cheon
- Department of Mathematical Sciences, Seoul National University, Seoul, 08826, Republic of Korea.,Crypto Lab Inc., Seoul, 08826, Republic of Korea
| | | | - Wonhee Cho
- Department of Mathematical Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | | | - Nicolas Gama
- Inpher, EPFL Innovation Park Bàtiment A, 3rd Fl, 1015 Lausanne, Switzerland
| | - Mariya Georgieva
- Inpher, EPFL Innovation Park Bàtiment A, 3rd Fl, 1015 Lausanne, Switzerland
| | - Seungwan Hong
- Department of Mathematical Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | | | - Duhyeong Kim
- Department of Mathematical Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | | | - Yiping Ma
- University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Lucila Ohno-Machado
- UCSD Health Department of Biomedical Informatics, University of California, San Diego, CA, 92093, USA
| | - Heidi Sofia
- National Institutes of Health (NIH) - National Human Genome Research Institute, Bethesda, MD, 20892, USA
| | | | - Yongsoo Song
- Department of Computer Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | | | - Xiaoqian Jiang
- Center for Secure Artificial intelligence For hEalthcare (SAFE), School of Biomedical Informatics, University of Texas Health Science Center, Houston, TX, 77030, USA.,Corresponding authors: ,
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8
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Zhang Z, Xiao X, Zhou W, Zhu D, Amos CI. False positive findings during genome-wide association studies with imputation: Influence of allele frequency and imputation accuracy. Hum Mol Genet 2021; 31:146-155. [PMID: 34368847 DOI: 10.1093/hmg/ddab203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 06/21/2021] [Accepted: 07/12/2021] [Indexed: 11/12/2022] Open
Abstract
Genotype imputation is widely used in genetic studies to boost the power of GWAS, to combine multiple studies for meta-analysis and to perform fine mapping. With advances of imputation tools and large reference panels, genotype imputation has become mature and accurate. However, the uncertain nature of imputed genotypes can cause bias in the downstream analysis. Many studies have compared the performance of popular imputation approaches, but few investigated bias characteristics of downstream association analyses. Herein, we showed that the imputation accuracy is diminished if the real genotypes contain minor alleles. Although these genotypes are less common, which is particularly true for loci with low minor allele frequency, a large discordance between imputed and observed genotypes significantly inflated the association results, especially in data with a large portion of uncertain SNPs. The significant discordance of p-values happened as the p-value approached 0 or the imputation quality was poor. Although elimination of poorly imputed SNPs can remove false positive (FP) SNPs, it sacrificed, sometimes, more than 80% true positive (TP) SNPs. For top ranked SNPs, removing variants with moderate imputation quality cannot reduce the proportion of FP SNPs, and increasing sample size in reference panels did not greatly benefit the results as well. Additionally, samples with a balanced ratio between cases and controls can dramatically improve the number of TP SNPs observed in the imputation based GWAS. These results raise concerns about results from analysis of association studies when rare variants are studied, particularly when case-control studies are unbalanced.
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Affiliation(s)
- Zhihui Zhang
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030.,Institute of Clinical and Translational Medicine, Department of Medicine, Baylor College of Medicine, Houston, TX 77030
| | - Xiangjun Xiao
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030
| | - Wen Zhou
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030
| | - Dakai Zhu
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030
| | - Christopher I Amos
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030.,Institute of Clinical and Translational Medicine, Department of Medicine, Baylor College of Medicine, Houston, TX 77030
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9
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Alseekh S, Kostova D, Bulut M, Fernie AR. Genome-wide association studies: assessing trait characteristics in model and crop plants. Cell Mol Life Sci 2021; 78:5743-54. [PMID: 34196733 DOI: 10.1007/s00018-021-03868-w] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 05/28/2021] [Accepted: 05/29/2021] [Indexed: 01/19/2023]
Abstract
GWAS involves testing genetic variants across the genomes of many individuals of a population to identify genotype–phenotype association. It was initially developed and has proven highly successful in human disease genetics. In plants genome-wide association studies (GWAS) initially focused on single feature polymorphism and recombination and linkage disequilibrium but has now been embraced by a plethora of different disciplines with several thousand studies being published in model and crop species within the last decade or so. Here we will provide a comprehensive review of these studies providing cases studies on biotic resistance, abiotic tolerance, yield associated traits, and metabolic composition. We also detail current strategies of candidate gene validation as well as the functional study of haplotypes. Furthermore, we provide a critical evaluation of the GWAS strategy and its alternatives as well as future perspectives that are emerging with the emergence of pan-genomic datasets.
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10
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Sarkar E, Chielle E, Gürsoy G, Mazonka O, Gerstein M, Maniatakos M. Fast and Scalable Private Genotype Imputation Using Machine Learning and Partially Homomorphic Encryption. IEEE Access 2021; 9:93097-93110. [PMID: 34476144 PMCID: PMC8409799 DOI: 10.1109/access.2021.3093005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The recent advances in genome sequencing technologies provide unprecedented opportunities to understand the relationship between human genetic variation and diseases. However, genotyping whole genomes from a large cohort of individuals is still cost prohibitive. Imputation methods to predict genotypes of missing genetic variants are widely used, especially for genome-wide association studies. Accurate genotype imputation requires complex statistical methods. Due to the data and computing-intensive nature of the problem, imputation is increasingly outsourced, raising serious privacy concerns. In this work, we investigate solutions for fast, scalable, and accurate privacy-preserving genotype imputation using Machine Learning (ML) and a standardized homomorphic encryption scheme, Paillier cryptosystem. ML-based privacy-preserving inference has been largely optimized for computation-heavy non-linear functions in a single-output multi-class classification setting. However, having a large number of multi-class outputs per genome per individual calls for further optimizations and/or approximations specific to this application. Here we explore the effectiveness of linear models for genotype imputation to convert them to privacy-preserving equivalents using standardized homomorphic encryption schemes. Our results show that performance of our privacy-preserving genotype imputation method is equivalent to the state-of-the-art plaintext solutions, achieving up to 99% micro area under curve score, even on real-world large-scale datasets up to 80,000 targets.
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Affiliation(s)
- Esha Sarkar
- Tandon School of Engineering, New York University, New York, NY 11201, USA
| | - Eduardo Chielle
- New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Gamze Gürsoy
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
| | - Oleg Mazonka
- New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
| | - Michail Maniatakos
- Tandon School of Engineering, New York University, New York, NY 11201, USA
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11
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Shumake J, Mallard TT, McGeary JE, Beevers CG. Inclusion of genetic variants in an ensemble of gradient boosting decision trees does not improve the prediction of citalopram treatment response. Sci Rep 2021; 11:3780. [PMID: 33580158 PMCID: PMC7881144 DOI: 10.1038/s41598-021-83338-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 10/27/2020] [Accepted: 02/02/2021] [Indexed: 12/28/2022] Open
Abstract
Identifying in advance who is unlikely to respond to a specific antidepressant treatment is crucial to precision medicine efforts. The current work leverages genome-wide genetic variation and machine learning to predict response to the antidepressant citalopram using data from the Sequenced Treatment Alternatives to Relieve Depression (STAR*D) trial (n = 1257 with both valid genomic and outcome data). A confirmatory approach selected 11 SNPs previously reported to predict response to escitalopram in a sample different from the current study. A novel exploratory approach selected SNPs from across the genome using nested cross-validation with elastic net logistic regression with a predominantly lasso penalty (alpha = 0.99). SNPs from each approach were combined with baseline clinical predictors and treatment response outcomes were predicted using a stacked ensemble of gradient boosting decision trees. Using pre-treatment clinical and symptom predictors only, out-of-fold prediction of a novel treatment response definition based on STAR*D treatment guidelines was acceptable, AUC = .659, 95% CI [0.629, 0.689]. The inclusion of SNPs using confirmatory or exploratory selection methods did not improve the out-of-fold prediction of treatment response (AUCs were .662, 95% CI [0.632, 0.692] and .655, 95% CI [0.625, 0.685], respectively). A similar pattern of results were observed for the secondary outcomes of the presence or absence of distressing side effects regardless of treatment response and achieving remission or satisfactory partial response, assuming medication tolerance. In the current study, incorporating SNP variation into prognostic models did not enhance the prediction of citalopram response in the STAR*D sample.
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Affiliation(s)
- Jason Shumake
- Department of Psychology, Institute for Mental Health Research, University of Texas At Austin, 305 E. 23rd St., E9000, Austin, TX, 78712, USA.
| | - Travis T Mallard
- Department of Psychology, Institute for Mental Health Research, University of Texas At Austin, 305 E. 23rd St., E9000, Austin, TX, 78712, USA
| | - John E McGeary
- Providence Veterans Affairs Hospital and Brown University School of Medicine, Providence, RI, USA
| | - Christopher G Beevers
- Department of Psychology, Institute for Mental Health Research, University of Texas At Austin, 305 E. 23rd St., E9000, Austin, TX, 78712, USA.
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12
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Shah S, Henry A, Roselli C, Lin H, Sveinbjörnsson G, Fatemifar G, Hedman ÅK, Wilk JB, Morley MP, Chaffin MD, Helgadottir A, Verweij N, Dehghan A, Almgren P, Andersson C, Aragam KG, Ärnlöv J, Backman JD, Biggs ML, Bloom HL, Brandimarto J, Brown MR, Buckbinder L, Carey DJ, Chasman DI, Chen X, Chen X, Chung J, Chutkow W, Cook JP, Delgado GE, Denaxas S, Doney AS, Dörr M, Dudley SC, Dunn ME, Engström G, Esko T, Felix SB, Finan C, Ford I, Ghanbari M, Ghasemi S, Giedraitis V, Giulianini F, Gottdiener JS, Gross S, Guðbjartsson DF, Gutmann R, Haggerty CM, van der Harst P, Hyde CL, Ingelsson E, Jukema JW, Kavousi M, Khaw KT, Kleber ME, Køber L, Koekemoer A, Langenberg C, Lind L, Lindgren CM, London B, Lotta LA, Lovering RC, Luan J, Magnusson P, Mahajan A, Margulies KB, März W, Melander O, Mordi IR, Morgan T, Morris AD, Morris AP, Morrison AC, Nagle MW, Nelson CP, Niessner A, Niiranen T, O'Donoghue ML, Owens AT, Palmer CNA, Parry HM, Perola M, Portilla-Fernandez E, Psaty BM, Rice KM, Ridker PM, Romaine SPR, Rotter JI, Salo P, Salomaa V, van Setten J, Shalaby AA, Smelser DT, Smith NL, Stender S, Stott DJ, Svensson P, Tammesoo ML, Taylor KD, Teder-Laving M, Teumer A, Thorgeirsson G, Thorsteinsdottir U, Torp-Pedersen C, Trompet S, Tyl B, Uitterlinden AG, Veluchamy A, Völker U, Voors AA, Wang X, Wareham NJ, Waterworth D, Weeke PE, Weiss R, Wiggins KL, Xing H, Yerges-Armstrong LM, Yu B, Zannad F, Zhao JH, Hemingway H, Samani NJ, McMurray JJV, Yang J, Visscher PM, Newton-Cheh C, Malarstig A, Holm H, Lubitz SA, Sattar N, Holmes MV, Cappola TP, Asselbergs FW, Hingorani AD, Kuchenbaecker K, Ellinor PT, Lang CC, Stefansson K, Smith JG, Vasan RS, Swerdlow DI, Lumbers RT. Genome-wide association and Mendelian randomisation analysis provide insights into the pathogenesis of heart failure. Nat Commun 2020; 11:163. [PMID: 31919418 PMCID: PMC6952380 DOI: 10.1038/s41467-019-13690-5] [Citation(s) in RCA: 360] [Impact Index Per Article: 90.0] [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: 07/08/2019] [Accepted: 11/18/2019] [Indexed: 12/20/2022] Open
Abstract
Heart failure (HF) is a leading cause of morbidity and mortality worldwide. A small proportion of HF cases are attributable to monogenic cardiomyopathies and existing genome-wide association studies (GWAS) have yielded only limited insights, leaving the observed heritability of HF largely unexplained. We report results from a GWAS meta-analysis of HF comprising 47,309 cases and 930,014 controls. Twelve independent variants at 11 genomic loci are associated with HF, all of which demonstrate one or more associations with coronary artery disease (CAD), atrial fibrillation, or reduced left ventricular function, suggesting shared genetic aetiology. Functional analysis of non-CAD-associated loci implicate genes involved in cardiac development (MYOZ1, SYNPO2L), protein homoeostasis (BAG3), and cellular senescence (CDKN1A). Mendelian randomisation analysis supports causal roles for several HF risk factors, and demonstrates CAD-independent effects for atrial fibrillation, body mass index, and hypertension. These findings extend our knowledge of the pathways underlying HF and may inform new therapeutic strategies.
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Affiliation(s)
- Sonia Shah
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, 4072, Australia
- Institute of Cardiovascular Science, University College London, London, UK
- British Heart Foundation Research Accelerator, University College London, London, UK
| | - Albert Henry
- Institute of Cardiovascular Science, University College London, London, UK
- British Heart Foundation Research Accelerator, University College London, London, UK
- Institute of Health Informatics, University College London, London, UK
| | - Carolina Roselli
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Cardiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Honghuang Lin
- Section of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
- National Heart, Lung, and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA, USA
| | | | - Ghazaleh Fatemifar
- British Heart Foundation Research Accelerator, University College London, London, UK
- Institute of Health Informatics, University College London, London, UK
- Health Data Research UK London, University College London, London, UK
| | - Åsa K Hedman
- Cardiovascular Medicine unit, Department of Medicine Solna, Karolinska Institute, Stockholm, Sweden
| | - Jemma B Wilk
- Pfizer Worldwide Research & Development, 1 Portland St, Cambridge, MA, USA
| | - Michael P Morley
- Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mark D Chaffin
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Anna Helgadottir
- deCODE genetics/Amgen Inc., Sturlugata 8, 101, Reykjavik, Iceland
| | - Niek Verweij
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Cardiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Abbas Dehghan
- Department of Epidemiology and Biostatistics, Imperial College London, St Mary's Campus, London, W2 1PG, UK
- MRC-PHE Centre for Environment and Health, Department of Epidemiology and Biostatistics, Imperial College London, St Mary's Campus, London, W2 1PG, UK
| | - Peter Almgren
- Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Charlotte Andersson
- National Heart, Lung, and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA, USA
- Department of Cardiology, Herlev Gentofte Hospital, Herlev Ringvej 57, 2650, Herlev, Denmark
| | - Krishna G Aragam
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Johan Ärnlöv
- Department of Neurobiology, Care Sciences and Society/ Section of Family Medicine and Primary Care, Karolinska Institutet, Stockholm, Sweden
- School of Health and Social Sciences, Dalarna University, Falun, Sweden
| | - Joshua D Backman
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA
| | - Mary L Biggs
- Department of Biostatistics, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Heather L Bloom
- Division of Cardiology, Department of Medicine, Emory University Medical Center, Atlanta, GA, USA
| | - Jeffrey Brandimarto
- Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael R Brown
- Department of Epidemiology, Human Genetics, and Environmental Sciences, The University of Texas School of Public Health, Houston, Texas, USA
| | - Leonard Buckbinder
- Pfizer Worldwide Research & Development, 1 Portland St, Cambridge, MA, USA
| | - David J Carey
- Department of Molecular and Functional Genomics, Geisinger, Danville, PA, USA
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, 02215, USA
- Harvard Medical School, Boston, MA, 02115, USA
| | - Xing Chen
- Pfizer Worldwide Research & Development, 1 Portland St, Cambridge, MA, USA
| | - Xu Chen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Jonathan Chung
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA
| | - William Chutkow
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - James P Cook
- Department of Biostatistics, University of Liverpool, Liverpool, UK
| | - Graciela E Delgado
- Vth Department of Medicine (Nephrology, Hypertensiology, Endocrinology, Diabetology, Rheumatology), Medical Faculty of Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Spiros Denaxas
- British Heart Foundation Research Accelerator, University College London, London, UK
- Institute of Health Informatics, University College London, London, UK
- Health Data Research UK London, University College London, London, UK
- The National Institute for Health Research University College London Hospitals Biomedical Research Centre, University College London, London, UK
- The Alan Turing Institute, London, United Kingdom
| | - Alexander S Doney
- Division of Molecular & Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, DD1 9SY, UK
| | - Marcus Dörr
- Department of Internal Medicine B, University Medicine Greifswald, Greifswald, Germany
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
| | - Samuel C Dudley
- Cardiovascular Division, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Michael E Dunn
- Regeneron Pharmaceuticals, Cardiovascular Research, 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA
| | - Gunnar Engström
- Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Tõnu Esko
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, 51010, Estonia
| | - Stephan B Felix
- Department of Internal Medicine B, University Medicine Greifswald, Greifswald, Germany
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
| | - Chris Finan
- Institute of Cardiovascular Science, University College London, London, UK
- British Heart Foundation Research Accelerator, University College London, London, UK
| | - Ian Ford
- Robertson Center for Biostatistics, University of Glasgow, Glasgow, UK
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Sahar Ghasemi
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Vilmantas Giedraitis
- Department of Public Health and Caring Sciences, Geriatrics, Uppsala University, Uppsala, 75185, Sweden
| | - Franco Giulianini
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, 02215, USA
| | - John S Gottdiener
- Department of Medicine, Division of Cardiology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Stefan Gross
- Department of Internal Medicine B, University Medicine Greifswald, Greifswald, Germany
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
| | - Daníel F Guðbjartsson
- deCODE genetics/Amgen Inc., Sturlugata 8, 101, Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, 101, Reykjavik, Iceland
| | - Rebecca Gutmann
- Division of Cardiovascular Medicine, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | | | - Pim van der Harst
- Department of Cardiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Durrer Center for Cardiogenetic Research, ICIN-Netherlands Heart Institute, Utrecht, The Netherlands
| | - Craig L Hyde
- Pfizer Worldwide Research & Development, 1 Portland St, Cambridge, MA, USA
| | - Erik Ingelsson
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, 94305, USA
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, 94305, USA
| | - J Wouter Jukema
- Department of Cardiology, Leiden University Medical Center, Leiden, The Netherlands
- Einthoven Laboratory for Experimental Vascular Medicine, LUMC, Leiden, The Netherlands
| | - Maryam Kavousi
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Kay-Tee Khaw
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Marcus E Kleber
- Vth Department of Medicine (Nephrology, Hypertensiology, Endocrinology, Diabetology, Rheumatology), Medical Faculty of Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Lars Køber
- Department of Cardiology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Andrea Koekemoer
- Department of Cardiovascular Sciences, University of Leicester and NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Claudia Langenberg
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0QQ, UK
| | - Lars Lind
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Cecilia M Lindgren
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Big Data Institute at the Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Barry London
- Division of Cardiovascular Medicine and Abboud Cardiovascular Research Center, University of Iowa, Iowa City, IA, USA
| | - Luca A Lotta
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0QQ, UK
| | - Ruth C Lovering
- Institute of Cardiovascular Science, University College London, London, UK
- British Heart Foundation Research Accelerator, University College London, London, UK
| | - Jian'an Luan
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0QQ, UK
| | - Patrik Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Anubha Mahajan
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Kenneth B Margulies
- Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Winfried März
- Department of Biostatistics, University of Liverpool, Liverpool, UK
- Synlab Academy, Synlab Holding Deutschland GmbH, Mannheim, Germany
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Graz, Austria
| | - Olle Melander
- Department of Internal Medicine, Clinical Sciences, Lund University and Skåne University Hospital, Malmö, Sweden
| | - Ify R Mordi
- Division of Molecular & Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, DD1 9SY, UK
| | - Thomas Morgan
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
- Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Andrew D Morris
- Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, United Kingdom
| | - Andrew P Morris
- Department of Biostatistics, University of Liverpool, Liverpool, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Alanna C Morrison
- Department of Epidemiology, Human Genetics, and Environmental Sciences, The University of Texas School of Public Health, Houston, Texas, USA
| | - Michael W Nagle
- Pfizer Worldwide Research & Development, 1 Portland St, Cambridge, MA, USA
| | - Christopher P Nelson
- Department of Cardiovascular Sciences, University of Leicester and NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Alexander Niessner
- Department of Internal Medicine II, Division of Cardiology, Medical University of Vienna, Vienna, Austria
| | - Teemu Niiranen
- National Institute for Health and Welfare, Helsinki, Finland
- Department of Medicine, Turku University Hospital and University of Turku, Turku, Finland
| | - Michelle L O'Donoghue
- TIMI Study Group, Cardiovascular Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Anjali T Owens
- Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Colin N A Palmer
- Division of Molecular & Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, DD1 9SY, UK
| | - Helen M Parry
- Division of Molecular & Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, DD1 9SY, UK
| | - Markus Perola
- National Institute for Health and Welfare, Helsinki, Finland
| | - Eliana Portilla-Fernandez
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Division of Vascular Medicine and Pharmacology, Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Bruce M Psaty
- Department of Medicine, Epidemiology, and Health Services, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, WA, USA
| | - Kenneth M Rice
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Paul M Ridker
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, 02215, USA
- Harvard Medical School, Boston, MA, 02115, USA
| | - Simon P R Romaine
- Department of Cardiovascular Sciences, University of Leicester and NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Departments of Pediatrics and Medicine, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Perttu Salo
- National Institute for Health and Welfare, Helsinki, Finland
| | - Veikko Salomaa
- National Institute for Health and Welfare, Helsinki, Finland
| | - Jessica van Setten
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, University of Utrecht, Utrecht, The Netherlands
| | - Alaa A Shalaby
- Division of Cardiology, Department of Medicine, University of Pittsburgh Medical Center and VA Pittsburgh HCS, Pittsburgh, PA, USA
| | - Diane T Smelser
- Department of Molecular and Functional Genomics, Geisinger, Danville, PA, USA
| | - Nicholas L Smith
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Seattle Epidemiologic Research and Information Center, Department of Veterans Affairs Office of Research & Development, Seattle, WA, USA
| | - Steen Stender
- Department of Clinical Biochemistry, Copenhagen University Hospital, Herlev and Gentofte, København, Denmark
| | - David J Stott
- Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Per Svensson
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
- Department of Cardiology, Södersjukhuset, Stockholm, Sweden
| | - Mari-Liis Tammesoo
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, 51010, Estonia
| | - Kent D Taylor
- Institute for Translational Genomics and Population Sciences, LABiomed and Departments of Pediatrics at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - Maris Teder-Laving
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, 51010, Estonia
| | - Alexander Teumer
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Guðmundur Thorgeirsson
- deCODE genetics/Amgen Inc., Sturlugata 8, 101, Reykjavik, Iceland
- Division of Cardiology, Department of Internal Medicine, Landspitali, National University Hospital of Iceland, Hringbraut, 101, Reykjavik, Iceland
| | - Unnur Thorsteinsdottir
- deCODE genetics/Amgen Inc., Sturlugata 8, 101, Reykjavik, Iceland
- Faculty of Medicine, Department of Medicine, University of Iceland, Saemundargata 2, 101, Reykjavik, Iceland
| | - Christian Torp-Pedersen
- Department of Epidemiology and Biostatistics, Aalborg University Hospital, Aalborg, Denmark
- Department of Health, Science and Technology, Aalborg University Hospital, Aalborg, Denmark
- Departments of Cardiology, Aalborg University Hospital, Aalborg, Denmark
| | - Stella Trompet
- Department of Cardiology, Leiden University Medical Center, Leiden, The Netherlands
- Section of Gerontology and Geriatrics, Department of Internal Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Benoit Tyl
- Translational and Clinical Research, Servier Cardiovascular Center for Therapeutic Innovation, 50 rue Carnot, 92284, Suresnes, France
| | - Andre G Uitterlinden
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Abirami Veluchamy
- Division of Molecular & Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, DD1 9SY, UK
| | - Uwe Völker
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Adriaan A Voors
- Section of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Xiaosong Wang
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Nicholas J Wareham
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0QQ, UK
| | | | - Peter E Weeke
- Department of Cardiology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Raul Weiss
- Division of Cardiovascular Medicine, Department of Internal Medicine, The Ohio State University Medical Center, Columbus, OH, USA
| | - Kerri L Wiggins
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Heming Xing
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | | | - Bing Yu
- Department of Epidemiology, Human Genetics, and Environmental Sciences, The University of Texas School of Public Health, Houston, Texas, USA
| | - Faiez Zannad
- Université de Lorraine, CHU de Nancy, Inserm and INI-CRCT (F-CRIN), Institut Lorrain du Coeur et des Vaisseaux, 54500, Vandoeuvre Lès, Nancy, France
| | - Jing Hua Zhao
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0QQ, UK
| | - Harry Hemingway
- British Heart Foundation Research Accelerator, University College London, London, UK
- Institute of Health Informatics, University College London, London, UK
- Health Data Research UK London, University College London, London, UK
- BHF Cardiovascular Research Centre, University of Glasgow, Glasgow, United Kingdom
| | - Nilesh J Samani
- Department of Cardiovascular Sciences, University of Leicester and NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - John J V McMurray
- BHF Cardiovascular Research Centre, University of Glasgow, Glasgow, United Kingdom
| | - Jian Yang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, 4072, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Peter M Visscher
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, 4072, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Christopher Newton-Cheh
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA
| | - Anders Malarstig
- Cardiovascular Medicine unit, Department of Medicine Solna, Karolinska Institute, Stockholm, Sweden
- Pfizer Worldwide Research & Development, 1 Portland St, Cambridge, MA, USA
| | - Hilma Holm
- deCODE genetics/Amgen Inc., Sturlugata 8, 101, Reykjavik, Iceland
| | - Steven A Lubitz
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiac Arrhythmia Service and Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Naveed Sattar
- BHF Cardiovascular Research Centre, University of Glasgow, Glasgow, United Kingdom
| | - Michael V Holmes
- Medical Research Council Population Health Research Unit at the University of Oxford, Oxford, UK
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, Big Data Institute, University of Oxford, Oxford, UK
- National Institute for Health Research Oxford Biomedical Research Centre, Oxford University Hospital, Oxford, UK
| | - Thomas P Cappola
- Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Folkert W Asselbergs
- Institute of Cardiovascular Science, University College London, London, UK
- British Heart Foundation Research Accelerator, University College London, London, UK
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, University of Utrecht, Utrecht, The Netherlands
| | - Aroon D Hingorani
- Institute of Cardiovascular Science, University College London, London, UK
- British Heart Foundation Research Accelerator, University College London, London, UK
| | - Karoline Kuchenbaecker
- Division of Psychiatry, University College of London, London, W1T 7NF, UK
- UCL Genetics Institute, University College London, London, WC1E 6BT, UK
| | - Patrick T Ellinor
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiac Arrhythmia Service and Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Chim C Lang
- Division of Molecular & Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, DD1 9SY, UK
| | - Kari Stefansson
- deCODE genetics/Amgen Inc., Sturlugata 8, 101, Reykjavik, Iceland
- Faculty of Medicine, Department of Medicine, University of Iceland, Saemundargata 2, 101, Reykjavik, Iceland
| | - J Gustav Smith
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Cardiology, Clinical Sciences, Lund University and Skåne University Hospital, Lund, Sweden
- Wallenberg Center for Molecular Medicine and Lund University Diabetes Center, Lund University, Lund, Sweden
| | - Ramachandran S Vasan
- National Heart, Lung, and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA, USA
- Sections of Cardiology, Preventive Medicine and Epidemiology, Department of Medicine, Boston University Schools of Medicine and Public Health, Boston, MA, USA
| | - Daniel I Swerdlow
- Institute of Cardiovascular Science, University College London, London, UK
| | - R Thomas Lumbers
- British Heart Foundation Research Accelerator, University College London, London, UK.
- Institute of Health Informatics, University College London, London, UK.
- Health Data Research UK London, University College London, London, UK.
- Bart's Heart Centre, St. Bartholomew's Hospital, London, UK.
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Homburger JR, Neben CL, Mishne G, Zhou AY, Kathiresan S, Khera AV. Low coverage whole genome sequencing enables accurate assessment of common variants and calculation of genome-wide polygenic scores. Genome Med 2019; 11:74. [PMID: 31771638 PMCID: PMC6880438 DOI: 10.1186/s13073-019-0682-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [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: 08/02/2019] [Accepted: 11/01/2019] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Inherited susceptibility to common, complex diseases may be caused by rare, pathogenic variants ("monogenic") or by the cumulative effect of numerous common variants ("polygenic"). Comprehensive genome interpretation should enable assessment for both monogenic and polygenic components of inherited risk. The traditional approach requires two distinct genetic testing technologies-high coverage sequencing of known genes to detect monogenic variants and a genome-wide genotyping array followed by imputation to calculate genome-wide polygenic scores (GPSs). We assessed the feasibility and accuracy of using low coverage whole genome sequencing (lcWGS) as an alternative to genotyping arrays to calculate GPSs. METHODS First, we performed downsampling and imputation of WGS data from ten individuals to assess concordance with known genotypes. Second, we assessed the correlation between GPSs for 3 common diseases-coronary artery disease (CAD), breast cancer (BC), and atrial fibrillation (AF)-calculated using lcWGS and genotyping array in 184 samples. Third, we assessed concordance of lcWGS-based genotype calls and GPS calculation in 120 individuals with known genotypes, selected to reflect diverse ancestral backgrounds. Fourth, we assessed the relationship between GPSs calculated using lcWGS and disease phenotypes in a cohort of 11,502 individuals of European ancestry. RESULTS We found imputation accuracy r2 values of greater than 0.90 for all ten samples-including those of African and Ashkenazi Jewish ancestry-with lcWGS data at 0.5×. GPSs calculated using lcWGS and genotyping array followed by imputation in 184 individuals were highly correlated for each of the 3 common diseases (r2 = 0.93-0.97) with similar score distributions. Using lcWGS data from 120 individuals of diverse ancestral backgrounds, we found similar results with respect to imputation accuracy and GPS correlations. Finally, we calculated GPSs for CAD, BC, and AF using lcWGS in 11,502 individuals of European ancestry, confirming odds ratios per standard deviation increment ranging 1.28 to 1.59, consistent with previous studies. CONCLUSIONS lcWGS is an alternative technology to genotyping arrays for common genetic variant assessment and GPS calculation. lcWGS provides comparable imputation accuracy while also overcoming the ascertainment bias inherent to variant selection in genotyping array design.
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Affiliation(s)
| | - Cynthia L Neben
- Color Genomics, 831 Mitten Road, Suite 100, Burlingame, CA, 94010, USA
| | - Gilad Mishne
- Color Genomics, 831 Mitten Road, Suite 100, Burlingame, CA, 94010, USA
| | - Alicia Y Zhou
- Color Genomics, 831 Mitten Road, Suite 100, Burlingame, CA, 94010, USA
| | | | - Amit V Khera
- Center for Genomic Medicine and Cardiology Division, Department of Medicine, Massachusetts General Hospital, Simches Research Building | CPZN 6.256, Boston, MA, 02114, USA.
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Harvard Medical School, Boston, MA, 02115, USA.
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14
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Budiarto BR, Pohan PU, Desriani. Nucleic acid amplification-based HER2 molecular detection for breast cancer. Journal of Oncological Sciences 2019. [DOI: 10.1016/j.jons.2018.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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15
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Chen LS, Hartz SM, Baker TB, Ma Y, L Saccone N, Bierut LJ. Use of polygenic risk scores of nicotine metabolism in predicting smoking behaviors. Pharmacogenomics 2018; 19:1383-1394. [PMID: 30442082 DOI: 10.2217/pgs-2018-0081] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
AIM This study tests whether polygenic risk scores (PRSs) for nicotine metabolism predict smoking behaviors in independent data. MATERIALS & METHODS Linear regression, logistic regression and survival analyses were used to analyze nicotine metabolism PRSs and nicotine metabolism, smoking quantity and smoking cessation. RESULTS Nicotine metabolism PRSs based on two genome wide association studies (GWAS) meta-analyses significantly predicted nicotine metabolism biomarkers (R2 range: 9.2-16%; minimum p = 7.6 × 10-8). The GWAS top hit variant rs56113850 significantly predicted nicotine metabolism biomarkers (R2 range: 14-17%; minimum p = 4.4 × 10-8). There was insufficient evidence for these PRSs predicting smoking quantity and smoking cessation. CONCLUSION Results suggest that nicotine metabolism PRSs based on GWAS meta-analyses predict an individual's nicotine metabolism, so does use of the top hit variant. We anticipate that PRSs will enter clinical medicine, but additional research is needed to develop a more comprehensive genetic score to predict smoking behaviors.
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Affiliation(s)
- Li-Shiun Chen
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO 63110, USA.,Siteman Cancer Center, Washington University in St Louis, St Louis, MO 63110, USA
| | - Sarah M Hartz
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Timothy B Baker
- Department of Medicine, University of Wisconsin School of Medicine & Public Health, Madison, WI 53711, USA
| | - Yinjiao Ma
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Nancy L Saccone
- Department of Genetics, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Laura J Bierut
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO 63110, USA.,Siteman Cancer Center, Washington University in St Louis, St Louis, MO 63110, USA
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16
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Marenholz I, Grosche S, Rüschendorf F, Kalb B, Blumchen K, Schlags R, Harandi N, Price M, Hansen G, Seidenberg J, Yürek S, Homuth G, Schmidt CO, Nöthen MM, Hubner N, Niggemann B, Beyer K, Lee YA. Evaluation of food allergy candidate loci in the Genetics of Food Allergy study. J Allergy Clin Immunol 2018; 142:1368-1370.e2. [PMID: 29969633 DOI: 10.1016/j.jaci.2018.06.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 04/19/2018] [Accepted: 06/08/2018] [Indexed: 01/03/2023]
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17
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Vergara C, Parker MM, Franco L, Cho MH, Valencia-Duarte AV, Beaty TH, Duggal P. Genotype imputation performance of three reference panels using African ancestry individuals. Hum Genet 2018; 137:281-292. [PMID: 29637265 PMCID: PMC6209094 DOI: 10.1007/s00439-018-1881-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [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: 01/10/2018] [Accepted: 03/31/2018] [Indexed: 12/22/2022]
Abstract
Genotype imputation estimates unobserved genotypes from genome-wide makers, to increase genome coverage and power for genome-wide association studies. Imputation has been successful for European ancestry populations in which very large reference panels are available. Smaller subsets of African descent populations are available in 1000 Genomes (1000G), the Consortium on Asthma among African ancestry Populations in the Americas (CAAPA) and the Haplotype Reference Consortium (HRC). We compared the performance of these reference panels when imputing variation in 3747 African Americans (AA) from two cohorts (HCV and COPDGene) genotyped using Illumina Omni microarrays. The haplotypes of 2504 (1000G), 883 (CAAPA) and 32,470 individuals (HRC) were used as reference. We compared the number of variants, imputation quality, imputation accuracy and coverage between panels. In both cohorts, 1000G imputed 1.5-1.6× more variants than CAAPA and 1.2× more than HRC. Similar findings were observed for variants with imputation R2 > 0.5 and for rare, low-frequency, and common variants. When merging imputed variants of the three panels, the total number was 62-63 M with 20 M overlapping variants imputed by all three panels, and a range of 5-15 M variants imputed exclusively with one of them. For overlapping variants, imputation quality was highest for HRC, followed by 1000G, then CAAPA, and improved as the minor allele frequency increased. 1000G, HRC and CAAPA provided high performance and accuracy for imputation of African American individuals, increasing the number of variants available for subsequent analyses. These panels are complementary and would benefit from the development of an integrated African reference panel.
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Affiliation(s)
| | - Margaret M Parker
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Liliana Franco
- National School of Public Health, Universidad de Antioquia, Medellín, Colombia
- School of Medicine, Universidad Pontificia Bolivariana, Medellín, Colombia
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Terri H Beaty
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD, USA
| | - Priya Duggal
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD, USA.
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18
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Guerreiro R, Ross OA, Kun-Rodrigues C, Hernandez DG, Orme T, Eicher JD, Shepherd CE, Parkkinen L, Darwent L, Heckman MG, Scholz SW, Troncoso JC, Pletnikova O, Ansorge O, Clarimon J, Lleo A, Morenas-Rodriguez E, Clark L, Honig LS, Marder K, Lemstra A, Rogaeva E, St George-Hyslop P, Londos E, Zetterberg H, Barber I, Braae A, Brown K, Morgan K, Troakes C, Al-Sarraj S, Lashley T, Holton J, Compta Y, Van Deerlin V, Serrano GE, Beach TG, Lesage S, Galasko D, Masliah E, Santana I, Pastor P, Diez-Fairen M, Aguilar M, Tienari PJ, Myllykangas L, Oinas M, Revesz T, Lees A, Boeve BF, Petersen RC, Ferman TJ, Escott-Price V, Graff-Radford N, Cairns NJ, Morris JC, Pickering-Brown S, Mann D, Halliday GM, Hardy J, Trojanowski JQ, Dickson DW, Singleton A, Stone DJ, Bras J. Investigating the genetic architecture of dementia with Lewy bodies: a two-stage genome-wide association study. Lancet Neurol 2018; 17:64-74. [PMID: 29263008 PMCID: PMC5805394 DOI: 10.1016/s1474-4422(17)30400-3] [Citation(s) in RCA: 164] [Impact Index Per Article: 27.3] [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: 06/21/2017] [Revised: 08/17/2017] [Accepted: 11/03/2017] [Indexed: 01/22/2023]
Abstract
BACKGROUND Dementia with Lewy bodies is the second most common form of dementia in elderly people but has been overshadowed in the research field, partly because of similarities between dementia with Lewy bodies, Parkinson's disease, and Alzheimer's disease. So far, to our knowledge, no large-scale genetic study of dementia with Lewy bodies has been done. To better understand the genetic basis of dementia with Lewy bodies, we have done a genome-wide association study with the aim of identifying genetic risk factors for this disorder. METHODS In this two-stage genome-wide association study, we collected samples from white participants of European ancestry who had been diagnosed with dementia with Lewy bodies according to established clinical or pathological criteria. In the discovery stage (with the case cohort recruited from 22 centres in ten countries and the controls derived from two publicly available database of Genotypes and Phenotypes studies [phs000404.v1.p1 and phs000982.v1.p1] in the USA), we performed genotyping and exploited the recently established Haplotype Reference Consortium panel as the basis for imputation. Pathological samples were ascertained following autopsy in each individual brain bank, whereas clinical samples were collected after participant examination. There was no specific timeframe for collection of samples. We did association analyses in all participants with dementia with Lewy bodies, and also only in participants with pathological diagnosis. In the replication stage, we performed genotyping of significant and suggestive results from the discovery stage. Lastly, we did a meta-analysis of both stages under a fixed-effects model and used logistic regression to test for association in each stage. FINDINGS This study included 1743 patients with dementia with Lewy bodies (1324 with pathological diagnosis) and 4454 controls (1216 patients with dementia with Lewy bodies vs 3791 controls in the discovery stage; 527 vs 663 in the replication stage). Results confirm previously reported associations: APOE (rs429358; odds ratio [OR] 2·40, 95% CI 2·14-2·70; p=1·05 × 10-48), SNCA (rs7681440; OR 0·73, 0·66-0·81; p=6·39 × 10-10), an GBA (rs35749011; OR 2·55, 1·88-3·46; p=1·78 × 10-9). They also provide some evidence for a novel candidate locus, namely CNTN1 (rs7314908; OR 1·51, 1·27-1·79; p=2·32 × 10-6); further replication will be important. Additionally, we estimate the heritable component of dementia with Lewy bodies to be about 36%. INTERPRETATION Despite the small sample size for a genome-wide association study, and acknowledging the potential biases from ascertaining samples from multiple locations, we present the most comprehensive and well powered genetic study in dementia with Lewy bodies so far. These data show that common genetic variability has a role in the disease. FUNDING The Alzheimer's Society and the Lewy Body Society.
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Affiliation(s)
- Rita Guerreiro
- UK Dementia Research Institute, University College London, London, UK; Department of Molecular Neuroscience, UCL Institute of Neurology, University College London, London, UK; Department of Medical Sciences and Institute of Biomedicine, iBiMED, University of Aveiro, Aveiro, Portugal
| | - Owen A Ross
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Celia Kun-Rodrigues
- Department of Molecular Neuroscience, UCL Institute of Neurology, University College London, London, UK
| | - Dena G Hernandez
- Laboratory of Neurogenetics, National Institutes on Aging, National Institutes of Health, Bethesda, MD, USA; German Center for Neurodegenerative Diseases, Tubingen, Germany
| | - Tatiana Orme
- Department of Molecular Neuroscience, UCL Institute of Neurology, University College London, London, UK
| | | | - Claire E Shepherd
- Neuroscience Research Australia, Sydney, NSW, Australia; School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Laura Parkkinen
- Nuffield Department of Clinical Neurosciences, Oxford Parkinson's Disease Centre, University of Oxford, Oxford, UK
| | - Lee Darwent
- Department of Molecular Neuroscience, UCL Institute of Neurology, University College London, London, UK
| | - Michael G Heckman
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Jacksonville, FL, USA
| | - Sonja W Scholz
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Juan C Troncoso
- Department of Pathology (Neuropathology), Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Olga Pletnikova
- Department of Pathology (Neuropathology), Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Olaf Ansorge
- Nuffield Department of Clinical Neurosciences, Oxford Parkinson's Disease Centre, University of Oxford, Oxford, UK
| | - Jordi Clarimon
- Memory Unit, Department of Neurology, IIB Sant Pau, Hospital de la Santa Creu i Sant Pau, Universitat Autonoma de Barcelona, Barcelona, Spain; Centro de Investigacion Biomedica en Red en Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - Alberto Lleo
- Memory Unit, Department of Neurology, IIB Sant Pau, Hospital de la Santa Creu i Sant Pau, Universitat Autonoma de Barcelona, Barcelona, Spain; Centro de Investigacion Biomedica en Red en Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - Estrella Morenas-Rodriguez
- Memory Unit, Department of Neurology, IIB Sant Pau, Hospital de la Santa Creu i Sant Pau, Universitat Autonoma de Barcelona, Barcelona, Spain; Centro de Investigacion Biomedica en Red en Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - Lorraine Clark
- Taub Institute for Alzheimer Disease and the Aging Brain and Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Lawrence S Honig
- Taub Institute for Alzheimer Disease and the Aging Brain and Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Karen Marder
- Taub Institute for Alzheimer Disease and the Aging Brain and Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Afina Lemstra
- Department of Neurology and Alzheimer Center, Neuroscience Campus Amsterdam, VU University Medical Center, Amsterdam, Netherlands
| | - Ekaterina Rogaeva
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, ON, Canada; Department of Medicine, University of Toronto, ON, Canada
| | - Peter St George-Hyslop
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, ON, Canada; Department of Medicine, University of Toronto, ON, Canada; Department of Clinical Neurosciences, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Elisabet Londos
- Clinical Memory Research Unit, Institution of Clinical Sciences Malmo, Lund University, Sweden
| | - Henrik Zetterberg
- UK Dementia Research Institute, University College London, London, UK; Department of Molecular Neuroscience, UCL Institute of Neurology, University College London, London, UK; Clinical Neurochemistry Laboratory, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Molndal, Sweden
| | - Imelda Barber
- Human Genetics, School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, UK
| | - Anne Braae
- Human Genetics, School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, UK
| | - Kristelle Brown
- Human Genetics, School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, UK
| | - Kevin Morgan
- Human Genetics, School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, UK
| | - Claire Troakes
- Department of Basic and Clinical Neuroscience and Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Safa Al-Sarraj
- Department of Basic and Clinical Neuroscience and Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Tammaryn Lashley
- Queen Square Brain Bank, Department of Molecular Neuroscience, UCL Institute of Neurology, University College London, London, UK
| | - Janice Holton
- Queen Square Brain Bank, Department of Molecular Neuroscience, UCL Institute of Neurology, University College London, London, UK
| | - Yaroslau Compta
- Queen Square Brain Bank, Department of Molecular Neuroscience, UCL Institute of Neurology, University College London, London, UK; Parkinson's Disease & Movement Disorders Unit, Neurology Service, Hospital Clinic, IDIBAPS, CIBERNED, Department of Biomedicine, University of Barcelona, Barcelona, Spain
| | - Vivianna Van Deerlin
- Department of Pathology and Laboratory Medicine, Center for Neurodegenerative Disease Research, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | - Suzanne Lesage
- Inserm U1127, CNRS UMR7225, Sorbonne Universites, UPMC Univ Paris 06, UMR, Paris, France; S1127, Institut du Cerveau et de la Moelle epiniere, Paris, France
| | - Douglas Galasko
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA; Veterans Affairs San Diego Healthcare System, La Jolla, CA, USA
| | - Eliezer Masliah
- Laboratory of Neurogenetics, National Institutes on Aging, National Institutes of Health, Bethesda, MD, USA; Division of Neurosciences, National Institutes of Health, Bethesda, MD, USA
| | - Isabel Santana
- Neurology Service, University of Coimbra Hospital, Coimbra, Portugal
| | - Pau Pastor
- Centro de Investigacion Biomedica en Red en Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain; Memory Unit, Department of Neurology, University Hospital Mutua de Terrassa, University of Barcelona, Barcelona, Spain; Fundacio de Docencia I Recerca Mutua de Terrassa, Terrassa, Barcelona, Spain
| | - Monica Diez-Fairen
- Centro de Investigacion Biomedica en Red en Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain; Memory Unit, Department of Neurology, University Hospital Mutua de Terrassa, University of Barcelona, Barcelona, Spain; Fundacio de Docencia I Recerca Mutua de Terrassa, Terrassa, Barcelona, Spain
| | - Miquel Aguilar
- Centro de Investigacion Biomedica en Red en Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain; Memory Unit, Department of Neurology, University Hospital Mutua de Terrassa, University of Barcelona, Barcelona, Spain; Fundacio de Docencia I Recerca Mutua de Terrassa, Terrassa, Barcelona, Spain
| | - Pentti J Tienari
- Molecular Neurology, Research Programs Unit, University of Helsinki, Helsinki, Finland; Department of Neurology, Helsinki University Hospital, Helsinki, Finland
| | - Liisa Myllykangas
- Department of Pathology, Haartman Institute, University of Helsinki, Helsinki, Finland; HUSLAB, Helsinki, Finland
| | - Minna Oinas
- Department of Neurosurgery, University of Helsinki, Helsinki, Finland; Department of Neuropathology and Neurosurgery, Helsinki University Hospital, Helsinki, Finland
| | - Tamas Revesz
- Queen Square Brain Bank, Department of Molecular Neuroscience, UCL Institute of Neurology, University College London, London, UK
| | - Andrew Lees
- Queen Square Brain Bank, Department of Molecular Neuroscience, UCL Institute of Neurology, University College London, London, UK
| | - Brad F Boeve
- Department of Neurology, Mayo Clinic, Rochester, MN, USA
| | | | - Tanis J Ferman
- Department of Psychiatry, Mayo Clinic, Jacksonville, FL, USA
| | - Valentina Escott-Price
- MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, UK
| | | | - Nigel J Cairns
- Knight Alzheimer's Disease Research Center, Department of Neurology, Washington University School of Medicine, Saint Louis, MO, USA
| | - John C Morris
- Knight Alzheimer's Disease Research Center, Department of Neurology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Stuart Pickering-Brown
- Institute of Brain, Behaviour and Mental Health, Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK
| | - David Mann
- Institute of Brain, Behaviour and Mental Health, Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK
| | - Glenda M Halliday
- Neuroscience Research Australia, Sydney, NSW, Australia; School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia; Brain and Mind Centre, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - John Hardy
- UK Dementia Research Institute, University College London, London, UK; Department of Molecular Neuroscience, UCL Institute of Neurology, University College London, London, UK
| | - John Q Trojanowski
- Department of Pathology and Laboratory Medicine, Center for Neurodegenerative Disease Research, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Andrew Singleton
- Laboratory of Neurogenetics, National Institutes on Aging, National Institutes of Health, Bethesda, MD, USA
| | | | - Jose Bras
- UK Dementia Research Institute, University College London, London, UK; Department of Molecular Neuroscience, UCL Institute of Neurology, University College London, London, UK; Department of Medical Sciences and Institute of Biomedicine, iBiMED, University of Aveiro, Aveiro, Portugal.
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19
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Hartz SM, Horton A, Oehlert M, Carey CE, Agrawal A, Bogdan R, Chen LS, Hancock DB, Johnson EO, Pato C, Pato M, Rice JP, Bierut LJ. Association Between Substance Use Disorder and Polygenic Liability to Schizophrenia. Biol Psychiatry 2017; 82:709-715. [PMID: 28739213 PMCID: PMC5643224 DOI: 10.1016/j.biopsych.2017.04.020] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 04/19/2017] [Accepted: 04/30/2017] [Indexed: 12/21/2022]
Abstract
BACKGROUND There are high levels of comorbidity between schizophrenia and substance use disorder, but little is known about the genetic etiology of this comorbidity. METHODS We tested the hypothesis that shared genetic liability contributes to the high rates of comorbidity between schizophrenia and substance use disorder. To do this, polygenic risk scores for schizophrenia derived from a large meta-analysis by the Psychiatric Genomics Consortium were computed in three substance use disorder datasets: the Collaborative Genetic Study of Nicotine Dependence (ascertained for tobacco use disorder; n = 918 cases; 988 control subjects), the Collaborative Study on the Genetics of Alcoholism (ascertained for alcohol use disorder; n = 643 cases; 384 control subjects), and the Family Study of Cocaine Dependence (ascertained for cocaine use disorder; n = 210 cases; 317 control subjects). Phenotypes were harmonized across the three datasets and standardized analyses were performed. Genome-wide genotypes were imputed to the 1000 Genomes reference panel. RESULTS In each individual dataset and in the mega-analysis, strong associations were observed between any substance use disorder diagnosis and the polygenic risk score for schizophrenia (mega-analysis pseudo-R2 range 0.8-3.7%; minimum p = 4 × 10-23). CONCLUSIONS These results suggest that comorbidity between schizophrenia and substance use disorder is partially attributable to shared polygenic liability. This shared liability is most consistent with a general risk for substance use disorder rather than specific risks for individual substance use disorders and adds to increasing evidence of a blurred boundary between schizophrenia and substance use disorder.
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Affiliation(s)
| | - Amy Horton
- Washington University in St. Louis, MO, USA
| | - Mary Oehlert
- VA Eastern Kansas Health Care System, Leavenworth, KS, USA,The University of Kansas Medical Center, Kansas City, KS, USA
| | | | | | | | | | | | | | - Carlos Pato
- SUNY Downstate Medical Center, Brooklyn, NY, USA
| | - Michele Pato
- SUNY Downstate Medical Center, Brooklyn, NY, USA
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20
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Marenholz I, Grosche S, Kalb B, Rüschendorf F, Blümchen K, Schlags R, Harandi N, Price M, Hansen G, Seidenberg J, Röblitz H, Yürek S, Tschirner S, Hong X, Wang X, Homuth G, Schmidt CO, Nöthen MM, Hübner N, Niggemann B, Beyer K, Lee YA. Genome-wide association study identifies the SERPINB gene cluster as a susceptibility locus for food allergy. Nat Commun 2017; 8:1056. [PMID: 29051540 PMCID: PMC5648765 DOI: 10.1038/s41467-017-01220-0] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 08/31/2017] [Indexed: 02/08/2023] Open
Abstract
Genetic factors and mechanisms underlying food allergy are largely unknown. Due to heterogeneity of symptoms a reliable diagnosis is often difficult to make. Here, we report a genome-wide association study on food allergy diagnosed by oral food challenge in 497 cases and 2387 controls. We identify five loci at genome-wide significance, the clade B serpin (SERPINB) gene cluster at 18q21.3, the cytokine gene cluster at 5q31.1, the filaggrin gene, the C11orf30/LRRC32 locus, and the human leukocyte antigen (HLA) region. Stratifying the results for the causative food demonstrates that association of the HLA locus is peanut allergy-specific whereas the other four loci increase the risk for any food allergy. Variants in the SERPINB gene cluster are associated with SERPINB10 expression in leukocytes. Moreover, SERPINB genes are highly expressed in the esophagus. All identified loci are involved in immunological regulation or epithelial barrier function, emphasizing the role of both mechanisms in food allergy.
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Affiliation(s)
- Ingo Marenholz
- Max-Delbrück-Center (MDC) for Molecular Medicine, 13125, Berlin, Germany.,Clinic for Pediatric Allergy, Experimental and Clinical Research Center, Charité University Medical Center, 13125, Berlin, Germany
| | - Sarah Grosche
- Max-Delbrück-Center (MDC) for Molecular Medicine, 13125, Berlin, Germany.,Clinic for Pediatric Allergy, Experimental and Clinical Research Center, Charité University Medical Center, 13125, Berlin, Germany
| | - Birgit Kalb
- Max-Delbrück-Center (MDC) for Molecular Medicine, 13125, Berlin, Germany.,Clinic for Pediatric Allergy, Experimental and Clinical Research Center, Charité University Medical Center, 13125, Berlin, Germany.,Department of Pediatric Pneumology and Immunology, Charité University Medical Center, 13353, Berlin, Germany
| | - Franz Rüschendorf
- Max-Delbrück-Center (MDC) for Molecular Medicine, 13125, Berlin, Germany
| | - Katharina Blümchen
- Department of Allergy, Pulmonology and Cystic Fibrosis, Children's Hospital, Goethe University, 60590, Frankfurt am Main, Germany
| | - Rupert Schlags
- Department of Pediatric Pneumology and Allergology, Wangen Hospital, 88239, Wangen, Germany
| | - Neda Harandi
- Department of Pediatric Pneumology and Allergology, Wangen Hospital, 88239, Wangen, Germany
| | - Mareike Price
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, 30625, Hannover, Germany
| | - Gesine Hansen
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, 30625, Hannover, Germany
| | - Jürgen Seidenberg
- Department of Pediatric Pneumology and Allergology, Neonatology and Intensive Care, Medical Campus of University Oldenburg, 26133, Oldenburg, Germany
| | - Holger Röblitz
- Department of Pediatrics and Adolescent Medicine, Sana Klinikum Lichtenberg, 10365, Berlin, Germany
| | - Songül Yürek
- Department of Pediatric Pneumology and Immunology, Charité University Medical Center, 13353, Berlin, Germany
| | - Sebastian Tschirner
- Department of Pediatric Pneumology and Immunology, Charité University Medical Center, 13353, Berlin, Germany
| | - Xiumei Hong
- Department of Population, Family and Reproductive Health, Center on the Early Life Origins of Disease, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Xiaobin Wang
- Department of Population, Family and Reproductive Health, Center on the Early Life Origins of Disease, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Georg Homuth
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine and Ernst-Moritz-Arndt-University Greifswald, 17487, Greifswald, Germany
| | - Carsten O Schmidt
- Institute for Community Medicine, Study of Health in Pomerania/KEF, University Medicine Greifswald, 17475, Greifswald, Germany
| | - Markus M Nöthen
- Institute of Human Genetics and Department of Genomics, Life & Brain Center, University of Bonn, 53127, Bonn, Germany
| | - Norbert Hübner
- Max-Delbrück-Center (MDC) for Molecular Medicine, 13125, Berlin, Germany
| | - Bodo Niggemann
- Department of Pediatric Pneumology and Immunology, Charité University Medical Center, 13353, Berlin, Germany
| | - Kirsten Beyer
- Department of Pediatric Pneumology and Immunology, Charité University Medical Center, 13353, Berlin, Germany
| | - Young-Ae Lee
- Max-Delbrück-Center (MDC) for Molecular Medicine, 13125, Berlin, Germany. .,Clinic for Pediatric Allergy, Experimental and Clinical Research Center, Charité University Medical Center, 13125, Berlin, Germany.
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21
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Folsom AR, Roetker NS, Kelley ST, Tang W, Pankratz N. Failure to replicate thrombomodulin genetic variant predictors of venous thromboembolism in African Americans. Blood 2017; 130:688-90. [PMID: 28619983 DOI: 10.1182/blood-2017-03-771329] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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22
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Lindström S, Loomis S, Turman C, Huang H, Huang J, Aschard H, Chan AT, Choi H, Cornelis M, Curhan G, De Vivo I, Eliassen AH, Fuchs C, Gaziano M, Hankinson SE, Hu F, Jensen M, Kang JH, Kabrhel C, Liang L, Pasquale LR, Rimm E, Stampfer MJ, Tamimi RM, Tworoger SS, Wiggs JL, Hunter DJ, Kraft P. A comprehensive survey of genetic variation in 20,691 subjects from four large cohorts. PLoS One 2017; 12:e0173997. [PMID: 28301549 PMCID: PMC5354293 DOI: 10.1371/journal.pone.0173997] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [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: 06/08/2016] [Accepted: 03/01/2017] [Indexed: 12/18/2022] Open
Abstract
The Nurses' Health Study (NHS), Nurses' Health Study II (NHSII), Health Professionals Follow Up Study (HPFS) and the Physicians Health Study (PHS) have collected detailed longitudinal data on multiple exposures and traits for approximately 310,000 study participants over the last 35 years. Over 160,000 study participants across the cohorts have donated a DNA sample and to date, 20,691 subjects have been genotyped as part of genome-wide association studies (GWAS) of twelve primary outcomes. However, these studies utilized six different GWAS arrays making it difficult to conduct analyses of secondary phenotypes or share controls across studies. To allow for secondary analyses of these data, we have created three new datasets merged by platform family and performed imputation using a common reference panel, the 1,000 Genomes Phase I release. Here, we describe the methodology behind the data merging and imputation and present imputation quality statistics and association results from two GWAS of secondary phenotypes (body mass index (BMI) and venous thromboembolism (VTE)). We observed the strongest BMI association for the FTO SNP rs55872725 (β = 0.45, p = 3.48x10-22), and using a significance level of p = 0.05, we replicated 19 out of 32 known BMI SNPs. For VTE, we observed the strongest association for the rs2040445 SNP (OR = 2.17, 95% CI: 1.79-2.63, p = 2.70x10-15), located downstream of F5 and also observed significant associations for the known ABO and F11 regions. This pooled resource can be used to maximize power in GWAS of phenotypes collected across the cohorts and for studying gene-environment interactions as well as rare phenotypes and genotypes.
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Affiliation(s)
- Sara Lindström
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America
- Department of Epidemiology, University of Washington, Seattle, WA, United States of America
- * E-mail:
| | - Stephanie Loomis
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA, United States of America
| | - Constance Turman
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America
| | - Hongyan Huang
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America
| | - Jinyan Huang
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America
| | - Hugues Aschard
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America
| | - Andrew T. Chan
- Gastrointestinal Unit, Massachusetts General Hospital, Boston, MA, United States of America
| | - Hyon Choi
- Section of Rheumatology and Clinical Epidemiology Unit, Boston University School of Medicine, Boston, MA, United States of America
| | - Marilyn Cornelis
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, United States of America
| | - Gary Curhan
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States of America
- Renal Division, Department of Medicine, Brigham and Women's Hospital, Boston, MA, United States of America
| | - Immaculata De Vivo
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States of America
| | - A. Heather Eliassen
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States of America
| | - Charles Fuchs
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States of America
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, United States of America
| | - Michael Gaziano
- Division of Aging, Department of Medicine, Brigham and Women's Hospital, Boston, MA, United States of America
| | - Susan E. Hankinson
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States of America
- Department of Biostatistics and Epidemiology, University of Massachusetts, Amherst, MA, United States of America
| | - Frank Hu
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America
| | - Majken Jensen
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States of America
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America
| | - Jae H. Kang
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States of America
| | - Christopher Kabrhel
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States of America
- Department of Emergency Medicine, Center for Vascular Emergencies, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Liming Liang
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America
| | - Louis R. Pasquale
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA, United States of America
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States of America
| | - Eric Rimm
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States of America
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America
| | - Meir J. Stampfer
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States of America
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America
| | - Rulla M. Tamimi
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States of America
| | - Shelley S. Tworoger
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States of America
| | - Janey L. Wiggs
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA, United States of America
| | - David J. Hunter
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States of America
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America
| | - Peter Kraft
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America
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23
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Johnson EO, Hancock DB, Levy JL, Gaddis NC, Page GP, Glasheen C, Saccone NL, Bierut LJ, Kral AH. KAT2B polymorphism identified for drug abuse in African Americans with regulatory links to drug abuse pathways in human prefrontal cortex. Addict Biol 2016. [PMID: 26202629 DOI: 10.1111/adb.12286] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Drug abuse is a common and heritable set of disorders, but the underlying genetic factors are largely unknown. We conducted genome-wide association studies of drug abuse using 7 million imputed single nucleotide polymorphisms (SNPs) and insertions/deletions in African Americans (AAs; n = 3742) and European Americans (EAs; n = 6845). Cases were drawn from the Urban Health Study of street-recruited people, who injected drugs and reported abusing opioids, cocaine, marijuana, stimulants and/or other drugs 10 or more times in the past 30 days, and were compared with population controls. Independent replication testing was conducted in 755 AAs and 1131 EAs from the Genetic Association Information Network. An intronic SNP (rs9829896) in the K(lysine) acetyltransferase 2B (KAT2B) gene was significantly associated with drug abuse in AAs (P = 4.63 × 10-8 ) and independently replicated in AAs (P = 0.0019). The rs9829896-C allele (frequency = 12%) had odds ratios of 0.68 and 0.53 across the AA cohorts: meta-analysis P = 3.93 × 10-10 . Rs9829896-C was not associated with drug abuse across the EA cohorts: frequency = 36% and meta-analysis P = 0.12. Using dorsolateral prefrontal cortex data from the BrainCloud cohort, we found that rs9829896-C was associated with reduced KAT2B expression in AAs (n = 113, P = 0.050) but not EAs (n = 110, P = 0.39). KAT2B encodes a transcriptional regulator in the cyclic adenosine monophosphate and dopamine signaling pathways, and rs9829896-C was associated with expression of genes in these pathways: reduced CREBBP expression (P = 0.011) and increased OPRM1 expression (P = 0.016), both in AAs only. Our study identified the KAT2B SNP rs9829896 as having novel and biologically plausible associations with drug abuse and gene expression in AAs but not EAs, suggesting ancestry-specific effects.
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Affiliation(s)
- Eric O. Johnson
- Fellow Program and Behavioral Health and Criminal Justice Division; RTI International; Research Triangle Park NC USA
| | - Dana B. Hancock
- Behavioral and Urban Health Program, Behavioral Health and Criminal Justice Division; RTI International; Research Triangle Park NC USA
| | - Joshua L. Levy
- Research Computing Division; RTI International; Research Triangle Park NC USA
| | - Nathan C. Gaddis
- Research Computing Division; RTI International; Research Triangle Park NC USA
| | - Grier P. Page
- Fellow Program, Center for Genomics in Public Health and Medicine, and Genomics, Statistical Genetics, and Environmental Research Program; RTI International; Atlanta GA USA
| | - Cristie Glasheen
- Behavioral and Urban Health Program, Behavioral Health and Criminal Justice Division; RTI International; Research Triangle Park NC USA
| | - Nancy L. Saccone
- Department of Genetics; Washington University School of Medicine; St. Louis MO USA
| | - Laura J. Bierut
- Department of Psychiatry; Washington University School of Medicine; St. Louis MO USA
| | - Alex H. Kral
- Behavioral and Urban Health Program, Behavioral Health and Criminal Justice Division; RTI International; San Francisco CA USA
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Codoni V, Blum Y, Civelek M, Proust C, Franzén O, Björkegren JL, Le Goff W, Cambien F, Lusis AJ, Trégouët DA; Cardiogenics Consortium., IDEM Leducq Consortium CADGenomics. Preservation Analysis of Macrophage Gene Coexpression Between Human and Mouse Identifies PARK2 as a Genetically Controlled Master Regulator of Oxidative Phosphorylation in Humans. G3 (Bethesda) 2016; 6:3361-71. [PMID: 27558669 DOI: 10.1534/g3.116.033894] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Macrophages are key players involved in numerous pathophysiological pathways and an in-depth characterization of their gene regulatory networks can help in better understanding how their dysfunction may impact on human diseases. We here conducted a cross-species network analysis of macrophage gene expression data between human and mouse to identify conserved networks across both species, and assessed whether such networks could reveal new disease-associated regulatory mechanisms. From a sample of 684 individuals processed for genome-wide macrophage gene expression profiling, we identified 27 groups of coexpressed genes (modules). Six modules were found preserved (P < 10−4) in macrophages from 86 mice of the Hybrid Mouse Diversity Panel. One of these modules was significantly [false discovery rate (FDR) = 8.9 × 10−11] enriched for genes belonging to the oxidative phosphorylation (OXPHOS) pathway. This pathway was also found significantly (FDR < 10−4) enriched in susceptibility genes for Alzheimer, Parkinson, and Huntington diseases. We further conducted an expression quantitative trait loci analysis to identify SNP that could regulate macrophage OXPHOS gene expression in humans. This analysis identified the PARK2 rs192804963 as a trans-acting variant influencing (minimal P-value = 4.3 × 10−8) the expression of most OXPHOS genes in humans. Further experimental work demonstrated that PARK2 knockdown expression was associated with increased OXPHOS gene expression in THP1 human macrophages. This work provided strong new evidence that PARK2 participates to the regulatory networks associated with oxidative phosphorylation and suggested that PARK2 genetic variations could act as a trans regulator of OXPHOS gene macrophage expression in humans.
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Ramnarine S, Zhang J, Chen LS, Culverhouse R, Duan W, Hancock DB, Hartz SM, Johnson EO, Olfson E, Schwantes-An TH, Saccone NL. When Does Choice of Accuracy Measure Alter Imputation Accuracy Assessments? PLoS One 2015; 10:e0137601. [PMID: 26458263 DOI: 10.1371/journal.pone.0137601] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 08/19/2015] [Indexed: 11/20/2022] Open
Abstract
Imputation, the process of inferring genotypes for untyped variants, is used to identify and refine genetic association findings. Inaccuracies in imputed data can distort the observed association between variants and a disease. Many statistics are used to assess accuracy; some compare imputed to genotyped data and others are calculated without reference to true genotypes. Prior work has shown that the Imputation Quality Score (IQS), which is based on Cohen’s kappa statistic and compares imputed genotype probabilities to true genotypes, appropriately adjusts for chance agreement; however, it is not commonly used. To identify differences in accuracy assessment, we compared IQS with concordance rate, squared correlation, and accuracy measures built into imputation programs. Genotypes from the 1000 Genomes reference populations (AFR N = 246 and EUR N = 379) were masked to match the typed single nucleotide polymorphism (SNP) coverage of several SNP arrays and were imputed with BEAGLE 3.3.2 and IMPUTE2 in regions associated with smoking behaviors. Additional masking and imputation was conducted for sequenced subjects from the Collaborative Genetic Study of Nicotine Dependence and the Genetic Study of Nicotine Dependence in African Americans (N = 1,481 African Americans and N = 1,480 European Americans). Our results offer further evidence that concordance rate inflates accuracy estimates, particularly for rare and low frequency variants. For common variants, squared correlation, BEAGLE R2, IMPUTE2 INFO, and IQS produce similar assessments of imputation accuracy. However, for rare and low frequency variants, compared to IQS, the other statistics tend to be more liberal in their assessment of accuracy. IQS is important to consider when evaluating imputation accuracy, particularly for rare and low frequency variants.
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26
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Hancock DB, Reginsson GW, Gaddis NC, Chen X, Saccone NL, Lutz SM, Qaiser B, Sherva R, Steinberg S, Zink F, Stacey SN, Glasheen C, Chen J, Gu F, Frederiksen BN, Loukola A, Gudbjartsson DF, Brüske I, Landi MT, Bickeböller H, Madden P, Farrer L, Kaprio J, Kranzler HR, Gelernter J, Baker TB, Kraft P, Amos CI, Caporaso NE, Hokanson JE, Bierut LJ, Thorgeirsson TE, Johnson EO, Stefansson K. Genome-wide meta-analysis reveals common splice site acceptor variant in CHRNA4 associated with nicotine dependence. Transl Psychiatry 2015; 5:e651. [PMID: 26440539 PMCID: PMC4930126 DOI: 10.1038/tp.2015.149] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 08/19/2015] [Indexed: 01/04/2023] Open
Abstract
We conducted a 1000 Genomes-imputed genome-wide association study (GWAS) meta-analysis for nicotine dependence, defined by the Fagerström Test for Nicotine Dependence in 17 074 ever smokers from five European-ancestry samples. We followed up novel variants in 7469 ever smokers from five independent European-ancestry samples. We identified genome-wide significant association in the alpha-4 nicotinic receptor subunit (CHRNA4) gene on chromosome 20q13: lowest P=8.0 × 10(-9) across all the samples for rs2273500-C (frequency=0.15; odds ratio=1.12 and 95% confidence interval=1.08-1.17 for severe vs mild dependence). rs2273500-C, a splice site acceptor variant resulting in an alternate CHRNA4 transcript predicted to be targeted for nonsense-mediated decay, was associated with decreased CHRNA4 expression in physiologically normal human brains (lowest P=7.3 × 10(-4)). Importantly, rs2273500-C was associated with increased lung cancer risk (N=28 998, odds ratio=1.06 and 95% confidence interval=1.00-1.12), likely through its effect on smoking, as rs2273500-C was no longer associated with lung cancer after adjustment for smoking. Using criteria for smoking behavior that encompass more than the single 'cigarettes per day' item, we identified a common CHRNA4 variant with important regulatory properties that contributes to nicotine dependence and smoking-related consequences.
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Affiliation(s)
- D B Hancock
- Behavioral and Urban Health Program, Behavioral Health and Criminal Justice Research Division, Research Triangle Institute International, Research Triangle Park, NC, USA,Behavioral and Urban Health Program, Behavioral Health and Criminal Justice Research Division, Research Triangle Institute International, 3040 East Cornwallis Road, P.O. Box 12194, Research Triangle Park, NC 27709, USA. E-mail:
| | | | - N C Gaddis
- Research Computing Division, Research Triangle Institute International, Research Triangle Park, NC, USA
| | - X Chen
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA,Nevada Institute of Personalized Medicine and Department of Psychology, University of Nevada, Las Vegas, NV, USA
| | - N L Saccone
- Department of Genetics, Washington University in St. Louis, St. Louis, MO, USA
| | - S M Lutz
- Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - B Qaiser
- Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - R Sherva
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
| | | | - F Zink
- deCODE Genetics/Amgen, Reykjavik, Iceland
| | - S N Stacey
- deCODE Genetics/Amgen, Reykjavik, Iceland
| | - C Glasheen
- Behavioral and Urban Health Program, Behavioral Health and Criminal Justice Research Division, Research Triangle Institute International, Research Triangle Park, NC, USA
| | - J Chen
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
| | - F Gu
- Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, United States Department of Health and Human Services, Bethesda, MD, USA
| | | | - A Loukola
- Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | | | - I Brüske
- Institute of Epidemiology I, German Research Center for Environmental Health, Neuherberg, Germany
| | - M T Landi
- Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, United States Department of Health and Human Services, Bethesda, MD, USA
| | - H Bickeböller
- Department of Genetic Epidemiology, University of Göttingen—Georg-August University Göttingen, Göttingen, Germany
| | - P Madden
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - L Farrer
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA,Department of Neurology, Boston University School of Medicine, Boston, MA, USA,Department of Ophthalmology, Boston University School of Medicine, Boston, MA, USA,Department of Genetics and Genomics, Boston University School of Medicine, Boston, MA, USA,Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA,Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - J Kaprio
- Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland,National Institute for Health and Welfare, Helsinki, Finland,Institute for Molecular Medicine, University of Helsinki, Helsinki, Finland
| | - H R Kranzler
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA,VISN 4 Mental Illness Research, Education and Clinical Center, Philadelphia VA Medical Center, Philadelphia, PA, USA
| | - J Gelernter
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA,Department of Genetics, Yale University School of Medicine, New Haven, CT, USA,Department of Neurobiology, Yale University School of Medicine, New Haven, CT, USA,VA CT Healthcare Center, Department of Psychiatry, West Haven, CT, USA
| | - T B Baker
- Center for Tobacco Research and Intervention, University of Wisconsin, Madison, WI, USA
| | - P Kraft
- Department of Epidemiology, Harvard University School of Public Health, Boston, MA, USA,Department of Biostatistics, Harvard University School of Public Health, Boston, MA, USA
| | - C I Amos
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth, Hanover, NH, USA,Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH, USA,Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanoven, NH, USA
| | - N E Caporaso
- Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, United States Department of Health and Human Services, Bethesda, MD, USA
| | - J E Hokanson
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - L J Bierut
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | | | - E O Johnson
- Fellow Program and Behavioral Health and Criminal Justice Research Division, Research Triangle Institute International, Research Triangle Park, NC, USA
| | - K Stefansson
- deCODE Genetics/Amgen, Reykjavik, Iceland,Faculty of Medicine, University of Iceland, Reykjavik, Iceland
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Hancock DB, Levy JL, Gaddis NC, Glasheen C, Saccone NL, Page GP, Hulse G, Wildenauer D, Kelty E, Schwab S, Degenhardt L, Martin NG, Montgomery GW, Attia J, Holliday EG, McEvoy M, Scott RJ, Bierut LJ, Nelson EC, Kral A, Johnson EO. Cis-Expression Quantitative Trait Loci Mapping Reveals Replicable Associations with Heroin Addiction in OPRM1. Biol Psychiatry 2015; 78:474-84. [PMID: 25744370 PMCID: PMC4519434 DOI: 10.1016/j.biopsych.2015.01.003] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 12/18/2014] [Accepted: 01/08/2015] [Indexed: 12/25/2022]
Abstract
BACKGROUND No opioid receptor, mu 1 (OPRM1) gene polymorphisms, including the functional single nucleotide polymorphism (SNP) rs1799971, have been conclusively associated with heroin/other opioid addiction, despite their biological plausibility. We used evidence of polymorphisms altering OPRM1 expression in normal human brain tissue to nominate and then test associations with heroin addiction. METHODS We tested 103 OPRM1 SNPs for association with OPRM1 messenger RNA expression in prefrontal cortex from 224 European Americans and African Americans of the BrainCloud cohort. We then tested the 16 putative cis-expression quantitative trait loci (cis-eQTL) SNPs for association with heroin addiction in the Urban Health Study and two replication cohorts, totaling 16,729 European Americans, African Americans, and Australians of European ancestry. RESULTS Four putative cis-eQTL SNPs were significantly associated with heroin addiction in the Urban Health Study (smallest p = 8.9 × 10(-5)): rs9478495, rs3778150, rs9384169, and rs562859. Rs3778150, located in OPRM1 intron 1, was significantly replicated (p = 6.3 × 10(-5)). Meta-analysis across all case-control cohorts resulted in p = 4.3 × 10(-8): the rs3778150-C allele (frequency = 16%-19%) being associated with increased heroin addiction risk. Importantly, the functional SNP allele rs1799971-A was associated with heroin addiction only in the presence of rs3778150-C (p = 1.48 × 10(-6) for rs1799971-A/rs3778150-C and p = .79 for rs1799971-A/rs3778150-T haplotypes). Lastly, replication was observed for six other intron 1 SNPs that had prior suggestive associations with heroin addiction (smallest p = 2.7 × 10(-8) for rs3823010). CONCLUSIONS Our findings show that common OPRM1 intron 1 SNPs have replicable associations with heroin addiction. The haplotype structure of rs3778150 and nearby SNPs may underlie the inconsistent associations between rs1799971 and heroin addiction.
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Affiliation(s)
- Dana B. Hancock
- Behavioral Health Epidemiology Program, Research Triangle Institute, Research Triangle Park, NC
| | - Joshua L. Levy
- Research Computing Division, RTI International, Research Triangle Park, NC
| | - Nathan C. Gaddis
- Research Computing Division, RTI International, Research Triangle Park, NC
| | - Cristie Glasheen
- Behavioral Health Epidemiology Program, Research Triangle Institute, Research Triangle Park, NC
| | - Nancy L. Saccone
- Department of Genetics, Washington University in St. Louis, St. Louis, MO
| | - Grier P. Page
- Center for Public Health Genomics, RTI International, Atlanta, GA
| | - Gary Hulse
- School of Psychiatry and Clinical Neurosciences, University of Western Australia, Crawley, Western Australia, Australia
| | - Dieter Wildenauer
- School of Psychiatry and Clinical Neurosciences, University of Western Australia, Crawley, Western Australia, Australia
| | - Erin Kelty
- School of Psychiatry and Clinical Neurosciences, University of Western Australia, Crawley, Western Australia, Australia
| | - Sibylle Schwab
- Department of Psychiatry and Psychotherapy, University of Erlangen-Nuremberg, Erlangen, Germany,Faculty of Science, Medicine, and Health, University of Wollongong, Wollongong, Australia
| | - Louisa Degenhardt
- National Drug and Alcohol Research Centre, University of New South Wales, Sydney, Australia
| | - Nicholas G. Martin
- Queensland Institute of Medical Research (QIMR) Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Grant W. Montgomery
- Queensland Institute of Medical Research (QIMR) Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - John Attia
- Centre for Clinical Epidemiology and Biostatistics, School of Medicine and Public Health, University of Newcastle, Newcastle, New South Wales, Australia,Clinical Research Design, IT and Statistical Support Unit, Hunter Medical Research Institute, Newcastle, New South Wales, Australia
| | - Elizabeth G. Holliday
- Centre for Clinical Epidemiology and Biostatistics, School of Medicine and Public Health, University of Newcastle, Newcastle, New South Wales, Australia,Clinical Research Design, IT and Statistical Support Unit, Hunter Medical Research Institute, Newcastle, New South Wales, Australia
| | - Mark McEvoy
- Centre for Clinical Epidemiology and Biostatistics, School of Medicine and Public Health, University of Newcastle, Newcastle, New South Wales, Australia,Public Health Research Program, Hunter Medical Research Institute, Newcastle, New South Wales, Australia
| | - Rodney J. Scott
- Center for Bioinformatics, Biomarker Discovery and Information-Based Medicine, Hunter Medical Research Institute, Newcastle, New South Wales, Australia,School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, New South Wales, Australia,Division of Genetics, Hunter Area Pathology Service, Newcastle, New South Wales, Australia
| | - Laura J. Bierut
- Department of Psychiatry, Washington University in St. Louis, St. Louis, MO
| | - Elliot C. Nelson
- Department of Psychiatry, Washington University in St. Louis, St. Louis, MO
| | - Alex Kral
- Urban Health Program, Research Triangle Institute, San Francisco, CA
| | - Eric O. Johnson
- Behavioral Health Epidemiology Program, Research Triangle Institute, Research Triangle Park, NC
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Hancock DB, Wang JC, Gaddis NC, Levy JL, Saccone NL, Stitzel JA, Goate A, Bierut LJ, Johnson EO. A multiancestry study identifies novel genetic associations with CHRNA5 methylation in human brain and risk of nicotine dependence. Hum Mol Genet 2015. [PMID: 26220977 DOI: 10.1093/hmg/ddv303] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Nicotine dependence is influenced by chromosome 15q25.1 single nucleotide polymorphisms (SNPs), including the missense SNP rs16969968 that alters function of the α5 nicotinic acetylcholine receptor (CHRNA5) and noncoding SNPs that regulate CHRNA5 mRNA expression. We tested for cis-methylation quantitative trait loci (cis-meQTLs) using SNP genotypes and DNA methylation levels measured across the IREB2-HYKK-PSMA4-CHRNA5-CHRNA3-CHRNB4 genes on chromosome 15q25.1 in the BrainCloud and Brain QTL cohorts [total N = 175 European-Americans and 65 African-Americans (AAs)]. We identified eight SNPs that were significantly associated with CHRNA5 methylation in prefrontal cortex: P ranging from 6.0 × 10(-10) to 5.6 × 10(-5). These SNP-methylation associations were also significant in frontal cortex, temporal cortex and pons: P ranging from 4.8 × 10(-12) to 3.4 × 10(-3). Of the eight cis-meQTL SNPs, only the intronic CHRNB4 SNP rs11636753 was associated with CHRNA5 methylation independently of the known SNP effects in prefrontal cortex, and it was the most significantly associated SNP with nicotine dependence across five independent cohorts (total N = 7858 European ancestry and 3238 AA participants): P = 6.7 × 10(-4), odds ratio (OR) [95% confidence interval (CI)] = 1.11 (1.05-1.18). The rs11636753 major allele (G) was associated with lower CHRNA5 DNA methylation, lower CHRNA5 mRNA expression and increased nicotine dependence risk. Haplotype analyses showed that rs11636753-G and the functional rs16969968-A alleles together increased risk of nicotine dependence more than each variant alone: P = 3.1 × 10(-12), OR (95% CI) = 1.32 (1.22-1.43). Our findings identify a novel regulatory SNP association with nicotine dependence and connect, for the first time, previously observed differences in CHRNA5 mRNA expression and nicotine dependence risk to underlying DNA methylation differences.
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Affiliation(s)
- Dana B Hancock
- Behavioral and Urban Health Program, Behavioral Health and Criminal Justice Division,
| | - Jen-Chyong Wang
- Department of Neuroscience and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | | | | | - Jerry A Stitzel
- Department of Integrative Physiology, University of Colorado, Boulder, CO 80309, USA
| | - Alison Goate
- Department of Neuroscience and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Laura J Bierut
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO 63110, USA and
| | - Eric O Johnson
- Fellow Program and Behavioral Health and Criminal Justice Division, Research Triangle Institute (RTI) International, Research Triangle Park, NC 27709, USA
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29
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Mosley JD, Shaffer CM, Van Driest SL, Weeke PE, Wells QS, Karnes JH, Velez Edwards DR, Wei WQ, Teixeira PL, Bastarache L, Crawford DC, Li R, Manolio TA, Bottinger EP, McCarty CA, Linneman JG, Brilliant MH, Pacheco JA, Thompson W, Chisholm RL, Jarvik GP, Crosslin DR, Carrell DS, Baldwin E, Ralston J, Larson EB, Grafton J, Scrol A, Jouni H, Kullo IJ, Tromp G, Borthwick KM, Kuivaniemi H, Carey DJ, Ritchie MD, Bradford Y, Verma SS, Chute CG, Veluchamy A, Siddiqui MK, Palmer CN, Doney A, MahmoudPour SH, Maitland-van der Zee AH, Morris AD, Denny JC, Roden DM. A genome-wide association study identifies variants in KCNIP4 associated with ACE inhibitor-induced cough. Pharmacogenomics J 2016; 16:231-7. [PMID: 26169577 DOI: 10.1038/tpj.2015.51] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Revised: 04/13/2015] [Accepted: 06/03/2015] [Indexed: 12/30/2022]
Abstract
The most common side effect of angiotensin-converting enzyme inhibitor (ACEi) drugs is cough. We conducted a genome-wide association study (GWAS) of ACEi-induced cough among 7080 subjects of diverse ancestries in the Electronic Medical Records and Genomics (eMERGE) network. Cases were subjects diagnosed with ACEi-induced cough. Controls were subjects with at least 6 months of ACEi use and no cough. A GWAS (1595 cases and 5485 controls) identified associations on chromosome 4 in an intron of KCNIP4. The strongest association was at rs145489027 (minor allele frequency=0.33, odds ratio (OR)=1.3 (95% confidence interval (CI): 1.2–1.4), P=1.0 × 10−8). Replication for six single-nucleotide polymorphisms (SNPs) in KCNIP4 was tested in a second eMERGE population (n=926) and in the Genetics of Diabetes Audit and Research in Tayside, Scotland (GoDARTS) cohort (n=4309). Replication was observed at rs7675300 (OR=1.32 (1.01–1.70), P=0.04) in eMERGE and at rs16870989 and rs1495509 (OR=1.15 (1.01–1.30), P=0.03 for both) in GoDARTS. The combined association at rs1495509 was significant (OR=1.23 (1.15–1.32), P=1.9 × 10−9). These results indicate that SNPs in KCNIP4 may modulate ACEi-induced cough risk.
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30
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Germain M, Chasman DI, de Haan H, Tang W, Lindström S, Weng LC, de Andrade M, de Visser MCH, Wiggins KL, Suchon P, Saut N, Smadja DM, Le Gal G, van Hylckama Vlieg A, Di Narzo A, Hao K, Nelson CP, Rocanin-Arjo A, Folkersen L, Monajemi R, Rose LM, Brody JA, Slagboom E, Aïssi D, Gagnon F, Deleuze JF, Deloukas P, Tzourio C, Dartigues JF, Berr C, Taylor KD, Civelek M, Eriksson P, Psaty BM, Houwing-Duitermaat J, Goodall AH, Cambien F, Kraft P, Amouyel P, Samani NJ, Basu S, Ridker PM, Rosendaal FR, Kabrhel C, Folsom AR, Heit J, Reitsma PH, Trégouët DA, Smith NL, Morange PE. Meta-analysis of 65,734 individuals identifies TSPAN15 and SLC44A2 as two susceptibility loci for venous thromboembolism. Am J Hum Genet 2015; 96:532-42. [PMID: 25772935 DOI: 10.1016/j.ajhg.2015.01.019] [Citation(s) in RCA: 189] [Impact Index Per Article: 21.0] [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: 09/08/2014] [Accepted: 01/29/2015] [Indexed: 11/18/2022] Open
Abstract
Venous thromboembolism (VTE), the third leading cause of cardiovascular mortality, is a complex thrombotic disorder with environmental and genetic determinants. Although several genetic variants have been found associated with VTE, they explain a minor proportion of VTE risk in cases. We undertook a meta-analysis of genome-wide association studies (GWASs) to identify additional VTE susceptibility genes. Twelve GWASs totaling 7,507 VTE case subjects and 52,632 control subjects formed our discovery stage where 6,751,884 SNPs were tested for association with VTE. Nine loci reached the genome-wide significance level of 5 × 10(-8) including six already known to associate with VTE (ABO, F2, F5, F11, FGG, and PROCR) and three unsuspected loci. SNPs mapping to these latter were selected for replication in three independent case-control studies totaling 3,009 VTE-affected individuals and 2,586 control subjects. This strategy led to the identification and replication of two VTE-associated loci, TSPAN15 and SLC44A2, with lead risk alleles associated with odds ratio for disease of 1.31 (p = 1.67 × 10(-16)) and 1.21 (p = 2.75 × 10(-15)), respectively. The lead SNP at the TSPAN15 locus is the intronic rs78707713 and the lead SLC44A2 SNP is the non-synonymous rs2288904 previously shown to associate with transfusion-related acute lung injury. We further showed that these two variants did not associate with known hemostatic plasma markers. TSPAN15 and SLC44A2 do not belong to conventional pathways for thrombosis and have not been associated to other cardiovascular diseases nor related quantitative biomarkers. Our findings uncovered unexpected actors of VTE etiology and pave the way for novel mechanistic concepts of VTE pathophysiology.
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Affiliation(s)
- Marine Germain
- Institut National pour la Santé et la Recherche Médicale (INSERM), Unité Mixte de Recherche en Santé (UMR_S) 1166, 75013 Paris, France; Sorbonne Universités, Université Pierre et Marie Curie (UPMC Univ Paris 06), UMR_S 1166, Team Genomics & Pathophysiology of Cardiovascular Diseases, 75013 Paris, France; Institute for Cardiometabolism and Nutrition (ICAN), 75013 Paris, France
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02215, USA
| | - Hugoline de Haan
- Department of Thrombosis and Hemostasis, Department of Clinical Epidemiology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Weihong Tang
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, MN 55454, USA
| | - Sara Lindström
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
| | - Lu-Chen Weng
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, MN 55454, USA
| | - Mariza de Andrade
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55905, USA
| | - Marieke C H de Visser
- Einthoven Laboratory for Experimental Vascular Medicine, Department of Thrombosis and Hemostasis, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Kerri L Wiggins
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
| | - Pierre Suchon
- Laboratory of Haematology, La Timone Hospital, 13385 Marseille, France; INSERM, UMR_S 1062, Nutrition Obesity and Risk of Thrombosis, 13385 Marseille, France; Nutrition Obesity and Risk of Thrombosis, Aix-Marseille University, UMR_S 1062, 13385 Marseille, France
| | - Noémie Saut
- Laboratory of Haematology, La Timone Hospital, 13385 Marseille, France; INSERM, UMR_S 1062, Nutrition Obesity and Risk of Thrombosis, 13385 Marseille, France; Nutrition Obesity and Risk of Thrombosis, Aix-Marseille University, UMR_S 1062, 13385 Marseille, France
| | - David M Smadja
- Université Paris Descartes, Sorbonne Paris Cité, 75006 Paris, France; AP-HP, Hopital Européen Georges Pompidou, Service d'Hématologie Biologique, 75015 Paris, France; Faculté de Pharmacie, INSERM, UMR_S 1140, 75006 Paris, France
| | - Grégoire Le Gal
- Université de Brest, EA3878 and CIC1412, 29238 Brest, France; Ottawa Hospital Research Institute at the University of Ottawa, Ottawa, ON K1Y 4E9, Canada
| | - Astrid van Hylckama Vlieg
- Department of Thrombosis and Hemostasis, Department of Clinical Epidemiology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Antonio Di Narzo
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA
| | - Christopher P Nelson
- Department of Cardiovascular Sciences, University of Leicester, LE1 7RH Leicester, UK; National Institute for Health Research (NIHR) Leicester Cardiovascular Biomedical Research Unit, Leicester LE3 9QP, UK
| | - Ares Rocanin-Arjo
- Institut National pour la Santé et la Recherche Médicale (INSERM), Unité Mixte de Recherche en Santé (UMR_S) 1166, 75013 Paris, France; Sorbonne Universités, Université Pierre et Marie Curie (UPMC Univ Paris 06), UMR_S 1166, Team Genomics & Pathophysiology of Cardiovascular Diseases, 75013 Paris, France; Institute for Cardiometabolism and Nutrition (ICAN), 75013 Paris, France
| | - Lasse Folkersen
- Department of PharmacoGenetics, Novo Nordisk Park 9.1.21, 2400 Copenhagen, Denmark
| | - Ramin Monajemi
- Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Lynda M Rose
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA 02215, USA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Services, University of Washington, Seattle, WA 98195-5852, USA
| | - Eline Slagboom
- Department of Molecular Epidemiology, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Dylan Aïssi
- Institut National pour la Santé et la Recherche Médicale (INSERM), Unité Mixte de Recherche en Santé (UMR_S) 1166, 75013 Paris, France; Sorbonne Universités, Université Pierre et Marie Curie (UPMC Univ Paris 06), UMR_S 1166, Team Genomics & Pathophysiology of Cardiovascular Diseases, 75013 Paris, France; Institute for Cardiometabolism and Nutrition (ICAN), 75013 Paris, France
| | - France Gagnon
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7, Canada
| | - Jean-Francois Deleuze
- Commissariat à l'Energie Atomique/Direction des Sciences du Vivant/Institut de Génomique, Centre National de Génotypage, 91057 Evry, France
| | - Panos Deloukas
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 4NS, UK; Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Christophe Tzourio
- Inserm Research Center U897, University of Bordeaux, 33000 Bordeaux, France
| | | | - Claudine Berr
- Inserm Research Unit U1061, University of Montpellier I, 34000 Montpellier, France
| | - Kent D Taylor
- Los Angeles Biomedical Research Institute and Department of Pediatrics, Harbor-UCLA Medical Center, Torrence, CA 90502, USA
| | - Mete Civelek
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Per Eriksson
- Atherosclerosis Research Unit, Center for Molecular Medicine, Department of Medicine, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Services, University of Washington, Seattle, WA 98195-5852, USA; Group Health Research Institute, Group Health Cooperative, Seattle, WA 98101, USA
| | - Jeanine Houwing-Duitermaat
- Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Alison H Goodall
- Department of Cardiovascular Sciences, University of Leicester, LE1 7RH Leicester, UK; National Institute for Health Research (NIHR) Leicester Cardiovascular Biomedical Research Unit, Leicester LE3 9QP, UK
| | - François Cambien
- Institut National pour la Santé et la Recherche Médicale (INSERM), Unité Mixte de Recherche en Santé (UMR_S) 1166, 75013 Paris, France; Sorbonne Universités, Université Pierre et Marie Curie (UPMC Univ Paris 06), UMR_S 1166, Team Genomics & Pathophysiology of Cardiovascular Diseases, 75013 Paris, France; Institute for Cardiometabolism and Nutrition (ICAN), 75013 Paris, France
| | - Peter Kraft
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
| | - Philippe Amouyel
- Institut Pasteur de Lille, Université de Lille Nord de France, INSERM UMR_S 744, 59000 Lille, France; Centre Hospitalier Régional Universitaire de Lille, 59000 Lille, France
| | - Nilesh J Samani
- Department of Cardiovascular Sciences, University of Leicester, LE1 7RH Leicester, UK; National Institute for Health Research (NIHR) Leicester Cardiovascular Biomedical Research Unit, Leicester LE3 9QP, UK
| | - Saonli Basu
- Division of Biostatistics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Paul M Ridker
- Division of Preventive Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02215, USA
| | - Frits R Rosendaal
- Department of Thrombosis and Hemostasis, Department of Clinical Epidemiology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Christopher Kabrhel
- Department of Emergency Medicine, Massachusetts General Hospital, Channing Network Medicine, Harvard Medical School, Boston, MA 2114, USA
| | - Aaron R Folsom
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, MN 55454, USA
| | - John Heit
- Division of Cardiovascular Diseases, Mayo Clinic, Rochester, MN 55905, USA
| | - Pieter H Reitsma
- Einthoven Laboratory for Experimental Vascular Medicine, Department of Thrombosis and Hemostasis, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - David-Alexandre Trégouët
- Institut National pour la Santé et la Recherche Médicale (INSERM), Unité Mixte de Recherche en Santé (UMR_S) 1166, 75013 Paris, France; Sorbonne Universités, Université Pierre et Marie Curie (UPMC Univ Paris 06), UMR_S 1166, Team Genomics & Pathophysiology of Cardiovascular Diseases, 75013 Paris, France; Institute for Cardiometabolism and Nutrition (ICAN), 75013 Paris, France
| | - Nicholas L Smith
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA; Group Health Research Institute, Group Health Cooperative, Seattle, WA 98101, USA; Seattle Epidemiologic Research and Information Center, VA Office of Research and Development, Seattle, WA 98108, USA.
| | - Pierre-Emmanuel Morange
- Laboratory of Haematology, La Timone Hospital, 13385 Marseille, France; INSERM, UMR_S 1062, Nutrition Obesity and Risk of Thrombosis, 13385 Marseille, France; Nutrition Obesity and Risk of Thrombosis, Aix-Marseille University, UMR_S 1062, 13385 Marseille, France.
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Aïssi D, Dennis J, Ladouceur M, Truong V, Zwingerman N, Rocanin-Arjo A, Germain M, Paton TA, Morange PE, Gagnon F, Trégouët DA. Genome-wide investigation of DNA methylation marks associated with FV Leiden mutation. PLoS One 2014; 9:e108087. [PMID: 25265411 PMCID: PMC4179266 DOI: 10.1371/journal.pone.0108087] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [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: 05/07/2014] [Accepted: 08/12/2014] [Indexed: 12/31/2022] Open
Abstract
In order to investigate whether DNA methylation marks could contribute to the incomplete penetrance of the FV Leiden mutation, a major genetic risk factor for venous thrombosis (VT), we measured genome-wide DNA methylation levels in peripheral blood samples of 98 VT patients carrying the mutation and 251 VT patients without the mutation using the dedicated Illumina HumanMethylation450 array. The genome-wide analysis of 388,120 CpG probes identified three sites mapping to the SLC19A2 locus whose DNA methylation levels differed significantly (p<3 10−8) between carriers and non-carriers. The three sites replicated (p<2 10−7) in an independent sample of 214 individuals from five large families ascertained on VT and FV Leiden mutation among which 53 were carriers and 161 were non-carriers of the mutation. In both studies, these three CpG sites were also associated (2.33 10−11<p<3.02 10−4) with biomarkers of the Protein C pathway known to be influenced by the FV Leiden mutation. A comprehensive linkage disequilibrium (LD) analysis of the whole locus revealed that the original associations were due to LD between the FV Leiden mutation and a block of single nucleotide polymorphisms (SNP) located in SLC19A2. After adjusting for this block of SNPs, the FV Leiden mutation was no longer associated with any CpG site (p>0.05). In conclusion, our work clearly illustrates some promises and pitfalls of DNA methylation investigations on peripheral blood DNA in large epidemiological cohorts. DNA methylation levels at SLC19A2 are influenced by SNPs in LD with FV Leiden, but these DNA methylation marks do not explain the incomplete penetrance of the FV Leiden mutation.
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Affiliation(s)
- Dylan Aïssi
- Sorbonne Universités, UPMC Univ Paris 06, UMR_S 1166, Team Genomics & Pathophysiology of Cardiovascular Diseases, Paris, France
- INSERM, UMR_S 1166, Team Genomics & Pathophysiology of Cardiovascular Diseases, Paris, France
- ICAN Institute for Cardiometabolism and Nutrition, Paris, France
| | - Jessica Dennis
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Martin Ladouceur
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
- Centre de Recherches du CHUM, Montréal, Canada
| | - Vinh Truong
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Nora Zwingerman
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Ares Rocanin-Arjo
- Sorbonne Universités, UPMC Univ Paris 06, UMR_S 1166, Team Genomics & Pathophysiology of Cardiovascular Diseases, Paris, France
- INSERM, UMR_S 1166, Team Genomics & Pathophysiology of Cardiovascular Diseases, Paris, France
- ICAN Institute for Cardiometabolism and Nutrition, Paris, France
| | - Marine Germain
- Sorbonne Universités, UPMC Univ Paris 06, UMR_S 1166, Team Genomics & Pathophysiology of Cardiovascular Diseases, Paris, France
- INSERM, UMR_S 1166, Team Genomics & Pathophysiology of Cardiovascular Diseases, Paris, France
- ICAN Institute for Cardiometabolism and Nutrition, Paris, France
| | - Tara A. Paton
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Pierre-Emmanuel Morange
- Aix-Marseille University, UMR_S 1062, Nutrition Obesity and Risk of Thrombosis, Marseille, France
- INSERM, UMR_S 1062, Nutrition Obesity and Risk of Thrombosis, Marseille, France
- Laboratory of Haematology, La Timone Hospital, Marseille, France
| | - France Gagnon
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - David-Alexandre Trégouët
- Sorbonne Universités, UPMC Univ Paris 06, UMR_S 1166, Team Genomics & Pathophysiology of Cardiovascular Diseases, Paris, France
- INSERM, UMR_S 1166, Team Genomics & Pathophysiology of Cardiovascular Diseases, Paris, France
- ICAN Institute for Cardiometabolism and Nutrition, Paris, France
- * E-mail:
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Gusareva ES, Van Steen K. Practical aspects of genome-wide association interaction analysis. Hum Genet 2014; 133:1343-58. [DOI: 10.1007/s00439-014-1480-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 08/18/2014] [Indexed: 12/31/2022]
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Napolioni V. The relevance of checking population allele frequencies and Hardy-Weinberg Equilibrium in genetic association studies: the case of SLC6A4 5-HTTLPR polymorphism in a Chinese Han Irritable Bowel Syndrome association study. Immunol Lett. 2014;162:276-278. [PMID: 25151208 DOI: 10.1016/j.imlet.2014.08.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 08/13/2014] [Indexed: 12/27/2022]
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Rocanin-arjo A, Cohen W, Carcaillon L, Frère C, Saut N, Letenneur L, Alhenc-gelas M, Dupuy A, Bertrand M, Alessi M, Germain M, Wild PS, Zeller T, Cambien F, Goodall AH, Amouyel P, Scarabin P, Trégouët D, Morange P; and the CardioGenics Consortium. A meta-analysis of genome-wide association studies identifies ORM1 as a novel gene controlling thrombin generation potential. Blood 2014; 123:777-85. [DOI: 10.1182/blood-2013-10-529628] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Key PointsGenetic variations at the ORM1 locus and concentrations of the encoded protein associate with thrombin generation. These findings may guide the development of novel antithrombotic treatments.
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