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OTTERS: a powerful TWAS framework leveraging summary-level reference data

Dai, Qile (författare)
Department of Biostatistics and Bioinformatics, Emory University School of Public Health, Atlanta, GA, 30322, USA; Center for Computational and Quantitative Genetics, Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
Zhou, Geyu (författare)
Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06511, USA
Zhao, Hongyu (författare)
Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06511, USA; Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06520, USA
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Võsa, Urmo (författare)
Estonian Genome Centre, Institute of Genomics, University of Tartu, 50090, Tartu, Estonia
Franke, Lude (författare)
Department of Genetics, University of Groningen, University Medical Center Groningen, 9700 RB, Groningen, The Netherlands; Oncode Institute, 3521 AL, Utrecht, The Netherlands
Battle, Alexis (författare)
Department of Computer Science, and Departments of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
Teumer, Alexander (författare)
Institute for Community Medicine, University Medicine Greifswald, 17489, Greifswald, Germany
Lehtimäki, Terho (författare)
Department of Clinical Chemistry, Fimlab Laboratories and Finnish Centre for Cardiovascular Disease Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, 33520, Finland
Raitakari, Olli T. (författare)
Centre for Population Health Research, University of Turku and Turku University Hospital, 20520, Turku, Finland; Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, 20520, Turku, Finland; Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, 20521, Turku, Finland
Esko, Tõnu (författare)
Estonian Genome Centre, Institute of Genomics, University of Tartu, 50090, Tartu, Estonia
Agbessi, Mawussé (författare)
Computational Biology, Ontario Institute for Cancer Research, Toronto, ON, Canada
Ahsan, Habibul (författare)
Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
Alves, Isabel (författare)
Computational Biology, Ontario Institute for Cancer Research, Toronto, ON, Canada
Andiappan, Anand Kumar (författare)
Singapore Immunology Network, Agency for Science Technology and Research, Singapore, Singapore
Arindrarto, Wibowo (författare)
Leiden University Medical Center, Leiden, The Netherlands
Awadalla, Philip (författare)
Computational Biology, Ontario Institute for Cancer Research, Toronto, ON, Canada
Battle, Alexis (författare)
Institute for Community Medicine, University Medicine Greifswald, 17489, Greifswald, Germany
Beutner, Frank (författare)
Heart Center Leipzig, Universität Leipzig, Leipzig, Germany
Jan Bonder, Marc (författare)
Department of Genetics, University of Groningen, University Medical Center Groningen, 9700 RB, Groningen, The Netherlands; European Molecular Biology Laboratory, Genome Biology Unit, 69117, Heidelberg, Germany
Boomsma, Dorret I. (författare)
Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
Christiansen, Mark W. (författare)
Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
Claringbould, Annique (författare)
Department of Genetics, University of Groningen, University Medical Center Groningen, 9700 RB, Groningen, The Netherlands; Oncode Institute, 3521 AL, Utrecht, The Netherlands
Deelen, Patrick (författare)
Department of Genetics, University of Groningen, University Medical Center Groningen, 9700 RB, Groningen, The Netherlands; Oncode Institute, 3521 AL, Utrecht, The Netherlands; Genomics Coordination Center, University Medical Centre Groningen, Groningen, The Netherlands; Department of Genetics, University Medical Centre Utrecht, P.O. Box 85500, 3508 GA, Utrecht, The Netherlands
Favé, Marie-Julie (författare)
Computational Biology, Ontario Institute for Cancer Research, Toronto, ON, Canada
Frayling, Timothy (författare)
Genetics of Complex Traits, University of Exeter Medical School, Royal Devon & Exeter Hospital, Exeter, UK
Gharib, Sina A. (författare)
Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA; Department of Medicine, University of Washington, Seattle, WA, USA
Gibson, Greg (författare)
School of Biological Sciences, Georgia Tech, Atlanta, GA, USA
Heijmans, Bastiaan T. (författare)
Leiden University Medical Center, Leiden, The Netherlands
Hemani, Gibran (författare)
MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
Jansen, Rick (författare)
Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
Kähönen, Mika (författare)
Department of Clinical Physiology, Tampere University Hospital and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
Kalnapenkis, Anette (författare)
Estonian Genome Centre, Institute of Genomics, University of Tartu, 50090, Tartu, Estonia
Kasela, Silva (författare)
Estonian Genome Centre, Institute of Genomics, University of Tartu, 50090, Tartu, Estonia
Kettunen, Johannes (författare)
University of Helsinki, Helsinki, Finland
Kim, Yungil (författare)
Department of Computer Science, and Departments of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA; Genetics and Genomic Science Department, Icahn School of Medicine at Mount Sinai, New York, NY, USA
Kirsten, Holger (författare)
Institut für Medizinische InformatiK, Statistik und Epidemiologie, LIFE – Leipzig Research Center for Civilization Diseases, Universität Leipzig, Leipzig, Germany
Kovacs, Peter (författare)
IFB Adiposity Diseases, Universität Leipzig, Leipzig, Germany
Krohn, Knut (författare)
Interdisciplinary Center for Clinical Research, Faculty of Medicine, Universität Leipzig, Leipzig, Germany
Kronberg, Jaanika (författare)
Estonian Genome Centre, Institute of Genomics, University of Tartu, 50090, Tartu, Estonia
Kukushkina, Viktorija (författare)
Estonian Genome Centre, Institute of Genomics, University of Tartu, 50090, Tartu, Estonia
Kutalik, Zoltan (författare)
Lausanne University Hospital, Lausanne, Switzerland
Lee, Bernett (författare)
Singapore Immunology Network, Agency for Science Technology and Research, Singapore, Singapore
Loeffler, Markus (författare)
Institut für Medizinische InformatiK, Statistik und Epidemiologie, LIFE – Leipzig Research Center for Civilization Diseases, Universität Leipzig, Leipzig, Germany
Marigorta, Urko M. (författare)
School of Biological Sciences, Georgia Tech, Atlanta, GA, USA; Integrative Genomics Lab, CIC bioGUNE, Bizkaia Science and Technology Park, Derio, Bizkaia, Basque Country, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
Mei, Hailang (författare)
Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands
Milani, Lili (författare)
Estonian Genome Centre, Institute of Genomics, University of Tartu, 50090, Tartu, Estonia
Montgomery, Grant W. (författare)
Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
Müller-Nurasyid, Martina (författare)
Institute of Genetic Epidemiology, Helmholtz Zentrum München – German Research Center for Environmental Health, Neuherberg, Germany; Department of Medicine I, University Hospital Munich, Ludwig Maximilian’s University, München, Germany; DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany
Nauck, Matthias (författare)
Institute of Clinical Chemistry and Laboratory Medicine, Greifswald University Hospital, Greifswald, Germany; German Center for Cardiovascular Research (partner site Greifswald), Greifswald, Germany
Nivard, Michel G. (författare)
Department of Biological Psychology, Faculty of Behaviour and Movement Sciences, VU, Amsterdam, The Netherlands
Penninx, Brenda (författare)
Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
Perola, Markus (författare)
National Institute for Health and Welfare, University of Helsinki, Helsinki, Finland
Pervjakova, Natalia (författare)
Estonian Genome Centre, Institute of Genomics, University of Tartu, 50090, Tartu, Estonia
Pierce, Brandon L. (författare)
Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
Powell, Joseph (författare)
Garvan Institute of Medical Research, Garvan-Weizmann Centre for Cellular Genomics, Sydney, NSW, Australia
Prokisch, Holger (författare)
Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany; Institute of Human Genetics, Technical University Munich, Munich, Germany
Psaty, Bruce M. (författare)
Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA; Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
Ripatti, Samuli (författare)
Statistical and Translational Genetics, University of Helsinki, Helsinki, Finland
Rotzschke, Olaf (författare)
Singapore Immunology Network, Agency for Science Technology and Research, Singapore, Singapore
Rüeger, Sina (författare)
Lausanne University Hospital, Lausanne, Switzerland
Saha, Ashis (författare)
Department of Computer Science, and Departments of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
Scholz, Markus (författare)
Institut für Medizinische InformatiK, Statistik und Epidemiologie, LIFE – Leipzig Research Center for Civilization Diseases, Universität Leipzig, Leipzig, Germany
Schramm, Katharina (författare)
Institute of Genetic Epidemiology, Helmholtz Zentrum München – German Research Center for Environmental Health, Neuherberg, Germany; Department of Medicine I, University Hospital Munich, Ludwig Maximilian’s University, München, Germany
Seppälä, Ilkka (författare)
Department of Clinical Chemistry, Fimlab Laboratories and Finnish Centre for Cardiovascular Disease Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, 33520, Finland
Slagboom, Eline P. (författare)
Leiden University Medical Center, Leiden, The Netherlands
Stehouwer, Coen D. A. (författare)
Department of Internal Medicine and School for Cardiovascular Diseases (CARIM), Maastricht University Medical Center, Maastricht, The Netherlands
Stumvoll, Michael (författare)
Department of Medicine, Universität Leipzig, Leipzig, Germany
Sullivan, Patrick (författare)
Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
‘t Hoen, Peter A. C. (författare)
Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center Nijmegen, Nijmegen, The Netherlands
Thiery, Joachim (författare)
Institute for Laboratory Medicine, LIFE – Leipzig Research Center for Civilization Diseases, Universität Leipzig, Leipzig, Germany
Tong, Lin (författare)
Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
Tönjes, Anke (författare)
German Center for Cardiovascular Research (partner site Greifswald), Greifswald, Germany
van Dongen, Jenny (författare)
Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
van Iterson, Maarten (författare)
Leiden University Medical Center, Leiden, The Netherlands
van Meurs, Joyce (författare)
Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, The Netherlands
Veldink, Jan H. (författare)
UMC Utrecht Brain Center, University Medical Center Utrecht, Department of Neurology, Utrecht University, Utrecht, The Netherlands
Verlouw, Joost (författare)
Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, The Netherlands
Visscher, Peter M. (författare)
Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
Völker, Uwe (författare)
Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
Westra, Harm-Jan (författare)
Department of Genetics, University of Groningen, University Medical Center Groningen, 9700 RB, Groningen, The Netherlands; Oncode Institute, 3521 AL, Utrecht, The Netherlands
Wijmenga, Cisca (författare)
Department of Genetics, University of Groningen, University Medical Center Groningen, 9700 RB, Groningen, The Netherlands
Yaghootkar, Hanieh (författare)
Luleå tekniska universitet,Medicinsk vetenskap,Genetics of Complex Traits, University of Exeter Medical School, Royal Devon & Exeter Hospital, Exeter, UK; School of Life Sciences, College of Liberal Arts and Science, University of Westminster, 115 New Cavendish Street, London, UK
Yang, Jian (författare)
Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia; School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
Zeng, Biao (författare)
School of Biological Sciences, Georgia Tech, Atlanta, GA, USA
Zhang, Futao (författare)
Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
Epstein, Michael P. (författare)
Center for Computational and Quantitative Genetics, Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
Yang, Jingjing (författare)
Center for Computational and Quantitative Genetics, Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
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 (creator_code:org_t)
Springer Nature, 2023
2023
Engelska.
Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 14:1
  • Tidskriftsartikel (refereegranskat)
Abstract Ämnesord
Stäng  
  • Most existing TWAS tools require individual-level eQTL reference data and thus are not applicable to summary-level reference eQTL datasets. The development of TWAS methods that can harness summary-level reference data is valuable to enable TWAS in broader settings and enhance power due to increased reference sample size. Thus, we develop a TWAS framework called OTTERS (Omnibus Transcriptome Test using Expression Reference Summary data) that adapts multiple polygenic risk score (PRS) methods to estimate eQTL weights from summary-level eQTL reference data and conducts an omnibus TWAS. We show that OTTERS is a practical and powerful TWAS tool by both simulations and application studies.

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MEDICIN OCH HÄLSOVETENSKAP  -- Medicinska och farmaceutiska grundvetenskaper -- Medicinsk genetik (hsv//swe)
MEDICAL AND HEALTH SCIENCES  -- Basic Medicine -- Medical Genetics (hsv//eng)

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Dai, Qile
Zhou, Geyu
Zhao, Hongyu
Võsa, Urmo
Franke, Lude
Battle, Alexis
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Teumer, Alexande ...
Lehtimäki, Terho
Raitakari, Olli ...
Esko, Tõnu
Agbessi, Mawussé
Ahsan, Habibul
Alves, Isabel
Andiappan, Anand ...
Arindrarto, Wibo ...
Awadalla, Philip
Beutner, Frank
Jan Bonder, Marc
Boomsma, Dorret ...
Christiansen, Ma ...
Claringbould, An ...
Deelen, Patrick
Favé, Marie-Juli ...
Frayling, Timoth ...
Gharib, Sina A.
Gibson, Greg
Heijmans, Bastia ...
Hemani, Gibran
Jansen, Rick
Kähönen, Mika
Kalnapenkis, Ane ...
Kasela, Silva
Kettunen, Johann ...
Kim, Yungil
Kirsten, Holger
Kovacs, Peter
Krohn, Knut
Kronberg, Jaanik ...
Kukushkina, Vikt ...
Kutalik, Zoltan
Lee, Bernett
Loeffler, Markus
Marigorta, Urko ...
Mei, Hailang
Milani, Lili
Montgomery, Gran ...
Müller-Nurasyid, ...
Nauck, Matthias
Nivard, Michel G ...
Penninx, Brenda
Perola, Markus
Pervjakova, Nata ...
Pierce, Brandon ...
Powell, Joseph
Prokisch, Holger
Psaty, Bruce M.
Ripatti, Samuli
Rotzschke, Olaf
Rüeger, Sina
Saha, Ashis
Scholz, Markus
Schramm, Kathari ...
Seppälä, Ilkka
Slagboom, Eline ...
Stehouwer, Coen ...
Stumvoll, Michae ...
Sullivan, Patric ...
‘t Hoen, Peter A ...
Thiery, Joachim
Tong, Lin
Tönjes, Anke
van Dongen, Jenn ...
van Iterson, Maa ...
van Meurs, Joyce
Veldink, Jan H.
Verlouw, Joost
Visscher, Peter ...
Völker, Uwe
Westra, Harm-Jan
Wijmenga, Cisca
Yaghootkar, Hani ...
Yang, Jian
Zeng, Biao
Zhang, Futao
Epstein, Michael ...
Yang, Jingjing
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