Abstract

Scalable, integrative methods to understand mechanisms that link genetic variants with phenotypes are needed. Here we derive a mathematical expression to compute PrediXcan (a gene mapping approach) results using summary data (S-PrediXcan) and show its accuracy and general robustness to misspecified reference sets. We apply this framework to 44 GTEx tissues and 100+ phenotypes from GWAS and meta-analysis studies, creating a growing public catalog of associations that seeks to capture the effects of gene expression variation on human phenotypes. Replication in an independent cohort is shown. Most of the associations are tissue specific, suggesting context specificity of the trait etiology. Colocalized significant associations in unexpected tissues underscore the need for an agnostic scanning of multiple contexts to improve our ability to detect causal regulatory mechanisms. Monogenic disease genes are enriched among significant associations for related traits, suggesting that smaller alterations of these genes may cause a spectrum of milder phenotypes.

Details

Title
Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics
Author
Barbeira, Alvaro N 1   VIAFID ORCID Logo  ; Dickinson, Scott P 1 ; Bonazzola, Rodrigo 1 ; Zheng, Jiamao 1 ; Wheeler, Heather E 2   VIAFID ORCID Logo  ; Torres, Jason M 3 ; Torstenson, Eric S 4 ; Shah, Kaanan P 1 ; Garcia, Tzintzuni 5 ; Edwards, Todd L 6   VIAFID ORCID Logo  ; Stahl, Eli A 7 ; Huckins, Laura M 7 ; Aguet, François 8 ; Ardlie, Kristin G 8 ; Cummings, Beryl B 9 ; Gelfand, Ellen T 8 ; Getz, Gad 10 ; Kane, Hadley 8 ; Handsaker, Robert E 11 ; Huang, Katherine H 8 ; Kashin, Seva 11 ; Karczewski, Konrad J 9 ; Lek, Monkol 9 ; Li, Xiao 8 ; MacArthur, Daniel G 9 ; Nedzel, Jared L 8 ; Nguyen, Duyen T 8 ; Noble, Michael S 8 ; Segrè, Ayellet V 8 ; Trowbridge, Casandra A 8 ; Tukiainen, Taru 9 ; Abell, Nathan S 12 ; Balliu, Brunilda 13 ; Barshir, Ruth 14 ; Basha, Omer 14 ; Battle, Alexis 15 ; Bogu, Gireesh K 16 ; Brown, Andrew 17 ; Brown, Christopher D 18 ; Castel, Stephane E 19 ; Chen, Lin S 20 ; Chiang, Colby 21 ; Conrad, Donald F 22 ; Damani, Farhan N 15 ; Davis, Joe R 12 ; Delaneau, Olivier 17 ; Dermitzakis, Emmanouil T 17 ; Engelhardt, Barbara E 23 ; Eskin, Eleazar 24 ; Ferreira, Pedro G 25 ; Frésard, Laure 12 ; Gamazon, Eric R 26 ; Garrido-Martín, Diego 16 ; Gewirtz, Ariel D H 27 ; Gliner, Genna 28 ; Gloudemans, Michael J 29 ; Guigo, Roderic 30 ; Hall, Ira M 31 ; Han, Buhm 32 ; He, Yuan 33 ; Hormozdiari, Farhad 34 ; Howald, Cedric 17 ; Jo, Brian 27 ; Eun Yong Kang 34 ; Kim, Yungil 15 ; Kim-Hellmuth, Sarah 19 ; Lappalainen, Tuuli 19 ; Li, Gen 35 ; Li, Xin 13 ; Liu, Boxiang 36 ; Serghei Mangul 34 ; McCarthy, Mark I 37 ; McDowell, Ian C 38 ; Mohammadi, Pejman 19 ; Monlong, Jean 39 ; Montgomery, Stephen B 12 ; Muñoz-Aguirre, Manuel 40 ; Ndungu, Anne W 41 ; Nobel, Andrew B 42 ; Oliva, Meritxell 43 ; Ongen, Halit 17 ; Palowitch, John J 44 ; Panousis, Nikolaos 17 ; Papasaikas, Panagiotis 16 ; Park, YoSon 18 ; Parsana, Princy 15 ; Payne, Anthony J 41 ; Peterson, Christine B 45 ; Quan, Jie 46 ; Reverter, Ferran 47 ; Sabatti, Chiara 48 ; Saha, Ashis 15 ; Sammeth, Michael 49 ; Scott, Alexandra J 21 ; Shabalin, Andrey A 50 ; Sodaei, Reza 16 ; Stephens, Matthew 51 ; Stranger, Barbara E 52 ; Strober, Benjamin J 33 ; Sul, Jae Hoon 53 ; Tsang, Emily K 54 ; Urbut, Sarah 55 ; van de Bunt, Martijn 56 ; Wang, Gao 55 ; Wen, Xiaoquan 57 ; Wright, Fred A 58 ; Xi, Hualin S 46 ; Yeger-Lotem, Esti 59 ; Zappala, Zachary 12 ; Zaugg, Judith B 60 ; Yi-Hui, Zhou 58 ; Akey, Joshua M 61 ; Bates, Daniel 62 ; Chan, Joanne 63 ; Claussnitzer, Melina 64 ; Demanelis, Kathryn 20 ; Diegel, Morgan 62 ; Doherty, Jennifer A 65 ; Feinberg, Andrew P 66 ; Fernando, Marian S 43 ; Halow, Jessica 62 ; Hansen, Kasper D 67 ; Haugen, Eric 62 ; Hickey, Peter F 68 ; Hou, Lei 69 ; Farzana Jasmine 20 ; Ruiqi Jian 63 ; Jiang, Lihua 63 ; Johnson, Audra 62 ; Kaul, Rajinder 62 ; Kellis, Manolis 69 ; Kibriya, Muhammad G 20 ; Lee, Kristen 62 ; Jin Billy Li 63 ; Li, Qin 63 ; Lin, Jessica 70 ; Lin, Shin 71 ; Linder, Sandra 12 ; Linke, Caroline 43 ; Liu, Yaping 69 ; Maurano, Matthew T 72 ; Molinie, Benoit 8 ; Nelson, Jemma 62 ; Neri, Fidencio J 62 ; Park, Yongjin 69 ; Pierce, Brandon L 20 ; Rinaldi, Nicola J 69 ; Rizzardi, Lindsay F 73 ; Sandstrom, Richard 62 ; Skol, Andrew 52 ; Smith, Kevin S 12 ; Snyder, Michael P 63 ; Stamatoyannopoulos, John 74 ; Tang, Hua 63 ; Wang, Li 8 ; Wang, Meng 63 ; Nicholas Van Wittenberghe 8 ; Wu, Fan 43 ; Zhang, Rui 63 ; Nierras, Concepcion R 75 ; Branton, Philip A 76 ; Carithers, Latarsha J 77 ; Guan, Ping 76 ; Moore, Helen M 76 ; Rao, Abhi 76 ; Vaught, Jimmie B 76 ; Gould, Sarah E 78 ; Lockart, Nicole C 78 ; Casey, Martin 78 ; Struewing, Jeffery P 78 ; Volpi, Simona 78 ; Addington, Anjene M 79 ; Koester, Susan E 79 ; Little, A Roger 80 ; Brigham, Lori E 81 ; Hasz, Richard 82 ; Hunter, Marcus 83 ; Johns, Christopher 84 ; Johnson, Mark 85 ; Kopen, Gene 86 ; Leinweber, William F 86 ; Lonsdale, John T 86 ; McDonald, Alisa 86 ; Mestichelli, Bernadette 86 ; Myer, Kevin 83 ; Roe, Brian 83 ; Salvatore, Michael 86 ; Saboor Shad 86 ; Thomas, Jeffrey A 86 ; Walters, Gary 85 ; Washington, Michael 85 ; Wheeler, Joseph 84 ; Bridge, Jason 87 ; Foster, Barbara A 88 ; Gillard, Bryan M 88 ; Karasik, Ellen 88 ; Kumar, Rachna 88 ; Miklos, Mark 87 ; Moser, Michael T 88 ; Jewell, Scott D 89 ; Montroy, Robert G 89 ; Rohrer, Daniel C 89 ; Valley, Dana R 89 ; Davis, David A 90 ; Mash, Deborah C 90 ; Undale, Anita H 91 ; Smith, Anna M 92 ; Tabor, David E 92 ; Roche, Nancy V 92 ; McLean, Jeffrey A 92 ; Vatanian, Negin 92 ; Robinson, Karna L 92 ; Sobin, Leslie 92 ; Barcus, Mary E 93 ; Valentino, Kimberly M 92 ; Qi, Liqun 92 ; Hunter, Steven 92 ; Hariharan, Pushpa 92 ; Singh, Shilpi 92 ; Ki Sung Um 92 ; Matose, Takunda 92 ; Tomaszewski, Maria M 92 ; Barker, Laura K 94 ; Mosavel, Maghboeba 95 ; Siminoff, Laura A 94 ; Traino, Heather M 94 ; Flicek, Paul 96 ; Juettemann, Thomas 96 ; Ruffier, Magali 96 ; Sheppard, Dan 96 ; Taylor, Kieron 96 ; Trevanion, Stephen J 96 ; Zerbino, Daniel R 96 ; Craft, Brian 97 ; Goldman, Mary 97 ; Haeussler, Maximilian 97 ; Kent, W James 97 ; Lee, Christopher M 97 ; Paten, Benedict 97 ; Rosenbloom, Kate R 97 ; Vivian, John 97 ; Zhu, Jingchun 97 ; Nicolae, Dan L 1 ; Cox, Nancy J 4 ; Im, Hae Kyung 1   VIAFID ORCID Logo 

 Section of Genetic Medicine, The University of Chicago, Chicago, IL, USA 
 Department of Biology, Loyola University Chicago, Chicago, IL, USA; Department of Computer Science, Loyola University Chicago, Chicago, IL, USA 
 Committee on Molecular Metabolism and Nutrition, The University of Chicago, Chicago, IL, USA 
 Vanderbilt Genetic Institute, Vanderbilt University Medical Center, Nashville, TN, USA 
 Center for Research Informatics, The University of Chicago, Chicago, IL, USA 
 Division of Epidemiology, Department of Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA 
 Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, NYC, NY, USA; Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, NYC, NY, USA 
 The Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA 
 The Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA 
10  The Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA; Massachusetts General Hospital Cancer Center, Department of Pathology, Massachusetts General Hospital, Boston, MA, USA 
11  The Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA 
12  Department of Genetics, Stanford University, Stanford, CA, USA; Department of Pathology, Stanford University, Stanford, CA, USA 
13  Department of Pathology, Stanford University, Stanford, CA, USA 
14  Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, BenGurion University of the Negev, Beer-Sheva, Israel 
15  Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA 
16  Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain 
17  Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland; Institute for Genetics and Genomics in Geneva (iG3), University of Geneva, Geneva, Switzerland; Swiss Institute of Bioinformatics, Geneva, Switzerland 
18  Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA 
19  New York Genome Center, New York, NY, USA; Department of Systems Biology, Columbia University Medical Center, New York, NY, USA 
20  Department of Public Health Sciences, The University of Chicago, Chicago, IL, USA 
21  McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA 
22  Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA; Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA 
23  Department of Computer Science, Center for Statistics and Machine Learning, Princeton University, Princeton, NJ, USA 
24  Department of Computer Science, University of California, Los Angeles, CA, USA; Department of Human Genetics, University of California, Los Angeles, CA, USA 
25  Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal; Institute of Molecular Pathology and Immunology (IPATIMUP), University of Porto, Porto, Portugal 
26  Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands; Department of Psychiatry, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands 
27  Lewis Sigler Institute, Princeton University, Princeton, NJ, USA 
28  Department of Operations Research and Financial Engineering, Princeton University, Princeton, NJ, USA 
29  Department of Genetics, Stanford University, Stanford, CA, USA; Department of Pathology, Stanford University, Stanford, CA, USA; Biomedical Informatics Program, Stanford University, Stanford, CA, USA 
30  Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), Barcelona, Spain 
31  McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA 
32  Department of Convergence Medicine, University of Ulsan College of Medicine, Asan Medical Center, Seoul, South Korea 
33  Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA 
34  Department of Computer Science, University of California, Los Angeles, CA, USA 
35  Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY, USA 
36  Department of Genetics, Stanford University, Stanford, CA, USA; Department of Pathology, Stanford University, Stanford, CA, USA; Department of Biology, Stanford University, Stanford, CA, USA 
37  Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK; Oxford NIHR Biomedical Research Centre, Churchill Hospital, Oxford, UK 
38  Computational Biology & Bioinformatics Graduate Program, Duke University, Durham, NC, USA 
39  Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Human Genetics Department, McGill University, Montreal, QC, Canada 
40  Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Departament d’Estadística i Investigació Operativa, Universitat Politècnica de Catalunya, Barcelona, Spain 
41  Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK 
42  Department of Statistics and Operations Research, University of North Carolina, Chapel Hill, NC, USA; Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA 
43  Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, USA; Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, USA 
44  Department of Statistics and Operations Research, University of North Carolina, Chapel Hill, NC, USA 
45  Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA 
46  Computational Sciences, Pfizer Inc, Cambridge, MA, USA 
47  Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Universitat de Barcelona, Barcelona, Spain 
48  Department of Biomedical Data Science, Stanford University, Stanford, CA, USA; Department of Statistics, Stanford University, Stanford, CA, USA 
49  Institute of Biophysics Carlos Chagas Filho (IBCCF), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil 
50  Department of Psychiatry, University of Utah, Salt Lake City, UT, USA 
51  Department of Statistics, The University of Chicago, Chicago, IL, USA; Department of Human Genetics, The University of Chicago, Chicago, IL, USA 
52  Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, USA; Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, USA; Center for Data Intensive Science, The University of Chicago, Chicago, IL, USA 
53  Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, CA, USA 
54  Department of Pathology, Stanford University, Stanford, CA, USA; Biomedical Informatics Program, Stanford University, Stanford, CA, USA 
55  Department of Human Genetics, The University of Chicago, Chicago, IL, USA 
56  Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK 
57  Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA 
58  Bioinformatics Research Center and Departments of Statistics and Biological Sciences, North Carolina State University, Raleigh, NC, USA 
59  Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, BenGurion University of the Negev, Beer-Sheva, Israel; National Institute for Biotechnology in the Negev, Beer-Sheva, Israel 
60  European Molecular Biology Laboratory, Heidelberg, Germany 
61  Lewis Sigler Institute, Princeton University, Princeton, NJ, USA; Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA 
62  Altius Institute for Biomedical Sciences, Seattle, Washington, USA 
63  Department of Genetics, Stanford University, Stanford, CA, USA 
64  The Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA; Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA; University of Hohenheim, Stuttgart, Germany 
65  Huntsman Cancer Institute, Department of Population Health Sciences, University of Utah, Salt Lake City, UT, USA 
66  Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA; Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Mental Health, Johns Hopkins University School of Public Health, Baltimore, MD, USA 
67  Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Biostatistics, Johns Hopkins University, Baltimore, MD, USA 
68  Department of Biostatistics, Johns Hopkins University, Baltimore, MD, USA 
69  The Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA 
70  Department of Genetics, Stanford University, Stanford, CA, USA; Department of Medicine, University of Washington, Seattle, Washington, USA 
71  Department of Genetics, Stanford University, Stanford, CA, USA; Division of Cardiology, University of Washington, Seattle, Washington, USA 
72  Institute for Systems Genetics, New York University Langone Medical Center, New York, NY, USA 
73  Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA 
74  Altius Institute for Biomedical Sciences, Seattle, Washington, USA; Department of Medicine, University of Washington, Seattle, Washington, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA 
75  Office of Strategic Coordination, Division of Program Coordination, Planning and Strategic Initiatives, Office of the Director, NIH, Rockville, MD, USA 
76  Biorepositories and Biospecimen Research Branch, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD, USA 
77  Biorepositories and Biospecimen Research Branch, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD, USA; National Institute of Dental and Craniofacial Research, Bethesda, MD, USA 
78  Division of Genomic Medicine, National Human Genome Research Institute, Rockville, MD, USA 
79  Division of Neuroscience and Basic Behavioral Science, National Institute of Mental Health, NIH, Bethesda, MD, USA 
80  Division of Neuroscience and Behavior, National Institute on Drug Abuse, NIH, Bethesda, MD, USA 
81  Washington Regional Transplant Community, Falls Church, VA, USA 
82  Gift of Life Donor Program, Philadelphia, PA, USA 
83  LifeGift, Houston, TX, USA 
84  Center for Organ Recovery and Education, Pittsburgh, PA, USA 
85  LifeNet Health, Virginia Beach, VA, USA 
86  National Disease Research Interchange, Philadelphia, PA, USA 
87  Unyts, Buffalo, NY, USA 
88  Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, NY, USA 
89  Van Andel Research Institute, Grand Rapids, MI, USA 
90  Brain Endowment Bank, Miller School of Medicine, University of Miami, Miami, FL, USA 
91  National Institute of Allergy and Infectious Diseases, NIH, Rockville, MD, USA 
92  Biospecimen Research Group, Clinical Research Directorate, Leidos Biomedical Research, Inc., Rockville, MD, USA 
93  Leidos Biomedical Research, Inc, Frederick, MD, USA 
94  Temple University, Philadelphia, PA, USA 
95  Department of Health Behavior and Policy, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA 
96  European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK 
97  UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA 
Pages
1-20
Publication year
2018
Publication date
May 2018
Publisher
Nature Publishing Group
e-ISSN
20411723
Source type
Scholarly Journal
Language of publication
English
ProQuest document ID
2036170303
Copyright
© 2018. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.