It appears you don't have support to open PDFs in this web browser. To view this file, Open with your PDF reader
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.
You have requested "on-the-fly" machine translation of selected content from our databases. This functionality is provided solely for your convenience and is in no way intended to replace human translation. Show full disclaimer
Neither ProQuest nor its licensors make any representations or warranties with respect to the translations. The translations are automatically generated "AS IS" and "AS AVAILABLE" and are not retained in our systems. PROQUEST AND ITS LICENSORS SPECIFICALLY DISCLAIM ANY AND ALL EXPRESS OR IMPLIED WARRANTIES, INCLUDING WITHOUT LIMITATION, ANY WARRANTIES FOR AVAILABILITY, ACCURACY, TIMELINESS, COMPLETENESS, NON-INFRINGMENT, MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. Your use of the translations is subject to all use restrictions contained in your Electronic Products License Agreement and by using the translation functionality you agree to forgo any and all claims against ProQuest or its licensors for your use of the translation functionality and any output derived there from. Hide full disclaimer
Details




1 Section of Genetic Medicine, The University of Chicago, Chicago, IL, USA
2 Department of Biology, Loyola University Chicago, Chicago, IL, USA; Department of Computer Science, Loyola University Chicago, Chicago, IL, USA
3 Committee on Molecular Metabolism and Nutrition, The University of Chicago, Chicago, IL, USA
4 Vanderbilt Genetic Institute, Vanderbilt University Medical Center, Nashville, TN, USA
5 Center for Research Informatics, The University of Chicago, Chicago, IL, USA
6 Division of Epidemiology, Department of Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
7 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
8 The Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
9 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