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Committee on A Framework for Developing a New Taxonomy of Disease Board on Life Sciences Division on Earth and Life Studies

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THE NATIONAL ACADEMIES PRESS 500 Fifth Street NW Washington, DC 20001 NOTICE: The project that is the subject of this report was approved by the Governing Board of the National Research Council, whose members are drawn from the councils of the National Academy of Sciences, the National Academy of Engineering, and the Institute of Medicine. The members of the Committee responsible for the report were chosen for their special competences and with regard for appropriate balance. This study was supported by Contract/Grant No. N01-0D-4-2139 between the National Academy of Sciences and the National Institutes of Health. Any opinions, findings, con- clusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the views of the organizations or agencies that provided support for the project. International Standard Book Number-13: 978-0-309-22222-8 International Standard Book Number-10: 0-309-22222-2 Library of Congress Control Number: 2011943146 Additional copies of this report are available from the National Academies Press, 500 Fifth Street, N.W., Lockbox 285, Washington, DC 20055; (800) 624-6242 or (202) 334- 3313 (in the Washington metropolitan area); Internet, http://www.nap.edu Cover art: Nicolle Rager Fuller, Sayo-Art LLC Photo: © Graham Bell/Corbis Copyright 2011 by the National Academy of Sciences. All rights reserved. Printed in the United States of America

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The National Academy of Sciences is a private, nonprofit, self-perpetuating society of distinguished scholars engaged in scientific and engineering research, dedicated to the furtherance of science and technology and to their use for the general welfare. Upon the authority of the charter granted to it by the Congress in 1863, the Academy has a mandate that requires it to advise the federal government on scientific and technical matters. Dr. Ralph J. Cicerone is president of the National Academy of Sciences. The National Academy of Engineering was established in 1964, under the charter of the National Academy of Sciences, as a parallel organization of outstanding engineers. It is autonomous in its administration and in the selection of its members, sharing with the National Academy of Sciences the responsibility for advising the federal government. The National Academy of Engineering also sponsors engineering programs aimed at meeting national needs, encourages education and research, and recognizes the superior achievements of engineers. Dr. Charles M. Vest is president of the National Academy of Engineering. The Institute of Medicine was established in 1970 by the National Academy of Sciences to secure the services of eminent members of appropriate professions in the examina - tion of policy matters pertaining to the health of the public. The Institute acts under the responsibility given to the National Academy of Sciences by its congressional charter to be an adviser to the federal government and, upon its own initiative, to identify issues of medical care, research, and education. Dr. Harvey V. Fineberg is president of the Institute of Medicine. The National Research Council was organized by the National Academy of Sciences in 1916 to associate the broad community of science and technology with the Academy’s purposes of furthering knowledge and advising the federal government. Functioning in accordance with general policies determined by the Academy, the Council has become the principal operating agency of both the National Academy of Sciences and the Na - tional Academy of Engineering in providing services to the government, the public, and the scientific and engineering communities. The Council is administered jointly by both Academies and the Institute of Medicine. Dr. Ralph J. Cicerone and Dr. Charles M. Vest are chair and vice chair, respectively, of the National Research Council. www.national-academies.org

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COMMITTEE ON A FRAMEWORK FOR DEVELOPING A NEW TAXONOMY OF DISEASE SUSAN DESMOND-HELLMANN, (Co-Chair), University of California, San Francisco, CA CHARLES L. SAWYERS, (Co-Chair), Memorial Sloan-Kettering Cancer Center, New York, NY DAVID R. COX, Applied Quantitative Genotherapeutics Unit, Pfizer Inc., San Francisco, CA CLAIRE FRASER-LIGGETT, University of Maryland, School of Medicine, College Park, MD STEPHEN J. GALLI, Stanford University, Stanford, CA DAVID B. GOLDSTEIN, Duke University School of Medicine, Durham, NC DAVID J. HUNTER, Harvard School of Public Health, Boston, MA ISAAC S. KOHANE, Harvard Medical School, Boston, MA MANUEL LLINÁS, Princeton University, Princeton, NJ BERNARD LO, University of California, San Francisco, CA TOM MISTELI, National Cancer Institute, Bethesda, MD SEAN J. MORRISON, University of Texas, Southwestern, TX DAVID G. NICHOLS, The Johns Hopkins University School of Medicine, Baltimore, MD MAYNARD V. OLSON, University of Washington, Seattle, WA CHARMAINE D. ROYAL, Duke University, Durham, NC KEITH R. YAMAMOTO, University of California, San Francisco, CA Staff INDIA HOOK-BARNARD, Study Director MIRSADA KARALIC-LONCAREVIC, Senior Program Associate CARL-GUSTAV ANDERSON, Program Associate ORIN LUKE, Senior Program Assistant AMANDA MAZZAWI, Senior Program Assistant MELINDA DIVITO, Christine Mirzayan Fellow v

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BOARD ON LIFE SCIENCES KEITH R. YAMAMOTO (Chair), University of California, San Francisco, CA BONNIE L. BASSLER, Princeton University, Princeton, NJ VICKI L. CHANDLER, Gordon and Betty Moore Foundation, Palo Alto, CA SEAN EDDY, Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA MARK D. FITZSIMMONS, John D. and Catherine T. MacArthur Foundation, Chicago, IL DAVID R. FRANZ, Midwest Research Institute, Frederick, MD LOUIS J. GROSS, University of Tennessee, Knoxville, TN CATO T. LAURENCIN, University of Connecticut Health Center, Farmington, CT BERNARD LO, University of California, San Francisco, CA ROBERT M. NEREM, Georgia Institute of Technology, Atlanta, GA CAMILLE PARMESAN, University of Texas, Austin, TX MURIEL E. POSTON, Skidmore College, Saratoga Springs, NY ALISON G. POWER, Cornell University, Ithaca, NY BRUCE W. STILLMAN, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY CYNTHIA WOLBERGER, Johns Hopkins University School of Medicine, Baltimore, MD MARY WOOLLEY, Research!America, Alexandria, VA Staff FRANCES E. SHARPLES, Director JO L. HUSBANDS, Scholar/Senior Project Director JAY B. LABOV, Senior Scientist/Program Director for Biology Education KATHERINE BOWMAN, Senior Program Officer MARILEE K. SHELTON-DAVENPORT, Senior Program Officer INDIA HOOK-BARNARD, Program Officer KEEGAN SAWYER, Program Officer ANNA FARRAR, Financial Associate CARL-GUSTAV ANDERSON, Program Associate SAYYEDA AYESHA AHMED, Senior Program Assistant ORIN LUKE, Senior Program Assistant AMANDA MAZZAWI, Senior Program Assistant vi

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Acknowledgments This report has been reviewed in draft form by individuals chosen for their diverse perspectives and technical expertise in accordance with procedures approved by the National Research Council’s Report Review Committee. The purpose of this independent review is to provide candid and critical comments that will assist the institution in making its published report as sound as pos - sible and to ensure that the report meets institutional standards of objectivity, evidence, and responsiveness to the study charge. The review comments and draft manuscript remain confidential to protect the integrity of the deliberative process. We thank the following individuals for their review of this report: Leslie Biesecker, National Institutes of Health • Martin J. Blaser, New York University Langone Medical Center • Wylie Burke, University of Washington • Christopher G. Chute, University of Minnesota and Mayo Clinic • Sean Eddy, Howard Hughes Medical Institute Janelia Farm Research • Elaine Jaffe, National Cancer Institute • Brian J. Kelly, Aetna • Chaitan Khosla, Stanford University • Daniel R. Masys, University of Washington • Stephen M. Schwartz, University of Washington • Although the reviewers listed above have provided many constructive comments and suggestions, they were not asked to endorse the conclusions or recommendations, nor did they see the final draft of the report before its release. The review of the report was overseen by Dennis Ausiello, Harvard Medical School, Massachusetts General Hospital and Partners Healthcare, and vii

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viii ACKNOWLEDGMENTS Queta Bond, Burroughs Wellcome Fund. Appointed by the National Research Council, they were responsible for making certain that an independent exami - nation of this report was carried out in accordance with institutional procedures and that all review comments were carefully considered. Responsibility for the final content of the report rests entirely with the authoring committee and the institution. We thank Dr. Theresa O’Brien, Director of Research Strategy and Special Projects, UCSF School of Medicine, for thoughtful suggestions and support to the Committee and NRC staff, throughout this study process. We thank Steve Olson for his writing and editorial assistance. We are grateful to those who attended and participated in the workshop “Toward a New Taxonomy of Disease,” held March 1 and 2, 2011 (Appendix C) and those who discussed data sharing with the Committee during the course of this study. These individuals, named below, were generous with their time, expertise, and ideas, and their insights were helpful to the Committee’s work: Charles Baum, Vice President of Global R&D, Pfizer • Leslie Biesecker, Chief & Senior Investigator, Genetic Disease Research • Branch, NHGRI Martin Blaser, Frederick H. King Professor of Internal Medicine and • Chairman of the Department of Medicine, NYU School of Medicine John Brownstein, Instructor, Harvard Medical School • Atul Butte, Chief and Assistant Professor, Division of Systems Medicine, • Department of Pediatrics, Stanford Lewis Cantley, Chief, Division of Signal Transduction, Harvard Medical • School Alta Charo, Professor of Law and Bioethics, University of Wisconsin • Law School Christopher G. Chute, Professor of Medical Informatics, Mayo Clinic • College of Medicine Andrew Conrad, Chief Scientific Officer, LabCorp • Elissa Epel, Associate Professor in Residence, Department of Psychiatry • at University of California, San Francisco Kathy Giusti, Founder and Chief Executive Officer, Multiple Myeloma • Research Foundation (MMRF) John Glaser, Chief Executive Officer, Health Services Business Unit, • Siemens Health Services Corey Goodman, Managing Director and Co-Founder, venBio • Brian J. Kelly, Head of Informatics and Strategic Alignment, Aetna • Debra Lappin, President, Council for American Medical Innovation • Jason Lieb, Professor, Department of Biology, University of North Caro- • lina at Chapel Hill Klaus Lindpaintner, Vice President of R&D, Strategic Diagnostics Inc. •

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ix ACKNOWLEDGMENTS Jon Lorsch, Professor of Biophysics and Biophysical Chemistry, Johns • Hopkins University, School of Medicine Daniel Masys, Chair of the Department of Biomedical Informatics, • Vanderbilt University Medical Center William Pao, Director, Personalized Cancer Medicine at the Vanderbilt- • Ingram Cancer Center Erin Ramos, Epidemiologist, National Human Genome Research • Institute Neil Risch, Institute for Human Genetics, University of California, San • Francisco Catherine Schaefer, Kaiser Permanente Northern California Division of • Research Ingrid Scheffer, Professor of Paediatric Neurology Research, University • of Melbourne Sanford Schwartz, Professor of Medicine, Health Care Management, • and Economics, University of Pennsylvania Janet Woodcock, Director, Center for Drug Evaluation and Research at • the U.S. Food and Drug Administration Helmut Zarbl, University of Medicine and Dentistry of New Jersey- • Robert Wood Johnson Medical School, Environmental & Occupational Medicine, Rutgers University

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Contents SUMMARY 1 1 INTRODUCTION 9 The Current Opportunity, 9 The Charge to the Committee, 10 A Brief History of Disease Taxonomies, 12 The Taxonomic Needs of the Biomedical Research and Medical Practice Communities, 13 Missed Opportunities of Current Taxonomies, 14 An Information Commons, a Knowledge Network, and a New Taxonomy that Would Integrate Many Types of Information and Serve All Stakeholders, 17 Rationale and Organization of the Report, 19 2 WHY NOW? 21 Biology Has Become a Data-Intensive Science, 22 The Opportunity to Integrate Data-Intensive Biology with Medicine, 24 The Urgent Need to Better Understand Phenotype-Genotype Correlations, 28 Dramatic Advances in Information Technology Are Driving Systemic Change, 29 Gathering Information from Informal Data Sources, 33 Integrating Clinical Medicine and Basic Science, 34 Multiple Stakeholders Are Ready for Change, 36 Public Attitudes Toward Information and Privacy Are in Flux, 39 The Proposed Knowledge Network of Disease Could Catalyze xi

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xii CONTENTS Changes in Biology, Information Technology, Medicine, and Society, 39 3 WHAT WOULD A KNOWLEDGE NETWORK AND NEW TAXONOMY LOOK LIKE? 41 The Knowledge Network of Disease Would Incorporate Multiple Parameters and Enable a Taxonomy Heavily Rooted in the Intrinsic Biology of Disease, 42 The Information Commons on which the Knowledge Network and New Taxonomy Would be Based Would Incorporate Much Information that Cannot Presently be Described in Molecular Terms, 43 The Proposed Knowledge Network of Disease Would Include Information about Pathogens and Other Microbes, 46 The Proposed Knowledge Network of Disease Would Go Beyond Description, 46 A Hierarchy of Large Datasets Would Be the Foundation of the Knowledge Network of Disease and Its Practical Applications, 50 The Proposed Knowledge Network Would Fundamentally Differ from Current Biomedical Information Systems, 54 A Knowledge Network of Disease Would Continuously Evolve, 55 The New Taxonomy Would Require Continuous Validation, 56 The New Taxonomy Would Develop in Parallel with the Continued Use of Current Taxonomies, 57 The Proposed Informational Infrastructure Would Have Global Health Impact, 57 4 HOW DO WE GET THERE? 59 A New Discovery Model for Disease Research, 60 Pilot Studies Should Draw Upon Observational Studies, 62 Example Pilot Study 1: The Million American Genomes Initiative (MAGI), 64 Example Pilot Study 2: Metabolomic Profiles in Type 2 Diabetes, 65 Anticipated Outcomes of the Pilot Studies, 65 A Research Model Based on Open Data Sharing Requires Changes to Data Access, Consent, and Sharing Policies, 66 Precompetitive Collaborations, 69 Competition and Sharing in the Health-Care System, 70 The Development of a Knowledge Network of Disease Will Require and Inform the Education of Health-Care Providers at All Levels, 71 5 EPILOGUE 75

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xiii CONTENTS REFERENCES 81 APPENDIXES A The Statement of Task, with Additional Context 93 B Committee Biographies 97 C March 1& 2, 2011—Workshop Agenda 109 D eMERGE Consortium Data Use Agreement 115 E Glossary 119 BOXES 1-1 Statement of Task, 11 1-2 A Flexnerian Moment?, 15 2-1 Distinguishing Types of Lung Cancer, 26 2-2 Prospective Cohort Studies—A Special Role, 30 2-3 eMERGE Consortium, 32 2-4 Precision Medicine for Drug Development, 38 3-1 The Exposome, 44 3-2 Distinguishing Disease Types, 47 3-3 Information to Guide Treatment Decisions, 49 FIGURES S-1 A Knowledge Network of Disease Would Enable a New Taxonomy, 2 1-1 Integration Would Benefit All Stakeholder Communities, 14 1-2 A Information Commons Might Use a GIS-Type Structure, 17 1-3 A Knowledge Network of Disease Would Enable a New Taxonomy, 18 2-1 The Plummeting Cost of Complete Genome Sequencing, 23 2-2 Knowledge of Non-Small-Cell Lung Cancer Has Evolved Substantially in Recent Decades, 27 3-1 Building a Biomedical Knowledge Network for Basic Discovery and Medicine, 52 4-1 Curriculum for Biomedical Graduate Program—Proposed New Model, 72

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