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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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