INTEGRATING LARGE-SCALE GENOMIC INFORMATION INTO CLINICAL PRACTICE

WORKSHOP SUMMARY

Steve Olson, Sarah H. Beachy, Claire F. Giammaria, and Adam C. Berger, Rapporteurs

Roundtable on Translating Genomic-Based Research for Health

Board on Health Sciences Policy

INSTITUTE OF MEDICINE
     OF THE NATIONAL ACADEMIES

THE NATIONAL ACADEMIES PRESS
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Steve Olson, Sarah H. Beachy, Claire F. Giammaria, and Adam C. Berger, Rapporteurs Roundtable on Translating Genomic-Based Research for Health Board on Health Sciences Policy

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THE NATIONAL ACADEMIES PRESS 500 Fifth Street, N.W. Washington, DC 20001 NOTICE: The project that is the subject of this report was approved by the Govern- ing Board of the National Research Council, whose members are drawn from the councils of the National Academy of Sciences, the National Academy of Engineer- ing, and the Institute of Medicine. This project was supported by contracts between the National Academy of Sciences and the American College of Medical Genetics (unnumbered contract); Ameri- can Medical Association (unnumbered contract); American Nurses Association (unnumbered contract); Blue Cross and Blue Shield Association (unnumbered con- tract); Centers for Disease Control and Prevention (Contract No. 200-2011-38807); College of American Pathologists (unnumbered contract); Department of the Air Force (Contract No. FA7014-10-P-0072); Department of Veterans Affairs (Con- tract No. V101(93) P-2238); Eli Lilly and Company (Contract No. LRL-0028-07); Genetic Alliance (unnumbered contract); Health Resources and Services Adminis- tration (Contract No. HHSH250201100119P); Johnson & Johnson (unnumbered contract); Kaiser Permanente (unnumbered contract); National Cancer Institute (Contract No. N01-OD-4-2139, TO#189); National Heart, Lung, and Blood Insti- tute (Contract No. N01-OD-4-2139, TO#189); National Human Genome Research Institute (Contract No. N01-OD-4-2139, TO#189 and 264); National Society of Genetic Counselors (unnumbered contract); and Pfizer Inc. (Contract No. 140-N- 1818071). Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the authors and do not necessarily reflect the views of the organizations or agencies that provided support for the project. International Standard Book Number-13: 978-0-309-22034-7 International Standard Book Number-10: 0-309-22034-3 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. For more information about the Institute of Medicine, visit the IOM home page at www.iom.edu. Copyright 2012 by the National Academy of Sciences. All rights reserved. Printed in the United States of America The serpent has been a symbol of long life, healing, and knowledge among almost all cultures and religions since the beginning of recorded history. The serpent adopted as a logotype by the Institute of Medicine is a relief carving from ancient Greece, now held by the Staatliche Museen in Berlin. Suggested citation: IOM (Institute of Medicine). 2012. Integrating Large-Scale Genomic Information into Clinical Practice: Workshop Summary. Washington, DC: The National Academies Press.

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“Knowing is not enough; we must apply. Willing is not enough; we must do.” — Goethe Advising the Nation. Improving Health.

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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 Acad- emy 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 engineer- ing programs aimed at meeting national needs, encourages education and research, and recognizes the superior achievements of engineers. Dr. Charles 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 examination of policy matters pertaining to the health of the public. The Insti- tute 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 Sci- ences 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 National Academy of Engineering in providing services to the government, the public, and the scientific and engineering communities. The Coun- cil is administered jointly by both Academies and the Institute of Medicine. Dr. Ralph J. Cicerone and Dr. Charles Vest are chair and vice chair, respectively, of the National Research Council. www.national-academies.org

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PLANNING COMMITTEE1 BRUCE BLUMBERG (Cochair), Institutional Director of Graduate Medical Education, Northern California Kaiser Permanente, The Permanente Medical Group, Oakland, CA CATHERINE A. WICKLUND (Cochair), Past President, National Society of Genetic Counselors; Director, Graduate Program in Genetic Counseling; Associate Professor, Department of Obstetrics and Gynecology, Northwestern University, Chicago, IL PAUL R. BILLINGS, Chief Medical Officer, Life Technologies Corporation, Carlsbad, CA DENISE E. BONDS, Medical Officer, Division of Prevention and Population Sciences, National Heart, Lung, and Blood Institute, Bethesda, MD W. GREGORY FEERO, Special Advisor to the Director for Genomic Medicine, National Human Genome Research Institute, Bethesda, MD KATHERINE JOHANSEN-TABER, Senior Scientist, American Medical Association, Chicago, IL SHARON KARDIA, Professor and Chair of Epidemiology; Director, Public Health Genetics Program; Director, Life Science and Society Program; Codirector, Center for Public Health and Community Genomics, University of Michigan School of Public Health, Ann Arbor MOHAMED KHAN, Leader of Radiation Oncology, Vancouver Cancer Centre, BC Cancer Agency, Vancouver, BC, Canada MUIN KHOURY, Director, National Office of Public Health Genomics, Centers for Disease Control and Prevention, Atlanta, GA DEBRA LEONARD, Professor and Vice Chair for Laboratory Medicine; Director of the Clinical Laboratories; Director of the Pathology Residency Training Program, Weill Cornell Medical Center of Cornell University, New York, NY MICHELE LLOYD-PURYEAR, Chief, Genetic Services Branch, Health Resources and Services Administration, Rockville, MD MARTHA TURNER, Assistant Director, American Nurses Association Center for Ethics and Human Rights, Silver Spring, MD MICHAEL S. WATSON, Executive Director, American College of Medical Genetics, Bethesda, MD 1 Institute of Medicine planning committees are solely responsible for organizing the work- shop, identifying topics, and choosing speakers. The responsibility for the published workshop summary rests with the workshop rapporteurs and the institution. v

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IOM Staff ADAM C. BERGER, Project Director CLAIRE F. GIAMMARIA, Research Associate TONIA E. DICKERSON, Senior Program Assistant vi

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ROUNDTABLE ON TRANSLATING GENOMIC-BASED RESEARCH FOR HEALTH1 WYLIE BURKE (Chair), Professor and Chair, Department of Bioethics and Humanities, University of Washington, Seattle NAOMI ARONSON, Executive Director, Technology Evaluation Center, Blue Cross and Blue Shield Association, Chicago, IL BRUCE BLUMBERG, Institutional Director of Graduate Medical Education, Northern California Kaiser Permanente, The Permanente Medical Group, Oakland, CA DENISE E. BONDS, Medical Officer, Division of Prevention and Population Sciences, National Heart, Lung, and Blood Institute, Bethesda, MD C. THOMAS CASKEY, Professor, Baylor College of Medicine, Houston, TX W. GREGORY FEERO, Special Advisor to the Director for Genomic Medicine, National Human Genome Research Institute, Bethesda, MD ANDREW N. FREEDMAN, Branch Chief, Clinical and Translational Epidemiology Branch, Epidemiology and Genetics Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute, Rockville, MD GEOFFREY GINSBURG, Director, Center for Genomic Medicine, Institute for Genomic Sciences and Policy, Duke University, Durham, NC SHARON KARDIA, Professor and Chair of Epidemiology; Director, Public Health Genetics Program; Director, Life Science and Society Program; Codirector, Center for Public Health and Community Genomics, University of Michigan School of Public Health, Ann Arbor MOHAMED KHAN, representative of the American Medical Association; Leader of Radiation Oncology, Vancouver Cancer Centre, BC Cancer Agency, Vancouver, BC, Canada MUIN KHOURY, Director, National Office of Public Health Genomics, Centers for Disease Control and Prevention, Atlanta, GA DEBRA LEONARD, representative of the College of American Pathologists; Professor and Vice Chair for Laboratory Medicine; Director of the Clinical Laboratories; Director of the Pathology Residency Training Program, Weill Cornell Medical Center of Cornell University, New York, NY MICHELE LLOYD-PURYEAR, Chief, Genetic Services Branch, Health Resources and Services Administration, Rockville, MD 1 Institute of Medicine forums and roundtables do not issue, review, or approve individual documents. The responsibility for the published workshop summary rests with the workshop rapporteurs and the institution. vii

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ELIZABETH MANSFIELD, Director of the Personalized Medicine Staff, Office of In Vitro Diagnostic Device Evaluation and Safety, Center for Devices and Radiological Health, U.S. Food and Drug Administration, Silver Spring, MD GARRY NEIL, Corporate Vice President, Corporate Office of Science and Technology, Johnson & Johnson, New Brunswick, NJ ROBERT L. NUSSBAUM, Chief, Division of Medical Genetics, Department of Medicine and Institute of Human Genetics, University of California, San Francisco, School of Medicine MICHELLE A. PENNY, Senior Director, Translational Medicine Group, Eli Lilly and Company, Indianapolis, IN AIDAN POWER, Vice President and Global Head of Molecular Medicine, Pfizer Inc., Groton, CT VICTORIA M. PRATT, Chief Director, Molecular Genetics, Quest Diagnostics Nichols Institute, Chantilly, VA RONALD PRZYGODZKI, Associate Director for Genomic Medicine, Biomedical Laboratory Research and Development, Department of Veterans Affairs, Washington, DC ALLEN D. ROSES, President and Chief Operating Officer, Cabernet, Shiraz and Zinfandel Pharmaceuticals; and Jefferson-Pilot Professor of Neurobiology and Genetics, Professor of Medicine (Neurology); Director, Deane Drug Discovery Institute; Senior Scholar, Fuqua School of Business, R. David Thomas Executive Training Center, Duke University, Durham, NC KEVIN A. SCHULMAN, Professor of Medicine and Business Administration; Director, Center for Clinical and Genetic Economics; Associate Director, Duke Clinical Research Institute, Duke University School of Medicine, Durham, NC SHARON TERRY, President and Chief Executive Officer, Genetic Alliance, Washington, DC MARTHA TURNER, Assistant Director, American Nurses Association Center for Ethics and Human Rights, Silver Spring, MD MICHAEL S. WATSON, Executive Director, American College of Medical Genetics, Bethesda, MD DANIEL WATTENDORF, Deputy Chief, Medical Innovations, Department of the Air Force; Program Manager, DARPA/Defense Sciences Office, Arlington, VA CATHERINE A. WICKLUND, Past President, National Society of Genetic Counselors; Director, Graduate Program in Genetic Counseling; Associate Professor, Department of Obstetrics and Gynecology, Northwestern University, Chicago, IL viii

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IOM Staff ADAM C. BERGER, Project Director SARAH H. BEACHY, Christine Mirzayan Science and Technology Policy Graduate Fellow (August to November 2011) CLAIRE F. GIAMMARIA, Research Associate TONIA E. DICKERSON, Senior Program Assistant ANDREW POPE, Director, Board on Health Sciences Policy ix

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Reviewers 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 possible and to ensure that the report meets institutional standards for objectivity, evidence, and responsiveness to the study charge. The review comments and draft manuscript remain confidential to protect the integrity of the process. We wish to thank the following individuals for their review of this report: James P. Evans, Bryson Distinguished Professor of Genetics & Medicine, Department of Genetics, University of North Carolina at Chapel Hill W. Andrew Faucett, Director, Policy and Education, Genomic Medicine Institute, Geisinger Health System, Danville, PA Henry T. Greely, Deane F. and Kate Edelman Johnson Professor of Law; Professor, by courtesy, of Genetics; Director, Center for Law and the Biosciences, Stanford University Mary V. Relling, Chair, Pharmaceutical Department, St. Jude Children’s Research Hospital, Memphis, TN Cindy L. Vnencak-Jones, Professor, Departments of Pathology and Pediatrics; Director, Molecular Diagnostics Laboratory, Vanderbilt University Medical Center, Nashville, TN xi

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xii REVIEWERS Although the reviewers listed above have provided many construc- tive comments and suggestions, they were not asked to endorse the final draft of the report before its release. The review of this report was over- seen by Harold J. Fallon, Dean Emeritus of the University of Alabama at Birmingham School of Medicine. Appointed by the Institute of Medicine, he was responsible for making certain that an independent examination 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 this report rests entirely with the author and the institution.

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Acknowledgments The support of the sponsors of the Institute of Medicine Roundta- ble on Translating Genomic-Based Research for Health was crucial to the planning and conduct of the workshop Integrating Large-Scale Genomic Information into Clinical Practice. Federal sponsors are the Centers for Dis- ease Control and Prevention; Department of the Air Force; Department of Veterans Affairs; Health Resources and Services Administration; National Cancer Institute; National Heart, Lung, and Blood Institute; and National Human Genome Research Institute. Non-federal sponsorship was provided by the American College of Medical Genetics, American Medical Associa- tion, American Nurses Association, Blue Cross and Blue Shield Association, College of American Pathologists, Eli Lilly and Company, Genetic Alliance, Johnson & Johnson, Kaiser Permanente, National Society of Genetic Coun- selors, and Pfizer Inc. The Roundtable wishes to express its gratitude to the expert speakers whose presentations helped outline the challenges and opportunities in integrating large-scale genomic information into clinical practice. The Roundtable also wishes to thank the members of the planning committee for their work in developing an excellent workshop agenda. The project director would like to thank project staff who worked diligently to develop both the workshop and the resulting summary. Christine Mirzayan Science and Technology Policy Fellow Sarah H. Beachy was involved in writ- ing and editing of the report, as was research associate Claire F. Giammaria. Tonia E. Dickerson arranged meetings and handled administrative tasks that resulted in a highly successful workshop. xiii

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Contents ABBREVIATIONS AND ACRONYMS xix 1 INTRODUCTION 1 2 THE REALIZATION OF GENOMIC MEDICINE 5 Shifting Research Paradigms, 6 Clinical Applications of Genomics-Based Medicine, 6 Addressing Obstacles and Defining a Path Forward, 7 The ClinSeq Project, 8 An Evolution of Medicine, 10 3 THE ANALYSIS OF GENOMIC DATA 11 Challenges for Laboratories, 12 Laboratory-Based Solutions, 14 Meaningful Use of Test Results, 17 Genomic Medicine in Practice, 20 4 THE INTERPRETATION OF GENOMIC DATA 25 Data Interpretation from a Clinician’s Perspective, 26 Integrating Genomic Data with Pathology, 29 Using a Bioinformatics Model for Interpretation, 33 Envisioning Clinical Genomics in 2020, 36 xv

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xvi CONTENTS 5 THE DELIVERY OF GENOMIC DATA 39 Implementing Pharmacogenetics in Clinical Practice, 40 Granting Access to Personal Health Information, 43 Advancing the Utilization of Genomic Information, 45 Building a Business Case for Genetic Testing, 46 6 ETHICAL AND LEGAL ISSUES 47 Regulatory Issues, 48 Ethical Issues: The Doctor–Patient Relationship, 49 Privacy Issues, 50 Other Issues, 51 7 WORKFORCE DEVELOPMENT 53 Knowledge, Skill Sets, and Training Opportunities, 54 A Generation of Effort, 55 8 ENVISIONING THE FUTURE 57 Maintaining Curated Databases, 57 Databases for Genetic Variants Involved in Cancer, 59 A Public Health Approach to Genomic Medicine, 60 Return of Results, 62 Getting Health Care Providers Interested, 62 Reimbursement for Interpretative Services, 63 The Role of Industry, 63 Final Words, 63 REFERENCES 65 APPENDIXES A WORKSHOP AGENDA 69 B SPEAKER BIOGRAPHICAL SKETCHES 75 C REGISTERED ATTENDEES 87

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Figures and Box FIGURES 3-1 Genetic tests undergo a characteristic progression from gene discovery to test application, 15 4-1 A model for future cancer care demonstrates how genomic sequencing and network biology will enable personalized medicine, 30 BOX 8-1 Goals to Realize the Vision of Genomic Medicine, 61 xvii

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Abbreviations and Acronyms ATM automated teller machine BRCA1 breast cancer 1, early onset BRCA2 breast cancer 2, early onset CAP College of American Pathologists CDC Centers for Disease Control and Prevention CDG congenital disorders of glycosylation CK creatine kinase CLIA Clinical Laboratory Improvement Amendments CLL chronic lymphocytic leukemia CMAMMA combined malonic and methylmalonic aciduria CMD congenital muscular dystrophy CPMC Coriell Personalized Medicine Collaborative CT computed tomography EGFR epidermal growth factor receptor EMR electronic medical record FDA U.S. Food and Drug Administration FISH fluorescent in situ hybridization HCM hypertrophic cardiomyopathy HIV human immunodeficiency virus xix

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xx ABBREVIATIONS AND ACRONYMS ICOB Informed Cohort Oversight Board IRB institutional review board IT information technology NCBI National Center for Biotechnology Information NIH National Institutes of Health PCPGM Partners HealthCare Center for Personalized Genetic Medicine PGRN Pharmacogenomics Research Network PHR personal health record SNP single nucleotide polymorphism TPMT thiopurine S-methyltransferase XLID X-linked intellectual disability