Evaluating Human Genetic Diversity

Committee on Human Genome Diversity

Commission on Life Sciences

NATIONAL RESEARCH COUNCIL

NATIONAL ACADEMY PRESS
Washington, DC
1997



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Evaluating Human Genetic Diversity Evaluating Human Genetic Diversity Committee on Human Genome Diversity Commission on Life Sciences NATIONAL RESEARCH COUNCIL NATIONAL ACADEMY PRESS Washington, DC 1997

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Evaluating Human Genetic Diversity NATIONAL ACADEMY PRESS 2101 Constitution Ave., N.W. Washington, D.C. 20418 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. In preparing its report, the committee invited people with different perspectives to present their views. Such invitation does not imply endorsement of those views. This report has been reviewed by a group other than the authors according to procedures approved by a Report Review Committee consisting of members of the National Academy of Sciences, the National Academy of Engineering, and the Institute of Medicine. This study by the National Research Council's Commission on Life Sciences was sponsored by the National Institutes of Health and the National Science Foundation under contract no. N01-OD-4-2139. Points of view in this document are those of the authors and do not necessarily represent the official position of the sponsoring agencies. Library of Congress Catalog Card Number 97-81059 International Standard Book Number 0-309-05931-3 Additional copies of this report are available from: National Academy Press 2101 Constitution Ave., NW Box 285 Washington, DC 20055 800-624-6242 202-334-3313 (in the Washington Metropolitan Area) http://www.nap.edu Copyright 1997 by the National Academy of Sciences. All rights reserved. Printed in the United States of America

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Evaluating Human Genetic Diversity COMMITTEE ON HUMAN GENOME DIVERSITY WILLIAM J. SCHULL (Chair) University of Texas Health Center, Houston, TX GEORGE J. ANNAS, Boston University Schools of Medicine and Public Health, Boston, MA NORMAN ARNHEIM, University of Southern California, Los Angeles, CA JOHN BLANGERO, Southwest Foundation for Biomedical Research, San Antonio, TX ARAVINDA CHAKRAVARTI, Case Western Reserve University, Cleveland, OH VIRGINIA R. DOMINGUEZ, University of Iowa, Iowa City, IA GEORGIA DUNSTON, Howard University, Washington, DC WARD H. GOODENOUGH, University of Pennsylvania, Philadelphia, PA RICHARD R. HUDSON, University of California, Irvine, CA ERIC JUENGST, Case Western Reserve University, Cleveland, OH MICHAEL M. KABACK, University of California, San Diego, CA DANIEL R. MASYS, University of California, San Diego, CA KATHRYN MOSELEY, Henry Ford Hospital, Detroit, MI ROBERT SOKAL, State University of New York, Stony Brook, NY ALAN R. TEMPLETON, Washington University, St. Louis, MO LAP-CHEE TSUI, The Hospital for Sick Children, Toronto, ON, Canada GEORGE C. WILLIAMS, State University of New York, Stony Brook, NY NRC Staff TANIA WILLIAMS, Study Director ERIC A. FISCHER, Study Director (through December 1996) NORMAN GROSSBLATT, Editor ERIKA SCHUGART, Research Assistant KATHLEEN BEIL, Project Assistant PAULETTE A. ADAMS, Senior Project Assistant (through August 1996)

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Evaluating Human Genetic Diversity BOARD ON BIOLOGY MICHAEL T. CLEGG (Chair) University of California, Riverside, CA JOHN C. AVISE, University of Georgia, Athens, GA DAVID EISENBERG, University of California, Los Angeles, CA GERALD D. FISCHBACH, Harvard Medical School, Cambridge, MA DAVID J. GALAS, Darwin Molecular Corporation, Bothell, WA DAVID GOEDDEL, Tularik, Incorporated, South San Francisco, CA ARTURO GOMEZ-POMPA, University of California, Riverside, CA COREY S. GOODMAN, University of California, Berkeley, CA BRUCE R. LEVIN, Emory University, Atlanta, GA OLGA F. LINARES, Smithsonian Tropical Research Institute, Panama ELLIOTT M. MEYEROWITZ, California Institute of Technology, Pasadena, CA ROBERT T. PAINE, University of Washington, Seattle, WA COREY S. GOODMAN, University of California, Berkeley, CA RONALD R. SEDEROFF, North Carolina State University, Raleigh, NC DANIEL SIMBERLOFF, Florida State University, Tallahassee, FL ROBERT R. SOKAL, State University of New York, Stony Brook, NY SHIRLEY TILGHMAN, Princeton University, Princeton, NJ RAYMOND L. WHITE, University of Utah, Salt Lake City, UT Staff PAUL GILMAN, Acting Director ERIC A. FISCHER, Director (through December 1996) TANIA WILLIAMS, Program Officer KATHLEEN BEIL, Administrative Assistant ERIKA SHUGART, Research Assistant

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Evaluating Human Genetic Diversity COMMISSION ON LIFE SCIENCES THOMAS D. POLLARD (Chair) The Salk Institute for Biological Studies, La Jolla, CA FREDERICK R. ANDERSON, Cadwalader, Wickersham & Taft, Washington, DC JOHN C. BAILAR, III, University of Chicago, IL PAUL BERG, Stanford University, Stanford, CA JOANNA BURGER, Rutgers University, Piscataway, NJ SHARON L. DUNWOODY, University of Wisconsin, Madison, WI JOHN L. EMMERSON, Indianapolis, IA NEAL L. FIRST, University of Wisconsin, Madison, WI URSULA W. GOODENOUGH, Washington University, St. Louis, MO HENRY W. HEIKKINEN, University of Northern Colorado, Greeley, CO HANS J. KENDE, Michigan State University, East Lansing, MI CYNTHIA J. KENYON, University of California, San Francisco, CA DAVID M. LIVINGSTON, Dana-Farber Cancer Institute, Washington, DC DONALD R. MATTISON, University of Pittsburgh, Pittsburgh, PA JOSEPH E. MURRAY, Wellesley Hills, MA EDWARD E. PENHOET, Chiron Corporation, Emeryville, CA MALCOLM C. PIKE, Norris/USC Comprehensive Cancer Center, Los Angeles, CA JONATHAN M. SAMET, The Johns Hopkins University, Baltimore, MD CHARLES F. STEVENS, The Salk Institute for Biological Studies, La Jolla, CA JOHN L. VANDEBERG, Southwest Foundation for Biomedical Research, San Antonio, TX Staff PAUL GILMAN, Executive Director SOLVEIG PADILLA, Administrative Assistant

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Evaluating Human Genetic Diversity 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. Bruce Alberts 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. William Wulf 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 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. Kenneth I. Shine 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 National 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. Bruce Alberts and Dr. William A. Wulf are chairman and vice chairman, respectively, of the National Research Council.

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Evaluating Human Genetic Diversity Preface Over the last three-fourths of this century or so, an enormous body of data has accumulated on the extent of genetic variation among human beings, but most of this information has arisen opportunistically, having been driven by individual investigator initiatives and collected under widely varied conditions. Moreover, the information and samples that have been collected are dispersed in laboratories around the world, and access to them is often difficult. Therefore, it has proved difficult to compare results from different studies, and this difficulty has narrowed the value of the information and samples for the study of many problems of current evolutionary and biologic interest. To remedy those shortcomings, support has been growing in the international scientific community for a worldwide, geographically comprehensive survey of variation in the human genome. The Committee on Human Genome Diversity, in the Board on Biology of the National Research Council's Commission on Life Sciences, came into being as a result of a request from the National Science Foundation and the National Institutes of Health for the Research Council to assess the scientific value, technical aspects, and organizational requirements of a systematic worldwide survey of human genetic variability and the ethical, legal, and social issues that would be raised by it before the commitment of substantial funds to any survey. The committee was organized in early 1996 and was structured to include members with expertise in all the major fields relevant to the project: population, human, and molecular genetics; evolutionary biology; anthropology (cultural and biologic); biostatistics; informatics; ethics; and law. In its fact-finding, it became apparent to the committee that the precise

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Evaluating Human Genetic Diversity nature of the proposed survey was more elusive than the committee had envisioned; different participants in the formulation of its consensus document had quite different perceptions of the intent of the project and even of its organizational structure. The committee reviewed the consensus document for the proposed Human Genome Diversity Project (HGDP) and was briefed by persons involved in formulating it. The committee found that there was no sharply defined proposal that it could evaluate; as a result, it chose to look at the issues posed by such a global survey of human genetic variation more broadly. The committee held 4 meetings; at 3, members of the public and persons acting on the public's behalf were invited to discuss the issues with the committee, whereas the fourth was devoted entirely to the writing of this report. To elicit as wide a spectrum of opinions on the merits of the proposed survey as practical, the committee circulated a questionnaire encouraging those who could not attend the public sessions to submit their opinions in writing. Their comments were tabulated and taken into account in the committee's deliberations and this report. The committee gratefully acknowledges the support of staff of the National Research Council. Eric Fischer and Tania Williams helped to refine the report and contributed to the preparation and administrative work of the project; Norman Grossblatt edited the manuscript; and invaluable support was provided by Kathleen Beil, Erika Shugart, and Paulette Adams.

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Evaluating Human Genetic Diversity Contents     EXECUTIVE SUMMARY   1     Sampling Issues   2     Sample Collection and Data Management   5     Human Rights Considerations   6     Organization and Management   8 1   INTRODUCTION AND BACKGROUND   10     The Committee, Its Charge, and Its Activities   11     The Proposed Human Genome Diversity Project   12     This Report   14 2   SCIENTIFIC AND MEDICAL VALUE OF RESEARCH ON HUMAN GENETIC VARIATION   16     Human History and Evolution   17     Basic Mechanisms of Genome Evolution   19     Biomedical Applications   20     Conclusion   22 3   SAMPLING ISSUES   23     Basic Sampling Strategies   24     Strategies That Are Not Population Based   25     Strategies That Are Population Based   25     Which Sampling Strategy Should Be Used?   30     How to Select Which Human Populations to Sample   32

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Evaluating Human Genetic Diversity     Considerations in Choosing Subject Populations   32     Number of Populations to Sample, and Number of People to Sample in a Population   33     Summary and Conclusions   35 4   SAMPLE COLLECTION AND DATA MANAGEMENT   36     Sources of DNA to Be Sampled   36     Characterization of Genetic Variation   39     Classes of DNA Markers   40     DNA Polymorphisms Based on Single Nucleotide Substitutions   42     Should There Be a Core Set of DNA Markers That Will Be Scored for All Samples in the Repository?   43     Research-Materials Management   44     Data Management   47     Functional Requirements for Human Genetic Variation Data   49     Data Acquisition Methods   50     Quality Control and Annotation   50     Communication Via Public Networks   51     Archival Storage   51     Distribution and Access   52     Security Issues Related to Human Genetic Variation Data   52     Summary and Conclusions   53 5   HUMAN RIGHTS AND HUMAN GENETIC-VARIATION RESEARCH   55     Context of Concerns About Studying Human Genetic Variation   56     Ethical Considerations in the Design of Human Genetic-Variation Research   58     Control   65     Commercialization and Reciprocity Agreements   66     Conclusion   68 6   ORGANIZATIONAL AND OTHER ISSUES   69     REFERENCES   74 APPENDIX A:   Committee on Human Genome Diversity: Biographical Information   81 APPENDIX B:   Acknowledgments   89