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  1. 1. Molecular Diagnostics For the Clinical Laboratorian Edited by William B. Coleman Gregory J. Tsongalis Molecular Diagnostics For the Clinical Laboratorian SECOND EDITION Edited by William B. Coleman Gregory J. Tsongalis SECOND EDITION
  3. 3. MOLECULAR DIAGNOSTICS Edited by WILLIAM B. COLEMAN Department of Pathology and Laboratory Medicine University of North Carolina School of Medicine Chapel Hill, NC and GREGORY J. TSONGALIS Department of Pathology Dartmouth Medical School Dartmouth-Hitchcock Medical Center Lebanon, NH Foreword by LAWRENCE M. SILVERMAN Department of Pathology and Laboratory Medicine University of Virginia Charlottesville, VA For the Clinical Laboratorian Second Edition
  4. 4. © 2006 Humana Press Inc. 999 Riverview Drive, Suite 208 Totowa, New Jersey 07512 humanapress.com For additional copies, pricing for bulk purchases, and/or information about other Humana titles, contact Humana at the above address or at any of the following numbers: Tel.: 973-256-1699; Fax: 973-256-8341; E-mail:orders@humanapr.com; Website: http://humanapress.com All rights reserved. No part of this book may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, microfilming, recording, or otherwise without written permission from the Publisher. All articles, comments, opinions, conclusions, or recommendations are those of the author(s), and do not necessarily reflect the views of the publisher. Due diligence has been taken by the publishers, editors, and authors of this book to assure the accuracy of the information published and to describe generally accepted practices. The contributors herein have carefully checked to ensure that the drug selections and dosages set forth in this text are accurate and in accord with the standards accepted at the time of publication. Notwithstanding, as new research, changes in govern- ment regulations, and knowledge from clinical experience relating to drug therapy and drug reactions constantly occurs, the reader is advised to check the product information provided by the manufacturer of each drug for any change in dosages or for additional warnings and contraindi- cations. This is of utmost importance when the recommended drug herein is a new or infrequently used drug. It is the responsibility of the treating physician to determine dosages and treatment strategies for individual patients. Further it is the responsibility of the health care pro- vider to ascertain the Food and Drug Administration status of each drug or device used in their clinical practice. The publisher, editors, and authors are not responsible for errors or omissions or for any consequences from the application of the information presented in this book and make no warranty, express or implied, with respect to the contents in this publication. Cover illustrations: Background—Figure 4 from Chapter 15. Foreground—Figure 6B from Chapter 2; Figure 5B from Chapter 13; Figure 1 from Chapter 22; and Figure 3A,B from Chapter 32. Cover design by Patricia F. Cleary This publication is printed on acid-free paper. ∞ ANSI Z39.48-1984 (American National Standards Institute) Permanence of Paper for Printed Library Materials. Photocopy Authorization Policy: Authorization to photocopy items for internal or personal use, or the internal or personal use of specific clients, is granted by Humana Press Inc., provided that the base fee of US $30.00 per copy is paid directly to the Copyright Clearance Center at 222 Rosewood Drive, Danvers, MA 01923. For those organizations that have been granted a photocopy license from the CCC, a separate system of payment has been arranged and is acceptable to Humana Press Inc. The fee code for users of the Transactional Reporting Service is: [1-58829-356-4/06 $30.00]. Printed in the United States of America. 10 9 8 7 6 5 4 3 2 1 Library of Congress Cataloging-in-Publication Data Molecular diagnostics : for the clinical laboratorian / edited by William B. Coleman and Gregory J. Tsongalis.— 2nd ed. p. cm. Previously published in 1997. Includes bibliographical references and index. ISBN 1-58829-356-4 (alk. paper) eISBN 1-59259-928-1 1. Molecular diagnosis. 2. Pathology, Molecular. I. Coleman, William B. II. Tsongalis, Gregory J. RB43.7.M6338 2004 616.07’56—dc22 2004023555
  5. 5. DEDICATION First and foremost, we would like to dedicate this book to our wives, Monty and Nancy, for their unprecedented support of our careers and families. To all of our colleagues, students, trainees, and mentors over the many years, we thank you for your continued support.
  6. 6. FOREWORD In 1994 I coedited a book, Molecular Pathology: Ap- proaches to Diagnosing Human Disease in the Clinical Laboratory, that coined the phrase “molecular pathology” to refer to applications of molecular biology in the tradi- tional areas of laboratory medicine. That compilation of clinical molecular techniques included 11 chapters and an epilogueon“NewDirectionsfortheClinicalLaboratory.” Chapter headings included: automation, neoplasia, heri- table diseases, and infectious diseases. Threeyearslater,in1997,BillColemanandGregTson- galis edited Molecular Diagnostics: For the Clinical Laboratorian,whichcontained18chaptersandintroduced the new areas of RT-PCR and In Situ PCR, and included a section on gene therapy. Now, ten years after the intro- duction of molecular pathology, we are looking at the second edition of Bill Coleman and Greg Tsongalis’ text. This second edition now comprises 44 chapters, and contains new chapters on bioinformatics, microarrays, methylation assays, FISH, laser capture microdissection, quality assurance, chimerism studies for bone marrow transplantation, and separate chapters on genetic counsel- ingandELSI(ethical,legal,andsocialissues). Thesenew chapters represent developments in the past decade that have fundamentally changed the scope from molecular pathology to molecular diagnostics, highlighting the changingroleoftheclinicallaboratorianswhodirectthese efforts. It should be evident that molecular pathology and diagnostics impact almost every conceivable subspecialty in laboratory medicine and, particularly in the case of pharmacogenomics, have led to the development of new areas of investigation. What is less evident is the burden placed upon the laboratorians directing these efforts. Issues regarding training, certification, continuing education, and reim- bursement (just to name a few) have demanded enormous time and effort from professional organizations and gov- ernmental agencies. In addition, because conventional approaches cannot always be applied to molecular diag- nostics, unique solutions for quality assurance and quality control must be developed. These challenges have engen- dered committees, subcommittees, taskforces, and workgroups from regulatory agencies and professional organizations, representing worldwide constituencies. As in any situation involving so many players, consensus- building and communication are mandatory. To these ends,professionaljournalsandtextbooksareourbesthope forremainingcurrentwiththisrapidlychangingfield. One needs only to compare the wealth of knowledge in this current edition with our efforts of only ten years ago to appreciate the magnitude of this challenge. Lawrence M. Silverman, PhD vii
  7. 7. It has been almost ten years since the concept for producing the first edition of Molecular Diagnostics: For the Clinical Laboratorian was conceived. In those ten years the field of molecular pathology and diagnostics has exploded as many predicted. The clinical diagnostic labo- ratory continues to function as the playing field for this expansion that includes vast and dynamic changes in test menus, instrumentation, and clinical applications. The impact of this field on the routine practice of clinical medicine and management of patients continues to be felt as new developments that span all areas of laboratory medicine exceed our expectations. The success of this technology in a clinical setting is highly dependent upon the training of well-qualified tech- nologists,residents,andcliniciansalike,whowillnotonly have to perform and interpret results of these tests but also understand the limitations of the technology and resulting clinicalimplications.Theproductionofthissecondeditionis a testament to our passion and commitment for the teaching and training of qualified individuals who wish to embark on this journey. The numerous training programs, educational venues, and board certification examinations that have evolved over the past ten years also sends a strong vow of commitment by others in the field to ensure the successful useofthesenewtoolsinsupportingthebestpossiblepatient care that is available. The second edition of Molecular Diagnostics: For the Clinical Laboratorian begins with a historical perspec- tive of laboratory medicine followed by an overview of basic molecular biology techniques and concepts. Part III provides a more in depth examination of some advanced molecular technologies and their potential uses. Part IV describes other technologies found in the clinical labora- tory that can complement or be complemented by molecu- lar diagnostic technologies. The increasing need for awareness and practice of quality assurance in this field led us to include a complete section (Part V) that examines some of these issues. Although the first edition included clinical applications all in one section, the increased num- ber of applications led us to develop separate sections for genetic disease, human cancers, infectious diseases, and identity testing (Parts VI–IX). Finally, the book concludes with a section on genetic counseling and ethical/social issues involved with nucleic acid testing. Although no such book could possibly be all encom- passing in such a rapidly developing field, we feel that the material covered herein will provide the reader with an excellent overview. William B. Coleman Gregory J. Tsongalis PREFACE ix
  8. 8. CONTENTS Dedication......................................................................................................................................v Foreword..................................................................................................................................... vii Preface ..........................................................................................................................................ix Color Plates .................................................................................................................................xv Contributors .............................................................................................................................. xvii Value Added eBook Instructions ...............................................................................................xix Part I. Introduction 1 An Historical Perspective on the Clinical Diagnostic Laboratory ........................................3 Robert E. Moore Part II. Basic Molecular Biology 2 An Overview of Nucleic Acid Chemistry, Structure, and Function: The Foundations of Molecular Biology ...............................................................................13 William B. Coleman 3 Extraction of Nucleic Acids .................................................................................................25 Paul N. Bogner and Anthony A. Killeen 4 Nucleic Acid Blotting Techniques: Theory and Practice....................................................31 Terry Amiss and Sharon Collins Presnell 5 The Polymerase Chain Reaction ..........................................................................................47 William B. Coleman and Gregory J. Tsongalis 6 Bioinformatics: Computer-Based Approaches to Genetic Analysis....................................57 Sharon L. Ricketts Part III. Molecular Diagnostic Technologies 7 PCR-Based Methods for Mutation Detection ......................................................................65 Ian M. Frayling, Emma Monk, and Rachel Butler 8 Alternative Methods for Amplified Nucleic Acid Testing ..................................................75 Deborah A. Payne and Laurie E. Sower 9 Electrophoretic Methods for Mutation Detection and DNA Sequencing ...........................85 W. Edward Highsmith, Jr. xi
  9. 9. xii Contents 10 Single-Nucleotide Polymorphisms: Testing DNA Variation for Disease Association .....111 Ulrich Broeckel and Martin J. Hessner 11 Microarray Approaches to Gene Expression Analysis ......................................................121 David Neil Hayes and Matthew Meyerson 12 Methods for Analysis of DNA Methylation.......................................................................149 Alexander Dobrovric Part IV. Other Clinical Diagnostic Technologies 13 Flow Cytometry ..................................................................................................................163 Joseph A. DiGiuseppe 14 Medical Cytogenetics .........................................................................................................173 Martha B. Keagle 15 Fluorescence In Situ Hybridization: A Major Milestone in Luminous Cytogenetics........189 Suneel D. Mundle and Robert J. Koska 16 Immunohistochemistry .......................................................................................................203 John Hunt, Larissa Davydova, Richard W. Cartun, and Maria Baiulescu 17 Laser Capture Microdissection ...........................................................................................219 C. Robert Bagnell, Jr. Part V. Quality Assurance in the Molecular Diagnostics Laboratory 18 Framework for Quality Assurance in Molecular Diagnostics ...........................................227 Marlene Sabbath-Solitare, Selwyn J. Baptist, and Teresita Cuyegkeng Redondo 19 Verification of Molecular Assays.......................................................................................237 Brent L. Seaton 20 Standards and Standardization of Molecular Diagnostics .................................................243 John P. Jakupciak and Catherine D. O’Connell 21 Laboratory-Developed Tests in Molecular Diagnostics ....................................................247 Andrea Ferreira-Gonzalez and Carleton T. Garrett Part VI. Applications of Molecular Diagnostics for Genetic Diseases 22 An Overview of Molecular Genetics..................................................................................259 Elaine Weidenhammer and Gregory J. Tsongalis 23 Genetic Basis of Neurologic and Neuromuscular Diseases ..............................................267 Narasimhan Nagan, Christopher J. Klein, D. Brian Dawson, Myra J. Wick, and Stephen N. Thibodeau
  10. 10. Contents xiii 24 Molecular Mechanisms of Endocrine Disorders................................................................281 Amy Potter and John A. Phillips III 25 Molecular Pathogenesis of Cardiovascular Disease ..........................................................295 Alan H. B. Wu 26 Molecular Diagnostics in Coagulation ...............................................................................311 Enrique Ballesteros 27 Cystic Fibrosis ....................................................................................................................321 Eugene H. Lewis III, Myra J. Lewis, Jean A. Amos, and Gregory J. Tsongalis 28 Prenatal Genotyping for Identification of Fetuses at Risk for Immune Cytopenic Disorders .......................................................................................329 Martin J. Hessner and Brian R. Curtis 29 Personalized Medicine ........................................................................................................341 Karen McCullough Part VII. Applications of Molecular Diagnostics for Human Cancers 30 Molecular Pathogenesis of Human Cancer ........................................................................349 William B. Coleman and Gregory J. Tsongalis 31 Application of Molecular Diagnostics to Hereditary Nonpolyposis Colorectal Cancer ...............................................................................................................375 Ian M. Frayling, Lisa Happerfield, Christopher Mattocks, Kim Oakhill, and Mark J. Arends 32 Molecular Genetic Applications to the Diagnosis of Lymphoma .....................................393 William N. Rezuke, Jr. and Gregory J. Tsongalis 33 Molecular Genetic Abnormalities in Acute and Chronic Leukemias ...............................415 Pei Lin and L. Jeffrey Medeiros Part VIII. Applications of Molecular Diagnostics for Infectious Diseases 34 Molecular Testing for Chlamydia trachomatis and Neisseria gonorrhoeae ....................437 Alexandra Valsamakis 35 Human Papillomavirus .......................................................................................................447 Theresa M. Voytek and Gregory J. Tsongalis 36 Molecular Diagnosis for HIV-1..........................................................................................453 Angela M. Caliendo and Charles E. Hill 37 Hepatitis C...........................................................................................................................461 D. Robert Dufour
  11. 11. 38 Cytomegalovirus .................................................................................................................473 Angela M. Caliendo and Nell S. Lurain Part IX. Applications of Molecular Diagnostics for Identity-Based Testing 39 HLA Typing Using Molecular Methods ............................................................................485 John L. Schmitz 40 Molecular Analysis for Forensic Casework and Parentage Testing..................................495 Tracey Dawson Cruz 41 Molecular Assessment of Bone Marrow Transplant Engraftment .................................... 511 Jessica K. Booker 42 The Use of DNA-Based Identity Testing for Specimen Identification .............................517 Andrew Ricci Jr. and Gregory J. Tsongalis Part X. Issues for the Clinical Molecular Pathology Laboratory 43 Genetic Counseling Considerations in Molecular Diagnosis ............................................525 Myra I. Roche 44 Ethical, Social, and Legal Issues Related to Molecular Genetic Testing..........................545 Jennifer L. Herbst and Jon F. Merz Index ..........................................................................................................................................555 xiv Contents
  12. 12. COLOR PLATES COLOR PLATE 1: Fig. 1 (Ch. 11, p. 124). cDNA microarray manufacturing process. COLOR PLATE 2: Fig. 2 (Ch. 11, p. 125). Example of cDNA microarray image file. COLOR PLATE 3: Fig. 11 (Ch. 11, p. 138). Dendrogram. COLOR PLATE 4: Fig. 1 (Ch. 15, p. 191). In situ hybridization for detection of mRNA. COLOR PLATE 5: Fig. 2 (Ch. 15, p. 194). Different types of DNA FISH probes. COLOR PLATE 6: Fig.3(Ch.15,p.196).M-FISHanalysisofametaphaseobtainedfromthebonemarrowofMDSpatient. COLOR PLATE 7: Fig. 4 (Ch. 15, p. 197). Tyramide amplification of FISH signals. COLOR PLATE 8: Fig. 1 (Ch. 31, pp. 379–380). Examples of DNA mismatch repair immunohistochemistry. COLOR PLATE 9: Fig. 3 (Ch. 31, p. 383). Examples of microsatellite instability. COLOR PLATE 10: Fig. 4 (Ch. 31, p. 385). Comparative sequence analysis. COLOR PLATE 11: Fig. 15 (Ch. 32, p. 404). FISH analysis utilizing a dual-color translocation probe system. xv
  13. 13. Color Plate 1, Fig. 1. (See full caption and discussion in Ch. 11, p. 124). cDNA microarray manufacturing process. Color Plate 2, Fig. 2. (See full caption and discussion in Ch. 11, p. 125). Example of cDNA microarray image file. Magnified view showing approx 10% of the “spots” from a selected cDNA microarray. Color Plate 3, Fig. 11. (See full caption and discussion in Ch. 11, p. 138). Dendrogram. Color Plate 4, Fig. 1. (See full caption and discussion in Ch. 15, p. 191). In situ hybridization for detection of mRNA. Color Plate 5, Fig. 2. (See full caption and discussion in Ch. 15, p. 194). Different types of DNA FISH probe.
  14. 14. Color Plate 6, Fig. 3. (See full caption and discussion in Ch. 15, p. 196). M-FISH analysis of a metaphase obtained from a bone mar- row of MDS patient. Color Plate 7, Fig. 4. (See full caption and discussion in Ch. 15, p. 197). Tyramide amplification of FISH signals. Color Plate 8, Fig. 1. (See full caption and discussion in Ch. 31, p. 379). Examples of DNA mismatch repair immunohistochemistry.
  15. 15. Color Plate 8, Fig. 1. (Continued)
  16. 16. Color Plate 9, Fig. 3. (See full caption and discussion in Ch. 31, p. 383). Examples of microsatellite instability. Color Plate 10, Fig. 4. (See full caption and discussion in Ch. 31, p. 385). Comparative sequence analysis. Color Plate 11, Fig. 15. (See full caption and discussion in Ch. 32, p. 404). FISH analysis utilizing a dual-color translocation probe system.
  17. 17. CONTRIBUTORS TERRY AMISS, PhD • BD Technologies/Biosensors, Research Triangle Park, NC JEAN A. AMOS, PhD • Scientific Director, Molecular Genetics, Specialty Laboratorie, Inc., Santa Monica, CA MARK J. ARENDS, MA, MB ChB(Hons), BSc(Hons), PhD, FRCPath • Department of Pathology, Addenbrooke’s Hospital, University of Cambridge, Cambridge, UK C. ROBERT BAGNELL, JR., PhD • Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, NC MARIA BAIULESCU, MD • Department of Pathology and Laboratory Medicine, Charlotte-Hungerford Hospital, Torrington, CT ENRIQUE BALLESTEROS, MD • Department of Pathology and Laboratory Medicine, Hartford Hospital, Hartford, CT SELWYN J. BAPTIST, MD • Department of Pathology, Saint Barnabas Medical Center, Livingston, NJ PAUL N. BOGNER, MD • Department of Pathology, University of Michigan, Ann Arbor, MI JESSICA BOOKER, PhD, FACMG • Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, NC ULRICH BROECKEL, MD • Department of Medicine and Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI RACHEL BUTLER, BSc(Hons), MRCPath • Molecular Genetics Laboratory, Institute of Medical Genetics, Cardiff, UK ANGELA M. CALIENDO, MD, PhD • Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA RICHARD W. CARTUN, PhD • Department of Pathology and Laboratory Medicine, Hartford Hospital, Hartford, CT WILLIAM B. COLEMAN, PhD • Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, NC TRACEY DAWSON CRUZ, PhD • Forensic Science Program & Department of Biology, Virginia Commonwealth University, Richmond, VA BRIAN R. CURTIS, MS, MT (ASCP)SBB • Platelet and Neutrophil Laboratory, The Blood Center of Southeastern Wisconsin, Milwaukee, WI D. BRIAN DAWSON, PhD • Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN xvii LARISSA DAVYDOVA, MD • Department of Pathology and Laboratory Medicine, Hartford Hospital, Hartford, CT JOSEPH A. DIGIUSEPPE, MD, PhD • Director, Special Hematology Laboratory, Acting Director, Molecular Pathology Laboratory, Department of Pathology and Laboratory Medicine, Hartford Hospital, Hartford, CT ALEXANDER DOBROVIC, PhD • Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Australia D. ROBERT DUFOUR, MD • Pathology and Laboratory Medicine Service, Veterans Affairs Medical Center, Washington, DC ANDREA FERREIRA-GONZALEZ, PhD • Department of Pathology, Virginia Commonwealth University, Richmond, VA IAN M. FRAYLING, MA, MB, BChir, PhD, MRCPath • Clinical Genetics Laboratory, Institute of Medical Genetics, University Hospital of Wales, Cardiff, UK CARLETON T. GARRETT, MD, PhD • Department of Pathology, Virginia Commonwealth University, Richmond, VA LISA HAPPERFIELD, FIBMS, MSc • Department of Histopathology, Addenbrooke’s Hospital, Cambridge, UK DAVID NEIL HAYES, MD, MPH • Division of Hematology/ Oncology, Department of Internal Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC JENNIFER L. HERBST, JD, M.Bioethics • Montgomery, McCracken, Walker & Rhoads, LLC, Philadelphia, PA MARTIN J. HESSNER, PhD • Department of Pediatrics and Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI W. EDWARD HIGHSMITH, JR., PhD • Division of Laboratory Genetics, Department of Laboratory Medicine Pathology, Mayo Clinic, Rochester, MN CHARLES E. HILL, MD, PhD • Department of Pathology and Laboratory Medicine, Emory University Hospital, Atlanta, GA JOHN HUNT, MD • Department of Pathology, Baystate Medical Center, Springfield, MA JOHN P. JAKUPCIAK, PhD • DNA Technologies Group, Biotechnology Division, National Institute of Standards and Technology, Gaithersburg, MD
  18. 18. MARTHA B. KEAGLE, MEd, CLSp(CG) • Diagnostic Cytogenetic Sciences, School of Allied Health, University of Connecticut, Storrs, CT ANTHONY A. KILLEEN, MD, PhD • Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN CHRISTOPHER J. KLEIN, MD • Department of Neurology, Mayo Clinic, Rochester, MN ROBERT J. KOSKA, BSMT (ASCP), MBA • Cepheid, Sunnyvale, CA EUGENE H. LEWIS III, DO • Department of Pathology and Laboratory Medicine, Hartford Hospital, Hartford, CT MYRA J. LEWIS, DO • Department of Pathology and Laboratory Medicine, Hartford Hospital, Hartford, CT PEI LIN, MD • Department of Hematopathology, University of Texas M.D. Anderson Cancer Center, Houston, TX NELL S. LURAIN, PhD • Department of Immunology/ Microbiology, Rush-Presbyterian-St. Luke’s Medical Center, Chicago, IL CHRISTOPHER MATTOCKS, BSc(Hons) • National Genetics Reference Laboratory, Salisbury District Hospital, Salisbury, UK KAREN MCCULLOUGH, PhD • Vanda Pharmaceuticals, Rockville, MD L. JEFFREY MEDEIROS, MD • Department of Hematopathology, University of Texas M.D. Anderson Cancer Center, Houston, TX JON F. MERZ • Center for Bioethics, and Center for Clinical Epidemiology and Biostatistics, Department of Medical Ethics, University of Pennsylvania School of Medicine, Philadelphia PA. MATTHEW MEYERSON, MD, PhD • Division of Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA EMMA MONK, BSc • East Anglian Regional Genetics Service, Molecular Genetics Laboratory, Addenbrooke’s Hospital, Cambridge, UK ROBERT E. MOORE, PhD • Department of Pathology and Laboratory Medicine, Hartford Hospital, Hartford, CT SUNEEL D. MUNDLE, PhD • Rush Cancer Institute, Chicago, IL; Technical Services Manager, Vysis Inc., Downers Grove, IL NARASIMHAN NAGAN, PhD • Laboratory Director, Athena Diagnostics, Worcester, MA KIM OAKHILL, BSc(Hons), DipRCP • East Anglian Regional Genetics Service, Molecular Genetics Laboratory, Addenbrooke’s Hospital, Cambridge, UK CATHERINE D. O’CONNELL, PhD • Tetracore Inc., Gaithersburg, MD DEBORAH A. PAYNE, PhD, CLSp(MB), CLSDir(NCA) • Department of Pathology and Otolaryngology, Division of Molecular Diagnostics, The University of Texas Medical Branch, Galveston, TX JOHN A. PHILLIPS III, MD • Division of Medical Genetics, Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN AMY POTTER, MD • Division of Endocrinology and Metabolism, Departments of Pediatrics and Medicine, Vanderbilt University School of Medicine, Nashville, TN SHARON COLLINS PRESNELL, PhD • BD Technologies/ Biotherapy, Research Triangle Park, NC TERESITA CUYEGKENG REDONDO, MD • Department of Pathology, Saint Barnabas Medical Center, Livingston, NJ WILLIAM N. REZUKE JR., MD • Department of Pathology and Laboratory Medicine, Hartford Hospital, Hartford, CT ANDREW RICCI JR., MD • Department of Pathology and Laboratory Medicine, Hartford Hospital, Hartford, CT SHARON L. RICKETTS • Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, NC MYRA I. ROCHE, MS, CGC • Department of Pediatrics, University of North Carolina School of Medicine, Chapel Hill, NC MARLENE SABBATH-SOLITARE, PhD • Department of Pathology, Saint Barnabas Medical Center, Livingston, NJ JOHN L. SCHMITZ, PhD • Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, NC BRENT L. SEATON, PhD • Focus Technologies Inc., Cypress, CA LAWRENCE M. SILVERMAN, PhD • Department of Pathology and Laboratory Medicine, University of Virginia, Charlottesville VA LAURIE E. SOWER, PhD • Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX STEPHEN N. THIBODEAU, PhD • Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN GREGORY J. TSONGALIS, PhD • Department of Pathology, Dartmouth Medical School, Dartmouth-Hitchcock Medical Center, Lebanon, NH ALEXANDRA VALSAMAKIS, MD, PhD • Department of Pathology, Division of Microbiology, Johns Hopkins University School of Medicine, Baltimore, MD THERESA M. VOYTEK, MD • Department of Pathology and Laboratory Medicine, Hartford Hospital, Hartford, CT ELAINE WEIDENHAMMER, PhD • Senior Manager, Strategic Development, Nanogen, San Diego, CA MYRA J. WICK, PhD • Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN ALAN H. B. WU, PhD • Department of Laboratory Medicine, University of California, San Francisco, CA Contributors xviii
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  21. 21. 1. INTRODUCTION As the clinical diagnostic laboratory has entered the 21st century, it is interesting to reflect on past scientific and social events that have influenced the status of the laboratory and to anticipate future problems and opportunities. It would be a mis- take to suggest that all of the significant medical and social events that had an impact on the present laboratory function can be discussed or evaluated in a short introductory chapter. It is also possible to mistakenly attribute more influence to some events than they deserve simply because they are being inter- preted with a 21st century bias. However, some threads of com- monality have influenced the evolution of diagnostic laboratories from earliest times. It is the objective of this chap- ter to highlight events that, in my opinion, have shaped how and/or why clinical laboratories have arrived at their present position in the practice of medicine. A history of diagnostic testing can be started by reviewing the evolution of diagnostic tests from isolated procedures to organized diagnostic laboratory testing. Originally, laboratory tests were performed at the side of the patient with small, sim- ple equipment, rapid evaluation of the result, and a diagnostic opinion rendered. Test choice, performance, and interpretation were all left to the individual practitioner. There was no profes- sional support staff to assist at any point in the process. Little exchange took place between practitioners because the individ- ual’s success was directly related to which procedures were done and the manner in which they were done. A premium was paid for showmanship as well as successful treatments. The modern laboratory is a physical place, either standing alone or as a component of a health care institution, with numerous pieces of complicated capital equipment, where hun- dreds and sometimes thousands of specimens per day are processed for dozens of tests. Usually, the laboratory accepts a teaching and a research responsibility to accompany this patient service obligation. Today’s laboratories are staffed by professionals trained in several subspecialties, who are avail- able for consultation in all aspects of diagnostic testing. This structure underlines the current complexity and sophistication From: Molecular Diagnostics: For the Clinical Laboratorian, Second Edition Edited by: W. B. Coleman and G. J. Tsongalis © Humana Press Inc., Totowa, NJ 1 An Historical Perspective on the Clinical Diagnostic Laboratory ROBERT E. MOORE 3 of the modern laboratory operation. There are a myriad of pro- fessional organizations, meetings, and publications that have developed to make information exchange convenient and effi- cient. This exchange is also necessary to ensure a single level of care. The system that supported showmanship and theatrics has been replaced by one that only tolerates scientifically based medical practices. Today’s laboratory is in a state of flux—faced with issues of near-patient testing, outreach programs, utilization, extensive regulation, and stringent fiscal controls. The first three of these issues are reminiscent of the early beginnings of diagnostic testing. The laboratory organization has replaced the individual practitioner, but testing is moving back toward the patient in the form of near-patient testing or outreach programs. In the past, a few individuals spoke about appropriate use of diagnostic testing, whereas, today, committees and organizations are ded- icated to the control of laboratory utilization—an ontogeny recapitulating phylogeny phenomenon. A review of history gives some insight into relationships and similarities of past activity with current practice. What are perceived as new prob- lems and opportunities can be traced to antiquity. The development of the modern laboratory required several conditions to be met at appropriate times in history. Obviously, technology was and is the primary force behind advances in med- icine. This has been both a blessing and a curse. It is a blessing because the understanding and treatment of disease requires sophisticated tools that only technological advances can produce. It can be a curse because there is a direct relationship between sophistication and health care cost. Other social issues dealing with availability and ethics assume a much greater importance than in the past.Angiography, computer-aided tomography (CAT) scans, organ transplantation, and DNA analysis are just a few of the expensive but valuable technologies available to the modern physician. Such questions as when are they used, to whom are they available, and what is done with the result are dilemmas of the 21st-century laboratory. Another result of current technology is that it removes a large number of tests and procedures from the primary physician. The expertise required to perform these and other
  22. 22. procedures combined with the significant cost of the equipment precludes the primary physician from being the laboratorian. A second condition that had to be met was logistics. Laboratory testing had to be convenient. All the concerns of collection, preservation, testing, and reporting had to be easy and fast for both patient and physician. A practical consequence of this was the proliferation of laboratories with increased resources to deliver the service. In the beginning, these resources were human and consisted of having specimens transported to the primary laboratory site. This later became multiple collection sites, courier services, mechanical process- ing, and electronic reporting. These logistical issues led directly to a third condition for laboratory development: economics. There are two components to economic considerations. First, the laboratory service has to be an economically viable option for the ordering physician. The service must be delivered in a way so the physician does not experience any cost or significant loss of income from referring tests to a diagnostic laboratory. Second, there must be a mechanism to support the cost of laboratory testing. The lat- ter problem was solved, for a short time, by the third-party reimbursement system. As one of the social reform programs of the 20th century, the widespread availability of insurance made the cost of health services invisible to the patient. Without proper controls, the effect of this reimbursement system was to encourage the proliferation of technology and make services accessible to large segments of the population. The incentive was for every testing center to have all the best technology and make it available to everyone. This chapter will highlight some historical events and prac- tices that demonstrate how this evolution took place. The events outlined here are not absolute in defining the practice of labo- ratory medicine, but they suggest how concepts could evolve and develop into the practice of diagnostic laboratory testing as it is today, including some events that could be precursors of molecular diagnostics. 2. EARLIEST MEDICINE Long before there were laboratories, there were accepted practices for patient evaluation. Early health care providers (not all were physicians) attempted to determine the health status of the person under evaluation by any means possible. The diagno- sis and the prescribed treatment were not always an accurate or scientifically based pronouncement. The process was motivated by a combination of altruism, vanity, greed, scientific thought, and philosophical and religious edict. This is not meant to imply that all was quackery and incantation. The procedures that had medical value are the ones that laid the foundation for legitimiz- ing diagnostic medicine along with its subsequent support func- tions, one of which is the clinical laboratory. One major obstacle that physicians faced in ancient times was that it was illegal to practice invasive procedures. The patient could be observed and touched, but the only specimens that could be taken were those that naturally passed from the body. Because of these limitations, urine has been the sample with the longest history of evaluation. There is some evidence that the Sumerians and Babylonians used urine for diagnosis as early as 4000 BCE (1). The diagnosis of pregnancy was probably made by 4 SECTION I / INTRODUCTION ancient Egyptians using the urine of the woman to germinate seeds (1). Hindu medicine describes the sweet taste of urine and that black ants are attracted to this urine if it is poured on the ground (2). Hippocrates (460–355 BCE) described the character- istics and colors of urine from his patients and mentioned bub- bles being present in urine from patients with long-standing kidney disease (2,3). Over the next 600 years, the study of urine was advanced very little. Galen (129–200 AD) wrote and taught that urine was a filtrate of blood and, as such, could indicate the type and location of illnesses (2). The teachings of these two men were the information base for urinalysis, or uroscopy as it was called, for the next 9–10 centuries. During this time, approximately 800 AD, the first treatise on urine was written by Theophilus Protospatharius; in it is men- tioned the first chemical test done on urine. Urine collected from patients with kidney disease was heated over a candle flame and became cloudy (2). Other physicians repeated the process, some substituting acid for heat, and although it took centuries before the precipitating substance was identified as protein, the association with disease had been recognized (3). Other observations were made concerning the quality of the urine sample. The differences between morning and afternoon urine samples and factors like age, food, and medicaments exerted effects on the composition of urine. These were noted as early as the 10th century by Avacinna (2). It was realized as early as the 11th century that the first voided specimen in the morning was the best urine specimen for analysis and that when 24-h urine collections were required, they should be pro- tected from light and heat (2). Urinalysis continued to be such a focus of study that Gilles de Corbeil developed a glass vessel (called a matula), shaped like a urinary bladder, specifically for the examination of urine. The concept was that the urine sediments and discoloration would occur in the vessel at a place that corresponded to the site of pathology in the body. These early urine vessels were among the first pieces of laboratory equipment and were so common and identifiable that they were one of the predecessors to the caduceus as the symbol of medicine. Other tests and procedures were added to urinalysis and var- ious aids were developed to make the process easier. One device of this type was the urine wheel. This wheel was the original color chart similar in purpose to those that accompany most modern dipstick packages. Along with matching the urine color on the wheel, there was an interpretive text included to assist in making a diagnosis (3). Uroscopy soon took on a life of its own. Samples were sent to physicians without any explanation of the patient’s com- plaint and it was expected that the analyzing practitioner would return a diagnosis and therapy (3). Expectedly, uroscopy was ripe for abuse and, assuredly, this happened. The prominence of the practitioner was enhanced if he was perceived as being able to do more than other uroscopists. Consequently, claims were made concerning the interpretive powers of the analyst that far exceeded the limits of observation. It was during this period, when there was an opportunity to make a handsome income from urine analysis, that Joannes Actuarius began to write about the limitations of urine examination. He was one of the first to caution that urine examination, independent of how well
  23. 23. it was done, could not be used to the exclusion of all other clin- ical findings (3). It should not be inferred that uroscopy was always a ques- tionable effort. Proteinuria, although protein as such had not been identified, nephritis, type I diabetes, hematuria, infection, concentration, and limited assessment of liver disease were all recognized through urinalysis. In most cases, it took centuries to identify the specific component in urine and its association with a disease; nevertheless, urine testing was a valuable diag- nostic tool (3). These early attempts to diagnose disease, through the study of the only practical body fluid available, gives some insight into the development of laboratory medicine. First, the progres- sion from pure observation to the use of some elementary aids and procedures suggests that the seed of intellectual curiosity was germinating. If simple observation was useful, then employing procedures to define components was better. Second, equipment was being generated for a specific medical application. The equipment was primarily small, and portable but with such procedures as distillation, precipitation and evap- oration, the need for a place to do this work was becoming an issue. A permanent site or address for the practitioner to do his laboratory work enabled patients to “send” their urine for analysis (an early precursor to the outpatient laboratory). Third, because uroscopy was becoming a routine practice, some mem- bers of the legitimate medical community were discussing the appropriate use of these procedures. This might be the first sug- gestion of test utilization in history. 3. THE TRANSITION Progress requires an advance in technology or the appear- ance of a gifted individual. Science and technology had advanced to a point where a breakthrough on some other front was required. Two historic events that meet this requirement are the invention of movable type by Johann Gutenberg in the 15th century and the Reformation. Movable type and the print- ing press had the potential to make information available to large numbers of scholars. Experiments and data could be cor- roborated by other professionals, and groundless claims could become less common. Education, in all its forms, would be a benefactor. Education needs an appropriate environment. The Reformation provided that environment. The individual was acquiring more freedom in life, and the old way or restricted and regimented thought was passing. In this time of change, there were individuals of the proper education and personality to take advantage of the situation. Andreas Vesalius, who is credited as the founder of modern anatomy, was such an individual. He was the first to do exten- sive dissections and accurately document the anatomical infor- mation in text and illustration (4). The importance of this lies in the transition from animal to human dissections. Accurate anatomical data would become available and true progress in the other anatomical sciences, histology and zoology, could take place (4). Another individual of this type was Giovanni Battista Morgagni, a successor to Vesalius, who combined anatomic dissection with clinical history to describe pathologic anatomy (4). This was arguably the beginning of modern pathology. CHAPTER 1 / HISTORICAL PERSPECTIVE 5 It was during the 17th century that the science of laboratory medicine began to acquire the characteristics that are easily rec- ognized today. Laboratories were being established in homes in which research and development was being conducted (4). The results of this cottage industry were the development of equip- ment for laboratory and diagnostic use. Thermometers and hydrometers were two such pieces of equipment (4). Although the thermometer was described by Galileo in the late 1500s, it was not used for patient evaluation until the 17th century. The arguments waged as to which fluid was the best indicator of change and the best way to calibrate the instrument (4). Given these and other practical problems, some physicians were quick to realize that a quantitative measure of body temperature was an improvement over using one’s hand. For other physicians, the problems with obtaining and using the thermometer were too great. After this brief flurry of activity, the thermometer returned to a quiescent state until the 1800s. By the 1800s, many of the original problems had been either resolved or minimized, so it became a more practical matter to measure temperature.Articles appeared regarding the value of temperature in diagnosis and prognosis in major medical journals (5). The hydrometer had relatively little difficulty in its accept- ance. The instruments were made small and reliable, so they could be taken on home visits to the sick. Specific gravity was one of the well-entrenched measurements of uroscopy. A reli- able and simple instrument catered to the needs of the common practitioner. Urinalysis was still king. The home lab contributed to the refinement of equipment and methods. It should be remembered that alchemy was slowly giving way to organic chemistry, which was defined as the chemistry of living organisms (6). It was not until the syn- thesis of urea in 1828 that organic chemistry became the chem- istry of carbon compounds. Consequently, the efforts of the more inquisitive chemist-physicians turned to chemical proce- dures on body fluids (6). Paracelsus and, later, Willis suggested chemical analysis of urine (6). To separate the fluid into its component parts was thought to yield better diagnostic or prog- nostic information (6). True to history, a new hypothesis always has its detractors. Perseverance by the investigators and posi- tive, predictable results from the applications generated broader acceptance. It was an extension of this philosophy of active investigation rather than passive observation that led Robert Boyle to analyze blood. He had done chemical analysis on urine and continued this approach on human blood (5,6). Boyle had the disadvan- tage of not being a physician and so did not have the opportu- nity to analyze the blood of sick patients (5). He did have the insight to propose that knowing the results of his chemical analysis on healthy people, the evaluation of the sick would be made easier (5). Boyle was obviously an early proponent of normal reference intervals. This concept was carried further by the French physician Raymond Vieussens, who chemically analyzed the blood of large numbers of people of all descrip- tions (5). Normals, abnormals, men, women, and those of different temperaments were included in his study. These stud- ies of defined populations were exceptional in their time. Diagnostic testing had achieved a credibility that made it acceptable to perform chemical analysis on blood and urine and
  24. 24. use the information in a diagnostic workup. Laboratories were beginning to grow in number and they were developing tech- niques that could be applied to medicine. Laboratory skills were gaining respectability along with laboratory testing and laboratory data. 4. EARLY MODERN MEDICINE Chemistry as a science was developing rapidly in the 18th and early 19th centuries. Diabetes was the subject of intensive investigation by the medical chemists. Physicians like John Rollo and William Cruikshank demonstrated the presence or absence of sugar in the urine of diabetics, depending on the state of the patient’s disease (5). They were proponents of being able to monitor a patient’s status by knowing if there was sugar in the patient’s urine (5). The conventional wisdom of the time was that most of the practicing physicians were not sophisti- cated enough to do this type of analysis routinely (5). However, the concept of monitoring through repeated testing was being considered. In 1827, Richard Bright published his Reports of Medical Cases, in which he described albumin in the urine of patients with dropsy, which is the collection of serous fluid in body cav- ities or cellular tissue. Bright was aware of the anatomical lesions that were associated with this condition and he made the link between chemical findings and anatomic findings (5,7). This condition was later referred to as Bright’s disease in honor of the association made by Bright (7). This undoubtedly gave considerable credence to the analysis of specimens to diagnose disease. The test was simple: Heat the urine and observe the white precipitate that formed. The presence of kid- ney disease could be predicted by the outcome of the test. The test was not perfect, and as more people performed the test, conflicting results were obtained. Some “albuminous” material did not precipitate unless chemicals were added, and some nor- mal people had precipitates in their urine (5). These and other arguments were responsible for the slow acceptance of Bright’s albumin procedure and its use in diag- nostic medicine. However, the principle of laboratory testing and the additional insight that it gave the physician was devel- oping slowly. Progress was on the front side of a geometric curve, and by the end of the first half of the 19th century, greater utilization and faster development of laboratory diag- nostic medicine would be commonplace. A major driving force for this increased activity was the work of Gabrial Andral. Recognizing the value of chemical analysis of body fluids, he argued effectively for increased research by the medical community (5,6). He was a believer in chemical and microscopic examination of the liquid as well as the solid components of the body (5,6). His work, Pathological Hematology, examined blood chemically, microscopically, and visually in both the healthy and diseased populations (6). He measured or calculated the major components of blood and was able to demonstrate a decreased red cell mass in anemia and a decreased blood albumin in albuminuria (6). The success of Andral’s work coupled with his enthusiasm led other workers to pursue similar investigations. The studies of sugar in the blood of diabetics and uric acid in the blood of those who suf- fered from gout are prime examples of this effort (5). 6 SECTION I / INTRODUCTION The hematology specialties were benefiting from Andral’s work. The invention of counting chambers for red cell quanti- tation and their use in diagnosing anemia was discussed in medical publications (8). All the work in chemical analysis of fluids and the microscopic analysis of blood was facilitated because bloodletting was still an acceptable form of therapy. This was a Catch 22 situation. As more information was gained about diseases like anemia through these new methodologies, it became apparent that bloodletting was not appropriate therapy and this inexhaustible source of study material would become less available. The last half of the 19th century was a prolific time for the development of laboratory methods. So many methods began to appear that the practicing physician had difficulty in choos- ing which assays were reliable and which were not (8). Time and equipment were also becoming impediments to the routine use of these new tests. Physicians complained that the time required to conduct these analyses and the expertise involved in their performance exceeded their capabilities (8). The problem would get worse before it ever got better. Chemistry was becoming a tool to be used by all the medical disciplines. Dr. Paul Ehrlich used chemical dyes to test urine in the diagno- sis of typhoid fever and aniline dyes to distinguish different types of leukocytes (7,8). The study of gastric disturbances was accomplished by chemical analysis of stomach contents removed by gastric tube (8). The medical literature was replete with discussions of new methods and of the failures and shortcomings of older ones. If technological advances were the only requirement for legiti- macy, then laboratory medicine was an established discipline. However, true acceptance can only be established through aca- demic credentials. Throughout the 19th century, there was a parallel development of the academic and political status of diagnostic laboratories. Initially, medical schools did not have the status of universities and it was well into the 19th century before they became equivalent to colleges (9). Around the same time, medical chemistry was being split from chemistry, which was either general or organic chemistry (9). The latter subjects were considered to be more pure science and, therefore, more prestigious. The result was that physiological chemistry was the domain of physiology with no academic standing of its own (9). There were notable exceptions, one being the University of Tübingen, at which the first chair of physiological chemistry was established in 1845 (9). The first chairman was Julius Schlossberger, who was responsible for all the chemistry teach- ing in the medical facility (9). He was followed by Felix Hoppe-Seyler under whom the chair was transferred to the philosophical faculty (9). The chair survived until the 20th century, primarily because of the stature of the chairmen, all of whom were both organic and physiologic chemists (9). Similar aca- demic structures were not as successful at other universities. It was not until the position was established in the medical schools of the United States that physiological chemistry became secure. The first laboratory of physiological chemistry in the United States was established in 1874 at the Sheffield Scientific School of Yale University under the direction of Russell H. Chittenden (10). This was rapidly followed by similar laboratories being
  25. 25. established at other major universities. Faculty members were expected to teach and conduct research, and professional posi- tions were awarded on the academic credentials of the appli- cant (10). These facilities were a permanent part of universities and, later, medical schools. The premedical and medical train- ing of physicians included laboratory training in the biological and chemical sciences. Another development in the late 1800s was the appearance of hospitals in the United States. By midcentury, these hospi- tals were designing laboratory space for purposes of urinalysis (7). Resources were being made available for laboratory work, of which the overwhelming volume was urinalysis (7). There is some indication that urinalysis was routine in at least one pres- tigious Eastern hospital (7). At the end of the century, the hospital laboratory had been joined by the ward laboratory (8)—a smaller version of the main laboratory. The rationale was that a small lab space near patients would reduce the length of time required to get results and could be staffed by physi- cians and house staff. In practice, these two types of laboratory grew, each requiring more resources to make them operational. Two physicians added considerable credence to the concept of a professionally staffed, hospital-based laboratory. Otto Folin, at a lecture in 1908, proposed that laboratories should be hospital based and staffed by professional physiological chemists (11). William Osler judged the value of the laboratory to be indispen- sable to the clinical physician. When physicians as influential and respected as these were become proponents of laboratory testing, the position of the laboratory was permanently secured (8). With the continued acceptance of the laboratory and hospi- tals considering them to be integral to their service, a subtle change began to take place. Once the lab became established, work was generated. A review of several hospitals’ records at the beginning of the 20th century indicates that urine testing was being done on most patients even if there were no indica- tions for such a test (7). These urine tests were being refined by investigators who now had positions in the laboratory. New tests were being added for blood and other body fluids. Many of the famous names associated with clinical laboratory medi- cine such as Folin, Benedict, Garrod, Koch, Van Slyke, and Ehrlich, among others, came from this era. This was a very pro- ductive time for research and development; many of these find- ings were being transferred to the diagnostic service laboratory. Urine and diabetes have been studied for centuries in the hope of providing better care. There are records at the Pennsylvania Hospital that urine sugar measurements were used to monitor the therapy for a diabetic woman (7). The end point was a negative urine sugar finding and so urine was ana- lyzed every day. This was one of the first records of using lab tests to monitor treatment. After insulin was discovered, it became more important to monitor sugar because of the diffi- culty in controlling insulin therapy. Insulin preparations were of different purities, and external factors such as exercise and diet made insulin dosing very difficult. Blood sugar analysis was possible but difficult and so it became routine to do regu- lar urine sugar measurements (7). Methods continued to be developed and clinical applications were tested. Each test or procedure found its way into the serv- ice offerings of the clinical lab. It was apparent that at least two CHAPTER 1 / HISTORICAL PERSPECTIVE 7 problems were continuing to plague the lab. First, the volume of work was increasing and projections indicated that the trend would continue. Second, laboratory tests were difficult and tedious to do and, as a result, showed significant variability from imprecision. A partial solution to these issues came from Dr. Leonard Skeggs. His design of a continuous flow analyzer was the first practical unit for the laboratory (12). These first designs were essentially mechanical duplicators of hand proce- dures but enabled the lab to increase throughput and improve the precision of the analysis. Automation for laboratory testing has undergone several generations of change. These instru- ments are now found in all sections of the laboratory and encompass a wide spectrum of methodologies. 5. THE MOLECULAR LINE As the 21st century begins, the clinical diagnostic laboratory is entering into a new phase. Biotechnology, in all its forms, is the fastest growing discipline in the modern clinical laboratory. From the original experiments of Gregor Mendel in 1865 describing hybridization of plants, to the Human Genome Project, molecular biology is presenting the laboratory profes- sional with new challenges. These challenges are not limited to the laboratory professional and questions of science. Ethical, legal, and commercial questions are every bit as daunting as the scientific issues. Molecular biology appears to be a relatively recent disci- pline, but it is possible to point to events in the distant past that can be considered precursors of the current science. The Assyrians and Babylonians, between 5000 and 2000 BCE, rec- ognized the existence of gender in the date palm tree and under- took artificial pollination (13). It can be surmised that the purpose was to enhance those traits that were considered desir- able. Between the 6th and 4th centuries BCE, the Greeks dis- cussed inherited traits and the relative influence of inheritance versus the environment with respect to birth defects (13). Arguments were put forth as to how humans developed and what was the source of the traits that were easily recognized between parent and offspring. Progress was slow until Maupertius described the first inher- ited genetic disorder through four generations of a family in 1752 (13). Joseph Adams published on the hereditary proper- ties of disease, delayed expression of hereditary diseases, and environmental exposure as a trigger for disease (13). This was quickly followed by Schleiden and Schwann proposing that nucleated cells were the fundamental units of life and Virchow’s theory that cells could only come from the division of existing cells (13). In 1859, Darwin published “On the Origin of the Species,” a significant work that was lacking in genetic theory (13). The point in history where most people agree that molecular genetics began is 1865 when Gregor Mendel presented his work with peas to explain hereditary traits (14). As important as this work is now viewed, it must be remembered that it went essentially unrecognized for 35 years. For the remainder of the 1800s, there were many discoveries and theories of cell physi- ology and structure. Some of the current terms in molecular biology and genetics such as nucleic acid, chromosomes, and mitosis come from this era.
  26. 26. The first half of the 20th century was fueled by Mendel’s work. Traits in plants and animals were re-evaluated in light of the Mendalian ratio. Remarkable studies by remarkable scien- tists contributed a large volume of basic science to this bur- geoning discipline. Such contributions as chromosomes are paired (1902), X andY chromosomes determine gender (1905), genes are physically on chromosomes (1910), the first gene map (1913), and DNA isolated and purified (1935) were oblig- atory precursors to the Human Genome Project (13,14). There were other events during this period that have an interesting relationship with modern molecular biology. First, the stress of every first-year genetics student can be traced to 1910, at Columbia University, when T. H. Morgan determined the sex-linked character of some traits in Drosophila melanogaster. A choice of model that allowed the study of many generations in a short time span. This became important because Hermann Muller used the fruit fly model to demon- strate how ionizing radiation accelerated the formation of genetic mutations. This was important several years later to the Department of Energy. Second, X-ray crystallography studies of DNA and proteins led to the origination of the term molecular biology, the implication being that there had been a movement from the relatively gross studies of biology to a more refined study on a molecular level. Third, the concept of one gene, one enzyme was proposed by George Beadle and Edward Tatum (15). This theory unified several of the discrete pieces of infor- mation that had preceded it and also unified genetics and bio- chemistry (15). This is the first major discovery of molecular biology (15). Up until 1950, information was being gathered, unified, and converging to a point that is now called molecular biology. However, as the computer scientists say, there is another thread, one that is more closely related to the practice of current molec- ular biology. In the early part of the 20th century, Archibald Garrod published his findings about the hereditary nature of alkaptonuria (15). The significant issue here was that he was able to show this to be a metabolic or chemical disorder (15). Of the cases he studied, all were the product of a union between first-degree relatives, and Garrod was able to reason that this particular mating practice allowed a recessive character to sur- face, as predicted by a Mendelian distribution (15). This find- ing was followed a few years later by his book The Inborn Errors of Metabolism. The exact chemistry of the involved metabolic pathways would not be known for several years, but this is the first instance of laboratory work yielding a diagnosis, similar to today’s practice. A similar discovery took place in 1934. Asbjorn Folling was able to relate mental retardation to the metabolic disorder phenylketonuria (PKU), an inborn error in the metabolism of phenylalanine. The error arises because of a mutant gene in the synthesis of the enzyme phenylalanine hydroxylase (13). This represents another application of molecular biology; a genetic disease is detected very early in life and a treatment regimen can be started to prevent the disastrous sequelae. In 1949, Linus Pauling and his research group published an article in the journal Science that described sickle cell anemia as a molecular disease (15). This is the first description of a medical disease on a molecular basis and attributed to a mutant 8 SECTION I / INTRODUCTION gene. Pauling followed this with a description of the α-helix structure of proteins (14,15). This elucidation of the three- dimentional structures of proteins was a remarkable feat; yet Pauling did not discover the structure of DNA. These efforts continued in the 1950s with the establishment of the number of human chromosomes at 46 and the discovery of the chromosome abnormalities Down syndrome (trisomy 21), Turner syndrome (45,X), and Klienfelter syndrome (47,XXY) (13). This was an impressive start for the discipline of cytogenetics. Although these advances are some of the earli- est representations of how medical molecular biology is prac- ticed, the fundamental science was advancing at a remarkable rate. Chargaff determined that the ratio of the nucleic acid bases was always 1 : 1, an important breakthrough for deter- mining the structure of DNA (13,14). Combined with the crys- tallography work of Rosalind Franklin and Maurice Wilkins that showed an orderly, multiple polynucleotide chain, helix structure, James Watson and Francis Crick were able to pro- pose a structure for DNA (16). Many pieces of the puzzle were being put in place by the extraordinary work of many groups. The gross structure and many technical details of the components of DNA were becom- ing available to the research world. One very important ques- tion about how this package of information was translated to actual proteins remained. Marshall Nirenberg and Heinrich Matthaei conducted a series of experiments with RNAs to see if they would synthesize proteins. From this series came the “poly U” discovery that UUU was the code for phenylalanine (16). Along with significant contributions from Gobind Khorana (polynucleotide synthesis), Philip Leder (tRNA bind- ing to ribosomes to determine code), and many others, this opened the way for the remainder of the code to be broken. As important as the fundamental discoveries were, equally important developments were made in methods and technolo- gies. This period saw the isolation and characterization of reverse transcriptase, DNA ligase, and restriction enzymes, methods for staining chromosomes, the Southern blot assay for DNA fragments, an approach to determining the nucleic acids in DNA, phage and plasmid development, and the polymerase chain reaction. The polymerase chain reaction was a sort of integration of all that had gone before. This relatively simple procedure made it possible to characterize DNA, even though the source material was of limited quantity. It was an active time that was making all of the tools available for cloning. Cloning, as a process, was accomplished before the word was coined. In 1952, Robert Briggs and Thomas King used the technique to clone frogs (17). The method was a nuclear trans- fer procedure that was later improved and replicated by John Gurdon at Cambridge (17). There were other experiments with the fruit fly and bacteria, but in the early 1970s, Paul Berg cre- ated the first recombinant DNA and Stan Cohen, Herb Boyer, and colleagues created the first recombinant DNA organisms (16). They had successfully amplified toad DNA in Escherichia coli. This was the beginning of genetic engineering and began the discussion of the social impact of this new science. The ability to alter genes and to amplify them in another species was a source of concern to say the least. Could these new “agents” cause deadly diseases that would ravage mankind?
  27. 27. This was truly uncharted territory, and for the next few years, the scientific community discussed what, if anything, should be done to control the science. An international conference in February 1975, held in Pacific Grove, CA (Asilomar Conference), gener- ated a set of provisional recommendations that were later used by the National Institutes of Health (NIH) to formulate a set of mandatory guidelines. All NIH-funded programs were obligated to follow these guidelines (16). Other agencies around the world soon adopted similar restraints on recombinant DNA research. An unusual situation was now developing. The potential of cloning was not lost on anyone and each experiment received wide exposure in both the popular press and scientific journals. Therefore, enterprising individuals saw the commercial possi- bilities and the early biotech companies were born. Genentech, Cetus, Genex, Biogen, and Amgen were some of the early entries into genetic engineering (16). In 1980, it became legal to patent genetically engineered organisms. This encouraged the pharmaceutical and research companies to pursue protein hormones, drugs, and specific links between genetic abnormal- ities and diseases. Somatostatin was the first genetically engi- neered hormone and was followed in the next year by insulin and shortly thereafter by erythropoietin. It was clear that this was the new approach to the production of pharmaceuticals. The cloning experiments that were conjecture in the 1950s and 1960s became reality in the 1980s. Nuclear transplant cloning of mammals was accomplished on mice, sheep, bovines, pigs, goats, and rabbits (17). These experiments and others paved the way for the cloning of Dolly, the first animal cloned from adult cells. Dolly was born in July of 1996 at the Roslin Institute in Scotland (17). The theories had been turned into practice and the pharmaceutical industry as well as all of biological science would embark on an exciting and daunting future. One of the greatest success stories in molecular biology has to be the Human Genome Project. Some time after WWII, the Atomic Energy Commission (AEC), later known as the Department of Energy (DOE), was intensely interested in study- ing the health effects of ionizing radiation (18). The AEC had been consumed with the Manhattan Project and the creation of the atomic bomb and one can reasonably assume that the interest in ionizing radiation was piqued by those events. The AEC was the largest funder of genetic research in the United States. By the 1980s, the DOE was supporting research on the health impact of non-nuclear sources of energy (18). In this environment, Charles DeLisi began to muse about mapping the human genome. The obstacles were tremendous. Initially, it was thought that the process that would be required to accomplish such a feat was impossible. Techniques were not available yet to make this prac- tical. Major agencies like the NIH were not interested and neither were many of the ranking scientists throughout the country. The idea persisted, and as technologies were developed and computer power was improved, there began to be more interest. The DOE announced in 1987 the formation of the Human Genome Project Initative that would order and sequence the human genome (18). In science as in all of life, nothing becomes more interesting than when someone else has an interest. This announcement by the DOE stirred the interest of the NIH or, more specifically, the director, James Wingaarden (18). The scientific community was still divided because the perception was that the money used for CHAPTER 1 / HISTORICAL PERSPECTIVE 9 this project would jepordize all the other funded research. The cost of this project was estimated in the billions of dollars. The National Academy of Sciences wrote a report for the NIH that supported the genome project. The funding war was on. DOE and NIH were cosponsors of the project in the early days, but funding gradually shifted to the NIH (18). The official announcement of the Human Genome Project was made in 1990 and it was expected to take 15 years and 3 billion dollars. The original goals were to generate a high res- olution gene and physical map of the human genome, to deter- mine the complete DNA sequence in humans and other organisms, to develop the technology to store, analyze, and interpret the data, and to assess the ethical, legal, and social implications of genomics. It is interesting to note that the ethi- cal, social, and legal issues were funded from the same source as the scientific project. Remarkable progress and cooperation, as evidenced by the sharing of sequence data within 24 h, was a hallmark of the project. That is not to say there was not some competition from the commercial side. Celera Corporation was created to compete with the NIH project and had set as its goal a 3-year timetable and a significantly reduced cost. President Clinton announced in June 2000 the completion of the first draft of the Human Genome Project. It was a joint pres- entation, with both the commercial company Celera and the International Human Genome Consortium represented. At the time of the announcement, the project had cost about 300 million dollars and was several years early (13). It was truly a first draft in that the entire genome had not been mapped, but by 2001, about half was finished and available in the public database (13). Fifty years after the announcement of the structure of DNA, the Human Genome Project has accomplished virtually all of its goals. From this brief overview, it can be said that molecular biol- ogy has developed, more than any other science, by the coop- erative effort of many diverse disciplines. There was the mathematical approach of Mendel employing algebraic logic (19). The isolation of protein-free nucleic acid by Richard Altman and the experiments to convert nonvirulent to virulent bacteria by Fred Griffith and Oswald Avery are significant developmental landmarks (20). The application of the princi- ples of theoretical chemistry by Max Delbrück and Erwin Schrödinger allowed others to proceed using the principles of physical science (19). James Watson and Francis Crick eluci- dated the mathematically satisfying structure of DNA (21). There were the developments in computer science that made the software and hardware available for the storage and data analysis possible. Even the legal issues of patenting have to be considered as contributing to the development of this science. For the first time in the history of the diagnostic laboratory, molecular biology is extending the range of information avail- able. Until this time, the laboratory has been descriptive in nature. It could measure events that were currently going on by evaluating the chemistry, hematology, or anatomical pathology. Molecular biology allows the laboratory to be predictive in nature. Now, statements can be made about events that might occur in the future. This is different from an elevated value for blood glucose, when the diagnosis of diabetes can be made. This new technology returns results that indicate the patient might be at risk for a disease. Because of the ability of this
  28. 28. technology to detect carriers of a mutation and predict risk for disease development, ethical considerations and genetic coun- seling have become an inseparable part of the laboratory proce- dure. Preventive medicine, therefore, will benefit from this new technology. In cases of a family history that suggests high risk for a particular disease, a lab test might indicate that there is no risk to a specific family member. If there is a significant risk, then medical care might be able to intervene at a much earlier stage. This has significant financial benefits for those that have to control the costs of healthcare. The pharmaceutical industry will benefit greatly from the genetic engineering approach to drug production and even to synthesizing drugs specific for an individual patient. Perhaps that synthesis will take the form of modifying genes in animals so the animal will synthesize the human product, greatly reduc- ing the need for organic synthesis. 6. OTHER FACTORS As has been discussed, the laboratory has developed through a series of advances and setbacks. Until recently, the volume of test- ing has gone up dramatically every year in excess of what is pre- dicted for diagnostic purposes. One contributing factor may be that in the mid-20th century, health insurance became available to a large portion of the working population. Under this type of pro- gram, medical care was delivered with little concern about the cost. These costs were passed along to the insurance company, which paid the charges. This put the laboratory in a revenue- generating position, and more tests translated to more income. There was no incentive to control costs; in fact, there was an incen- tive to do more tests, hire more staff, and buy more equipment. This led to a considerable growth in laboratory services, and although test costs were coming down, the increased volume made the total cost higher. As this new technology matures, there might be a par- adoxical financial shift; that is, the individual laboratory tests might currently be more expensive to perform than more traditional assays, but the benefit from earlier intervention and genetic coun- seling could reduce the long-term aggregate cost of health care. The subsequent chapters will outline a wide variety of diag- nostic testing that is available, along with the benefits and med- ical options that are available to the patient and the health care team. This technology will carry laboratory diagnostic medi- cine into the 21st century. 10 SECTION I / INTRODUCTION REFERENCES 1. Rubin, L. P. A Young Woman Taken to the Doctor by Her Family. Mezzotint by Johann Andreas Pfeffel after an original painting by Jan Josef Horemans. J. Hist. Med. Allied Sci. 36(4):488–489, 1981. 2. Haber, M. H. Pisse prophecy: a brief history of urinalysis. Clin. Lab. Med. 8(3):415–430, 1988. 3. White, W. I. A new look at the role of urinalysis in the history of diagnostic medicine. Clin. Chem. 37(1):119–125, 1991. 4. Camac, C. N. B. Imhotep to Harvey: Backgrounds of Medical History, Milford House, Boston, 1973. 5. Flint, A. Remarks on the use of the thermometer in diagnosis and prognosis, in Technology and American Medical Practice 1880–1930, Howell J. D., ed, pp. 1–14. Garland, New York, 1988. 6. Caraway, W. The scientific development of clinical chemistry to 1948. Clin. Chem. 19(4):373–383, 1973. 7. Howell, J. D. Technology in the Hospital, The Johns Hopkins University Press. Baltimore, MD, 1995. 8. Reiser, S. J. Medicine and the Reign of Technology, Cambridge University Press, Cambridge, 1978. 9. Kohler, R. E. From Medical Chemistry to Biochemistry, Cambridge University Press, New York, 1982. 10. Chittenden, R. H. The Development of Physiological Chemistry in the United States. The Chemical Catalog Company, NewYork, 1930. 11. Meites, S. First call for clinical chemists in U.S. Clin. Chem. 29(10):1852–1853, 1983. 12. Lewis, L. Leonard Skeggs—a multifaceted diamond. Clin. Chem. 27(8):1465–1468, 1981. 13. Lorentz, C. P., Wieben, E. D., Tefferi, A., et al. Primer on medical genomics; Part I: History of genetics and sequencing of the human genome. Mayo Cli. Proc. 77, 2002. 14. Terry, M. Spiraling through genetic history. Adv. Med. Lab. Professionals, May 28, 2001. 15. Morange, M. A History of Molecular Biology, Harvard University Press, Cambridge, MA, 1998. 16. Echols, H. Operators and Promoters, the Story of Molecular Biology and Its Creators, University of California Press, Berkeley, CA, 2001. 17. Baldi, P. The Shattered Self, the End of Natural Selection, MIT Press, Cambridge, MA, 2001. 18. Wickelgren, I. The Gene Masters. Times Books, Henry Holt and Co., New York, 2002. 19. Miclos, D. A. and Freyer, G. A. DNA Science—A First Course in Recombinant DNA Technology, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp. 4–9, 1990. 20. Blackburn, M. G. and Gait, M. J., eds. Nucleic Acids in Chemistry and Biology, IRL Press/Oxford University Press, New York, pp. 3–4, 1990. 21. Kay, L. E. The Molecular Vision of Life, Caltech, The Rockefeller Foundation, and the Rise of the New Biology, Oxford University Press, New York, 1993.
  30. 30. 1. INTRODUCTION Chemists and early biochemists determined the essential building blocks of living cells and characterized their chemical nature. Among these building blocks were nucleic acids, long- chain polymers composed of nucleotides. Nucleic acids were named based partly on their chemical properties and partly on the observation that they represent a major constituent of the cell nucleus. That nucleic acids form the chemical basis for the trans- mission of genetic traits was not realized until about 60 years ago (1,2). Prior to that time, there was considerable disagreement among scientists as to whether genetic information was contained in and transmitted by proteins or nucleic acids. It was recognized that chromosomes contained deoxyribonucleic acid as a primary constituent, but it was not known if this DNA carried genetic information or merely served as a scaffold for some undiscovered class of proteins that carried genetic information. However, the demonstration that genetic traits could be transmitted through DNA formed the basis for numerous investigations focused on elucidation of the nature of the genetic code. During the last half- century, numerous investigators have participated in the scientific revolution leading to modern molecular biology. Of particular sig- nificance were the elucidation of the structure of DNA (3–9), determination of structure–function relationships between DNA and RNA (10,11), and acquisition of basic insights into the processes of DNA replication, RNA transcription, and protein synthesis (12–19). Molecular pathology represents the applica- tion of the principles of basic molecular biology to the investiga- tion of human disease processes. Our ever broadening insights into the molecular basis of disease processes continues to provide an opportunity for the clinical laboratory to develop and imple- ment new and novel approaches for diagnosis and prognostic assessment of human disease. 2. THE CENTRAL DOGMA OF MOLECULAR BIOLOGY Molecular biology has developed into a broad field of scien- tific pursuit and, at the same time, has come to represent a basic From: Molecular Diagnostics: For the Clinical Laboratorian, Second Edition Edited by: W. B. Coleman and G. J. Tsongalis © Humana Press Inc., Totowa, NJ 2 An Overview of Nucleic Acid Chemistry, Structure, and Function The Foundations of Molecular Biology WILLIAM B. COLEMAN 13 component of most other basic research sciences. This has come about through the rapid expansion of our insights into numerous basic aspects of molecular biology and the develop- ment of an understanding of the fundamental interaction among the several major processes that comprise the larger field of investigation. A theory, referred to as the “central dogma,” describes the interrelationships among these major processes (20,21). The central dogma defines the paradigm of molecular biology that genetic information is perpetuated as sequences of nucleic acid, but that genes function by being expressed in the form of protein molecules (20). The flow of genetic informa- tion among DNA, RNA, and protein that is described by the central dogma is illustrated in Fig. 1. Individual DNA mole- cules serve as templates for either complementary DNA strands during the process of replication or complementary RNA mol- ecules during the process of transcription. In turn, RNA mole- cules serve as blueprints for the ordering of amino acids by ribosomes during protein synthesis or translation. This simple representation of the complex interactions and interrelation- ships among DNA, RNA, and protein was proposed and commonly accepted shortly after the discovery of the struc- ture of DNA. Nonetheless, this paradigm still holds more than 45 years later and continues to represent a guiding princi- ple for molecular biologists involved in all areas of basic bio- logical, biomedical, and genetic research. 3. CHEMICAL NATURE OF DNA Deoxyribonucleic acid is a polymeric molecule that is com- posed of repeating nucleotide subunits. The order of nucleotide subunits contained in the linear sequence or primary structure of these polymers represents all of the genetic information car- ried by a cell. Each nucleotide is composed of (1) a phosphate group, (2) a pentose (5 carbon) sugar, and (3) a cyclic nitrogen- containing compound called a base. In DNA, the sugar moiety is 2-deoxyribose. Eukaryotic DNA is composed of four differ- ent bases: adenine, guanine, thymine, and cytosine. These bases are classified based on their chemical structure into two groups:
  31. 31. Adenine and guanine are double-ring structures termed purines, and thymine and cytosine are single-ring structures termed pyrimidines (Fig. 2). Within the overall composition of DNA, the concentration of thymine is always equal to the concentra- tion of adenine, and the concentration of cytosine is always equal to guanine (22,23). Thus, the total concentration of pyrim- idines always equals the total concentration of purines. These monomeric units are linked together into the polymeric structure by 3′, 5′-phosphodiester bonds (Fig. 3). Natural DNAs display widely varying sizes depending on the source. Relative molecu- lar weights range from 1.6 × 106 Daltons for bacteriophage DNA to 1 × 1011 Daltons for a human chromosome. 4. STRUCTURE OF DNA The structure of DNA is a double helix, composed of two polynucleotide strands that are coiled about one another in a spi- ral (3,4). Each polynucleotide strand is held together by phospho- diester bonds linking adjacent deoxyribose moieties. The two polynucleotide strands are held together by a variety of noncova- lent interactions, including lipophilic interactions between adja- cent bases and hydrogen-bonding between the bases on opposite strands. The sugar-phosphate backbones of the two complemen- tary strands are antiparallel; that is, they possess opposite chemi- cal polarity. As one moves along the DNA double helix in one direction, the phosphodiester bonds in one strand will be oriented 5′–3′, whereas in the complementary strand, the phosphodiester bonds will be oriented 3′–5′. This configuration results in base- pairs being stacked between the two chains perpendicular to the axis of the molecule. The base-pairing is always specific:Adenine is always paired to thymidine, and guanine is always paired to cytosine. This specificity results from the hydrogen-bonding capacities of the bases themselves.Adenine and thymine form two hydrogen bonds, and guanine and cytosine form three hydrogen bonds. The specificity of molecular interactions within the DNA molecule allows one to predict the sequence of nucleotides in one polynucleotide strand if the sequence of nucleotides in the com- plementary strand is known (24). Although the hydrogen bonds themselves are relatively weak, the number of hydrogen bonds within a DNA molecule results in a very stable molecule that would never spontaneously separate under physiological condi- tions. There are many possibilities for hydrogen-bonding between pairs of heterocyclic bases. Most important are the hydrogen- bonded basepairs A:T and G:C that were proposed by Watson and Crick in their double-helix structure of DNA (3,24). However, other forms of base-pairing have been described (25,26). In addi- tion, hydrophobic interactions between the stacked bases in the double helix lend additional stability to the DNA molecule. 14 SECTION II / BASIC MOLECULAR BIOLOGY Three helical forms of DNA are recognized to exist: A, B, and Z (27). The B conformation is the dominate form under physiological conditions. In B DNA, the basepairs are stacked 0.34 nm apart, with 10 basepairs per turn of the right-handed double helix and a diameter of approx 2 nm. Like B DNA, the A conformer is also a right-handed helix. However, A DNA exhibits a larger diameter (2.6 nm), with 11 bases per turn of the helix, and the bases are stacked closer together in the helix (0.25 nm apart). Careful examination of space-filling models of A and B DNA conformers reveals the presence of a major groove and a minor grove (27). These grooves (particularly the minor groove) contain many water molecules that interact favorably with the amino and keto groups of the bases. In these grooves, DNA-binding proteins can interact with specific DNA sequences without disrupting the base-pairing of the molecule. In contrast to the A and B conformers of DNA, Z DNA is a left- handed helix. This form of DNA has been observed primarily in synthetic double-stranded oligonucleotides, especially those with purine and pyrimidines alternating in the polynucleotide strands. In addition, high salt concentrations are required for the maintenance of the Z DNA conformer. Z DNA possesses a minor groove but no major groove, and the minor groove is suf- ficiently deep that it reaches the axis of the DNA helix. The nat- ural occurrence and potential physiological significance of Z DNA in living cells has been the subject of much speculation. However, these issues with respect to Z DNA have not yet been fully resolved. 5. SEQUENCE OF THE HUMAN GENOME The diploid genome of the typical human cell contains approx 3 × 109 basepairs of DNA that is subdivided into 23 pairs of chromosomes (22 autosomes and sex chromosomes X and Y). It has long been suggested that discerning the complete sequence of the human genome would enable the genetic causes of human disease to be investigated (28–30). Practical methods for DNA sequencing appeared in the mid to late 1970s (31–33), and numerous reports of DNA sequences corresponding to segments of the human genome began to appear. In the mid-1980s, a proj- ect to sequence the complete human genome was proposed, and this project began in the later years of that decade. The develop- ment of automated methods for DNA sequencing (34,35) made the ambitious goals of the Human Genome Project attainable (36,37). Subsequently, detailed genetic and physical maps of the human genome appeared (38–43), expressed sequences were identified and characterized (44–46), and gene maps of the human genome were constructed (47,48). Efforts by several con- sortiums using differing approaches (49–51) to large-scale sequencing of human DNA and sequence contig assembly cul- minated in 2001 with the publication of a draft sequence of the human genome (52,53). The actual number of genes contained in the human genome is not yet known. Early estimates suggested that the human genome might contain 70,000 to 100,000 genes (54–56). However, more recently, the number of genes contained in the human genome has been estimated to be approximately 30,000–40,000 (52,53,57,58). Early analysis of the draft sequences of the human genome revealed considerable variabil- ity between individuals, including in excess of 1.1–1.4 million single-nucleotide polymorphisms (SNPs) distributed throughout Fig. 1. The central dogma of molecular biology. The central dogma defines the paradigm of molecular biology that genetic information is perpetuated as sequences of nucleic acid, but that genes function by being expressed in the form of protein molecules. (From ref. 20.)
  32. 32. the genome (53,59). Refinement of the human genome sequence, identification and characterization of the genes contained, and description of the features of the genome (SNPs and other varia- tions) continues at a rapid pace (http://www.nhgri.nih.gov/). In early 2003, it was announced that the Human Genome Project had completely sequenced 99% of the gene-containing portion of the human genome, and new plans and goals for genomics research were described (60,61). 6. ORGANIZATION OF GENOMIC DNA The human genomic DNA is packaged into discreet structural units that vary in size and genetic composition. The structural unit of DNA is the chromosome, which is a large continuous segment of DNA (62). A chromosome represents a single genetically spe- cific DNA molecule to which are attached a large number of pro- tein molecules that are involved in the maintenance of chromosome structure and regulation of gene expression (63). Genomic DNA contains both “coding” and “noncoding” sequences. Noncoding sequences contain information that does not lead to the synthesis of an active RNA molecule or protein (54,64). This is not to suggest that noncoding DNA serves no function within the genome. On the contrary, noncoding DNA sequences have been suggested to function in DNA packaging, chromosome structure, chromatin organization within the nucleus, or in the regulation of gene expression (65,66). A portion of the noncoding sequences represent intervening sequences that split the coding regions of structural genes. However, the majority of noncoding DNA falls into several families of repetitive DNA whose exact functions have not been entirely elucidated (67,68). Coding DNA sequences give rise to all of the transcribed RNAs of the cell, including mRNA. The organization of tran- scribed structural genes consists of coding regions that are inter- rupted by intervening noncoding regions of DNA (Fig. 4). Thus, CHAPTER 2 / NUCLEIC ACID CHEMISTRY, STRUCTURE, AND FUNCTION 15 the primary RNA transcripts contain both coding and noncoding sequences. The noncoding sequences must be removed from the primary RNA transcript during processing to produce a func- tional mRNA molecule appropriate for translation. 7. DNA FUNCTION DNA serves two important functions with respect to cellular homeostasis: the storage of genetic information and the trans- mission of genetic information. In order to fulfill both of these functions, the DNA molecule must serve as a template. The cel- lular DNA provides the source of information for the synthesis of all the proteins in the cell. In this respect, DNA serves as a template for the synthesis of RNA. In cell division, DNA serves as the source of information inherited by progeny cells. In this case, DNA serves as a template for the faithful replication of the genetic information that is ultimately passed into daughter cells. 7.1. TRANSCRIPTION OF RNA Contained within the linear nucleotide sequence of the cellular DNA is the informa- tion necessary for the synthesis of all the protein constituents of a cell (Table 1). Transcription is the process in which mRNA is synthesized with a sequence complementary to the DNA of a gene to be expressed. The correct start and end points for tran- scription of a specific gene are identified in the DNA by a pro- moter sequence upstream of the gene and a termination signal downstream (Fig. 4). In the case of RNA transcription, only one strand of the DNA molecule serves as a template. This strand is referred to as the “sense” strand. Transcription of the sense strand ultimately yields a mRNA molecule that encodes the proper amino acid sequence for a specific protein. 7.2. REPLICATION OF DNA The double-stranded model of the structure of DNA strongly suggests that replica- tion of the DNA can be achieved in a semiconservative manner (69–72). In semiconservative replication, each strand of the Fig. 2. The chemical structure of purine and pyrimidine deoxyribonucleosides.
  33. 33. DNA helix serves as a template for the synthesis of comple- mentary DNA strands. The result is the formation of two com- plete copies of the DNA molecule, each consisting of one strand derived from the parent DNA molecule and one newly synthesized complementary strand. The utilization of the DNA strands as the template for the synthesis of new DNA ensures the faithful reproduction of the genetic material for transmis- sion into daughter cells (19). 7.3. GENETIC RECOMBINATION Genetic recombina- tion represents one mechanism for the generation of genetic diversity through the exchange of genetic material between two homologous nucleotide sequences (73,74). Such an exchange of genetic material often results in alterations of the primary struc- ture (nucleotide sequence) of a gene and, subsequently, alter- ation of the primary structure of the encoded protein product. In 16 SECTION II / BASIC MOLECULAR BIOLOGY organisms that reproduce sexually, recombination is initiated by formation of a junction between similar nucleotide sequences carried on the same chromosome from the two different parents. The junction is able to move along the DNA helix through branch migration, resulting in an exchange of the DNA strands. 7.4. DNA REPAIR Maintenance of the integrity of the informational content of the cellular DNA is absolutely required for cellular and organismal homeostasis (75,76). The cellular DNA is continuously subjected to structural damage through the action of endogenous or environmental mutagens. In the absence of efficient repair mechanisms, stable mutations can be introduced into DNA during the process of replication at damaged sites within the DNA. Mammalian cells possess sev- eral distinct DNA repair mechanisms and pathways that serve to maintain DNA integrity, including enzymatic reversal repair, Fig. 3. The chemical structure of repeating nucleotide subunits in DNA and RNA. Each panel shows the sugar-phosphate backbone of a single polynucleotide strand of nucleic acid composed of four nucleotide subunits. The stippled area highlights a 3′–5′ phosphodiester bond.