METHODS IN MOLECULAR BIOLOGY™ 336 CClliinniiccaall AApppplliiccaattiioonnss ooff PPCCRR SS EE EECCOONNDD DDIITTIIOONN EEddiitteedd bbyy YY.. MM.. DDeennnniiss LLoo RRoossssaa WW.. KK.. CChhiiuu KK.. CC.. AAlllleenn CChhaann Clinical Applications of PCR M E T H O D S I N M O L E C U L A R B I O L O G Y™ John M. Walker, SERIES EDITOR 352. Protein Engineering Protocols, edited by Kristian 328. New and Emerging Proteomic Techniques, Müller and Katja Arndt, 2006 edited by Dobrin Nedelkov and Randall W. Nelson, 351. C. elegans: Methods and Applications, edited by 2006 Kevin Strange, 2006 327. Epidermal Growth Factor: Methods and Protocols, 350. Protein Folding Protocols, edited by Yawen Bai edited by Tarun B. Patel and Paul J. Bertics, 2006 and Ruth Nussinov 2006 326. In Situ Hybridization Protocols, Third Edition, 349. YAC Protocols, Second Edition, edited by Alasdair edited by Ian A. Darby and Tim D. Hewitson, 2006 MacKenzie, 2006 325. Nuclear Reprogramming: Methods and 348. Nuclear Transfer Protocols: Cell Reprogramming Protocols, edited by Steve Pells, 2006 and Transgenesis, edited by Paul J. Verma and Alan 324. Hormone Assays in Biological Fluids, edited by Trounson, 2006 Michael J. Wheeler and J. S. Morley Hutchinson, 347. Glycobiology Protocols, edited by Inka 2006 Brockhausen-Schutzbach, 2006 323. Arabidopsis Protocols, Second Edition, edited by 346. Dictyostelium discoideum Protocols, edited by Julio Salinas and Jose J. Sanchez-Serrano, 2006 Ludwig Eichinger and Francisco Rivero-Crespo, 2006 322. Xenopus Protocols: Cell Biology and Signal 345. Diagnostic Bacteriology Protocols, Second Edi- Transduction, edited by X. Johné Liu, 2006 tion, edited by Louise O'Connor, 2006 321. Microfluidic Techniques: Reviews and Protocols, 344.Agrobacterium Protocols, Second Edition: edited by Shelley D. Minteer, 2006 Volume 2, edited by Kan Wang, 2006 320. Cytochrome P450 Protocols, Second Edition, 343.Agrobacterium Protocols, Second Edition: edited by Ian R. Phillips and Elizabeth A. Volume 1, edited by Kan Wang, 2006 Shephard, 2006 342. MicroRNA Protocols, edited by Shao-Yao Ying, 2006 319. Cell Imaging Techniques, Methods and Protocols, edited by Douglas J. Taatjes and Brooke T. 341.Cell–Cell Interactions: Methods and Protocols, Mossman, 2006 edited by Sean P. Colgan, 2006 318. Plant Cell Culture Protocols, Second Edition, 340.Protein Design: Methods and Applications, edited by Victor M. Loyola-Vargas and Felipe edited by Raphael Guerois and Manuela López de la Vázquez-Flota, 2005 Paz, 2006 317. Differential Display Methods and Protocols, 339.Microchip Capillary Electrophoresis: Methods Second Edition, edited by Peng Liang, Jonathan and Protocols, edited by Charles Henry, 2006 Meade, and Arthur B. Pardee, 2005 338.Gene Mapping, Discovery, and Expression: 316. Bioinformatics and Drug Discovery, edited by Methods and Protocols, edited by M. Bina, 2006 Richard S. Larson, 2005 337.Ion Channels: Methods and Protocols, edited by 315. Mast Cells: Methods and Protocols, edited by James D. Stockand and Mark S. Shapiro, 2006 Guha Krishnaswamy and David S. Chi, 2005 336.Clinical Applications of PCR: Second Edition, 314. DNA Repair Protocols: Mammalian Systems, edited by Y. M. Dennis Lo, Rossa W. K. Chiu, and K. C. Second Edition, edited by Daryl S. Henderson, 2006 Allen Chan, 2006 313.Yeast Protocols: Second Edition, edited by 335.Fluorescent Energy Transfer Nucleic Acid Wei Xiao, 2005 Probes: Designs and Protocols, edited by Vladimir V. Didenko, 2006 312.Calcium Signaling Protocols: Second Edition, edited by David G. Lambert, 2005 334.PRINS and In Situ PCR Protocols: Second Edition, edited by Franck Pellestor, 2006 311. Pharmacogenomics: Methods and Protocols, edited by Federico Innocenti, 2005 333. Transplantation Immunology: Methods and Protocols, edited by Philip Hornick and Marlene 310. Chemical Genomics: Reviews and Protocols, Rose, 2006 edited by Edward D. Zanders, 2005 332. Transmembrane Signaling Protocols: Second 309. RNA Silencing: Methods and Protocols, edited by Edition, edited by Hydar Ali and Bodduluri Haribabu, Gordon Carmichael, 2005 2006 308. Therapeutic Proteins: Methods and Protocols, 331. Human Embryonic Stem Cell Protocols, edited edited by C. Mark Smales and David C. James, by Kursad Turksen, 2006 2005 330. Embryonic Stem Cell Protocols, Second Edition, 307.Phosphodiesterase Methods and Protocols, Vol. II: Differentiation Models, edited by Kursad edited by Claire Lugnier, 2005 Turksen, 2006 306.Receptor Binding Techniques: Second Edition, 329. Embryonic Stem Cell Protocols, Second Edition, edited by Anthony P. Davenport, 2005 Vol. I: Isolation and Characterization, edited by 305.Protein–Ligand Interactions: Methods and Kursad Turksen, 2006 Applications, edited by G. Ulrich Nienhaus, 2005 M E T H O D S I N M O L E C U L A R B I O L O G Y™ Clinical Applications of PCR Second Edition Edited by Y. M. Dennis Lo Rossa W. K. Chiu K. C. Allen Chan Department of Chemical Pathology The Chinese University of Hong Kong Hong Kong SAR © 2006 Humana Press Inc. 999 Riverview Drive, Suite 208 Totowa, New Jersey 07512 www.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. Methods in Molecular BiologyTM is a trademark of The Humana Press Inc. All papers, comments, opinions, conclusions, or recommendations are those of the author(s), and do not necessarily reflect the views of the publisher. This publication is printed on acid-free paper. ∞ ANSI Z39.48-1984 (American Standards Institute) Permanence of Paper for Printed Library Materials. Production Editor: Jennifer Hackworth Cover illustration: Sunny Wong Cover design by Patricia F. Cleary 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: [email protected]; or visit our Website: www.humanapress.com 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: [1-58829-348-3/06 $30.00]. Printed in the United States of America. 10 9 8 7 6 5 4 3 2 1 1-59745-074-X (e-book) ISSN 1064-3745 Library of Congress Cataloging-in-Publication Data Clinical applications of PCR / edited by Y.M. Dennis Lo, Rossa W.K. Chiu, K.C. Allen Chan.-- 2nd ed. p. ; cm. -- (Methods in molecular medicine ; 336) Includes bibliographical references and index. ISBN 1-58829-348-3 (alk. paper) 1. Polymerase chain reaction--Diagnostic use. [DNLM: 1. Polymerase Chain Reaction--methods. QU 450 C241 2006] I. Lo, Y. M. Dennis. II. Chiu, Rossa W. K. III. Chan, K. C. Allen IV. Series. RB43.8.P64C55 2006 616.07'56--dc22 2005022727 Preface Since the invention of the polymerase chain reaction (PCR) in the early 1980s, this technique has rapidly become an indispensable part of modern molecular diagnostics. Without this powerful technology, many of the impor- tant developments in modern sciences, including the Human Genome Project, would probably have progressed much more slowly. In the area of molecular diagnostics, PCR has allowed target detection to be performed with unprec- edented sensitivity and ease. It has been several years since the first edition of Clinical Applications of PCR was published. During these few years, it is amazing how rapidly techno- logical advances in PCR-based technologies have developed. Important technological advances, notably real-time PCR and mass spectrometry, have revolutionized the field. In particular, real-time PCR has allowed the technique to be performed with improved sensitivity, robustness, and resilience to carryover contamination, as well as in a quantitative manner. These techno- logical developments, together with the indispensable nature of PCR in molecular laboratories everywhere, have led to a vast expansion in the number of clinical applications of PCR. In the second edition of Clinical Applications of PCR, we hope to share with readers the exciting applications of some of these innovations, including PCR for gene expression, methylation, trace molecule, gene dosage, and single cell analysis. It is hoped that the step-by-step protocols and the explanatory notes will help readers to harness the power of these techniques in their laboratories. Y. M. Dennis Lo Rossa W. K. Chiu K. C. Allen Chan v Contents Preface ..............................................................................................................v Contributors .....................................................................................................ix 1 Introduction to the Polymerase Chain Reaction Y. M. Dennis Lo and K. C. Allen Chan..................................................1 2 Setting Up a Polymerase Chain Reaction Laboratory Y. M. Dennis Lo and K. C. Allen Chan................................................11 3 Real-Time Polymerase Chain Reaction and Melting Curve Analysis Robert J. Pryor and Carl T. Wittwer...................................................19 4 Qualitative and Quantitative Polymerase Chain Reaction-Based Methods for DNA Methylation Analyses Ivy H. N. Wong...................................................................................33 5 In-Cell Polymerase Chain Reaction: Strategy and Diagnostic Applications T. Vauvert Hviid..................................................................................45 6 Qualitative and Quantitative DNA and RNA Analysis by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry Chunming Ding...................................................................................59 7 Analysis of Polymerase Chain Reaction Products by Denaturing High-Performance Liquid Chromatography Ching-Wan Lam..................................................................................73 8 Use of Real-Time Polymerase Chain Reaction for the Detection of Fetal Aneuploidies Bernhard Zimmermann, Lisa Levett, Wolfgang Holzgreve, and Sinuhe Hahn............................................................................83 9 Noninvasive Prenatal Diagnosis by Analysis of Fetal DNA in Maternal Plasma Rossa W. K. Chiu and Y. M. Dennis Lo.............................................101 10 Clinical Applications of Plasma Epstein-Barr Virus DNA Analysis and Protocols for the Quantitative Analysis of the Size of Circulating Epstein-Barr Virus DNA K. C. Allen Chan and Y. M. Dennis Lo..............................................111 vii viii Contents 11 Molecular Analysis of Circulating RNA in Plasma Nancy B. Y. Tsui, Enders K. O. Ng, and Y. M. Dennis Lo.................123 12 Molecular Analysis of Mitochondrial DNA Point Mutations by Polymerase Chain Reaction Lee-Jun C. Wong, Bryan R. Cobb, and Tian-Jian Chen....................135 13 Novel Applications of Polymerase Chain Reaction to Urinary Nucleic Acid Analysis Anatoly V. Lichtenstein, Hovsep S. Melkonyan, L. David Tomei, and Samuil R. Umansky.....................................145 14 Detection and Quantitation of Circulating Plasmodium falciparum DNA by Polymerase Chain Reaction Shira Gal and James S. Wainscoat....................................................155 15 Molecular Diagnosis of Severe Acute Respiratory Syndrome Enders K. O. Ng and Y. M. Dennis Lo..............................................163 16 Genomic Sequencing of the Severe Acute Respiratory Syndrome-Coronavirus Stephen S. C. Chim, Rossa W. K. Chiu, and Y. M. Dennis Lo.............177 Index ............................................................................................................195 Contributors K. C. ALLEN CHAN • Department of Chemical Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR TIAN-JIAN CHEN • Department of Medical Genetics, University of South Alabama, Mobile, AL STEPHEN S. C. CHIM • Department of Obstetrics and Gynaecology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR ROSSA W. K. CHIU • Department of Chemical Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR BRYAN R. COBB • Institute for Molecular and Human Genetics, Georgetown University Medical Center, Washington, DC CHUNMING DING • Centre for Emerging Infectious Diseases, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR SHIRA GAL • Nuffield Department of Clinical Laboratory Sciences, University of Oxford, John Radcliffe Hospital, Oxford, UK SINUHE HAHN • Laboratory for Prenatal Medicine, University Women’s Hospital, Basel, Switzerland WOLFGANG HOLZGREVE • Laboratory for Prenatal Medicine, University Women’s Hospital, Basel, Switzerland T. VAUVERT HVIID • Department of Clinical Biochemistry, H:S Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark CHING-WAN LAM • Department of Chemical Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR LISA LEVETT • Cytogenetic DNA Services Ltd., London, UK ANATOLY V. LICHTENSTEIN • Cancer Research Center, Moscow, Russia Y. M. DENNIS LO • Department of Chemical Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR HOVSEP S. MELKONYAN • Xenomics Inc., New York, NY/Princeton, NJ ENDERS K. O. NG • Department of Health, Centre for Health Protection, Government of Hong Kong Special Administrative Region, Hong Kong SAR ROBERT J. PRYOR • Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT L. DAVID TOMEI • Xenomics Inc., New York, NY/Princeton, NJ ix