CARL WITTWER MEINHARD HAHN KAREN KAUL (Eds.) Rapid Cycle Real-Time PCR - Methods and Applications Quantification

Transcription

1 CARL WITTWER MEINHARD HAHN KAREN KAUL (Eds.) Rapid Cycle Real-Time PCR - Methods and Applications Quantification

2 EM Springer-Verlag Berlin Heidelberg GmbH

3 Carl Wittwer Meinhard Hahn Karen Kaul (Eds.) Rapid Cycle Real-Time PCR - Methods and Applications Quantification With 78 Figures and 108 Tables Springer

4 EU Professor Dr. CARL WITTWER Director of Flow Cytometry & New Technology Department of Pathology University of Utah School of Medicine Salt Lake City, UT USA Dr. MEINHARD HAHN Deutsches Krebsforschungszentrum Abt. Molekulare Genetik Im Neuenheimer Feld Heidelberg Germany Dr. KAREN KAUL Evanston Northwestern Healthcare Department of Pathology 2650 Ridge Avenue Evanston, IL USA ISBN We thank Mr. Olfert Landt, TIB MOLBIOL Syntheselabor, Berlin, Germany, for carefully reviewing the sequence and technical information and for his valuable comments. Cataloging-in-Publication Data applied for Bibliographic information published by Die Deutsche Bibliothek Die Deutsche Bibliothek lists this publication in the Deutsche Nationalbibliografie; detailed bibliographic data is available in the Internet at < ISBN ISBN (ebook) DOI / This work is subject to copyright. All rights are reserved, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilm or in any other way, and storage in data banks. Duplication of this publication or parts thereof is permitted only under the provisions of the German copyright Law of September 9, 1965, in its current version, and permission for use must always be obtained from Springer-Verlag. Violations are liable for prosecution under the German Copyright Law. Springer-Verlag Berlin Heidelberg 2004 Originally published by Springer-Verlag Berlin Heidelberg New York in 2004 Softcover reprint of the hardcover 1st edition 2004 The use of general descriptive names, registered names, trademarks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. Product liability: The publisher cannot guarantee the accuracy of any information about dosage and application thereof contained in this book. In every individual case the user must check such information by consulting the relevant literature. Cover Design: design & production GmbH, Heidelberg, Germany Typesetting: TypoStudio Tobias Schaedla, Heidelberg, Germany Printed on acid free paper SPIN /

5 Table of Contents Part I Methods Housekeeping Genes: AGold Standard? ONNO BAKKER, DAPHNE C.TIMMER 3 The Choice ofhouse Keeping Genes inmrd-quantification ofamll-eto Positive Acute Myeloid Leukemia 11 MARTIN WEISSER, CLAUDIA SCHOCH, TORSTEN HAFERLACH, WOLFGANG HIDDEMANN, SUSANNE SCHNITTGER Quantification ofmrna Using linearregression oflog-linear PCR Data-Points as an Alternative forthestandard Curve Approach 21 CHRISTIAN RAMAKERS, DAPHNE TIMMER, ONNO BAKKER, RONALD H. LEKANNE DEPREZ, JAN M. RUIJTER, ANTOON EM. MOORMAN Measuring Genome Sizes by Absolute Quantification JOCHEN WILHELM, MEINHARD HAHN 31 Part 11 Applications Regulation and Development Relative Quantification ofinsulin Gene Expression on thelightcycler Using SYBR Green I 45 NICOLE NEUBAUER Quantification ofbrec-'!'ja Signal Joint T-Cell Receptor Excision Circle DNA inpatients after Autologous and Allogeneic Stem Cell Transplantation 53 JUERGEN LOEFFLER, HOLGER HEBART, LUTZ LOCHMANN, THOMAS DAIKELER, PETER BAD ER, RALF BAUER, KATHRIN SCHMIDT, HERMANN EINSELE

6 171 Table of Contents Expression Analysis ofmitochondrial Components inavariety ofplant Species Using Real-Time Quantitative PCR 61 KATHARINE A. HowELL, RYAN LISTER, JAMES WHELAN Quantification ofikaros Splice Variants by Real-Time PCR 73 ELLI VEISTINEN, KALLE-PEKKA NERA, JUKKA ALINIKULA, OLLI LASSILA Methods to Quantify Cytokine Gene Expression by Real-Time PCR PATRICK STORDEUR 83 Oncology Profiling Breast Cancer Using Real-Time Quantitative PCR SCOT G. FRANK, PHILIP S. BERNARD 95 HER-2/neuGene Copy Number Quantified by Real-Time PCR incell lines and BreastCancer Tissue 107 MELANIE KONIGSHOFF, JOCHEN WILHELM, MEINHARD HAHN Quantification ofseveral Components offibrinolytic and Matrix Metalloproteinase Systems inprimary Breast Cancer REMEDIOS CASTELLO, FRANCISCO ESPANA, JUSTO AZNAR, AMPARO ESTELLES 117 ARapid Cycle Real-Time Quantitative P-9lobin PCR for Quantification ofhuman DNA infeces 125 CORNE H.W. KLAASSEN, CLEMENS EM. PRINSEN, FREDERIK B.J.M. THUNNISSEN Quantification oftumor Load for Follicular Lymphoma by Quantifying BCL2/IGH Using Real-Time Quantitative PCR by lightcycler 131 CHUNG-CHE CHANG, BERNARD C. SCHUR, B.S. Real-Time Quantification oftheaml Rearrangements, AML 1-ETO and TEL-AML 1, inacute Leukemia 141 EVA BARRAGAN, PASCUAL BOLUFER, MIGUEL ANGEL SANZ Genetics Rapid Detection ofgene Duplications incharcot-marie-tooth 1ADisease by SNP Genotyping Using Real-Time PCR 159 C. RUIZ-PONTE, A. VEGA, A. CARRACEDO, E BARROS

7 Table of Contents QD Cytochrome P4S0 2D6 Deletion Genotyping Using Derivative Curve Analysis on the LightCycler 171 ALISON MILLSON, ELIZABETH L. FRANK, ELAINE LYON Trisomy 21 Detected by SNP Allele Ratios 179 GENEVIEVE PONT-KINGDON, ELAINE LYON Quantitative Chimerism Analysis by Allele-Specific Real-Time PCR ofa 10bp Insertion/Deletion Polymorphism within thepromotor Region offactor Vllc 187 HENDRIK REUTER, BJORN TEWS, JOCHEN WILHELM, MEIN HARD HAHN Microbiology Detection ofsars-coronavirus inthe LightCycler by S'-Nuclease Real-Time RT-PCR 199 CHRISTIAN DROSTEN Normalized Quantitative Rapid-Cycle Real-Time PCR for theassessment ofcmv-dna Copies 211 MARKUS STOCHER, JORG BERG