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M E T H O D S I N M O L E C U L A R B I O L O G YT M
Prenatal Diagnosis Edited by
Sinuhe Hahn Laboratory for Prenatal Medicine and Gynecological Oncology, Department of Biomedicine, University Womens’s Hospital, Basel, Switzerland
and
Laird G. Jackson Department of Obstetrics and Gynecology, Drexel University College of Medicine, Philadelphia, Pennsylvania
Editors Sinuhe Hahn Laboratory for Prenatal Medicine and Gynecological Oncology, Department of Biomedicine University Womens’s Hospital Basel, Switzerland
[email protected]
Laird G. Jackson Department of Obstetrics and Gynecology Drexel University College of Medicine Philadelphia, PA
[email protected]
Series Editor John M. Walker School of Life Sciences University of Hertfordshire Hatfield, Hertfordshire, UK
ISBN: 978-1-58829-803-4 ISSN: 1064-3745
e-ISBN: 978-1-59745-066-9 e-ISSN: 1940-6029
Library of Congress Control Number: 2007940754 © 2008 Humana Press, a part of Springer Science+Business Media, LLC All rights reserved. This work may not be translated or copied in whole or in part without the written permission of the publisher (Humana Press, 999 Riverview Drive, Suite 208, Totowa, NJ 07512 USA), except for brief excerpts in connection with reviews or scholarly analysis. Use in connection with any form of information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed is forbidden. The use in this publication of trade names, trademarks, service marks, and similar terms, even if they are not identified as such, is not to be taken as an expression of opinion as to whether or not they are subject to proprietary rights. While the advice and information in this book are believed to be true and accurate at the date of going to press, neither the authors nor the editors nor the publisher can accept any legal responsibility for any errors or omissions that may be made. The publisher makes no warranty, express or implied, with respect to the material contained herein. Cover illustration: Figure 1, Chapter 3, “Rapid Prenatal Aneuploidy Screening by Fluorescene In Situ Hybridization (FISH),” by Anja Weise and Thomas Liehr. Printed on acid-free paper 987654321 springer.com
Preface
Molecular biology has transformed prenatal diagnosis because it permits an accurate diagnosis to be made from very small quantities of fetal material, even single cells. Although the latter permits the analysis of preimplantation embryos and, perhaps in the future, the analysis of fetal cells enriched from maternal blood, a major current focus is to facilitate rapid, cost-effective diagnoses. In this manner, the use of fluorescence in situ hybridization (FISH) or polymerase chain reaction (PCR)-based approaches on uncultured amniocytes or chorionic villi already permits a rapid assessment of the most common fetal aneuploidies (chromosomes 13, 18, 21, X, and Y) to be obtained within 24 h, thereby obviating the need for a 2-week culture period previously required for a traditional karyotype. Although the accuracy of karyotypic analysis is greatly enhanced by methodologies such as spectral karyotyping (SKY) or comparative genomic hybridization (CGH), the advent of high-density nucleotide arrays (chips) facilitates rapid assessment of the fetal genotype for a large number of mutations of frequent Mendelian disorders, e.g., cystic fibrosis, the hemoglobinopathies, and Tay-Sachs syndrome. A further focus is the development of noninvasive, and hence, risk-free alternatives for prenatal diagnosis that no longer rely on invasive procedures such as amniocentesis or chorionic villus sampling. The most successful of these approaches is the analysis of placentally derived cell-free DNA in maternal blood. This approach has been found to be very reliable for the assessment of fetal loci absent from the maternal genome, and it is consequently already being used clinically for the determination of the fetal Rhesus D status and sex in pregnancies at risk for X-linked disorders. As such, cutting-edge applications for the rapid assessment of fetal aneuploidies and Mendelian disorders on fetal material gained by invasive approaches and procedures being validated for routine clinical analysis of cellfree fetal DNA are covered in Prenatal Diagnosis. In addition, several chapters address developments that are on the brink of clinical applications.
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We thank all the authors for their excellent contributions and trust that Prenatal Diagnosis will be useful to molecular biologists interested in clinical applications and those involved in basic research in prenatal medicine. Sinuhe Hahn Basel, Switzerland and Laird G. Jackson Philadelphia, Pennsylvania
Contents
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Contributors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Part I:
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Invasive Approaches
1
Spectral Karyotyping (SKY): Applications in Prenatal Diagnostics . . . . 3 Susanne Mergenthaler-Gatfield, Wolfgang Holzgreve, and Sinuhe Hahn 2 Characterization of Prenatally Assessed De Novo Small Supernumerary Marker Chromosomes by Molecular Cytogenetics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27 Thomas Liehr 3 Rapid Prenatal Aneuploidy Screening by Fluorescence In Situ Hybridization (FISH) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39 Anja Weise and Thomas Liehr 4
Application of Multi-PRINS to Simultaneously Identify Chromosomes 18, X, and Y in Prenatal Diagnosis. . . . . . . . . . . . . . . . 49 Macoura Gadji, Kada Krabchi, Ju Yan, and Régen Drouin
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Prenatal Diagnosis Using Array CGH . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Catherine D. Kashork, Aaron Theisen, and Lisa G. Shaffer Prenatal Detection of Chromosome Aneuploidy by Quantitative Fluorescence PCR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Kathy Mann, Erwin Petek, and Barbara Pertl Real-Time Quantitative PCR for the Detection of Fetal Aneuploidies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bernhard G. Zimmermann and Lech Dudarewicz MLPA for Prenatal Diagnosis of Commonly Occurring Aneuploidies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Jan Schouten and Robert-Jan Galjaard MALDI-TOF Mass Spectrometry for Trisomy Detection . . . . . . . . . . . . . Dorothy J. Huang, Matthew R. Nelson, and Wolfgang Holzgreve
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Rapid Detection of Fetal Mendelian Disorders: Thalassemia and Sickle Cell Syndromes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133 Joanne Traeger-Synodinos, Christina Vrettou, and Emmanuel Kanavakis 11 Rapid Detection of Fetal Mendelian Disorders: Tay-Sachs Disease . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147 Esther Guetta and Leah Peleg 12 Arrayed Primer Extension Reaction for Genotyping on Oligonucleotide Microarray. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161 Janne Pullat and Andres Metspalu 13 A Fast Microelectronic Array for Screening and Prenatal Diagnosis of -Thalassemia . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169 Barbara Foglieni, Silvia Galbiati, Maurizio Ferrari, and Laura Cremonesi
Part II:
Noninvasive Approaches
14 RHD Genotyping from Maternal Plasma: Guidelines and Technical Challenges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 185 Neil D. Avent 15 Isolation of Cell-Free DNA from Maternal Plasma Using Manual and Automated Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 203 Dorothy J. Huang, Susanne Mergenthaler-Gatfield, Sinuhe Hahn, Wolfgang Holzgreve, and Xiao Yan Zhong 16 Fetal DNA: Strategies for Optimal Recovery . . . . . . . . . . . . . . . . . . . . . . . . 209 Tobias J. Legler, Klaus-Hinrich Heermann, Zhong Liu, Aicha Ait Soussan, and C. Ellen van der Schoot 17 Quantification of Circulatory Fetal DNA in the Plasma of Pregnant Women . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 219 Bernhard G. Zimmermann, Deborah G. Maddocks, and Neil D. Avent 18 Detection and Quantification of Fetal DNA in Maternal Plasma by Using LightCycler Technology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 231 Yuditiya Purwosunu, Akihiko Sekizawa, and Takashi Okai 19 Size Fractionation of Cell-Free DNA in Maternal Plasma and Its Application in Noninvasive Detection of Fetal Single Gene Point Mutations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 239 Ying Li, Wolfgang Holzgreve, and Sinuhe Hahn 20 MALDI-TOF Mass Spectrometry for Analyzing Cell-Free Fetal DNA in Maternal Plasma . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 253 Chunming Ding
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Isolation of Cell-Free RNA from Maternal Plasma . . . . . . . . . . . . . . . . . . . 269 Xiao Yan Zhong, Wolfgang Holzgreve, and Dorothy J. Huang 22 A Microarray Approach for Systematic Identification of Placental-Derived RNA Markers in Maternal Plasma . . . . . . . . . . 275 Nancy B. Y. Tsui and Y. M. Dennis Lo 23 A Novel Method to Identify Syncytiotrophoblast-Derived RNA Products Representative of Trisomy 21 Placental RNA in Maternal Plasma . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 291 Attie T. J. J. Go, Allerdien Visser, Marie van Dijk, Monique A. M. Mulders, Paul Eijk, Bauke Ylstra, Marinus A. Blankenstein, John M. G. van Vugt, and Cees B. M. Oudejans 24 Method for Extraction of High-Quantity and -Quality Cell-Free DNA from Amniotic Fluid. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 303 Olav Lapaire, Kirby L. Johnson, and Diana W. Bianchi 25
Detection of New Screening Markers for Fetal Aneuploidies in Maternal Plasma: A Proteomic Approach . . . . . . . . . . . . . . . . . . . . . 311 Chinnapapagari Satheesh Kumar Reddy, Wolfgang Holzgreve, and Sinuhe Hahn
Index. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 327
Contributors
Neil D. Avent • Centre for Research in Biomedicine, University of the West of England, Bristol, UK Diana W. Bianchi • Division of Genetics, Departments of Pediatrics, Obstetrics, and Gynecology, Tufts-New England Medical Center and Floating Hospital for Children, Tufts University School of Medicine, Boston, MA Marinus A. Blankenstein • Department of Clinical Chemistry, VU University Medical Center, Amsterdam, The Netherlands Laura Cremonesi • Genomic Unit for Diagnosis of Human Pathologies, San Raffaele Scientific Institute, Milan, Italy; and Diagnostica e Ricerca San Raffaele S.p.A, Milan, Italy Chunming Ding • Centre for Emerging Infectious Diseases, Chinese University of Hong Kong, Hong Kong, China Régen Drouin • Science of Genetics, Department of Pediatrics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Quebec, Canada Lech Dudarewicz • Department of Genetics, Polish Mother’s Memorial Hospital, Lodz, Poland Paul Eijk • Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands Maurizio Ferrari • Genomic Unit for Diagnosis of Human Pathologies, San Raffaele Scientific Institute, Milan, Italy; Diagnostica e Ricerca San Raffaele S.p.A.; and Universita` Vita-Salute San Raffaele, Milan, Italy Barbara Foglieni • Genomic Unit for Diagnosis of Human Pathologies, San Raffaele Scientific Institute, Milan, Italy Macoura Gadji • Science of Genetics, Department of Pediatrics, Faculty of Medicine and Health Sciences, Universit´e de Sherbrooke, Quebec, Canada Silvia Galbiati • Genomic Unit for Diagnosis of Human Pathologies, San Raffaele Scientific Institute, Milan, Italy Robert-Jan Galjaard • Erasmus University of Rotterdam, Rotterdam, The Netherlands xi
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Contributors
Attie T. J. J. Go • Department of Obstetrics/Gynecology, VU University Medical Center, Amsterdam, The Netherlands Esther Guetta • Danek Gertner Institute of Human Genetics, Chaim Sheba Medical Center, Tel-Hashomer, Israel Sinuhe Hahn • Laboratory of Prenatal Medicine and Gynecological Oncology, Department of Biomedicine, University Women’s Hospital, Basel, Switzerland Klaus-Hinrich Heermann • Department of Virology, University of Göttingen, Göttingen, Germany Wolfgang Holzgreve • Laboratory of Prenatal Medicine, University Women’s Hospital/Department of Research, Basel, Switzerland Dorothy J. Huang • Laboratory of Prenatal Medicine, University Women’s Hospital/Department of Research, Basel, Switzerland Laird G. Jackson • Department of Obstetrics and Gynecology, Drexel University College of Medicine, Philadelphia, PA Kirby L. Johnson • Division of Genetics, Departments of Pediatrics, Obstetrics, and Gynecology, Tufts-New England Medical Center and Floating Hospital for Children, Tufts University School of Medicine, Boston, MA Emmanuel Kanavakis • Department of Medical Genetics, National and Kapodistiran University of Athens, St. Sophia’s Children’s Hospital, Athens, Greece Catherine D. Kashork • Signature Genomics Laboratories, LLC, Spokane, WA Kada Krabchi • Science of Genetics, Department of Pediatrics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Quebec, Canada Olav Lapaire • Division of Genetics, Departments of Pediatrics, Obstetrics, and Gynecology, Tufts-New England Medical Center and Floating Hospital for Children, Tufts University School of Medicine, Boston, MA; University Women’s Hospital/Department of Obstetrics and Gynecology, Basel, Switzerland Tobias J. Legler • Department of Transfusion Medicine, University of Göttingen, Göttingen, Germany Ying Li • Laboratory of Prenatal Medicine, University Women’s Hospital/Department of Research, Basel, Switzerland Thomas Liehr • Institute of Human Genetics and Anthropology, Friedrich-Schiller-University Jena, Jena, Germany Zhong Liu • Hefei Red Cross Blood Center, Hefei, People’s Republic of China
Contributors
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Y. M. Dennis Lo • Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China Deborah G. Maddocks • Centre for Research in Biomedicine, University of the West of England, Bristol, UK Kathy Mann • Cytogenetics Department, Guy’s Hospital, London, UK Susanne Mergenthaler-Gatfield • Laboratory of Prenatal Medicine, University Women’s Hospital/Department of Research, Basel, Switzerland Andres Metspalu • Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia; The Estonian Biocentre, MDC of United Laboratories of the Tartu University Hospital, Tartu, Estonia; Estonian Genome Project Foundation, Tartu, Estonia Monique A. M. Mulders • Department of Clinical Chemistry, VU University Medical Center, Amsterdam, The Netherlands Matthew R. Nelson • Sequenom, Inc., San Diego, CA Takashi Okai • Department of Obestetrics and Gynecology, Showa University School of Medicine, Tokyo, Japan Cees B. M. Oudejans • Department of Clinical Chemistry, VU University Medical Center, Amsterdam, The Netherlands Leah Peleg • Danek Gertner Institute of Human Genetics, Chaim Sheba Medical Center, Tel-Hashomer, Israel Erwin Petek • Department of Human Biology and Medical Genetics, Medical University of Graz, Graz, Austria Barbara Pertl • Department of Obstetrics and Gynecology, Medical University of Graz, Graz, Austria Janne Pullat • Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia; The Estonian Biocentre, Tartu, Estonia Yuditiya Purwosunu • Department of Obstetrics and Gynecology, Showa University School of Medicine, Tokyo, Japan Chinnapapagari Satheesh Kumar Reddy • Laboratory of Prenatal Medicine, University Women’s Hospital/Department of Research, Basel, Switzerland Jan Schouten • MRC-Holland bv, Amsterdam, The Netherlands Akihiko Sekizawa • Department of Obstetrics and Gynecology, Showa University School of Medicine, Tokyo, Japan Lisa G. Shaffer • Signature Genomics Laboratories, LLC, Spokane, WA; Health Research and Education Center, Washington State University, Spokane, WA Aicha Ait Soussan • Sanquin Research, Amsterdam, The Netherlands Aaron Theisen • Signature Genomics Laboratories, LLC, Spokane, WA
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Contributors
Joanne Traeger-Synodinos • Department of Medical Genetics, National and Kapodistiran University of Athens, St. Sophia’s Children’s Hospital, Athens, Greece Nancy B. Y. Tsui • Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China C. Ellen van der Schoot • Sanquin Research, Amsterdam, The Netherlands Marie van Dijk • Department of Clinical Chemistry, VU University Medical Center, Amsterdam, The Netherlands John M. G. van Vugt • Department of Obstetrics/Gynecology, VU University Medical Center, Amsterdam, The Netherlands Allerdien Visser • Department of Clinical Chemistry, VU University Medical Center, Amsterdam, The Netherlands Christina Vrettou • Department of Medical Genetics, National and Kapodistiran University of Athens, St. Sophia’s Children’s Hospital, Athens, Greece; Athens University Research Institute for Prevention and Treatment of Genetic and Malignat Diseases of Childhood, St. Sophia’s Children’s Hospital, Athens, Greece Anja Weise • Institute of Human Genetics and Anthropology, Friedrich-Schiller-University Jena, Jena, Germany Ju Yan • Science of Genetics, Department of Paediatrics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Quebec, Canada Bauke Ylstra • Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands Bernhard G. Zimmermann • Centre for Research in Biomedicine, University of the West of England, Bristol, UK; DRI (Dental Research Institute), Center for Health Sciences, University of California, Los Angeles, CA Xiao Yan Zhong • Laboratory of Prenatal Medicine, University Women’s Hospital/Department of Research, Basel, Switzerland
