Thomas Liehr Editor Fluorescence In Situ Hybridization (FISH) – Application Guide 123 .

The use of general descriptive names. All rights are reserved. in this publication does not imply. reproduction on microfilm or in any other way. 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. USA. reprinting. and storage in data banks. whether the whole or part of the material is concerned.com .de Cover illustration: Mapping of a gene-specific plasmid clone along circular P1 molecules (photo by Heinz-Ulli G. Germany Printed on acid-free paper 9 8 7 6 5 4 3 2 1 springer. Violations are liable for prosecution under the German Copyright Law. recitation. etc. Berkeley CA. Cover design: deblik Berlin. specifically the rights of translation. Duplication of this publication or parts thereof is permitted only under the provisions of the German Copyright Law of September 9. Thomas Liehr Institut für Humangenetik und Anthropologie Kollegiengasse 10 07743 Jena Germany i8lith@mti. broadcasting.uni-jena. and permissions for use must always be obtained from Springer-Verlag. University of California. trademarks. in its current version. see Chap. registered names. 1965. reuse of illustrations. 25) ISBN 978-3-540-70580-2 e-ISBN 978-3-540-70581-9 Library of Congress Control Number: 2008930215 © 2009 Springer-Verlag Berlin Heidelberg This work is subject to copyright.Editor Dr. Weier.

cell biology. The FISH Application Guide initially provides an overview of the (historical) development of molecular cytogenetics. as well as the application of molecular cytogenetics to zoology. Apart from cytogeneticists. and applications of them are presented in 36 chapters by authors from ten different countries around the world. Jena April 2008 Thomas Liehr v . an exclusive collection of internet resources related to cytogenetics. newcomers to the field of cytogenetics. including array CGH. The book not only provides the reader with basic and background knowledge on the topic. the multiple approaches and probe sets that are now available for these techniques are described. molecular cytogeneticists. oncology. its basic procedures. and human and clinical geneticists. and their potential for use in combination with other approaches. comprehensive and unique book is a valuable resource for lecturers and students. This up-to-date. the equipment required. Finally. As comparative genomic hybridization (CGH). as well as specialists in FISH techniques. this book is also of the greatest relevance to those working in the fields of reproduction medicine. botany. their availability. is currently indispensable for precisely characterizing minimal chromosomal aberrations. These are followed by chapters on various multicolor FISH probe sets. hematology. pathology. CGH and array-based chip techniques are reviewed. The possible applications that are shown encompass the characterization of marker chromosomes. molecular cytogenetics and molecular genetics is given.Preface This book is a unique source of information on the present state of the exciting field of molecular cytogenetics and how it can be applied in research and diagnostics. The book then describes tips and tricks for making different tissues available for molecular cytogenetic studies. cryptic cytogenetic aberrations and epigenetic changes in humans by interphase and metaphase cytogenetics. botany and microbiology. and probe generation. but also gives detailed protocols that show how molecular cytogenetics is currently performed by specialists in this field. and protocols that describe how to perform them are also provided. evolutionary biology and microbiology. The basic techniques of fluorescence in situ hybridization and primed in situ hybridization (PRINS) are outlined. studies of nuclear architecture. zoology.

............................... and Joan Aurich-Costa Microscopy and Imaging Systems . Nadezda Kosyakova.......... Fengtang Yang............................. Petra Paulasova....... Bee Ling Ng.. Carter ISH Probes Derived from BACs.................................................... Probes and Equipment Molecular Cytogenetic Applications in Diagnostics and Research: An Overview..... Leah Zamechek...................... Ivan Iourov 3 2 23 3 35 4 53 5 61 6 67 7 75 vii .Contents Part I 1 Molecular Cytogenetics.... Vivien Klaschka. Nadezda Kosyakova................ Nedime Serakinci and Steen Kølvraa Molecular Cytogenetics: The Standard FISH and PRINS Procedure ................................ Thomas Liehr and Franck Pellestor Generation of Paint Probes by Flow-Sorted and Microdissected Chromosomes ........... Anja Weise. and Thomas Liehr PNA-FISH Technique for In Situ Assessment of Aneuploidy ...... Kristin Mrasek..... Vladimir Trifonov................... Hasmik Mkrtchyan.. and Nigel P............... Sean Bradley..................... Madeleine Gross.. Including Microwave Treatment for Better FISH Results ............ Franck Pellestor............................... and Samir Hamamah Oligonucleotide FISH Probes...................................................................................

.............................................. Hasmik Mkrtchyan... Katja Behr.... and Thomas Liehr Application of FISH to Archival Cytogenetic Slides ..... Amniocytes................... and Fibroblasts................................ Vladimir A............... and Willem Rens FISH Applications in Different Tissue Preparations 85 9 99 Part II 10 Pre............. Including Nucleus Extraction ..... Anja Weise and Thomas Liehr Prenatal Diagnostics on Uncultured Amniocytes ... Hasmik Mkrtchyan.............. Maria Oliver-Bonet Characterization of Marker Chromosomes 113 11 123 12 131 13 137 14 141 15 147 16 157 Part III 17 Multiplex FISH and Spectral Karyotyping . Thomas Liehr and Erich Gebhart Characterization of Mosaicism in Various Easy-to-Acquire Body Tissues Such as Buccal Smears... Spermatocytes and Oocytes ............... Anna Polityko........ and Hans-Jürgen Arens Tumorcytogenetic Diagnostics and Research on Uncultured Blood or Bone Marrow and Smears ..... Vera Witthuhn............... Hair Root Cells or Urine ....................................................... Nadezda Kosyakova........................... Anja Weise......... Madeleine Gross...... Nadezhda N. Joana Melo............ Thomas Liehr.................. Michael Sommerauer and Ingrid Feuerbacher FISH With and Without COT1 DNA ..... Thomas Liehr and Marina Manvelyan FISH on Sperms.. and Lukrecija Brecevic 175 .... Madeleine Gross............ Vorobieva........... Chorion.and Postnatal Diagnostics and Research on Peripheral Blood.. Ralf Glaubitz........... Anita Heller...... Hasmik Mkrtchyan... Sophie Hinreiner................................. Kristin Mrasek....... Trifonov...................... and Thomas Liehr Characterization of Archived Formalin-Fixed/ Paraffin-Embedded or Cryofixed Tissue........ Bernd Eiben.................viii Contents 8 Optical Filters for FISH .. Kristin Mrasek......

............... Daniela Reich......... Anja Weise..................... and Thomas Liehr Characterization of Cryptic and Epigenetic Aberrations 183 19 193 20 217 21 231 22 243 23 251 Part IV 24 Subtelomeric and/or Subcentromeric Probe Sets . and Roderick A........ Kristin Mrasek... Greulich-Bode........ Madeleine Gross.... Sophie Hinreiner... Ulrike Keller... Christine J................................. Anja Weise........ and Thomas Liehr 261 25 269 26 293 .... and Heinz-Ulli G.. Kristin Mrasek.... Hasmik Mkrtchyan..... Vladimir Trifonov........ Luitpold Distel....... Kristin Mrasek. Lesley Lawrenson..... Anja Weise........ Nadezda Kosyakova... Nadezda Kosyakova..... Vivien Klaschka..... Elisabeth Ewers......... Weier... and Henry H.. Steve Bremer.......... Heike Nelle................................. Thomas Liehr................... Ye... and Thomas Liehr Quantitative DNA Fiber Mapping.....F.......... Weier Parental Origin Determination FISH: Pod-FISH ... Hasmik Mkrtchyan......... Joshua Stevens.... Karin M.... Kristin Mrasek. Madeleine Gross......................Q......... Maren Kaufmann........ MacLeod Simultaneous Fluorescence Immunostaining and FISH .......................................... Octavian Henegariu Three-Color FISH for the Detection of Individual Radiosensitivity .............. Heng Color-Changing Karyotyping (CCK)..... Karen J.... Karin M........ Ye................ Guo Liu........... Jingly F...... and Susann Neubauer FISH Banding Techniques.. Greulich-Bode........... Vivien Klaschka.................. and Anja Weise cenM-FISH Approaches ....... Klaus Gilbertz... an M-FISH/SKY Alternative ....Contents ix 18 Tips and Tricks for mFISH . Chun-Mei Lu.......... Mei Wang...................... Marina Manvelyan....... Nadine Rüdiger.....

........ Ilia V.. Iourov................. and Erasmo Neviani Comparative Genomic Hybridization (CGH) and Array CGH 323 30 347 31 361 32 365 33 395 Part VII 34 Micro-CGH: Microdissection-Based Comparative Genomic Hybridization ....................................................... Peng Zhang and Bernd Friebe FISH in Food Microbiology .................. Joris R.................................. Marina Manvelyan...... and Yuri B..x Contents Part V 27 Interphase FISH and Characterization of the Nuclear Architecture Interphase FISH: Detection of Intercellular Genomic Variations and Somatic Chromosomal Mosaicism ............................ Ivan Y......................... Anita Heller and Thomas Liehr Array CGH: Opening New Horizons ............................................................. and Thomas Liehr Applications of FISH in Zoology................................ Monica Gatti..... Fengtang Yang and Alexander S...................... Yurov Three-Dimensional Interphase Analysis Enabled by Suspension FISH .......................................... Thomas Liehr FISH on Plant Chromosomes..... Soloviev............ Ulf Steinhaeuser...... Samarth Bhatt.................. Danilo Ercolini...... Vermeesch Internet Links for FISH 411 35 421 Part VIII 36 FISH and Chips on the Internet ................................................................................................................ Svetlana G.... Friederike Hunstig............................. Botany and Microbiology 301 28 313 Part VI 29 Animal Probes and ZOO-FISH ....................................... Harry Scherthan FISH on Insect Cells Transfected with Heterologous DNA: A Single-Cell-Directed Approach .... Benedetta Bottari... Vorsanova.............. 447 .......................... Thomas Liehr and Anja Weise 441 Index ................................... Graphodatsky FISH Targeting of Chromosomes and Subchromosomal Regions in Yeast.......

KG.unipr. USA.com Nigel P. 65205 Wiesbaden. Cambridge CB10 1SA. Cambridge. Montpellier. e-mail: lbr25@hotmail.Arens@abbott. Max-Planck-Ring 2. Germany.com Katja Behr Institut für Humangenetik und Anthropologie. via Usberti 11/A. Inc. Evolution.com Joan Aurich-Costa One Cell Systems. UK. France. Cambridge. Montpellier. e-mail: ssbhatt@bcm. France and University of Montpellier I. e-mail: Hans-Juergen. Italy. Department of Reproduction Biology. Montpellier.bottari@nemo. Wellcome Trust Genome Campus.tmc. Biology of Microorganisms. USA. e-mail: sean. Abbott GmbH & Co.edu Benedetta Bottari Department of Genetics.ac. MA 02139.it Sean Bradley One Cell Systems. Croatia. 43100 Parma. University of Parma.com Lukrecija Brecevic School of Medicine. Anthropology.de Samarth Bhatt INSERM U847. e-mail: joan@onecell. Salata 12.Contributors Hans-Jürgen Arens Abbott Molecular. 100 Inman Street. 07743 Jena. HR-10000 Zagreb.. Croatian Institute for Brain Research. e-mail: benedetta. Inc. MA. e-mail: npc@sanger. Germany. MA. Hinxton.uni-jena. MA 02139.bradley@onecell. e-mail: i3beka@mti. Carter Wellcome Trust Sanger Institute.uk xi .. Kollegiengasse 10. 100 Inman Street. CHU Montpellier. France.

91054 Erlangen.de Klaus Gilbertz Institut für Radiobiologie der Bundeswehr in Verbindung mit der Universität Ulm. Germany. e-mail: eiben@eurogen. Germany. University Erlangen Nürnberg. KS 66506-5502. e-mail: glaubitz@eurogen. Neuherbergstraße 11.gatti@unipr. e-mail: ercolini@unina. e-mail: friebe@ksu. e-mail: if@ahf. e-mail: KlausGilbertz@bundeswehr. Schwabachanlage 10.org Ralf Glaubitz Institut für Laboratoriumsmedizin und klinische Genetik Nordrhein und Labor wagnerstibbe. 07743 Jena.distel@uk-erlangen. Kansas State University. e-mail: ewel@mti. e-mail: monica.de Danilo Ercolini School of Biotechnological Sciences. 72005 Tübingen. Germany. Wheat Genetic and Genomic Resources Center. Biology of Microorganisms. via Usberti 11/A. e-mail: egebhart@t-online. e-mail: Luitpold.it Elisabeth Ewers Institut für Humangenetik und Anthropologie. Department of Food Science. Germany.xii Contributors Luitpold Distel Department of Radiation Oncology. 80937 München. Portici. Evolution. Germany. Anthropology. 27. 45127 Essen. 43100 Parma. Kollegiengasse 10. Manhattan. University of Naples Federico II.edu Monica Gatti Department of Genetics. Germany.de . University of Parma. Italy. Universtätstr. 45127 Essen. Willy Brandt Platz 4. USA. Germany. Italy.de Bernd Friebe Department of Plant Pathology.uni-jena. via Università 100. 80055.de Ingrid Feuerbacher AHF analysentechnik AG.it Erich Gebhart Institut für Humangenetik.de Bernd Eiben Institut für Laboratoriumsmedizin und klinische Genetik Nordrhein und Labor wagnerstibbe. Willy Brandt Platz 4. 91054 Erlangen.

edu Henry H. Iourov National Research Center of Mental Health.ru Karin M. 10 Amistad Street. Germany. Abteilung Genetik der Hautkarzinogenese.de Octavian Henegariu Department of Immunobiology. 371 avenue du Doyen Gaston Giraud.uni-jena. Yale University. New Haven. DKFZ/ZMBH Allianz. MI 48201.henegariu@yale. Kollegiengasse 10. 07743 Jena. e-mail: hheng@med. e-mail: s-hamamah@chu-montpellier.Hunstig@mti. Russian Academy of Medical Sciences.. Detroit. e-mail: octavian.de Friederike Hunstig Institut für Humangenetik und Anthropologie. CHRU Montpellier. Heng Center for Molecular Medicine and Genetics. e-mail: Friederike. USA. 630090 Novosibirsk.Contributors xiii Alexander S.com . Germany. e-mail: madeleine. Zagorodnoe sh. Germany. Kollegiengasse 10. Wayne State University School of Medicine.gross@dkfz-heidelberg. e-mail: ahel@mti. 07743 Jena. Graphodatsky Institute of Cytology and Genetics. Russian Federation. 07743 Jena. e-mail: graf@bionet. Detroit. Russian Academy of Sciences. Germany. e-mail: ivan_iourov@yahoo. Germany. 34295 Montpellier Cedex 5. Karmanos Cancer Institute.greulich@dkfz-heidelberg.wayne.edu Sophie Hinreiner Institut für Humangenetik und Anthropologie.uni-regensburg. 69120 Heidelberg. e-mail: k. MI 48201. Russian Federation. USA. 102A. Wayne State University School of Medicine. France.hinreiner@klinik. CT 06519.Q.uni-jena. 07743 Jena.de Ivan Y.nsc. Greulich-Bode Deutsches Krebsforschungszentrum (DKFZ). Im Neuenheimer Feld 280. Service de Médecine et Biologie de la Reproduction. Hôpital Arnaud de Villeneuve.de Madeleine Gross Institut für Humangenetik und Anthropologie. USA.fr Anita Heller Institut für Humangenetik und Anthropologie. Kollegiengasse 10. e-mail: sophie. 2. Kollegiengasse 10.de Samir Hamamah INSERM U847. 119152 Moscow.

Wayne State University School of Medicine. e-mail: gliu@med.uni-jena. e-mail: Ulrike. Universtätstr. Tai Ping.edu Thomas Liehr Institut für Humangenetik und Anthropologie. 07743 Jena. Germany.de Marina Manvelyan Department of Genetic and Laboratory of Cytogenetics. Institut für Humangenetik und Anthropologie. Armenia. Berkeley. Germany. e-mail: marina_manv@yahoo. e-mail: llawrens@med. Kollegiengasse 10. Department of Cell Cultures.com . Germany. Germany. Detroit. Vejle County Hospital. Alex Manoukian Str. USA. MI 48201.ncit.uni-jena. CA.regionsyddanmark. Vejle. 27. Kollegiengasse 10. e-mail: rml@dsmz.de Vivien Klaschka Institut für Humangenetik und Anthropologie.de Lesley Lawrenson Center for Molecular Medicine and Genetics. 07743 Jena. ROC.wayne. 1. e-mail: klavi@mti. MacLeod DSMZ – German Collection of Microorganisms and Cell Cultures. Germany. State University.wayne. Present address: Department of Chemical Engineering.de Steen Koelvraa Department of Clinical Genetics. USA. Detroit. 91054 Erlangen.edu Chun-Mei Lu E. 07743 Jena. Wayne State University School of Medicine. USA. Taichung. Germany.Keller@uk-erlangen. e-mail: kosna@mti. 07743 Jena. e-mail: Steen. Denmark.xiv Contributors Ulrike Keller Department of Radiation Oncology.dk Nadezda Kosyakova Institut für Humangenetik und Anthropologie. MI 48201. Kollegiengasse 10.uni-jena. e-mail: i8lith@mti. University of California.F.edu. Life Sciences Division.de Guo Liu Center for Molecular Medicine and Genetics. University Erlangen Nürnberg. e-mail: lucm@chinyi. National Chin-Yi University of Technology. 38124 Braunschweig. 375025 Jerewan. Inhoffenstraße 7B. Lawrence Berkeley National Laboratory (LBNL). Taiwan 411. 35 Chungshan Road.Koelvraa@vgs.O.tw Roderick A. Section 1. Kollegiengasse 10.

uni-jena. 375025 Jerewan.pt Hasmik Mkrtchyan Department of Genetic and Laboratory of Cytogenetics. e-mail: maria. V uvalu 84. Universitat Autònoma de Barcelona. France. Czech Republic. Service de Médecine et Biologie de la Reproduction.it Bee Ling Ng Wellcome Trust Sanger Institute. Kollegiengasse 10.neviani@unipr. Germany.de Heike Nelle Institut für Humangenetik und Anthropologie.fr . 34295 Montpellier Cedex 5. Kollegiengasse 10.uni-jena. and Klinik für Kinder & Jugendmedizin.cj. Biology of Microorganisms. Faculdade de Medicina da Universidade de Coimbra.de Susann Neubauer Praenatalmedicine and Genetics Nürnberg. 3004-504 Coimbra.cat Petra Paulasova Centre of Assisted Reproduction and Reproductive Genetics. 07743 Jena.de Kristin Mrasek Institut für Humangenetik und Anthropologie. Edifici M. Bankgasse 3. e-mail: erasmo. Rua Larga.uk Maria Oliver-Bonet Unitat de Biologia Cellular i Genètica Mèdica. via Usberti 11/A.ac. Bellaterra. 43100 Parma. Kochstraße 2. Spain. e-mail: kmra@mti. University of Parma. Armenia. 08193. 1. Anthropology.uc. e-mail: hene@mti. Evolution. 90402 Nürnberg. CHRU Montpellier. Germany. Kollegiengasse 10.com Erasmo Neviani Department of Genetics.cz Franck Pellestor INSERM U847. 371 avenue du Doyen Gaston Giraud. 07743 Jena.Contributors xv Joana Melo Laboratório de Citogenética – Diagnóstico Prénatal. e-mail: s. Facultat de Medicina. e-mail: jbmelo@cnc. e-mail: f-pellestor@chu-montpellier. Portugal. e-mail: hamk@mti.paulas@post. Hôpital Arnaud de Villeneuve. UK. 07743 Jena.neubauer@praenatal. and Institut für Humangenetik und Anthropologie. Alex Manoukian Str. Cambridge CB10 1SA. 150 06 Prague 5. e-mail: petra. Italy. e-mail: bln@sanger.uni-jena. Wellcome Trust Genome Campus.oliver@uab. Hinxton. State University. Germany. Motol Hospital.

Vejle.. Russian Federation. 72005 Tübingen. Kollegiengasse 10. 80937 Munich. Kollegiengasse 10. Russian Federation. Germany. Belarus. e-mail: ustein@tele2. MI 48201. 119152 Moscow. e-mail: ivan_iourov@yahoo. e-mail: nadine_ruediger81@web. 07743 Jena. Germany. Germany.nsc.de Joshua Stevens Center for Molecular Medicine and Genetics. Southern Denmark University.de Nedime Serakinci Institute of Regional Health Services. 630090 Novosibirsk. e-mail: polityko@yahoo. e-mail: wr203@mole. 07743 Jena. 07743 Jena. e-mail: scherth@web. University of Cambridge. Telomere and Aging Group.cam.com Michael Sommerauer AHF analysentechnik AG. Neuherbergstr. Cambridge CB3 OES. Madingley Road. Vejle County Hospital.wayne. USA. Denmark.xvi Contributors Anna Polityko Institut of Hereditary Diseases. e-mail: jstevens@genetics.de Willem Rens Department of Veterinary Medicine. Germany. 2.ac. e-mail: vlad@bionet.de Harry Scherthan Institut für Radiobiologie der Bundeswehr. Russian Academy of Medical Sciences. Germany.com Daniela Reich Institut für Humangenetik und Anthropologie. e-mail: nedser@biopark-vejle.uk Nadine Rüdiger Institut für Humangenetik und Anthropologie. Wayne State University School of Medicine. Zagorodnoe sh.ru . and Department of Clinical Genetics. Soloviev National Research Center of Mental Health.bio. 220053 Minsk. Detroit. e-mail: ms@ahf. Orlovska Street 66.(IRS). 11.edu Vladimir Trifonov Institute of Cytology and Genetics.uni-jena. Russian Academy of Sciences. Kollegiengasse 10. e-mail: Reich@mti. UK.de Ulf Steinhaeuser Institut für Humangenetik und Anthropologie.dk Ilia V.

e-mail: svorsanova@mail. University of California.. 119152 Moscow. Hinxton. Wayne State University School of Medicine. USA. Kollegiengasse 10.gov Heinz-Ulli G. Russian Academy of Medical Sciences.ac. 400 Oyster Point Blvd. Lavrentev av. 3000 Leuven. LLC.uni-jena. e-mail: jinglyw@gmail. Russian Federation.nsc. e-mail: ugweier@lbl. USA. MI 48201.be Nadezhda N. Russian Federation. Detroit. 10. Weier Life Sciences Division. 127412 Moscow.ru Mei Wang US DOE Joint Genome Institute/E. Weier Life Sciences Division. LBNL. SeeDNA Biotech Inc. MS 74-157. 2800 Mitchell Drive.. Herestraat 49. Rosmedtechnologii.uk Christine J. e-mail: Christine@seedna.gov Jingly F. LBNL.O. Yurov National Research Center of Mental Health. Germany. Cambridge CB10 1SA. 1 Cyclotron Road. Berkeley. Ye Center for Molecular Medicine and Genetics.ru Svetlana G. USA.vermeesch@med. University Hospital Gasthuisberg. e-mail: vorn@bionet. Germany. Canada.com .uni-jena. Zagorodnoe sh. e-mail: mwang@lbl. e-mail: i8lith@mti. CA 94598. LBNL. Vorobieva Institute of Cytology and Genetics.Contributors xvii Joris Vermeesch Center for Human Genetics. Wellcome Trust Genome Campus..de Fengtang Yang Wellcome Trust Sanger Institute. e-mail: y_yurov@yahoo. CA 94720.com Anja Weise Institut für Humangenetik und Anthropologie. Kollegiengasse 10. Taldomskaya 2. Windsor.O. Russian Federation. South San Francisco. University of California. E. e-mail: fy1@sanger. CA. CA 94080. Reprogenetics. 07743 Jena. ON. E. Walnut Creek. USA. 2. e-mail: aweise@mti.O. Berkeley.com Yuri B. Vorsanova Institute of Pediatrics and Children Surgery. e-mail: joris. USA. Belgium.kuleuven. UK.de Vera Witthuhn Institut für Humangenetik und Anthropologie. 07743 Jena. 630090 Novosibirsk.

au . University of Sydney. e-mail: pengzhang@camden. Inc. e-mail: leah. Cambridge.zamechek@onecell. MA 02139.usyd. Australia. USA. Camden NSW 2570. 107 Cobbitty Road. 100 Inman Street.xviii Contributors Leah Zamechek One Cell Systems.com Peng Zhang Plant Breeding Institute.edu..

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