Fluorescence In Situ Hybridization (FISH): Application Guide

588 Pages·2016·11.52 MB·English

by  Thomas Liehr

Thomas Liehr Editor
Fluorescence In
Situ Hybridization
(FISH)
Application Guide
Second Edition
S P H
PRINGER ROTOCOLS ANDBOOKS
Moreinformation aboutthis series athttp://www.springer.com/series/8623
Fluorescence In Situ
Hybridization (FISH)
Application Guide
Editor
Thomas Liehr
€
Institut fur Humangenetik, Jena, Germany
Second Edition
Editor
ThomasLiehr
Institutfu€rHumangenetik
Jena,Germany
ISSN1949-2448 ISSN1949-2456 (electronic)
SpringerProtocolsHandbooks
ISBN978-3-662-52957-7 ISBN978-3-662-52959-1 (eBook)
DOI10.1007/978-3-662-52959-1
LibraryofCongressControlNumber:2016954653
©Springer-VerlagBerlinHeidelberg2009,2017
Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpartofthematerialis
concerned,specificallytherightsoftranslation,reprinting,reuseofillustrations,recitation,broadcasting,reproduction
onmicrofilmsorinanyotherphysicalway,andtransmissionorinformationstorageandretrieval,electronicadaptation,
computersoftware,orbysimilarordissimilarmethodologynowknownorhereafterdeveloped.
Theuseofgeneraldescriptivenames,registerednames,trademarks,servicemarks,etc.inthispublicationdoesnotimply,
evenintheabsenceofaspecificstatement,thatsuchnamesareexemptfromtherelevantprotectivelawsandregulations
andthereforefreeforgeneraluse.
Thepublisher,theauthorsandtheeditorsaresafetoassumethattheadviceandinformationinthisbookarebelievedto
betrueandaccurateatthedateofpublication.Neitherthepublishernortheauthorsortheeditorsgiveawarranty,
expressorimplied,withrespecttothematerialcontainedhereinorforanyerrorsoromissionsthatmayhavebeenmade.
Printedonacid-freepaper
ThisSpringerimprintispublishedbySpringerNature
TheregisteredcompanyisSpringer-VerlagGmbHBerlinHeidelberg
Foreword
Of all biological structures, chromosomes are the most fascinating. They embody the
essence of life, containing the DNA blueprint of evolution and the source of variation in
allorganisms.Onlybylearningaboutchromosomescanoneunderstandthelifecycleofthe
cell and the mechanisms of heredity. A full appreciation of genetics and molecular biology
requiresknowledgeofchromosomestructureandfunction.Thereisbeautyintheimageof
the chromosome, fixed, stained and observed with the compound microscope. The stains
used in the discovery of bacteria in the nineteenth century led also to the serendipitous
discovery of chromosomes. As methods improved, their detailed structure became more
apparent. Chromosome variation in number and morphology were found to be species
characteristics, and a pair associated with sex determination could be identified in many
species. Each advance in chromosome biology followed an advance in chromosome tech-
nology.Thisisthehistoryofcytogenetics.
My fascination with chromosomes makes it a great pleasure for me to read about
modern methods for examining them. The second edition of this Application Guide to
FISHcontainstheessentialprotocolsrequiredbyanyoneembarkingonastudyofmolecular
cytogenetics and its various applications. These protocols are laid out by an international
group of experts with a track record of publications based on firsthand experience of the
techniques they describe. The book contains all the well-tried recipes required by the
beginner for making fluorescence-labelled probes used in the diagnosis of chromosome
aberrationsinpatientswithcomplexdisordersincludingcancer,fortheprenataldiagnosisof
genetic disease, for gene mapping and for the elucidation of phylogenetic relationships
through cross-species chromosome painting. The preparation of the three main types of
DNA probes is described: whole chromosome painting probes made from chromosome-
specific DNA labelled by PCR and obtained by flow sorting or microdissection; locus-
specific probes isolated from DNA libraries and cloned in bacteria (BACs); and probes
containing tandem repeats of DNA sequence, such as centromeric, telomeric or ribosomal
DNA.Mostoftheseprobesarehybridizedtometaphasechromosomes,butcanbeusedalso
in interphase nuclei (to determine chromosome copy number) or in DNA fibre-FISH
(to determine order of close sequences). Other cytogenetic methods are not forgotten,
including several array-based comparative genome hybridization techniques useful for
identifying small duplications and deletions and for assessing genomic variation at the
molecularlevel.
Thefirsteditionwaswidelyused,andthissecondeditionnowfollowsaftersevenyears
andisgreatlyenhancedbytheadditionof17chaptersandthecarefulrevisionand/ornew
arrangement of all the original 36. The new additions include methods for breakpoint
mapping, for the measurement of telomere length, for the analysis of micronuclei, for the
study of epigenetic modifications and for much more. Also the aspect the exciting field of
chromosomesequencingisincludedinthelastchapterofthisedition.
ThomasLiehrhasnotonlygatheredtogetheradistinguishedteamofcontributorsbut
hasbeenpersonallyinvolvedascoauthorinmanyofthechaptersandhaseditedthemall.His
v
vi Foreword
outstandingcontributionstomolecularcytogeneticsarewellknownandservetoguarantee
the scientific quality of the publication. This is more than a global cookbook of delightful
chromosomefareandwillsurelyleadtomanyenjoyablefeaststocome!
CambridgeUniversityDepartmentofVeterinary MalcolmA.Ferguson-Smith
Medicine
Cambridge,UKJune2016
Preface to First Edition
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 basic
techniques offluorescence in situhybridization and primed insitu hybridization(PRINS)
are outlined, the multiple approaches and probe sets that are now available for these
techniquesaredescribed,and applicationsofthemarepresentedin36chaptersbyauthors
fromtendifferentcountriesaroundtheworld.Thebooknotonlyprovidesthereader with
basic and background knowledge on the topic but also gives detailed protocols that show
howmolecularcytogeneticsiscurrentlyperformedbyspecialistsinthisfield.
The FISH Application Guide initially provides an overview of the (historical) develop-
ment of molecular cytogenetics, its basic procedures, the equipment required, and probe
generation.Thebookthendescribestipsandtricksformakingdifferenttissuesavailablefor
molecularcytogeneticstudies.ThesearefollowedbychaptersonvariousmulticolorFISH
probe sets, their availability, and their potential for use in combination with other
approaches. The possible applications that are shown encompass the characterization of
markerchromosomes,crypticcytogeneticaberrations,andepigeneticchangesinhumansby
interphase and metaphase cytogenetics, studies of nuclear architecture, as well as the
applicationofmolecularcytogeneticstozoology,botany,andmicrobiology.Ascomparative
genomic hybridization (CGH), including array CGH, is currently indispensable for pre-
ciselycharacterizingminimalchromosomalaberrations,CGHandarray-basedchiptechni-
ques are reviewed, and protocols that describe how to perform them are also provided.
Finally, an exclusive collection of Internet resources related to cytogenetics, molecular
cytogenetics,andmoleculargeneticsisgiven.
This up-to-date, comprehensive, and unique book is a valuable resource for lecturers
and students, newcomers to the field of cytogenetics, as well as specialists in FISH techni-
ques.Apartfromcytogeneticists,molecularcytogeneticists,andhumanandclinicalgeneti-
cists,thisbookisalsoofthegreatestrelevancetothoseworkinginthefieldsofreproduction
medicine, oncology, hematology, pathology, cell biology, botany, zoology, evolutionary
biology,andmicrobiology.
Jena,Germany ThomasLiehr
April2008
vii
Contents
PrefacetoFirstEdition ....................................................... vii
AbouttheEditor............................................................. xiii
Background ................................................................ 1
ThomasLiehrandAnjaWeise
PART I REQUIRED EQUIPMENTAND PROBES FOR FISH PROCEDURES
MicroscopyandImaging..................................................... 17
IvanY.Iourov
OpticalFiltersandLightSourcesforFISH..................................... 27
MichaelSommerauer,IngridFeuerbacher,andAlexanderKrause
ClassificationofFISHProbes................................................. 43
ThomasLiehr
CommercialFISHProbes.................................................... 49
ThomasLiehr
GenerationofPaintProbesfromFlow-SortedandMicrodissected
Chromosomes .............................................................. 63
FengtangYang,VladimirTrifonov,BeeLingNg,NadezdaKosyakova,
andNigelP.Carter
FISH-Microdissection ....................................................... 81
NadezdaKosyakova,ThomasLiehr,andAhmedB.HamidAl-Rikabi
HomemadeLocus-SpecificFISHProbes:BacterialArtificialChromosomes ........ 101
ThomasLiehr
PART II FISH PROCEDURE
TheStandardFISHProcedure................................................ 109
ThomasLiehr,KatharinaKreskowski,MonikaZiegler,KatjaPiaszinski,
andKatharinaRittscher
MicrowaveTreatmentforBetterFISHResultsinaShorterTime ................. 119
AnjaWeiseandThomasLiehr
FISHwithandWithoutCOT1DNA.......................................... 123
VladimirA.Trifonov,NadezhdaV.Vorobieva,NataliaA.Serdyukova,
andWillemRens
Formamide-FreeFluorescenceInSituHybridization(FISH)..................... 135
EmanuelaV.Volpi
One-DayQuickFISH ....................................................... 141
Ga´borMe´hes,Tama´sCsonka,andKatalinHegyi
TelomereLengthMeasurementbyFISH....................................... 147
GordanaJoksic,IvanaJoksic,JelenaFilipovic´,andThomasLiehr
ix
x Contents
RNAImaginginLivingCells................................................. 153
BinMaandNaokoTanese
TheReplicativeDetargetingFISH(ReD-FISH)TechniqueinStudies
ofTelomereReplication...................................................... 159
NikolayRubtsovandNatalyaZhdanova
PART III MATERIAL SUITED FOR FISH APPLICATIONS IN HUMANS
Pre-andPostnatalDiagnosticsandResearchonPeripheralBlood,Bone
Marrow,Chorion,Amniocytes,andFibroblasts................................. 171
AnjaWeiseandThomasLiehr
ApplicationofFISHtoPreviouslyGTG-Bandedand/orEmbedded
CytogeneticSlides........................................................... 181
ThomasLiehrandMonikaZiegler
FISHinUncultivatedAmniocytes............................................. 185
AnjaWeise,MonikaZiegler,andThomasLiehr
TumorcytogeneticDiagnosticsandResearchonBloodandBoneMarrow
SmearsorEffusions.......................................................... 189
EyadAlhourani,MoneebA.K.Othman,ShaymaaS.HusseinAzawi,
andThomasLiehr
CharacterizationofMosaicisminDifferentEasy-to-AcquireBodyTissues
SuchAsBuccalSmears,SkinAbrasions,HairRootCells,orUrine ................ 195
ThomasLiehrandNadezdaKosyakova
CharacterizationofArchivedFormalin-Fixed/Paraffin-EmbeddedorCryofixed
Tissue,IncludingNucleusExtraction.......................................... 201
ThomasLiehr
FISHonSperm,SpermatocytesandOocytes ................................... 209
MariaOliver-Bonet
PART IV MULTICOLOR-FISH-PROBE SETS (MFISH) AND IMMUNOSTAINING
Two-toThree-ColorFISH .................................................. 227
ThomasLiehr,SvenHauke,andBrittaMeyer
MultiplexFISHandSpectralKaryotyping...................................... 233
ThomasLiehrandNadezdaKosyakova
FISHBandingTechniques ................................................... 241
ThomasLiehr,NadezdaKosyakova,andAnjaWeise
cenM-FISHApproaches ..................................................... 249
ThomasLiehr,AnjaWeise,andNadezdaKosyakova
Heterochromatin-DirectedmFISH(HCM-FISH) .............................. 257
ThomasLiehr,NadezdaKosyakova,AnjaWeise,andAhmedB.HamidAl-Rikabi
Subtelomericand/orSubcentromericProbeSets................................ 261
AnjaWeiseandThomasLiehr
BarCodingIsBack.......................................................... 271
ThomasLiehr,AhmedB.HamidAl-Rikabi,andAnjaWeise