Prenatal Diagnosis

357 Pages·2019·6.938 MB·English

by  Brynn Levy

Methods in
Molecular Biology 1885
Brynn Levy Editor
Prenatal
Diagnosis
Second Edition
M M B
ETHODS IN OLECULAR IO LO GY
SeriesEditor
JohnM.Walker
School of Lifeand MedicalSciences
University ofHertfordshire
Hatfield, Hertfordshire,AL109AB,UK
Forfurther volumes:
http://www.springer.com/series/7651
Prenatal Diagnosis
Second Edition
Edited by
Brynn Levy
Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia
University Irving Medical Center, New York, NY, USA
Editor
BrynnLevy
DepartmentofPathologyandCellBiology
VagelosCollegeofPhysiciansandSurgeons
ColumbiaUniversityIrvingMedicalCenter
NewYork,NY,USA
ISSN1064-3745 ISSN1940-6029 (electronic)
MethodsinMolecularBiology
ISBN978-1-4939-8887-7 ISBN978-1-4939-8889-1 (eBook)
https://doi.org/10.1007/978-1-4939-8889-1
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Preface
Ithasbeentenyearssincethefirsteditionofthisbookwaspublished.Overthisperiod,the
conceptof“genetictesting,”whichhistoricallyconjuredupthenotionofsingleassaysand
pinpoint precision in clinical diagnostics, has evolved to include a broader whole genome
testingapproachthatoftenleveragesbigdataandcomplexalgorithms.Assuch,wecannow
consider ourselves to be deeply entrenched in the genomics era where bioinformatics and
terabytes of data are an integral part of analysis and diagnostics. Indeed, the American
College of Medical Genetics officially changed their name to the American College of
MedicalGeneticsandGenomicstorecognizethisparadigmshift.
The biggest change in the field of prenatal diagnosis has been observed in the area of
cytogenomicswheremicroarrayandnext-generationsequencingtechnologieshavebecome
the preferable genomic tool for the assessment of preimplantation embryos and first and
second trimester fetuses. The introduction of these newer genomic technologies has had a
major effectonthesuccess rates ofIVF as demonstrated inrecent prospectiverandomized
clinicaltrials.Intraditionalprenataldiagnosis,chromosomalmicroarrayanalysis(CMA)has
been recommended for all pregnancies with a fetal structural anomaly and currently offers
themostcomprehensiveassessmentof fetalaneuploidy,aneusomy,andmicrodeletionsand
microduplicationspossible.
Whilemicroarraydiagnosticscurrentlyprovidesthemostcompletecytogenomicassess-
mentofthefetus,theappealofahighlysensitivenoninvasivebloodtestthatscreensforthe
common aneuploidies has made noninvasive prenatal testing (NIPT) one of the fastest-
adoptedgenetictests.Infact,intheUnitedStates,themassadoptionofNIPTisbelievedto
be the primary reason for the decline in the number of invasive prenatal diagnosis proce-
duresperformed.ItisimportanttoemphasizethatNIPT,initscurrentform,isascreening
test while CMA is a diagnostic test. As a screening test, NIPToffers superior detection of
Downsyndromeandtheothercommonaneuploidiescomparedtotraditionalbiochemical
markersandnuchaltranslucency(NT)measurements.However,asascreeningtest,itdoes
not cover the vast scope of genomic abnormalities that are detectable by CMA. NIPT has
alsobeendevelopedtopredictthefetalRhDgenestatusinordertoguidetargetedprenatal
anti-D prophylaxis and prevent hemolytic disease of the fetus and the newborn. This
approachhasbeenparticularlywellreceivedinEurope,especiallyinScandinavia.
Next-generation sequencing (NGS) entered the prenatal world predominantly for
aneuploidydetectioninpreimplantationembryosandfornoninvasivecopynumberassess-
mentofcell-freeDNA.Itisnowincreasinglyutilizedtoevaluatesinglenucleotidevariations
(SNVs)infetuseswithstructuralanomaliesaswellasassesscrypticcomplexrearrangements
andimbalancesinfetusescarryingapparentlybalancedtranslocations.Itislikelythatinthe
future NGS will serve to assess both SNVs and copy number changes in a single assay. In
order to replace CMA, NGS as a single test will need to match the current resolution and
accuracyofCMAtesting.Thiswillcertainlyrequiregreatercoverageofthegenomewhich
willonlybecomearealityforroutinetestingwhenwholegenomesequencingcostsdecrease.
Overthepastdecade,noveltechnologieshavebeenutilizedforthedevelopmentofnew
diagnostic tests. However, the newer prenatal tests have not necessarily replaced the older
ones. A prime reason pertains to payment/reimbursement of the new and often more
expensive tests. Payment/reimbursement in countries with national health systems and
v
vi Preface
evenbyprivatehealthinsurancecompaniesisoftennotapprovedasthenewtestsareusually
deemed“experimental”with“insufficientevidence”tosupportclinicalutility.Inaddition,
thereisoftenalargetimegapbeforethesetestsareuniversallyadoptedworldwideandeven
withinindividualcountries.Insomeinstances,thetimegapisdirectlyrelatedtotheamount
oftimeittakesfortheappropriateclinicaltrialstobeperformedtosupportclinicalutility.In
other cases, there may be a lack of the necessary expertise to interpret the more complex
genomicassays.Inmanycases,thedelayinadoptionhastodowiththeeconomicresources
available to purchase the genomic equipment as well as validate and implement the new
tests.Assuch,thereremainstremendousutilityformanyoftheoldstyleandlessexpensive
targetedtestslikeFISH,QF-PCRandMLPA.
This second edition of Prenatal Diagnosis is divided into three major sections; preim-
plantation genetic testing, traditional prenatal testing and finally non-invasive prenatal
testing. The first part of the book begins with a historical introduction to each of the
three major sections. Traditional prenatal testing methodologies that have served as the
goldstandardfordecadesremainanimportantaspectofthisbookastheycontinuetoserve
astheprimarytestingassaysinmanyregionsoftheworld.Newtothisbookaremethodol-
ogiesthatemploynextgenerationsequencingtechniquesandthesecanbefoundineachof
thethreeprimarysections.
Myappreciationandthanksgoestotheauthorsfortheirindividualcontributions.Their
willingness to share their protocols and experience provides a valuable resource to clinical
laboratoriesaroundtheglobe.
NewYork,NY,USA BrynnLevy
Contents
Preface ..................................................................... v
Contributors................................................................. ix
PART I HISTORICAL INTRODUCTION
1 TraditionalPrenatalDiagnosis:PasttoPresent ............................. 3
BrynnLevyandMelissaStosic
2 OverviewofPreimplantationGeneticDiagnosis(PGD):
HistoricalPerspectiveandFutureDirection................................ 23
JoeLeighSimpson,AnverKuliev,andSvetlanaRechitsky
3 NoninvasiveApproachestoPrenatalDiagnosis:Historical
PerspectiveandFutureDirections......................................... 45
LisaHui
PART II PREIMPLANTATION GENETIC TESTING
4 MolecularTestingforPreimplantationGeneticDiagnosis
ofSingleGeneDisorders ................................................ 61
RebekahS.Zimmerman,JenniferEccles,ChaimJalas,
NathanR.Treff,andRichardT.ScottJr.
5 DetectionofAneuploidyandUnbalancedRearrangements
UsingComparativeGenomicHybridizationMicroarrays .................... 73
LorenaRodrigoViv(cid:1)o andCarmenRubioLluesa
6 AneuploidyScreeningusingNextGenerationSequencing ................... 85
CengizCinnioglu,RefikKayali,TristanDarvin,AdedoyinAkinwole,
MilenaJakubowska,andGaryHarton
PART III TRADITIONAL PRENATAL DIAGNOSIS
7 DNAExtractionfromVariousTypesofPrenatalSpecimens.................. 105
OdeliaNahum,AmandaThomas,andBrynnLevy
8 AssessmentofMaternalCellContaminationinPrenatalSamples
byQuantitativeFluorescentPCR(QF-PCR)............................... 117
ChristieM.Buchovecky,OdeliaNahum,andBrynnLevy
9 RapidPrenatalAneuploidyScreeningbyFluorescenceInSitu
Hybridization(FISH) ................................................... 129
AnjaWeiseandThomasLiehr
10 PrenatalDetectionofChromosomeAneuploidybyQuantitative
FluorescencePCR ...................................................... 139
KathyMann,ErwinPetek,andBarbaraPertl
vii
viii Contents
11 MultiplexLigation-DependentProbeAmplification(MLPA)
forPrenatalDiagnosisofCommonAneuploidies ........................... 161
JanSchouten,PaulvanVught,andRobert-JanGaljaard
12 ChromosomalMicroarrayAnalysisUsingArrayComparative
GenomicHybridizationonDNAfromAmnioticFluid
andChorionicVillusSampling ........................................... 171
AnkitaPatel
13 PrenatalDiagnosisUsingChromosomalSNPMicroarrays................... 187
MythilyGanapathi,OdeliaNahum,andBrynnLevy
14 RapidDetectionofFetalMendelianDisorders:Thalassemia
andSickleCellSyndromes ............................................... 207
JoanneTraeger-Synodinos,ChristinaVrettou,
andEmmanuelKanavakis
15 PrenatalDiagnosisofCysticFibrosis ...................................... 221
AnastasiaM.Fedick,JinglanZhang,LisaEdelmann,
andRuthKornreich
16 PrenatalDiagnosisofTay-SachsDisease................................... 233
JinglanZhang,HongjieChen,RuthKornreich,andChunliYu
17 NextGenerationSequencingofPrenatalStructural
ChromosomalRearrangementsUsingLarge-InsertLibraries................. 251
BenjaminB.Currall,CarolineW.Antolik,
RyanL.Collins,andMichaelE.Talkowski
18 PrenatalDiagnosisbyWholeExomeSequencinginFetuses
withUltrasoundAbnormalities........................................... 267
VanessaFelice,AvinashAbhyankar,andVaidehiJobanputra
19 IsolationandCharacterizationofAmnioticFluid-Derived
ExtracellularVesiclesforBiomarkerDiscovery.............................. 287
BlakeEbertandAlexJ.Rai
PART IV NON-INVASIVE PRENATAL TESTING
20 QuadScreenTest,AMultiplexedBiomarkerAssayforPrenatalScreening
toAssessBirthDefects:TheColumbiaUniversityExperience
UsingtheBeckmanAccess2ImmunoassayAnalyzerandBenetechPRA....... 297
AwetTecleab,AlexK.Lyashchenko,andAlexJ.Rai
21 IsolationofCell-FreeDNAfromMaternalPlasma.......................... 309
JamesStrayandBernhardZimmermann
22 NoninvasiveDetectionofFetalAneuploidyUsingNext
GenerationSequencing.................................................. 325
KirstenJ.Curnow,RebeccaK.Sanderson,andSueBeruti
23 NoninvasiveAntenatalScreeningforFetalRHDinRhDNegative
WomentoGuideTargetedAnti-DProphylaxis............................. 347
FrederikBanchClausen,KlausRieneck,GretheRisumKrog,
BirgitteSuhrBundgaard,andMortenHanefeldDziegiel
Index ...................................................................... 361
Contributors
AVINASH ABHYANKAR (cid:1) MolecularDiagnostics,NewYorkGenomeCenter,NewYork,NY,
USA
ADEDOYINAKINWOLE (cid:1) IGENOMIXUSA,Torrance,CA,USA
CAROLINEW.ANTOLIK (cid:1) MassachusettsGeneralHospital,Boston,MA,USA;BroadInstitute,
HarvardMedicalSchool,Cambridge,MA,USA
SUEBERUTI (cid:1) Illumina,Inc.,SanDiego,CA,USA
CHRISTIEM.BUCHOVECKY (cid:1) DepartmentofPathologyandCellBiology,VagelosCollegeof
PhysiciansandSurgeons,ColumbiaUniversityIrvingMedicalCenter,NewYork,NY,
USA
BIRGITTESUHRBUNDGAARD (cid:1) DepartmentofClinicalImmunology,Section2034,
CopenhagenUniversityHospital,Copenhagen,Denmark
HONGJIECHEN (cid:1) MountSinaiGenomics,Inc.,DBASema4,NewYork,NY,USA;
DepartmentofGeneticsandGenomicSciences,IcahnSchoolofMedicineatMountSinai,
NewYork,NY,USA
CENGIZCINNIOGLU (cid:1) IGENOMIXUSA,Torrance,CA,USA
FREDERIKBANCHCLAUSEN (cid:1) DepartmentofClinicalImmunology,Section2034,Copenhagen
UniversityHospital,Copenhagen,Denmark
RYANL.COLLINS (cid:1) MassachusettsGeneralHospital,Boston,MA,USA;BroadInstitute,
HarvardMedicalSchool,Cambridge,MA,USA
KIRSTEN J.CURNOW (cid:1) Illumina,Inc.,FosterCity,CA,USA
BENJAMINB.CURRALL (cid:1) MassachusettsGeneralHospital,Boston,MA,USA;BroadInstitute,
HarvardMedicalSchool,Cambridge,MA,USA
TRISTANDARVIN (cid:1) IGENOMIXUSA,Torrance,CA,USA
MORTENHANEFELDDZIEGIEL (cid:1) DepartmentofClinicalImmunology,Section2034,
CopenhagenUniversityHospital,Copenhagen,Denmark;InstituteofClinicalMedicine
(IKM),CopenhagenUniversity,Copenhagen,Denmark
BLAKEEBERT (cid:1) DepartmentofPathologyandCellBiology,VagelosCollegeofPhysiciansand
Surgeons,ColumbiaUniversityIrvingMedicalCenter,NewYork,NY,USA
JENNIFERECCLES (cid:1) BaylorGenetics,Houston,TX,USA
LISAEDELMANN (cid:1) DepartmentofGeneticsandGenomicSciences,IcahnSchoolofMedicineat
MountSinai,NewYork,NY,USA;MountSinaiGenomics,Inc.,DBASema4Genomics,
NewYork,NY,USA
ANASTASIA M.FEDICK (cid:1) DepartmentofGeneticsandGenomicSciences,IcahnSchoolof
MedicineatMountSinai,NewYork,NY,USA;MountSinaiGenomics,Inc.,DBASema4
Genomics,NewYork,NY,USA
VANESSAFELICE (cid:1) MolecularDiagnostics,NewYorkGenomeCenter,NewYork,NY,USA
ROBERT-JANGALJAARD (cid:1) DepartmentofClinicalGenetics,ErasmusUniversityMedical
Center,Rotterdam,TheNetherlands
MYTHILYGANAPATHI (cid:1) DepartmentofPathologyandCellBiology,VagelosCollegeof
PhysiciansandSurgeons,ColumbiaUniversityIrvingMedicalCenter,NewYork,NY,
USA
GARYHARTON (cid:1) IGENOMIXUSA,Torrance,CA,USA
ix
x Contributors
LISAHUI (cid:1) DepartmentofPerinatalMedicine,MercyHospitalforWomen,Heidelberg,VIC,
Australia;DepartmentofObstetricsandGynaecology,UniversityofMelbourne,Parkville,
VIC,Australia;ReproductiveEpidemiology,MurdochChildren’sResearchInstitute,
Parkville,VIC,Australia
MILENAJAKUBOWSKA (cid:1) IGENOMIXUSA,Torrance,CA,USA
CHAIMJALAS (cid:1) FoundationforEmbryonicCompetence,BaskignRidge,NJ,USA
VAIDEHIJOBANPUTRA (cid:1) MolecularDiagnostics,NewYorkGenomeCenter,NewYork,NY,
USA;DepartmentofPathologyandCellBiology,VagelosCollegeofPhysiciansand
Surgeons,ColumbiaUniversityIrvingMedicalCenter,NewYork,NY,USA
EMMANUELKANAVAKIS (cid:1) DepartmentofMedicalGenetics,St.Sophia’sChildren’sHospital,
NationalandKapodistrianUniversityofAthens,Athens,Greece;GenesisGenomaLab,
Athens,Greece
REFIKKAYALI (cid:1) IGENOMIXUSA,Torrance,CA,USA
RUTHKORNREICH (cid:1) DepartmentofGeneticsandGenomicSciences,IcahnSchoolofMedicine
atMountSinai,NewYork,NY,USA;MountSinaiGenomics,Inc.,DBASema4
Genomics,NewYork,NY,USA
GRETHE RISUMKROG (cid:1) DepartmentofClinicalImmunology,Section2034,Copenhagen
UniversityHospital,Copenhagen,Denmark
ANVERKULIEV (cid:1) FloridaInternationalUniversity,Miami,FL,USA;ReproductiveGenetics
Institute,Inc.(RGI),Northbrook,IL,USA
BRYNNLEVY (cid:1) DepartmentofPathologyandCellBiology,VagelosCollegeofPhysiciansand
Surgeons,ColumbiaUniversityIrvingMedicalCenter,NewYork,NY,USA
THOMASLIEHR (cid:1) JenaUniversityHospital,InstituteofHumanGenetics,FriedrichSchiller
University,Jena,Germany
CARMENRUBIOLLUESA (cid:1) Igenomix,Valencia,Spain
ALEXK.LYASHCHENKO (cid:1) DepartmentofPathologyandCellBiology,VagelosCollegeof
PhysiciansandSurgeons,ColumbiaUniversityIrvingMedicalCenter,NewYork,NY,
USA
KATHYMANN (cid:1) ViapathAnalytics,Guy’sHospital,London,UK
ODELIANAHUM (cid:1) DepartmentofPathologyandCellBiology,VagelosCollegeofPhysicians
andSurgeons,ColumbiaUniversityIrvingMedicalCenter,NewYork,NY,USA
ANKITAPATEL (cid:1) Lineagen,SaltLakeCity,UT,USA
BARBARAPERTL (cid:1) PrenatalCentre,RagnitzHospital,Graz,Austria
ERWINPETEK (cid:1) InstituteofHumanGenetics,MedicalUniversityofGraz,Graz,Austria
ALEXJ.RAI (cid:1) DepartmentofPathologyandCellBiology,VagelosCollegeofPhysiciansand
Surgeons,ColumbiaUniversityIrvingMedicalCenter,NewYork,NY,USA
SVETLANARECHITSKY (cid:1) FloridaInternationalUniversity,Miami,FL,USA;Reproductive
GeneticsInstitute,Inc.(RGI),Northbrook,IL,USA
KLAUSRIENECK (cid:1) DepartmentofClinicalImmunology,Section2034,CopenhagenUniversity
Hospital,Copenhagen,Denmark
REBECCA K.SANDERSON (cid:1) Illumina,Inc.,FosterCity,CA,USA
JANSCHOUTEN (cid:1) DepartmentofClinicalGenetics,ErasmusUniversityMedicalCenter,
Rotterdam,TheNetherlands
RICHARDT.SCOTTJR. (cid:1) ThomasJeffersonUniversity,BaskingRidge,NJ,USA;Rutgers-
RobertWoodJohnsonMedicalSchool,PiscatawayTownship,NJ,USA
JOELEIGHSIMPSON (cid:1) MarchofDimesFoundation,WhitePlains,NY,USA;Florida
InternationalUniversity,Miami,FL,USA;ReproductiveGeneticsInstitute,Inc.(RGI),
Northbrook,IL,USA