基因芯片技术的临床应用

基因芯片技术(microarray)的临床应用人类基因及基因组DominantRecessive线粒体病多基因病Genes+

Environments肿瘤也是基因及基因组病23

对染色体---

2

x30

亿个碱基编码

21,000

个基因

---编码序列占整个基因组

的1.5%基因及基因组病

（遗传病）染色体数量异常Trisomy

21

（唐氏综合症）Trisomy

18Trisomy

13Sexchromosomal

aneuploidiesMosaictrisomiesofother

chromosomes染色体结构变化Morethan200known

disordersMorethan1000rare

abnormalities单基因病

(more

than

8,000)人类有60多种恶性肿瘤所有肿瘤都含有基因及基因组异常中国年出生1600万，出生缺陷发生率在5.6%,

每年新增出生缺陷数约90万例。(婴儿在出生的一年内，体格上出现明显的结构异常和需要手术矫正的畸形）智力低下迟发性疾病-------Thompson&ThompsonGeneticsInMedicine.Eighth

Edition遗传病的实验室诊断二代测序（NGS）原位荧光杂交（FISH）一代测序（Sanger

Sequencing）非测序分子生物学技术（non-DNA

techniques）核型分析（Karyotyping）基因/基因组检测基因芯片（Microarray）酶学检测高效液相色谱-串联质谱电感耦合等离子体质谱气相色谱-质谱超高效液相色谱蛋白质及代谢产物检测ChromosomeMicroarrayAnalysis

(CMA)Principlesof

CMACurrentStatusofCMAApplicationforClinical

ServiceFutureTrendsofCMAforClinical

ServiceaCGH

techniquesSNP

microarray199220032005

Indicatingthepresenceofuniparentaldisomy

(UPD)Indicatingthepresenceof

consanguinityIndicatingthepresenceofshared

ancestryIdentifyrecessivegene

mutationsConfirmCNVcallsbycheckingSNPallele

patternsIncreasesensitivityfordetectionof

mosaicismIdentifytriploidyforwhichaCGHfailsto

detectDetermineparentaloriginofadenovo

CNVImprovesourunderstandingofgenetic

aberrationsEnhancesthequalitycontrolinthediagnosticlaboratory

workflowIdentifygenomicregionswithLOHrelatedto

tumorigenesisPrinciplesof

CMAsPathogenicLikely

pathogenicUncertainclinicalsignificanceLikely

benignbenignClassificationofCopyNumberVariantsidentifiedbyCMAbasedontheirclinical

significancesCMAapplicationsforclinical

service受孕胚胎植入前的基因及基因组检测产前筛查及诊断新生儿筛查及诊断遗传病病人（儿童及成人）诊断健康人群隐性遗传病携带者检出健康及亚健康人群疾病易感基因检测遗传病的基因及基因组检测

肿瘤的基因及基因组检测遗传性肿瘤携带者检出无症状早期筛查分子诊断靶向药物的选择预后判断治疗监控复发基因克隆检出ValidationsofCMAplatformsforClinical

ServicesTechnical

ValidationsClinical

ValidationsValidation-Agilent

aCGH-244KYu,

S.

Bittel,

DC.

Kibiryeva,

N.

Zwick,

DL.

Cooley,

LD.ValidationoftheAgilent244Koligonucleotidearray-basedcomparativegenomichybridizationplatformforclinicalcytogeneticdiagnosis.AmJClinPathol

2009;132(3):349-60.VerificationofaCGH

findingsYuS,

Kielt,M,StegnerA,Bittel,DC.Cooley,

LD.ApplicationofQuantitativeReal-Time

PCRMethodsfortheVerificationofGenomicImbalancesDetectedbyMicroarray-basedComparativeGenomicHybridization.GenetTestMolBiomarkers

2009;13(6):751-60.aCGHforpostnataldiagnosis

(1)IdentifyNovelGenomic

DisordersBelloneRRetal.DifferentialgeneexpressionofTRPM1,thepotential

cause

of

congenital

stationary

night

blindness

(先天性静止性夜盲症)andcoatspottingpatterns(LP)intheAppaloosahorse(Equuscaballus).Genetics.2008

Aug;179(4):1861-70.LepichonJB,BittelDC,GrafWD,Yu

S.A15q13.3homozygousmicrodeletionassociatedwithasevereneurodevelopmentaldisordersuggestsputativefunctionsoftheTRPM1,CHRNA7,andotherhomozygouslydeletedgenes.AmJMedGenetA.2010

May;152A(5):1300-4.LepichonJB,YuS,GrafWD,andBittelDC.Genomewidegeneexpressioninapatientwith15q13.3homozygousmicrodeletionsyndromeEurJHumGenet.2013,

1-7.15q13.3

homozygousmicrodeletionAbdelmoityAT,HallJJ,BittelDC,Yu

S.1.39Mbinheritedinterstitialdeletionin12p13.33associatedwithdevelopmentaldelay.EurJMedGenet.2011

Mar-Apr;54(2):198-203.12p13.33

deletionRamalingamA,ZhouXG,FiedlerSD,BrawnerSJ,JoyceJM,LiuHY,Yu

S.16p13.11duplicationisariskfactorforawidespectrumofneuropsychiatricdisorders.JHumGenet.2011

Jul;56(7):541-416p13.11

duplicationYuSandGraf

WD.BRAFgenedeletionbroadenstheclinicalspectrumneuro-cardio-facial-cutaneoussyndromes.JChildNeurol.2011

Dec;26(12):1593-6.BRAFgene

deletionYuS,ShaoL,KilbrideH,Zwick

DL.HaploinsufficienciesofFOXF1andFOXC2genesassociatedwithlethalalveolarcapillary

dysplasiaandcongenitalheart

disease.AmJMedGenetA.2010

May;152A(5):1257-62.16q24.1

microdeletionaCGHforpostnataldiagnosis

(2)DiscoverNovelGenetic

MechanismsTelomerecaptureasafrequentmechanismforstabilizationoftheterminalchromosomaldeletionassociatedwithinverted

duplication.YuS

andGraf

WD.Telomerecaptureasafrequentmechanismforstabilizationoftheterminalchromosomaldeletionassociatedwithinverted

duplication.CytogenetGenomeRes.

2010;129(4):265-74.Genomicprofileofcopynumbervariantson

theshortarmofhumanchromosome

8YuS,

FiedlerS,StegnerA,andGraf

WD.Genomicprofileofcopynumbervariantsontheshortarmofhumanchromosome8.EurJHum

Genet.2010Oct;18(10):1114-20.YuS,ZhouXG,FiedlerSD,BrawnerSJ,JoyceJM,Liu

HY.Cardiac

defects

are

infrequent

findings

in

individuals

with

8p23.1

genomic

duplications

containing

GATA4.CircCardiovascGenet.2011

Dec;4(6):620-5.8p23.1genomic

duplicationsaCGHforpostnataldiagnosis

(3)Refinebreakpointsofgenomic

disordersGenomicDisorders

onchromosome

22YuS,BittelDC,YuS,NewkirkH,KibiryevaN,ButlerMG,CooleyLD.Refiningthe22q11.2deletionbreakpointsinDiGeorgesyndromebyaCGH.CytogenetGenomeRes

2009;124(2):113-20.YuS,GrafWD,RamalingamA,BrawnerSJ,JoyceJM,FiedlerDS,ZhouXG,andLiuHY(2001)Identificationofcopynumber

variants

(CNV)

on

human

chromosome

22

in

patients

with

a

variety

of

clinical

findings.

Cytogenet

GenomeRes.2011;134(4):260-8.Epub2011Aug

17.ButlerMG,BittelDC,KibiryevaN,CooleyLD,YuS.

Aninterstitial15q11-q14deletion:expandedPrader-Willisyndromephenotype.AmJMedGenetA.2010Feb;152A(2):404-8.expandedPrader-WillisyndromeaCGHforpostnataldiagnosis

(4)Characterizeoriginofmarker

chromosomeAneocentricsupernumerarymarkerchromosomeoriginatingfromtheXpdistal

regionYuS,BarbouthD,BenkePJ,WarburtonPE,Fan

YS.CharacterizationofaneocentricsupernumerarymarkerchromosomeoriginatingfromtheXpdistalregionbyFISH,CENP-Cstaining,andarray

CGH.CytogenetGenomeRes

2007;116(1-2):141-5.YuS,FiedlerDS,BrawnerSJ,JoyceJM,ZhouXG,andLiu

HY.CharacterizingSupernumeraryMarkerChromosomes(SMCs)withCombinationofMultiple

Techniques.CytogenetGenomeRes.

2012;136(1):6-14.Characterizing

SupernumeraryMarkerChromosomes

(SMCs)SNPMicroarrayforClinical

ApplicationsWhyshouldSNPmicroarraybeusedtoreplaceaCGH

?Whatisa

SNP?WhatisaSNP

array?Advantages

of SNParraysover

aCGH?ApplicationsofSNPMicroarraySingleNucleotidePolymorphism

(SNP)Definition:asinglenucleotidechangeinaDNAsequencethatoccursin

asignificantproportion(≥1%)inalarge

population.DifferentLevelsofpolymorphismsinhuman

genomeinv(9)SNP

factsRepresent90%of

genomic

variations inhuman

genome,ThereisaSNPper100-300bpinhuman

genome,SNPscanoccurincoding(gene)andnoncodingregionsofthe

genome,ManySNPshavenoeffectoncellfunction,butotherscouldpredisposepeopletodiseaseorinfluencetheirresponsetomedicines,environmental

factors.DNA

SequencingHybridizationMicroarraysTaqMan,Molecular

BeaconsAllele-specific

PCRFRETIntercalating

DyesPrimer

ExtensionMALDI-tofSNaPshotLigationPadlock

ProbesRollingCircle

AmplificationEndonuclease

CleavageRFLPPIRA/RFLPMethodstodiscovernovelSNPsanddetectknown

SNPsClinicalSNP

arraysNumbersofMarkers

(probes)AverageMarkerSpacing(base

pairs)Genescovered(25markers/100

kb)AgilentIlluminaAffymetrixTheCytoScan™HDArrayfrom

Affymetrix

Indicatethepresenceofuniparentaldisomy

(UPD)Indicatethepresenceof

consanguinityIndicatethepresenceofshared

ancestry

Identifyrecessivegene

mutationsConfirmCNVcallsbycheckingSNPallele

patternsIncreasesensitivityfordetectionof

mosaicismIdentifytriploidyforwhichaCGHfailsto

detectDetermineparentaloriginofadenovo

CNVImprovesourunderstandingofgenetic

aberrationsEnhancesthequalitycontrolinthediagnosticlaboratory

workflowIdentifygenomicregionswithLOHrelatedto

tumorigenesisSNPMicroarrayAnalysisforClinical

ServiceSNParrayforClinicalService

(5)Indicatethepresenceofuniparentaldisomy

(UPD)UPDchromosomesassociatedwithimprinting

disordersSNParrayforClinicalService

(6)Indicatethepresenceof

consanguinityROH

indicatingconsanguinityTwosiblingswithhighpercentage

ROHindicatingconsanguinity

marriageGlobalConsanguinity

RatesHamamyH.Consanguineousmarriages:Preconceptionconsultationinprimaryhealthcaresettings.JCommunityGenet.2012

Jul;3(3):185-92.SNParrayforClinicalService

(7)Identifyrecessivegene

mutationsROHfacilitatingidentificationofrecessive

genesmonth-oldboywithmultipleendocrine

&structural

issues:congenitalprimary

hypothyroidismhyperinsulinisminthefaceof

hypoglycemiagrowthhormone

deficiencycortisol

deficiencyresolveddirectandindirect

hyperbilirubinemiacorticalvisual

impairmentrespiratoryissues,

aspirationsignificantdevelopmental

delayhypotoniadysmorphicfacial

featureshirsutismwithlowanterior

hairlineCMAtestingforCNVisrecommendedasafirst-linetestintheinitialpostnatalevaluationofindividualswiththefollowing:Multipleanomaliesnotspecifictoawell-delineatedgenetic

syndrome.Apparentlynonsyndromic

DD/ID.Autismspectrum

disorders.FurtherdeterminationoftheuseofCMAtestingfortheevaluationofthechildwithgrowthretardation,

speechdelay,andotherlesswell-studiedindicationsisrecommended,particularlybyprospectivestudiesandaftermarketanalysis.Appropriatefollow-upisrecommendedincasesofchromosomeimbalanceidentifiedbyCMA,toincludecytogenetic/FISHstudiesofthepatient,parentalevaluation,andclinicalgeneticevaluationand

counseling.GrafWD,LePichonJB,BittelDC,AbdelmoityAT,andYuS.Practiceparameter:evaluationofthechildwithmicrocephaly(anevidence-basedreview):reportofthequalitystandardssubcommitteeoftheAmericanAcademyofNeurologyandthePracticeCommitteeoftheChildNeurologySociety.Neurology.

2010;74(13):1080-1.LedbetterDH.Cytogenetictechnology--genotypeandphenotype.NEnglJMed.

2008;359(16):1728-30.BejjaniBAandShafferLG.Clinicalutilityofcontemporarymolecularcytogenetics.AnnuRevGenomicsHumGenet.

2008;9:71-86.Clinical

indication Testing不孕不育(

about

1/3duetogenetic/genomic

defects)已知基因\基因组异常核型分析原位荧光杂交基因芯片(BlueGnome)MES,WES,

WGS胚胎植入前检测(PGS

&

PGD)已知基因\基因组异常原位荧光杂交基因芯片单基因检测，WGSCMAforPGS/PGD(preimplantationgeneticscreening/diagnosis

(8)Colls,P.etal.Validationofarraycomparativegenomehybridizationfordiagnosisoftranslocationsinpreimplantationhumanembryos.ReprodBiomedOnline.2012;24:

621–629.Treff,N.R.etal.Singlenucleotidepolymorphismmicroarray-basedconcurrentscreeningof24-chromosomeaneuploidyandunbalancedtranslocationsinpreimplantationhumanembryos.FertilSteril.2011;95:

1606–1612.Johnson,D.S.etal.Preclinicalvalidationofamicroarraymethodforfullmolecularkaryotypingofblastomeresina24-hprotocol.HumReprod.2010;25:1066–1075.PetersBAetal.