拷貝數(shù)缺失（Deletion/Lost1copyor0 Her2gene6copiesofthesegeneisindicativeofresponseto曲妥獲得性突變機(jī)制（SomaticMutationsmechanism 單堿基點(diǎn)突變i.e.AtoTorCtoaG為什 BRAFV600EWildBRAFV600E

雜合子缺失（LossOf為什么要研究雜合子缺失 癥的機(jī)制-單倍體與LOH:一個拷貝的抑癌 變.Thenadeletion/lossoccursintheothercopyoralleleoftheTSG.Nowboth“brakes”havefailedleadingto(mutation+-cnLOH:OnecopyofaTSGhasamutation.Thenadeletion/lossoftheothercopyoralleleoftheTSGoccursANDthecopywiththemutationgetsnormaldiploid),both“brakesthatcontrolcellmultiplicationhavefailedleadingtocancer.(mutation+loss+

正常細(xì)胞 (LOH) 中,LOHregions一般cnLOH現(xiàn)象在實(shí)體瘤樣本中非常普Rateofcopy-neutralLOHdependsonwhatcancertype,sampletype, EvidencesofCNVand3,299TumorsamplesfromCancerGenome12cancerTumorscanbedividedintotwogroups,onecharacterizedmostlybymutations,andtheothermostlybycopynumberIn11tumors,includingseverallargeincidencesolidtumorslikelungandbreastcancer,thereareseveralgeneswithcopynumberchanges,thataretargetablewithdrugsrightnowGenomic tionsconsideredincludednumber 151deletedregionsand11614ofalltheseCNVsaremostfrequent 9p21,3q26,8q24,1q21,11q13,8q22,5p15,8p23,7p11,20q13,19q12,1q32,8p21, Effectedgenes:CDKN2A,MYC,CCND1,EGFR,CCNE1,somatic199199mutatedgenesfoundinthose12typeofMainlySomaticmutationsonly40%ofthosemutationsaredirectlytargetedinand30%areundirectlytargetedindrugMapoffunctionalandactionable GenesGenes(rows)encodingcomponentsoffourmajoroncogenicRTK-RAS-RAF,PI3K-AKT-mTOR,cellcycleandp53–DNASomaticMutationgenesInBRAF/EGFR/IDH1/IDH2/KRAS/NRAS/PIK3CA/PTEN/組 組 客戶總是比我們 TechnicalV與肺癌的部分相關(guān) 結(jié)果：該位點(diǎn)4拷貝時平均存活率只有9比，4MAPKAPK2LargeAndGrowingListOfActionableCopyNumberChanges!MDAnderson2012–200genesactionableforMDAnderson2013-Same200genesnowactionableforCNasCPartialListOfMDAnderson200Largeandgrowinglistofactionablecopynumberchanges ISHpanelsandmplexcountingUseOncoScanISHpanelsandmplexcountingUseOncoScanandgetanswerinminutesCRUK1stList–OnlySM,noCRUK2ndList-15CN123456789Use5performExample---HER2）

又名HER2/neu，c-erbB-2，表皮生長因子受體成員；原 ，位于17q21，編碼相對分子質(zhì)量185KD的膜糖蛋白（跨膜酪氨酸激酶受體）；研究表明：30％以上的人類腫瘤中存在H2 的擴(kuò)增/過度表達(dá)（如 、 癌、 內(nèi)膜癌 癌、胃癌 癌等）；其中20％－30％ 性浸潤有 的擴(kuò)增/過度表達(dá)中 擴(kuò)增/過度表達(dá)的臨床意義無病生存期和總生存期短相關(guān),腫瘤預(yù)后差。在多變量分析結(jié)HER2是腫瘤復(fù)發(fā)和總生存期長短的獨(dú)立預(yù)后因HER2是目前公認(rèn)的一 重要。HER2陽性狀態(tài)預(yù)示腫瘤對常規(guī)治療的反應(yīng)。.內(nèi)分泌治療HER2陽性患者相對.CMF方案HER2陽性患者相對

BreastCancerERBB2/Her26FISHERBB2/Her2UseOncoScanandgetanswerinminutesOncoScan?FFPEAssayKitisforResearchUse

BreastCancer–MDCopyNeutralLOHregionasamarkeroftherapy

MYCGain

High臨床對分子標(biāo)記的數(shù)量和 組拷貝數(shù)的分布需求的不斷增需要 不可能把每個樣品都在-80度或者液氮中保存DNA，F(xiàn)FPE為病理科及腫瘤科通用保存方法，涵蓋和癌旁；各種stage、各種預(yù)后、以及藥物不同年年限較長，有些樣品已經(jīng)存放年DNA雜質(zhì)較高度降樣品間差異DNA量有限，樣品Untilnowtherehasbeennoeffectivesolutionforsolidtumorcopynumber KeyaCGHTargeted

HighinputDNA-500ng-1ug(cannotgetthisinFFPE!)PoorlossofheterozygosityLowconfidencein“mosaic”cancerNotreliableforHighdepthsequencingHHighfailurerateinFFPE(15-PoorresolutionNeedsexpertNotgenomeWholegenomesequencingnotviableforFFPEan80Xcoveragewouldgenerate bytesofdatathattakesmonthsto 實(shí)體瘤FFPE樣本解決方案---OncoScan存放10年的FFPE樣本都能后的很好的結(jié)對高度降解的(>=150bps)FFPE樣本也同樣適從DNA到結(jié)果只需要48統(tǒng)一的參考數(shù)探針設(shè) 加密覆蓋~900 (50kb- 組范圍的拷貝數(shù)覆蓋(300kb- 組LOH(3-10Mb)檢測能在9 中檢測~70種體細(xì)胞突變亞克隆檢測及嵌合體最廣的拷貝數(shù)變異范圍,0,1,2,3,4,5-6,7-10,11-2020-50高可以檢測50倍變---CopyNumberandSomatic NexusExpress

Simplified,streamlined,andquality-forprocessingGeneChip?Scanner(GCS)30007GGCS3000Dxv.2,HybOven645,FS450/450OncoScanOncoScan?FFPEAssayCopynumberCopynumberpanelof~220Kprobes,~100%SNPprobes,enablinglowlevelmosaicandLOHdetectionProbesvalidatedforhighCancergeneSolidtumorfocuseddesignwithhighresolutionin~900cancerGenomewidecoverageoutsideofthe~900cancer~90%ofthegenomehas300Kbresolutionor1+97%ofthegenomehasatleast380Kbresolutionor1+GenomewideLOHresolutionof3Mb*-*3MbwhenaberrantcellfractionisOncoScan?FFPEAssaySomaticmutationsSomaticmutation74mutationsin99genes-BRAF,KRAS,EGFR,IDH1,IDH2,PTEN,PIK3CA,NRAS,TP53observedformultiplesomaticToolprovidedforvisualizationofmutantcallversusreference(wildtype)Sensitivityclaimvalidatedby studies(oligoswithmutant edinatvariousmutant%levelsinnormalFFPEMajorityofmutationsweredetected20%Inrealworldsamples,therewereexamplesofdetectiondownto~10%

Distributionof74mutationsbyOverviewofOncoScanMIPProbe240KSNPprobesusedforCopyNumber(CN)ProbesaresingleThereare3copiesofeachalleleontheSNPislocatedintheGapFillSizeofprobes:GenomicpartofMIPis40-70ntandthetagis2574SNPprobesforSomaticMutation(SM)ProbesaresingleOneprobeforeachsomaticmutationandtheyinterrogatetheSNPandbasessurroundingtheThereare3copiesofthesametagontheSizeofprobes:GenomicpartofMIPis40-70ntandthetagis25ProbeSNPcanbelocatedintheGapFillSNPcanbelocatedadjacenttotheGapFillSomaticMutationandActionalDrug藥物名稱（英PatientswhosetumorsharboredV600EandV600Ktrametinib,thantochemotherapy同24229OncoScan?AssayPanelMolecularInversionProbeStructureCleavagesite

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MolecularInversionProbe(MIP)Step1.Linear

Homology

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MolecularInversionProbe(MIP):BeforeandAfterCleavageStep1.Linear

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Site#2(RestrictionDigestafterPCR)Step4.dNTP,LigaseAddition,GapFillStep5.ExoNuclease Step6.Cleaved,linearizedprobeisNowtheprimerbindingsitesfaceoneanothersoprobeissaidtobeAmplificationofInvertedAmplification plishedbyPCRasshownhere.Wearegeneratingmultiplecopiesofasequenceincludesthetagsequencetoberecognizedonthearrayandtheamplifi