oncoscan培训及相关芯片昂飞材料

拷贝数缺失（Deletion/Lost1copyor0 Her2gene6copiesofthesegeneisindicativeofresponseto曲妥获得性突变机制（SomaticMutationsmechanism 单碱基点突变i.e.AtoTorCtoaG为什 BRAFV600EWildBRAFV600E

杂合子缺失（LossOf为什么要研究杂合子缺失 症的机制-单倍体与LOH:一个拷贝的抑癌 变.Thenadeletion/lossoccursintheothercopyoralleleoftheTSG.Nowboth“brakes”havefailedleadingto(mutation+-cnLOH:OnecopyofaTSGhasamutation.Thenadeletion/lossoftheothercopyoralleleoftheTSGoccursANDthecopywiththemutationgetsnormaldiploid),both“brakesthatcontrolcellmultiplicationhavefailedleadingtocancer.(mutation+loss+

正常细胞 (LOH) 中,LOHregions一般cnLOH现象在实体瘤样本中非常普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/组 组 客户总是比我们 TechnicalV与肺癌的部分相关 结果：该位点4拷贝时平均存活率只有9比，4MAPKAPK2LargeAndGrowingListOfActionableCopyNumberChanges!MDAnderson2012–200genesactionableforMDAnderson2013-Same200genesnowactionableforCNasCPartialListOfMDAnderson200Largeandgrowinglistofactionablecopynumberchanges ISHpanelsandmplexcountingUseOncoScanISHpanelsandmplexcountingUseOncoScanandgetanswerinminutesCRUK1stList–OnlySM,noCRUK2ndList-15CN123456789Use5performExample---HER2）

又名HER2/neu，c-erbB-2，表皮生长因子受体成员；原 ，位于17q21，编码相对分子质量185KD的膜糖蛋白（跨膜酪氨酸激酶受体）；研究表明：30％以上的人类肿瘤中存在H2 的扩增/过度表达（如 、 癌、 内膜癌 癌、胃癌 癌等）；其中20％－30％ 性浸润有 的扩增/过度表达中 扩增/过度表达的临床意义无病生存期和总生存期短相关,肿瘤预后差。在多变量分析结HER2是肿瘤复发和总生存期长短的独立预后因HER2是目前公认的一 重要。HER2阳性状态预示肿瘤对常规治疗的反应。.内分泌治疗HER2阳性患者相对.CMF方案HER2阳性患者相对

BreastCancerERBB2/Her26FISHERBB2/Her2UseOncoScanandgetanswerinminutesOncoScan™FFPEAssayKitisforResearchUse

BreastCancer–MDCopyNeutralLOHregionasamarkeroftherapy

MYCGain

High临床对分子标记的数量和 组拷贝数的分布需求的不断增需要 不可能把每个样品都在-80度或者液氮中保存DNA，FFPE为病理科及肿瘤科通用保存方法，涵盖和癌旁；各种stage、各种预后、以及药物不同年年限较长，有些样品已经存放年DNA杂质较高度降样品间差异DNA量有限，样品Untilnowtherehasbeennoeffectivesolutionforsolidtumorcopynumber KeyaCGHTargeted

HighinputDNA-500ng-1ug(cannotgetthisinFFPE!)PoorlossofheterozygosityLowconfidencein“mosaic”cancerNotreliableforHighdepthsequencingHHighfailurerateinFFPE(15-PoorresolutionNeedsexpertNotgenomeWholegenomesequencingnotviableforFFPEan80Xcoveragewouldgenerate bytesofdatathattakesmonthsto 实体瘤FFPE样本解决方案---OncoScan存放10年的FFPE样本都能后的很好的结对高度降解的(>=150bps)FFPE样本也同样适从DNA到结果只需要48统一的参考数探针设 加密覆盖~900 (50kb- 组范围的拷贝数覆盖(300kb- 组LOH(3-10Mb)检测能在9 中检测~70种体细胞突变亚克隆检测及嵌合体最广的拷贝数变异范围,0,1,2,3,4,5-6,7-10,11-2020-50高可以检测50倍变---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药物名称（英PatientswhosetumorsharboredV600EandV600Ktrametinib,thantochemotherapy同24229OncoScan™AssayPanelMolecularInversionProbeStructureCleavagesite

(HaeIII)

Hybridizestothe

MolecularInversionProbe(MIP)Step1.Linear

Homology

CleavageStep2.MIPProbereadytobindgDNA

MolecularInversionProbe(MIP):BeforeandAfterCleavageStep1.Linear

Homology

CleavageSiteStep3.AnnealingofProbeto

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