affymetrix-optima.pptx

affymetrix-optima.pptx

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1CytoScanOptimaSuite简介2CytoScanOptima的探针设计，来自于丰富的临床经验累积与产前专家的推荐1.NICHD（国家儿童健康和人类发展研究所）5年近4,000例临床试验病例积累超声异常使用芯片检测，阳性检出率比核型分析提高6%以上约90个基因区域2.近15,000个CytoScan（HD）病例的积累CytoScanOptima产前专家共同推荐的396个基因区域，加密覆盖总共315,608features、探针:

296,900SNPmarkers18,018CNmarkersControlfeatures3CytoScanOptimaSuite:

专为产前诊断设计无需再外购试剂，Optima包括PCR扩增酶包括一个全新为产前和流产物样本优化的referencefile对于实验室而言，所有的操作步骤与CytoScanHD/750K一致使用ChAS软件分析CytoScanOptima特点为产前诊断和流产物分析设计经济可靠含所有试剂，无需外购数据解读简易分辨率和覆盖度全基因组范围检测在396个产前诊断相关基因区域加密（分辨率100kb）.全基因组大于5MbLOH设计策略探针全部精选自CytoscanHD可检测CNV/LOH，染色体不平衡等SNP探针可分析三倍体，亲源性，嵌合体等，适合用于临床诊断与报告45Optima实例6A0014084:

正常样本此例为完全正常的健康人样本未检测到任何异常区域.7A0002869:

7号染色体的缺失和扩增该样本的7号染色体发生拷贝数的变化（copynumber=1,2,and3）7号染色体短臂发生微重复，及长臂末端有微重复8A0013758:

POC流产物样本的缺失和重复该样本为POC流产物样本在四号染色体长臂末端，发生了46MB的扩增，紧接着是2.2MB的缺失9143400:

在目标基因（CREBBP）发现一处170kb的缺失该样本在396个加密基因区发现了170KB的微缺失（CREBBP）10CytoScanOptima检测整三倍体该流产物为整三倍体ThisPOCsamplehasaTriploidgenomeSNPs有四条信号带而llog2ratio值为正常，即可判断为检测到了三倍体仅拷贝数探针的信号为“正常”值11嵌合体该样本在1号染色体末端发生了嵌合型扩增130086:

1号染色体嵌合型扩增12从smoothsignalandallelepeakstracks可见50%的嵌合型扩增130086：

全基因组视图，一目了然Thesamesamplevisualizedinwhole-genomeview1350%mosaicisclearlyvisibleonthealleledifferencetrackandsmoothsignal14158:

POC样本的6号染色体的嵌合（约35%）POC样本的6号染色体整条为嵌合型缺失通14过smoothsignal和allelepeakstracks可推测到嵌合比例为35%1514158:

Mosaicmonosomy6（35%）onaPOCsampleWhole-genomeviewaidsintheidentificationofthemosaicmonosomy635%mosaicisclearlyvisibleonthealleledifferencetrackandsmoothsignal16ROH/AOH/LOH实例17130080:

RegionsidenticalbydescentGenomicprofileofconsanguinityThisexampleillustratesblocksofLOH5MbacrossamajorityoftheChromosomes.18RegionsidenticalbydescentDetailedviewofchromosome2ThisisanexampleoftwoblocksofLOH5MbonChromosome2.19Genotypes基因型Trio亲源性分析Aidintheconfirmationofcopy-numberEventsHigh-densitySNPsallowforalloftheseperformanceattributestobemeasuredatgene-levelresolution.AidinbreakpointdeterminationAOH/LOHThepowerofSNPsIdentificationofgenomiccontamination（MCC）IdentificationofMosaicismeventscorroborationMendelianconsistencycheckingTriploidyHighdensitySNPsPrenatalResearchDoyourunparent（s）asareflexinsomeofyoursamples?

Areyousurethetrio/duoisconsistentbeforemakingconclusions?

WithCytoScanCytogeneticsSuiteandChASsoftware,youcanusethegenotypesandrunaconsistencycheckfirst!

21ConcordancematConcordancePatConcordancetotal1-FAM199.89%99.89%99.57%2-FAM299.89%99.83%99.49%3-MIX99.89%91.69%84.91%22Chas3.0TrioTool亲源性分析工具-Optima/750K/HD都适用SampleIDRef#Trio#RelationFamilyA-0015275A-0012037A-0012038A-0015266A-0012011A-0012010A-0015275A-0012037A-0012010NA10847NA12239NA12146NA07029NA07000NA06994NA10847NA12239NA06994111222112motherCEPH1334matgrandmotherCEPH1334matgrandfatherCEPH1334fatherCEPH1340patgrandmotherCEPH1340patgrandfatherCEPH1340motherCEPH1334matgrandmotherCEPH1334patgrandfatherCEPH1340CytoScanOptima有丰富的可检测基因表型的SNP探针，可运行亲源性分析Chas3.0TrioTool可检测亲缘不一致23可重复性实例24Chr7的一致性25ChrX一致性26Optima与ILMN和Agilent的比较高密度的SNP探针能实现以上遗传学信息的检测.有助于breakpoint的确认对拷贝数探针检出的变异的再次确认SNP探针的功能母源性污染的检出AOH/LOH的检测检测嵌合体亲源性鉴定整三倍体的检测HighdensitySNPs28ILMN300K是一款来源于GWAS设计的芯片Cyto-12来自于GWAS设计的局限性（Cyto-12or300KfromILMN）：

由于SNP探针分布不均匀造成的检测区域的GAPS为GWAS设计的低MAFSNPs不适用于检测LOH批间差效应，低重复性，不适用于临床诊断611121314111213141516171811192021222324212223242526272821293031323334313233343536373831394041424344414243444546474841495051525354515253545556575851596061626364616263646566676861697071727374717273747576777871798029919192929393949495959696979798989999818283848182838485868788818990919293949192939495969798919910093949192939495969798999596979899100929596979899100919293949596979899Affymetrixtechnology:

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