高通量测序技术简介

高通量测序技术简介本文档共29页；当前第1页；编辑于星期六\18点53分NextGenerationSequencingSamplefragmentationLibrarypreparationSequencingreactionDataanalysisRoche454焦磷酸测序PyrophosphateSequencingIlluminaSolexa合成测序SequencebySynthesizeABISOLiD连接法测序SequencebyLigation第六部分高通量测序技术简介本文档共29页；当前第2页；编辑于星期六\18点53分Roche454焦磷酸测序PyrophosphateSequencing基本原理本文档共29页；当前第3页；编辑于星期六\18点53分454sequencing：EmulsionPCR(emPCR)MixDNALibrary&capturebeads(limiteddilution)“Breakmicro-reactors”IsolateDNAcontainingbeadsGenerationofmillionsofclonallyamplifiedtemplatesoneachbeadNocloningandcolonypickingCreate“Water-in-oil”emulsion+PCRReagents+EmulsionOilPerformemulsionPCRAdaptercarryinglibraryDNAABMicro-reactorsAdaptercomplementEnrichAnnealSeqprimer本文档共29页；当前第4页；编辑于星期六\18点53分CentrifugeStepLoadEnzymeBeads454sequencing：DepositionofDNAbeadsinto thePicoTiter™PlateLoadbeadsintoPicoTiter™Plate本文档共29页；当前第5页；编辑于星期六\18点53分IlluminaSolexa合成测序SequencebySynthesize基本原理本文档共29页；当前第6页；编辑于星期六\18点53分ClonalSingleMoleculeArrays

单分子克隆~1000moleculesper~1µmcluster

~1000clustersper100µmsquare~40millionclustersperexperimentPrepareDNAfragmentsLigateadaptersAttachsinglemoleculestosurfaceAmplifytoformclusters20micronsSequence本文档共29页；当前第7页；编辑于星期六\18点53分ReversibleTerminatorChemistry

可逆终止反应OPPPHNNOOcleavagesitefluor3’blockNextcycleIncorporationDetectionDeblock;fluorremovalODNAHNNOO3’O5’free3’endXOHAll4labellednucleotidesin1reaction本文档共29页；当前第8页；编辑于星期六\18点53分Sequencing-by-Synthesis(SBS)

5’GTCAGTCAGTCAGT3’5’CAGTCATCACCTAGCGTA FirstbaseincorporatedCycle1: Addsequencingreagents Removeunincorporatedbases DetectsignalCycle2-n:Addsequencingreagentsandrepeat1、每轮测序反应加入四种带有荧光标记的dNTP，末端带有可以被去除的阻断基团2、每轮反应只能整合一个核苷酸，仪器读取相应的荧光信号3、信号读取结束，用化学方法去除阻断基团，进行下一轮测序反应本文档共29页；当前第9页；编辑于星期六\18点53分123789456TTTTTTT

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T…Theidentityofeachbaseofaclusterisreadofffromsequentialimages根据每个点每轮反应读取的荧光信号序列，转换成相应的DNA序列Basecallingfromtherawdata本文档共29页；当前第10页；编辑于星期六\18点53分Solexa测序Workflow本文档共29页；当前第11页；编辑于星期六\18点53分ABISOLiD连接法测序SequencebyLigation基本原理本文档共29页；当前第12页；编辑于星期六\18点53分文库制备：微珠单分子克隆本文档共29页；当前第13页；编辑于星期六\18点53分1024种8碱基探针4色荧光，4种双核苷酸，每色荧光有256个探针(4^6)SOLiD利用探针的连接反应读取模板的DNA序列本文档共29页；当前第14页；编辑于星期六\18点53分连接法测序

（一）每个探针进行检测的两个碱基后面有三个匹配碱基，因此一条测序引物读取的序列是不完整的测序引物与adapter退火探针连接，检测荧光切除荧光基团第二轮探针连接，检测荧光切除荧光基团本文档共29页；当前第15页；编辑于星期六\18点53分连接法测序

（二）测序引物沿着Adapter移动5次，确保每个位点都被检测本文档共29页；当前第16页；编辑于星期六\18点53分连接法测序

（三）0位置是Adapter的最后一个碱基，因此只检测一次，该碱基是进行解码所必须的。本文档共29页；当前第17页；编辑于星期六\18点53分Advantage&disadvantage454sequencing读取长度大，400bp可以对未知基因组进行从头测序denovosequencing当遇到polymer时，如AAAAAA等，荧光强度和碱基个数不成线性关系，判定重复碱基个数有困难Solexasequencing高度自动化的系统读取片段多，适合进行大量小片段的测序，如microRNAprofiling基于可逆反应，随反应轮数增加，效率降低，信号衰减，读取序列较短，给denovosequencing拼接带来困难SOLiDsequencing每个碱基读取两次非常高的准确性，特别是对于SNP的检测灵活的系统，完善的磁珠编码系统，可以进行样品的pooling，分割测序区域读取长度受连接反应的轮数限制，给denovosequencing拼接带来困难本文档共29页；当前第18页；编辑于星期六\18点53分高通量测序的应用Denovo测序基因深度测序（genomere-sequencing）转录组深度测序（transcriptomere-sequencing）DigitalexpressionprofilingChIP-seqMethy-seq本文档共29页；当前第19页；编辑于星期六\18点53分Transcriptomeresequencing：malignantpleuralmesotheliomas(MPMs)：恶性胸膜间皮瘤pulmonaryadenocarcinoma(ADCA)：肺腺癌本文档共29页；当前第20页；编辑于星期六\18点53分TranscriptomecharacteristicsSolidline：atleastonereadDashedline：atleast20readsExpressiondifferencebetweenMPMandADCAsamplecomparetoalungtissuecontrolAnalysisofpercent-ageofreadscontainingknowncodingregionSNVsinthesixtissuesamples.SNV：SingleNucleotideSubstitutionVariant本文档共29页；当前第21页；编辑于星期六\18点53分Digitalexpressionprofiling（1）：

人大脑组织与UHR（UniversalHumanReference）的表达差异本文档共29页；当前第22页；编辑于星期六\18点53分DigitalexpressionprofilingµRNAre-sequencing：hESC：humanembryonicstemcellsEB：embryoidbodies本文档共29页；当前第23页；编辑于星期六\18点53分ChIP-seq（1）：人一号染色体DNA-蛋白相互作用本文档共29页；当前第24页；编辑于星期六\18点53分ChIP-seq（2）：Sequencedshortreads(typically
25–50bp)fromChIP-Seqexperimentsarefirstmappedontothereferencegenome.Themappedreadsarethenusedtoestimatestatisticalparameters,whichincludetheestimationoftheaveragelengthFofsequencedDNAfragments.本文档共29页；当前第25页；编辑于星期六\18点53分Methy-seq（1）：肿瘤和MCF7细胞系中BRCA!启动子区域的甲基化差异本文档共29页；当前第26页；编辑于星期六\18点53分Somehighlights:

CorrelationbetweenChIP-SeqandhispriorSAGE-likemethod(calledGMAT)hasr=0.906

‘HowevertheresolutionwithChIP-Seqwasdramaticallyhigher.Furthermore,ChIP-Seqwasmoresensitiveandgeneratedlessfalse-negativeregions’

12,726geneswhosetranscriptionlevelsareknowninCD4+T-cellswerecorrelatedwiththehistonemodificationsand35,961PolIIbindingsite‘islands’wereidentified

‘Thiscost-effectivemethodproducesdigital-qualitydataandshouldfindbroadapplicationsinoureffortstounderstandthecontributionofthehumanepigenomesingeneexpressionandepigeneticinheritance’

Methy-seq（2）：本文档共29页；当前第27页；编辑于星期六\18点53分部分参考文献阅读Genomere-sequencing

vanOrsouwNJ,HogersRC,JanssenA,etal.Complexityreductionofpolymorphicsequences(CRoPS):anovelapproachforlarge-scalepolymorphismdiscoveryincomplexgenomes.PLoSONE,2007,2(11):e1172HillierLW,MarthGT,QuinlanAR,etal.Whole-genomesequencingandvariantdiscoveryinC.elegans.NatMethods,2008,5(2):183—188Transcriptomere-sequencingMortazaviA,WilliamsBA,McCueK,etal.MappingandquantifyingmammaliantranscriptomesbyRNA-Seq.NatMethods,2008,5(7):621—628SugarbakerDJ,RichardsWG,GordonGJ,etal.Transcriptomesequencingofmalignantpleuralmesotheliomatumors.ProcNatlAcadSciUSA,2008,105(9):3521—3526DigitalexpressionprofilingRubyJG,JanC,PlayerC,etal.Large-scalesequencingreveals21U-RNAsandadditionalmicroRNAsandendogenoussiRNAsinC.elegans.Cell,2006,127(6):1193—1207MorinRD,O'ConnorMD,GriffithM,etal.ApplicationofmassivelyparallelsequencingtomicroRNAprofilinganddiscoveryinhumanembryonicstemcells.GenomeRes,2008,18(4):610—621ChIP-seqJohnsonDS,MortazaviA,MyersRM,etal.Genome-widemappingofinvivoprotein-DNAinteractions.Science,2007,316(5830):1497—1502RobertsonG,HirstM,BainbridgeM,etal.Genome-wideprofilesofSTAT1DNAassoci