高通量测序技术简介

高通量测序技术简介目前一页\总数二十九页\编于二十一点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目前二页\总数二十九页\编于二十一点Roche454焦磷酸测序PyrophosphateSequencing基本原理目前三页\总数二十九页\编于二十一点454sequencing：EmulsionPCR(emPCR)MixDNALibrary&capturebeads(limiteddilution)“Breakmicro-reactors”IsolateDNAcontainingbeadsGenerationofmillionsofclonallyamplifiedtemplatesoneachbeadNocloningandcolonypickingCreate“Water-in-oil”emulsion+PCRReagents+EmulsionOilPerformemulsionPCRAdaptercarryinglibraryDNAABMicro-reactorsAdaptercomplementEnrichAnnealSeqprimer目前四页\总数二十九页\编于二十一点CentrifugeStepLoadEnzymeBeads454sequencing：DepositionofDNAbeadsinto thePicoTiter™PlateLoadbeadsintoPicoTiter™Plate目前五页\总数二十九页\编于二十一点IlluminaSolexa合成测序SequencebySynthesize基本原理目前六页\总数二十九页\编于二十一点ClonalSingleMoleculeArrays

单分子克隆~1000moleculesper~1µmcluster

~1000clustersper100µmsquare~40millionclustersperexperimentPrepareDNAfragmentsLigateadaptersAttachsinglemoleculestosurfaceAmplifytoformclusters20micronsSequence目前七页\总数二十九页\编于二十一点ReversibleTerminatorChemistry

可逆终止反应OPPPHNNOOcleavagesitefluor3’blockNextcycleIncorporationDetectionDeblock;fluorremovalODNAHNNOO3’O5’free3’endXOHAll4labellednucleotidesin1reaction目前八页\总数二十九页\编于二十一点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目前九页\总数二十九页\编于二十一点123789456TTTTTTT

G

T…T

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C

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A

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G

A

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目前十页\总数二十九页\编于二十一点Solexa测序Workflow目前十一页\总数二十九页\编于二十一点ABISOLiD连接法测序SequencebyLigation基本原理目前十二页\总数二十九页\编于二十一点文库制备：微珠单分子克隆目前十三页\总数二十九页\编于二十一点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序列目前十四页\总数二十九页\编于二十一点连接法测序

（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目前十五页\总数二十九页\编于二十一点连接法测序

（二）测序引物沿着Adapter移动5次，确保每个位点都被检测目前十六页\总数二十九页\编于二十一点连接法测序

（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。目前十七页\总数二十九页\编于二十一点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拼接带来困难目前十八页\总数二十九页\编于二十一点高通量测序的应用Denovo测序基因深度测序（genomere-sequencing）转录组深度测序（transcriptomere-sequencing）DigitalexpressionprofilingChIP-seqMethy-seq目前十九页\总数二十九页\编于二十一点Transcriptomeresequencing：malignantpleuralmesotheliomas(MPMs)：恶性胸膜间皮瘤pulmonaryadenocarcinoma(ADCA)：肺腺癌目前二十页\总数二十九页\编于二十一点TranscriptomecharacteristicsSolidline：atleastonereadDashedline：atleast20readsExpressiondifferencebetweenMPMandADCAsamplecomparetoalungtissuecontrolAnalysisofpercent-ageofreadscontainingknowncodingregionSNVsinthesixtissuesamples.SNV：SingleNucleotideSubstitutionVariant目前二十一页\总数二十九页\编于二十一点Digitalexpressionprofiling（1）：

人大脑组织与UHR（UniversalHumanReference）的表达差异目前二十二页\总数二十九页\编于二十一点DigitalexpressionprofilingµRNAre-sequencing：hESC：humanembryonicstemcellsEB：embryoidbodies目前二十三页\总数二十九页\编于二十一点ChIP-seq（1）：人一号染色体DNA-蛋白相互作用目前二十四页\总数二十九页\编于二十一点ChIP-seq（2）：Sequencedshortreads(typically
25–50bp)fromChIP-Seqexperimentsarefirstmappedontothereferencegenome.Themappedreadsarethenusedtoestimatestatisticalparameters,whichincludetheestimationoftheaveragelengthFofsequencedDNAfragments.目前二十五页\总数二十九页\编于二十一点Methy-seq（1）：肿瘤和MCF7细胞系中BRCA!启动子区域的甲基化差异目前二十六页\总数二十九页\编于二十一点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）：目前二十七页\总数二十九页\编于二十一点部分参考文献阅读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-wideprofilesofSTAT1DNAassociationusi