IlluminaSNPgenotyping_精品文档资料下载.pdf

IlluminaSNPgenotyping_精品文档资料下载.pdf

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IlluminaSNPGenotypingTechnologiesBeadArrayandBeadChipPlatformSNPGenotypingAssayandSNPMultiplexingLevelperSampleGoldenGateAssayOPAsynthesiscontaining48,96,144,192,384,768,1536,or3072-plexSNPspersampleassayInfiniumAssayCustommadeiSelectchipstoassay3072upto1MSNPspersample.5InfiniumproductstargetedtowardAgriculturalmarketsBovineHDBeadChip8samples,777,962SNPsBovineSNP50BeadChip24samples,54,609SNPsCanineHDBeadChip12samples,172,115SNPsOvineSNP50BeadChip12samples,54,241SNPsPorcineSNP60BeadChip12-samples,62,163SNPsMaizeSNP50BeadChip24samples,56,110SNPsiSelectCustomPanels6iSelectBeadChipFormatsandSupportedMarkerDensitiesBeadChipFormat24-sample12-sample4-samplePreviousplexrange3,07260,80060,801200,000n/aNewplexrange3,07290,00090,001250,000250,0011MAdd-oncontentrange*Uptolimitof90,000Uptolimitof250,000Uptolimitof1M*Add-oncontentrangeallowed=（maximumattemptedbeadtypesonBeadChip）MINUS（existingbeadtypesinoriginalpool）7RatCitrusWheatHoneyBeeArmadilloCacaoRhesusCatCanolaRiceAtlanticCodLettuceFalseBromeSheepSwineHorseCattleHumanPeachPoplarRyegrassTurkeySoyBeanBarleyCitrusCottonRapeseedSpruceMouseCornPineChickenDogTomatoAtlanticSalmonGrapeVineSweetSorghumP.falciparumZebraFinchZebraFishApplicationsCustomGenotypingontheInfiniumAssayGenome-wideselectionGeneticPredictionSNPdiscoveryCommercialAgriculturescreeningpanelsTargetedfollow-upstudiesafterGWASTargeteddiseasepanelsTargetedrarevariantpanelsSampleQCandtrackingpanelsConsumerGenomicsForensicsTheRightContentLetsYouCaptureMoreBiology8BeadArraytechnologyandBeadChipmanufacturing9photo-resistsiliconwaferplasmaetchingcleaningMicrofabricationofBeadChipWells2mbeadsinwells11BeadsandBeadTypesFull-lengthOligos（800,000/bead）BeadRedundancy:

@#@averageof15beadsperbeadtype13BeadPreparationandArrayProductionUniqueoligoforeachbeadtypeBeadPoolcanbe1,000,000beadtypesRandomself-assemblyofbeadsAverage15beadsperbeadtypeFunctionalvalidationofarray14Decoderhybridization2Decoderhybridization1DecoderOligo12345678910111213141516Decodehyb1Decodehyb2BeadDecodingExample:

@#@16BeadTypesGeneratinga.dmapfileGoldenGateAssayBiochemistry14GoldenGateAssay:

@#@PrimerDesignAGillumiCodeAddressUniversalPCRSequence1UniversalPCRSequence2UniversalPCRSequence3GenomicDNAT/CT/AASOsLSOAlleleSpecificRegionLocusSpecificRegion（1-20bpgap）SNP335515Allele-specificextensionandligationGoldenGateAssay:

@#@Biochemistry/AssayDiagramAGillumiCodeAddressAlleleSpecificExtension&@#@LigationASO1UniversalPCRSequence3GenomicDNATLigasePolymeraseASO216AmplificationGoldenGateAssay:

@#@Biochemistry/AssayDiagramAillumiCode#561AmplificationTemplatePCRwithCommonPrimersCy3UniversalPrimer1Cy5UniversalPrimer2UniversalPrimerP317HybridizationtoVBPGoldenGateAssay:

@#@Biochemistry/AssayDiagram/illumiCode#561illumiCode#217illumiCode#1024/A/AG/GC/TSNP#561SNP#217SNP#1024InfiniumAssayBiochemistry17Whole-genomeamplificationOptimizedWGAreactionminimizesGCbiasUpto1000-foldamplification18FragmentationRobustendpointfragmentationAllowsaccesstovastmajorityofgenome10InfiniumProbesandBeadTypesProbeAddressLocus-Specific22bp50bp19HybridizationAATCGG20SingleBaseExtensionAATCGGTTAGCCACTGdintrophenol-labeledddNTPsbiotin-labeledddNTPs21StainTTAGCCstreptavidin-greenanti-DNP-redanti-streptavidin-biotinanti-Ab-DNP22ImageTTAGCCINTENSITYINTENSITYINTENSITYBeadChipScanningandSNPAssayDetectionInputfile.dmapfilescontainingbeadlocationsOutputfile.idatfilescontaininghybridizationintensitydataBeadStationToscanBeadChipsandgeneraterawdataBeadChipsBeadChipscanninginprogressEachbeadtranslatestorawdataforoneSNPDataAnalysisandGenotypeCallingusingGenomeStudioSoftware2LoadingData3FileTypesDECODE*.dmapINTENSITYDATA*.idatPROJECT*.bscREPORT*.csvMANIFEST*.bpmor*.opaSAMPLESHEET*.csvCLUSTER*.egtGenomeStudioBeadScanorGenomeScan4LoadDataFileExtensionDescriptionSourceRequired?

@#@Data*.idatContainsthemeanredandgreensignalintensitiesforeachbeadtypeGenomeScanYesManifest*.bpm*.opaListstheSNPIDandannotationforeachbeadtypeiComYesCluster*.egtForeachlocus,definestheallowablesignalintensityrangesforAA,AB,andBBgenotypesiCom/User-createdNoSampleSheet*.csvForeachsample,liststhemicrotiterplatelocations,replicateandfamilyrelationshipinformationUser-createdNo5Signalintensitiesfor96samplesatonelocusYaxisisgreensignalintensityXaxisisredsignalintensityPlottingintensitiesinCartesianspace6NormalizationProprietarynormalizationalgorithm7SNPGraph-PolarCoordinates=anglefromXaxisR=A+B8Clustering?

@#@GenCallscorereflectsthedistanceofadatapointtothecentroidofacluster?

@#@GenCallscoreisarepresentationoftheconfidencewithwhichagenotypecallismade（GenTrainscoreanddatatomodelfit）?

@#@Darkshadedregionsarecallregions（GenCallscore