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Infinium® LCG Quad Assay Protocol Guide For Research Use Only. Not for use in diagnostic procedures. ILLUMINA PROPRIETARY Catalog # WG-901-5 001 Part # 15025908 Rev. D June 2015 ThisdocumentanditscontentsareproprietarytoIllumina,Inc.anditsaffiliates("Illumina"),andareintendedsolelyforthecontractualuseof itscustomerinconnectionwiththeuseoftheproduct(s)describedhereinandfornootherpurpose.Thisdocumentanditscontentsshallnot beusedordistributedforanyotherpurposeand/orotherwisecommunicated,disclosed,orreproducedinanywaywhatsoeverwithoutthe priorwrittenconsentofIllumina.Illuminadoesnotconveyanylicenseunderitspatent,trademark,copyright,orcommon-lawrightsnor similarrightsofanythirdpartiesbythisdocument. Theinstructionsinthisdocumentmustbestrictlyandexplicitlyfollowedbyqualifiedandproperlytrainedpersonnelinordertoensurethe properandsafeuseoftheproduct(s)describedherein.Allofthecontentsofthisdocumentmustbefullyreadandunderstoodpriortousing suchproduct(s). FAILURETOCOMPLETELYREADANDEXPLICITLYFOLLOWALLOFTHEINSTRUCTIONSCONTAINEDHEREINMAYRESULTIN DAMAGETOTHEPRODUCT(S),INJURYTOPERSONS,INCLUDINGTOUSERSOROTHERS,ANDDAMAGETOOTHERPROPERTY. ILLUMINADOESNOTASSUMEANYLIABILITYARISINGOUTOFTHEIMPROPERUSEOFTHEPRODUCT(S)DESCRIBEDHEREIN (INCLUDINGPARTSTHEREOFORSOFTWARE). ©2015Illumina,Inc.Allrightsreserved. Illumina,24sure,BaseSpace,BeadArray,BlueFish,BlueFuse,BlueGnome,cBot,CSPro,CytoChip,DesignStudio,Epicentre,GAIIx, GeneticEnergy,GenomeAnalyzer,GenomeStudio,GoldenGate,HiScan,HiSeq,HiSeqX,Infinium,iScan,iSelect,MiSeq,NeoPrep, Nextera,NextBio,NextSeq,PoweredbyIllumina,SeqMonitor,SureMDA,TruGenome,TruSeq,TruSight,UnderstandYourGenome, UYG,VeraCode,verifi,VeriSeq,thepumpkinorangecolor,andthestreamingbasesdesignaretrademarksofIllumina,Inc.and/orits affiliate(s)intheU.S.and/orothercountries.Allothernames,logos,andothertrademarksarethepropertyoftheirrespectiveowners. ii Part#15025908Rev.D Revision History Part # Revision Date Descriptionof Change 15025908 D June2015 CorrectedtheAmplificationtemperatureto 37°C. 15025908 C May2012 Indicatedthatupto24BeadChipscanbe washedwith550mlofPB1. 15025908 B September ReagentsSuppliedtableamendedtodelete 2011 partnumbersandmovedescriptionsto secondcolumn. 15025908 A June2011 Initialrelease. iii InfiniumLCGQuadAssayProtocolGuide iv Part#15025908Rev.D Table of Contents RevisionHistory iii TableofContents v ListofTables vii Chapter1 Overview 1 IntroductiontoInfiniumLCGQuadAssay 2 AudienceandPurpose 3 InfiniumLCGQuadAssay 4 IlluminaInfiniumBeadChips 9 IlluminaLabProtocols 10 TrackingTools 11 TecanGenePaint 14 ImagingSystems 15 GenomeStudioIntegrated InformaticsPlatform 16 Chapter2 ManualProtocol 17 IntroductiontoInfiniumLCGQuadManualProtocol 18 InfiniumLCGQuadManualWorkflow 19 Equipment,Materials,andReagents 21 QuantifyDNA(Optional)(Pre-Amp) 23 MaketheAMP5Plate 31 IncubateDNA(Post-Amp) 35 FragmentDNA(Post-Amp) 36 PrecipitateDNA(Post-Amp) 39 ResuspendDNA(Post-Amp) 43 HybridizetoBeadChip(Post-Amp) 46 WashBeadChips(Post-Amp) 61 ExtendandStain(XStain)BeadChip(Post-Amp) 73 ImageBeadChip 93 IlluminaGenomeStudio 94 Chapter3 AutomatedProtocol 95 IntroductiontoInfiniumLCGQuadAutomatedProtocol 96 InfiniumLCGQuadAutomatedWorkflow 97 Equipment,Materials,andReagents 99 QuantifyDNA(Optional)(Pre-Amp) 102 v InfiniumLCGQuadAssayProtocolGuide MaketheAMP5Plate 112 IncubateDNA(Post-Amp) 121 FragmentDNA(Post-Amp) 123 PrecipitateDNA(Post-Amp) 129 ResuspendDNA(Post-Amp) 137 HybridizetoBeadChip(Post-Amp) 142 WashBeadChips(Post-Amp) 160 ExtendandStain(XStain)BeadChip(Post-Amp) 172 ImageBeadChip 195 IlluminaGenomeStudio 196 Index 197 TechnicalAssistance 199 vi Part#15025908Rev.D List of Tables Table1 SampleSheetGuidelines 11 Table2 AutoLoader2andAutoLoader2xFeatures 15 Table3 ConcentrationsofLambdaDNA 25 Table4 VolumesforPicoGreenReagents 27 Table5 ScanSettingsforInfiniumLCGQuad 93 Table6 ConcentrationsofLambdaDNA 104 Table7 VolumesforPicoGreenReagents 106 Table8 ListofReactions 182 Table9 ScanSettingsforInfiniumLCGQuad 195 Table10 IlluminaGeneralContactInformation 199 Table11 IlluminaCustomerSupportTelephoneNumbers 199 vii InfiniumLCGQuadAssayProtocolGuide viii Part#15025908Rev.D Chapter1 Overview Overview C h a p t e IntroductiontoInfiniumLCGQuadAssay 2 r AudienceandPurpose 3 1 InfiniumLCGQuadAssay 4 IlluminaInfiniumBeadChips 9 IlluminaLabProtocols 10 TrackingTools 11 TecanGenePaint 14 ImagingSystems 15 GenomeStudioIntegrated InformaticsPlatform 16 1 InfiniumLCGQuadAssayProtocolGuide w IntroductiontoInfinium LCGQuadAssay e i v er TheIllumina®Infinium LCGQuadAssayis an evolution forDNAanalysis,by v streamliningsamplepreparation andenablinghigh multiplexing.UsingInfinium Iand O Infinium IIprobedesigns anddual colorchannel approach,theInfinium LCGQuadAssay allows DNAanalysis ofuptoseveral million ofSNPs andCNV markers persample. TheInfinium LCGQuadAssayaccomplishes this unlimitedmultiplexingbycombining whole-genomeamplification (WGA)samplepreparation with direct,array-basedcapture andenzymatic scoringoftheSNPloci.Locus discrimination orcopynumber(CNV) determination is providedbya combination ofhigh beadtyperepresentation perfeature, sequence-specific hybridization captureandarray-based,single-baseprimerextension.In thecaseoftheInfinium IIprobedesign,the3' endoftheprimeris positioneddirectly adjacenttotheSNPsite,orthenonpolymorphic sitein thecaseofnonpolymorphic probes. In thecaseoftheInfinium Iprobedesign,the3' endoftheprimeroverlaps with theSNP site.Ifthereis a perfectmatch,extension occurs andsignal is generated.Ifthereis a mismatch,extension does notoccurandnosignal is generated. Allele-specific singlebaseextension oftheprimerincorporates a biotin nucleotideora dinitrophenyl labelednucleotide.CandGnucleotides arebiotin labeled;AandT nucleotides aredinitrophenyl labeled.Signal amplification oftheincorporatedlabel further improves theoverall signal-to-noiseratiooftheassay. TheInfinium LCGQuadAssayoffers: } High multiplexing } High call rateandaccuracy } UnlimitedGenome-widemarkerselection } Singletubeamplification,singlechip,noPCR } Minimal riskofcarryovercontamination } LowDNAinput—400 ngpersample. } Walk-awayautomation usingTecan Genesis orFreedom EVORobots andTecan GenePaintsystem } Compatibilitywith both Illumina iScan® andHiScan Systems } Multiple-SampleBeadChipformat 2 Part#15025908Rev.D

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Then smack the plate down on a dry area of the pad, avoiding the This protocol uses an aliphatic amide that is a probable reproductive toxin.
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Infinium® LCG Quad Assay Protocol Guide For Research Use Only. Not for use in diagnostic procedures. ILLUMINA PROPRIETARY Catalog # WG-901-5 001 Part # 15025908 Rev. D June 2015 ThisdocumentanditscontentsareproprietarytoIllumina,Inc.anditsaffiliates("Illumina"),andareintendedsolelyforthecontractualuseof itscustomerinconnectionwiththeuseoftheproduct(s)describedhereinandfornootherpurpose.Thisdocumentanditscontentsshallnot beusedordistributedforanyotherpurposeand/orotherwisecommunicated,disclosed,orreproducedinanywaywhatsoeverwithoutthe priorwrittenconsentofIllumina.Illuminadoesnotconveyanylicenseunderitspatent,trademark,copyright,orcommon-lawrightsnor similarrightsofanythirdpartiesbythisdocument. Theinstructionsinthisdocumentmustbestrictlyandexplicitlyfollowedbyqualifiedandproperlytrainedpersonnelinordertoensurethe properandsafeuseoftheproduct(s)describedherein.Allofthecontentsofthisdocumentmustbefullyreadandunderstoodpriortousing suchproduct(s). FAILURETOCOMPLETELYREADANDEXPLICITLYFOLLOWALLOFTHEINSTRUCTIONSCONTAINEDHEREINMAYRESULTIN DAMAGETOTHEPRODUCT(S),INJURYTOPERSONS,INCLUDINGTOUSERSOROTHERS,ANDDAMAGETOOTHERPROPERTY. ILLUMINADOESNOTASSUMEANYLIABILITYARISINGOUTOFTHEIMPROPERUSEOFTHEPRODUCT(S)DESCRIBEDHEREIN (INCLUDINGPARTSTHEREOFORSOFTWARE). ©2015Illumina,Inc.Allrightsreserved. Illumina,24sure,BaseSpace,BeadArray,BlueFish,BlueFuse,BlueGnome,cBot,CSPro,CytoChip,DesignStudio,Epicentre,GAIIx, GeneticEnergy,GenomeAnalyzer,GenomeStudio,GoldenGate,HiScan,HiSeq,HiSeqX,Infinium,iScan,iSelect,MiSeq,NeoPrep, Nextera,NextBio,NextSeq,PoweredbyIllumina,SeqMonitor,SureMDA,TruGenome,TruSeq,TruSight,UnderstandYourGenome, UYG,VeraCode,verifi,VeriSeq,thepumpkinorangecolor,andthestreamingbasesdesignaretrademarksofIllumina,Inc.and/orits affiliate(s)intheU.S.and/orothercountries.Allothernames,logos,andothertrademarksarethepropertyoftheirrespectiveowners. ii Part#15025908Rev.D Revision History Part # Revision Date Descriptionof Change 15025908 D June2015 CorrectedtheAmplificationtemperatureto 37°C. 15025908 C May2012 Indicatedthatupto24BeadChipscanbe washedwith550mlofPB1. 15025908 B September ReagentsSuppliedtableamendedtodelete 2011 partnumbersandmovedescriptionsto secondcolumn. 15025908 A June2011 Initialrelease. iii InfiniumLCGQuadAssayProtocolGuide iv Part#15025908Rev.D Table of Contents RevisionHistory iii TableofContents v ListofTables vii Chapter1 Overview 1 IntroductiontoInfiniumLCGQuadAssay 2 AudienceandPurpose 3 InfiniumLCGQuadAssay 4 IlluminaInfiniumBeadChips 9 IlluminaLabProtocols 10 TrackingTools 11 TecanGenePaint 14 ImagingSystems 15 GenomeStudioIntegrated InformaticsPlatform 16 Chapter2 ManualProtocol 17 IntroductiontoInfiniumLCGQuadManualProtocol 18 InfiniumLCGQuadManualWorkflow 19 Equipment,Materials,andReagents 21 QuantifyDNA(Optional)(Pre-Amp) 23 MaketheAMP5Plate 31 IncubateDNA(Post-Amp) 35 FragmentDNA(Post-Amp) 36 PrecipitateDNA(Post-Amp) 39 ResuspendDNA(Post-Amp) 43 HybridizetoBeadChip(Post-Amp) 46 WashBeadChips(Post-Amp) 61 ExtendandStain(XStain)BeadChip(Post-Amp) 73 ImageBeadChip 93 IlluminaGenomeStudio 94 Chapter3 AutomatedProtocol 95 IntroductiontoInfiniumLCGQuadAutomatedProtocol 96 InfiniumLCGQuadAutomatedWorkflow 97 Equipment,Materials,andReagents 99 QuantifyDNA(Optional)(Pre-Amp) 102 v InfiniumLCGQuadAssayProtocolGuide MaketheAMP5Plate 112 IncubateDNA(Post-Amp) 121 FragmentDNA(Post-Amp) 123 PrecipitateDNA(Post-Amp) 129 ResuspendDNA(Post-Amp) 137 HybridizetoBeadChip(Post-Amp) 142 WashBeadChips(Post-Amp) 160 ExtendandStain(XStain)BeadChip(Post-Amp) 172 ImageBeadChip 195 IlluminaGenomeStudio 196 Index 197 TechnicalAssistance 199 vi Part#15025908Rev.D List of Tables Table1 SampleSheetGuidelines 11 Table2 AutoLoader2andAutoLoader2xFeatures 15 Table3 ConcentrationsofLambdaDNA 25 Table4 VolumesforPicoGreenReagents 27 Table5 ScanSettingsforInfiniumLCGQuad 93 Table6 ConcentrationsofLambdaDNA 104 Table7 VolumesforPicoGreenReagents 106 Table8 ListofReactions 182 Table9 ScanSettingsforInfiniumLCGQuad 195 Table10 IlluminaGeneralContactInformation 199 Table11 IlluminaCustomerSupportTelephoneNumbers 199 vii InfiniumLCGQuadAssayProtocolGuide viii Part#15025908Rev.D Chapter1 Overview Overview C h a p t e IntroductiontoInfiniumLCGQuadAssay 2 r AudienceandPurpose 3 1 InfiniumLCGQuadAssay 4 IlluminaInfiniumBeadChips 9 IlluminaLabProtocols 10 TrackingTools 11 TecanGenePaint 14 ImagingSystems 15 GenomeStudioIntegrated InformaticsPlatform 16 1 InfiniumLCGQuadAssayProtocolGuide w IntroductiontoInfinium LCGQuadAssay e i v er TheIllumina®Infinium LCGQuadAssayis an evolution forDNAanalysis,by v streamliningsamplepreparation andenablinghigh multiplexing.UsingInfinium Iand O Infinium IIprobedesigns anddual colorchannel approach,theInfinium LCGQuadAssay allows DNAanalysis ofuptoseveral million ofSNPs andCNV markers persample. TheInfinium LCGQuadAssayaccomplishes this unlimitedmultiplexingbycombining whole-genomeamplification (WGA)samplepreparation with direct,array-basedcapture andenzymatic scoringoftheSNPloci.Locus discrimination orcopynumber(CNV) determination is providedbya combination ofhigh beadtyperepresentation perfeature, sequence-specific hybridization captureandarray-based,single-baseprimerextension.In thecaseoftheInfinium IIprobedesign,the3' endoftheprimeris positioneddirectly adjacenttotheSNPsite,orthenonpolymorphic sitein thecaseofnonpolymorphic probes. In thecaseoftheInfinium Iprobedesign,the3' endoftheprimeroverlaps with theSNP site.Ifthereis a perfectmatch,extension occurs andsignal is generated.Ifthereis a mismatch,extension does notoccurandnosignal is generated. Allele-specific singlebaseextension oftheprimerincorporates a biotin nucleotideora dinitrophenyl labelednucleotide.CandGnucleotides arebiotin labeled;AandT nucleotides aredinitrophenyl labeled.Signal amplification oftheincorporatedlabel further improves theoverall signal-to-noiseratiooftheassay. TheInfinium LCGQuadAssayoffers: } High multiplexing } High call rateandaccuracy } UnlimitedGenome-widemarkerselection } Singletubeamplification,singlechip,noPCR } Minimal riskofcarryovercontamination } LowDNAinput—400 ngpersample. } Walk-awayautomation usingTecan Genesis orFreedom EVORobots andTecan GenePaintsystem } Compatibilitywith both Illumina iScan® andHiScan Systems } Multiple-SampleBeadChipformat 2 Part#15025908Rev.D

Description:
Then smack the plate down on a dry area of the pad, avoiding the This protocol uses an aliphatic amide that is a probable reproductive toxin.
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