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HOLOTYPEHLA™24/7
A1&A2USERMANUAL
FORRESEARCHUSEONLY
V2.1
OmixonLimited2017
.
OmixonHolotypeHLA24/7UserManualv2.1.Forresearchuseonly.Copyright©2017,OmixonBiocomputingLtd.Confidential&Proprietary Page2│48
TableofContentsDOCUMENTHISTORY...........................................................................................................................................4THEPRINCIPLEOFTHEMETHOD:NGS-BASEDHLATYPINGFORTHEILLUMINAMISEQ.........................................6HOLOTYPEHLAPACKINGLIST...............................................................................................................................7
PRIMERCOMPONENTBOX..............................................................................................................................................7LIBRARYPREPARATIONREAGENTSCOMPONENTBOX...........................................................................................................796-WELLADAPTORPLATE...............................................................................................................................................7EXCELWORKBOOK........................................................................................................................................................7SOFTWARE–OMIXONHLATWIN....................................................................................................................................8
RECOMMENDATIONS...........................................................................................................................................9DNAEXTRACTIONRECOMMENDATIONS............................................................................................................................9TECHNICALANDEQUIPMENTRECOMMENDATIONS..............................................................................................................9ASSOCIATEDREAGENTRECOMMENDATIONS.......................................................................................................................9
MiSeqReagentKitcapacity...............................................................................................................................10RECOMMENDEDSUPPLIES.............................................................................................................................................10
LEGALNOTICE....................................................................................................................................................12SUMMARYOFSTEPS..........................................................................................................................................13GLOSSARY/DEFINITIONS.....................................................................................................................................15STEP0–GENOMICDNAPREPARATION..............................................................................................................16STEP1–HLAAMPLIFICATIONMASTERMIXPREPARATION................................................................................17
REAGENTLIST.............................................................................................................................................................17PROTOCOL.................................................................................................................................................................17
MasterMix:HLA-A,B,C,DRB1,DPB1,andDQA1.............................................................................................17MasterMix:HLA-DQB1Set3.............................................................................................................................18
STEP2–HLACLASSIANDIIAMPLIFICATION......................................................................................................19REAGENTLIST.............................................................................................................................................................19PROTOCOL.................................................................................................................................................................19
TaqPolymerase-LoadedMasterMix:HLA-DQB1set3......................................................................................20ClassIAmplification(HLA-A,BandC)...............................................................................................................20ExpectedAmpliconSizes....................................................................................................................................21
STEP3–AMPLICONQUANTITATIONANDNORMALIZATION(USINGAPLATEFLUOROMETER)...........................22REAGENTLIST.............................................................................................................................................................22PROTOCOL.................................................................................................................................................................22
Ampliconpooling...............................................................................................................................................23ExoSAP-ITExpressPCRPurification....................................................................................................................24
STEP4–LIBRARYPREPARATION........................................................................................................................25REAGENTLIST.............................................................................................................................................................25PROTOCOL.................................................................................................................................................................25
FragmentationMasterMix................................................................................................................................25FragmentationProgram....................................................................................................................................26EndRepairMasterMix......................................................................................................................................27EndRepairProgram...........................................................................................................................................27
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LigationMasterMix...........................................................................................................................................28LigationProgram...............................................................................................................................................28Poolingandlibrarypurification.........................................................................................................................29
STEP5–LIBRARYSIZESELECTION.......................................................................................................................31REAGENTLIST.............................................................................................................................................................31PROTOCOL.................................................................................................................................................................31
STEP6–LIBRARYQUANTIFICATIONUSINGANINTERCALATINGDSDNAFLUORESCENTDYE...............................32REAGENTLIST.............................................................................................................................................................32PROTOCOL.................................................................................................................................................................32
STEP7–SEQUENCINGONILLUMINAMISEQ......................................................................................................34REAGENTLIST.............................................................................................................................................................34
MiSeqReagentKitcapacity...............................................................................................................................34PROTOCOL.................................................................................................................................................................34
STEP8–ANALYSISOFHLASEQUENCINGDATA..................................................................................................36AUTOMATEDPROTOCOL...............................................................................................................................................36
ITSetupandConfiguration................................................................................................................................36ProtocolperAnalysis.........................................................................................................................................36
MANUALSERVERPROTOCOL.........................................................................................................................................36ITSetupandConfiguration................................................................................................................................36ProtocolperAnalysis.........................................................................................................................................36
MANUALDESKTOPPROTOCOL.......................................................................................................................................36ITSetupandConfiguration................................................................................................................................36ProtocolperAnalysis.........................................................................................................................................37
TECHNICALASSISTANCE.....................................................................................................................................38PhoneSupport:..................................................................................................................................................38
SUPPLEMENTALFIGURES....................................................................................................................................39PLATEEXAMPLEFORAMPLICONPLATE,AMPLIFICATIONPLATE,DILUTIONPLATE,AMPLICONQUANTITATIONPLATE(FORANINDIVIDUALLOCUS)&REACTIONPLATE...........................................................................................................................39STANDARDSQUANTITATIONPLATEEXAMPLE....................................................................................................................40KAPALIBRARYQUANTITATIONQPCRPLATEEXAMPLE......................................................................................................40
APPENDIX1:PIPPINPREP...................................................................................................................................41PROGRAMMINGTHEPIPPINPREP...................................................................................................................................41RUNNINGTHEPIPPINPREP...........................................................................................................................................41
APPENDIX2:AMPLICONQUANTITATIONUSINGAQPCRINSTRUMENT..............................................................44REAGENTLIST.............................................................................................................................................................44PROTOCOL.................................................................................................................................................................44
APPENDIX3:LIBRARYQUANTITATIONUSINGAQPCRINSTRUMENT..................................................................46REAGENTLIST.............................................................................................................................................................46PROTOCOL.................................................................................................................................................................46
qPCRPrimerMix................................................................................................................................................46qPCRMasterMix...............................................................................................................................................47
OmixonHolotypeHLA24/7UserManualv2.1.Forresearchuseonly.Copyright©2017,OmixonBiocomputingLtd.Confidential&Proprietary Page4│48
DocumentHistoryVersion Date DescriptionofChanges ApprovalName
1.5 January,2015 InitialVersion PeterMeintjes
1.6 March,2015 DQB Enhancer combination, general edits,Appendix2:SampleSheet
PeterMeintjes
1.7 June,2015ExoSAP-ITStepChange,DQB1Set1&2pooling,DQB1 Set 1 optional, <16 samples/run, PippinPrep0.8
PeterMeintjes
1.7.1 June,2015DPB1capschangedfromCleartoPurple,DQA1caps changed from Clear to Brown. MiSeqReagentNanoKitv2requirementsupdated.
PeterMeintjes
1.7.2 July,2015 MiSeqReagentKitv2andMiSeqReagentNanoKitv2requirementsupdated.
PeterMeintjes
1.7.3 November,2015
Amplificationverificationandquantitationmaybe optional after sufficient and consistentexperience.
PeterMeintjes
1.7.4 February,2016
Increased volume of Enhancer 2, Enhancer 2should now be saved after Combined DQBEnhancerismade,addednewDRB4MasterMixformulation, increased the volume used inFragmentation and End Repair master mix forfull plate, and rounded some values to thenearesttenth.
EfiMelista
1.7.5 April,2016
Changed wording from “LR-PCR enzyme” to“Taq Polymerase” based on Qiagen’sdocumentation change. Removed X2 fromHolotype HLA product configuration name.Approval name has been added on documenthistory.
EfiMelista
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1.7.6 April,2016 DQB1set1andset2statementupdate EfiMelista
1.7.7 July,2016 Updated library preparation reagent volumes,additionofadaptorplateA2andBinformation.
EfiMelista
2.0 January,2017
“DQB” removal from the DQB Enhancers, gelverification after LR-PCR made optional,amplicon quantitation simplification, per-samplepoolingvolumechangein11-locuskits,ExoSAP-IT replacement by ExoSAP-IT Express,Qubituseforlibraryquantitation.
EfiMelista
2.1 July,2017 DQB1 set 1 and set 2 primer mix replaced byDQB1set3,endrepairreactiontimedecrease,ligation reaction time decrease libraryquantitation method update, Sample sheetremovedfromAppendices
OmixonHolotypeHLA24/7UserManualv2.1.Forresearchuseonly.Copyright©2017,OmixonBiocomputingLtd.Confidential&Proprietary Page6│48
ThePrincipleoftheMethod:NGS-basedHLAtypingfortheIlluminaMiSeqFormany years theHLA community has beenworking toward amethod thatwill accuratelyidentifytheextensivepolymorphismoftheHLAgenesandoftheirgeneproducts.TheadventofPCR,combinedwithothertechnologies(Sangersequencing,SSOP,SSP,Luminex),providedaformula for significantly improving the detection of HLA polymorphisms albeit with severallimitationsthatcontinuetoinhibitourabilitytocomprehensivelycharacterizetheHLAgenes.Technologies developed over the last several years, cumulatively called Next GenerationSequencing (NGS),haveprovidednewopportunities thatallowthecompletecharacterizationoftheHLAgenesinhaploidfashion.NGShastwodistinctfeatures,1)clonalsequencingofDNAfragments, and 2) tremendously high throughput. NGS provides the capability to phasepolymorphismstherebyeliminatingallambiguitiesandprovidesHLAtypingatthethreetofourfieldlevelwithoutreflexivetesting,therebyintroducingapotentiallytotalsolutiontotheHLAtypingproblem.Theprotocoldescribedheretakesadvantageofthistechnologyandcombineslong-range PCR amplification of HLA geneswith sequencing on the IlluminaMiSeq platform.MorespecificallytheHLAgenesA,B,C,DQA1andDQB1areamplifiedfortheirentirecodinglength,includingelementsofthe5’and3’untranslatedregions,whileDRB1isamplifiedfromintron 1 to intron 4 and DPB1 is amplified from intron 1 to the 3’ untranslated region. Theampliconsarethenprocessedthroughaseriesofstepsthat:
1. FragmenttheampliconstoasizeappropriateforsequencingontheIlluminaplatform,
2. Blunt-endandadenylatetheendsofthefragmentedampliconsand
3. LigateadaptorsequencesthatareusedthroughouttheprocessontheMiSeqtocapture,amplify, and sequence the DNA. The adaptors also include an index which is a shortsequence, unique to each adaptor, which identifies the origins of the library(sample/locus).
Afterpoolingtheindexedlibraries,sizeselectionandquantitation,thesampleisloadedontheMiSeqforsequencing.Thewholeprocesstakes3-5daysdependingontheselectionoftheflowcellontheIlluminaplatform.ThegenerateddataareanalyzedusingtwodifferentalgorithmsinHLATwin™(www.omixon.com).TheuseoftwoindependentalgorithmsinHLATwinprovidesthehighestlevelofconfidencesothattheHLAgenotypingresultscanbereportedimmediatelywithoutfurtherattention.Sampleswithquestionableorambiguousgenotypingsareflaggedbythesoftwaretobeanalyzedmanually.
OmixonHolotypeHLA24/7UserManualv2.1.Forresearchuseonly.Copyright©2017,OmixonBiocomputingLtd.Confidential&Proprietary Page7│48
HolotypeHLAPackingList
PrimerComponentBoxPrimermix Rxns Vol/tube #Tubes ColorcodeHLA-A 24 60μL 1 YellowHLA-B 24 60μL 1 RedHLA-C 24 60μL 1 OrangeHLA-DRB1 24 60μL 1 GreenHLA-DPB1 24 60μL 1 PurpleHLA-DQA1 24 60μL 1 BrownHLA-DQB1(Set3) 24 60μL 1 BlueEnhancer1 96 1100μL 1 ClearEnhancer2 96 300μL 1 Clear
LibraryPreparationReagentsComponentBoxReagent Rxns Vol/tube #Tubes ColorcodeFragmentationEnzyme(A) 24 70μL 1 YellowFragmentationBuffer(B) 24 70μL 1 RedEndRepairEnzyme(C) 24 41μL 1 GreenEndRepairBuffer(D) 24 82μL 1 OrangeLigationEnzyme(E) 24 81μL 1 BlueLigationBuffer(F) 24 900μL 2 Black
96-wellAdaptorPlateIndexedadaptorsina5μLsolutionforgenerating24individualsequencinglibraries.Two (2) Adaptor Plate configurations are available containing 24 individual indices. Adaptorplates,thatcontain24indicesonlyareavailableinthefollowingconfigurations:A1(i1-i24),A2(i25-i48).
ExcelWorkbookAnExcelWorkbookisprovidedtosupporttheHolotypeHLAprotocolwithvolumecalculations,platelayouts,reagenttraceability,recordkeepingandMiSeqSampleSheetgenerationofallofthesupportedadaptorplateconfigurations(A1,A2).Ifyoudonothaveacopy,[email protected].
OmixonHolotypeHLA24/7UserManualv2.1.Forresearchuseonly.Copyright©2017,OmixonBiocomputingLtd.Confidential&Proprietary Page8│48
Software–OmixonHLATwinContact [email protected] for Omixon HLA Twin license associated with your purchase ofHolotypeHLA.
OmixonHolotypeHLA24/7UserManualv2.1.Forresearchuseonly.Copyright©2017,OmixonBiocomputingLtd.Confidential&Proprietary Page9│48
Recommendations
DNAExtractionRecommendations§ HighqualitygenomicDNA(gDNA)extractedfromwholeblood,bloodcells(B-celllines,
buffycoats,cordbloodoranyfractionofwhitebloodcells),salivaandbuccalswabscanbeused.FortheamplificationofHLA-A,HLA-B,HLA-C,HLA-DRB1,HLA-DPB1,HLA-DQA1andHLA-DQB1,0.8-1.2µgofgDNAisrequired.
TechnicalandEquipmentRecommendations§ Thermalcyclerwith96-wellformat§ Platefluorometer(oranyinstrumentcapableoffluorescencedetectionin96-wellplate
format,forusewiththePromegaQuantiFluordsDNASystem)§ PippinPrep(Cat#PIP0001)orBluePippin(Cat#BLU0001)bySAGEScience§ Qubitfluorometer(Cat#Q33216,ThermoFisherScientific)§ qPCRinstrumentwith96or384-wellplateformat(optional)§ IlluminaMiSeq(Cat#SY-410-1003)§ 64-bitcomputerwithminimum4Coresand16GBofRAM§ Long-termdatastorage(approximately2TBofdataperMiSeqperyear)
AssociatedReagentRecommendations§ LongRangePCRkitsfromQiagen(Cat#206401,206402or206403)
§ Eachsamplerequires3.2μLofTaqPolymerase§ Cat#206401LongRangePCRkit(20)contains8μLofTaqPolymerase§ Cat#206402LongRangePCRkit(100)contains40μLofTaqPolymerase§ Cat#206403LongRangePCRkit(250)contains100μLofTaqPolymerase
§ ExoSAP-IT Express from Affymetrix (Cat#75001-200, 75001-1ML, 75001-4X-1ML or75001-10ML)
§ Eachpooledsamplerequires4μLofExoSAP-ITExpressenzyme§ Cat#75001-200contains200μLofExoSAP-ITExpressenzyme§ Cat#75001-1-MLcontains1mLofExoSAP-ITExpressenzyme§ Cat#75001-4X-1MLcontains4mLofExoSAP-ITExpressenzyme§ Cat#75001-10MLcontains10mLofExoSAP-ITExpressenzyme
§ QubitdsDNABRAssayKit(Cat#Q32850orQ32853)§ Cat#Q32850contains100assays§ Cat#Q32853contains500assays
§ Library Quantification Kit – Illumina/Universal from KAPA Biosystems (Cat# KK4824)(optionalifusingaqPCRinstrument)
§ QuantiFluordsDNASystemfromPromega(Cat#E2670)§ AgencourtAMPureXPbeadsfromBeckmanCoulter(Cat#A63880,A63881,orA63882)
§ EachHolotypeHLArunrequiresamaximumof900μLofAMpureXPbeads
OmixonHolotypeHLA24/7UserManualv2.1.Forresearchuseonly.Copyright©2017,OmixonBiocomputingLtd.Confidential&Proprietary Page10│48
§ Cat#A63880contains5mLofAMPureXPbeads§ Cat#A63881contains60mLofAMPureXPbeads§ Cat#A63882contains450mLofAMPureXPbeads
§ Gelcassette,1.5%agarose,dyefreewithinternalstandard(MarkerK/R2),forthePippinPrep/BluePippin(Cat#CDF1510forPippinPrepandBDF1510forBluePippin)
§ Moleculargradeethanol(AnhydrousAlcohol)§ Moleculargradewater(DNaseandRNasefree)§ Sodiumhydroxide§ 1×TEbuffer(pH8.0)§ MiSeqReagentKitfromIllumina
MiSeqReagentKitcapacityIlluminaMiSeqReagentKit
TimeHours
24/7Samples
24/11Samples
96/5Samples
96/7Samples
96/11Samples
Std300Cycle(MS-102-2002) ~24 24 24 96 96 72
Micro300Cycle(MS-103-1002) ~19 24 20 40 28 20
Nano300Cycle(MS-103-1001) ~17 6 4 8 6 4
Std500Cycle(MS-102-2003) ~39 24 24 96 96 96
Nano500Cycle(MS-103-1003) ~28 12 8 16 12 8
RecommendedSupplies§ 1.5mLmicrocentrifugetubes§ 1.5mLlow-bindmicrocentrifugetubes§ 2.0mLlow-bindmicrocentrifugetubes(EppendorfDNALoBindCat#022431048
recommended)§ 0.5mlthinwalltubesforQubitinstrument(QubitAssaytubesCat#Q32856
recommended)§ Adjustablevolumepipettes(1.0–1000μLcapacity)§ 8-channeladjustablevolumepipettes(1.0-100μLcapacity)§ 96-wellplatescompatiblewiththethermalcycler§ 96-wellopticalplatescompatiblewiththeplatefluorometer§ 96-wellplatescompatiblewiththeqPCRinstrument§ Platesealsforgeneraluse§ Platesealscompatiblewiththethermalcyclers(testedforlongrangePCR)§ OpticalplatesealscompatiblewiththeqPCRinstrument(optional)§ Magneticstandcompatiblewith2mLmicrocentrifugetubes§ 96-wellcoolerracks(2pieces)§ 50mLconicaltubes
OmixonHolotypeHLA24/7UserManualv2.1.Forresearchuseonly.Copyright©2017,OmixonBiocomputingLtd.Confidential&Proprietary Page11│48
§ 50mLreservoirs
OmixonHolotypeHLA24/7UserManualv2.1.Forresearchuseonly.Copyright©2017,OmixonBiocomputingLtd.Confidential&Proprietary Page12│48
LegalNoticeThe Holotype HLA User Manual and all contents are proprietary to Omixon Biocomputing("Omixon"), and are intended solely for the contractual useby its customer in regard to theproduct(s)describedhereinandfornootherpurpose.Thisdocumentanditscontentsshallnotbe used or distributed for any other purpose and/or otherwise communicated, disclosed, orreproducedinanywaywhatsoeverwithoutthepriorwrittenconsentofOmixon.Omixondoesnotconveyanylicenseunderitspatent,trademark,copyright,orcommon-lawrightsnorsimilarrightsofanythirdpartiesbythisdocument.UseofOmixonHolotypeorMonotypeHLA(includingsoftwareandassay)isgovernedbyTermsandConditionsGoverningOmixonProducts(www.omixon.com/supply-agreement/),whichreferencestheOmixonHLATwinEULA(www.omixon.com/hla-twin-eula/).
UseofOmixonTargetsoftwareisgovernedbytheOmixonTargetEULA(www.omixon.com/omixon-target-eula/).
UseofOmixonHLATwinsoftwarealoneisgovernedbytheOmixonHLATwinEULA(www.omixon.com/hla-twin-eula/).
UseofOmixonHLAExploresoftwareisgovernedbytheOmixonHLAExploreEULA(www.omixon.com/hla-explore-eula/).
The instructions in this document must be strictly and explicitly followed by qualified andproperly trained personnel in order to ensure the proper and safe use of the product(s)describedherein.Allofthecontentsofthisdocumentmustbefullyreadandunderstoodpriortousingsuchproduct(s).FAILURE TO COMPLETELY READ AND EXPLICITLY FOLLOW ALL OF THE INSTRUCTIONSCONTAINED HEREIN MAY RESULT IN DAMAGE TO THE PRODUCT(S), INJURY TO PERSONS,INCLUDINGTOUSERSOROTHERS,ANDDAMAGETOOTHERPROPERTY.OMIXON DOES NOT ASSUME ANY LIABILITY ARISING OUT OF THE IMPROPER USE OF THEPRODUCT(S)DESCRIBEDHEREIN(INCLUDINGPARTSTHEREOFORSOFTWARE)ORANYUSEOFSUCHPRODUCT(S)OUTSIDETHESCOPEOFTHEEXPRESSWRITTENLICENSESORPERMISSIONSGRANTED BY OMIXON IN CONNECTION WITH CUSTOMER'S ACQUISITION OF SUCHPRODUCT(S).FORRESEARCHUSEONLY©2017OmixonBiocomputingLtd.Allrightsreserved.
OmixonHolotypeHLA24/7UserManualv2.1.Forresearchuseonly.Copyright©2017,OmixonBiocomputingLtd.Confidential&Proprietary Page13│48
SummaryofSteps
OmixonHolotypeHLA24/7UserManualv2.1.Forresearchuseonly.Copyright©2017,OmixonBiocomputingLtd.Confidential&Proprietary Page14│48
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Glossary/Definitions§ AmpliconPlate–AlternativenameforanAmplificationPlate§ AmpliconQuantitationPlate–96-wellplate compatiblewith theplate fluorometeror
qPCRmachinewheretheampliconsarequantitated.§ AmplificationPlate–96-wellPCRplateusedtoamplifytheHLAloci.§ Final Library – Library that includes all Sample Libraries ready to be sequenced in a
singleMiSeqrun.§ Reaction Plate – Platewhere the sequential reactions that fragment, end repair, and
ligatetheindexedadaptorstotheSampleLibrariesareperformed.§ ReagentPlate–PlateusedtoaliquotthevariousreagentsusedtopreparetheLibraries§ Sample Library – A library prepared by combining (pooling) all HLA loci for a given
sample.§ PooledAmpliconsPlate–Platecontainingasamplelibrary(alllocicombined)perwell.§ StandardsQuantitationPlate–96-wellplatecompatiblewiththeplatefluorometeror
qPCRmachinewhereDNAstandardsareplacedtoallowforampliconquantitation.
OmixonHolotypeHLA24/7UserManualv2.1.Forresearchuseonly.Copyright©2017,OmixonBiocomputingLtd.Confidential&Proprietary Page16│48
Step0–GenomicDNAPreparationDuration:~45minutesIsolategDNAfromwholeblood,bloodcells(B-celllines,buffycoats,cordbloodoranyfractionofwhitebloodcells),salivaandbuccalswabs.gDNAshouldbedissolvedinwaterastheEDTAinTE buffer can inhibit long-range PCR reactions and its recommended concentration is 20-30ng/μl.Wehighlyrecommendtouseafluorescence-basedquantitationmethodtodeterminethegDNAconcentration.Itsquality,asevaluatedbyspectrophotometry,shouldbe:
1. A260nm/280nmabsorbanceratiobetween1.7and1.9.2. A260nm/230nmabsorbanceratioof1.7orgreater.3. Minimal degradation. DNA that is old or has gone through repeated
freeze/thawswillsufferfrommoredegradation.FortheamplificationofHLA-A,HLA-B,HLA-C,HLA-DRB1,HLA-DPB1,HLA-DQA1andHLA-DQB1,0.8-1.2µgofgDNAisrequiredforeachsample.
OmixonHolotypeHLA24/7UserManualv2.1.Forresearchuseonly.Copyright©2017,OmixonBiocomputingLtd.Confidential&Proprietary Page17│48
Step1–HLAAmplificationMasterMixPreparationDuration:~45minutesThepurposeofthisstepistopreparelocus-specificMasterMixestoamplifyeachtargetedHLAlocusindividually.ThelociamplifiedbythisprotocolareHLA-A,HLA-B,HLA-C,HLA-DRB1,HLA-DPB1,HLA-DQA1andHLA-DQB1,Note: TheMasterMixes prepared in this step include all reagents needed for amplificationexcepttheTaqPolymerase.
ReagentlistItem Storage SuppliedbyHLA-APrimerMix -20°C OmixonHLA-BPrimerMix -20°C OmixonHLA-CPrimerMix -20°C OmixonHLA-DRB1PrimerMix -20°C OmixonHLA-DPB1PrimerMix -20°C OmixonHLA-DQA1PrimerMix -20°C OmixonHLA-DQB1Set3PrimerMix -20°C OmixonEnhancer1 -20°C OmixonEnhancer2 -20°C OmixonLongRangePCRBuffer(10×) -20°C QiagendNTPs(10mMeach) -20°C QiagenMoleculargradeH2O -20°C Qiagen
Protocol1.1 - Removeall primermixes, Enhancer 1 and2, thedNTPs and the Long-RangePCRBuffer
(10×),fromstorageandthawatroomtemperature.
1.2 - Prepare the Combined Enhancer: add 132 μL of Enhancer 2 into the Enhancer 1 tube.RelabelEnhancer1tubeasCombinedEnhancer.
1.3 -PrepareaMasterMixforeachPrimerMixaccordingtothetablesbelow:
MasterMix:HLA-A,B,C,DRB1,DPB1,andDQA1Reagent Volume/sample/locus Volume/24samples/locusPrimerMix 2μL 51μLLongRangePCRBuffer(10×) 2.5μL 63.8μLdNTPMix(10mMeach) 1.25μL 31.9μLMoleculargradeH2O 13.85μL 353.2μL
OmixonHolotypeHLA24/7UserManualv2.1.Forresearchuseonly.Copyright©2017,OmixonBiocomputingLtd.Confidential&Proprietary Page18│48
TotalVolume 19.6μL 499.9μL
MasterMix:HLA-DQB1Set3
Reagent Volume/sample/locus Volume/24samples/locusPrimerMix 2μL 51μLLongRangePCRBuffer(10×) 2.5μL 63.8μLdNTPMix(10mMeach) 1.25μL 31.9μLCombinedEnhancer 5.6μL 142.8μLMoleculargradeH2O 7.85μL 200.2μLTotalVolume 19.2μL 489.7μL1.4 –VortexeachMasterMixandspinitdownfor1second.PlaceMasterMixesonice.
1.5 -DiluteallgDNAstoaconcentrationof20-30ng/μL(minimumvolumeis45μL).
Note: Holotype HLA includes sufficient reagents for 24 reactions plus additionalvolumeforpipettinglossandfailedamplification.
OmixonHolotypeHLA24/7UserManualv2.1.Forresearchuseonly.Copyright©2017,OmixonBiocomputingLtd.Confidential&Proprietary Page19│48
Step2–HLAClassIandIIAmplificationDuration:~6hours45minutesThepurposeof Step2 is to amplify theHLA loci.HLAClass I andClass II amplificationshavebeen optimized using two separate sets of PCR conditions. Once the PCR reactions arecompleted,amplificationisverifiedbyagarosegelelectrophoresis(optional).
Quicktip–Theagarosegelelectrophoresis,whilerecommended,isnotrequiredtosuccessfullycompletetheHolotypeHLAprotocol.Whenampliconsarequantitated(Step3),anyconcentrationabove50ng/μLisconsideredasuccessfulamplification.AgarosegelelectrophoresisisanimportantqualitycontrolstepandshouldnotbeskippedwithoutsufficientexperiencewiththecompleteHolotypeHLAprotocol.
ReagentlistItem Storage SuppliedbyHLA-AMasterMix -20°C Step1HLA-BMasterMix -20°C Step1HLA-CMasterMix -20°C Step1HLA-DRB1MasterMix -20°C Step1HLA-DPB1MasterMix -20°C Step1HLA-DQA1MasterMix -20°C Step1HLA-DQB1Set3MasterMix -20°C Step1TaqPolymerase -20°C QiagengDNA 4°C UserMoleculargradeH2O 20°C User
Protocol2.1–RemovetheTaqPolymerasefromstorage,spin itdown,andadd it toeachMasterMixaccordingtothetablesbelow,rinsingthepipettetipsthoroughlybypipetting:TaqPolymerase-LoadedMasterMix:HLA-A,B,C,DRB1,DPB1,andDQA1Reagent Volume/sample/locus Volume/24samples/locusMasterMixfromStep1 19.6μL 499.9μLTaqPolymerase 0.4μL 10.2μLTotal 20μL 510.1μL
OmixonHolotypeHLA24/7UserManualv2.1.Forresearchuseonly.Copyright©2017,OmixonBiocomputingLtd.Confidential&Proprietary Page20│48
TaqPolymerase-LoadedMasterMix:HLA-DQB1set3Reagent Volume/sample/locus Volume/24samples/locusMasterMixfromStep1 19.2μL 489.7μLTaqPolymerase 0.8μL 20.4μLTotal 20μL 510.1μL2.2 -Briefly vortexand spindownall TaqPolymerase-loadedMasterMixes.Aliquot20μLofeachTaqPolymerase-loadedMasterMixintoseparatewellsof96-wellPCRplates.
Note:Class IandClass IIamplificationhavebeenoptimizedusing twodifferentPCRconditions,soClassIandClassIIMasterMixesshouldnotbeinthesameplate.
2.3–Add5μLof eachdilutedgDNA into theappropriatewell of theplatesprepared in thepreviousstep.Mixbypipetting.Seal themwitha thermalsealandvisually inspecteachwell.Spin-downallAmplificationPlatesinacentrifuge.
2.4 -Place theAmplificationPlates into thermalcyclersandrun theprograms forClass IandClassIIamplificationaccordingtothetablesbelow:
ClassIAmplification(HLA-A,BandC)NumberofCycles Temperature Time
1 95°C 3minutes 95°C 15seconds
35 65°C 30seconds 68°C 5minutes1 68°C 10minutes1 4°C ∞
ClassIIAmplification(HLA-DRB1,DPB1,DQA1andDQB1)NumberofCycles Temperature Time
1 95°C 3minutes 93°C 15seconds
35 60°C 30seconds 68°C 9minutes1 68°C 10minutes1 4°C ∞
Note: Amplification success canbe verified by running 2 μL from each amplicon in astandard2%agarosegelat250Vfor30minutes.(Optional)
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ExpectedAmpliconSizes
HLAlocus Expectedampliconsize(kb)HLA-A,BandC ~3HLA-DRB1 ~4.3HLA-DPB1 ~6.6HLA-DQA1 ~5.5
HLA-DQB1(Set3) ~6.5Safestoppingpoint.Ampliconscanbestoredat4°Covernightorat-20°Cforlonger.
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Step 3 – Amplicon Quantitation and Normalization(usingaPlateFluorometer)Duration:~35minutesAmplicon Quantitation and Normalization is recommended to ensure precise input into thelibrarypreparationstep(Optional).AmpliconconcentrationismeasuredusingtheQuantiFluordsDNA System that contains a fluorescent DNA-binding dye and DNA standard for sensitivequantitation of small amounts of double-stranded DNA (dsDNA). Refer to Appendix 2 forInstructionsonhowtodotheAmpliconQuantitationusingaqPCRmachine.
Quick tip – The amplicon quantitation, while recommended, is not required tosuccessfullycompletetheHolotypeHLAprotocol.Ampliconnormalizationdoesnotrequireprecisemeasurementofampliconconcentration.Anestimateofampliconconcentrations based on experience or agarose gel electrophoresis can be usedinstead. Amplicon quantitation should not be skipped without consistentexperiencewiththecompleteHolotypeHLAprotocol.
ReagentlistItem Storage SuppliedbyClassIAmplificationPlate 4°C Step2ClassIIAmplificationPlate 4°C Step2LambdaDNAStandard(100ng/μL) 4°C PromegaQuantiFluordsDNADye(200×) 4°C Promega20×TEBuffer(pH7.5) 4°C PromegaMoleculargradeH2O 20°Cto25°C UserExoSAP-iTExpress -20°C Affymetrix
Protocol3.1 – Prepare DNA standards by serial dilution of the Lambda DNA standard (100 ng/μL)
providedintheQuantiFluorkitaccordingtothedilutiontablebelow:Labelontube InputDNA VolumeDNA
(μL)Volume1xTE
(μL)FinalConc.(ng/μL)
Standard1 LambdaDNA 7.5μL 492.5μL 1.5ng/μLStandard2 Standard1 250μL 250μL 0.75ng/μLStandard3 Standard2 250μL 250μL 0.38ng/μLStandard4 Standard3 250μL 250μL 0.19ng/μLStandard5 Standard4 250μL 250μL 0.09ng/μLStandard6 Standard5 250μL 250μL 0.05ng/μLBlank Blank 0μL 250μL 0ng/μL
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3.2 -PreparetheAmpliconQuantitationplates(seesupplementalfigures).Aliquot99μL1xTE
buffer to the wells of a 96-well optical plate for the total number of amplicons to bequantitated.
3.3 -Add1μLofampliconsfromcorrespondingwellsintheAmpliconPlatestoindividualwellsintheAmpliconQuantitationPlates.Mixbypipetting.
3.4 - Prepare 1× QuantiFluor Dye working solution using the following formula: 0.5 μL
QuantiFluor Dye (200X) + 99.5 μL 1× TE buffer. Prepare sufficient 1× QuantiFluor Dyeworkingsolutionsothateachsample(totalsamples inAmpliconPlates)andstandard(14total)willreceivea100μLaliquot.
3.5 -PrepareaStandardsQuantitationPlateandAmpliconQuantitationplates.Aliquot100μL
of1×QuantiFluorDyeworkingsolutiontowellsofthe96-wellopticalplatethatwillbetheStandardsQuantitationPlateandtotheAmpliconQuantitationPlatesfromStep3.2.
3.6 - Using the standards prepared above, add 100 μL of each standard, in duplicate, to
individualwellsintheStandardsQuantitationPlate(14wellstotal).Mixbypipetting.
3.7 -Vortexwelltomixandspindown.3.8 -RuntheStandardsQuantitationPlateontheplatefluorometerfollowedbytheAmplicon
QuantitationPlates.3.9 -Calculate theconcentrationofDNA in theAmpliconQuantitationPlatesusingRFUdata
generatedbytheplatefluorometer.RefertotheDilutionTabintheprovidedworkbookforassistancewithcalculations.
3.10 - Dilute DNA in the Amplicon Plates with molecular grade H2O so that the final
concentrationofDNAisapproximately67ng/μL.§ IfDNAconcentrationis150ng/μLorgreater:add25μLofH2O§ IfDNAconcentrationis100-150ng/μL:add10μLofH2O§ IfDNAconcentrationislessthan100ng/μL:donotaddanyH2O
Ampliconpooling3.11 - Pool all loci for each sample into a single Pooled Amplicons Plate. Combine the
volumesindicatedforeachlocusasinthefollowingtabletoobtainafinalvolumeof35μL:
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HLAlocus Pooledvolume
A 5μLB 5μLC 5μL
DRB1 5μLDPB1 5μLDQA1 5μL
DQB1set3 5μL3.12 – Add 4 μL of ExoSAP-iT Express into each sample library. Rinse the pipette tips bypipetting.Sealtheplatewithathermalsealandspindown.3.13-PlacethePooledAmpliconsPlateintoathermalcyclerandrunthefollowingprogram:
ExoSAP-ITExpressPCRPurification
NumberofCycles Temperature Time1 37°C 4minutes1 80°C 1minutes1 4°C ∞
Safestoppingpoint.Ampliconscanbestoredat4°Covernightorat-20°Cforlonger.
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Step4–LibraryPreparationDuration:~3hoursDuringthisstep,thepooledampliconsarepreparedforsequencingontheIlluminaMiSeq.Theampliconsareenzymatically fragmented, theendsare repairedandadenylated, and indexedadaptorsareligatedtotheends.ThelibrariesarethenpooledfollowedbyasinglecleanupandconcentrationstepperformedusingAMPureXPbeads.
Note:Omixonrecommendsvolumesgreaterthanisnecessaryfor24samplesbecausemanyoftheenzymesandbuffersareviscous,resultinginexcesspipettingloss.
ReagentlistItem Storage SuppliedbyPooledAmpliconsPlate 4°C Step3AdaptorPlate -20°C OmixonFragmentationEnzyme(A) -20°C OmixonFragmentationBuffer(B) -20°C OmixonEndRepairEnzyme(C) -20°C OmixonEndRepairBuffer(D) -20°C OmixonLigationEnzyme(E) -20°C OmixonLigationBuffer(F) -20°C OmixonAMPureXPbeads 4°C BeckmanCoulter80%Ethanol(freshlyprepared) 20°Cto25°C UserMoleculargradeH2O 20°Cto25°C User
Protocol4.1-Turnonthethermalcycler.Verifythattheheatedlidiswarmingup.
Note:BesuretovortextheFragmentationEnzyme(A)thoroughlybeforeuse.4.2-PrepareFragmentationMasterMixaccordingtothetablebelow:
FragmentationMasterMix
Reagent Volumeperlibrary(μL)
Recommendedvolumesfor24libraries(μL)
Colorcode
FragmentationEnzyme(A) 2μL 55.2μL YellowFragmentationBuffer(B) 2μL 55.2μL RedTotalVolume 4μL 110.4μL
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4.3-PrepareaReagentPlate:placeanew96-wellPCRplateonaPCRcoolerrackandaliquotandequalamountoftheFragmentationMasterMixintoeachwellofasinglecolumn.
Note:Thefragmentationreactionhasbeendesignedtoprovide ideallysizedDNAforsequencingonthe IlluminaMiSeq. It is important tokeepthereagentscolduntil thereaction is started in the thermal cycler to prevent excessive fragmentation. Use ofmulti-channel pipettes is recommended to minimize opportunities for excessivefragmentation.
4.4-CentrifugethePooledAmpliconsPlatefor10seconds,andplaceitoniceoracoldblock.4.5-PrepareaReactionPlate:placeafresh96-wellPCRplateonaPCRcoldblock.4.6-Add4μLofFragmentationMasterMixfromtheReagentPlateintowellsoftheReactionPlate, correspondingwith samples in thePooledAmpliconsPlate.Theuseofamulti-channelpipetteisrecommended.4.7 -Transfer16μLofeachamplicon fromthePooledAmpliconsPlate to thecorrespondingwellontheReactionPlateusingamulti-channelpipette.Mixbypipetting.4.8-CovertheReactionPlatewithathermalsealandcentrifugefor10seconds.4.9-IncubatetheReactionPlateinathermalcyclerwiththefollowingprogram:
FragmentationProgram
NumberofCycles Temperature Time1 37°C 10minutes1 70°C 15minutes1 4°C ∞
Safestoppingpoint.Librariescanbestoredat4°Covernightorat-20°Cforlonger.
4.10-PreparetheEndRepairMasterMixaccordingtothetablebelow:
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EndRepairMasterMix
Reagent Volumeperlibrary(μL)
Recommendedvolumesfor24libraries(μL)
Colorcode
MoleculargradeH2O 1.25μL 34.8μL EndRepairEnzyme(C) 1.25μL 34.8μL GreenEndRepairBuffer(D) 2.5μL 69.6μL OrangeTotalVolume 5μL 139.2μL 4.11-AliquotanequalamountofEndRepairMasterMix intoasingleunusedcolumnoftheReagentPlate.4.12-CentrifugetheReactionPlate(containingthefragmentedSamples)for10seconds.Add5μLofEndRepairMasterMixfromtheReagentPlateintoeachwelloftheReactionPlate.Theuseofamulti-channelpipetteisrecommended.Mixbypipetting.4.13-CovertheReactionPlatewithathermalsealandcentrifugefor10seconds.4.14-IncubatetheReactionPlateinathermalcyclerwiththefollowingprogram:
EndRepairProgram
NumberofCycles Temperature Time1 20°C 30minutes1 70°C 5minutes1 4°C ∞
Safestoppingpoint.Librariescanbestoredat4°Covernightorat-20°Cforlonger.
4.15-Removethe IndexedAdaptorsPlatefromstorageandthawatroomtemperatureafterthe End Repair Program starts in the thermal cycler. When the Adaptor Plate is at roomtemperature,centrifugeitfor3minutesat3000rpm.4.16-CarefullypullthesealoffoftheAdaptorPlate.DonotshaketheAdaptorPlateoncethesealisremovedtopreventcrosscontamination.4.17 – Transfer the entire volume of each well from the Reaction Plate (25 μL) to thecorrespondingwellintheAdaptorPlate.
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Note: IftheentireAdaptorPlateisNOTgoingtobeused, it ispossibletouseonlythenecessarynumberofadaptors.Cuttheplatesealbetweenthewellstobeusedand thewells tobekept.Carefullypull the sealoff theAdaptorPlate, leaving thesealinplaceoverthewellstobekept.a. Transfer25μLfromeachend-repairedsampleoftheReactionPlatetoawellin
theAdaptorPlate,mixingwellwithapipette.
b. TransfertheentiretyofeachsamplefromtheAdaptorPlateintotheoriginalwelloftheReactionPlate.
c. ResealtheAdaptorPlateandreturnitto-20°C.UsetheReactionPlateinsteadoftheAdaptorPlatefortheremainingstepsinthemanual.
4.18-PreparetheLigationMasterMix.PrepareenoughLigationMasterMixforeachsample.
LigationMasterMix
Reagent Volume(μL) Recommendedvolumesfor24libraries(μL)
Colorcode
LigationEnzyme(E) 2.5μL 63.2μL BlueLigationBuffer(F) 30μL 757.5μL BlackTotalVolume 32.5 820.7μL
4.19-AliquottheLigationMasterMixintoanunusedcolumnoftheReagentPlate.Theuseofamulti-channelpipetteisrecommended.4.20 -Add32.5μLof LigationMasterMix intoeachwell of theReactionPlate. Theuseof amulti-channelpipetteisrecommended.Mixbypipetting.4.21-CovertheReactionPlatewithathermalsealandcentrifugefor10seconds.4.22-IncubatetheReactionPlateinthethermalcyclerwiththefollowingprogram:
LigationProgramNumberofCycles Temperature Time
1 25°C 10minutes1 70°C 10minutes1 4°C ∞
Safestoppingpoint.Librariescanbestoredat4°Covernightorat-20°Cforlonger.
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Poolingandlibrarypurification4.23-AllowAMPureXPbeadstocometoroomtemperature.Ensuretheyarehomogeneous(noclumpsorpellets).Preparefreshlymade5mLof80%ethanol(4mLEtOH+1mLH2O).4.24-CreatetheLibrarybycombininganaliquotfromeachpooledamplicon,nowasample-specificlibrary,intoasingle2.0mLlowbindmicrocentrifugetube.
I. For 16 ormore samples - Calculate the amount of each sample library to pooltogetherasasingleLibraryof900μLtotalvolume.Divide900μLbythenumberofsamplelibraries.ThisisthevolumeofaliquottobetakenfromeachsamplelibraryandpipettedintotheLibrary.
II. Forfewerthan16samples–Transfer60μLofeachsamplelibraryintoaLibrary.4.25 -Add900μLofAMPureXPbeads to theLibrary tube.Mix thoroughlybyvortexingandcentrifugebriefly.Donotallowthebeadstoseparate. IncubatetheLibrary for10minutesatroomtemperature.
Note: If there is less than 900 μL of library in the Final Pool, add an equivalentamountofAMPureXPbeads.Thereshouldbea1:1ratioofFinalPoolandAMPureXPbeads.
4.26-PlacetheLibrarytubeontoamagneticstandandincubatefor10minutes.4.27–Keepingthetubeonthemagneticstand,carefullyremoveanddiscardthesupernatantfromtheLibrarytube,withouttouchingthebeads.4.28-Keepingthetubeonthemagneticstand,add~1.5–2mLoffreshlyprepared80%ethanoltotheLibrarytube.Thevolumeofethanoladdedshouldbesufficienttocoverthebeads.
Note:Applytheethanoltothesideofthetubewithoutbeads.4.29 - Incubate the Library tube at room temperature for 30 seconds; afterwards, carefullyremoveanddiscardthesupernatant.4.30-Repeatsteps4.28and4.29.4.31-QuicklyspindowntheLibrarytubeandplaceitbackonthemagneticstandwiththelidopen.Removeresidualethanolwithapipette.Donottouchthebeads.
Note: Ensure the bead pellet does not contain residual ethanol. This may requirerotating the tubeon themagnetic stand to removeethanolwithoutdisturbing thebeadpellet.
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4.32-Allowthebeadstoairdryfor5-8minutesonthemagneticstanduntilthebeadpelletisdry.4.33 - Remove the Library tube from the magnetic stand and elute the Library with 31 μLmoleculargradewater.Donotletthepipettetiptouchthebeads,astheywillsticktoit.4.34 - Vortex the Library to fully resuspend the beads. Centrifuge briefly if some dropletsremainonthesidewalls.Ensurethebeadsremaininsuspension.4.35-IncubatetheLibraryatroomtemperaturefor2minutes.4.36-PlacetheLibrarytubeonthemagneticstandfor2minutes.4.37-CollecttheLibrary:keepingtheFinalLibrarytubeinthemagneticstand,collect31μLofthesupernatantintoanew1.5mllowbindmicrocentrifugetube.
Safestoppingpoint.Librariescanbestoredat-20°Cforextendedperiodsoftime.
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Step5–LibrarySizeSelectionDuration:~1hourStep 5 takes the Library from Step 4 and performs size selection using the Pippin Prep. ThePippin Prep can automatically select a range of DNA fragment sizes and elute them into acollection chamber. Note: Blue Pippin may be used instead of the Pippin Prep. Refer toAppendix1forPippinPrepInstructionsforUse.
ReagentlistItem Storage Suppliedby1.5%AgaroseGelCassette,DyeFree 20°Cto25°C SageSciencePippinloadingsolution/markermix(labeledK)
4°C SageScience
PooledLibrary 4°C Step4Note:MarkerKisusedwiththePippinPrep.TheBluePippinusesMarkerR2.
Protocol5.1-BringtheMarkerKloadingsolutiontoroomtemperature.5.2-Combine31μLofthePoolwith10μLofMarkerKloadingsolution.5.3-Mixbyvortexingandspindown.5.4-ConfigurethePippinPreptocollectDNAfragmentsbetween650and1300bps.Loadthe40μLsampleintothesampleportandrun.Runtimeis45-50minutes.5.5-Collectthewholecontent(approximately40μL)withintheelutionportofthePippinPrepandtransferittoanew1.5mllowbindmicrocentrifugetube.Thisisthesize-selectedlibrary.
Safestoppingpoint.Librariescanbestoredat-20°Cforextendedperiodsoftime.
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Step 6 – Library Quantification using an intercalatingdsDNAfluorescentdyeDuration:~15minutesIt isnecessarytoquantifythesize-selectedlibrary inordertooptimallyusetheoutputoftheIllumina MiSeq sequencer. The concentration of the size-selected library can be accuratelymeasured by an intercalating dsDNA fluorescent dye, such as SYBR green or equivalent.Commerciallyavailablekitsandinstrumentsforthispurposeinclude,butarenotlimitedto,theQubit reader by Thermo Fisher (uses the Qubit Broad-Range dsDNA assay kit), the QuantusreaderbyPromega(usestheQuantifluordsDNAfluorescentdye)andothers.Here,theQubitmethod isdescribedas it isthemostcommonlyused instrument. Incaseanother instrumentandkitisused,followthemanufacturer’sstandardinstructions.
Note: This dsDNA fluorometric method is a quick but accurate enough way todeterminetheconcentrationof thefinalsize-selected library. Itmeasuresallof thedsDNA that is present in the library.Optionally youmay use the KAPA BiosystemsLibraryQuantitationkitandqPCRmachine foramorespecificmeasurementof thelibraryconcentration.ForthisprotocolSeeAppendix3.
ReagentlistItem Storage SuppliedbyQubitdsDNABRAssayKit roomtemperature ThermoFisherQubitdsDNABRStandards 4°C ThermoFisherSizeSelectedLibrary 4°C Step5
Protocol6.1–BringtheQubitStandardstoroomtemperature.PrepareQubitassaytubes(500µL,thin-
walled) for your library in duplicate and the two standards. Vortex and centrifuge thestandardsandthelibrary.
6.2–Add995µL Bufferand5µLdyetoa1.5mlcentrifugetube.Vortexandspindown.
6.3–Transfer190µL fromthereagentmixtotheQubittubesforthetwostandards.Transfer198µL fromthereagentmixtothetwoQubittubesfortheduplicatesofthelibrary.
6.4–Add10µLfromstandard1tothecorrespondingQubittubeandvortexitfor2seconds.Repeatwithstandard2.
6.5–Add2µL fromthelibrarytothetwocorrespondingQubittubesandvortexfor2seconds.
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6.6–IncubatetheQubittubesatroomtemperaturefor2minutes.
6.7–SwitchonQubitmachineandchooseBRprotocol.6.8–Putstandard1QubittubeinandpushGO.Repeatwithstandard2.6.9–PutthelibrarytubeinQubitandpushGO.Repeatforthereplicate.6.10 – To convert the Qubit result from ng/μL to nM concentration, enter the meanconcentration of the two library replicates in the Omixon Workbook tab called “LibraryQuantitation”.6.11–UsingtheresultsfromtheQubitmeasurement,dilute10μLoftheSizeSelectedLibrarytoaconcentrationof2nMwithsterileH2O ina fresh1.5-mL lowbindmicrocentrifuge tube.StoretheremainingSizeSelectedLibraryat-20°C.
Safestoppingpoint.Librariescanbestoredat-20°Cforextendedperiodsoftime.Incase of long-term storage, re-quantification of the library is highly recommendedbeforerunningitontheMiSeq.
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Step7–SequencingonIlluminaMiSeqDuration:~24hoursTheIlluminaMiSeqisanautomatedNGSinstrumentthatcansequencethesize-selectedlibraryprepared intheprevioussteps.De-multiplexingofthe indexedsamples isdoneautomaticallyfollowingcompletionofthesequencingrun.
Quicktip–Youcanusea1%PhiXspike-inasanadditionalcontrol tomonitor thesequencing reaction. Refer to Illumina documentation on the PhiX control foradditionalinformation.
ReagentlistItem Storage SuppliedbyReagentCartridge -20°C IlluminaHT1 -20°C IlluminaPR2 4°C IlluminaMiSeqFlowCell 4°C IlluminaLibraryat2nM 4°C Step6NaOH1Nor2N 20°Cto25°C UserMoleculargradeH2O 20°Cto25°C User
MiSeqReagentKitcapacityIlluminaMiSeqReagentKit
TimeHours
24/7Samples
24/11Samples
96/5Samples
96/7Samples
96/11Samples
Std300Cycle(MS-102-2002) ~24 24 24 96 96 72
Micro300Cycle(MS-103-1002) ~19 24 20 40 28 20
Nano300Cycle(MS-103-1001) ~17 6 4 8 6 4
Std500Cycle(MS-102-2003) ~39 24 24 96 96 96
Nano500Cycle(MS-103-1003) ~28 12 8 16 12 8
Protocol7.1-PreparetheMiSeqaccordingtostandardIlluminaprotocols.7.2-Preparea1nMDenaturedLibrary:Combine10μLoffreshlyprepared0.2NNaOHand10μLof the2nMDilutedSizeSelectedLibrary inanew1.5mL lowbindmicrocentrifuge tube.
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Vortex and spin down. Incubate this 1 nM Denatured Library at room temperature for 5minutes.7.3-Preparea20pMDenaturedLibrary:Add980μLofchilledHT1tothe20μLofthe1nMDenaturedLibrary.Vortexandspindown.7.4 -Preparea9pMDenaturedLibrary:Add550μLofchilledHT1and450μLof the20pMDenaturedLibrarytoafresh1.5mLlowbindmicrocentrifugetube.Vortexandspindown.7.5 – Transfer 600μLof the9pMDenatured Library into the Load Samples reservoir of theMiSeqreagentcartridge.
Quicktip–ItisadvisabletousetheprovidedworkbooktocreatetheSampleSheetthat is requiredby theMiseq.Ensure that thecorrectAdaptorPlate configuration(A1orA2) is selectedon theOmixonWorkbookSequencing tab that contains theappropriateindexedadaptorsequences.
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Step8–AnalysisofHLASequencingDataTheIlluminaMiSeqwillprocessthe9pMPooledLibraryandgeneratesequencingdataasfastqfiles. Please refer to theHLATwinmanual for assistancewith the correct installationofHLATwinandforinformationoninterpretingthegenotypinganalysisofyoursequencingdata.Forimplementing the Automated Protocol and issues relating to installation or analyzing data,[email protected].
AutomatedProtocol
ITSetupandConfiguration1. InstallHLATwinServerontheServer.2. InstallHLATwinClientonaclientcomputer–multipleHLATwinClientsmayconnectto
theserver.3. ContactOmixonSupport([email protected])forcustominstallationinstructionsfor
Automation.
ProtocolperAnalysis1. LaunchHLATwinClientandlogin.2. Data is already processed or is being processed. Review the results using the Traffic
LightSysteminHLATwin.3. Exportthegenotypingresultsand/orconsensussequencesasrequired.
ManualServerProtocol
ITSetupandConfiguration1. InstallHLATwinServerontheServer.2. InstallHLATwinClientonaclientcomputer.
ProtocolperAnalysis1. LaunchHLATwinClientandlogin.2. SelecttheMiSeqdatainfastqorfastq.gzformatandstarttheHolotypeHLAtypingrun.3. After the Holotype HLA typing has finished, review the results using the Traffic Light
SysteminHLATwin.4. Exportthegenotypingresultsand/orconsensussequencesasrequired.
ManualDesktopProtocol
ITSetupandConfiguration1. InstallHLATwinDesktop.
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ProtocolperAnalysis1. LaunchHLATwinandlogin.2. SelecttheMiSeqdatainfastqorfastq.gzformatandstarttheHolotypeHLAtypingrun.3. After the Holotype HLA typing has finished, review the results using the Traffic Light
SysteminHLATwin.4. Exportthegenotypingresultsand/orconsensussequencesasrequired.
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TechnicalAssistanceForgeneralassistancewiththisprotocolcontactsupport@omixon.com.SafetyDataSheetsareavailableatwww.omixon.com/holotype-hla-documentation/msds.
PhoneSupport:UnitedStates|+1(617)500-0790Europe|+36705748001RestofWorld|+1(617)500-0790
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SupplementalFigures
PlateexampleforAmpliconPlate,AmplificationPlate,DilutionPlate,AmpliconQuantitationPlate(foranindividuallocus)&ReactionPlate
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StandardsQuantitationPlateExample
KAPALibraryQuantitationqPCRPlateExample
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Appendix1:PippinPrep
ProgrammingthePippinPrep1. ClicktheProtocolEditorTabandclickthe“New”button.
2. ClickthefoldericonnexttotheCassettefieldandselect“1.5%DFMarkerK”forthePippinPrepor“1.5%DFMarkerR2”fortheBluePippin.
3. Inthelanethatyouareprogramming:
a. Highlightthe“Range”field.b. Setthe“RefLane”tomatchthelanenumberyouareworkingin.c. Setthe“Start*”fieldto650.d. Setthe“End*”fieldto1300.
4. IntheReferenceLanefield,selectthelanethatyouareworkingin.
5. Clickthe“SaveAs”buttonandnameyourprogram.
RunningthePippinPrep1. TurnonthePippinPrepbypushingthepowerbuttoninthebackofthedevice.
2. Visually inspect thePippinPrep.Make sure the5 LEDsareonand that the insideof thedeviceiscleananddry.
3. Click on the Sage Science logo on the bottom right of the screen. Thiswill allow you toenterapassword.Thefactorydefaultpasswordis“pips”.
4. ClicktheFactorySetupTabandmakesuretheBase-to-Thresholdvalueissetto0.02.
5. PlacethecalibrationfixtureinsidethePippinPrep,makingsurethedarkstripisfacedownandovertheLEDlights.
6. IntheMaintab,clickthe“Calibration”button.
7. IntheCalibrationwindow,makesurethe“TargetIpHmA”fieldissetto0.80(0.60forBluePippin)andthenhitthe“Calibrate”button.
8. GototheProtocolsTab.Clickthe“Load”buttonandselecttheprogramforHolotypeHLAandthespecificlaneyouwillbeusing.Makesurethat:
a. Thecorrectlaneisturnedon
b. Broadspectrumselectionindicatorison
c. Thereferencelaneisthesamelanethatwillberunning.
9. GototheMainTab.Makesurethat:
a. Theprogramyouloadedistheonethatisselected.
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b. Theappropriatereferencelaneisselectedandthatitisalsothelanethesamplewillberunin.
10. Inspect thecassette.Beforetakingoff thetapesealing thewells, looktosee if thereareany bubbles behind the elution port. If there are any bubbles behind the elution port,gentlytapandrollthecassetteinyourhandtoworkthebubblesout.
11. Placethecassette,withthetapestilloverthewells,insideofthePippinPrep.
12. Carefully peel off the tape,making sure to remove the tape from the clean side of thecassette (lane5) to theused sideof the cassette (lane1). Take carenot to splash liquidwhenthetapeisremovedtopreventcontamination.
13. Removetheentirevolumeofbufferfromtheelutionportofthelaneyouwillbeusingandadd40μLoffreshelectrophoresisbufferinthatelutionport.
14. Addathinstripoftapeovertheelutionports.
15. Any reservoirs that are less than 3/4ths full should be topped off with electrophoresisbuffer.Donotoverfillthewells!Theedgeofthebuffershould‘just’reachtheplasticnothighertopreventdraggingwhenthelidslides.Applybufferfromthecleanwells(Lane5)totheusedwells(Lane1).
16. Make sure each of the loadingwells (wells with agarose) are filledwith electrophoresisbuffer.Thebuffershouldbe‘just’overtheagarose,appearingcompletelyflat.
17. ClosethePippinPrepslowly,watchingtomakesurenobufferistouchingthelidasyouareclosingthedevice.
18. Perform the continuity test. When the sensors dry out slightly, it is common for thecontinuitytesttofailonce.Ifthecontinuitytestfails,runthetestonemoretime.Oncethecontinuity test completes, open the Pippin slowly. Make sure no fluid is getting pulledacrossthecassettebythelidofthePippinPrep.
19. Briefly vortex the Marker K loading solution and spin it down. Add 10 μL of Marker Kloadingsolutiontoyour~30μLoflibrary.
20. Brieflyvortexyourlibraryandspinitdown.
21. Remove40μLofbufferfromthesamplewellthatyouwillbeusing.
22. Add~40μLofyourlibraryloadedwithMarkerKtothesamplewellthatyouwillbeusing.
23. Markthelanethatyouareusingwiththetechnician’sinitialsandthedate.
24. Close the Pippin Prep and click the “Start” button.Make sure the appropriate lane hasbeenturnedon.Thesampleshouldrunforabout45minutes.
25. Aftertherunhascompleted,carefullyopenthePippinPrep.Watchtoseeiftheliddragsanyliquidacrossthecassette.
26. Removethetapeovertheelutionports,beingcarefulnottoflickanyliquid.
27. Transferallthevolumefromtheelutionportintoanew1.5mllowbindtube.
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28. Coveralloftheopenwellswithtwopiecesofplatesealingtape.Remembertoleaveatabonthecleanside.Thiswillmakeitsimpletoremovethetapefromcleantoused.
29. Placethesealedcassetteintoitsbagandsetitaside.
30. TakethewashcassetteandfillitwithMiliQwater.GentlyclosethelidofthePippinPrep,watchingtoseeifyoupullanyliquidacrossthewashcassette.
32. LeavethePippinPrepclosedforseveralseconds.
33. OpenthePippinPrep,watchingtoseeifyoupullanyliquidacrossthewashcassette.
34. Removethewashcassette,emptyitofwater,andletitdry.
35. CleananywateroffofthePippinPrepandcloseitgently.
36. Selectthe“ShutDown”buttoninthePippinPrepmenu.
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Appendix 2: Amplicon Quantitation using a qPCRinstrumentDuration:35min
ReagentlistItem Storage Suppliedby20×TEBuffer(pH7.5) 4°C PromegaLambdaDNAStandard(100ng/μL) 4°C Promega200×QuantiFluordsDNADye 4°C PromegaSterileH2O 20°Cto25°C UserClassIAmplificationPlate(s) 4°C Step2ClassIIAmplificationPlate(s) 4°C Step2
Protocol1. Createaserialdilutionusing1.5mLmicrocentrifugetubesandtheQuantiFluorLambda
DNAstandard(100ng/μL).Followthedilutiontablebelow:
Labelontube InputDNA VolumeDNA(μL)
Volume1xTE(μL)
FinalConc.(ng/μL)
Standard1 LambdaDNA 7.5μL 492.5μL 1.5ng/μLStandard2 Standard1 250μL 250μL 0.75ng/μLStandard3 Standard2 250μL 250μL 0.38ng/μLStandard4 Standard3 250μL 250μL 0.19ng/μLStandard5 Standard4 250μL 250μL 0.09ng/μLStandard6 Standard5 250μL 250μL 0.05ng/μLStandard7,Blank
Blank 0μL 250μL 0ng/μL
2. PreparetheAmpliconQuantitationplates(seesupplementalfigures).Aliquot49.5μL1x
TEbuffertothewellsofaclean96-wellplateforthetotalnumberofampliconstobequantitated.
3. Add0.5μLofampliconsfromcorrespondingwells intheAmpliconPlatesto individualwellsintheAmpliconQuantitationPlates.Mixbypipetting.
4. Prepare 1× QuantiFluor Dye working solution using the following formula: 0.25 μLQuantiFluorDye(200X)+49.75μL1×TEbuffer.Preparesufficient1×QuantiFluorDyeworkingsolutionso thateachsample (total samples inAmpliconPlates)andstandard(14total)willreceivea50μLaliquot.
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5. PrepareaStandardsQuantitationPlateandAmpliconQuantitationplates.Aliquot50μLof1×QuantiFluorDyeworkingsolutiontowellsofthe96-wellopticalplatesusingtheformatof theStandardsQuantitationPlateandtheAmpliconQuantitationPlates (seesupplementalfigures).
6. Using the standards prepared above, add 50 μL of each standard, in duplicate, toindividualwellsintheStandardsQuantitationPlate(14wellstotal).
7. Vortextomixthoroughlyandspindown.
8. PuteachQuantitationPlate in theqPCRmachineoneata timeandrun the followingprogram:NumberofCycles Temperature Time
1 25°C 10seconds 25°C 15seconds2 25°C 30seconds(dataacquisition)
9. CalculatetheconcentrationofDNA in theAmpliconQuantitationPlatesusingtherawRFUdatageneratedbytheqPCRinstrument.
10. DiluteDNA in the Amplicon Plateswith sterile H2O so that the final concentration ofDNAisapproximately67ng/μL.
§ IfDNAconcentrationis150ng/μLorgreater:add25μLofH2O
§ IfDNAconcentrationis100-150ng/μL:add10μLofH2O
§ IfDNAconcentrationislessthan100ng/μL:add0μLofH2O
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Appendix 3: Library Quantitation using a qPCRinstrumentDuration:~1hourItisnecessarytoquantifytheSize-selectedLibraryinordertooptimallyusetheoutputoftheIllumina MiSeq sequencer. The concentration of the Size-selected Library can be accuratelymeasuredbyqPCR.
ReagentlistItem Storage Suppliedby10×IlluminaPrimerPremix -20°C KAPABiosystems2×KAPASYBRFASTqPCRMasterMix -20°C KAPABiosystemsStd1(20.00pM) -20°C KAPABiosystemsStd2(2.00pM) -20°C KAPABiosystemsStd3(0.20pM) -20°C KAPABiosystemsStd4(0.02pM) -20°C KAPABiosystemsIlluminaDNAStandards -20°C KAPABiosystemsMoleculargradeH2O 20°Cto25°C User1×TEBuffer(pH8.0) 20°Cto25°C UserSizeSelectedLibrary 4°C Step5
Protocol1-PreparetheqPCRPrimerMixusingthe10×IlluminaPrimerPremixandthe2×KAPASYBRFASTqPCRMasterMix:
Note:TheKAPASYBRFASTqPCRkitreagents(qPCRMasterMix,PrimerPremixandROXsolutions)arecombinedduringthefirstuseofthekit.Thiscombinedsolutionisstableforatleast30freeze/thawcycles.FollowKAPAdocumentationtodetermineifROXisrecommendedforyourqPCRinstrument.
qPCRPrimerMix
Reagent Volume(mL)10×IlluminaPrimerPremix 1mL2×KAPASYBRFASTqPCRMasterMix 5mLTotalVolume 6mL2–PreparetheqPCRMasterMix.
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qPCRMasterMix
Reagent Volume(μL)qPCRPrimerMix 228μLMoleculargradeH2O 76μLTotalVolume 304μL3-PrepareaserialdilutionoftheSizeSelectedLibrary.
a. Preparea1:1000dilutionbyadding1μLofSizeSelectedLibrary to999μLof1×TEbuffer(pH8.0),thoroughlyrinsingthepipettetip.Vortexandspindown.
b. Prepare a 1:2000 dilution by adding 100 μL of the 1:1000 dilution to 100 μL 1× TEbuffer(pH8.0).Vortexandspindown.
4-PrepareaqPCRQuantitationPlateinafreshPCRplatecompatiblewithyourqPCRsystem.5-Aliquot16μLoftheqPCRMasterMixintriplicateforstandards1-4,the1:1000dilutionand
the1:2000dilution(seesupplementalfigures).6 - Aliquot 4 μL of standards 1-4, the 1:1000 dilution and the 1:2000 dilution into the
correspondingwells.7-SealtheqPCRQuantitationPlateandcentrifugeitfor10seconds.
Note: Avoid creating bubbles in the qPCRQuantitation Platewells. Centrifuge asneededtoeliminatebubbles.
8 Setthe1:1000and1:2000triplicatesastargetedsamples,anddefinethestandards(points:
4, starting concentration: 20pM, dilution: 1:10). Run the following program on the qPCRmachine in order to determine the DNA concentration of the Size Selected Library:
NumberofCycles Temperature Time1 95°C 5minutes25
(nomeltcurve)95°C 30seconds60°C 90seconds(dataacquisition)
9 ToconverttheqPCRresultfrompMtonMconcentration,enterthe“Quantitymean”results
of the two library replicates in the Omixon Workbook tab called “Library Quantitation”.
10 - Using the volumes from the workbook, dilute 10 μL of the Size Selected Library to aconcentration of 2 nMwith sterile H2O in a fresh 1.5-mL low bindmicrocentrifuge tube.StoretheremainingSizeSelectedLibraryat-20°C.
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Safestoppingpoint.Librariescanbestoredat-20°Cforextendedperiodsoftime.Incase of long-term storage, re-quantification of the library is highly recommendedbeforerunningitontheMiSeq.