labvantage-reports external v2 - university of chicago · 2017-08-01 · irb protocol “test123”...
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LabVantage UserManual:ReportingFeatures• SampleFamily• SampleLifecycle• Searching&ViewingData• CreatingReports
1Disclaimer:Printedcopiesarenottheofficialdocument.PleaseseetheonlinePDFfileforthemostup-to-dateversion.http://htrc.uchicago.edu 8/1/17
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BringsyoubacktothispageLogoff
Changepassword
Clickonanyofthetramstops toaccess
thatpage
ThePI/RADashboardprovidesyouwithanoverviewofyourIRB
protocols2
NavigatingTheDatabase
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• LabVantage usestheconceptofasamplefamilytoorganizespecimensandsamples.Asamplefamilyconsistsofaparentsample(thisisthespecimen,e.g.,wholebloodortonsil)anditschildsamples(thesearethesamplesthatcamefromtheparent,e.g.,plasmaorOCTtumor)
• Youcantellwhichsamplesareparentsbylookingforthebeakericon:• Hint:parentsampleswillhaveastatusofdisposedandadispositionof
consumed
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ParentSample
ChildSamples
UnderstandingTheSampleFamily
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• IfyouwouldliketoviewfurtherinformationontheSampleFamily,clickontheboxnexttothesampleandselectSampleNavigator
• FromhereyouviewtheSampleDetailReportorexpandthefamilytree
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UnderstandingTheSampleFamily
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• Thestatusofasample,incombinationwithdispositionandcustodialdomain,explainswherethesampleisinthesamplelifecycle
• ThebelowchartwillhelpyouunderstandifthesampleisstoredintheHTRC,hasbeenpickedupandisnolongerintheHTRC’sstorage,orifasamplewasnotbankedduetoadverseconditions
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Status Disposition CustodialDomain MeaningInCirculation n/a HTRC Storedinbiobank
InCirculation n/a Transit Samplewaspreviouslywithdrawnfromthebiobank
3rd PartyTransfer n/a HTRC Samplewaspickedupsameday(ie.freshtissuepickedupsameday)
InPrep n/a HTRC Sampleisbeingprocessedandisnotreadytobedispersed/stored
Disposed Rejected HTRC Thisisasamplethatwascreatedautomaticallybythesoftwareandtherewasnotenoughbiospecimentofullfill it
Disposed SpecificReason HTRC Thesearesamplesthatwerenotbankedforspecificreasons,like"entirelysubmittedfordiagnostics”
Disposed Consumed HTRC Thisisaparentsamplethatwasconsumedinordertocreatechildsamples
UnderstandingSampleLifecycle
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• Nowthatyouunderstandtheconceptofthesamplefamilyandthesamplelifecycle,itistimetolearnhowtoviewdataandcreatereports
• TherearemanywaystoviewyourdatawithinLabVantage.TheeasiestwaytoseeaoverviewofyourdataistoutilizethePI/RADashboard
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• Youcanclickonthesliceofthepiegraphyou’reinterestedintoviewallofthedataassociatedwiththatprotocol
• Youcanalsoclickonthebargraphstoseespecificdataonsampletypes
AccessingData- Dashboard
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• Alternately,ifyouarelookingforspecificdataormorecomplexsearchingability,gototheSamplesTramstop
• Fromthispage,youcaneitherdoaquicksearchusingtheSearchByQueryoptions
• OryoucandoamorecomplexsearchbyusingtheNewAdhoc Queryfeature
• TheSearchByQueryoptionworkswellforquickandsimplesearches,likelookingforallsamplesfromapatientwithaspecificMRNorlookingforallsamplesbankedunderaspecificIRBprotocolnumber
• TheAdhoc Queryoptionworkswellformorecomplicatedsearches,likesearchingforallDNAsamplescollectedforaspecificprotocolthatwerepreviouslywithdrawn
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SearchingandViewingData
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UsingSearchByQueryOption• Let’ssayyouwanttoviewall
samplescollectedforaspecificpatient:– “JoeTest”– MRN=45689996
• SelecttheSearchByQueryOptionforMRN
• Type45689996intothesearchfieldandclickoktoviewthesearchresults
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SearchingandViewingData:SearchbyQuery
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• Herearethesearchresults:
• TrytochangetheGroupByoptiontoNone.Thiswillchangetheorderinwhichyoursamplesaredisplayed.Now,youshouldbeabletoviewaparentsamplewithitschildrentogether
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SearchingandViewingData:SearchbyQuery
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• Oursearchresultsshowthattherewere2parentsamplesbankedforJoeTest:
• Thefirstparentsampleisawholebloodsamplethathas3children,2plasmasamplesand1PBMCsample
• Thesecondparentsampleisatissuesamplethatwasnotbanked,withthereasonbeing“Other.”Inthiscase,youwillneedtoviewthesampledetailstoseethenotesinthecommentstab.Todothis,clickontheboxnexttothesample,selectview,andthenclickonthecommentstab
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SearchingandViewingData:SearchbyQuery
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• YoucanexporttheinformationdisplayedfromthesearchbyclickingeitherViewasPDForViewasExcel
• Youcanclickonthehyperlinkstoviewadditionalinformation
**Rememberthatparentsampleswillhavethebeakericon
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SearchingandViewingData:SearchbyQuery
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• Ifyouclickonthesamplenumberhyperlink,itwillopenupthesampledetails• Herearethedetailsforaparentspecimen,S091500009• YoucanclickontheSampleDetailReport,forevenmoredetails
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SearchingandViewingData:SearchbyQuery
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• Herearesomeofthemostutilizedsearchbyqueryelements:– ByMRN
• SearchbyMRN
– ByLastName• Searchbylastname
– ByProtocol• SearchbyIRBprotocolnumber
– ByProtocolandSampleType• SearchbyIRBprotocolnumberandsampletype
– PairedSamplesbyProtocol• Searchforpairedsamples(e.g.,tumorandnormalfromsameparent
sample)collectedunderaspecificIRBprotocol
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SearchingandViewingData:SearchbyQuery
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UsingAdHoc QueryOption• Adhoc QueriesworkbetterthanSearchByQueriesformorecomplicatedsearches• Let’ssayyouwanttoviewallsamplesthatwerecollectedfortheIRBprotocol“Test123”
betweenthedatesof4/1/2015- 9/21/2015• SelectNewAdHoc Queryandselectthesearchcriteriafromtheleftsideofthe
screenbyclickingontheicon• Important!Usethemagnifyingglassicontolookupdataelementsinsteadoftypinginto
thefield• Forthissearch,youwouldcreateanadhoc querylikethis:
Sinceyouwanttolookforsamplesthatareintheprotocol“Test123”and werereceivedbetween4/1/2015-9-21-2015,youshouldselectMeetALLoftheCriteria
Youwouldincludeprotocolandreceiveddate(usethereceiveddatefromthe
samplefamilynode)inthecriteriagroup
SearchingandViewingData:AdHocQuery
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• Onceyou’vecreatedyourAdHoc query,hitsearchtoviewresults• SelectspecificsamplesorallandexportthispageasaPDFortoExcel
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SearchingandViewingData:AdHocQuery
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UsingAdHoc QueryOptionwithmoredetails• Let’ssayyouwanttoviewallDNAandPBMCsamplesthatwerecollectedforthe
IRBprotocol“Test123”betweenthedatesof4/1/2015- 9/21/2015• SelectNewAdHoc Queryandselectthesearchcriteriafromtheleftside
ofthescreenbyclickingontheicon• Forthissearch,youwouldcreateanadhoc querylikethis:
Youwillneed2CriteriaGroupsforthissearch.UsetheNewCriteriaGroupbuttontoadd
CriteriaGroups
YourfirstCriteriaGroupwilllookforPMBCsamplesORDNAsamples.UseMeetANY
oftheCriteriaforthisCriteriaGroup
YoursecondCriteriaGroupwilllookfortheprotocol“Test123”ANDthedate
range.UseMeetALLoftheCriteriaforthisCriteriaGroup
Lastly,selectMeetALLoftheCriteriaGroups– thismeansthatALLofthecriteriafromtheCriteriaGroupsmustbemet
SearchingandViewingData:AdHocQuery
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• Onceyou’vecreatedyourAdHoc query,hitsearchtoviewresults• SelectspecificsamplesorallandexportthispageasaPDFortoExcel
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SearchingandViewingData:AdHocQuery
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SearchingandViewingData:AdHocQueryDataElementDictionaryPart1
AdHoc Search AdHoc SearchDescription BFExample TissueExampleSample SampleNumber S031606245 S031606247SampleType SampleType(child) DNA OCTDiseasedSampletypeDescription SampleType(child) DNA OCTDiseasedSampleFamily SampleFamilyID# SF-160325-00013 SF-160325-00014 StudySite StudySiteID# SS-00001279 SS-00001279StudysiteDescription StudySiteDesc.(WhereSpecimenWasProcessed) _P524 _P524CollectionDate SpecimenReceivedDate/Time 3/2/1610:25AM 3/25/1612:39PM RecievedDate DateSamplewasenteredintoLVbyHTRC 3/25/1612:26PM 3/25/1612:45PM Subject SubjectID# ST-00076083 ST-00076083BirthDate DOB 5/26/8112:00AM 5/26/8112:00AM GenderFlag Gender(MORFORU) M MMRN# MRN# 666666666666666 666666666666666Race Race WhiteorCaucasian. WhiteorCaucasian.Ethnicity Ethnicity NotHispanic/NotLatino NotHispanic/NotLatino
FirstName FirstName Testing TestingMiddleName MiddleName Nick NickLastName LastName Tester1 Tester1Disease DiseaseID# DS-00000002Tissue TissueOnly:TissueID# TS-00000110TissueDescription TissueDescription ColonInitialmass TissueParentSpecimenMass 1.0000000000InitialmassUnits TissueParentSpecimenMassUnit gInitialvolume BFParentSpecimenVolume 4.0000000000InitialvolumeUnits BFParentSpecimenVolumeUnit mlParticipant ParticipantID# P-00058724 P-00058724Externalparticipant ExternalParticipantID ExternalIDTest123 ExternalIDTest123ParticipantStatus ParticipantStatus Enrolled EnrolledEnrollDate ParticipantEnrollDate 10/6/1512:00AM 10/6/1512:00AM CompletedDate ParticipantCompletedDateWithdrawalDate ParticipantWithdrawalDateHeight TissueChildSampleHeight 0.5000000000Length TissueChildSampleLength 0.5000000000Width TissueChildSampleWidth 0.5000000000DimensionUnit TissueChildSampleDimensionUnit cmParticipantConsented ParticipantConsented(YorN) Y YSurgeryProcessTime TissueOnly:SurgerytoProcessTime 0-30MinutesActualCollectionDate&Time BFOnly:ActualCollection(DrawDate/Time) 3/1/1612:53PM
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SearchingandViewingData:AdHocQueryDataElementDictionaryPart2
AdHoc Search AdHocSearchDescription BFExample TissueExampleProcessedDate BFOnly:ProcessingDate/Time 3/2/1611:02AM SurgicalMethods TissueOnly:SurgicalMethod TotalColectomyConfirmedBy ConfirmedBy HTRC HTRCSysuserDescription SysuserDescription HTRCUserID HTRCUserIDDisabledFlag DisabledFlag N NEmail Email [email protected] [email protected] Defaultdepartment HTRC HTRCConfirmedDate DateSamplewasconfirmedinLVbyHTRC 3/25/1612:00AM 3/25/1612:00AM Protocol Protocol Test2015 Test2015StudyDescription StudyDescription IRBProtocolTemplate IRBProtocolTemplateDelinkableFlag DelinkableFlag(YorN) N NDuration DurationofProtocol 369 369UnitsofMeasurement DurationofProtocolUnits Years YearsAnticipatedStartDate AnticipatedStartDateofProtocol 7/31/1512:00AM 7/31/1512:00AM PIUser PIUser TestPI TestPIStorageStatus StorageStatusofSample InCirculation InCirculationStoragedisposalStatus StoragedisposalStatusIsitanExternallyprocessedSample? ExternallyProecessedSample(YorBlank) ySurgicalMethod surgicalmethodSurgicalPathologyNumber SurgicalPathologyNumber S-13123456 ParentSampleTypeID ParentSampleType(DRLOOKINTOTHIS) WholeBlood TissueSampletypeDescription ParentSampleType WholeBlood TissueNotes n/a ActiveFlag ActiveFlag Y YCustodialDomain CustodialDomain HTRC HTRCContainerType ParentSampleContainerType(ielavendertube)CurrentLocation CurrentStorageLocation /B031600052/A2 /B031600052/A3 Custodian Custodian drufo drufoQuantity CurrentSampleQuantity(VolumeorMass) 0.5000000000 0.5000000000ReservedLocation ReservedLocationSampleType Sampletype(child) DNA OCTDiseased260/280 Attribute- 260/280 2CellConcentration Attribute- cellconcentration 4CellViability Attribute- cellviability 5DNAConcentration Attribute- DNAconcentration 3OD260 Attribute- OD260 1SpecificTissueLocation Attribute- specifictissuelocation SpecificColonLocationBreast-ER(var:Breast-ERdataset:1)Breast-ER(Standard)rep:1 TissueOnly:TestResults PositiveBreast-HER2(var:Breast-HER2dataset:1)Breast-HER2(Standard)rep:1 TissueOnly:TestResults NegativeBreast-PR(var:Breast-PRdataset:1)Breast-PR(Standard)rep:1 TissueOnly:TestResults Negative
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• YounowhavetheskillstouseanAdhoc QuerytosearchfordatawithinLabVantage
• Next,youwilllearnhowtoutilizetheAdhoc Querytocreatecustomizedreports
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CreatingReports
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UsingAdHoc Querytocreateareport
• GototheAdhoc QueryBiobanking LIMSpage
• Important!YoumustperformtheAdhoc Queryfromthistramstop inordertocreateareport.AccessingtheAdhoc QueryfromotherpagesusingtheNewAdHoc Searchbuttonwillnotallowyoutoutilizethereportingfeatures
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CreatingReports
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• Let’ssayyouwanttoviewALL DNAandPBMCsamplesthatwerecollectedfortheIRBprotocol“Test123”betweenthedatesof4/1/2015-9/21/2015andyouwantyourreporttoincludethefollowingelements:firstname,lastname,MRN,externalpatientID,IRBprotocol,samplenumber,sampletype,anddatereceived
• First,setupyourAdhoc Queryasthoughyouweredoingasimplesearch
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CreatingReports
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• Now,addtheelementsthatyouwanttoappearinthereportbyclickingontheViewColumnsicon
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CreatingReports
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• NowaddtheelementthatyouwouldlikethereportsortedbyusingtheAddtoSortByColumnicon
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CreatingReports
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• Now,clickeitherSearchNow(andthenExporttoExcelorExporttoPDF)orSearchandExportAlltoviewyourreport
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CreatingReports
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ForAdditionalHelp…
• PleaseseetheHTRCwebsiteformoreinformationandtofindadditionaltrainingresources:https://htrc.uchicago.edu
• OremailtheLabVantage administratorsat:[email protected]
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