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UNC Health Registry Data Source Documentation TableofContents
i.HealthRegistryDataCollectionOverview...............................................................................2
Section1:TrackingStudyEvents.....................................................................................................3
Section2:Enrollment..........................................................................................................................7
Section3:Biospecimens.....................................................................................................................8
BiospecimenProcessFacility–BloodSamples.....................................................................................8
TissueProcurementFacility–Tissue........................................................................................................9
Section4:Questionnaires................................................................................................................10
EnrollmentQuestionnaire..........................................................................................................................10
BaselineQuestionnaire(CDART).............................................................................................................10
Cancer‐SpecificQuestionnaires(CDART).............................................................................................10
AnnualFollow‐up(CDART)........................................................................................................................11
Section5:MedicalRecordsAbstraction......................................................................................12
CDW‐HBillingCodes–CancerSpecificQuestionnaireAssignment............................................12
AbstractedMedicalRecordDataElements..........................................................................................13
MedicalRecordHand‐Abstraction..........................................................................................................15
Appendix1.System‐SpecificInformation..................................................................................17
PatientTrackingSystem.............................................................................................................................17
OverviewofBSPLIMSQualityAssurance/QualityControl..........................................................18
BioSpecimenFacilityInformationTechnologies(LIMS).................................................................20
FutureTPFLIMSSystem..............................................................................................................................21
ElectronicRegistrySystem(ERS).............................................................................................................21
Appendix2.System‐SpecificDataMappings.............................................................................23
CPR‐ORTissueCollectionTracking.....................................................................................................................23
i. Health Registry Data Collection Overview Figure1–StagesofDataCollection
Section 1: Tracking Study Events Withalargeandcomplexstudy,ensuringaproscribedsequenceofeventsrequires
operationalsystemsthataccuratelyandregularlyrecordsubjectstatussothatthenext
eventcanbeascertainedandfutureworkloadsbedetermined.
SubjectsenrolledintheUNCHealthRegistrycantakeavarietyoftrajectoriesthrough
studyeventsdependingondateofenrollment,specificcancertype,andlengthoffollow‐up.
Trackingprogressthroughstudyparticipationeventsrequiresasystemforloggingthe
sequenceofeventsforeachindividual.
Uponasubject’senrollmentintothestudyinthehospital(RecruitmentSchedule
SuccessfulConsentEnrollment)theybecomeeligibletoreceivethetelephone‐based
baselinequestionnaire.Ascancer‐specificbillingcodesaregeneratedduringvisitstoUNC
Hospitals,thetrackingsystemautomaticallymatchescodesthattriggercancer‐specific
questionnaires.
Interviewerdashboard,patientlookup,schedulingofinterviews,andcancer‐specific
questionnairearekeyfeaturesofthesysteminterface.Additionally,thesystemisusedfor
generationofpatientcontactmaterialsandisakeyadministrativeinterface,andisa
methodforloadingsubject‐specificstudyconsentandHIPAAdocuments.Theinterfacealso
providesstaffwithawaytorecordandverifyasubject’svital/deathstatus.
DetailsonthespecificuseofthestudytrackingsystemaredetailedintheInterviewer
ProtocolDocument.
Screenshots
Figure2.PaTSyHomeScreen.ThisdashboardprovidessummaryinformationonInterviewStatus,ThankYou
letters,andAncillaryStudyTasks
Figure3.PatientSummaryPage‐ContainscontactanddemographicinformationandlinkstoInformedConsent
anHIPAADocuments
Figure4.PatientContactInformationandCallLog
Figure5.ParticipantEventStatusPage.SpecificInformationonEventsandCancer‐SpecificInterview.
Figure6.ICD‐9EntryScreen.Cancer‐specificICD‐9Codestriggerspecificquestionnaires.
Figure7.InterviewerAppointmentQueue.TheHotListindicatesinterviewsscheduledforthecurrentday,while
theQueuelistsindividualswithanoutstandinginterviewstatus.
Section 2: Enrollment EnrollmentintotheHealthRegistryoccurswhenanindividualisdeemedtobeeligible
basedonclinicscheduledata,isapproachedbyahealthregistryrecruiter,andinformed
consentisprovidedbythepatientafterlearningabouttherisksandbenefitsof
participation.
Theenrollmentprocessbeginswithalistofeligibleindividualsvisitingcancerclinicsatthe
NCCancerHospitaleachday.ClinicscheduledataisobtainedfromUNCHealthcare
appointmentschedulingsystemsthroughtheCarolinaDataWarehouseforHealth(CDW‐
H)andispreparedonadailybasis.
Theclinicschedulereportispopulatedwithalistofindividualswhoscreentobeeligible
basedondateofbirthandresidence,whichareavailablefromthehospitalappointment
schedulingsystem.SchedulereportsaregenerateddailyforHealthRegistryrecruiters,
whousethisinformationtoapproachpatientsaroundthetimeoftheirappointment.
Onceapproached,anindividualisinformedaboutthepurposeofthestudy,shownabrief
videosummarizingthepurposeandscopeoftheHealthRegistry,andmadeawareof
potentialrisks.
Ifconsentisnotgiven,theindividual’sfinalstatuswillbesetas“Refused.”Iftheindividual
isinterestedbuthasnotprovidedconsent,thestatusissetto“CheckBack”whichcanbe
setto
Abriefintakequestionnaireiscompletedduringtheconsentingvisit.Basicdemographic
andcontactinformationisobtained,includingname,address,dateofbirth,gender,and
race.Additionally,maritalstatus,employmentstatus,andinformationaboutthereferring
physicianarerecorded.
Toobtainthemostup‐to‐datecontactinformationforeachsubject,thisinformationis
confirmedduringtelephoneinterviews.
HealthRegistryrecruitersutilizecomputertabletsrunningMiFormssoftware(Mi‐Co,
Durham,NC)torecordnotes,conducttheintakequestionnaire,andtoprocessconsent
documentsignatures.Thetabletsareconnectedtoasecurewirelessnetwork,anddatais
senttoadatabaseandfileserveroveranencryptednetworkconnection.Papercopiesofall
consentdocumentsareused,filed,andback‐enteredintheeventofconnectivityissues.
Section 3: Biospecimens UponenrollmentintotheHealthRegistry,asubjectmayprovidebiospecimenssuchas
bloodortumortissue.
Onoraftertheparticipant’sdateofconsent,bloodsamplesaredrawnbyaphlebotomist,
loggedandcollectedbyhealthregistrystaff,andtransportedtotheUNCBiospecimen
ProcessFacility.Bloodsamplesarenotcollectedforpartipantswhohaveaportacath
installed.Subjectsmaychoosedelayorrefusetheblooddrawprocedure.Asaresult,the
finalblooddrawstatusandnumberofapproachesarerecordedinthestudydatabase.
AllblooddraweventsareloggedbyHealthRegistryrecruitmentstaffusingcomputer
tabletsrunningMiFormssoftware.Participantsareassignedauniquebarcodenumber
usedtotrackbloodsamples.Arecruitmentstaffmemberbringsthepatienttoa
phlebotomysuitefortheblooddrawandgivesthephlebotomistbarcodedredand
lavendertubevials.ThetimeofbloodcollectionisloggedinMiFormsandsamplesare
temporarilyrefrigeratedon‐site.Withintwohoursofcollection,batchesofrefrigerated
participantbloodsamplesaretransportedandloggedintotheBSPforfurtherprocessing,
aliquoting,andbanking.
Biospecimen Process Facility – Blood Samples Onceparticipantbloodsamplesaretakenfollowingconsentintothestudy,theyaresentto
theUNCBiospecimenProcessFacility(BSP).Eachsampletakeniscollectedinatubewitha
serialnumberlinkedtotheindividual.Samplesarebatched,packedinacooler,andwalked
totheBSPlaboratorybyaHealthRegistrystaffmember(atripthatlasting5to10
minutes).OncethesamplesaredeliveredtotheBSP,theyareenteredintotheBSP
laboratoryinformationmanagementsystem(LIMS)bythelaboratorytechnicianand
HealthRegistrystaffmember.
OncebloodsamplesaresignedintotheLIMS,BSPstaffareassignednewworkandapplya
protocoltomeasure,aliquot,andstorechildsamples–thesequenceofwhichhasbeenpre‐
programmedintotheLIMS.AllprotocolstepsareproscribedbytheBSPLIMSsystem,
whichprovidesaninterfacetoinputmeasurements,recordnotes,andtoassignchild
samplecontaineridentificationnumbers.
Childsamplesarebankedinfreezersintwoseparatelocationstoprovideafail‐safeagainst
equipmentfailureorphysicalbreach,allowingsamplestobesecurelystored.Requeststo
pullsamples(toperformadditionalprotocols,tomail,todestroy)arehandledby
communicationbetweenHealthRegistrystaffandBSPtechnicians.Onceatechnicianis
requestedtohandleasample,thedetailoftherequestislogged.Sample(s)areidentifiedin
theLIMSsystem,pulledfromstorage,andpreparedaccordingtotherequest.A
confirmationissentbacktoHealthRegistrystafftonotifythattherequesthasbeen
completed.
Tissue Procurement Facility – Tissue TheTissueProcurementFacilityisagroupsponsoredbyUNCLinebergerComprehensive
CancerCenterandpartneroftheUNCHealthRegistrystudy.Astaffmemberfromthe
TissueProcurementFacilityidentifies”targetable”surgicalproceduresscheduledamong
consentedpatientsthatinvolvetumortissue.Intheeventthataresearchspecimencanbe
saved,theTPFbanksthesampleforfutureuse.
TPFstaffarepresenteachmorningandincludedocumentationforsurgicalstaffindicating
patientconsentinastudyrequestingtissueforresearch.Aftersurgeryisperformed,TPF
staffthentakecustodyoftissueandsenditontopathologyfortissueanalysis.
Afterthepathologylabhassampledthetissue,anyremainderissenttotheTPFfor
processingandbanking.Theprocessoftransportingasamplefromthesurgicalsuitetothe
sample’sfinalbankingnormallytakesanhourorless.
TheTPFusestwointerfacestoperformtheirwork.Scheduledsurgicalproceduresare
cross‐referencedwithalistofconsentedsubjectsfromtheHealthRegistrystudy.Matching
surgeryeventsareexaminedbystudystaffandplacedonatargetlist.Surgical
appointmenttargetlistsareprintedforTPFstaffeachmorning.
TheTPFLIMSsystemisusedtorecordinformationonanysamplescollected.Information
includedintheLIMSsystemincludesspecimenID,bankingstatus,andnotesfromthe
pathologyreport.
Section 4: Questionnaires Interview‐baseddataiscollectedduringtheenrollmentprocessandsubsequentbaseline
andfollow‐upinterviews.
Limiteddemographicdataiscollectedatthetimeofenrollmentontotabletcomputers.The
tabletsincludedatapre‐populatedfromtheCDW‐Hschedule.Theenrollment
questionnaireprovidesanopportunitytocollectandconfirmbasicdataincludingname,
dateofbirth,referringphysician,andcontactinformation.
OnceanindividualisconsentedandenrolledintotheUNCHealthRegistry,subsequent
questionnairedataisstoredinCDART–CarolinaDataAcquisitionandReportingTool–a
web‐basedapplicationthatiswellsuitedforcomputer‐assistedtelephoneinterviewing
(CATI).
Thebaselinequestionnaireconsistsofacommonsetofinterviewelementscollectedofall
subjectsshortlyafterconsent.Questionnaireelementscoverawideselectionoftopics
includinghistoricheightandweight,exposuretoalcohol,qualityoflife,andaccessto
healthcare.
Annualfollow‐upconsistsofquestionnaireformsadministeredonanannualbasis.
Enrollment Questionnaire Atthetimeofconsent,abriefenrollmentquestionnaireisadministeredtorecordbasic
demographicdetailsincludingname,dateofbirth,gender,race,ethnicity,language,
educationstatus,maritalstatus,referringphysicianinformationandcontactdetails.This
questionnaireisadministeredbyconsentingstaffintheclinic.Questionnairedatais
recordedoncomputertabletswithasecurewirelessconnectionandisstoredinastudy‐
maintaineddatabase. Baseline Questionnaire (CDART) Afterenrollmentintothestudy,subjectscompleteabaselinequestionnaireconsistingof
morethan20constituentquestionnairesmeasuringhealth,symptoms,qualityoflife,and
relatedvariables.Thesequestionnaireshavebeenvalidatedintheliteratureand
underwenttestingandIRBapproval.Thebaselineinterviewlastsbetween45minutesto
anhourandcanbecompletedovermultiplecalls.
Afewofthequestionnairescontainskippatternsthatenableordisablefurtherquestions
inasequencedependingonoutcome.Examplesincludeinformationonrateofalcohol
consumption(dependentonansweringalifetimealcoholconsumption)inthealcohol
informationformaswellasage‐basedskipsthatareutilizedinthehistoricheightand
weightform(questionsrefertoheightandweightatages40,50,and60).
Cancer‐Specific Questionnaires (CDART) Aseriesofcancer‐specificquestionnairesweredevelopedtocapturedataonspecific
disease‐relatedpointsofinterestandareincludedinbaselineandfollow‐upquestionnaires
administeredtostudyparticipants.ExampleareasincludeBreast,Prostate,Colorectal,and
Hepatobiliarycancers.
Assignmentofcancer‐specificquestionnairesoccursthroughanICD‐9billing‐codebased
classification.TheresultsofthisclassificationappeartointerviewersinthePatient
TrackingSystem.Amanualmethodofassignmentisalsospecifiedintheeventthatthe
billingcodefeedfailstocorrectlyclassifyanindividual’sdisease.
Annual Follow‐up (CDART) Aftercompletionofthebaselinequestionnaireandapplicablecancer‐specificquestionnaire
forms,anannualfollow‐upinterviewservestocapturechangesinthisinformation,aswell
asanysubsequentcancer‐specificinformationastheresultofnewdiagnoses.
Section 5: Medical Records Abstraction Medicalrecordsinformationcomesfrommultiplesourcesystems.Billingcodedatafrom
theCarolinaDataWarehouseforHealth(CDW‐H)isusedatthebeginningofenrollmentto
assigncancer‐specificquestionnairesbasedonsubject‐specificICD‐9billingcodes.
Atapproximatelythesametimethatanindividualvisitstheclinic,thehospitaltumor
registrarbeginstorecordinformationfromasubject’smedicalrecordsinordertofulfill
statecancer‐reportingrequirements.Thisdataiselectronicallystoredusingasoftware
productcalledERS(ElectronicRegistrySystems,CincinnatiOH).Asdiagnostic,tumor
staging,andcourseoftreatmentinformationbecomeavailable,thisinformationis
abstractedintosoftwarethatcanformatstate‐compliantreports.
TheUNCHealthRegistryStudypurchasedaninstanceoftheERSmedicalrecord
abstractionsoftwareinordertoenablestafftoviewabstractedinformationonthesubset
ofUNCHospitalpatientswhohaveconsentedtotheHealthRegistrystudyandenter
additionalinformationontreatmentsreceived.(SeeHand‐Abstractionformore
information).
Finally,theSAS‐UNCpartnershipisworkingtodevelopingahealthoutcomesanalysistool
basedusingasecuremedicalworkspaceconcept.ThistoolwilllinktoUNCHealthcaredata
andenableresearcherstodiscoveranalyticcohortsandrunanalysesinasecured
environment.
CDW‐H Billing Codes – Cancer Specific Questionnaire Assignment Cancer‐specificquestionnaireassignmentisdrivenbyICD‐9billingcodesfromUNC
Hospitalsbillingsystemsandservesasan“initialdiagnosis”untilmorespecificinformation
isacquiredthroughpathologicdata.Arule‐basedalgorithmhasbeenimplementedto
assignquestionnairesbasedonICD‐9billingcodes.
SourcedataoriginatesfromCDW‐Hbillingcodereports.Thesereportscontainmedical
recordnumber(MRN)correspondingtoeachsubject,thepatient’sdateofvisit,andICD‐9
code.
CDW‐HDataSourcesUsedbytheBillingCode/QuestionnaireAssignmentAlgorithm
HospitalPastDiagnosisReport
Allhospital‐sidebillingdiagnosessince4/2009for
patientswhowereseenataUNCcancerclinicin
thelast14days
P&APastDiagnosisReport
AllPhysician/Associatesbillingdiagnosessince
4/2009forpatientswhowereseenataUNC
Cancerclinicinthelast14days
Thisdataisusedinconjunctionwithindividualdateofconsenttoselectthebillingrecords
correspondingtothevisitclosesttothedateofconsent(thisisoften,butnotalwaysavisit
onthesubject’sdateofconsent).
Billingcodesfromtheselecteddateforeachpatientarematchedagainstaquestionnaire‐
mappingtable.Themappingtableidentifies220specificICD‐9codes.
QuestionnaireassignmentsaredisplayedtointerviewersinthePatientTrackingSystemso
thattheappropriateformsareselectedduringthetimeofinterview.
Abstracted Medical Record Data Elements MedicalRecordinformationonconsentedpatientsconsistsofdemographicdata,tumorstaging
information,treatmentinformation,andfollow‐upinformation.Thefollowingtablecontainsthe
patientandcancer‐specificinformationforresearchpurposes.
UNCCancerRegistryabstractedmedicalrecordvariables
Demographics
PatientUNCHRID
Firstname
Middlename
Maidenname
Lastname
Nameprefix
Namesuffix
Dateofbirth
Currentcounty
Ethnicity
Sex
Race
Tobaccohistory
Familycancerhistory
Alcoholhistory
DiagnosisandStaging Sequenceoftheprimary
Sitecode
Topographycode
Grade
Histology
Dateofdiagnosis
Surgery
Diagnosiszipcode
Comorbidities
Sitedescription
Tumorsize
Tumorextension/involvement
Lymphnodeinvolvement
Numberofpositivenodes
Numberofnodesexamined
Prostatetumorextension/involvement
Pathologyreportnumber
Primarypayer/insurance
Survivalmonthssincediagnosis
Tumorrecordnumber
Generalstage
AJCCstagebasis
PathologicT
PathologicN
PathologicM
PathologyAJCCstagegroup
ClinicalTstage
ClinicalNstage
ClinicalAJCCstagegroup
Clinicalstagedby
TNMeditionnumber
Justificationforclinicalstagingelements
Justificationforpathologicstagingelements
Generalstagetext
Typeofsourcedocuments
Diagnosiscomments
Operativefindings
Comments
Surgerydate
Surgerytype
Scopeoflymphnodesurgery
Lymphnoderemoved
Surgeryofregionalsites
Firstorsubsequentsurgery
Treatinghospitalcode
Treatment
Recurrence
Other
Treatmentdate
Regionaltreatmentmodality
Boosttreatmentmodality
Chemotherapy
Hormone/steroidtherapy
Immunotherapy
Hematologictransplant/endocrineprocedure
Othertreatment
Palliativeprocedure
Firstorsubsequenttreatment
Treatinghospitalcode
Recurrencedate
Recurrencetype
Recurrencemetastasissite
Cancerstatus
Patientstatus
Dateoflastcontact
Follow‐upmethod
Cancerstatus
Patientstatus
Dateoflastcontact
Follow‐upmethod
Medical Record Hand‐Abstraction AsetoffieldsiscreatedintheERSsystemtodetailinformationonfirstcourseoftreatment
forastudysubject.ThesefieldsareenteredbyUNCHR/CSCstaffandappendedtotheERS
record.
Hand‐abstractedfieldsincludeavariabletosignifywhetherfirstcourseoftreatmentwas
performedoutsideoftheUNCcancerhospital.Inaportionofthosecases,documentation
fromoutsideclinicsarescannedandreceivedbythehospitaltumorregistrarandare
availableforenumerationoftreatments.
Becausefirstcourseoftreatmentwillvarybycancersiteandotherindividualfactors,the
detailofeachrecordwillvary.Theavailabilityofinformationforanindividual’streatment
willinfluencethecompletenessofthesehand‐abstractedfields.Inmanycases,this
additionalabstractionwillserveasabasistovalidatetreatmentinformationfoundinother
sectionsoftheERSrecord.
Hormone,immunotherapy,andchemotherapyagentsinvolvedinthefirstcourseof
therapyarenotedinappropriatesectionsofthefreefields.Abestestimateoftreatment
startdateisrecordedbasedonrecords.Thisestimateisbasedonrecordof
dispensing/administrationwithinvisitnotes.Eachagent’sNSC(NCINationalService
Center)numberisrecorded.Often,coursesoftreatmentconsistofregimens.Fora
particulardrugregimen,multipledrugsmaybeadministered,eachwithit’sownNSC
number.Eachdrugintheregimenisrecorded.
Treatmentcompletionstatusisrecordedandcorrespondstoreasonsforinterruptionor
suspensionoftreatment.Successfulcompletionandunknowncompletionstatusarealso
recordedinthisfield.
UNCHR/CRCabstractedmedicalrecordsvariables*
ChemoAgent1‐6**
ChemoAgentNSC
StartDate
Enddate
NumberofCycles
Cycleduration
Completionstatus
HormoneAgent1
Startdate
HormoneAgentNSC
ImmunotherapyAgent1 Startdate
ImmunotherapyAgentNSC
Other
TreatmentsOutsideofUNC(Binary)
DateofHRabstraction
*ERSfreedatafieldsmodifiedtoincludethoselistedinthistable
**Datawillbeabstractedformultipletreatmentswhennecessary(1,2,etc)
Appendix 1. System‐Specific Information Patient Tracking System TheShepsIntegratedResearchSystem(“SIRS”)isasecure,enterprisedatabaseand
programmingframeworkspecificallydesignedtomeettheneedsofhealthresearch
projectsattheCecilG.ShepsCenteratUNCChapelHill(“Sheps”).SIRSprovidesreusable
modulesfordatacollection,management,andtrackingforadiversesetofstudies,
registries,andresearchcoordinatingunits.SIRSisspecificallydesignedtoprovidea
frameworkforprogrammingthatsimplifiescommonprogrammingtasksandallows
customizationwhilemeetingapplicablesecurityrequirements.TheSIRSframeworkis
completelywebbasedandopensourceutilizingMySQL,Apache,JavaScriptandPHP.
TheShepsIntegratedResearchSystemoffersmanyadvantagestoinvestigators
•
Security
•
Datamanagementexpertise
•
InputandfeedbackfromexperiencedSIRSprogrammers
•
Abilitytoincorporatedesignsfrompreviousstudies
•
Continuitywithinprojectsbutacrossprojectsovertime
•
Faster“intothefield”capability
•
Lowercost
•
Availabilityofcommoncomponentswithtestedandverifiedcode
•
Thoroughdataauditing
Allsystemloginproceduresanddatasubmissions(e.g.,fromstudystafforsurvey
respondentsthroughtheInternet)areencryptedviatheSecureSocketsLayer(SSL)
protocoltoasecurecentraldatabaseattheShepsCenter.User‐levelpermissionsarebased
onuserrolesandaredefinedwithintheprojectsystemtolimiteachuser’saccesstoonly
thoserecordstheyareauthorizedtosee.
Thecentraldatabaseforprojectsrunsonamirroredserversystemwithautomaticfail‐
overfeatures,dailybackupsandtransactionlogs.ThissystemisphysicallylocatedinaTier
IIDataCenterprovidingbackuppowersources,climatecontrol,fireprotectionand24x7
surveillance.
Auditlogsarereviewedroutinelytoverifysecuritymeasuresareoperational.Theservers
arescannedweeklyforvulnerabilitiesandarecurrentlymaintainedatthehighestlevelof
vendorandCERTsecurityrecommendations.Dataareneversharedoutsidetheproject
unlessauthorizedbytheprojectleader.Userauthenticationisbasedonuserpasswords.
Passwordcreationrequirementsareinplacetoguarantee“strongpasswords”asdefined
bytheCERTsecurityrecommendations.TheleadsystemsadministratorisGIACSecurity
EssentialscertifiedthroughMay,2014.
TheUNCShepsCenterendeavorstopreservetheprivacy,confidentiality,andsecurityof
protectedhealthinformationthatmaybepartofhealthrecordsorresearchdatasets.
ProtectedHealthInformation(PHI)ishandledaccordingtoappropriateHealthInsurance
PortabilityandAccountabilityActof1996(HIPAA)PrivacyandSecurityRegulations.Sheps
Centerprogrammersandresearchstaffwhoworkwithsensitivedataarerequiredto
completeappropriateHIPAAtrainingwithperiodicupdates,completeShepsCenter
internaltraining,complywiththeUNCITSecurityPolicies,andagreetotheprovisionsof
theShepsCenter’sRulesofBehaviorandSanctionPolicy.TheShepsCenterstrivesto
implementreasonablesecuritycontrolsguidedbyFISMA,HIPAA,andOMBCircularA‐130,
AppendixIII.
Overview of BSP LIMS Quality Assurance / Quality Control The Biospecimen Process Facility (BSP) Laboratory Information Management System
(LIMS)usesOracleasadatarepository.Therearethreedatabaseshostedontwoservers
supportedbyInstructional&InformationSystems,UNCSchoolofPublicHealth.Backups
occur on both servers on a daily basis. As the need arises, snapshots of the production
database are copied to the two additional databases (staging and development). In the
unlikelyeventofdatacorruptionontheproductionserver,theSchoolofPublicHealthwill
beabletorestorethesystemfromthelatestbackup.
Thepurposeofthestagingdatabaseistoprovideatestenvironmentforapplicationcode
priortoitsreleaseintothelaboratoryenvironment.WiththeuseofcustomSQLscripts,it
ispossibletorapidlysetupamirrorimageoftheproductiondatabase.Thisisusefulfor
rapidresponsetoLIMSmaintenanceissues.Userscanreportbugsbysendinganemailto
informaticshelp@unc.edu.ThiswillcreateahelprequestintheLinebergerBioinformatics
groupticketsystem.Applicationcoderunningagainstthestagingdatabaseisalwaysfound
inthehighestnumberedbranchwithinthecodeversioningsystem.
Thedevelopmentdatabaseisalsoperiodicallymirroredfromproductionbutwithpossible
schemamodifications.Thisdatabaseprovidesadataenvironmentformajorcodechanges,
whichsometimescontinueoveraperiodofmonths.Applicationcoderunningagainstthe
development database will always be found in the HEAD branch of the code versioning
system.
LIMS code development is done using the Eclipse software development tool. With few
exceptions, aspects of the LIMS application (Java source code, SQL scripts, database
packages,helpdocumentation,etc.)aremaintainedwithinEclipseandallofthesefilesare
backedupinacodeversioningsystemonbioinfostore.unc.edu.Therearetwobranchesof
codedevelopment:HEADandBranch_X,where Xrepresentsthebase‐versionnumberof
thelatest,orhighestrelease.Atthetimeofwritingthisdocumentthelatestreleaseis11,
e.g.Branch_11isthecurrentbranch.
Before releasing a new version of the LIMS, we conduct unit and integration testing.
During unit tests, developers verify that the newly added code functions properly and
solves reported bugs. Integration testing is used to make sure the changes don’t break
existingfunctionality.Wehaveaseriesofgeneraltestcasesthatwerunbeforereleasinga
new version. The steps for deploying a new version are documented and stored in our
group’sinternaldirectory.Weareimplementingcodereviewsasapartofthedeployment
process.
Eachreleaseistaggedwithaversionnumber.Thecodeversioningsystem(CVS)maintains
a history of the code versions and a change history for each file in the repository. From
Eclipse,youcanviewthechangehistoryforagivenfileandcompareittoanotherversion.
Wedocumentthechangesineachreleaseonourgroupwiki.
WhennewstudiesareaddedtoLIMS,theBSPlabmanagersmeetwiththeprincipal
investigatortodiscussthesampleprocessingworkflow.Then,theBSPlabmanagerscreate
protocolswithintheLIMStostandardizetheproceduresineachstepoftheworkflow.
Additionally,eachlabtechnicianreceivesperiodictrainingtolearnthelab’sstandard
operatingproceduresaswellastomaintaincertificationspertinenttotheworkinthelab
(iebloodbornepathogen,HIPAA,andCITItraining).TheLIMShasthefunctionalityto
maintainalistingofthecertificationsandvaliditydatesforeachuser.TheLIMSalsohas
thefunctionalitytotrackproject‐specificIRBcertifications.
Onamonthlybasis,theBSPlabmanagersgeneratecheck‐inreportsfromLIMStoverify
thevalidityofsamplecollectionanddrop‐offdates.IntheLIMSprojectsetup,thereisan
optiontosendcheck‐inreportstostudystaffandlabmanagersonaweeklyordailybasis.
Thereisascheduledtaskthatrunsdailyandemailsthereporttoregisteredusers.This
helpsthestudystaffandlabvalidatewhatsamplesweresentandreceivedeachweek.
TheLIMSmaintainsanaudittrailforeachsampleprocessedinthesystem.Eachaudit
recordcontainsthetechniciansnameandadateandtimestamp.Theaudittrailtracks
everythingthatisdonetothesamplefromthetimeitwascheckedintothesystemtowhen
itwasdiscardedorshippedtoanotherfacility.Thereareauditsforsamplecheck‐in,
storageassignment,extractions,openandclosingofprotocols,discards,planchanges,etc.
TheLIMSusesseveraldifferenttypesofinputfieldsontheinterfacedependingonthetype
ofdatabeingentered.Fornumericvaluessuchasvolumeandconcentration,theLIMS
displaysaninputfieldthatallowstheusertoselectanumberfromanorderedlist.There
areupanddownarrowsnexttothedatafieldforsteppingthroughthevaluesinthe
sequence.TheLIMSusescheckboxesforyesandnofields.Forexample,tomarkasample
asdiscarded,theusercancheckthediscardbox.Dropdownboxesareusedtoselectvalues
likeunits,containertypes,andprojectnames.Inputfieldsforcomments,participantids,
dropoffcourier,etcarefreetext.
TheLIMSprovidesdataqualityassuranceandqualitycontrolbyvalidatingdataentered
intothesystem.Forexample,OpticalDensitymeasurementsaretakenontheNanodrop
andtheDropSense.Theequipmentsavestheopticaldensitymeasurementsand
concentrationstoafile.WhenthatfileisloadedintotheLIMS,thesystemwillverifythat
thedataisnumeric.Ifit’snot,theLIMSwilldisplayanerrormessagetotheuser.Ifa
donorcodeformatisdefinedinaprojectcheck‐inprotocol,theLIMSwillchecktoseethat
theenteredtextfitsthedesiredformat.Theuserwillnotbeabletocheck‐inthesample
untilhe/sheentersaparticipantidinthecorrectformat.Eachprotocolcandefinecertain
fieldsasrequired.Whenprocessingsamplesthroughaprotocol,techniciansaren’tableto
completeaworksetuntiltheyhaveentereddataintoallrequiredfields.Thesearejusta
coupleexamplesofcaseswheretheLIMSvalidatesuserinput.
BioSpecimen Facility Information Technologies (LIMS) TheBSPutilizesastate‐of‐the‐artspecimentrackingsystemdesignedspecificallytomeet
theimmediate,inventory‐styletrackingneedsofmultiplehealthresearchprojects.Itis
referredtoastheLIMS(LaboratoryInformationManagementSystem).TheLIMShasbeen
designedtobeflexibleandextendibleforfutureneeds.Allsamplesenteringthelabreceive
2Dbarcodelabelsthatallowustofollowanysample’sprogressthroughthespecific
proceduresindicatedbytheappropriatestudyprotocol.Samplesthatenterthelabare
givenaBSPIDnumber,furtherprotectingastudysubject’srights.Theselabelsalsocontain
ahumanreadableportionandadditionalstudyencodedIDinformation.
TheBioSpecimenProcessingFacilityLIMSisOracle‐basedandmaintainedbytheSchoolof
PublicHealthwithsecurityandbackup.Theuserinterface(developedandmaintainedby
theSchoolofMedicine)isimplementedasaJavathick‐clientwithlimited(readonly)WEB
accessprovidedtoprincipleinvestigatorsandtheirstaff.Thethick‐clienttrackscreation,
storage,movement,anddiscardingofcontainers(vialsandplates)andthespecificsof
containercontents(materialtype,volume,concentration,techniciancomments,etc.)andis
accessedonlybyBSPFacilitystaff.Allcontainershaveastudycontext.BSPstaffhasaccess
toallstudiesbutonlyspecificPIstaff(assetupwithinthesystem)canaccessinformation
associatedwiththeirprojectviatheWEBclient.
LIMSusersarerequiredtologinusingtheiruseridandpassword.Thepasswordsmustbe
atleast8charactersandmustcontainanumberandaspecialcharacter(!,@,#,etc).The
LIMSwillnotallowuserstore‐usetheirlasttwopasswords.Eachuserisassignedarole,
whichdefineswhatfeaturesareavailabletothem.Inadditiontoroles,PIstaffmembers
areassociatedwithprojects.StaffmemberscanlogintotheWEBclienttoviewreportsfor
samplesintheirprojects.
EachcontainercreatedbythesystemisassignedaBSPidentifierthatisunique‐ineffect,
thisisthefacilityassetidentifierforthatcontainer/sample.Eachcontainerislabeledwith
theBSPidentifier,project/donoridentifiers,typeofcontainedmaterial,volume,
concentration(ifapplicable),dateofcreation,andcurrentstoragelocation.Containersmay
bepre‐assignedtoaprotocolpathwhicheventuallyleadstothedepartureofthe
containersfromthefacility,butmayalsoresultinlong‐termstoragewithinthe
facility.Throughaqueryinterface,setsofcontainersmaybeidentified,pulled,andbe
furtherprocessedwithinthefacilityorbeshippedtootherfacilities.
Anaudittrailismaintainedoncontainersandcontent.Thistrailrecordssuchthingsas
whenandwhodropsoffcontainerstotheBSP,whenthecontainerwascreatedasitmoves
throughprocessingintheBSPasdirectedbythestudiesprotocols,whichtechnician
createdit,whenandwhereitwasstored,whenandwhereitwaspulledfrom,etc.The
systemwilltrackmaterialsthataretransferredtootherfacilitiesorPIcollaboratorsas
well.
TheLIMShasthecapabilityofacceptingprocessinglogsgeneratedbytheAutopureLS
(DNAextractonrobot)andtheMultiprobeII(aliquotingrobot).Theselogscanbe
transferredtotheLIMSatthecompletionofeachrun.Theselogsarelinkedtothe
individualsampleshistoriesandcanbereferredtointhefutureforavarietyofreasons.
TheresultsfromanalysisdonewithinthefacilityarerecordedintheLIMSdatabase.This
includesagarosegelanalysis(withimage),opticaldensity(withwavegraph),real‐time
PCRandbioanalyzerresults.Analysisreportsareavailabletoboththefacilitystaffand
projectstaff(throughtheWebinterface).Thecurrentinventoryofagivenprojectisalso
availableasareport.Thisshowstheentireprojecthistoryintermsofmaterialthatwas
checkedintothefacility,createdbythefacility,andshippedfromthefacility.
NoPersonalHealthInformation(PHI)ismaintainedanywhereintheBSPsystems.When
donorsamplesarecheckedintothefacilitythesystemallowsforlimitingtheuseofthe
samplesbasedupondonorpreferences(i.e.allowgeneticresearch,destroyatproject
completion,orrestrictresearchtooriginalproject).
Onadailybasis,theLinebergerDatawarehouseandBiospecimensRepository(LDBR)
loadsLIMSproductiondataforreporting.Thedatawarehouseusesaread‐onlyaccountto
connecttotheLIMSdatabase.StoringLIMSdatainthedatawarehouseallowstheHealth
Registrystafftocreatereportsfortheirsamples.Thesereportsincludeinformationabout
thesamplesthathavebeencheckedin,thesampleinventory,andnucleicacidanalysis
data.
Future TPF LIMS System DevelopmentofthefutureTPFLIMSSystemwillbebasedontheBSPLIMSsystemandwill
besimilarinscope,development,andimplementation.TheFutureTPFLIMSsystemwill
storeinformationoncollectedtissue,pathologystatus,sampleprocessingprotocolsand
methods,andbankingandinventoryinformation.
Electronic Registry System (ERS) ElectronicRegistrySystem(ERS)isaCancerRegistrysoftwaretoolthatincludesthe
standarddatasetrequiredbytheCommissiononCancer(CoC)andmeetsthe
requirementsoftheNorthAmericanAssociationofCentralCancerRegistries(NAACCR).
TheUNCCancerRegistry’sCertifiedTumorRegistrarsuseERSasadatacollectiontoolfor
manualelectronicmedicalrecordsabstraction–requiredbystatelaw.Approximately
80%ofthehospitalsinNorthCarolinauseERS.
TheERSsoftwaretoolfortheUNCCancerRegistryismaintainedandhostedbyERSand
deliveredasavirtualizeddesktop.Itisaccessedviawebsiteandrequiresentryof
credentials.TheUNCHealthRegistry/CancerSurvivorshipCohort(HR/CRC)purchased
theERSsoftwaretooltofacilitatetransferofUNCCancerRegistrydatadirectlytoHR/CRC
viaanERSdevelopedsoftwarepatch.TheUNCHR/CRCERSwillbemanagedbythe
LinebergerDataWarehouseandHR/CSCITteamandERSprogrammingsupportgroupin
conjunctionwithISDtoassureversioningcomparability.InadditiontotherequiredCoC
datasets(seeTable1),ERSmakesavailabletotheUNCHR/CSCotherdatafields,including
thosethatcanbecustomized,tofitourspecificneeds.Theadditionalfieldsinclude
expandedresearchanddiagnosticfields,clinicaltrialfieldsaswellasuserdefinedfields
thatcanbecreatedandmaintainedbytheuser.TheHR/CRCstaffwillmanuallyabstract
theseadditionaldatafields(seeTable2)fromtheelectronicmedicalrecordtocomplement
thedatathatisprovideddirectlyinERSfromtheUNCCancerRegistry.Codingmanualsare
onlineandmaintainedbytheERSsoftwarecompany.ERSprovidesuserswithavery
extensivereportingmodulefordataanalysistocomparetreatmentanalysis,survival,
incidencebysite,stage,race,etc.Anydataiteminthesoftwarecanbeselectedandusedfor
reportingpurposes.Thesoftwarecontainsafollowupmodulethatallowstheuserto
automaticallyschedulefollowuplistsandletterswithpatients.
ERSprovidesthreedaysofinitialon‐sitetrainingfornewusersaswellasunlimitedonline
training.AcompleteusermanualisprovidedaswellasaVideoLibraryoftrainingtutorials
(seeonlineResourcelistbelow).Thesoftwareisupdatedquarterly(ERSnotifiesISDor
userviaemailthatthesoftwareupdateanddocumentdetailingupdatechangesis
available)andquarterlytrainingwebinarsareprovidedthatareawardedcontinuing
educationcreditsfromtheNationalCancerRegistrarsAssociation(NCRA).ERSprovides
unlimitedsupporttousersforallregistryandtechnicalissues.
TobeaCTR(CertifiedTumorRegistrar),oneisrequiredtohaveaminimumofa2year
degreeinahealthrelatedfieldandpassthenationalCTRtest.Asof2012,eachregistrar
mustbecertifiedtoperformabstraction.Thereareinternaleditcheckswithinthesoftware
thatcomeupifillogicalinformationisentered,suchasfemaleforprostatecancer,zipcode
andcountycodematchingerrorsaswellasprocedureandstagingconflicts,suchas
enteringpathologicstagingwhenthepatienthashadneoadjuvanttherapy.Requiredfields
cannotbeleftblank.Additionally,about10%ofthecasesareidentifiedbytheUNCCancer
Registrarandarereabstractedtocheckforaccuracy.Aqualitycontrolprotocolinvolving
reabstractionofaproportionofrecordstomonitordataqualityofadditionalHR/CSC
abstracteddataelementswillbeimplemented.Additionally,bothUNCCancerRegistryand
UNCHR/CSCmanuallyabstractedmedicalrecordsdataelementswillbecomparedwith
plannedEMRextractionsforadditionallyqualityassessment.
Resources:
1. ERSWebsite
http://www.ers‐can.com/
2. FORDSmanualfor2013
http://www.facs.org/cancer/coc/fords/fords‐manual‐2013.pdf
3. 7theditionAJCCstagingmanual:
http://www.cancerstaging.org/products/ajccproducts.html
ISBN:978‐0‐387‐88440‐0(mustpurchasefor$65–seewebsite)
Appendix 2. System‐Specific Data Mappings CPR‐OR Tissue Collection Tracking TheUNCHealthRegistryTPFReportcontainstissuebankingstatusinformationthatis
reportedincoarsergranularitybasedonseveralspecificbankingstatuscategories.This
tableexplainsthescenarioswheretissuesarenotcollected.
Status
Banked
After Hours
Surgery Stopped (updated
from Aborted)
Completely Submitted to
Path
Canceled
Improper Consent
Explanation
Tissue was received and
processed
Cases that run past 5:30pm
Monday through
Friday. Cases are then
targeted the next morning
before they are put on
formalin by pathology
(with the exception Friday
cases, after hours cases
will be updated the next
day)
Surgery was stopped (this
generally occurs when
frozen sections from
complex surgery cases
show metastatic disease,
and the surgeon decides
that the patient is better off
without continuation of
surgery) 
Cases in which tissue
procurement is not allowed
to take any tissue because
all of the tissue is needed
by pathology (examples
include: lymphoma
workups, spleens
submitted to hemepath,
medical kidneys, uterus
cases with complex
atypical hyperplasia,
BRCA ovaries)
Cases that were on the
schedule but were either
cancelled or moved to
another date 
Cases in which HIPAA
was not signed, the
consent form was not
signed, dates were invalid,
or surgeon did not consent
patient prior to surgery
Tissue Status
TISSUE
COLLECTED
Temporary status due
to pathology hours.
On TPF Report
Final status if collected
on a Friday.
NO TISSUE
COLLECTED
NO TISSUE
COLLECTED
“Not Enough
Tissue”
(Sample sent to
Surg Path)
NO TISSUE
COLLECTED
TISSUE NOT
COLLECTED
Infectious
Margins
Biopsies
Too Small
No Tumor Seen
Not Targetable Procedure
No Consent
Withdraw
Case that are known to be
infected with HIV, HBV,
HCV, or TB are not
banked by TPF
Wide local excision
(WLE) melanomas or
breast re-operative cases in
which margins were
previously positive are not
banked by TPF
Scope cases which
produce little or no tissue
are not banked by TPF
TISSUE NOT
COLLECTED
TISSUE NOT
COLLECTED
“Not Enough
Tissue”
(Sample sent to
Surg Path)
TISSUE NOT
COLLECTED
“Not Enough
Tissue”
Cases in which the PA can
see tumor, but there is not
enough tissue to be given
to TPF
TISSUE NOT
COLLECTED
(Sample sent to
Surg Path)
“Not Enough
Tissue”
- Cases in which there is
either no cancer diagnosis,
or the tumor cannot be
seen or palpated (examples
include: abnormal
mammograms, benign
disease cases, and cases
with only normal tissue)
are not banked by TPF
Cases that will not produce
tissue 
Cases that blank consent
form is found in the chart
(recently updated)
Cases that subject revoked
the consent signed prior
the surgery (recently
updated) 
TISSUE NOT
COLLECTED
(Sample sent to
Surg Path)
“No Tissue”
(No Sample Sent
to Surg Path)
TISSUE NOT
COLLECTED
TISSUE NOT
COLLECTED
TISSUE NOT
COLLECTED