iCaRe 2 Integrated Cancer Data Repository - PowerPoint Presentation

1. iCaRe2Integrated Cancer Data Repository for Cancer Research icare2.unmc.eduOleg Shatsoshats@unmc.eduFred & Pamela Buffett Cancer CenterUniversity of Nebraska Medical CenterMay 9, 2019

2. OutlineWhat is iCaRe2? TimelineSoftware architectureUser interfacesData being collectedOrganizational modelData feedsHow to obtain data for researchUtilizationDemos

3. AcknowledgementsThe iCare2 is supported predominantly by UNMC Fred and Pamela Buffett Cancer Center with some support from the UNMC College of Medicine.At various phases, iCaRe2 registries were also supported by National Institutes of Health (NIH), NE DHSS LB506 program, UNMC Clinical Research Center, NU Foundation, and the Leona M. and Harry B. Helmsley Foundation.

4. irequest.unmc.eduicare2.unmc.edu

5. What is iCaRe2?A multi-institutional resource that collects and manages standardized, multi-dimensional, longitudinal data and biospecimens on adult cancer patients, high-risk individuals, and normal controls. The goals are:to advance comprehensive studies of risk factors of cancer development and progressionto enable the design of novel strategies for prevention, screening, early detection, and personalized treatment of cancer.

6. What is iCaRe2?A HIPAA-compliant socio-technical system that addresses various aspects of interactions between: people (patients, clinical personnel, technicians, researchers, and administrators from multiple centers)technology (methods, tools, and databases) environment (governance procedures, laws and regulations, intellectual property issues, data and process flow, etc.)

7. Key CharacteristicsOpen to any cancer center/hospital to participateConfederation principle as an organizational modelEnrolls adult cancer patients (newly diagnosed and survivors), high-risk individuals and controlsPatient portal with extensive patient questionnaire Collect blood and provide access to tissue samplesMetadata-driven software architecture Automated workflows and pipelines for data integration

8. TimelineiCaRe2Pre-iCaRe2 registriesPancreaticThyroidBreastHealthy controls

9. iCaRe2 Registries  (investigator-initiated projects)Pancreatic Cancer (PI: Dr. Quan Ly)Breast Cancer (PIs: Drs. Ken Cowan, Jessica Maxwell)Thyroid Tumor & Cancer (PI: Dr. Whitney Goldner)Healthy Controls Registry / GPHID (PI: Dr. Ken Cowan)Genitourinary Cancers (PI: Dr. Shawna Boyle)Thoracic Oncology (PIs: Drs. David Berkheim, Apar Ganti)Head and Neck Cancers (PI: Dr. Zafar Sayed)Gastrointestinal & Abdominal Cavity Cancers (PIs: Drs. Jason Foster, Jean Grem)Central Nervous System Tumors (PI: Dr. Nicole Shonka)Leukemia and Myeloid Neoplasm (PI: Dr. Vijaya Bhatt)Melanoma (PI: Dr. Alissa Marr)Sarcoma (PI: Dr. Sean McGarry)Gynecologic Cancers (PI: Dr. Kerry Rodabaugh)Plasma Cell Dyscrasias Collaborative Registry (PI: Dr. Sarah Holstein)Neuroendocrine Tumors (PIs: Drs. Abbey Fingeret, Kelsey Klute)Unknown Primary cancers (PI: Dr. Apar Ganti)

10. Flashback: Working Groups for the Pancreatic Cancer Collaborative Registry (PCCR)PI: Randall Brand, M.D., U of Nebraska Medical Center Epi/Instrument (Drs. Lowenfels and Petersen)Henry Lynch, M.D., Creighton University Ralph H. Hruban, M.D., Johns Hopkins University Gloria Peterson, Ph.D., Mayo Clinic Rachael Stolzenberg-Solomon, M.P.H., Ph.D., NCI Albert B. Lowenfels, M.D., New York Medical College Richard H. Bell, Jr., M.D. , Northwestern UniversityWendy Rubinstein, Ph.D., Northwestern University Malcolm Bilimoria, M.D., Northwestern University Mark Talamonti, M.D., Northwestern University Simon Sherman, Ph.D., U of Nebraska Med Center Oleg Shats, M.S., U of Nebraska Medical Center David C Whitcomb M.D., Ph.D., U of Pittsburgh IRB (Dr. Prentice)Ernest Prentice, Ph.D., U of Nebraska Med CenterHenry Lynch, M.D., Creighton UniversityWendy Rubinstein, Ph.D., Northwestern University Pathology/Specimen (Drs. Hruban and Whitcomb)Ralph H. Hruban, M.D., Johns Hopkins University  Malcolm Bilimoria, M.D., Northwestern University Karen Kaul, M.D., Northwestern University Ernest Prentice, Ph.D., U of Nebraska Medical Center David Whitcomb, M.D., Ph.D., University of Pittsburgh Imaging (Dr. Brentnall)Mimi Canto, M.D., Johns Hopkins Hospital Teri Brentnall, M.D., University of Washington Babak (Bob) Etemad, M.D., U of Pittsburgh Med CenterJoe Anderson, M.D., U of Nebraska Medical Center Maurits Wiersema, M.D., Mayo Clinic  Chicago, October 31, 2001

11. Patient QuestionnaireiCaRe2 RegistriesUsersiCaRe2: Infrastructure and DataflowMetadata RepositoryIntegrated Data RepositoryInternal Staging DBPatient Master IndexiCaRe2 BiobankOpenSpecimenCancer RegistryCancer RegistryCancer RegistryDe-identification proceduresHonest Broker processMapping PipelinesMetadata-driven Extract-Transform-Load (ETL) proceduresMetadata-driven Automated Registry BuilderData elements, Permissible values, Units of measureValidation rules,Dependency rules,Customization rulesLook-n-feel attributesForm hierarchy, etc.Mapping rulesCancer-specificData ElementsClinical Data ElementsAdministrative Data ElementsExtended Data ElementsCore Data ElementsData Reporting & Mining ModuleVisualization Dashboard Tableau ServeriRequest:requests for dataiConsent:Electronic consentingTerminologiesSNOMED-CTICD-O-3NAACCRNCI’s cancer Data Standards Registry and Repository (caDSR)PHIDe-idAuthorized UsersResearchers from participating centersiCaRe2 personnel External Data SourcesHospital Cancer Registry…Frozen & Paraffin Tissue Banks…ParticipantsMetadata BuilderInternal ComponentsUser InterfacesETL procedures

12. iCaRe2 Dashboardhttp://cancerinformatics.unmc.edu/dashboards/icare2/

13. Metadata Builder (Oracle APEX)

14. Registry’s GUI

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17. Integration Dashboard (BC)

18. Sequencing Data

19. Bioinformatics Data

20. icaRe2 Biobank: OpenSpecimen

21. Data MiningSource code of OpenSpecimen, Krishagni Solutions is partially utilized (BSD-3 Style license)

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23. Workflow for Feedback

24. Electronic Consenting

25. Electronic Data Requests

26. Electronic Data Requests

27. Types of Collected DataPatient-provided dataClinical dataDemographicsOccupation Family HistoryMedical History Tobacco and Alcohol UsageDietary HabitsVitamins/SupplementsPhysical ActivityReason For Seeking CareSymptomsMedicationsQuality Of LifeSleep IndexDiagnostic PathologyBiomarkersGenetic TestsTreatmentRecurrenceOutcomeBiospecimensBloodTissues

28. Patient QuestionnairesCommon Core Questionnaire (CCQ) Standardized forms for demographic, family and medical history, tobacco and alcohol usage, etc.Extended/optional questionnaireLibrary of standardized forms for physical activity, dietary habits, vitamins, quality of life, etc.Cancer-specific forms reason for seeking care, medications, symptoms, etc.Follow-up questionnairesCCQ is mapped to the NCI’s Cancer Data Standards Registry and Repository (caDSR)

29. NCI's caDSR

30. Organizational ModelConfederation Principle:Allows centers, irrespective of their size or location, to participate in data collection and collaborative studiesProvides each participating institution with an equal representation in the steering committee Ensures that a center retains all rights to its own dataCollected data can be used by others only upon approval from data owners We act as an “honest broker”

31. OperationAll participating centers obtain an IRB approval from their institutions and accept the BylawsSubjects sign informed consent to participate (online or paper)Subjects complete detailed baseline questionnaire (online or paper)Follow-up questionnaires are optionalSubjects donate blood and allow access to tissue leftover after completion of routine diagnostic or clinical procedures Clinical personnel enters medical data (manual abstraction from EHR)Data is transferred from the hospital Ca registry (if available)Work is underway to link pathology and molecular studies data from NE-CARESThe goal is to feed structured clinical data from EHR

32. Data feed: Hospital Ca RegistryAll Ca patients treated at Nebraska MedicineThere is six months delayBi-weekly feed in NAACCR formatMapped to iCaRe2 cases by MRNData elements:Demographic (DOB, gender, race, ethnicity, occupation, marital status, address)Diagnostics (date, age, comorbidities, primary site, laterality, histologic type, grade, TNM staging)Treatment (surgeries, therapies with dates, agents)Cancer-specific factorsRecurrence (locoregional, distant mets, sites of mets, date)Outcome (date of last update, vital status, date of death, cause of death)

33. Data feed: NE-CARESUnder developmentAll records mapped to iCaRe2 cases by MRNData elements:Tissue availability in tissue banksStructured pathology data from synoptic reportsMolecular observations (sequence variants)

34. TissuesNE-CARESClinical samplesFrozen tissue bankParaffin tissue bankiCaRe2FreezerWorkscoPathManual review by PathologistiCaRe2 biobankOpenSpecimen

35. How can the data be obtained? irequest.unmc.eduResearch using identifiable data and/or biospecimens from iCaRe2 (may also have access to the medical record)iCaRe2 approvalExpedited IRBSRC approvalResearch using de-identified data (will not have access to the medical record)iCaRe2 approval onlyDoes not require IRB approval

36. Workflow for Data Requests

37. Projects utilizing iCaRe2 dataBreast cancer (BC) whole genome sequencing – Cowan/Guda/Agendia and IBM WatsonBC Inflammatory Biomarker – Cowan /BiodesixXPF-ERCC1 - predictable marker for chemotherapy BC – Bessho BC Tumor Margins detection using electrical and optical properties – WestBehavioral and Genetic Factors Associated with Sleep Quality in BC – BergerDietary intake and BC development – Hanson Familial BC – SanMing WangFormation of estrogen-DNA adducts as a biomarker of breast cancer risk – Rogan Prevalence of Colorectal Adenomas in Breast Cancer Survivors – Tandra Papillary Thyroid Cancer (TC) WES – GoldnerModifiable Risk Factors in TC – R. SmithMetabolomic Eval. of benign and malignant Thyroid nodules – Goldner Circulating Tumor Cells in Pancreatic Ca (PC) –GremPathobiology of PC: Identification & Evaluation of Biomarkers & Therapeutic Targets – Batra PC Rapid Autopsy Program – HollingsworthBiomarker validation for Pancreatic Neoplasms – Batra Identification of synergistic interactions between modifiable risk factors in PC development – Farazi Assessment of dietary microRNAs as confounders in cancer biomarker studies – CuiCancer Dx and phenotype in relation to Vit D status – Hanson Signaling Molecule Alterations in Colon Cancer – BlackMechanisms of TGF-B mediated suppression of metastasis in colon cancer – Jenny WangMucins in colorectal cancer – Batra HIPEC in abdominal cancers – Foster Serum MUC5AC levels in lung cancer – Ganti Stage IIIa NSC lung cancer WES – Trujillo Prostate Cancer microRNA – LaGrangeA prognosis marker for prostate cancer – Pi-Wan Cheng

38. Results are published in:Am J Gastroenterol.BMC CancerBreast J. Cancer Inform.Int J Endocrinol.International Journal of CancerJ of Oncology Navigation & SurvivorshipLaryngoscopeOtolaryngol Head Neck Surg. Supportive Care in CancerPLoS One

39. Participating centersiCaRe2 is currently utilized at 58 institutions (83 distinct sites) from 23 U.S. states and one center in Italy.

40. Numbers at a glance REGISTRY  # of all cases # of UNMC cases # of UNMC cases with bloodGI & Abdominal Cancers 28512851314Breast Cancer 727726181345Thoracic Oncology 23732373120Thyroid Tumor and Cancer 314619161414Genitourinary Cancers 12511251181Pancreatic Cancer54211212312Head & Neck Cancers 130375440Leukemia and Myeloid Neoplasm 66966930Central Nervous System Tumors 56756754Gynecologic Cancers 56156166Healthy Controls 406406274Unknown Primary Cancers 389389Melanoma 367367Plasma Cell Dyscrasias 3453452Sarcoma 2342342Total: 27,16016,5134,15459 Centers83 Distinct Sites27,160 Cases16,513 UNMC Patient Cases; 4,154 with Blood30 patients a month consented at UNMC in average

41. Next objectivesincrease enrollment broaden coverage improve data validation rulesexpand data feeds from clinical data sourcescontinue harmonizing data elements with standard terminologiesboost utilization

42. iCaRe2 key personnelKenneth Cowan, MD, PhD Executive DirectorWhitney Goldner, MD Lead PIBen Swanson, MD, PhD Lead PathologistMichelle Desler, MS Lead Research CoordinatorOleg Shats, MS IT / Informatics DirectorJianmin (JJ) Feng, MS Database Developer & AdministratorTaelyr Weekly, MPH, RN-BC Clinical Research CoordinatorPei Xian Chen, MD Research TechnologistAmy Wells, MS Research Technologist ALL Centers’ PIs and Coordinators

43. Questions?Technical: Oleg Shats - oshats@unmc.eduOperational: Michelle Desler - mdesler@unmc.eduOrganizational: Dr. Whitney Goldner – wgoldner@unmc.edu

44. iCaRe2 Resources Main website: icare2.unmc.edu Requests for Data: irequest.unmc.edu ‘iCaRe2 at a glance’ Dashboard (Intranet access only):cancerinformatics.unmc.edu/dashboards/icare2OpenSpecimen: openspecimen.unmc.edu 16 Registries: bccr.unmc.edu, tccr.unmc.edu, etc. Remote consent (prototype - pending IRB approval): www.unmc.edu/cancercenter/registry/enroll

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