Nagarajan Lab, 2010 Biomedical Informatics Infrastructure Integration using caBIG TM Tools Rakesh Nagarajan, MD PhD June 2, 2010 *Dr. Nagarajan is on the Scientific Advisory Board of Persistent Systems. Persistent Systems does not fund Dr. Nagarajan’s research.

Nagarajan Lab, 2010 Common Informatics Needs  Clinical Data Warehouse  Clinical Studies/Data Management System  Biospecimen Management System  Molecular Profiling Management Systems  Integration Systems  Analytical Systems

Nagarajan Lab, 2010 Problem Statement  Quality Improvement  Review Preparatory to Research  Clinical Studies Data Acquisition  Retrospective  Prospective  Biospecimen Selection  Participant Recruitment

Nagarajan Lab, 2010 Solution CIDER

Nagarajan Lab, 2010 Solution CIDER ~4.6 million patients ~34.5 million encounters ~63 million lab results ~14 million med. orders ~130 million vitals ~50 million text documents ~13 million scanned documents ~60,000 allergies (2009) ~780,000 microbiology results ( , 3 facilities)

Nagarajan Lab, 2010 Levels of Data Access

Nagarajan Lab, 2010 Getting Started

Nagarajan Lab, 2010 Executing a Query

Nagarajan Lab, 2010 Executing a Query

Nagarajan Lab, 2010 Executing a Query

Nagarajan Lab, 2010 Executing a Query

Nagarajan Lab, 2010 Curating De- identified Documents

Nagarajan Lab, 2010 Natural Language Processing Extract structured information from text documents (e.g. Tobacco and Alcohol History, Problem Lists, Medications) Make structured information available for query in CIDER

Nagarajan Lab, 2010 Running More Complex Workflows

Nagarajan Lab, 2010 Downloading Data

Nagarajan Lab, 2010 Downloading Data De-Identified

Nagarajan Lab, 2010 ClinPortal Overview  Web-based, data collection tool  Developed at Washington University School of Medicine  Designed for the following types of studies PI Initiated Studies Disease-oriented groups (Patient ‘databases’) Multi-institutional studies/trials  Application integration caTissue CIDER  Grant Supported Standardized vocabularies Reuses clinical variables/data elements Data sharing Identified, De-Identified (HIPAA compliant)

Nagarajan Lab, 2010 ClinPortal: Process Overview  Model data elements in UML  Import XMI into ClinPortal (Reuse of Dynamic Extensions from caTissue)  Import permissible value sets for enumerated value domains  Import case report form definitions

Nagarajan Lab, 2010 ClinPortal Study Details ClinPortal studies have 2 types of users: PI and Coordinator(s) Both roles have the same privileges: full identified PHI for all participants on all forms, unless otherwise specified by PI Complete Protocol Title per IRB approval Familiar shortened title IRB # IRB documented start date for protocol

Nagarajan Lab, 2010 Visit Details Event Visit Form

Nagarajan Lab, 2010 Tiered Consent

Nagarajan Lab, WUSTL Key Integration 2.eMPI Integration 3.SAS export 4.ClinPortal-caTissue User Interface Integration 5.Multi-Institutional Studies 6.Bulk Operations 7.Clinical Study Designer Recent ClinPortal Features

Nagarajan Lab, 2010 SAS Export

Nagarajan Lab, 2010 ClinPortal-caTissue Integration- Setup

Nagarajan Lab, 2010 ClinPortal- Visit View Based on Participant Name + Event

Nagarajan Lab, 2010 caTissue- Specimen Collection Group

Nagarajan Lab, 2010 Clinical Study Designer 1.0 Allows end users to design case report forms and define studies for use in ClinPortal a. Browse existing forms b. Design their study c. Create new forms d. Edit forms until ready for release e. Repurpose their own forms ( edit a form created for another study and insert it into a new study) f. Repurpose some else’s form (using another user’s forms, modify, rename and use as their own)

Nagarajan Lab, 2010 Clinical Study Designer 1.0

Nagarajan Lab, 2010 Build a new form + edit

Nagarajan Lab, 2010 Browse forms Preview

Nagarajan Lab, 2010 Design Study

Nagarajan Lab, 2010 Repurpose Forms

Nagarajan Lab, 2010  26 studies in production  ~4,000 participants registered across these studies  Additional ~30 studies in pipeline  Scope  First GCRC study  ~5 cancer studies in different phases of adoption  ADRC Integration (Center level Integration)  Dystonia Study (Multi-Institutional) ClinPortal Production

Nagarajan Lab, 2010 Authentication eIRB WUSTL Key (IdP) eMPI CIDERCSMSClinPortalcaTissueProfileDB Routine Inpatient and Outpatient Data Clinical Studies/ Disease-Oriented Groups Data Biospecimen Management System Molecular Profiling Data University-wide Informatics Architecture Person Identification Regulatory Approval

Nagarajan Lab, 2010 CIDERCSMSClinPortalcaTissueProfileDB Routine Inpatient and Outpatient Data Clinical Studies/ Disease-Oriented Groups Data Biospecimen Management System Molecular Profiling Data University-wide Informatics Architecture Medical Record Acquisition Linked by Biospecimen ID eIRB WUSTL Key (IdP) eMPI

Nagarajan Lab, 2010 Tissue Suite ClinPortal openMDRLexEVS a b d Clinical Studies c Desired Metadata Infrastructure Integration

Nagarajan Lab, 2010 Research Data Integration Find me all biospecimens procured from patients with Gleason grade 6 or more prostate cancer and a PSA value >= 10 mg/L who are also enrolled in RTOG P-0126 (a clinical trial comparing High Dose 3D-CRT versus Standard Dose 3D-CRT). CIDERClinPortal Tissue Suite Find me all biospecimens procured from patients with Gleason grade 6 or more prostate cancer and a PSA value >= 10 mg/L who are also enrolled in RTOG P-0126 (a clinical trial comparing High Dose 3D-CRT versus Standard Dose 3D-CRT).

Nagarajan Lab, 2010 Query Modes Tissue Suite ClinPortalTissueSuite ClinPortal caGrid caCORE-like API CIDER

Nagarajan Lab, 2010 Acknowledgments STL Team Sunita Koul George Joseph Rekha Meyer Yongkee Cho Li-Wei Chang Jasmine Owens Mukesh Sharma Caerie Houchins Jahangheer Shaik Dianne Oliver Ammar Halawa Daniel Fares David Mulvihill Nitin Shah Persistent Team Program Manager Srikanth Adiga BJC Team Tom Holdener Mindy Mass Robert Jost Brandon Ruiz Chris Champion Raghavendra Kalakota Leslie McIntosh Lori Scantlan Aniket Bhandare Sujay Narkar Bijoy George Nobish Varghese Kuldeep Matharasi Poornima Govindrao Mary Uhlmansiek Robby Begley Stewart Wang Collaborators Mark Watson Jeff Milbrandt Ken Polonsky Brad Evanoff Jackie Payton Abhijeet RanadiveNitesh MarwahaRukhsana Sameer Amit BidkarPathik ShethSachin Lale Amit DoshiPavan KalantriSagar Baldwa Anoop KunchukuttanPawan MaheshwariShika Sethi Baljeet DhindhwalPooja TavaseShital Lawhale Chetan PundhirPrachi SharmaShrishail Kalshetty Deepali AhiraoPradnya UnawaneSiddharth Shah Deepti ShelarPrajakta SakatSnehil Gupta Gaurav MehtaPrasanna KashikarSrinath Krishnamurthy Gaurav SawantPratha BudhraniSuhas Khot Geeta JaggalPritesh MehtaSumit Deshmukh Hemant PatilPulkit KumarSumit Gaurav Janhavi HasabanisRajesh VyasSupriya Dankh Kunal KambleRakhi GargSusmita Ghosh Madhumita ShrikhandeRashmi DixitVijay Pande Mandar ShahasrabuddheRashmi DixitVishvesh Mulay Niharika SharmaRinku RohraYogesh Leve