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Nagarajan Lab, 2010
Biomedical Informatics Infrastructure Integration using caBIGTM Tools
Rakesh Nagarajan, MD PhDJune 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 (2008-2009, 3 facilities)
Nagarajan Lab, 2010
Levels of Data Access
Data Privilege / Data First Name Last Name DOB Age Race
PSA Test date / Age @ Test
PSA Value
Anonymized xxxx xxxx xxxxxxxx 70 Caucasian 67 6De-Identified xxxx xxxx xxxxxxxx 70 Caucasian 67 6Limited xxxx xxxx 1/15/1939 70 Caucasian 2/1/2006 6Identified Tim Allen 1/15/1939 70 Caucasian 2/1/2006 6
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 titleIRB #IRB documented start date for protocol
Nagarajan Lab, 2010
Visit Details
Event
Visit
Form
Nagarajan Lab, 2010
Tiered Consent
Nagarajan Lab, 2010
1. 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
WUSTLKey (IdP)eMPI
CIDER CSMS ClinPortal caTissue ProfileDB
Routine Inpatient and
Outpatient Data
Clinical Studies/Disease-Oriented Groups
Data
Biospecimen Management
System
Molecular Profiling
Data
University-wide Informatics Architecture
Person IdentificationRegulatory Approval
Nagarajan Lab, 2010
CIDER CSMS ClinPortal caTissue ProfileDB
Routine Inpatient and
Outpatient Data
Clinical Studies/Disease-Oriented Groups
Data
Biospecimen Management
System
Molecular Profiling
Data
University-wide Informatics Architecture
Medical Record AcquisitionLinked by
Biospecimen ID
eIRB
WUSTLKey (IdP)eMPI
Nagarajan Lab, 2010
TissueSuite
ClinPortala
b
d
ClinicalStudies
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).
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).
CIDER ClinPortalTissueSuite
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
TissueSuite
ClinPortal
TissueTissueSuiteSuite ClinPortalClinPortal
caGrid
caCORE-likeAPICIDER
Nagarajan Lab, 2010
Acknowledgments
STL TeamSunita 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 ManagerSrikanth Adiga
BJC TeamTom HoldenerMindy MassRobert 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
CollaboratorsMark Watson
Jeff Milbrandt
Ken Polonsky
Brad Evanoff
Jackie PaytonAbhijeet Ranadive Nitesh Marwaha Rukhsana Sameer
Amit Bidkar Pathik Sheth Sachin Lale
Amit Doshi Pavan Kalantri Sagar Baldwa
Anoop Kunchukuttan Pawan Maheshwari Shika Sethi
Baljeet Dhindhwal Pooja Tavase Shital Lawhale
Chetan Pundhir Prachi Sharma Shrishail Kalshetty
Deepali Ahirao Pradnya Unawane Siddharth Shah
Deepti Shelar Prajakta Sakat Snehil Gupta
Gaurav Mehta Prasanna Kashikar Srinath Krishnamurthy
Gaurav Sawant Pratha Budhrani Suhas Khot
Geeta Jaggal Pritesh Mehta Sumit Deshmukh
Hemant Patil Pulkit Kumar Sumit Gaurav
Janhavi Hasabanis Rajesh Vyas Supriya Dankh
Kunal Kamble Rakhi Garg Susmita Ghosh
Madhumita Shrikhande Rashmi Dixit Vijay Pande
Mandar Shahasrabuddhe Rashmi Dixit Vishvesh Mulay
Niharika Sharma Rinku Rohra Yogesh Leve