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