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Clinical and Translational
Research
Overview of Informatics Tools and Services provided
by
Institute for Clinical and Translational Science(ICTS)
Monika Ahuja
Institute for Clinical and Translational Science, University of Iowa
Data Requests - Wordle
Clinical and Translational Research & Informatics
Image reference : Clinical research informatics: challenges, opportunities and definition for an emerging domain;J Am Med Inform Assoc. 2009 MayJun;16(3):316-27. doi: 10.1197/jamia.M3005. Epub 2009 Mar 4. Embi PJ1, Payne PR.
ICTS Tools
i2b2
CDR Explorer
StarMaker
TCGA
Data Exploration Tools
REDCap
UI BioShare
SCI-Link
Data Management Tools
XNAT
ICTS Tools
i2b2
CDR Explorer
StarMaker
Data Exploration Tools
– IRB Applications
– Grant Applications
– Study feasibility
TCGA
I2b2 User-base
• Researchers on Campus
• PCORENet Framework
– Definition from PCORI - “The goal of PCORI’s
National Patient-Centered Clinical Research
Network Program is to improve the nation’s
capacity to conduct comparative effectiveness
research (CER) efficiently, by creating a large,
highly representative electronic data
infrastructure for conducting clinical outcomes
research.”
http://www.pcori.org/funding-opportunities/funding-announcements/clinical-data-research-networks-cdrn-improvinginfrastructure-for-conducting-patient-centered-outcomes-research-pcor/
Data Usage Continuum
Many different levels of user sophistication are found
within the clinical enterprise.
Data access driven by knowledge model content,
with query generation tools for more advanced users.
Point-and-click data exploration
without query construction or data
manipulation.
Starmaker
Data Guru
Programmer
CDR Explorer
Report Writer
Slice and Dice
Dashboard
•Just show me the
numbers!
•Select data
•Organize results
Spreadsheets
& Tools
•Database logic
•Tables, columns
•Light scripting
•Math oriented
•Tabular data
•Often very
sophisticated!
*http://www.parkstreetsolutions.com/
•Applications
•Web pages
•Reports
•SQL author
•Data architect
•Datamarts
The Cancer Genome Atlas (TCGA) Browser
• Search, browse and integrate clinical,
expression(RNA SEQ), Methalation and MiRNA
data
• Used by 30 users (in Basic Science and Internal
Med)
ICTS Tools
• Data Management Tools
– Study Specific data
– Collaborative data
– Data security and data sharing
REDCap
UI BioShare
SCI-Link
Data Management Tools
XNAT
REDCap (Research Electronic Data Capture)
• Used to create web based forms and manage
databases to support data capture and
surveys for research studies.
• Over 2200 users across campus and externally
UI BioShare
• Integrated bio-specimen repository
• Centralized and standardized governance
– Team
– Data standards
– Workflows
• Integration with EPIC
• Implementation
underway available for General use in 2015
Placement at the University of Iowa
TPC
(CaTissue)
ICTS Genetics
(Progeny)
Existing
Databases
UI Biobank
(Progeny)
UI BioShare
OBGYN
Johnson
(Access)
EPIC
EHR & Research
Module Data
SCI-Link
SCI Link
• Tool developed by ICTS BMI for managing study specific data for
multiple studies under a single umbrella so that:
• Data is distributed in a controlled environment
• PHI is centrally managed
• PHI is centrally secured
• Distribution of patient population can be centrally monitored
• Data can be governed and standardized
• Evaluation of studies can be done centrally to know research community
and its spread
– Type of studies,
– Size of studies
– Collaboration
– Patient population
XNAT
• XNAT is an open-source software platform for
organizing, accessing, and sharing data
associated with medical imaging
• Approx. 350 projects used by Ophthalmology,
Psychiatry etc.
Growth: 2010 - 2014
XNAT
Instance
Server
Primary Users
XNAT
Projects
RPACS
rpacs.icts
General
Research
255
220
3.3TB
174GB
120 sessions
Predict-HD
xnat.predict-hd
Psychiatry
57
57
3.1TB
67GB
60 sessions
EYEXNAT
eyexnat.iibi
Ophthalmology
27
26
12.1TB
44GB
20 sessions
HDNI
xnat.hdni
Psychiatry
4
4
.65TB
2076GB
19.1TB in use
HDNI
Project PIs
known
21.5TB available
(variable)
1.9TB/6mo. growth
Storage (TB)
4
4
300
3
3
0
Avg. Session Growth
(6mo.)
20
RPACS
250
Avg. Storage
Growth (6mo.)
Project Count
EYEXNAT
350
Storage
Occupation
4
0.267
0.292
27
22
20
15
15
0.23
7
0.2
5
12.317
200
12.456
HDNI
0
0
246
205
0
100
0
7.317
213
50
36
0 1
Jul-10
36
Jan-11
Jul-11
0
0.314
5
94
40
40
Jan-12
RPACS
7.566
Predict-HD
0.117
184
115
0
EYEXNAT
10
229
0
150
255
42
Jul-12
43
Jan-13
54
Jul-13
57
Jan-14
57
0
0
0.035
0.024
0
Jul-10
0
0
0
0
2.128
0.597
2.48
2.673
2.88
2.968
2.28
2.586
1.379
1.15
0.764
Jan-11
1.746
2.108
2.305
2.385
2.465
2.565
Jul-11
Jan-12
Jul-12
Jan-13
Jul-13
Jan-14
Other Services
• Honest Broker Data Extraction
– Study specific data extraction (Honest broker
Services)
• Data Request form
• IRB needed
• Complex inclusion/exclusion criteria
• IRB / Grant application
• Letter printing and approaching patients
• Use of Epic for Research
Use of Epic for Research
• Research studies in Epic
– Setting up new studies
– Transferring existing studies in Epic
– Setting up Best Practice Advisories (BPA’s)
• Analysis
– BPA Effectiveness (Pre vs post Epic)
• Predictive modeling
UI Use Case- INSPPIRE
INSPPIRE
– Goal
• Setup an International
study across 14 sites
• Integration and analysis
of data
– Method:
• REDCap for patient
survey and other data
collection
*Design and Implementation of INSPPIRE (International Study Group of Pediatric Pancreatitis: in Search for a Cure). (Journal of
pediatric gastroenterology and nutrition (Impact Factor: 2.18). 05/2014; DOI: 10.1097/MPG.0000000000000417)
*http://www.medicine.uiowa.edu/pediatrics/insppire/
UI Use Case – BPA Analysis
• BPA Analysis (Epic UGM talks)
– Comprehensive Approach to DVT/PE Decision Support. EPIC UGM
(Sept 2013).
– Goal
Patient at Risk
Prescribe XX Rx
• Reduce DVT/PE cases
• Monitor if physician’s followed BPA’s
• Change in DVT/PE after BPA implementation
– Method
Patient at Risk
• EPIC BPA’s
DO NOT Prescribe
X
Patient at Risk
Prescribe XX Rx
Ignored BPA’s
XX Rx
UI USE Case: Patient Centered Outcome Research Institute(PCORI)
Greater Plains Collaborative (GPC)
Network:
1. KS, the University of Kansas Medical Center
(KUMC)
2. MO, Children’s Mercy Hospital
3. IA, University of Iowa Healthcare
4. WI, the University of Wisconsin - Madison; the
Medical College of Wisconsin; and Marshfield
Clinic
5. MN, the University of Minnesota Academic
Health Center
6. NE, the University of Nebraska Medical Center
7. TX, the University of Texas Health Sciences
Center at San Antonio and the University of
Texas Southwestern Medical Center
Focus areas:
Clinical Data Research Networks (CDRNs)
Patient Powered Research Networks (PPRNs)
*PCORI Structure: http://www.pcori.org/blog/how-pcori-is-marking-national-health-it-week/
1. Breast Cancer
2. Amyotrophic Lateral Sclerosis (ALS)
3. Obesity
http://www.gpcnetwork.org/
UI Use Case
• OBGYN
– Collection of a lifetime: A practical approach to developing a
longitudinal collection of women's healthcare biological samples.
European Journal of Obstetrics & Gynecology and Reproductive
Biology 01/2014; DOI: 10.1016/j.ejogrb.2014.05.023
– Goal
• Setup Maternal Fetal Tissue Bank
– Method
• SCI-Link
Web-Links
•
Request for tool and data use agreement signup
– https://www.icts.uiowa.edu/data-approval/index.html
•
Data request form (Honest Broker Services for getting study specific data)
– http://j.mp/oq22dJ
•
I2B2
– http://i2b2.icts.uiowa.edu/
•
CDR Explorer and StarMaker
– https://hedi.healthcare.uiowa.edu/CDR/ICTS/
•
REDCap
– https://redcap.icts.uiowa.edu
– https://redcap.icts.uiowa.edu/redcap/index.php?action=training
•
SCI-Link
– https://scilink.icts.uiowa.edu/
•
TCGA
– https://research.icts.uiowa.edu/compass
– http://cancergenome.nih.gov/abouttcga/overview
•
Other Tools
– SPARC ( Service Management tool - Coming up..)
– UI BioShare (Coming up..)
Acknowledgements
•
•
•
•
•
•
CTSA Grant- NIH 2 UL TR000442-06
Carver College of Medicine
Health Care Information Systems (HCIS)
Park Street Solutions Company
Department of Obstetrics and Gynecology
ICTS Team