adoption over the years johns hopkins university matthew marcetich johns hopkins university school...
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Adoption Over the YearsJohns Hopkins University
Matthew MarcetichJohns Hopkins University School of Medicine Institute for Clinical and Translational Research (ICTR)
Acknowledgements
Dan Ford – Vice Dean for Clinical ResearchMark Donowitz – GI Hopkins Conte PI/PDJim Potter – GI TREC PI/PDDiana Gumas – IT DirectorPam Murray – IT ManagerJoe DiMaggio – IT ManagerBob Lange – Software EngineerJen Parks – Software EngineerMatthew Marcetich – Domain Support
About Johns Hopkins
• Support for OpenSpecimen from JHU ICTR– Dan Ford: JHU SOM Vice Dean for Clinical Research– Service provided to JHU SOM Investigators
• Current biobanking landscape– Freezerworks– StarLims– LabMatrix– MDLogix– MS Excel, MS Access
Overview
• caTissue v1.2 Pilot – GI Translational Research Enhancement Core (TREC)
• caTissue Plus v3.0 Upgrade
• OpenSpecimen v1.0 Upgrade (in Progress)
Timeline
Pre September, 2011: JHU GI Biobank involved with caTissue since Persistent Systems
2011
September, 2011: caTissue v1.2 pilot
July, 2013: Upgrade to caTissue Plus v3.0
August – October, 2014: OS v1.0 Regression Testing
2012 2013 2014 2015
caTissue v1.2 Pilot caTissue Plus v3.0 OS v1.0
caTissue v1.2 Pilot
GI Translational Research Enhancement Core (TREC)
Specific Aims of the TREC
To support center members with all aspects of biospecimen collection including harvest, annotation, processing, storage, management, distribution, and ethical use.
To ensure that all specimens collected are of the highest quality through strict adherence to the latest Best Practices and Standard Operating Procedures.
To enhance the value of specimens for current and future research through annotation of pertinent preclinical (research) and clinical data.
Jim Potter, [email protected]
caTissue v1.2 Pilot, Continued
GI Translational Research Enhancement Core (TREC)
Specific Aims of the TREC
To ensure that the PI has primary ownership over all tissues directly related to his/her active study.
To provide fair and impartial access to specimens owned by the GI-TREC to Core Center investigators.
To educate and guide investigators conducting translational research requiring patient registries and associated databases (REDCap, CRMS, and i2b2 (Informatics for Integrating Biology and the Bedside).
Jim Potter, [email protected]
Hypothesis
Collection Protocol created on QA
server
Collection Protocol amended and
finalized with TREC
Final Collection Protocol created in
Prod
Specimen collection and storage begins
caTissue/OSUser meets with TREC to discuss
collection
Best Practices and SOPs
Example: use of sitagliptin to block DPP-4
for GLP1 assay
GI TREC Workflow
GI TREC: Specimen Collection Factors
• Purpose of the Biorepository (Hypothesis Driven)• Best Practices/SOPs
– The Scientific Foundation for Research– ISBER (International Society for Biological and Environmental
Repositories)• Consent• Governance / Oversight• Funding Support• Hardware• Software/Audit/Security (21 CFR part 11)• Enterprise Biomedical Informatics Systems• Personnel (FTE)
Jim Potter, [email protected]
caTissue v1.2 Pilot, Continued
First Two TREC Studies – Bulk Upload
1. Non-Alcoholic Fatty Liver Disease (NAFLD)– 10,000 specimens, 305 participants– Longitudinal study (0-8yr), all specimens collected– Freezer reorganization – 3 months– Snehil Gupta
caTissue v1.2 Pilot, Continued
2. Legacy Study: Barrett’s Esophagus– 3,500 specimens, 400 participants– Ongoing recruitment and specimen collection– Dynamic Extension Forms
• Participant Questionnaire• Specimen Pathology
– 6 months– Strength of dynamic extensions and queries, need for
better approach of surgical pathology data
Query Application: Barrett’s Esophagus Study
caTissue v1.2 Pilot: Summary
• September, 2011 to August, 2013
• 6 studies, 20,000 specimens
• Breadth of users
• To date (GI TREC):– Five major grants: R01, K08, ADA, ABMRF, ACS– 72 publications– Collaborations: GIM, Peds Allergy
caTissue Plus v3.0 Upgrade
• Significant improvements in usability– Quicker response from UI in general– Improved Query module– Creation of Event Points from Participant Page
• August, 2013 to present
• Regression Testing
• Major Bulk Upload: 70k specimens
caTissue Plus v3.0 Upgrade, Continued
Organizing Queries by Folder, Sharing Queries
caTissue Plus v3.0 Upgrade, Continued
Indexed Queries
OS v1.0 Upgrade
• Three rounds of regression testingAugust – October, 2014
• In use on JHU’s Development environment• Go-Live Q1 2015
• Show of hands…– Who has upgraded to OS v1.0?– Who plans to upgrade?– Maybe?
OS v1.0 Upgrade, Continued
Description Priority Reported Resolved Verified
Issue 1Received Dates and Collection Dates were swapped for one collection protocol
High 9/25/14 10/2/14 10/6/14
Issue 2Error message when using Create Parent Specimen bulk upload template
High 8/29/14 9/25/14 10/2/14 10/6/14
Issue 3 Unable to edit the specimen label format within saved CP Medium 8/29/14 9/1/14 9/25/14
CommentQuery results exported from Production (Plus v3.0) have a different format than those from Development (OS v1.0).
High 9/25/14
9/26/14 - Krishagni offered to implement an option to toggle between query layouts in OS v1.1
TBD
Commentsql queries appear to be more robust than Audit Report UI (new feature in OS v1.0)
n/a 8/29/14 n/a n/a
Work in Progress
• Surgical Pathology Reports
• Simplified Data Entry Screen
• Potential Use of SPREC codes– “Standard Preanalytical Code” (ISBER)– Show how specimen was collected– Annotate quality of specimen
• Increase User Base across JHU SOM
Lessons Learned
caTissue v1.2 Plus v3.0 OpenSpecimen v1.0
Pros• Dynamic
extensions • Robust advanced
queries
• Improved advanced query module
• Improved UI response time
• Subtle UI improvements in storage module
• Less training time for advanced queries
• Revamped dynamic extensions
• Flexible changes to collection protocols
• REST APIs
"Cons"
• High leaning curve for advanced queries
• Buggy• Relatively slow UI
response
• Similar "feel" to caTissue v1.2
• Some bugsTBD :)
Summary
• caTissue v1.2 Plus v3.0 OS v1.0• Team Effort• Use of “stock” code
As of December 4, 2014Users 155
Collection Protocols 13Specimens 94,835Groups 5Participants 5,725
Prospective New Users/Groups 5
Any Questions?
Johns Hopkins University School of Medicine Institute for Clinical and Translational Research
Jim Potter (Faculty Adviser)[email protected]
Pam Murray (Manager)[email protected]
Bob Lange (Developer)[email protected]
Matthew Marcetich (Domain Support)[email protected]