1. Adoption Over the Years Johns Hopkins University Matthew Marcetich Johns Hopkins University School of Medicine Institute for Clinical and Translational Research (ICTR)

2. Acknowledgements Dan Ford – Vice Dean for Clinical Research
Mark Donowitz – GI Hopkins Conte PI/PD
Jim Potter – GI TREC PI/PD
Diana Gumas – IT Director
Pam Murray – IT Manager
Joe DiMaggio – IT Manager
Bob Lange – Software Engineer
Jen Parks – Software Engineer
Matthew Marcetich – Domain Support

3. 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

4. Overview
caTissue v1.2 Pilot – GI Translational Research Enhancement Core (TREC)
caTissue Plus v3.0 Upgrade
OpenSpecimen v1.0 Upgrade (in Progress)

5. Timeline August – October, 2014: OS v1.0 Regression Testing
September, 2011: caTissue v1.2 pilot
July, 2013: Upgrade to caTissue Plus v3.0
2011
2012
2013
2014
2015
caTissue v1.2 Pilot
caTissue Plus v3.0
OS v1.0
Pre September, 2011: JHU GI Biobank involved with caTissue since Persistent Systems

6. 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,

7. 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,

8. Best Practices and SOPs User meets with TREC to discuss collection
Hypothesis
GI TREC Workflow
Best Practices and SOPs
caTissue/OS
User meets with TREC to discuss collection
Collection Protocol created on QA server
Example: use of sitagliptin to block DPP-4 for GLP1 assay
Collection Protocol amended and finalized with TREC
Final Collection Protocol created in Prod
Specimen collection and storage begins

9. 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,

10. caTissue v1.2 Pilot, Continued
First Two TREC Studies – Bulk Upload
Non-Alcoholic Fatty Liver Disease (NAFLD)
10,000 specimens, 305 participants
Longitudinal study (0-8yr), all specimens collected
Freezer reorganization
3 months
Snehil Gupta

11. caTissue v1.2 Pilot, Continued
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

12. Query Application: Barrett’s Esophagus Study

13. 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

14. 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

15. caTissue Plus v3.0 Upgrade, Continued
Organizing Queries by Folder, Sharing Queries

16. caTissue Plus v3.0 Upgrade, Continued
Indexed Queries

17. OS v1.0 Upgrade Three rounds of regression testing
August – 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?

18. OS v1.0 Upgrade, Continued Description Priority Reported Resolved
Description
Priority
Reported
Resolved
Verified
Issue 1
Received Dates and Collection Dates were swapped for one collection protocol
High
9/25/14
10/2/14
10/6/14
Issue 2
Error message when using Create Parent Specimen bulk upload template
8/29/14 9/25/14
Issue 3
Unable to edit the specimen label format within saved CP
Medium
8/29/14
9/1/14
Comment
Query results exported from Production (Plus v3.0) have a different format than those from Development (OS v1.0).
9/26/14 - Krishagni offered to implement an option to toggle between query layouts in OS v1.1
TBD
sql queries appear to be more robust than Audit Report UI (new feature in OS v1.0)
n/a

19. 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

20. Lessons Learned caTissue v1.2 Plus v3.0 OpenSpecimen v1.0 Pros
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 bugs
TBD :)

21. Summary caTissue v1.2  Plus v3.0  OS v1.0 Team Effort
Use of “stock” code
As of December 4, 2014
Users
155
Collection Protocols 13
Specimens
94,835
Groups 5
Participants
5,725
Prospective New Users/Groups

22. Any Questions?
Johns Hopkins University School of Medicine Institute for Clinical and Translational Research Jim Potter (Faculty Adviser) Pam Murray (Manager) Bob Lange (Developer) Matthew Marcetich (Domain Support)