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Adoption Over the Years Johns Hopkins University Matthew Marcetich Johns Hopkins University School of Medicine Institute for Clinical and Translational.

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Presentation on theme: "Adoption Over the Years Johns Hopkins University Matthew Marcetich Johns Hopkins University School of Medicine Institute for Clinical and Translational."— Presentation transcript:

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 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 20142015 caTissue v1.2 Pilot caTissue Plus v3.0 OS v1.0

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, jpotter@jhmi.edu

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, jpotter@jhmi.edu

8 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/OS User meets with TREC to discuss collection Best Practices and SOPs Example: use of sitagliptin to block DPP-4 for GLP1 assay GI TREC Workflow

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, jpotter@jhmi.edu

10 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

11 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

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 DescriptionPriorityReportedResolvedVerified Issue 1 Received Dates and Collection Dates were swapped for one collection protocol High9/25/1410/2/1410/6/14 Issue 2 Error message when using Create Parent Specimen bulk upload template High 8/29/14 9/25/14 10/2/1410/6/14 Issue 3 Unable to edit the specimen label format within saved CP Medium8/29/149/1/149/25/14 Comment Query results exported from Production (Plus v3.0) have a different format than those from Development (OS v1.0). High9/25/14 9/26/14 - Krishagni offered to implement an option to toggle between query layouts in OS v1.1 TBD Comment sql queries appear to be more robust than Audit Report UI (new feature in OS v1.0) n/a8/29/14n/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 v1.2Plus v3.0OpenSpecimen 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 Users155 Collection Protocols13 Specimens94,835 Groups5 Participants5,725 Prospective New Users/Groups5

22 Any Questions? Johns Hopkins University School of Medicine Institute for Clinical and Translational Research Jim Potter (Faculty Adviser) jpotter@jhmi.edu Pam Murray (Manager) pmurray@jhmi.edu Bob Lange (Developer) rlangea@jhmi.edu Matthew Marcetich (Domain Support) mmarcet1@jhmi.edu


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