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

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

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 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

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

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

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

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

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

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

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 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?

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

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   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 :)

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

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