Adoption Over the Years Johns Hopkins University Matthew Marcetich Johns Hopkins University School...

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

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, 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).

Hypothesis

Collection Protocol created on QA

server

Collection Protocol amended and

finalized with TREC

Final Collection Protocol created in

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)

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

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

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)jpotter@jhmi.edu

Pam Murray (Manager)pmurray@jhmi.edu

Bob Lange (Developer)rlangea@jhmi.edu

Matthew Marcetich (Domain Support)mmarcet1@jhmi.edu

Adoption Over the Years Johns Hopkins University Matthew Marcetich Johns Hopkins University School...

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