InterSPORE Biomarker Study Prostate SPORE Informatics

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Inter-SPORE Biomarker StudyProstate SPORE
Informatics

• Kevin Regan
• Memorial Sloan-Kettering Cancer Center

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Kevin Regan

• Vision
• Project History and Statement of Work
• Execution of Statement of Work
• Institutional Diversity

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IPBS Informatics Vision

• Establish a web-accessible catalog of specimens
  available from all the Prostate SPORE
  biorepositories
• allow catalogued specimens to be browsed,
  searched, requested, and approved online
• allow the manual or automated upload of IPBS
  Specimen Data consistent with the common data
  elements (CDEs) for distribution of specimen data
  to approved requestors
• interface with the installations of caTISSUE
  Suite at each Prostate SPORE
• tracks distributions of specimens and associated
  data
• Make it work!

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Project History

• Ongoing project since 2004
• Initially part of the National Biospecimen
  Network (NBN)
• Assessment of specimen management practices at
  each site
• IPBS Protocol was the motivation for this effort
• Project team looked to national efforts for
  guidance and found caBIG
• Developed a short term solution (pTracker) to
  allow the protocol to move forward with accrual
• Initiated a contract with the NCI to implement
  caTissue

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Implementation

• Weekly web conferences
• Review progress
• Divide workload
• Share experience and lessons learned
• Face to Face meetings
• Larger blocks of time to focus on specific tasks
• Generally scheduled around other meetings
• One meeting in St. Louis
• Maintain documentation in one central repository
  GForge
• Docs http//gforge.nci.nih.gov/docman/?group_id1
  59
• Files http//gforge.nci.nih.gov/frs/?group_id159
  
• Wiki http//gforge.nci.nih.gov/plugins/wiki/index
  .php?id159typeg

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Statement of Work

• Milestone 1
• Use Cases for Multi-centered specimen management
• System Requirements
• Evaluate IPBS Protocol requirements against the
  data elements in caTissue
• Milestone 2
• Deployment Plan
• Deployment of caTissue Suite
• UML domain object model for CDEs (IPBS
  requirements)
• Registered Model in caDSR
• Extended local instance of caTissue Suite
• Milestone 3
• Data migration plan
• Importing of Data
• Test Plan
• Testing
• Demonstration of adoption
• Adoption Report and Lessons Learned

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Statement of Work Extension

• Milestone 4
• Finalize UML models for category 3
• Generate XMI for category 3
• Deploy current build of caTissue Suite 1.0 at one
  site
• Extend Suite 1.0 using DE to load XMI for
  category 3
• Capture SOP for deployment of caTissue production
  instance and loading XMI
• Update test cases
• Milestone 5
• Set up caTissue Suite 1.0 at each site
• Extend with XMI for category 3 at each site
• Migrate relevant data from pTracker into Suite
  1.0
• Define 5 queries to demonstrate data sharing
• Adapt script to submit 5 queries against all live
  sites
• Execute query script
• Test
• Adopter report
• Lessons learned

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Intangible Milestones

• Established important and effective working
  relationships
• Maintained team focus and effort over a long
  period of time
• Provided valuable feedback to the caTissue
  development team
• Continue to make progress towards IPBS goals
• Identified issues that will be faced by any
  institutions collaborating and sharing patient
  data
• Continue to engage the Tissue Bank Workspace

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Institutional Diversity

• Team members
• Project management
• Software development
• Statistics
• Bioinformatics
• Hosting Environment
• Institutional security reviews
• Direct access to servers
• Operating System Windows, Linux, and Solaris
• Database MySQL and Oracle (numerous Versions)
• caTissue Implementation
• Primary Repository
• Mechanism for sharing data