Developing an EnterpriseScale Biobanking System in an Academic Environment

1
Developing an Enterprise-Scale Biobanking System
in an Academic Environment
Mark A. Watson, M.D., Ph.D. Dept. Pathology and
Immunology
2
The Evolution of Biospecimen Banking

• 1988

• 2008

3
WUMC Biobanking pre- 1998

• Scientists with individual biospecimen banking
  efforts
• Unregulated use of clinical paraffin tissue
  blocks
• Variable levels of informed consent and
  regulatory practices
• Issues of ownership
• Variable levels of biospecimen annotation
• Variables levels of biospecimen processing / QA
• Specimens often lost to follow-up
• Few mechanisms for biospecimen sharing

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4
WUMC Biobanking 1998

• Cancer Center Tissue Procurement Core
• Collection of tumor tissue specimens for future
  research use
• Support for the collection of biospecimens from
  cancer clinical trials
• Standardized protocols and data collection
• Biospecimen resources made available to a larger
  number of investigators
• Some investigators continue to maintain
  individual biospecimen banking efforts

SCC Tissue Procurement Core
5
WU Laboratory for Translational Pathology
Organization
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WUMC Biobanking 1998 - 2008

• Scope of Cancer Core extended for other funded
  efforts
• Use of specimens for several high-profile
  studies
• Efforts made to meet emerging NIH guidelines
  for biospecimen banking
• Fewer investigators maintain individual
  biospecimen banking efforts
• Centralized facility not scalable with available
  resources
• Space (Lab and storage)
• Personnel
• Informatics system outgrown by operations

SCC TPF ACOSOG CSB P30 Awards CTSA Award
Neuroscience Dept. Banks
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The Rationale for caTissue

• Many specimen resource centers have ad hoc,
  inadequate, and/or closed source specimen banking
  / tracking informatics systems.
• Many specimen resource centers have large,
  sophisticated legacy systems that still must be
  mapped to a common object model and data
  elements to make them interoperable.
• Most existing informatics systems are not
  modular and can not easily accommodate the
  expanding functionality of specimen resource
  centers.
• Different user classes (scientists, clinicians,
  specimen bank personnel) require remote,
  controlled access to different data types for
  different purposes.
• Data representation may be complex and
  hierarchical.
• Many specimen resource centers have common
  functionality, but each has unique workflows and
  end-user requirements.

8
caTissue General Requirements

• An informatics system for biospecimen data
  related to storage, processing, QA, tracking, and
  annotation.
• An ability to store complex and hierarchical
  biospecimen tracking data with high granularity.
• Use of data element standards.
• A user interface that can accommodate varying
  workflows present at diverse biospecimen resource
  centers, but that allows for simple, intuitive
  data entry.
• Alternate functionality for different user
  classes (scientists, clinicians, specimen bank
  personnel).
• An application that can be rapidly deployed and
  brought into production at any biospecimen
  resource center.
• Implementation of good software design practices
  that includes iterative development based on
  end-user feedback.

9
Biospecimen Banking in Multi-Site Trials
Process Store
Collect Ship
Collection Site
Specimen Bank
Investigative Lab
Distribute
Register Participant
Accession Specimen Create Specimen Distribute
Search
Biospecimen Inventory
Add Protocol Add User Add Site
Coordinating Center
Trials Database
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Biospecimen Banking in Multi-Site Trials
Biospecimen Bank Personnel
Study Scientist
Protocol PI and Coordinators
Bank
Study
Protocol
Participant
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caTissue Suite v1.1

• Web-based application for biospecimen
  information management
• Professional approach to software design
• Open source / Open access (Free)
• Iterative development cycle (Always improving)
• Flexible to meet the needs of varying biobank
  environments
• Multiple sources of electronic and human support

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caTissue Suite- Data Sharing
caTissue 2
caTissue 3
caTissue 4
caTissue Installation 1
caGrid Search
Repository A
Repository B
Repository C
Collection Protocols
caTissue Search (Web Interface)
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caTissue Suite- Data Sharing
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caTissue Suite Support

• Illustrated manuals for technical and biobanking
  staff

• Web-based, interactive training tools

• Web- and human-based Knowledge Center resources

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https//cabig-kc.nci.nih.gov/Biospecimen/KC
caBIG Tissue Bank Knowledge Center
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Community Portal

• Foster the exchange of ideas and best practices
  across institutions

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The Potential caTissue Community 2009
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WUMC Biobanking 2009
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WUMC Biobanking Beyond 2009

• Maintain a Central Repository
• Pathology biospecimen collection effort
• New / small collections
• Assumption of legacy collections
• Integrate / Harmonize All Other Repositories
  Across Campus
• Common Informatics (wuTissue)
• Common SOPs
• Common regulatory practices
• Publicize and Facilitate Resource Sharing and
  Utilization

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caTissue Resources

• The TBTT KC site-
• https//cabig-kc.nci.nih.gov/Biospecimen/KC/index.
  php/Main_Page
• Log on and try out the demo site for caTissue
  Suite v1.1- http//catissue.wustl.edu8080/catissu
  ecore
• View a narrated video overview of the tool and
  installation-
• https//cabig-kc.nci.nih.gov/Biospecimen/KC/index.
  php/Tissue/Biospecimen_Banking_and_Technology_Tool
  sCurrent_events
• Practice learning how to use the tool on the
  E-learning portal-http//cabigtrainingdocs.nci.nih
  .gov/caTissue/index.html
• Browse through the on-line manual-
• https//cabig-kc.nci.nih.gov/Biospecimen/KC/index.
  php/CaTissue_1.1_User_Manual
• For additional questions, post them to the TBTT
  KC Forum-
• https//cabig-kc.nci.nih.gov/Biospecimen/forums/

21
Acknowledgements
Rakesh Nagarajan MD, PhD Mark A. Watson MD,
PhD Dave Mulvihill Vicky Holtschlag Amy Brink
Aniket Pandit Ashish Gupta Deepti
Shellar Ganesh Naikwade Komal Gulati Poornima
Govindrao Prafull Kadam Sachin Lale Sayali
Salodkar Supriya Dankh Srikanth Adiga Vaishali
Khandelwal Vijay Pande Virender Mehta Rushikesh
Subedar Rajesh Patil Kalpana Thakur Snehil
Gupta Madhumita Shrikhande Abhishek Mehta Preeti
Munot