1 / 21

Developing an Enterprise-Scale Biobanking System in an Academic Environment

Developing an Enterprise-Scale Biobanking System in an Academic Environment. Mark A. Watson, M.D., Ph.D. Dept. Pathology and Immunology. ?. The Evolution of Biospecimen Banking. 1988. 2008. WUMC Biobanking pre- 1998. Scientists with individual biospecimen banking efforts

phiala
Download Presentation

Developing an Enterprise-Scale Biobanking System in an Academic Environment

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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 ?

  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

  6. 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

  7. 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 Distribute Investigative Lab Register Participant Accession Specimen Create Specimen Distribute Search Biospecimen Inventory Add Protocol Add User Add Site Coordinating Center Trials Database

  10. Biospecimen Banking in Multi-Site Trials Biospecimen Bank Personnel Study Scientist Protocol PI and Coordinators Bank Study Protocol Participant

  11. 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

  12. 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)

  13. caTissue Suite- Data Sharing

  14. caTissue Suite Support • Illustrated manuals for technical and biobanking staff • Web-based, interactive training tools • Web- and human-based Knowledge Center resources

  15. https://cabig-kc.nci.nih.gov/Biospecimen/KC caBIG™ Tissue Bank Knowledge Center

  16. Community Portal • Foster the exchange of ideas and best practices across institutions

  17. The Potential caTissue Community 2009

  18. WUMC Biobanking 2009

  19. 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

  20. 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.edu:8080/catissuecore • 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_Tools:Current_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

More Related