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Adoption and Use of caTissue Suite in a Multi-Repository Academic Environment

Adoption and Use of caTissue Suite in a Multi-Repository Academic Environment. ?. Biospecimen Banking has Evolved Highly Complex Informatics Requirements. 1990 . 2010 . Biospecimens Managed with caTissue . As of Feb 16, 2010 (pending follow up with ~10 more Grid instances).

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Adoption and Use of caTissue Suite in a Multi-Repository Academic Environment

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  1. Adoption and Use of caTissue Suite in a Multi-Repository Academic Environment

  2. ? Biospecimen Banking has Evolved Highly Complex Informatics Requirements • 1990 • 2010

  3. Biospecimens Managed with caTissue As of Feb 16, 2010 (pending follow up with ~10 more Grid instances) = specimens on the grid; = specimens available to internal researchers, but not on the grid; = specimens in caTissue, no information if they are grid-accessible

  4. caTissue Suite v1.2 • 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 • New features include performance and usability enhancements • Multiple sources of electronic and human support

  5. caTissue Suite End Users • Targeted Users: • Biospecimen resource staff who want to track and store data about their biospecimen collection, inventory, and distribution. • Scientists who want to search for biospecimens and associated data for their translational research projects. • Core Functions / Modules • Administration: Create and edit users, protocols, and storage systems associated with a biospecimen inventory. • Biospecimen: Create and edit data concerning participants and their corresponding biospecimens. • Query: Identify biospecimens and their data based upon one or more selection criteria.

  6. Types of Data Tracked by caTissue Suite Clinical Data PARTICIPANT (Patient) COLLECTION PROTOCOL (CP) (Protocol) PARTICIPANT PROTOCOL REGISTRATION (PPI) (Study Registration) DISTRIBUTION PROTOCOL (DP) (Study) SPECIMEN COLLECTION GROUP (SCG) SPECIMEN QA and Availability Data Aliquot Derivative Pathology Data and Reports

  7. Supporting Data Entry Workflows for Generic Biospecimen Banking • Pre-operative consent is obtained and operative frozen tissue specimens (tumor and non-malignant) are collected from surgical discards. Consent Patient Register to Protocol Provide Diagnosis Provide Operative Date Receive Specimen Store Specimen Collect Specimen CRA Pathologist Biobank TIME

  8. Support for ‘High-Throughput’ Banking of Cells and Biofluids • A tube of whole blood is collected which is then processed and aliquoted into individual components, as per a unique SOP for that protocol. Plasma Aliquot Collect Whole Blood WBC Aliquot STORE

  9. Support for Import and De-Identification of Surgical Pathology Reports and Block Archive • Pathology report texts that are loaded into the system are the basis for a search and block request. Blocks are requested, deidentified, sectioned, and distributed for a study. Retrieve requested blocks from pathology and accession as new specimens Path Report Loading Search for cases based on path report Cut slides and distribute

  10. Operation of Multiple, Independent Repositories Using Role-Based Access User Roles Role Privileges + Operation of Multiple Repositories / Protocols in a Single Instance Defining Users

  11. Participant Consent Tracking by Protocol at the Individual Specimen Level Registering Consent Updating Consent Validating Consent before Distribution

  12. Tracking Biospecimen Collection and Receipt Parameters Specimen Collection Group (Applies to all specimens collected in the group) When / who collected from the participant: Surgeon Clinician CRA Pathologist When / who received the specimen: Pathologist Pathology Assistant Biospecimen Bank Staff

  13. Tracking Specimen Collection Timepoints Time point with specimens collected (gold) Collected specimen (purple) Status of collection time point Pending or not collected specimen (black)

  14. Tracking Specimen Processing Events Recordable specimen events Recording when / who / how specimen was frozen

  15. Monitoring Biospecimen QA Tissue Specimen Review Event- Who / When Details

  16. Biospecimen QA Reporting QUERY REPORT Filter based on: RNA / DNA Fixed / Frozen Tissue Tissue Site Collector Collection Date Collection Site Processing Technician ANALYZE Distribution of RNA RIN Scores for Frozen Tissue Specimens

  17. caTissue Suite Pathology Annotation Dynamic Extensions (DE) Tool caTissue Suite Pathology Annotation Form CAP Cancer Checklist

  18. Creation and Management of Custom Searches and Result Views Customized Query Results View Saved Query Management and Keyword Search Bar

  19. Use of New Bulk Operations Tool to Migrate Legacy Data to caTissue 1. Participants 2. SCGs 3. Specimens caTissue Legacy “Tissue Log”

  20. Use of New Bulk Operations Tool to Perform Batch Data Import from External Data Sources

  21. Data Sharing and Interoperability through caGrid caTissue 2 caTissue 3 caTissue 4 caTissue Installation 1 caGrid Search Repository A Repository B Repository C Collection Protocols caB2B caTissue Search (Web Interface)

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

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

  24. caTissue at Washington University School of Medicine An expanding network of integrated repositories and biospecimen laboratories with associated users, protocols, and biospecimens

  25. The caTissue Biospecimen Network (2010) UK Netherlands Japan India Australia Testing Production Grid-enabled Production 48 institutions 10,000 specimens 13 institutions 470,000 specimens 5 institutions 716,000 specimens

  26. caTissue Resources • The TBTT KC site- • https://cabig-kc.nci.nih.gov/Biospecimen/KC • Log on and try out the demo site for caTissue Suite v1.2- http://catissuesuitetest.wustl.edu/cas/login • View narrated video overviews of the tool and installation- • https://cabig-kc.nci.nih.gov/Biospecimen/KC/index.php/Video_Archive • 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/

  27. 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

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