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

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Presentation on theme: "Adoption and Use of caTissue Suite in a Multi-Repository Academic Environment."— Presentation transcript:

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

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 PARTICIPANT (Patient) PARTICIPANT PROTOCOL REGISTRATION (PPI) (Study Registration) COLLECTION PROTOCOL (CP) (Protocol) SPECIMEN COLLECTION GROUP (SCG) SPECIMEN DISTRIBUTION PROTOCOL (DP) (Study) Aliquot Derivative Clinical Data Pathology Data and Reports QA and Availability Data

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

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

9 Support for Import and De-Identification of Surgical Pathology Reports and Block Archive Path Report LoadingSearch for cases based on path report Retrieve requested blocks from pathology and accession as new specimens Cut slides and distribute 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.

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

11 Participant Consent Tracking by Protocol at the Individual Specimen Level Registering ConsentUpdating 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 Status of collection time point Time point with specimens collected (gold) Collected specimen (purple) Pending or not collected specimen (black)

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

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

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

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

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

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

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

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

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) TestingProductionGrid-enabled Production 48 institutions 10,000 specimens 13 institutions 470,000 specimens 5 institutions 716,000 specimens Japan India UK Netherlands Australia

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 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 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 Aniket PanditAshish GuptaDeepti Shellar Ganesh NaikwadeKomal GulatiPoornima Govindrao Prafull KadamSachin LaleSayali Salodkar Supriya DankhSrikanth AdigaVaishali Khandelwal Vijay PandeVirender MehtaRushikesh Subedar Rajesh PatilKalpana ThakurSnehil Gupta Madhumita ShrikhandeAbhishek MehtaPreeti Munot Rakesh Nagarajan MD, PhD Mark A. Watson MD, PhD Dave Mulvihill Vicky Holtschlag Amy Brink


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