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Biospecimen Banking has Evolved Highly Complex Informatics Requirements

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Presentation on theme: "Biospecimen Banking has Evolved Highly Complex Informatics Requirements"— 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
As of Feb 16, 2010 (pending follow up with ~10 more Grid instances) Dark green = specimens on the grid Light green = specimens available to internal researchers, but not on the grid Orange = specimens in caTissue, no information if they are grid-accessible Also note there are 10 other organizations indicated as having caTissue data on the grid, but no information on how much data was available in the latest update. = 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 Repositories / Protocols in a Single Instance
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 Validating Consent before Distribution
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 Saved Query Management and Keyword Search Bar
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 https://cabig-kc.nci.nih.gov/Biospecimen/KC 23

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- 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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