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

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Adoption and Use of caTissue Suite in a
Multi-Repository Academic Environment
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Biospecimen Banking has Evolved Highly Complex
Informatics Requirements

• 1990

• 2010

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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
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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

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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.

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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
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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
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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
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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
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Operation of Multiple, Independent Repositories
Using Role-Based Access
User Roles
Role Privileges

Operation of Multiple Repositories / Protocols in
a Single Instance
Defining Users
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Participant Consent Tracking by Protocol at the
Individual Specimen Level
Registering Consent
Updating Consent
Validating Consent before Distribution
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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
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Tracking Specimen Collection Timepoints
Time point with specimens collected (gold)
Collected specimen (purple)
Status of collection time point
Pending or not collected specimen (black)
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Tracking Specimen Processing Events
Recordable specimen events
Recording when / who / how specimen was frozen
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Monitoring Biospecimen QA
Tissue Specimen Review Event- Who / When
Details
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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
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caTissue Suite Pathology Annotation
Dynamic Extensions (DE) Tool
caTissue Suite Pathology Annotation Form
CAP Cancer Checklist
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Creation and Management of Custom Searches and
Result Views
Customized Query
Results View
Saved Query Management and Keyword Search Bar
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Use of New Bulk Operations Tool to Migrate Legacy
Data to caTissue
1. Participants
2. SCGs
3. Specimens
caTissue
Legacy Tissue Log
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Use of New Bulk Operations Tool to Perform Batch
Data Import from External Data Sources
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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)
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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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caTissue at Washington University School of
Medicine
An expanding network of integrated repositories
and biospecimen laboratories with associated
users, protocols, and biospecimens
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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
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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/

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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