Transcript View Presentation - Pathology Informatics 2015

Adoption and Use of caTissue
Suite in a Multi-Repository
Academic Environment
Biospecimen Banking has Evolved Highly
Complex Informatics Requirements
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Biospecimens in caTissue
Biospecimens Managed with caTissue
As of Feb 16, 2010 (pending follow up with ~10 more Grid instances)
1000000
100000
10000
1000
100
10
1
= specimens on the grid;
= specimens available to internal researchers, but not on the grid;
= specimens in caTissue, no information if they are grid-accessible
caTissue Suite v1.2
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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
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.
Types of Data Tracked by caTissue Suite
Clinical Data
PARTICIPANT
COLLECTION
PROTOCOL (CP)
(Patient)
PARTICIPANT
PROTOCOL
REGISTRATION (PPI)
(Protocol)
(Study Registration)
DISTRIBUTION
PROTOCOL (DP)
SPECIMEN
COLLECTION
GROUP (SCG)
Pathology Data
and Reports
(Study)
SPECIMEN
Aliquot
Derivative
QA and
Availability
Data
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
CRA
Collect Specimen
Pathologist
TIME
Receive Specimen
Store Specimen
Biobank
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
Support for Import and De-Identification
of Surgical Pathology Reports and Block
Archive
•
Path Report Loading
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.
Search for cases based
on path report
Retrieve requested
blocks from pathology
and accession as new
specimens
Cut slides and distribute
Operation of Multiple, Independent
Repositories Using Role-Based Access
User Roles
+
Role Privileges
Defining Users
Operation of Multiple
Repositories / Protocols
in a Single Instance
Participant Consent Tracking by Protocol
at the Individual Specimen Level
Registering Consent
Updating Consent
Validating Consent before Distribution
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
Tracking Specimen Collection Timepoints
Time point with specimens
collected (gold)
Collected specimen (purple)
Pending or not collected specimen (black)
Status of collection
time point
Tracking Specimen Processing Events
Recordable
specimen events
Recording when / who / how
specimen was frozen
Monitoring Biospecimen QA
Tissue Specimen Review Event- Who / When
Details
Biospecimen QA Reporting
QUERY
REPORT
30
Filter based on:
20
15
10
5
RIN
ANALYZE
Distribution of RNA RIN Scores for Frozen
Tissue Specimens
9.8
9.4
9
8.6
8.2
7.8
7.4
7
6.6
6.2
5.8
5.4
5
4.6
4.2
3.8
3
0
3.4
Samples
25
RNA / DNA
Fixed / Frozen Tissue
Tissue Site
Collector
Collection Date
Collection Site
Processing Technician
caTissue Suite Pathology Annotation
Dynamic Extensions (DE) Tool
caTissue Suite Pathology Annotation
Form
CAP Cancer Checklist
Creation and Management of Custom
Searches and Result Views
Customized Query
Results View
Saved Query Management and Keyword Search Bar
Use of New Bulk Operations Tool to
Migrate Legacy Data to caTissue
1. Participants
2. SCGs
3. Specimens
caTissue
Legacy “Tissue Log”
Use of New Bulk Operations Tool to
Perform Batch Data Import from External
Data Sources
Data Sharing and Interoperability through
caGrid
caTissue
2
caTissue
Installation
1
caTissue
3
caGrid Search
Repository
A
Repository
B
Repository
C
Collection
Protocols
caTissue Search (Web Interface)
caB2B
caTissue
4
caTissue Suite Support
 Illustrated
manuals for
technical and
biobanking staff
 Web- and human-based
Knowledge Center
resources
 Web-based,
interactive
training tools
caBIG™ Tissue Bank Knowledge Center
https://cabig-kc.nci.nih.gov/Biospecimen/KC
caTissue at Washington University
School of Medicine
Biorepository
SCC Tissue Procurement Core
ADRC Neuropathology Bank
Kidney Disease Bank
ADRC Biomarker Core
ADRC Genetics Core
GI Disease Bank
Endometrial CA Bank
Cervical CA Bank
GI Serum Bank
Urology Biospecimen Bank
PI
Watson
Carins
Jain
Holtzman
Goate
Li
Goodfellow
Rader
Linehan
Andriole
Status
Done
Done
Done
Developing
Developing
Developing
Developing
Developing
Developing
Planning
An expanding network of integrated repositories and biospecimen
laboratories with associated users, protocols, and biospecimens
The caTissue Biospecimen Network
(2010)
UK
Netherlands
Japan
India
Australia
Testing
Production
Grid-enabled Production
48 institutions
13 institutions
5 institutions
10,000 specimens
470,000 specimens
716,000 specimens
caTissue Resources
• The TBTT KC sitehttps://cabig-kc.nci.nih.gov/Biospecimen/KC
• Log on and try out the demo site for caTissue Suite v1.2http://catissuesuitetest.wustl.edu/cas/login
• View narrated video overviews of the tool and installationhttps://cabig-kc.nci.nih.gov/Biospecimen/KC/index.php/Video_Archive
• Practice learning how to use the tool on the E-learning portalhttp://cabigtrainingdocs.nci.nih.gov/caTissue/index.html
• Browse through the on-line manualhttps://cabigkc.nci.nih.gov/Biospecimen/KC/index.php/CaTissue_1.1_User_Manual
• For additional questions, post them to the TBTT KC Forumhttps://cabig-kc.nci.nih.gov/Biospecimen/forums/
Acknowledgements
Rakesh Nagarajan MD, PhD
Mark A. Watson MD, PhD
Dave Mulvihill
Vicky Holtschlag
Amy Brink
Aniket Pandit
Ganesh Naikwade
Prafull Kadam
Supriya Dankh
Vijay Pande
Rajesh Patil
Madhumita Shrikhande
Ashish Gupta
Komal Gulati
Sachin Lale
Srikanth Adiga
Virender Mehta
Kalpana Thakur
Abhishek Mehta
Deepti Shellar
Poornima Govindrao
Sayali Salodkar
Vaishali Khandelwal
Rushikesh Subedar
Snehil Gupta
Preeti Munot