slide1 n.
Download
Skip this Video
Loading SlideShow in 5 Seconds..
Adoption and Use of caTissue Suite in a Multi-Repository Academic Environment PowerPoint Presentation
Download Presentation
Adoption and Use of caTissue Suite in a Multi-Repository Academic Environment

Loading in 2 Seconds...

play fullscreen
1 / 27

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


  • 101 Views
  • Uploaded on

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).

loader
I am the owner, or an agent authorized to act on behalf of the owner, of the copyrighted work described.
capcha
Download Presentation

PowerPoint Slideshow about 'Adoption and Use of caTissue Suite in a Multi-Repository Academic Environment' - trory


An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -
Presentation Transcript
slide2

?

Biospecimen Banking has Evolved Highly Complex Informatics Requirements

  • 1990
  • 2010
biospecimens managed with catissue
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

slide4

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
slide5

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.
slide6

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

slide7

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

slide8

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

slide9

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

slide10

Operation of Multiple, Independent Repositories Using Role-Based Access

User Roles

Role Privileges

+

Operation of Multiple Repositories / Protocols in a Single Instance

Defining Users

slide11

Participant Consent Tracking by Protocol at the Individual Specimen Level

Registering Consent

Updating Consent

Validating Consent before Distribution

slide12

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

slide13

Tracking Specimen Collection Timepoints

Time point with specimens collected (gold)

Collected specimen (purple)

Status of collection time point

Pending or not collected specimen (black)

slide14

Tracking Specimen Processing Events

Recordable specimen events

Recording when / who / how specimen was frozen

slide15

Monitoring Biospecimen QA

Tissue Specimen Review Event- Who / When

Details

slide16

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

slide17

caTissue Suite Pathology Annotation

Dynamic Extensions (DE) Tool

caTissue Suite Pathology Annotation Form

CAP Cancer Checklist

slide18

Creation and Management of Custom Searches and Result Views

Customized Query

Results View

Saved Query Management and Keyword Search Bar

slide19

Use of New Bulk Operations Tool to Migrate Legacy Data to caTissue

1. Participants

2. SCGs

3. Specimens

caTissue

Legacy “Tissue Log”

slide21

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)

slide22

caTissue Suite Support

  • Illustrated manuals for technical and biobanking staff
  • Web-based, interactive training tools
  • Web- and human-based Knowledge Center resources
https cabig kc nci nih gov biospecimen kc
https://cabig-kc.nci.nih.gov/Biospecimen/KC

caBIG™ Tissue Bank Knowledge Center

slide24

caTissue at Washington University School of Medicine

An expanding network of integrated repositories and biospecimen laboratories with associated users, protocols, and biospecimens

slide25

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

slide26

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/
slide27

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