Transcript Columbus Children’s Research Institute Center for

The Research Institute at Nationwide
Children’s Hospital
Center for Childhood Cancer
BioInformatics Group
Tom Barr
Dave Billiter, PMP
The Research Institute at Nationwide
Children’s Hospital
Overview
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Introduction
Center for Childhood Cancer
C3BIG
Biopathology Center
VIPER
C3BIG Image Dashboard
VM2M
Future Opportunities
Closing
Center for Childhood Cancer
Areas of Focus
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Molecular mechanisms involving pediatric
sarcomagenesis
Regulation of survivin gene expression
Stroma/tumor interactions in adult and pediatric
cancer
Tumor microenvironment
Gene expression profiling in pediatric leukemias
Signal transduction and pharmacologic interventions
Oncolytic viral therapy in pediatric brain tumors
Affiliations and Collaborations
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Children’s Oncology Group (COG)
Gynecologic Oncology Group (GOG)
Cooperative Human Tissue Network (pCHTN)
Cancer Therapy Evaluation Program (CTEP)
The Ohio State University Comprehensive Cancer
Center
Arthur G. James Cancer Hospital/Richard J. Solove
Research Institute
Nationwide Children’s Hospital Division of
Hematology and Oncology
Center for Childhood Cancer
BioInformatics Group (C3BIG)
Mission
The C3 BioInformatics Group of The
Research Institute at Nationwide
Children's Hospital, under the
direction of Dr. Stephen J. Qualman,
is a BioInformatics application
development team dedicated to
increasing cure rates and decreasing
side effects in therapy through
Information Technology.
C3BIG
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Dave Billiter- Informatics Development Manager
Tom Barr – Imaging Manager
Bob Neville- Senior Software Developer
Scott Hargrose- Software Developer/DBA
Bill Beyer- Business Analyst/Software Developer
Heather Bao- Software Developer
Heather Day- Quality Assurance/Tech Writer
Subha Krishnamachary- Software Developer
Andy Fox- Software Developer
Mark Plaskow- Consultant
C3BIG User Community
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Center for Childhood Cancer
Biopathology Center (BPC)
Biobehavioral Health
Center for Innovation in Pediatric Practice
Research Information Services
Children’s Hospital Inc.
Children’s Oncology Group (COG)
Gynecologic Oncology Group (GOG)
Cooperative Human Tissue Network (CHTN)
Childhood Cancer Survival Studies (CCSS)
Ohio Supercomputer Center (OSC)
Group Banking Committee (GBC)
C3BIG Focus Areas
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Customized Application Development
Informatics Consulting
Solution Analysis
Data Management
Project Management
Systems Architecture (SOA)
Web Site Development
Digital Imaging/Image Analysis
Biopathology Center
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The Biopathology Center (BPC) is largely a
government funded non-profit organization whose
primary objective is the long-term acquisition and
storage of a large number of cancer related tissue
samples and related data for the purpose of
supporting cutting edge research.
Normal tissue and other diseased specimens are
also managed by the BPC.
Directed by Dr. Nilsa Ramirez
http://www.biopathologycenter.org/
Biopathology Center Components
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Biospecimen Repository
Molecular Genetics
Core Morphology
Digital Imaging Core
Biopathology Center
Organization providing specimen management services for:
 Pediatric Cooperative Human Tissue Network (pCHTN)
 Children’s Oncology Group (COG)
 Gynecologic Oncology Group (GOG)
 Childhood Cancer Survivor Study (CCSS)
 Clinical Trials Evaluation Program (CTEP)
 The Cancer Genome Atlas (TCGA)
 Strategic Partnering for the Evaluation of Cancer Signatures
(SPECS)
BPC by the numbers
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Over 650,000 specimens currently in bank
Receive tissues from over 500 hospitals
Receive and process 100 cases or 500
aliquots each day
Distribute over 25,000 specimens annually to
over 130 academic and commercial
researchers
Quality Control
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Verification of institutional diagnosis
Documentation of % tumor and % necrosis
Specimens must go through quality control
process prior to being served to an
investigator
Virtual Microscopy
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The technique of digitizing microscope slides
with common objective magnifications
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may be equivalent to original glass slides on
microscopes
will provide diagnostic image quality
Why Virtual Microscopy?
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Eliminate distribution of glass slides, logistical
issues with rapid turnaround times, and costs
of tracking and lost or broken slides
Support image analysis
Better quality than static images
Accessible anytime via the Internet
VM Software/Hardware
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Scanscope Console
Spectrum Information
Manager
Virtual Slide Manager
Web Viewer
ImageScope
Digital Slide Studio
TMALab
Digital Slide Conferencing
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Aperio Scanscope XT (2)
Virtual Slide Repository
NAS Device
Project VIPER
10 Tb storage cluster at the
Ohio Supercomputer Center
6 Tb local storage cluster
Project VIPER
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Virtual microscopy Image Pilot EndeavoR
• Web-based pathology review system that is
extensible both for today and tomorrow’s research
needs
• Facilitates a more efficient and cost-effective quality
control review process of patient tissue submitted
by member institutions
• Integration of a virtual microscopy service into the
research workflow
• Acts as catalyst to advance collaborative pediatric
and gynecologic pathology research and research
in image analysis
Reviewers
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Online registration and
request for password resets
Notified via email of new
cases
Personalized screen with list
of cases and case status
after authenticating into
VIPER
System monitors new cases,
completed cases, and cases
under review
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Ability to annotate images
Online forms for completion
Email notification of
completed cases to the BPC
User’s manual available
online
Operations Staff
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Assign Password
Assign Cases and/or
groups of cases
Upload Pathology
Reports
Add Staff Accounts
Add or Remove
reviewers
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Manage Cases
Manage Slides
Manage Groups
Manage Institutions
Query for Case status
by reviewer or protocol
Image Directory
Assignment
Online User’s Manual
VIPER
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http://viper.epn.osc.edu/viper/
C3BIG Image Dashboard
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Slide processor for cancerous diseases
Allows users to query multiple images by
morphologic characteristics
Algorithm to detect and measure necrosis
Algorithm to detect and measure abnormal
nuclei clustering (anaplasia)
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Virtual Microscopy to Molecule (VM2M)
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Creates a system where Virtual Microscopy data will be
available alongside microarray data for disease diagnosis and
treatment
Web-based system where a pathologist can search for tissue
samples of interest
Reviewer can inspect the corresponding digital image using a
web based image viewer, with the ability to zoom and pan to
the desired parts of the image.
Reviewer will also have the ability to access the micro- array
data corresponding to the same tissue sample, along with
results from an automated analysis of the digital image.
VM2M Architecture
Home
Logged in
Search
Allow the user to search all files stored on the system for
the specific criteria.
Browse
Allow the user to quick search all files stored on the system
based on different disease types and Sub disease types
Upload Files
Download
Allow the user to upload different types of files such as
.svs (digital slides file), .cel (raw microarray file), and .chp
(processed microarray file). When .cel file uploaded, MIAME
Checklist is required.
Allow the user to download useful files online
Registration – Get Account
Forget Password? – Get Password
User Profile
Allow the user to edit the personal information.
VM2M Home Page
VM2M Login Page
VM2M Browser
VM2M Search Page
VM2M Search Detail Page
VM2M Slide Upload Page
VM2M Add New Case
VM2M Microarray Upload
VM2M Download
Future Opportunities
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COG/GOG Image Warehouse
Pediatric TARGET Tool
caBIG Image Service
Pathology Review Education
VIPER Integration with Aperio Spectrum
Further development of image analysis
algorithms
Closing
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Thank You
Questions??
[email protected]