The Research Institute at Nationwide Childrens Hospital Center for Childhood Cancer BioInformatics G

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The Research Institute at Nationwide Childrens
Hospital Center for Childhood Cancer
BioInformatics Group

• Tom Barr
• Dave Billiter, PMP

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The Research Institute at Nationwide Childrens
Hospital
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Overview

• Introduction
• Center for Childhood Cancer
• C3BIG
• Biopathology Center
• VIPER
• C3BIG Image Dashboard
• VM2M
• Future Opportunities
• Closing

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Center for Childhood Cancer Areas of Focus

• 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

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Affiliations and Collaborations

• Childrens 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 Childrens Hospital Division of
  Hematology and Oncology

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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.

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C3BIG

• 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

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C3BIG User Community

• Center for Childhood Cancer
• Biopathology Center (BPC)
• Biobehavioral Health
• Center for Innovation in Pediatric Practice
• Research Information Services
• Childrens Hospital Inc.
• Childrens 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)

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C3BIG Focus Areas

• Customized Application Development
• Informatics Consulting
• Solution Analysis
• Data Management
• Project Management
• Systems Architecture (SOA)
• Web Site Development
• Digital Imaging/Image Analysis

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Biopathology Center

• 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/

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Biopathology Center Components

• Biospecimen Repository
• Molecular Genetics
• Core Morphology
• Digital Imaging Core

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Biopathology Center

• Organization providing specimen management
  services for
• Pediatric Cooperative Human Tissue Network
  (pCHTN)
• Childrens 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)

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BPC by the numbers

• 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

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Quality Control

• Verification of institutional diagnosis
• Documentation of tumor and necrosis
• Specimens must go through quality control process
  prior to being served to an investigator

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Virtual Microscopy

• The technique of digitizing microscope slides
  with common objective magnifications
• may be equivalent to original glass slides on
  microscopes
• will provide diagnostic image quality

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Why Virtual Microscopy?

• 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

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VM Software/Hardware

• Scanscope Console
• Spectrum Information Manager
• Virtual Slide Manager
• Web Viewer
• ImageScope
• Digital Slide Studio
• TMALab
• Digital Slide Conferencing

• 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

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Project VIPER

• Virtual microscopy Image Pilot EndeavoR
• Web-based pathology review system that is
  extensible both for today and tomorrows 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

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Reviewers

• 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

• Ability to annotate images
• Online forms for completion
• Email notification of completed cases to the BPC
• Users manual available online

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Operations Staff

• Assign Password
• Assign Cases and/or groups of cases
• Upload Pathology Reports
• Add Staff Accounts
• Add or Remove reviewers

• Manage Cases
• Manage Slides
• Manage Groups
• Manage Institutions
• Query for Case status by reviewer or protocol
• Image Directory Assignment
• Online Users Manual

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VIPER

• http//viper.epn.osc.edu/viper/

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C3BIG Image Dashboard

• 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)

• 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.

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VM2M Architecture
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Search
Allow the user to search all files stored on the
system for the specific criteria.
VM2M Web Flow
Allow the user to quick search all files stored
on the system based on different disease types
and Sub disease types
Browse
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.
Logged in
Home
Upload Files
Download
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.
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VM2M Home Page
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VM2M Login Page
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VM2M Browser
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VM2M Search Page
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VM2M Search Detail Page
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VM2M Slide Upload Page
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VM2M Add New Case
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VM2M Microarray Upload
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VM2M Download
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Future Opportunities

• COG/GOG Image Warehouse
• Pediatric TARGET Tool
• caBIG Image Service
• Pathology Review Education
• VIPER Integration with Aperio Spectrum
• Further development of image analysis algorithms

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Closing

• Thank You
• Questions??
• Thomas.Barr_at_NationwideChildrens.org