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Sponsoring Cancer Center

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Integrative Cancer Research (developer) LCCC caBIG Representative. Robert Clarke, ... Integrative Cancer Research Workspace. Examples of Ongoing Funded Projects ... – PowerPoint PPT presentation

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Title: Sponsoring Cancer Center


1
Integrative Cancer Research
  • Sponsoring Cancer Center
  • Lombardi Comprehensive Cancer Center
  • Georgetown University
  • Workspaces
  • Architecture (developer)
  • Integrative Cancer Research (developer)
  • LCCC caBIG Representative
  • Robert Clarke, Ph.D., D.Sc.
  • clarker_at_georgetown.edu
  • (202) 687-3755

2
Integrated Cancer Research Teams
  • Georgetown University
  • Edmund Gehan (Biostatistics Biomathematics)
  • Stephen Moore (Advanced Research Computing)
  • Seong Ki Mun (Imaging Science Information
    Systems)
  • Cathy Wu (Protein Information Resource)
  • Virginia Tech
  • Joseph Wang (Engineering Computer Science)
  • Catholic University
  • Jason Xuan (Engineering Computer Science)
  • National Institutes of Health
  • Spiderweb Team (NCICB )
  • Javed Khan (NHGRI)
  • Aiyi Liu (NICHD)
  • University of Edinburgh, Scotland
  • William Miller (Oncology)

3
Overview
  • Project Activity
  • Tool development for exploring very high
    dimensional data sets
  • Deployment of grid enabled and integrated array
    (MIAME
  • compliant) and clinical research databases
    (Spiderweb)
  • Contribution of expression array and other data
    from multiple
  • clinical, translational, and basic research
    projects
  • Stage of Maturity
  • Tools at each stage of development
  • Technical Details/Standards
  • Open source currently most are written in C
    and/or MatLab
  • Points of Interoperability
  • Use of caCORE APIs caBIG-compatible APIs
  • Resources
  • Platform migration software engineering
    personnel

4
Examples of Ongoing Funded Projects
  • Bioengineering Research Partnership (NCI)
  • Large, prospective, molecular profiling study in
    breast cancer
  • Expression array tool development and deployment
  • Expression array and clinical data
  • Gene/Nutrition Interactions in Breast Cancer
    (NCI)
  • U54 program project array tool development and
    deployment data
  • Breast Cancer Center of Excellence (DOD)
  • Study of alcohol and breast cancer risk array
    tool deployment data
  • Clinical Translational Research Study (DOD)
  • Large, prospective and retrospective, molecular
    profiling study
  • of Letrozole and Tamoxifen in breast cancer
  • Array tool development and deployment data

5
Examples of Ongoing Funded Projects
  • Computational Decomposition of Composite
    Molecular
  • Signatures (NCBIB)
  • Expression array tool development, optimization,
    and deployment
  • Intelligent Mapping and Visual Exploration of
    Gene
  • Expression Profiles (NCI)
  • Expression array tool development, optimization,
    and deployment
  • Comprehensive Computational Analysis of Gene
    Expression
  • (NCI)
  • Expression array tool development, optimization,
    and deployment

6
Integrated Tool Development
7
Tools for Very High Dimensional Data Sets
  • General Approach
  • Probablistic approaches to address the
    properties of very high
  • dimensional data spaces (e.g., "curse of
    dimensionality",
  • "concentration of measure phenomenon")
  • Data Preprocessing
  • Normalization
  • Tissue heterogeneity correction
  • Multitask, goal-specific, gene selection tool
    (e.g., classification vs.
  • signaling/function)
  • Cluster Discovery and Visualization
  • Visual Statistical Data Analysis (VISDA) package
  • Classification and Prediction
  • Optimized multilayer perceptron classifiers
  • Expression array tool development

8
Comprehensive Data Analysis
Cluster Discovery Visualization
Data Preprocessing
Classification Prediction
Adaptive Hierarchical Subspace Experts
Cross-Phenotype Normalization
Tissue Heterogeneity Correction
Information Visualization
Optimized Mutlilayer Perceptron Classifiers
Visual Statistical Data Analyzer (VISDA)
Multitask Gene Selection
Matlab
Neural Networks
Pattern Recognition
Independent Component Analysis
9
Examples of Novel Tools
Discriminant Components Analysis
10
Dynamic Contrast Enhanced-MRI
Tumor angiogenesis in the breast
11
Integrating Imaging and Molecular Analysis
12
Integrate DataProtein Information Resource
13
SpiderWeb Collaboration Goals
  • Integration of multiple, varied information to
    achieve a basis for rational design of novel
    diagnostics and therapeutics
  • Integration of functional genomics information
    into clinical information so it can be used to
    diagnose genetic predisposition,
    sub-classification of disease and help with
    optimal selection of therapies
  • Bring new efficiencies to clinical research by
    integrating bench to bedside and back

14
SpiderWeb Project (LCCC/NCICB)
Approval
15
Timelines and Resources
  • Development Requirements (approx)
  • 3 programmers for data analysis tools
  • 3 programmers for PIR integration into caBIG
  • Infrastructure
  • C/Java development environment enhancements
  • software system administrator
  • Draft 12-month Work Plan and Milestones (approx)
  • 1-3 months VISDA caBIG interoperability
  • 4-6 months CPN and THC caBIG interoperability
  • 7-9 months MTGS and MLP/AHSE caBIG
    interoperability
  • 10-12 months software system integration and
    final testing
  • 12 months for PIR integration into caBIG
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