Methods Workshops

Application of Systems Genetics to Cancer Susceptibility

Models and foundations for systems genetics
David W. Threadgill

Embracing complexity: Using systems level data for predictive modeling
Alison Motsinger-Reif, North Carolina State University, Raleigh, NC

Systems analysis of inherited breast cancer metastasis susceptibility
Kent W. Hunter, National Cancer Institute, Bethesda, MD

Using systems genetics to understand the effects of low dose ionizing radiation
Brynn Voy, University of Animal Science, Knoxville, TN

Development and Characterization of Biomarkers for Epidemiological Studies

Introduction
Montserrat Garcia-Closas

Principles of biomarker characterization for epidemiological studies
Nathaniel Rothman, National Cancer Institute, Bethesda, MD

How to measure, control, and evaluate the impact of laboratory variation
Shelley S. Tworoger, Brigham and Women’s Hospital, Boston, MA

Use of biomarkers in case-control studies of etiology and prognosis: Functional assays
Xifeng Wu, UT M. D. Anderson Cancer Center, Houston, TX

Use of biomarkers in perspective cohort studies: Lessons learned from the UK Biobank
Paul Downey, UK Biobank, Cheshire, United Kingdom

Emerging Radiation Options with Charged Particles

Introduction
Stephen M. Hahn

Delivery and applications of proton therapy in the clinic
Torunn I. Yock, Massachusetts General Hospital, Boston, MA

Imaging and new technology development in charged particle therapy
Anthony Lomax, Paul Scherrer Institute, Villigen, Switzerland

Understanding the biology of charged particle therapy
W. Gillies McKenna, University of Oxford, Headington, United Kingdom

Translational research opportunities in charged particle therapy
Keith A. Cengel, University of Pennsylvania, Philadelphia, PA

Nanotechnology Platforms for Cancer Imaging

Nano-sized probes for imaging tumor compartments in vivo
Alexei A. Bogdanov, University of Massachusetts Medical School, Worcester, MA

Nanoliposomes for cancer imaging and therapy: Labeling methods and potential applications
William T. Phillips, UT Health Science Center, San Antonio, TX

Multifunctional, multimodality cancer imaging based on biodegradable water-soluble synthetic polymers
Chun Li, UT M. D. Anderson Cancer Center, Houston, TX

Magnetovaccination and magnetic resonance imaging as a means to investigate cancer vaccine dynamics
Jeff W. M. Bulte, Johns Hopkins University Medical School, Baltimore, MD

High-Throughput Approaches to Drug Discovery

Knowledge-driven strategies for exploring the chemosphere
Nathalie Meurice, Translational Genomics Research Institute, Scottsdale, AZ

File enhancement and high-throughput medicinal chemistry
Christopher Hulme, University of Arizona, Tucson, AZ

Cancer drug discovery by high-throughput screening at Sanofi-aventis
Ken Wertman, Sanofi-aventis, Tucson, AZ

Turning hits into leads
Gerald M. Maggiora, University of Arizona, Tucson, AZ

Integrating Imaging into Preclinical and Clinical Trials

Dynamic molecular imaging of signal transduction pathways as drug targets in preclinical models
David Piwnica-Worms, Washington University School of Medicine, St. Louis, MO

Application of imaging as a decision making tool in oncology
Timothy J. McCarthy, Pfizer Global Research and Development, New London, CT

Molecular imaging in tumor treatment response
Steven M. Larson, Memorial Sloan-Kettering Cancer Center, New York, NY

Integrating imaging into clinical trials: Challenges, pitfalls, and practical examples
Lawrence H. Schwartz

Methods in Cancer Epigenetics and Epigenomics

The MIRA method for methylation analysis of cancer genomes
Gerd P. Pfeifer, City of Hope, Duarte, CA

Validation of genome-wide DNA methylation data in CLL using the MassARRAY system
Christoph Plass

DNA methylation profiling by Illumina GoldenGate, Infinium, and Genome Analyzer Technology
Peter W. Laird, USC/Norris Comprehensive Cancer Center, Los Angeles, CA

Bisulfite based methods for genome-wide DNA methylation profiles using next-generation sequencers
Matteo Pellegrini, University of California, Los Angeles, CA

Whole Genome Approaches to Cancer Gene Discovery

Using next generation sequencing technologies to investigate structural rearrangements in human cancers
P. Andrew Futreal, Wellcome Trust Sanger Institute, Hinxton, United Kingdom

Statistical analysis of copy-number profiles to identify driver events
Rameen Beroukhim, Dana-Farber Cancer Institute, Boston, MA

Hitting cancer where it hurts most: The RNAi strategy to discover synthetic lethal interactions in cancer
Roderick L. Beijersbergen, The Netherlands Cancer Institute, Amsterdam, The Netherlands

Finding biomarkers of drug resistance through RNA interference-based genetic screens
René Bernards

Clinical Trial Designs Workshop: Design and Implementation of Innovative Clinical Trials Part 1: Early Phase Trials and Discovery

Scientifically driven “proof of principle” trials: Current and future value to drug development
Elizabeth M. Jaffee, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD

Tumor marker development and co-development: Potential pitfalls
Daniel F. Hayes, University of Michigan Comprehensive Cancer Center, Ann Arbor, MI

Biomarker driven clinical trial designs: Present and future
Heinz-Josef Lenz, USC/Norris Comprehensive Cancer Center, Los Angeles, CA

Adaptive designs for speeding up drug discovery
J. Jack Lee

GWAS, SNPs, and Copy Number Variants in Cancer

Speakers to be announced

Integrating Molecular Imaging with Biomarkers and Functional Measures

Imaging biomarkers in oncologic drug development: Potential uses and challenges
Patricia E. Cole, Eisai Global Medical Research, Inc., Ridgefield Park, NJ

Asking and answering questions: The role of molecular imaging in the oncology clinic
Peter Choyke, National Cancer Institute, Bethesda, MD

National efforts to improve imaging biomarkers in cancer clinical trials
Daniel C. Sullivan, Duke Comprehensive Cancer Center, Durham, NC

Imaging biomarkers and functional measures in the assessment of cancer patients
Nathan Hall, The Ohio State University Medical Center, Columbus, OH

Three-Dimensional Organotypic Models

Three-dimensional skin and melanoma models
Meenhard Herlyn, The Wistar Institute, Philadelphia, PA

Three-dimensional organotypic models to study transition from preinvasive ductal carcinoma in situ to invasive ductal carcinoma
Bonnie F. Sloane, Wayne State University School of Medicine, Detroit, MI

In vivo reconstruction and manipulation of prostate cancer using tissue recombination approaches
Simon W. Hayward

A liver organotypic bioreactor for cancer metastasis
Alan Wells, University of Pittsburgh, Pittsburgh, PA

Clinical Trial Designs Workshop: Design and Implementation of Innovative Clinical Trials Part 2: Late Phase Trials and Validation

Learning from the past to inform the future: What insights can we gain from the last three decades of clinical cancer trials
Monika K. Krzyzanowska, Princess Margaret Hospital, Toronto, ON, Canada

Speeding up the evaluation of new agents in cancer
Mahesh K. B. Parmar, Medical Research Council Clinical Trials Unit, London, United Kingdom

Biomarkers and non-survival endpoints: Current status and validation strategies to fulfill the promise
Daniel J. Sargent, Mayo Clinic College of Medicine, Rochester, MN

Methods in Cancer Metabolism

Imaging tumor metabolism: What do we need to see and how can we see it?
Ralph DeBerardinis, UT Southwestern Medical Center, Dallas, TX

Comprehensive metabolic analysis tools for dissecting chronic disease mechanisms
Christopher B. Newgard, Duke University Medical Center, Durham, NC

Real-time measurement of mitochondrial respiration and glycolysis rates of cancer cells in a microplate
Min Wu, Seahorse Bioscience, North Billerica, MA

Using computational genomics to discover transcriptional networks controlling metabolism
Daniel H. Arlow, Broad Institute of MIT and Harvard, Cambridge, MA

Proteomics Technology Platforms for the Cancer Biomarker Pipeline

Proteomics technologies and a biomarker pipeline
Steven A. Carr, Broad Institute of MIT and Harvard, Cambridge, MA

Interlaboratory studies of proteomics technology platforms for biomarker discovery and verification
Daniel C. Liebler

Breast cancer biomarker discovery in mouse models
Amanda G. Paulovich, Fred Hutchinson Cancer Research Center, Seattle, WA

A discovery-to-verification pipeline for biomarker development in breast cancer
Michael Gillette, Broad Institute of MIT and Harvard, Cambridge, MA

Pushing the Boundaries: New Tools for Molecular Epidemiology

Online resources for identifying candidate pathways and SNPs
Linda E. Kelemen, Alberta Cancer Board, Calgary, AB, Canada

Methods for genome-wide association studies
Ellen L. Goode, Mayo Clinic College of Medicine, Rochester, MN

Copy number variation and cancer risk
Christopher I. Amos, UT M. D. Anderson Cancer Center, Houston, TX

From DNA blueprint to protein: Additional considerations
Thomas A. Sellers

Single Molecule Sequencing Approaches, Methods, and Applications

Discovery and analysis of mutational burden in the human cancer genome using next generation sequencing technology
David A. Wheeler, Baylor College of Medicine, Houston, TX

High-throughput sequencing applications in cancer genomics
John McPherson, Ontario Institute for Cancer Research, Toronto, ON, Canada

Sequencing the cancer genome
Richard K. Wilson, Washington University School of Medicine, St. Louis, MO

Identification and somatically acquired genetic variation in whole cancer genomes
Peter Campbell, The Wellcome Trust Sanger Institute, Hinxton, United Kingdom