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RNA Summit

Co-located CHI Event:
RNA Interference Summit
June 8-10, 2009
San Francisco, CA


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Bio-IT World



Genome Medicine



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The Scientist


Translating Genomic Knowledge - Day 2


Day 1  |  Day 2  |  Download BrochurePrint


Wednesday, June 10


7:00– 8:00 am Facilitated Breakout Discussion Groups & Continental Breakfast

Grab a cup of coffee and join a facilitated discussion group focused around specific themes. This unique session allows conference participants to exchange ideas, experiences, and develop future collaborations around a focused topic.

Table 1: Translating New Genomic Tools to Clinical Testing
Host:  Wayne Grody, M.D., Ph.D., Professor, UCLA School of Medicine
Discussion topics include:

  • Potential applications of high-density arrays to clinical medicine
  • Will whole-genome sequencing ever be clinically useful?
  • Should these tests be offered direct-to-consumer?

 Table 2:  Post-Marketing Research
Host:  Felix Frueh, Ph.D., VP, R&D & Personalized Medicine, Medco Health Solutions
This discussion group will focus on:

  • What do we really want to know?
  • What type of data is needed to change clinical practice after a drug has entered the market?

Table 3:  Genomic Predictive Marker in Drug Development
Host: Yihong Yao, Ph.D., Principal Scientist, Medimmune
Discussion topics include:

  • Suitable analyses as predictive marker for efficacy or safety
  • Mechanism based markers or more ‘fishing’ like approach
  • Where to look: peripheral blood and/or disease tissues/tumors
  • The challenges that we face;
    When to begin the study
    How to generate and test the hypothesis in phase 2
     Phase 3 design: incorporate predictive marker into pivotal trial

Table 4:  Challenges in Next Generation Sequencing Data Analysis
Host: Doug Robinson, SAS Institute and Faye Schilkey, National Center for Genome Resources
Discussion to include:

  • Software/hardware for whole genome alignment  
  • QC and statistical analysis of summarized data
  • Exon-level analysis of next-gen sequencing data
  • Correlating paired genomic data types

 Table 5: Using Data Mining Techniques to Develop Models of Biologic Regulation
Host: John Eberhardt, EVP Life Sciences, DecisionQ Corporation

Discussion to Include:

  • Addressing the high-dimensionality data problem
  • Data mining techniques
  • Data curation
  • Casuality vs. Dependence in statistical models 

Table 6:  Bringing Biomarker Tests into Clinical Reality
Host:  Dan Burns, Ph.D., Senior Director, Cabernet Pharmaceuticals; Deane Drug Discovery Institute, Duke University

  • How do we integrate the various entities necessary to bring biomarker test to clinical reality?
  • Regulators, pharma, test developers, clinical labs, and payers.
  • Recent examples demonstrate the current mechanism is ad hoc at best.
  • We are not using the same language, benchmarks or incentives.  How can we break these barriers to innovation down?


8:15 Chairperson’s Remarks

8:20 Practical, Ethical and Regulatory Issues Involved in the Application of High-Density Genotyping Tools to Clinical Molecular Testing

Wayne Grody, M.D., Ph.D., Professor, Divisions of Medical Genetics and Molecular Pathology, University of California at Los Angeles School of Medicine

The advent of high-throughput, genome-wide analysis technologies has catapulted the field of clinical molecular diagnostics well beyond its traditional focus on targeted mutation and single-gene testing. While these new platforms have already proven themselves as powerful research tools, their ultimate place and application in clinical medicine remains to be elucidated. Even with the technology available, there is real concern that such comprehensive genomic analysis performed on individual patients may reveal far more information than we know what to do with, and may raise far more questions than it answers. This presentation will examine the medical, ethical, and regulatory issues that must be taken into account before these technologies can be so applied.

8:50 Integrative Translational Research in Three Phases

James Lyons-Weiler, MSc, Ph.D., Director, Bioinformatics Analysis Core, University of Pittsburgh

Biomarker development in a silo has rarely led to translational success. Integrative translational research, as defined by Shi & Lyons-Weiler, is a three-phase strategy that forces the consideration of biomarkers in a clinical context. The three phases are Clinical Decision Modeling, Model Validation, and Prospective Clinical Trial. The many advantages and risks of this approach are outlined.

9:20 Case Study: Discovering a Molecular Biomarker and Developing a Test

Andrew Grupe, Ph.D., Senior Director, Pharmacogenomics; Director, CNS Research, Celera Diagnostics

Genome-wide association and gene expression studies enable the characterization of molecular networks and a better understanding of disease etiologies. Careful study designs and stringent statistical analyses are required to identify variants that impact disease risk, disease progression, or response to treatment. Biomarkers that pass stringent analytical and clinical validation criteria and have clinical utility are useful candidates to guide decisions on diagnosis and treatment. This presentation will describe the discovery and validation of a specific molecular biomarker and its development as a molecular test.

9:50 Networking Coffee Break, Exhibit and Poster Viewing

10:45 Molecular Targets for Therapeutic Lymphangiogenesis in Lymphatic Dysfunction and Disease

Stanley Rockson, M.D., Director, Stanford Center for Lymphatic and Venous Disorders; Professor of Medicine, Stanford University School of Medicine

11:15 Biomarker Applications in Drug Development

Nicholas C. Dracopoli, Ph.D., Vice President, Biomarkers, Centocor R&D, Johnson & Johnson

While biomarkers are being broadly used in clinical development, very few have emerged as regulatory approved companion diagnostics. This presentation will provide an overview of companion diagnostics in oncology, and discuss some of the bottlenecks that delay the transition from exploratory biomarkers to validated endpoints.

11:45 Translation of New Technologies: From Basic Research to Drug Discovery and Development

Nirmala Bhogal, Ph.D., Scientific Director, FRAME
The impetus to apply new technologies originating from multiple disciplines to reduce drug attrition rates has resulted in a number of key global initiatives. The aim of this talk is to assess the value of new technologies and methodologies within the drug discovery and development arenas. A retrospective evaluation of approaches originally developed as research methods that have been adopted as drug discovery and development tools will be made to identify the key factors that are likely to influence whether such future technologies will gain industrial and regulatory acceptance.

12:15 pm Close of Morning Session

12:30 Luncheon Presentation Sponsored by   NextBio
Making Discoveries Using Combined Collections of Large-Scale Gene- and Sequence-Centric Data

Ilya Kupershmidt, Co-founder and Vice President Products, NextBio
This talk will describe NextBio’s latest addition to its novel knowledge discovery platform – a framework for integrating sequence-centric data from diverse microarray and next-generation sequencing platforms. The new platform allows hypotheses testing using public and internal data from diverse applications including studies on DNA methylation, protein-DNA interaction, transcriptomics, CNV and mutation analysis among others. In this session, we will share NextBio’s strategy of combining semantic framework, large-scale data and meta-analysis methods to enable real-time knowledge discovery.


1:45 Chairperson’s Remarks

Leo Sahelijo, Ph.D., Director of Pharmacogenomics, Takeda Global

1:50 Genotyping, Deep Phenotyping, and Clinical Utility

Clive Bowman, FRSS FLS FRSM, Professor, School of Biological Sciences, University of Reading; and School of Mathematics, University of Leeds

Information simultaneously extracted from clinical phenotypic and genomic databases is the key to translating wide-band investigations into medical practice. Detection of this in patients sequentially in real-time; and, recognition in terms of pre-existing knowledge; can make real-world acceptance rapid. Genetic information can be straight-forwardly deployed to adaptively recruit clinical trial subjects maximizing their treatment benefit and minimizing their risk of adverse events. The future challenge is to understand patients pharmaco-genomically in the context of clinically relevant groupings based upon deep phenotyping.

2:20 Establishing Clinical Utility of Genetic Tests

Felix Frueh, Ph.D., Vice President, R&D & Personalized Medicine, Medco Health Solutions Inc.

2:50 Networking Refreshment Break, Poster and Exhibit Viewing

3:30 Pharmacogenetics: Finding Value in Early Clinical Trials

Anahita Bhathena, Ph.D., Associate Research Investigator, Pharmacogenetics, Abbott

4:00 Integrating Pharmacogenetics Throughout the Pharma Value Chain

Daniel Burns, Ph.D., Senior Director, Pharmacogenetics Consulting, Cabernet Pharmaceuticals; Deane Drug Discovery Institute, Duke University

4:30 Characterization and Biomarker Analysis of Complex Wounds

John S. Eberhardt III, Executive Vice President, DecisionQ Corp.

Walter Reed Army Medical Center and National Naval Medical Center have access to a unique population of patients with traumatic battle wounds. These wounds represent a unique opportunity to understand biological factors that can be used to stratify patients into different healing categories and to identify potential novel diagnostic and therapeutic targets for exploration. The Combat Wound Initiative Program has detailed molecular and bacteriological characterization of over 50 combat wounds. Using this information, the Program is developing a bioinformatics driven strategy to develop diagnostic models capable of prospectively stratifying patients into different wound healing categories. Finally, the Program is using bioinformatics to identify potential targets of interest for future molecular mechanistic studies.

5:15 Conference Wrap-up

5:30 Close of Conference



Co-located Events:     Genotyping Tools          The Business of Genomics        Genomic Sample Prep