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The march of molecular genomics is progressing from the laboratory to the clinic. Within the pharmaceutical and diagnostic community, applications of clinical genomics promises to enhance the discovery of drug response markers, reduce the size and expense of clinical drug trials, and provide tools for addressing regulatory approval issues. Cambridge Healthtech Institute’s Translating Genomic Knowledge: Biological Discovery to Clinical Utility expounds the driving factors that are encouraging pharmacogenetic strategy development by:

  • Weeding out unpromising molecules earlier in the game
  • Compressing development timelines
  • Running smaller, more focused clinical trials and to adapt them mid-stream
  • Exploring secondary indications more quickly

Tuesday, June 9

9:50 Conference Registration

10:40 Chairperson's Remark's
Stephen Kingsmore, Ph.D., President and CEO, National Center For Genomic Resources



Translating Small Genetic Contributions into Large Effects Using Phylogenetic Analyses

RosesAllen D. Roses, M.D., Professor of Medicine, Jefferson-Pilot Professor of Neurobiology and Genetics; Director, Deane Drug Discovery Institute; Senior Scholar, Fuqua School of Business; Member, Duke Institute for Genome Sciences & Policy; President of Shiraz Pharmaceuticals, Inc.






Multilocus Analysis of Sequence and Genotype Data

SchorkNicholas J. Schork, Ph.D., Director of Research, Scripps Genomic Medicine, Director of Biostatistics and Bioinformatics,
The Scripps Translational Science

Most diseases of contemporary public health concern, such as diabetes, hypertension, and cancer, are influenced by a number of genetic and non-genetic factors, each with small to moderate effect. Identifying genetic factors via genotyping and sequencing-based association strategies will thus be difficult if the combined effects of these genetic factors are not taken into consideration in a relevant association analyses. This talk will describe ways in which multilocus effects can be accommodated in association analysis strategies.

12:15 pm Close of Morning Session


2:00 Chairperson’s Remarks

Eric Lai, Ph.D., Senior VP, R&D, Gen Probe, Inc.

2:05 Exome Sequencing and Human Disease

Jay Shendure, M.D., Ph.D., Department of Genome Sciences, University of Washington

Second-generation DNA sequencing is evolving rapidly, and has already enabled the complete resequencing of several human genomes. As an interim approach, we and others have developed “genomic partitioning” technologies for isolating complex subsets of the human genome at a scale matched to the current throughput of second-generation sequencers. We are primarily interested in developing a high-throughput pipeline for selectively capturing and comprehensively resequencing all protein-coding sequences, termed the “exome” (~1% split amongst ~180,000 subsequences) across multiple individuals. Thus far, we have applied genomic partitioning in tandem with second-generation sequencing to resequence the exomes of 10 individuals. Exome resequencing across multiple individuals provides an early window into the challenges and opportunities that complete genome resequencing will provide for investigating the role of rare variants in human disease.
Click here to listen to Jay's recent podcast 

2:35 Genomic Tools in Identifying Markers of Resistance: ABCC3 Co-Amplification in HER2 Positive Breast Cancer

Ajay Pandita, Ph.D., Scientist, Department of Oncology Diagnostics, Genentech Inc.

Breast cancer is a heterogeneous disease with distinct molecular subtypes, varied in their response to targeted and chemotherapeutic agents. Enhanced understanding of the genetic alterations underlying the different subtypes is needed to pave the way for a more personalized administration of therapeutic agents. Using a combination of genomic approaches on a well-characterized panel of breast cancer cell lines, we identified ABCC3 as a putative subtype specific biomarker of resistance to anti-mitotic agents such as paclitaxel and monomethyl-auristatin-E (MMAE) in HER2 amplified breast cancer. We further developed a FISH based assay to screen for the co-amplification of ABCC3 in HER2 amplified patient samples and will discuss potential clinical applications of this assay.

3:05 Multiple Biomarker Approaches to Guide the Clinical Development of Anti-IFN-α Mab Therapy

Yihong Yao, Ph.D., Principal Scientist, Translational Sciences, MedImmune Inc.

IFN-α-inducible genes are strongly over-expressed in the whole blood (WB) and disease sites of a fraction of patients with systemic lupus erythematosus, myositis and rheumatoid arthritis, as measured by both Affymetrix whole genome array and taqMan QRT-PCR. These results provided strong scientific rationale to apply anti-IFN-α therapy in these autoimmune diseases. The overexpression of IFN-α-inducible genes in WB of SLE patients provided an effective pharmacodynamic (PD) marker to evaluate the biological effect of the anti-IFN-α monoclonal antibody in a phase 1a clinical trial in SLE that showed evidence of clinical activity. We are currently evaluating the PD of the anti-IFN-α mAb in multi-dose trials evaluating anti-IFN-α therapy in SLE and myositis to obtain optimal doses to use in pivotal trials based on PK/PD modeling, and these genes as potential diagnostic markers to identify patients that respond to the therapy.

3:35 Diagnostics and Pharmacogenetic Solutions for Common Psychiatric Disorders and Addictions
Elena Pushnova, Ph.D., Founder & Chief Executive Officer

4:00 Refreshment Break, Poster and Exhibit Viewing

4:45 Panel Discussion – Successful Data Flow in Translation Discovery Research

Moderator: Eric Lai, Ph.D., Senior VP of R&D, Gen Probe Inc.
Panelists:  Nicholas Schork, Andrew Grupe, Felix Frueh, Anahita Bhathena, Clive Bowman

5:45 Close of Day