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Cambridge Healthtech Institute’s Inaugural
Microbes to Man and Back Again
March 7-8, 2012| Hilton San Diego Resort | San Diego, California 

Next-generation sequencing now makes it possible to determine the sequence of a genome at accessible prices and in a short period of time. Thus, DNA sequencing has revolutionized the scale, speed and economics of ecological studies. This application has led to a highly productive merger of clinical, experimental, and environmental microbiology. The merging and interrogation of diverse DNA datasets, including patient-based to experimental animal models, human to microbial, host to pathogen, and GWAS/gene expression, is becoming a rapid reality. We are now in a position to gain deeper insights into how host-microbes interactions impact health and disease.

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7:30-8:30 am Breakfast Presentation (Sponsorship Opportunity Available) or Morning Coffee

» 8:30 am - 12:30 pm • Plenary Keynote Session 

8:30 Chairperson's Opening Remarks

8:40 Recent Advances in Cancer Genome Sequencing

Richard WilsonRichard K. Wilson, Ph.D., Professor of Genetics, Director, The Genome Institute, Washington University School of Medicine

Our laboratory was the first to sequence the genome of a cancer patient and discover genetic signatures relevant to the pathogenesis of the disease. Building upon this achievement, our current focus is to utilize genome sequencing and analysis technology to discover clues that will facilitate more effective diagnosis and treatment of cancer and other human diseases. This presentation highlights some of the recent accomplishments and impact of The Genome Institute's cancer sequencing program.

9:25 Making a Definitive Diagnosis: Successful Clinical Application of Diagnostic Whole Genome Sequencing

Elizabeth WortheyElizabeth A. Worthey, Ph.D., Assistant Professor, The Human and Molecular Genetics Center, Pediatrics, Bioinformatics, Medical College of Wisconsin

We began deploying genomic sequencing in the clinic in the latter half 2009 to end a diagnostic odyssey in a specific child and continue to offer this service as a clinic to end such odysseys for other specific, very ill individuals being seen at the Children's Hospital and Health System of Wisconsin. So far we have received requests for clinical sequencing of more than 50 individuals. Eleven individuals have had their genomes sequenced; in a number of (but not all) cases a diagnosis has been rendered. Our approach to clinical whole genome sequencing, our analysis strategy and tools, and findings will be presented.

10:10 Networking Coffee Break in the Exhibit Hall with Poster Viewing

11:00 Can Genomes Improve Medical Outcomes?

Samuel LevySamuel Levy, Ph.D., Director of Genomic Sciences, Scripps Translational Science Institute and Scripps Genomic Medicine, Professor of Molecular and Experimental Medicine, The Scripps Research Institute

Pharmacogenomics and cancer benefit from the acquisition of DNA sequencing data in concert with relevant clinical phenotypes. The application of novel sequencing approaches in these areas enables the detection of molecular signatures that can be employed to determine appropriate treatment strategies that will positively impact medical outcomes.

11:45 RNA Editing – The Neo-Gold Rush of Diversity?

Robert BraunRobert Braun, Ph.D., Associate Director/Chair of Research, The Jackson Laboratory

RNA editing is a process that modifies RNA nucleotides and changes the efficiency and fidelity of the central dogma. Recent advances in sequencing have enabled the genome-wide identification of RNA editing sites in mammalian transcriptomes. We have demonstrated that tissue-specific canonical RNA editing (A-to-I and C-to-U) occurs in the mouse, and report that high-confidence canonical RNA editing sites can cause non-synonymous amino acid changes and are significantly enriched in 3? UTRs, specifically at microRNA target sites, suggesting both regulatory and functional consequences for RNA editing.

12:30 pm Close of Keynote Session

12:45 Luncheon Presentation (Sponsorship Opportunity Available) or Lunch on Your Own


Metagenomic Contributions to Health and Disease 

2:15 Chairperson's Remarks

Richard Moore, Ph.D., Sequencing Group Leader, Canada's Michael Smith Genome Sciences Centre



» 2:20 Featured Speaker 

Terabase-Scale Microbiology 

George WeinstockGeorge M. Weinstock, Ph.D., Professor of Genetics, Associate Director, The Genome Institute, Washington University School of Medicine

Traditional microbial sequencing projects focused on single organisms due to the high cost and relatively low throughput. Next-generation sequencing is in effect a more powerful microscope to study more complex microbial systems such as communities and populations. The higher density of data that is possible with NGS pushes microbial studies into new realms of biology for both cellular and viral micro-organisms.

2:55 Microbial Eukaryotes in the Human Microbiome: Ecology, Evolution, and Future Directions

Laura Wegener Parfrey, Ph.D., Research Scientist, Chemistry and Biochemistry, University of Colorado

The eukaryotes that reside in the human gut are relatively unexplored with high-throughput methods, yet many eukaryotic parasites are major sources of morbidity and mortality, especially in developing countries. Initial pyrosequencing results of geographically diverse populations demonstrate that the eukaryotic component of the microbiome is highly variable across individuals. Family members share a larger proportion of taxa than unrelated individuals. Co-occurrence patterns between eukaryotes and bacteria will also be discussed.

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3:30 Analyzing Multi-Sample Next-Gen Data from Sequence Reads to SNPs to Gene Expression and Ontology

Tom Schwei, Vice President and General Manager, DNASTAR, Inc.DNASTAR Lasergene is a desktop computer software solution that is affordable, easy to use and powerful.  This session is a brief overview of a workflow within Lasergene to assemble next-gen sequencing data from multiple DNA samples using a common reference, identify SNPs, assess gene expression for affected genes, and identify key gene ontology impact.

3:45 Networking Refreshment Break in Exhibit Hall with Poster Viewing

4:30 Detecting Infectious Agents Associated with Cancer

Richard Moore, Ph.D., Sequencing Group Leader, Canada's Michael Smith Genome Sciences Centre

We have developed a method for detecting potential infectious agents associated with cancer. Briefly, transcriptome data from massively parallel sequencing is analyzed for known bacterial and viral expression in comparison with adjacent normal tissue. This technique has been applied to colorectal carcinoma and a significant association with Fusobacterium nucleatum was detected. Data will also be presented on the expressed microbiome in colorectal carcinoma.

5:05 Investigating the Biological and Clinical Significance of Dysbiosis in Human Inflammatory Bowel Diseases

Daniel N. Frank, Ph.D., Assistant Professor, University of Colorado School of Medicine

Chronic diseases, such as the human inflammatory bowel diseases, arise through multifactorial processes involving host and environment. In many instances, disruptions to the human microbiome also have been proposed to contribute to disease etiology. I will discuss how my colleagues and I have merged human microbiome data with multiple additional high-throughput datasets and patient-based data to gain deeper understanding of how host–microbe interactions impact disease.

5:40 Close of Day

5:30-6:00 Dinner Short Course Registration

6:00-9:00 Dinner Short Courses*

SC4: Sequencing Data Analysis

SC5: The Key to Quality: Sample Preparation

*Separate registration required.

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