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Cambridge Healthtech Institute’s Sixth Annual
Successful Sequencing
March 7-8, 2012| Hilton San Diego Resort | San Diego, California 

To sequence or not to sequence is no longer the question. Sequencing projects are becoming more numerous and more complex. Matching the NGS platform(s) to your genomic research project includes not only decisions concerning read length and coverage but also efficient workflow strategies. Management of sequencing projects includes both upstream sequencing runs and downstream data management and analysis. Experienced researchers from large sequencing centers, core laboratories, and specialized groups share their practical knowledge, real-world experiences and solutions from project to pipeline to platform to progress.

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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 - 11:00 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 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 (Opportunity Available) or Lunch on Your Own


Managing A Sequencing Laboratory -
Breaking Down Sequencing Silos

2:15 Chairperson's Remarks

Gary T. Hardiman, Ph.D., Associate Professor; Director, Biomedical Genomics Microarray Facility, University of California, San Diego


»2:20 Featured Speaker: 

Application of Next-Generation Sequencing Technologies at JCVI

Yu-Hui Rogers, Ph.D., Vice President, Core Technology Development and Services, J. Craig Venter Institute

I will present an overview of the JTC research areas and how the next-generation sequencing technologies are being applied to support these activities. Specifically, I will discuss the sequencing technologies that are in use at JCVI including 454, Illumina and SOLiD, their capabilities and how we utilize different sequencing strategies for different applications.

2:55 Integrative Biomedical Informatics: A Multidisciplinary Approach at the City of Hope

Yate-Ching Yuan, Ph.D., Director, Bioinformatics Core Facility, Beckman Research Institute, City of Hope Medical Center

Sponsored byBioteam small logo3:30 Sponsored Technology PresentationAdam Kraut, Senior Scientific Consultant, Services, BioTeam


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

4:30 Resource Management in NGS: Getting Out From Under the 80-20 Rule

Ghia Euskirchen, Ph.D., Director, DNA Sequencing Program, Center for Genomics and Personalized Medicine, Stanford University

NGS has become a widespread tool in molecular biology and continues to play a critical role in personalized medicine, biodiversity, agriculture and other large-scale studies. Small-scale experiments and new projects tend to require disproportionately more support, yet they are often the sparks for eventual large-scale, systematic studies. Feasibility and project needs dictate process upgrades and frequent recalibrations are part of the realm. Illustrative examples from both internal research projects and the service center workflow will be presented and explored.

5:05 Application of High-Throughput Sequencing Technologies at the UCSD Biomedical Genomics Core Facility

Gary T. Hardiman, Ph.D., Associate Professor; Director, Biomedical Genomics Microarray Facility, University of California, San Diego 

The mission of the UCSD Biomedical Genomics Core (BIOGEM) is to provide state of the art sequencing services to the UCSD biomedical community. A major goal in biomedical research today is to understand how alterations in the epigenome and subsequent responses in gene expression impact disease phenotype and treatment regimens. BIOGEM provides complementary services to advance these efforts: conventional gene expression microarray analysis and deep sequencing-based approaches to help define transcriptional and epigenetic mechanisms. This presentation will cover the application of Illumina and Pacific Biosciences massively parallel sequencing technologies at UCSD BIOGEM.

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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