Archived Content

Cambridge Healthtech Institute's Second Annual
Insights into the Active Genome
March 7-8, 2012| Hilton San Diego Resort | San Diego, California 

RNA-Seq is perhaps the most complex NGS application. In nature, RNA transcripts are moving targets, making their characterization and quantification difficult. RNA-Seq methods are advancing and improving in transcription start site mapping, strand-specific measurements, gene fusion detection, small RNA and long non-coding RNA characterization, and detection of alternative splicing events. RNA-Seq is transforming our understanding of transcription and regulation, giving new biological insights into the "active genome."

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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 (Sponsorship Opportunity Available) or Lunch on Your Own


Comprehending Complex Disease 

2:15 Chairperson's Remarks

Andrew S. Weyrich, Ph.D., Professor of Internal Medicine, Molecular Medicine Program, University of Utah School of Medicine

2:20 RNA-seq Taps into the Molecular Signature of Anucleate Platelets

Andrew S. Weyrich, Ph.D., Professor of Internal Medicine, Molecular Medicine Program, University of Utah School of Medicine

Platelets are anucleate cells that sprout from the cytoplasm of parent megakaryocytes. During this process, which is referred to as thrombopoiesis, megakaryocytes invest platelets with thousands of transcripts that are capped, polyadenylated, and competent for translation. Using next-generation RNA-sequencing, we have shown that platelets have a complex molecular signature that varies in disease states. We have also used next-gen RNA-seq to identify genetic disorders and novel transcript isoforms unique to platelets. These results, as well as emerging platelet RNA-seq data, will be discussed.

2:55 Alternative Transcription Exceeds Alternative Splicing in Generating the Transcriptome Diversity of Cerebellar Development

Ramana Davuluri, Ph.D., Associate Professor, Computational Biology, Wistar Institute

Our laboratory studies two closely related fundamental aspects of mammalian genomics and cancer: (i) Alternative gene promoters and (ii) Isoform-level gene regulatory networks in brain development and brain tumors, by integrative genomics and computational biology approaches. We've recently built genome-wide inventory of non-coding and protein-coding transcripts and its variants, their promoters and histone modification states for developing and adult cerebellum using integrative massive-parallel sequencing and bioinformatics approach. I will discuss the bioinformatics methods and pipelines for integrative analysis of multiple RNA-seq and ChIP-seq datasets.

3:30 Selected Poster Presentation: FLIR Automated Universal Sample Prep Technologies

Milena Iacobelli Martinez, Ph.D., Senior Scientist, FLIR Systems, Inc.

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

4:30 RNA Misregulation in Neurodegeneration

Kasey Hutt, Ph.D., Research Scientist, University of California, San Diego

TDP-43 and FUS/TLS have recently been identified as major causative factors in a myriad of neurodegenerative diseases, including ALS. Found in cytoplasmic aggregates of diseased neurons, it is increasingly recognized that the disease is caused by both gain and loss-of-function of these proteins. To mimic the loss-of-function scenario and reveal the nuclear functions of these RNA binding proteins, we perform genome-wide sequencing studies aimed at which RNA species are bound using CLIP-seq technology, and which RNA species are misregulated using RNA-seq and splicing-specific microarrays.

5:05 Fusion Gene Detection and Characterization in NGS Data

Huanying "Gary" Ge, Ph.D., Bioinformatics Analyst, Amgen

NGS generates base-pair resolution data, which allows the detection and characterization of genomic aberrations at more levels of details. We have developed an efficient fusion aligner, FusionMap, which performs a sensitive and complete search of fusion junction-spanning single-end reads and intergene paired-end reads. It can be applied to both gDNA-Seq or RNA-Seq studies and characterize fusion events at base-pair resolution.

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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