2014 Archived Content


Cambridge Healthtech Institute’s Fifth Annual

Genome and Transcriptome Analysis

Next-Generation Sequencing of Disease Genomes, Epigenomes & Transcriptomes

February 10-12, 2014 | Moscone North Convention Center | San Francisco, CA


Over a decade following the completion of the Human Genome Project, next-generation sequencing has progressed from the future to the forefront of modern-day research. The advent of NGS– along with a shift toward precision medicine – has revolutionized the prevention, diagnosis, prognosis, treatment and understanding of the basic biology of complex disease, by offering unprecedented interrogation of the human genome at high resolution, and relatively low costs. With NGS becoming commonplace, and canvassing a wide range of applications within genome, epigenome, and transcriptome interrogation, holistic views of human diseases are emerging from the integration of varied NGS data - providing insights into the underlying genome, a regulatory epigenome, and a dynamic transcriptome. The Genome and Transcriptome Analysis meeting is designed to explore how NGS is continuing to shape our understanding human disease, by uncovering biological meaning from analyzing NGS data.


Day 1 | Day 2 | Day 3 | Download Brochure 

Wednesday, February 12

7:00 am Breakfast Presentation (Sponsorship Opportunity Available) or Morning Coffee

8:00 Plenary Keynote Session (Click Here For More Details)  

9:45 Refreshment Break and Poster Competition Winner Announced in the Exhibit Hall


10:35 Chairperson’s Remarks

Francisco M. De La Vega, D.Sc., Visiting Instructor, Department of Genetics, Stanford University School of Medicine

10:40 Concomitant Clonal Evolution of Leukemia Across the Genome, Epigenome, and Transcriptome

Christopher Mason, Ph.D., Assistant Professor, Computational Biomedicine, Weill Cornell Medical College

We have examined patients with acute myelogeneous leukemia (AML) during treatment with genome sequencing, epigenetic profiling (RRBS), and ribo-depleted RNA sequencing. Our results demonstrate a convergence of disrupted biological networks in DNA, RNA, and DNA methylation that mediate chemo-resistance. Also, we observe new prognostic features of epigenetic clones that can predict relapse time, allele-specific switching of damaging mutations, and completely novel, complex genetic rearrangements. Together, these data reveal an extremely dynamic evolutionary landscape of molecular changes, which tumors rapidly engage to survive.

11:10 From Outlier Cancer Phenotypes to Precision Genotypes

Barry S. Taylor, Ph.D., Assistant Professor, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco

Little is known about the basis of elusive exceptional responses to cancer therapy. I will describe their outlier phenotype-to-genotype approach that uses both whole-genome and deep targeted sequencing to identify the molecular genetic basis of complete and durable response to both targeted and systemic cancer therapies. Recent work will be discussed on the use of such approaches coupled to nuanced computational analyses to identify not only individual sensitizing mutations, but also synergistically acting genetic interactions and the contribution of tumor clonality to the durability of treatment response.

11:40 Computational Approaches for Analyzing Mutational Heterogeneity in Cancer Genomes

Ben Raphael, Ph.D., Associate Professor, Department of Computer Science & Center for Computational Molecular Biology, Brown University

Recent cancer sequencing studies have demonstrated extensive mutational heterogeneity within some tumors, with multiple subpopulations of tumor cells having different complements of somatic mutations. We describe computational techniques to characterize this intra-tumor heterogeneity from whole-genome sequencing data.

12:10 pm Session Break

12:20 Luncheon Presentation (Sponsorship Opportunity Available) or Lunch on Your Own

1:00 Refreshment Break in the Exhibit Hall and Last Chance for Poster Viewing


1:40 Chairperson’s Remarks

Ben Raphael, Ph.D., Associate Professor, Department of Computer Science & Center for Computational Molecular Biology, Brown University

1:45 Assembly and Variant Calling of High-Throughput Sequencing Data: Lessons from Large-Scale Sequencing Projects and Moving to the Clinic

Francisco M. De La Vega, D.Sc., Visiting Instructor, Department of Genetics, Stanford University School of Medicine

Here I discuss the principles to implement and validate such pipelines in terms of sensitivity and specificity of the full spectrum of genetic variation, turn-around time and quality, and what are the current open challenges based on experience gained at the 1000 Genomes Project and other large-scale sequencing studies. I will also discuss advanced methods to improve variant quality by leveraging family & population structures, individual germline references in cancer sequencing, and integrative analysis of orthogonal NGS data sets.

2:15 Novel Computational Methods for RNA-Seq Data Analysis

Colin N. Dewey, Ph.D., Associate Professor, Departments of Biostatistics & Medical Informatics and Computer Sciences, University of Wisconsin, Madison

One revolutionary aspect of RNA-Seq is its ability to provide information regarding transcript abundances in species whose genomes have not yet been sequenced. In such situations, transcript quantification involves a combination of de novo assembly and abundance estimation, both of which are challenging tasks when a reference genome is unavailable. I will present my group’s recent work in addressing these challenges. In particular, our novel methodology for evaluating the accuracy of de novo transcriptome assemblies and performing quantification with them.

2:45 Genomics & Sequencing Data Integration, Analysis and Visualization

Carl Meinhof, Manager, Research Informatics, IT, Ceres, Inc.

Scientists expect to navigate genomic data with the same ease and speed that they can navigate geographic data. We have developed a genome browser that uses algorithms from game development to provide high-performance visualization of genomics data. Data from multiple sources can be integrated in a relational database backend, but users can also visualize data from files. Due to its high speed and ease of use the browser facilitates playful exploration of data.

3:15 An Integrative Web Portal for the Biodiscovery and Visualization of Gliobalstoma

Uma Shankavaram, Ph.D., Staff Scientist, Bioinformatics, Radiation Oncology Branch, NCI, NIH

3:45 Refreshment Break


4:00 Chairperson’s Remarks

Gabe Rudy, Vice President, Product Development, Golden Helix

4:05 CLIA-Certified Cancer Genome Diagnostic Testing in a Rapidly Changing Environment

David Wheeler, Ph.D., Co-Director, Bioinformatics; Associate Professor, Department of Molecular and Human Genetics, Baylor College of Medicine

A CLIA lab seeks reproducibility and stability in the assays performed. However, the rapid accumulation of novel and exciting cancer genome discoveries is expanding our view of the genetic landscape of cancer and impacting how diagnostic testing can be performed. Here I will discuss analytical and biological advances that are changing the way we think about diagnostic services, and how we are integrating them into the CLIA lab.

4:35 Implementation of Next-Generation Sequencing in the Clinical Molecular Oncology Laboratory

Eric Duncavage, M.D., Assistant Professor; Director, Molecular Genetic Pathology Training Program, Department of Pathology and Immunology, Division of Clinical and Genomic Medicine, Washington University

This talk will focus on the design, informatics, and validation of clinical grade NGS-based oncology testing based on experience in the Washington University Genomics and Pathology Services Laboratory. Design considerations including enrichment methods and selecting the best genes for an oncology panel will be discussed and an evaluation of clinical-grade variant analysis tools will be provided. Finally, NGS validation practices, regulatory guidelines, and reimbursement issues will be reviewed.

5:05 Interpreting My DTC Exomes Using Public Access Clinical Databases

Gabe Rudy, Vice President, Product Development, Golden Helix

23andMe provided through a limited pilot the delivery of uninterpreted exomes in 2012. In this talk, I use GenomeBrowse and publicly available clinical databases such as ClinVar and OMIM, as well as many other integrative genomic annotations, to interpret the exomes of myself, wife and son. Recent improvements in alignment, variant calling and public annotation sources may be able to take my research grade exome to a clinical grade interpretation.

5:35 Close of Conference Program

Day 1 | Day 2 | Day 3 | Download Brochure 

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