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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.

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Monday, February 10


10:30 am Conference Program Registration


11:50 Chairperson’s Opening Remarks

Babak Alizadeh, Ph.D., Co-founder & COO, PrognosDx Health, Inc.

12:00 pm The Cancer Epigenome

Peter A. Jones, Ph.D., D.Sc., Director, USC Norris Comprehensive Cancer Center; Distinguished Professor, Urology, Biochemistry & Molecular Biology, Keck School of Medicine, University of Southern California

Recent genome sequencing projects have revealed a surprising number of unanticipated mutations in genes which modify the epigenome. These studies have revealed a much closer interaction between the genetic and epigenetic basis of human cancer. We have begun to explore the potential effects of these mutations on the epigenome, paying particular attention to the existence and roles of chromatin accessibility in carcinogenesis. There is also excitement at the potential to use drugs to target these changes and I will discuss the effects of DNA methylation inhibitors.

12:30 Crosstalk between 5-Methylcytosine, 5-Hydroxymethylcytosine and Histone Modifications in Cancer

Gerd Pfeifer, Ph.D., Lester M. and Irene C. Finkelstein Endowed Chair, Biology & Professor, Epigenetics and Genetics of Cancer, Cancer Biology, City of Hope

Although changes of the epigenome, such as perturbation of DNA methylation patterns, are common events in human cancer, their contribution to the initiation and progression of malignant tumors has remained unclear. We have analyzed histone and DNA cytosine modifications in human cancer and normal tissue. The relationship between chromatin marks and cytosine modifications will be discussed. We propose a model in which specific epigenetic changes are shown to be important for the selection of tumor-driving events and thus may play a major role in cancer progression.

1:00 Session Break

1:15 Luncheon Presentation I: Accelerating Large Scale Genomics and Translational Research Using an Integrated High Performance Computing Solution

Kathy Tzeng, Ph.D., Team Lead, Life Sciences Solution Enablement, IBM 

Scott Markel, Ph.D., Principal Bioinformatics Architect, Accelrys

Advancements in life science research and translational medicine drive the need for new technologies and computing approaches. These approaches pose challenges for IT leaders, researchers and developers to manage, share and store higher data volumes with greater efficiency at lower cost. Life sciences industry experts will discuss compute- and data-intensive challenges, the latest IBM genomic medicine solutions and real-world strategies adopted by leading genomic research institutes for large-scale data projects. 

1:45 Luncheon Presentation II: Beyond Known microRNAs: Exploring the Rest of the Small RNA Transcriptome

Todd M. Lowe, Ph.D., CSO, Maverix Biomics, Inc.

Within the human transcriptome, microRNAs have proven to be the most dynamic, functionally important class of small non-coding RNAs, influencing the regulation of the majority of protein coding genes. However, largely unexplored small RNA transcriptome data sets, both public (ENCODE, TCGA, SRA) and private, have revealed a very wide range of novel small RNA transcripts with potential to be new biomarkers or uncharacterized regulators. To enable hands-on exploration of RNA-seq data sets by a much larger community of biologists, we have developed the Maverix Analytic Platform, integrating tools and data at the command of any researcher. We show examples of these overlooked classes of small RNAs to illustrate the untapped opportunities for discovery.

2:15 Session Break


2:30 Chairperson’s Remarks

Kathy Tzeng, Ph.D., Team Lead, Life Sciences Solution Enablement, IBM 

2:35 What Does Our Genome ENCODE?

John Stamatoyannopoulos, M.D., Associate Professor, Genome Sciences and Medicine, School of Medicine, University of Washington

3:05 Pan-Cancer to Personalized Pathway Targets

Josh Stuart, Ph.D., Baskin Engineering Endowed Chair & Professor, Department of Biomolecular Engineering; Associate Director, Center for Biomolecular Science & Engineering, University of California, Santa Cruz

The Cancer Genome Atlas Research Network has profiled and analyzed large numbers of human tumors to discover molecular aberrations at the DNA, RNA, protein and epigenetic levels. The rich data resulting from that enterprise provides a major opportunity to develop a picture of commonalities, differences, and emergent themes across tumor lineages. In this talk I will discuss our efforts to create new tools to elucidate disrupted pathways in cancer cells to infer the “health”
of cellular circuitry.

3:35 Single Cell Genome Sequencing: Life at the Single Molecule Level

Xiaoliang Sunney Xie, Ph.D., Mallinckrodt Professor, Chemistry, Department of Chemistry and Chemical Biology, Harvard University

Point mutation and copy number variation, which are two major dynamical changes of DNA, can now be studied at the single cell level by whole genome amplification and sequencing. Experiments probing the biology of meiosis and cancer will be described. We demonstrate the proof of principle of selecting oocytes in in vitro fertilization in order to avoid miscarriage and genetic diseases. We also show that individual circulating tumor cells can be sequenced, providing tumor genetic signatures for personalized therapy.

4:05 Selected Poster Presentation: Genome-Wide Copy Number Profiling of Single Cells in S-Phase Reveals DNA Replication Domains 

Niels Van der Aa, Research Scientist, Laboratory for Cytogenetics and Genome Research, Katholieke Universiteit Leuven



4:35 Refreshment Break and Transition to Plenary Keynote 

5:00 Plenary Keynote Session (Click Here For More Details) 

6:15 Grand Opening Reception in the Exhibit Hall with Poster Viewing

7:45 Close of Day


Day 1 | Day 2 | Day 3 | Download Brochure 

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