CHI’s Seventh Annual
DNA-Seq: Advancing Clinical Applications
March 18-20, 2013
Hilton San Diego Resort, San Diego, CA


Next-generation sequencing (NGS) continues to drive the cost of generating genomic data to unprecedented lows. Opportunities for the analysis of clinically sequenced DNA are expanding, and new therapeutic strategies for personalized targeting of diseases are evolving. CHI’s DNA-Sequencing: Advancing Clinical Applications conference centers on NGS technical improvements to increase the accuracy, sensitivity and specificity of DNA to the single base pair level. As the quality of NGS data output increases, so does the analytical validity accelerating the transition into the clinic.

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Monday, March 18

8:30 am Short Course Registration

9:00 – 12:00 pm Short Courses



1:00 Conference Registration


Plenary Keynote Session 

2:00 Chairperson’s Opening Remarks

Abizar lakdawalla, Ph.D., Associate Director, New Sequencing Technologies, Illumina


2:15 Profiling Dynamic Regulation of the Epigenome Defines Linkages between Metabolism and Breast Cancer

Kevin GardnerKevin Gardner, M.D., Ph.D., Senior Investigator and Head, Transcription Regulation Section, Center for Cancer Research, NCI, NIH, DHHS
New findings linking epigenetic regulation to cellular processes that drive important hallmarks of cancer will be discussed. The broader impact of these findings on defining molecular and genomic mechanisms that uncover important connections between race, obesity and breast cancer will be reviewed.

3:00 Landscape of Somatic Retrotransposition in Human Cancers

Peter ParkPeter J. Park, Ph.D., Associate Professor, Center for Biomedical Informatics, Harvard Medical School; Informatics Program, Children’s Hospital Boston
Transposable elements (TEs) comprise close to half of the human genome, and some TE families are still able to copy and insert their sequences into other genomic loci through an RNA-mediated mechanism. We will describe our analysis of somatic retrotransposition events in cancer and their potential role in tumorigenesis, using a computational method called Tea (Transposable Element Analyzer) we developed for detecting TE integration sites at single-nucleotide resolution from paired-end whole-genome sequencing data. We have identified nearly 200 high-confidence somatic TE insertions in the cancer genomes of 43 patients across multiple tumor types, and our integrative analyses with other data types have indicated their potential impact in tumorigenesis. We will give an update on our efforts at characterizing TE activities in a more comprehensive panel of tumor types.

3:45 Afternoon Refreshment Break

4:00 Gene Regulation and Common Disease

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

5:00 Panel Discussion with Plenary Speakers

Moderator: Abizar lakdawalla, Ph.D., Associate Director, New Sequencing Technologies, Illumina

Thanks to the explosive power of NGS and extraordinary collaborative projects such as ENCODE and TCGA, researchers are gaining important new insights regarding genome function and architecture, including the role of non-coding RNAs and epigenetic modifications in health and disease. In this plenary panel discussion, our opening speakers will discuss the implications of current research and future directions and priorities.

6:00 Welcome Reception in the Exhibit Hall with Poster Viewing

7:00 Close of Day One



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