CHI’s Third Annual
RNA-Seq: Differential Expression in Depth
March 18-20, 2013 | Hilton San Diego Resort, San Diego, CA
RNA-Seq is perhaps the most complex NGS application. The range, depth, and complexity of a human transcriptome is far from fully characterized. RNA transcripts, by nature, are moving targets, making their characterization and quantification difficult. A single RNA-Seq experiment can provide relatively unbiased sequence information for analysis of gene expression, novel transcripts, novel isoforms, alternative splice sites, allele-specific expression, cSNPs, and rare transcripts, depending on read depth. CHI’s Third Annual RNA-Sequencing: Differential Expression in Depth conference centers on NGS technical improvements providing new insights into our active genome.
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Monday, March 18
8:30 am Short Course Registration
9:00 – 12:00 pm Short Courses
1:00 Conference Registration
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 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 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
Day 1 | Day 2 | Day 3 | Download Brochure