CHI’s Third Annual
RNA-Seq: Differential Expression in Depth
March 18-20, 2013 | Hilton San Diego Resort, San Diego, CA
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Tuesday, March 19
8:00 Java and Jive Discussion Groups
Grab a cup of coffee and join a discussion group. These are moderated discussions with brainstorming and interactive problem solving, allowing conference participants from diverse backgrounds to exchange ideas, experiences, and develop future collaborations around a focused topic.
Table 1: Vetting Clinical Interpretations of SNP Changes
Terry Gaasterland, Ph.D., Director, Genomics, University of California, San Diego
• How do we translate observations from the literature into clinical reports?
• How do we assign levels of evidence to published research papers that associate genome variants with a disease?
• How do we convey to the end user (physician or person)?
• What are the implications of this evidence?
• How do we define and enforce good interpretation of genomes?
Table 2: Utilization of Next-Generation Sequencing for Clinical Microbiology Applications
Andrew Camilli, Ph.D., Associate Professor, Molecular Biology & Microbiology, Tufts University; Investigator, Howard Hughes Medical Institute
• What are the critical limitations for use in diagnosis of infections?
• What measures are being taken to overcome these limitations?
• What are clear-cut and feasible opportunities?
Table 3: Cloud, Desktop Computer, Tablet or Phone – Where is the Best Place to Do My Sequence Assembly and Analysis?
Tom Schwei, Vice President & General Manager, DNASTAR, Inc.
• What tasks or functions are best done on what device?
• What are the major challenges in using each device?
• How do I effectively collaborate with others and share and transfer data?
• What will things look like two years from now?
Table 4: Understanding Non-Canonical DNA Modifications
Terry Kelly, Ph.D., R&D Manager, Active Motif
• Current evidence describing 5hmc, 5caC, 5fc
• What techniques are used to study these modifications?
• Are these modifications stable states or part of a demethylation pathway?
• What is the clinical relevance of these non-canonical DNA modifications?
Table 5: RNA-seq for Gene Expression Profiling
Melanie Lehman, Ph.D., Research Fellow, Australian Prostate Cancer Research Centre, Queensland University of Technology
• What analysis methods are available for RNA-seq analysis and how do they compare?
• Should microarray and RNA-seq data be compared?
• Is the term ‘gene’ useful in RNA-seq analysis given the prevalence of alternative splice variants?
• How can RNA-seq data be used for both clinical application and biological discovery?
9:10 Chairperson’s Remarks
Alexander Seitz, M.D., CEO , Lexogen
9:15 Single-Cell RNA-Seq Applied to Cancer and Stem Cell Biology
Louise Laurent, Ph.D., Assistant Professor, Reproductive Medicine, University of California, San Diego
We will present a new and robust method for single cell transcriptome sequencing, which we have applied to the characterization of circulating melanoma cells and the differentiation of human embryonic stem cells to hepatocytes. We will illustrate how these data can be used to determine the developmental lineage of cells, to determine the heterogeneity in cell populations, and to identify subpopulations of cells.
9:50 Using RNA-Seq to Better Understand Cancers of the Head and Neck
David I. Smith, Ph.D., Professor, Department of Laboratory Medicine and Pathology, Mayo Clinic
We have used RNA-Seq to characterize different head and neck cancers depending upon key risk factors, such as a history of drinking and smoking versus exposure to human papillomavirus. We also compared a variety of different platforms to validate the results that we detected with RNA-Seq. We present evidence that RNA-Seq could also be a powerful clinical tool.
10:25 Introducing Lexogen’s SENSE and SQUARE Technologies: Enabling Complete Transcriptome Sequencing
Alexander Seitz, M.D., CEO , Lexogen
Lexogen has developed technologies enabling complete transcriptome sequencing. SQUARE mRNA-Seq technology empowers discovery and quantification of transcript variants. SENSE mRNA-Seq library prep has a strand-specificity of over 99,9% and thus truly allows the analysis of antisense transcription.
10:40 Coffee Break in the Exhibit Hall with Poster Viewing
11:15 Non-Reference RNAs in the Prostate Cancer Transcriptome
Melanie Lehman, Ph.D., Research Fellow, Australian Prostate Cancer Research Centre, Queensland University of Technology
We have applied strand-specific RNA-seq and de novo transcriptome assembly methods to investigate RNA expression in prostate cancer cells. Many of the non-coding and protein-coding RNAs detected are not represented in RNA reference databases (e.g. RefSeq, Ensembl, Gencode) and therefore not measured by conventional gene expression profiling methods. A complete picture of the transcriptome is critical for developing a durable cure for men with late stage prostate cancer.
11:50 Seq Technologies to Understand the Human Malaria Parasite Infectious Cycle
Karine Le Roch, Ph.D., Associate Professor, Institute for Integrative Genome Biology, Center for Disease Vector Research, Cell Biology & Neuroscience, University of California, Riverside
Recent access to next-generation sequencing technologies, along with an increased number of genome-wide applications, is expanding the impact of the human malaria parasite genome on biomedical research, contributing to a paradigm shift in research activities that may possibly lead to new optimized diagnosis and treatments. Over the past few years, we have used a combination of seq technologies to provide a better understanding of the unusual mechanisms regulating chromatin and transcriptional regulation in the human malaria parasite.
12:25 pm Close of Session
12:30 Luncheon Presentation
Moving from Genomic Discovery to Translational Results: Highly Multiplexed, Automated Digital Enumeration of DNA and RNA Targets Using nCounter Technology
Joseph M. Beechem, Senior Vice President, Research & Development, NanoString Technologies
Converting insights from data-dense next-gen sequencing and expression-profiling into “clinical-strength” multi-gene diagnostic assays remains a challenge. Techniques developed by NanoString Technologies (Seattle WA), based on optical molecular barcoding (Nature Biotech (2008) 26:317-25), digitally counts nucleic-acid targets (up to 800-plex) from a wide range of difficult sample inputs:from single cells (10 pg input RNA) to 30-yr-old FFPE tumor specimens. Single-cell gene-expression, miRNA counting, and retrospective clinical studies (NanoString PAM50 breast-cancer panel) will be presented.
2:00 Chairperson’s Remarks
2:05 Global Analysis of RNA Alternative Splicing by Deep Sequencing
Yi Xing, Ph.D., Associate Professor, Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles
Ultra-deep RNA sequencing (RNA-Seq) has become a powerful approach for genome-wide analysis of pre-mRNA alternative splicing. We developed MATS (multivariate analysis of transcript splicing), a flexible statistical framework for detecting differential alternative splicing patterns from RNA-Seq data. Using RNA-Seq, we investigated the complete spectrum of alternative splicing events that are regulated by the epithelium-specific splicing regulatory proteins ESRP1 and ESRP2. Our study provides a comprehensive picture of an extensive epithelial alternative splicing program in development and disease.
2:40 RNA-Seq Analysis of Platelets and Their Precursors
Jesse Rowley, Ph.D., Research Fellow, Andrew Weyrich Lab, Eccles Institute of Human Genetics, University of Utah
Platelets, the only cell type that are at origin devoid of nuclei, contain nucleic acids including mRNA and miRNA that they acquire from their precursor cells, megakaryocytes. Novel properties of platelet and megakarycoyte transcriptomes identified through RNA-seq, and the clinical utility of RNA-seq in platelets will be discussed.
3:15 Selected Poster Presentation: A Robust Pipeline for Comparing RNA-Seq Samples of Two Classes
Xuegong Zhang, Ph.D., Professor, Automation Bioinformatics Institute, Tsinghua University
3:30 Refreshment Break in the Exhibit Hall with Poster Viewing
4:00 Identification of Transcription Factor Gene Targets Using Chromatin Immunoprecipitation (ChIP)-seq Combined with Transcriptome Analysis
Elizabeth Thomas, Ph.D., Associate Professor, Molecular Biology, The Scripps Research Institute
Transcription factors can control the expression of numerous genes, although the complete range of target genes for most transcription factors are unknown. This presentation will describe the use of chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) in combinmation with genome-wide expression profiling to define target genes for two CNS transcription factors, B-cell leukemia/lymphoma 11B (Bcl11b) and Forkhead box protein P1 (FoxP1). Therapeutic implications will also be discussed.
4:35 High-Throughput Sequencing of Extracurricular RNA and Decoding Their Functional Role in the UV-Response
Benjamin Yu, M.D., Ph.D., Associate Professor, Medicine and Dermatology, Institute for Genomic Medicine, Stem Cell Program, University of California, San Diego
Extracurricular RNAs (exRNAs) have been described in a number of tissues but their physiologic functions in humans are unknown. In the skin, we have recently discovered that exRNAs play a role during the initial stages of UV-induced sunburns. Using RNA-seq, the non-coding U1 RNA was identified as a possible trigger for the UV-inflammatory response. Further studies now provide high-resolution mapping of the physiologic mechanisms involved in the UtV-induced exRNA response.
5:10 Close of Day
5:30-8:30 Dinner Short Courses
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