WEDNESDAY, SEPTEMBER 23, 2009
7:30am Breakfast Presentation Sponsored by .JPG "JMP Software")
Next-Gen Biomarker Discovery Using Alpheus and JMP Genomics
Doug Robinson, Ph.D., JMP Genomics Applications Scientist Manager, SAS Institute Inc.
Faye D. Schilkey, Associate Director, NM Sequencing Center, National Center for Genome Resources
Please join us for a complimentary breakfast seminar and learn how scientists at the National Center for Genome Resources (NCGR) have integrated JMP Genomics into their standard workflows for next-generation Illumina sequence analysis. Co-presenters Faye Schilkey, Associate Director of NCGR’s New Mexico Genome Sequencing Center, and JMP Genomics Application Scientist Doug Robinson will discuss cutting-edge NCGR research projects that display the flexibility and power of next-generation sequencing technology when combined with JMP Genomics tools for dynamic data analysis and pathway exploration.
8:15 Chairperson’s Remarks
Murali Ramanathan, Ph.D., Assoc.Professor, Director, Graduate Studies, Pharmaceutical Sciences & Neurology, State University of NY
8:20 The Path to Personalized Cancer Treatment Utilizing the Molecular Gateway
Jae K. Lee, Ph.D., Associate Professor of Biostatistics and Epidemiology, University of Virginia School of Medicine
The actualization of personalized medicine in cancer requires combining conventional clinical patient data with different molecular assessment profiles based on their careful bioinformatics analyses. This synergistic approach offers tangible benefits such as heightened specificity in molecular classification of cancer subtypes, improved prognostic accuracy, targeted development of new therapies, novel applications for old therapies, and tailored selection and delivery of chemotherapeutics. Personalized medicine is poised for rapid growth as insight provided by new molecular platforms is integrated with current procedures for assessment and treatment of patients with cancer.
8:50 Sequencing in the Study of Psychiatric Diseases
Chunyu Liu, Ph.D., Department of Psychiatry, University of Chicago
Genetic dissection is the basis of personalized medicine. Identification of risk genes, variants and their associations with diseases, intermediate phenotypes, and drug responses could lead to better diagnosis and treatment of complex diseases. Large-scale deep sequencing, including next-generation sequencing, has been used in our study of psychiatric diseases, particularly Bipolar Disorder and Schizophrenia, to search for genetic variants and differential expression of microRNA genes. Both common and rare variant models for common diseases were investigated. Integration of genetics and genomics data has been explored. The Next-Gen may hold the key of the personalized treatment of psychiatric diseases.
9:20 Information-Theoretic Identification and Modeling of Gene-Gene, Environment-Environment and Gene-Environment Interactions
Murali Ramanathan, Ph.D., Associate Professor, Director of Graduate Studies, Pharmaceutical Sciences and Neurology, State University of New York
9:50 Statistical Model for Whole Genome Sequencing and its Application to Minimally Invasive Diagnosis of Fetal Genetic Disease
Tianjiao Chu, Ph.D., Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburg School of Medicine
10:20 Technology Spotlight Sponsored by
Next Generation Sequencing: Application Specific Data Analysis Pipelines
Heather Koshinsky, Ph.D., Chief Scientific Officer, Eureka Genomics
10:35 Networking Coffee Break, Exhibit & Poster Viewing
11:15 A Geometric Approach For Classification And Comparison of Structural Variants
Ben Raphael, Department of Computer Science and Center for Computational Molecular Biology, Brown University
Structural variants, including duplications, deletions, and inversions, are an important contributor to human genome variation. We introduce a geometric approach to classify and compare structural variants across multiple samples and multiple measurement platforms, including both paired-end sequencing and microarray hybridization data. Our method represents the uncertainty in the measurement of a structural variant, the breakpoint region, as a polygon in the plane, and identifies measurements supporting the same variant using techniques from computational geometry. We demonstrate our geometric approach on data from several normal and cancer genomes.
11:45 Exploring the Human Microbiome with Next-Generation Sequencing
Rob Knight, Ph.D., Assistant Professor, Department of Chemistry and Biochemistry, University of Colorado at Boulder
Over the past four years, a “large” microbiome sequencing study has expanded from ~1000 sequences to ~1,000,000 sequences, with the prospect of ~100,000,000 sequences near at hand. Each order of magnitude increase in the number of sequences, and, potentially, the number of samples, poses substantial new challenges but also new opportunities. Here I discuss how the software tools that my lab has developed have allowed us to use studies in the 100,000-1,000,000 sequence regime, split across hundreds of samples, to discover unexpected large-scale patterns in human microbiome data: the relationships among body habitats, trends within the microbiome of one individual over time, and the definition of the microbial core at the lineage and functional level. I also discuss the outlook for preparing for the next two orders of magnitude in sequencing ability.
12:15pm Luncheon Presentation (Sponsorship Opportunity Available) or Lunch on Your Own
2:00 Chairperson’s Remarks
Patrice Milos, Ph.D., VP & CSO, Helicos Biosciences
2:05 Observations of the Most Abundant and Active Genes in the Biosphere—The Ecology of Viral Genes
K. Eric Wommack, Ph.D., Associate Professor, University of Delaware, Delaware Biotechnology Institute
Shawn Polson, Ph.D., Postdoctoral Fellow, University of Delaware, Delaware Biotechnology Institute
Two decades of aquatic viral ecology research have established that marine microbial communities support large viral populations with rapid turnover rates. As a consequence we can assume that most genes within aquatic viral metagenomes are actively replicated and expressed within aquatic microbial communities. Thus, one challenge for the coming third decade of the ‘third age of phage’ is to leverage metagenomic resources for an increasingly sophisticated view of the role of viral processes within microbial communities. High-throughput sequencing of viral genomic nucleic acids from environmental samples is adding exquisite genetic detail to our view of natural viral assemblages. It is quite possible that dsDNA viruses alone are among the greatest reservoirs of genetic diversity in the biosphere. Our recent work indicates that even the most commonly encountered genes within viral assemblages are largely unknown, showing no homology to previously sequenced genes. This talk will review the current status of viral metagenomics and propose paths forward to meeting the challenge of understanding the ecological significance of abundant and active viral genes.
2:45 Transcriptome-Guided Characterization of Genomic Alterations
Qi Zhao, Ph.D., Assistant Professor, Human Genomics Medicine, J. Craig Venter Institute
We have identified new genomic alterations in a breast cancer cell line using high-throughput transcriptome sequencing. With cDNA sequences captured by 454 reads, we were able to identify genomic rearrangement events leading to fusions or truncations of genes already implicated in oncogenesis and other additional genes . Our approach demonstrates that high-throughput transcriptome sequencing is an effective strategy for the characterization of genomic changes in cancers.
3:15 Networking Refreshment Break and Final Exhibit and Poster Viewing
3:45 Detecting Signatures of Domestication in the Chicken Genome
Michael Zody, M.Sc., Chief Technologist, Broad Institute and Department of Medical Biochemistry and Microbiology, Uppsala University
We used SOLiD sequencing to generate whole genome shotgun sequence data from pools representing several different domestic chicken lines and a pool of red junglefowl. This sequencing yielded over 5 million high confidence SNPs (>99% validation rate) and more than 2,000 high confidence deletions. Analysis of variation within domestic lines showed a large number of regions of extended homozygosity within one or more domestic lines, indicating sites of likely selective sweeps during domestication or later specialization of domesticated lines.
4:15 The Vertebrate Microbiome in Health and Disease
Rob Knight, Ph.D., Assistant Professor, Department of Chemistry and Biochemistry, University of Colorado at Boulder
Frederic Bushman, Ph.D., Professor, Microbiology, University of Pennsylvania
Alterations in vertebrate-associated microbial communities have been implicated in maintaining health and alterations can accompany disease. Examples from recent studies will be presented that emphasize the dynamics and diversity of the vertebrate microbiome, and the value of Next-Generation Sequencing as an analytical tool.
5:00 Close of Meeting
Co-located Event: Exploring Next-Generation Sequencing
For more information, please contact:
Mary Ann Brown
Executive Director, Conferences
Cambridge Healthtech Institute
Email: mabrown@healthtech.com
Phone: 781-972-5497
For exhibit and sponsorship information, please contact:
Angela Parsons
VP, Business Development
Cambridge Healthtech Institute
Email: aparsons@healthtech.com
Phone: 781-972-5467