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Thursday, February 4
8:25 AM Chairperson’s Remarks
Megan Laurance, Ph.D., Senior Scientist, Ingenuity Systems, Inc.
8:30 Keynote Presentation
Kenneth H. Buetow, Ph.D., Associate Director, Bioinformatics and Information Technology, National Cancer Institute
9:00 Cooperative and Complementary Genetic Selection in Brain Tumors
Megan Laurance, Ph.D., Senior Scientist, Ingenuity Systems, Inc.
Brain tumors are a disease of the genome. These tumors show recurrent patterns of genetic aberrations. Dissecting which genetic events function cooperatively to deregulate principal signaling pathways in brain tumors and which are complementary to such deregulation will help developing refined therapeutic strategies to treat these complex diseases.
9:30 Expression Based Patient Stratification for Cancer Prognostics
Peter J. van der Spek, Ph.D., Department of Bioinformatics, Erasmus MC - Medical Faculty
Systems biology approaches in life sciences and health open new perspectives for patient stratification. Microarray and next-generation sequencing techniques provide vast volumes of data and detailed information about natural variants vs. mutations in the underlying molecular etiology of the disease. Knowledge bases allow scientists to place their research results in perspective.
Sponsored by
10:00 Functional Analysis of Omics Data in Cancer
Yuri Nikolsky, Ph.D., CEO, GeneGo, Inc.
High-throughput assays are indispensable in studies of complex human diseases. Numerous methods have been developed for Omics data analysis. I will describe GeneGo techniques of pathway, network, and interactome analysis, and summarize recent results of our collaborative studies on breast, colorectal, pancreatic, and glial cancers. I will also describe functional analysis of predictive gene signatures developed for FDA’s MAQCII project.
10:15 Sponsored by 
Cellular Target Profiling and Quantitative Phosphoproteomics Reveal Insight into a Drug’s Efficiency and Cellular Mode of Action
Jutta Fritz, Ph.D., Head of Technology, Kinaxo Biotechnologies
System-wide approaches integrating drug target identification and global phosphoproteomics depict a compound’s cellular mode of action and its impact on signal transduction. KINAXO’s chemical proteomics and global quantitative phosphoproteomics platform revealed Sorafenib’s target profile and allowed quantification of phosphorylation patterns in relation to drug administration, thereby facilitating monitoring of the integration of signaling and pointing at additional therapeutic applications.
10:30 Poster Competition Refreshment Break & Raffles in the Exhibit Hall
11:30 microRNA Expression Profiling for the Identification of Forensically Relevant Biological Fluids
Jack Ballantyne, Ph.D., Professor, Department of Chemistry, Associate Director for Research, National Center for Forensic Science, University of Central Florida
We performed the first miRNAome-wide evaluation of specific miRNA expression in dried, forensically relevant biological fluids (blood, semen, saliva, vaginal secretions and menstrual blood). A panel of nine differentially expressed miRNAs was identified that permit the identification of the body fluid using 50pg of total RNA. miRNA profiling provides a promising alternative approach to body fluid identification for forensic casework.
12:00 PM Gene Expression Signatures of Pathway Activity as Biomarkers in Oncology: RAS Pathway Signature
Andrey P. Loboda, Ph.D., Research Fellow, Oncology Molecular Profiling, Merck Research Laboratories
12:30 Luncheon Presentation I
Overview of Metabolomics
John Ryals, Ph.D., Chief Executive Officer, Metabolon, Inc.
Metabolomics is the global profiling of biochemicals and metabolites in biological samples and provides a snapshot of the metabolic state of a biological system. As such, it can rapidly characterize and identify metabolic changes caused by drugs, disease, diet or environment effects. This talk provides an overview of metabolomics and the technology requirements for profiling hundreds of biochemicals. The technology platform deployed at Metabolon involves the separation of analytes on three independent analytical platforms (GC-MS, LC-MS/MS(+), LC-MS/MS(-)). Proprietary software processes the mass spectral data and retention times by matching the run data to a database of biochemical standards. This “chemo-centric” approach results in the positive identification of hundreds of biochemicals in a single sample. Through statistical analysis, the significant changes are identified and mapped onto biochemical pathways. Because biochemicals are closely related to biological phenotype, identification of affected pathways not only provides insight into the biological mechanism but uncovers biomarkers useful in diagnosing and monitoring.
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1:00 Luncheon Presentation II
Regulatory Network Analysis of Cancer Gene Expression Profiles for Target and Biomarker Discovery Using the ExPlain™ Analysis System
Raymond DiDonato, Ph.D., Product Manager, BIOBASE Corporation
High-throughput gene expression analysis techniques generate large amounts of data, which pose a particular challenge of transforming expression data into meaningful hypotheses for target discovery and candidate biomarker identification. Traditional approaches for interpreting expression data rely on mapping differentially expressed genes to canonical pathways, biological processes, or disease states. However, understanding the transcriptional regulators and upstream signaling events that lead to differential gene expression can help better identify the molecular mechanisms that influence changes in gene expression profiles, facilitating discovery of targets which themselves are not differentially expressed, but which are key to underlying disease mechanisms. In this session we present a case study in which ExPlain™, a tool that employs the BIOBASE Knowledge Library™ for promoter and regulatory network analysis, was used to uncover target and biomarker candidates from a cancer gene expression experiment, by identifying upstream signaling molecules likely involved in the underlying pathways leading to the disease state.
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1:45 Ice Cream Refreshment Break in the Exhibit Hall
2:15 Plenary Keynote Introduction
2:25 Chips, Clones and Living Beyond 100
Paul J.H. Schoemaker, Ph.D., M.B.A., Chairman and Chief Executive Officer, Decision Strategies International, Inc.; Research Director, Mack Center for Technological Innovation, The Wharton School; Adjunct Professor of Marketing, The Wharton School Adjunct Professor, Wharton School of Business
As information technologies and life sciences continue to converge, new business opportunities and challenges will arise for the field of diagnostics and beyond. This keynote reviews the deeper forces shaping the future of the biosciences, from social and economic to technological and political, including the stresses they will introduce for existing business models and healthcare. Not only will bioconvergence introduce new products, services and competitors, it may create entirely new industries on a scale larger than the computer revolution has to date. Several broad scenarios will be painted for the state of the biosciences in 2025 and the forces that might take us there, summarizing a multi-year strategy study conducted and supervised by the speaker at the Wharton school.
3:05 Refreshment Break in the Exhibit Hall
3:45 Chairperson’s Remarks
David Haussler, Ph.D., Professor & Director, Biomolecular Science & Engineering, University of California, Santa Cruz
3:50 Whole Genome Sequencing in Cancer
Gad Getz, Ph.D., Head, Cancer Genome Analysis, The Broad Institute
4:20 Systematic Discovery of Cancer Gene Fusions using Paired End Transcriptome Sequencing
Chandan Kumar, Ph.D., Michigan Center for Translational Pathology, University of Michigan
Gene fusions represent common genetic aberrations in cancers that can serve as specific biomarkers and therapeutic targets. The recent discovery of recurrent gene fusions in prostate and lung cancers portends similar aberrations in other common carcinoma. We employ paired end transcriptome sequencing and customized bioinformatic pipelines to characterize gene fusions and chimeric transcripts in cancer.
4:50 Mapping Cancer Genomics Data to Pathways
David Haussler, Ph.D., Professor & Director, Biomolecular Science & Engineering, University of California, Santa Cruz
It is essential, but challenging to interpret cancer genomics data in terms of biological meaningful perturbations of molecular pathways within tumor cells. I will discuss a new Cancer Genomics Browser, on the web at genome-cancer.ucsc.edu, that accomplishes this through large-scale data analysis and probabilistic modeling. This methodology is currently being used in several large-scale cancer studies, including the ISPY breast cancer trial, the TCGA project and by one of the SU2C Dream Teams.
5:20 Analyzing Coding Variants
Pauline Ng, Ph.D., Senior Scientist, Human Genomic Medicine, J. Craig Venter Institute
Whole genome and whole exome sequencing are identifying a large number of coding variants. Some of these coding variants may have functional consequences that lead to disease. I will discuss the behavior of coding variants and the webtools we have made to analyze them.
5:50 Close of Day
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