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Download Final Agenda Day1 Day2 Day3   Main Conference Wednesday, April 11 7:30    Registration and Morning Coffee Sponsored by 8:30    Opening Introductions Keynote Presentations: 8:40    The Rosetta Stone of Cancer Genomics & Proteomics James L. Wittliff, Ph.D., M.D. hc, Professor of Biochemistry & Molecular Biology, James Graham Brown Cancer Center, University of Louisville Click here to view video interview 9:20    Preanalytical Variables in the Analysis of Biomarkers for Clinical Trials Scott D. Patterson, Ph.D., Senior Director, Medical Sciences, Amgen Inc. Much can be learned from the careful examination of analytes from samples collected from clinical trials. For example, PK:PD responses can be modeled to help guide dose-ranging studies. However, collected human tissue samples should be considered as responding to their perturbed environment until they are rendered incapable of doing so. Understanding what can happen to the analytes of interest in the period from collection of the tissue to analysis is critical to generating robust data. Click here to view video interview 10:00  Coffee Break 10:35  The Impact of Tissue Fixation Time and Whole Genomic Amplification on Array CGH Profiles Susan J. Done, MBA, Ph.D., MB, FRCPC, Bchir, Scientist, Division of Applied Molecular Oncology, Ontario Cancer Institute (OCI) 11:05  Using Microarrays to Assess microRNA Expression Changes in the Human Brain: Neurodegeneration and Brain Cancer Peter T. Nelson, M.D., Ph.D., Assistant Professor, Sanders-Brown Center on Aging, University of Kentucky Microarray experiments studying miRNA expression changes in human tissue hold much promise but researchers must be mindful of important pitfalls.  Besides the usual statistical issues, caveats include RNA quality issues; clinico-pathological correlates; cellular heterogeneity even in small tissue samples; post-microarray data validation (which must include in situ hybridization!); and some other technical considerations.  I will present data about miRNA microarray studies I have performed on RNA from human brain tissue with a focus both on the interesting conclusions that we have obtained, and the pitfalls that we have experienced. 11:35  Expression of Integrin alpha V (CD 51) in Colorectal Cancer using Tissue Microarrays Albert J. Kovatich, M.S., President and CSO, MDR Global Systems, LLC Integrins are involved in tumor cell- extracellular matrix interactions and receptor tyrosine kinase modulation.  A tissue micro-array was created to evaluate the expression of the alpha V integrin, alphaVbeta5 and the epidermal growth factor receptor (EGFR) in colorectal cancer samples.  Image analysis for TMA applications was used to score the expression of the markers. 12:05  Lunch on your own (Sponsorship for Technology Presentation Available) 1:30    Accelerating the Development of Targeted Therapeutics with Tissue Microarrays John Reilly, Ph.D., Research Fellow, Merck & Co, Inc. Sponsored by Identification of patient populations likely to respond to a particular compound is a key issue in clinical development for oncology indications.  Combining cancer tissue microarrays, immunohistochemistry and automated image  analysis allows rapid assessment of target activation in clinical samples to facilitate preclinical and clinical development of targeted therapies. 2:00    Luminescent, Fluorescent Nanoparticle and Rolling Circle Amplification Detection on Microelectronic Arrays  Michael J. Heller, Ph.D., Professor, Department of Bioengineering, University of California San Diego  Microelectronic array devices have been used to carry out a variety of DNA genotyping applications. Most often, the DNA probes used in these hybridization assays are labeled with organic fluorophores. However, after considerable time and effort the detection of low copy number targets (<10,000) still remains problematic. More recently, a new generation of fluorescent nanoparticles called quantum dots have become readily available and are being used for biomolecule detection applications. We are now developing methods for creating luminescent/quantum dot complexes in combination with rolling circle amplification techniques as a way to overcome the specificity/sensitivity limitations seen in classical DNA genotyping applications. This microarray technology is being developed for cancer genotyping diagnostics, in particular for p53 point mutation analysis. 2:30    Histological Staining Methods Preparatory to Laser Capture Microdissection Significantly Affect Detection of mRNAs in Microarray Hybridization  J. Frederic Mushinski, Ph.D., Senior Investigator, Laboratory of Genetics, Center for Cancer Research, National Cancer Institute, NIH To study the contribution of staining methods to degradation of results from GEP of LCM samples, we subjected pellets of the mouse plasmacytoma cell line TEPC1165 to direct RNA extraction and to parallel frozen sectioning for LCM and subsequent RNA extraction. We used microarray hybridization analysis to compare GEP of RNA from cell pellets with that of RNA from frozen sections that had been stained with hematoxylin and eosin (H&E), Nissl Stain (NS), and for immunofluorescence (IF) as well as with the plasma cell-revealing methyl green pyronin (MGP) stain. The MGP-stained samples showed the least introduction of mRNA loss, followed by H&E and immunofluorescence. Inclusion of RNAase inhibitor in aqueous staining solutions appears to be important in protecting RNA from loss of gene transcripts. 3:00    Meet-the-Experts Brainstorming discussion groups moderated by experts in the area. Attendees are invited to choose the table according to their main interest; however, they may switch between roundtables. We emphasize that this roundtable discussion is for an interactive exchange among scientists and is not meant to be, in any way, a corporate or product discussion Topics moderated: Table 1: The Importance of Protein Partitioning and Fractionation:  Enrichment before Downstream Analyses Host: TBA •“To partition or not to partition? That is the question.”  • Specificity & reproducibility? • Methods for high capacity proteome fractionation • Digging into the proteome using these tools. How deep can you go? Table 2: Gel Based Proteomic versus Peptide Labeling Proteomic Host: Sunny Tam, Ph.D., Director of Proteomic Fractionation Group, Research Associate Professor, UMMS Proteomic Consortium, University of Massachusetts Medical School • Pros and cons of 2D gel versus iTRAQ • What are the expected outcomes of the two approaches? • What are the future improvements for the two approaches? Table 3: Biorepositories/HIPAA/IRB Host: James L. Wittliff, Ph.D., M.D. hc, Professor of Biochemistry & Molecular Biology, James Graham Brown Cancer Center, University of Louisville Table 4: Influence of Sample Collection Parameters on Functional Assays Host: Scott D. Patterson, Ph.D., Senior Director, Medical Sciences, Amgen Inc. • Which analytes change rapidly following collection? • What realistic controls can be put in place? • Validity of ex vivo stimulation as oppose Table 5: RNA Amplification and Labeling for Array Profiling Host: Christoph Adams, Ph.D., Research Area Manager/Epigenetics, Life Sciences Division, Invitrogen Corporation • Normalizing RNA sample input • What constitute proper internal controls for array normalization? • When is RNA amplification a good idea?  • How many microRNAs are there in humans? Table 6: Fresh versus Frozen Tissue in Drug Discovery Research Host: James Eliason, CSO, Research and Development, Asterand, Inc.; Associate Professor, Barbara Ann Karmanos Cancer Institute, Wayne State University Table 7: Sample Collection and Processing, a Pivotal Stage of Transcript Profiling Host: Eric R. Fedyk, Ph.D., Senior Scientist II, Drug Safety Evaluation, Millennium Pharmaceuticals, Inc. • When to collect and store samples frozen versus formalin-fixed and    paraffin-embedded? • Isolate subpopulations of leukocytes or store whole blood? Table 8: Confidence in Multiplex Immunoassay Data Host: Robert S. Negm, Ph.D., Vice President, GenTel BioSciences  • Methods to array replicate antibody microspots?  • What defines confidence in dilutional recovery and precision data?  • What is the future of automating antibody chips? 4:30    Better Microarray Spots Using Continuous Flow Spotting Techniques Bruce Gale, Ph.D., Assistant Professor, Mechanical Engineering, University of Utah A microfluidic platform for manufacturing protein, lipid, and cell arrays has been developed that produces spots with less than a 5% CV between spots, making microarrays a more quantitative tool.  In addition, these systems have shown the ability to concentrate proteins from crude samples on spots without expensive purification steps, significantly reducing the cost of custom protein microarrays.  These same systems have been shown to be able to deposit cells, lipid bilayers, and sequential chemistries on a single spot with high quality. 5:30    End of Day One

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