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Module 2: Genomics Methodologies, Technologies and ProductsFACULTY Dr. Shawn Levy, Assistant Professor and Director of the Microarray Shared Resource Vanderbilt University Medical Center Module two will begin with a general overview of genomics technologies and continue to provide details on a variety of technologies, experimental designs, sample preparation and analysis techniques. Students will gain a level of understanding in genomic technologies to enable them to appropriately consider what impact they would have on their research program, how to more effectively use and evaluate the technologies, and finally to provide a knowledge base that prepares them for future advances of the increasing technology level that is common to modern research. TECHNOLOGY OVERVIEW. Genomic technologies are traditionally centered on the analysis of RNA and DNA molecules in a high-throughput manner or on a whole genome scale. RNA (gene expression), DNA (SNP genotyping or sequencing by hybridization) and Gene expression technologies from major vendors will be discussed along with options for production of custom arrays with user-defined content. Advantages and considerations for each will be presented along with biological material considerations. Low-throughput methodologies and technologies often used for the verification of high-density results such as RT-PCR will also be discussed. DNA genotyping technologies using microarray-based, PCR-based bead-based or mass spectrometry based techniques will be included in the course. By participating in this module, students are expected to be able to appreciate the diversity of technologies that are available for the analysis of DNA and RNA molecules, the overall application of these technologies to complex research questions, and begin to develop an appreciation of the importance of appropriate experimental and statistical design for the meaningful incorporation of the techniques into a basic or translational research program. SAMPLE PROCESSING: The Sample Processing portion of the genomics module with introduce students to the basics of nucleic acid isolation and the theory behind the most commonly used isolation techniques (organic separation and bind and elute methods. In this portion of the module, students will gain an appreciation for the basics of nucleic acid isolation, important considerations for the collection and isolation of clinical or challenging samples, and the importance of sample quality in the overall process. GENE EXPRESSION ANALYSIS USING MICROARRAYS: This portion of the module will provide a detailed description of the use of DNA microarrays for the analysis of gene expression. Students will gain an appreciation of how microarray experiments are performed as well as an appreciation of the diversity of technologies and methods that are available. They will also understand the fundamentals and theory behind the RNA labeling, hybridization, scanning, and data acquisition methods. GENOTYPING USING HIGH-DENSITY TECHNOLOGIES: This module will cover sample processing, technology diversity and details on specific platforms for high-throughput genotyping methodologies. Students will understand the fundamentals of high-throughput genotyping, its application in genomic research, and the capabilities and relative advantages of each platform. An appreciation of the data densities and tools available for their analysis will be introduced in this section. DATA ANALYSIS AND BIOINFORMATICS: This section will describe the overall data structures that are encountered in genomic analysis and detail data formats and file types. The challenges associated with the dimensionality of this type of data and the resulting unique statistical considerations will also be addressed. Key concepts such as experimental design as it relates to analysis options, data filtering and formatting tools, basic statistical tests used most routinely, supervised versus unsupervised clustering, machine learning techniques, data filtering, and open source data analysis tools and databases will be described. At the end of this section, students will be familiar with the general concepts of many of the major analytical tools commonly used today and be familiar with many of the open source efforts that are contributing to this field. The overall goal of this section is to provide the students with the basic knowledge and informational resources that they can evaluate for use in future work and experimentsGenNext's 2007 In Person Translational Courses have been completed. GenNext would like to thank its Education Partners and excellent instructors for another highly received Translational Research Program.Information regarding GenNext's 2008 program will become available shortly. Sign-up to find out about upcoming GenNext courses. For more information about this course, please contact GenNext Technologies at inform@gennexttech.com or call 650-563-9577.
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