Core--Genomics

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(Applicant's Abstract) Two factors make the Genomics Core (GC) a necessity in this SCOR proposal. First the GC avoids the potential wasted resources resulting from individual component projects assembling a genotyping, sequencing and data warehousing infrastructure. The molecular biological techniques used in DNA sequencing and in DNA genotyping are straightforward, however, organizing their implementation on a large scale requires the integration of molecular biology, production engineering "assembly line" design, and quality control process monitoring. Overlaid upon this is the requirement for efficient trafficking of the data, including sample tracking, software scripted interfaces between technicians and analytical instruments, between different analytical instruments, and between analytical instruments and databases. Finally the data must be accessible. This requires rational organization into database structures which can be queried with maximal flexibility. It is unnecessarily redundant and practically impossible for each Principle Investigator to design and build these elements into a coherent system. Second the Genomics Core is the most efficient way to deliver the best technical methodology to each project. The technology underlying DNA sequencing, DNA genotyping and genetic data management is in an extremely dynamic phase of development. In addition to providing a centralized technical service with genetic data as the work product, a goal of the Genomics Core is to enable each SCOR component project, at the conclusion of the funding period, to continue pursuing its research objectives using state of the art methods. Thus the Genomics Core mitigates the potential redundancy in both technical execution and in evaluating and assimilation emerging technologies into the component projects. Dr. Walt Klimecki, the Core Leader of the GC is ideally suited to direct this key SCOR component. He is currently directing high throughput genetic analysis at the University of Arizona Respiratory Sciences Center, a position he moved to after directing product development in polymorphism analysis at Motorola BioChip Systems, a biotechnology "start-up" within Motorola Incorporated. The Genomics Core will accomplish the first objective by providing a central facility with 1) All necessary equipment, 2) Existing, working, standard operating procedures (SOPs), 3) Skilled technical personnel with experience executing all necessary methods, and 4) The necessary computing infrastructure. Dr. Klimecki will interact extensively with each component project to develop an experimental plan. Each component project will provide technical personnel. The mission of the GC is to train the component projects' personnel in the execution of the experimental plan at the Core facility. Dr. Klimecki and the GC staff will monitor the progress of each project, including supervising quality control measures ("blinded" samples introduced into the sample chain). Emerging genetic analysis technologies will be continually evaluated for potential integration into component projects. The GC will supervise data management and work with project investigators to enable the data to be accessed and analyzed in the most efficient form for each project. The GC will accomplish the second objective by continually evaluating emerging technology in genetic analysis and data management. This includes evaluating scientific literature, attending national and international technology-focused meetings (for which we are requesting funding), and through internal technology development (an ongoing effort for which we are not requesting funding within this SCOR).