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Core D: Genomics and Bioinformatics

The Genomics and Bioinformatics Core will assist SPORE projects in experimental and analytic aspects of gene expression profiling. Initially, the Core bioinformatics team will assist SPORE project leaders in the design of expression profiling experiments, including issues of sample replication for statistical analysis. The Core will obtain RNA samples from investigators. Genomics and Bioinformatics Core staff will then in vitro transcribe and label complementary RNA (cRNA), hybridize the cRNA to oligonucleotide arrays, incubate with detection reagents, and scan the resulting fluorescent images. The data will be distributed to investigators using the database system and internet-based data pipeline of the Genomics and Bioinformatics Core. Investigators and affiliated members of the Genomics and Bioinformatics Core have extensive experience analyzing gene expression data. They will share this expertise--including image analysis, statistical analysis, data scaling, clustering, and supervised learning approaches--with members of the SPORE projects. In addition, the informatics staff of the Genomics and Bioinformatics Core will work to generate innovative approaches for data analysis where necessary. Because of its information-handling infrastructure, the Genomics and Bioinformatics Core will be able to readily share information between DF-HCC Lung SPORE projects. We expect that investigators in other lung cancer SPOREs will also wish to analyze the gene expression data generated in the DF/HCC Lung SPORE, and the Genomics and Bioinformatics Core will set up internet-based access systems for that purpose. Furthermore, investigators in the SPORE are active in other National Cancer Institute initiatives in lung cancer research, such as the Director's Challenge program and the Mouse Models of Human Cancer Consortium. The Genomics and Bioinformatics Core will set up systems for data sharing with these groups as well.