) The DNA Microarray Core will support the three research projects in colon, ovarian and lung cancer using two distinct platforms. The first platform will generate data pertaining to the expression of arrayed genes and the second will provide mutation data for a selected set of genes that are frequently mutated in cancer. All DNA microarray analyses will rely on microdissected tumors. A protocol has also been set up for expression analysis of tumor cells obtained by laser capture microdissection. It is expected that expression analysis will be undertaken for approximately 1,200 tumors from the three component projects. To this effect, a DNA microarray facility has been set up as part of the core using robotics for clone handling and for manufacturing of DNA arrays. The facility also includes a hybridization station and currently a CCD based scanner which will be upgraded in the coming year to a laser based scanner. Access to clones for arraying is provided by the Michigan Microarray Network, funded by the University of Michigan Medical Center. For the subset of genes for which proteins have been identified as part of the Proteomics Core activities, it is expected that data for expression at the RNA level will be integrated with data for expression and the protein level. We also propose to utilize the Affymetrix mutation chip to analyze colon, lung and ovarian tumors for point mutations in specific genes. In its current form the mutation chip is offered for the analysis of p53 mutations. However, it is envisaged that a more comprehensive chip will be developed for common mutations in cancer that will include K-ras as well as other genes. The DNA Microarray Core will also take advantage of work done by the applicant group through other funding, for the development of genomic microarrays that will allow identification of genomic alterations in tumors including amplification and methylation changes. The core will have access to these chips during the proposed funding period for their application to colon, ovarian and lung cancer.
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