We have developed a powerful technique (representational difference analysis, or RDA) for the comparison of the differences between two complex genomes. By performing RDA on DNA from human tumor cells and the DNA extracted from normal tissue or blood of the same patient, we can derive probes for loci that have undergone genetic alterations including deletions, translocations, inversions, insertions and amplifications in the tumor cells. Moreover, we can detect foreign genomes (such as viral genomes), if any are present. This methodology presents an unparalleled opportunity to discover the genetic lesions that underlie cancer. We propose to apply this methodology to a series of renal cell carcinoma cell lines and paired normal DNA in order to derive probes that detect genetic lesions in such cell lines. These probes will be used to detect similar types of lesions in other human cancers. We shall further attempt to define the critical genes affected by these lesions, and to test them for biological function. Special emphasis will be placed on tumor suppressor genes.
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