We have adapted a DNA fingerprinting approach to detect tumor specific genomic differences. The approach is based in the comparison of the genome fingerprints of normal and tumor tissues from the same individuals, after the amplification of DNA sequences by the Arbitrary Priming Polymerase Chain Reaction (AP-PCR). The method is able to detect in a single and simple experiment, both quantitative and qualitative genomic differences associated with neoplastic transformation. It also allows the cloning in a single step of these altered DNA sequences, including those deleted in the tumor cells. We propose to use this approach as a molecular alternative to the cytogenetic analysis of solid tumors; to estimate the extent and compare the spectrum of genetic alterations occurring in diverse tumors of the digestive tract at different stages of tumor progression; to explore its potential value as prognostic indicator for Cancer of the colon and rectum; and to search for unknown cancer genes in colorectal and other gastrointestinal tumors. We will test the hypothesis that the relative values of genetic damage obtained by the AP-PCR method reflect the degree of aneuploidy of the cancer cells, and that this information might have value for cancer diagnosis and prognosis. The existence of uncharacterized cancer genes involved in the development and/or progression of defined gastrointestinal neoplasms will be searched by isolating and characterizing the chromosomal localization of DNA sequences representing recurrent genetic alterations in these tumors. Genetic alterations will be identified in a panel of about 200 tumors of the gastrointestinal tract including adenomas and carcinomas of the colon and rectum, pancreas and stomach, by comparison of the AP-PCR patterns of tumor versus normal tissues. Genomic alterations specific to the metastatic process of any of these tumors will be searched by comparing primary versus metastatic tumors by the same approach (specific aim 1). We will continue the follow-up of a subset of these tumors (about 100 colorectal carcinomas), which have been already followed for an average of over 3 years for recurrence and survival. These tumors have been already characterized for mutations in the ras oncogene and in the p53 tumor suppressor gene. The relative values of genetic damage obtained for these colorectal carcinomas by the AP-PCR method will be correlated with ras and p53 gene mutations and recurrence and survival rates (specific aim 2). The chromosomal localization of DNA fragments corresponding to recurrent tumor specific genetic alterations will be determined by AP-PCR amplification of panels of human/hamster cell hybrids. When appropriate, these DNA fragments will be cloned and sequenced to further characterize by standard PCR approaches their chromosomal localization and their presence and frequency in other tumors (specific aim 3).
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