COMPARATIVE GENOMIC ANALYSIS OF TUMORS - DETECTION OF DNA LOSSES AND AMPLIFICATION

We demonstrate the use of representational difference analysis for clo ning probes that detect DNA loss and amplification in tumors. Using DN A isolated from human tumor cell lines to drive hybridization against matched normal DNA, we were able to identify six genomic regions that are homozygously deleted in cultured cancer cells. When this method wa s applied in the reverse way, using normal DNA to drive hybridization against tumor cell DNA, we readily isolated probes detecting amplifica tion. Representational difference analysis was also performed on DNAs derived from tumor biopsies, and we thereby discovered a probe detecti ng very frequent homozygous loss in colon cancer cell lines and locate d on chromosome 3p.