Cancer is a disorder brought upon by the accumulation of specific mutations in the cancerous cells. Our understanding of the disease, and potentially its diagnosis and therapeutic treatment, is enhanced by defining the genetic lesions that cause it. We are applying several new techniques to the discovery of new somatic genetic abnormalities in breast cancer: Representational difference analysis (RDA), a method that discovers probes for altered genomic DNA; high complexity representations (HCR), a method that facilitates the genomic analysis of minute, archived or fresh tumor specimens, and Rapid Isolation of cDNA by Hybridization (RICH), a method for rapid transcriptional mapping of large genomic regions. RDA is a DNA subtraction methodology that finds sequences present in one DNA population, the tester, that is absent or reduced in a second, the driver. RDA has been used to discover sequences lost or amplified in the genomic DNA of the cancerous cells. Genetic loss and gene amplification are hallmarks of tumor suppressor genes and oncogenes, respectively. We have been applying RDA to the discovery of sequences amplified in breast cancer. Over a dozen loci undergoing amplification in breast cancer have been identified. The transcriptional mapping of genomic regions. Additionally, HCR will facilitate the genetic analysis of minute samples of tumor biopsies, such as those produced by the InterSPORE DCIS Project. We expect that the continued execution of out stated plan will accomplish our stated goal, the identification of oncogenes that are commonly involved in breast cancer. This project will interface with other ongoing projects in our laboratory that aim to understand the function of the genes we discover.
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