California Pacific Medical Center

Helene S Smith

Ling-Chun Chen

You Lu

Guoren Deng

The present invention encompasses methods for determining the likelihood that benign hyperplastic breast tissue or normal breast tissue adjacent to carcinoma tissue will become malignant. The methods comprise substantially isolating the tissue; and determining loss of heterozygosity (LOH) at chromosome 3p24 in the tissue. LOH at chromosome 3p24 is a prognostic indicator that the tissue may become malignant.

Prognostic methods for prediction of progression of normal and hyperplastic mammary cells to carcinoma

New methods are disclosed for detecting cancer associated genes, and obtaining corresponding cDNA fragments. The methods involve supplying RNA preparations from control cells, and from a plurality of different cancer cells that share a duplicated or deleted gene in the same region of a chromosome. Amplified cDNA copies are displayed, and then selected based on differences in abundance of RNA between preparations. Optional additional screening steps involve surveying panels of cancer cells using the cDNA for RNA overabundance with or without gene duplication. By applying these methods, cDNA sequences derived from four novel genes associated with breast cancer were obtained and characterized. Each of the genes was duplicated in about 60% of the cancer cell lines tested; while other cells showed RNA overabundance without gene duplication. Genes with these properties are particularly useful in cancer diagnosis and treatment.

Methods for identifying genes amplified in cancer cells

cDNA sequences derived from four novel genes associated with breast cancer are provided. In over about 60% of the cancer cell lines tested, RNA hybridizing with the cDNAs were substantially more abundant than in normal cells. Most of the cell lines also showed a duplication of the corresponding gene, which probably contributed to the increased level of RNA in the cell. However, for each of the four genes, there were some cell lines which had RNA overabundance without gene duplication. This suggests that the gene product is sufficiently important to the cancer process that cells will use several alternative mechanisms to achieve increased expression. The polynucleotides, polypeptides, and antibodies provided by this invention are expected to be particularly useful in diagnosis and treatment of breast cancer. Also provided is a general method for obtaining cDNA with similar properties that may be associated with breast cancer and other malignancies.

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San Francisco, CA, United States of America

Helene S Smith