Structural Component Substantiation Methodology

We propose a breakthrough technique for ultra rapid, sensitive detection of cancer specific chromosome rearrangements in solution to facilitate bulk quantification of tumor cells for early detection of metastatic tumor cells in bone marrow, lymph nodes,and peripheral blood. Combining two separate, novel techniques (1) hybridization of chromosomes in suspension using (2) Repeat Sequence Depleted DNA probes, we will: (I) Apply DNA hybridization in suspension to human breast cancer cell lines. Chromosomeaberrations will be detected using reversible DNA-hybridization probes that uniquely bind to DNA normally present in a specified subset of the genome. A second set of reversible DNA hybridization probes is used to uniquely hybridize with a correspondingsecond subset of the genome. Any (aberrant) chromosomes containing both subsets will be rapidly, efficiently isolated and quantified. (II) We will determine the translocation detection sensitivity using serial dilutions of a human breast cancer cell line(with known translocation) with the human lymphoblast cell line AG122. We expect our technique will have sensitivity similar to PCR and far higher than FISH, with specificity similar to or better than PCR and FISH, thus revolutionizing FISH and PCRmedical diagnostics techniques. The research will lead to technology for licensing and commercial kits for early diagnoses of metastatic tumors as well as detecting minimal residual disorders in hematological malignancies. Pharmaceutical, biotech andhospitals will embrace this technology as it will lead to early detection of metastatic tumors cells and minimal residual leukemia cells. Early detection will increase patient survival, profoundlyimpact cancer patient management, and reduce cost.