The detailed cytogenetic analyses of human tumors and cancer tissues, in particular, have revealed the presence of structural chromosome abnormalities in most of cases. The underlying changes are often specific for the type of tumor or cancer and the cells' altered phenotype. Furthermore, investigators could demonstrate a correlation between the type or extent of chromosome changes, disease progression, and outcome. However, present laboratory techniques for the screening for structural abnormalities are very limited with respect to the detection of small, 'cryptic' translocations. For example, Giemsa (G)-banding of metaphase chromosomes or the fluorescence in situ hybridization (FISH)-based techniques of whole chromosome painting (WCP) and Spectral Karyotyping (SKY) analysis typically miss translocations that involve segments of less than 10 megabasepairs (Mbp), i.e., about the size of a chromosome band. We postulate that small cryptic translocations exist undetected in the genomes of individuals with a normal phenotype or diseases such as mental retardation, impaired fertility, precancerous lesions, or early stage tumors. Knowledge about structural alterations and chromosomal imbalances might help clinicians make more accurate predictions regarding the onset and course of a disease. This R21 project will investigate the feasibility to rapidly and inexpensively screen the human genome for the presence of occult cryptic translocations (OCTs). Specifically, we will develop and test FISH assays using collections of validated chromosome-specific bacterial artificial chromosomes (BACs) for the detection of OCTs in human cancer cells. With BAC probes spaced on average 0.9 Mbp apart and covering the entire euchromatic part of the human genome, we expect our 'BAC-FISH' assay to lead to greatly increased sensitivity compared to WCP or banding tests. Our innovative assay for sensitive genome-wide screening for translocations will be developed with cancer cell lines for which limited information about structural abnormalities is available. At the end of this project, we will be well positioned to conduct a larger study of the frequency of OCTs in the normal population as well as tumor cells and to offer BAC-FISH screening service and reagents to research and clinical laboratories for collaborative studies. ? ? ?
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