The general aim of the present application is to recruit newly available genomic technologies such as Bacterial Artificial Chromosome (BAC) library preparations, finished sequence of the human genome, and next- generation sequencing technologies developed by the 454 Life Sciences Corporation in the fight against cancer. This application aims to develop the Barcoded Tag Pooled Genomic Indexing (BT-PGI) method for highly multiplexed BAC-based mapping of chromosomal aberrations in cancer. The BT-PGI method achieves throughput and resolution by combining two types of multiplexing -- the pooling of BAC clones by the PGI method and the parallel sequencing of short mappable sequence tags by the newly developed 454 sequencing technology. A commercially available BAC library obtained from the well-established MCF-7 breast cancer cell line will be used for'testing and validation of these methods. Specific rearrangements detected in MCF-7 will then be measured in other breast cancer cell lines, and in breast cancer tissue. The biological function of these rearrangements will be tested by cloning and expression in both immortalized and transformed breast epithelial cells. Biological assays will depend upon the rearrangement or breakpoints of interest, but will focus on proliferation, survival, invasion and transformation. The improved understanding of chromosomal rearrangements will open new opportunities for charting the progression of cancer, understanding relevant molecular mechanisms, identifying biomarkers for informed therapy, and identifying targets for therapeutic intervention in breast cancer and other tumors.
