Mutation in Rpa1 results in defective DNA double-strand break repair, chromosomal instability, and cancer in mice
Authors: Stanislav V. Volik, Joseph Costello, Burt Feuerstein, Pavel Pevzner, Ben Raphael, John H. Brebner, David Kowbel, Quanzhou Tao, Pieter De Jong, Michael Stratton, Marco Marra, Pamela Paris, Jeffry Simko, Joe W. Gray, Colin C. Collins
Journal: Cancer Research (2004)

BA-1  Genomes of solid tumors can be highly rearranged. Recurrent genome rearrangements are known to involve genes that mediate a wide range of tumor functions including angiogenesis, immortality, survival, metastasis, and resistance to therapy. Genes linked to these rearrangements are increasingly targets of anti-tumor therapeutics. Tumor genomes are not collinear with their normal host genome and current technologies for studying tumor genome structure are not capable of elucidating the structural organization of tumor genomes at high resolution, or of relating it to he underlying sequence. Because of these inherent limitations, the role of translocations and inversions in solid tumors is not well understood. Indeed, even the structural organization of amplicons remains largely enigmatic due to indirect methods of analysis. ESP is a sequence-based method for directly determining the structural organization of tumor genomes, and for cloning structural rearrangements such as translocations, inversions, and complex rearrangements en masse. ESP begins with construction of a BAC library from a tumor. BAC end sequences are then generated for individual BAC clones and mapped onto the normal “reference” genome sequence. This process reveals all classes of structural aberrations including copy number changes, translocations, and inversions, and, importantly, identifies BAC clones spanning associated genome breakpoints. We first demonstrated the power of ESP in an analysis of the breast cancer cell line MCF7 and have now extended it to primary tumors of the brain and breast. For copy number analysis ESP and array CGH are highly concordant although ESP is capable of much higher resolution. In contrast to array CGH, ESP provides direct evidence for the packaging of amplified DNA from multiple loci, and that the packaged DNA may be highly rearranged. ESP provides evidence for independent mechanisms of amplification operating within a single tumor genome. Approximately 80% of identified translocations and inversions tested were confirmed, and evidence for chimeric transcripts is emerging. Whole genome ESP is being combined with robust mathematical methods for tumor genome assembly enabling the formal testing of hypotheses of tumor evolution. ESP is inherently integrative and thus brings the power of genetic analysis to interpretation of complex expression microarray and proteomic data. Further, it enables construction of mice transgenic for BAC clones carrying human tumor DNA, thus preserving the nuances of transcriptional regulation and alternative splicing and allowing for the functional dissection of inversions, translocations, and amplicons in model systems. Finally, ∼ 200 tumor genomes can be effectively immortalized and exhaustively analyzed by ESP for less than the cost of sequencing a single mammalian sized genome.