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Mutation Profiling of Mismatch Repair-deficient Colorectal Cancers Using an in Silico Genome Scan to Identify Coding Microsatellites¹

Centre for Cancer Genetics, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, and Departments of Laboratory Medicine and Pathobiology, Biochemistry, and Surgery, University of Toronto, Toronto, Ontario, Canada M5G 1X5 [J. P., D. B., R. G., K. M., N. D. N., S. G., C. W. V. H., M. R.], and Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115 [M. R.]

Human colorectal, endometrial, and gastric cancers with defective DNA mismatch repair (MMR) have microsatellite instability, a unique molecular alteration characterized by widespread frameshift mutations of repetitive DNA sequences. We developed "Kangaroo," a bioinformatics program for searches in nucleotide and protein sequence databases, and performed an in silico genome scan for DNA coding microsatellites that may have novel mutations in MMR-deficient cancers. Examination of 29 previously untested coding polyadenines revealed widespread mutations in MMR-deficient colorectal cancers, with the highest frequencies in ERCC5, CASP8AP2, p72, RAD50, CDC25, RECQL1, CBF2, RACK7, GRK4, and DNAPK (range, 10–33%). This algorithm allows comprehensive mutation profiling of MMR-deficient cancers, an important step in understanding the pathogenesis of these neoplasms.

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