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(American Journal of Pathology. 2004;164:285-293.)
© 2004 American Society for Investigative Pathology

Defining a 0.5-Mb Region of Genomic Gain on Chromosome 6p22 in Bladder Cancer by Quantitative-Multiplex Polymerase Chain Reaction

Andrew J. Evans^*, Brenda L. Gallie^¶||**, Michael A.S. Jewett, Gregory R. Pond, Kirk Vandezande^**, John Underwood, Yves Fradet, Gloria Lim^||, Paula Marrano^¶, Maria Zielenska^¶¶ and Jeremy A. Squire^*¶||

From the Department of Pathology,^* University Health Network/Princess Margaret Hospital, Toronto; the Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto; the Department of Biostatistics, UniversityHealth Network/Princess Margaret Hospital, Toronto; the Department of Surgical Oncology, Division of Urology, University Health Network/Princess Margaret Hospital, Toronto; the Department of Surgery, Laval University Cancer Research Centre, Laval, Quebec; the Division of Cancer Informatics, Ontario Cancer Institute/Princess Margaret Hospital, Toronto; the Department of Ophthalmology, University of Toronto, Toronto; the Division of Cellular and Molecular Biology,^¶ Ontario Cancer Institute/Princess Margaret Hospital, University Health Network, Toronto; the Department of Medical Biophysics,|| University of Toronto, Toronto; Solutions by Sequence Inc.,^** Toronto; and the Division of Pathology,^¶¶ Department of Pediatric Laboratory Medicine, Hospital for Sick Children, Toronto, Ontario, Canada

Metaphase-based comparative genomic hybridization (CGH) has identified recurrent regions of gain on different chromosomes in bladder cancer, including 6p22. These regions may contain activated oncogenes important in disease progression. Using quantitative multiplex polymerase chain reaction (QM-PCR) to study DNA from 59 bladder tumors, we precisely mapped the focal region of genomic gain on 6p22. The marker STS-X64229 had copy number increases in 38 of 59 (64%) tumors and the flanking markers, RH122450 and A009N14, had copy number gains in 33 of 59 (56%) and 26 of 59 (45%) respectively. Contiguous gain was present for all three markers in 14 of 59 (24%) and for two (RH122450 and STS-X64229) in 25 of 59 (42%). The genomic distance between the markers flanking STS-X64229 is 0.5 megabases, defining the minimal region of gain on 6p22. Locus-specific interphase fluorescence in situ hybridization confirmed the increased copy numbers detected by QM-PCR. Current human genomic mapping data indicates that an oncogene, DEK, is centrally placed within this minimal region. Our findings demonstrate the power of QM-PCR to narrow the regions identified by CGH to facilitate identifying specific candidate oncogenes. This also represents the first study identifying DNA copy number increases for DEK in bladder cancer.

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