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(American Journal of Pathology. 2003;162:763-770.)
© 2003 American Society for Investigative Pathology

Technical Advance

High-Resolution Analysis of Paraffin-Embedded and Formalin-Fixed Prostate Tumors Using Comparative Genomic Hybridization to Genomic Microarrays

Pamela L. Paris^*, Donna G. Albertson^*, Janneke C. Alers, Armann Andaya^*, Peter Carroll, Jane Fridlyand^*, Ajay N. Jain^*, Sherwin Kamkar^*, David Kowbel^*, Pieter-Jaap Krijtenburg, Daniel Pinkel^*, Fritz H. Schröder, Kees J. Vissers, Vivienne J. E. Watson^*, Mark F. Wildhagen, Colin Collins^* and Herman van Dekken

From the Comprehensive Cancer Center^* and the Department of Urology, University of California at San Francisco, San Francisco, California; and the Departments of Pathology and Urology, Erasmus Medical Center, University Medical Center Rotterdam, Rotterdam, The Netherlands

We have used prostate cancer, the most commonly diagnosed noncutaneous neoplasm among men, to investigate the feasibility of performing genomic array analyses of archival tissue. Prostate-specific antigen and a biopsy Gleason grade have not proven to be accurate in predicting clinical outcome, yet they remain the only accepted biomarkers for prostate cancer. It is likely that distinct spectra of genomic alterations underlie these phenotypic differences, and that once identified, may be used to differentiate between indolent and aggressive tumors. Array comparative genomic hybridization allows quantitative detection and mapping of copy number aberrations in tumors and subsequent associations to be made with clinical outcome. Archived tissues are needed to have patients with sufficient clinical follow-up. In this report, 20 formalin-fixed and paraffin-embedded prostate cancer samples originating from 1986 to 1996 were studied. We present a straightforward protocol and demonstrate the utility of archived tissue for array comparative genomic hybridization with a 2400 element BAC array that provides high-resolution detection of both deletions and amplifications.

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