1607 HIGH-RESOLUTION DETECTION OF PTEN GENOMIC DELETION BY FLUORESCENCE IN SITU HYBRIDIZATION (FISH) USING 330 FIXED PARAFFIN-EMBEDDED TISSUE SAMPLES

Abstract

You have accessJournal of UrologyProstate Cancer: Basic Research1 Apr 20111607 HIGH-RESOLUTION DETECTION OF PTEN GENOMIC DELETION BY FLUORESCENCE IN SITU HYBRIDIZATION (FISH) USING 330 FIXED PARAFFIN-EMBEDDED TISSUE SAMPLES Jeremy Squire, Olga Ludkovski, Dave DeGrace, Andrew Evans, Kanishka Sircar, Tarek Bismar, and Maisa Yoshimoto Jeremy SquireJeremy Squire Kingston, Canada More articles by this author , Olga LudkovskiOlga Ludkovski Toronto, Canada More articles by this author , Dave DeGraceDave DeGrace Kingston, Canada More articles by this author , Andrew EvansAndrew Evans Toronto, Canada More articles by this author , Kanishka SircarKanishka Sircar Houston, TX More articles by this author , Tarek BismarTarek Bismar Calgary, Canada More articles by this author , and Maisa YoshimotoMaisa Yoshimoto Kingston, Canada More articles by this author View All Author Informationhttps://doi.org/10.1016/j.juro.2011.02.1715AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookTwitterLinked InEmail INTRODUCTION AND OBJECTIVES Deletion of a tumour suppressor gene in routine formalin-fixed paraffin-embedded (FFPE) pathology sections is readily assayed by fluorescence in situ hybridization (FISH). However, the sectioning of the FFPE tissue samples often results in truncation artefacts of interphase nuclei leading to partitioning of the spherical shaped nucleus. As many as 20–40% of nuclei may be have been partially severed through the sectioning process leading to “false positive” signal losses and considerable interpretative difficulties. In this study a novel probe combination, for detecting gene deletions with high specificity was developed. METHODS Four color FISH probes were designed to detect genomic losses in the PTEN genomic region in 5 micron FFPE tissue sections. We evaluated the reliability of this assay using FFPE CaP tissue samples (tissue microarrays, n=330 patients), and mapping the breakpoint regions associated with PTEN deletions in this cohort derived from two institutions. RESULTS The probe combination selected reduced the rate of signal losses due to nuclear truncation by 50%. 132/330 (40%) of patient tumours were deleted for PTEN. The extent of deletion in each of the 132 tumors was mapped by FISH and the major class (41%) had an interstitial genomic deletion interval of 2Mb or less. The second most frequent class (28% of deleted tumors) involved genomic losses that were more heterogeneous in length, and involved PTEN deletions accompanied by adjacent genes on either side of the locus, with more losses extending in a telomeric direction. CONCLUSIONS FISH-based tumor suppressor deletion assay offers the advantage of highly specific and statistically significant quantitative evaluation of the gene locus of interest within individual cells in intact tissue. Consequently, CaP samples can be thoroughly characterized in an attempt to identify any PTEN heterogeneity, within or between foci in multifocal tumors. The clinical value of this assay is that presence of PTEN deletion by FISH is associated with earlier biochemical recurrence and increased mortality. For tumors with a homozygous deletion there is a strong association with hormone refractory CaP and metastatic disease. © 2011 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 185Issue 4SApril 2011Page: e645 Advertisement Copyright & Permissions© 2011 by American Urological Association Education and Research, Inc.MetricsAuthor Information Jeremy Squire Kingston, Canada More articles by this author Olga Ludkovski Toronto, Canada More articles by this author Dave DeGrace Kingston, Canada More articles by this author Andrew Evans Toronto, Canada More articles by this author Kanishka Sircar Houston, TX More articles by this author Tarek Bismar Calgary, Canada More articles by this author Maisa Yoshimoto Kingston, Canada More articles by this author Expand All Advertisement Advertisement PDF downloadLoading ...