Allelic loss detected on chromosomes 8, 10, and 17 by fluorescence in situ hybridization using single-copy P1 probes on isolated nuclei from paraffin-embedded prostate tumors.

We have implemented a reliable new technique for preparing isolated prostate cancer nuclei from paraffin-embedded tissue sections followed by analysis with single-copy fluorescence in situ hybridization (FISH). Our initial validation is described by comparison of our data with fresh prostate tumor tissue and loss of heterozygosity (LOH) studies. We also describe evaluation of 36 previously unstudied prostate cancer patients. Fifteen archival samples were selected from patients who underwent radical prostatectomy in which direct FISH and LOH data were available. Isolated nuclei were prepared and allelic loss was detected on 17q using a single-copy DNA (P1 phage) probe by FISH. A high (80%) concordance was found when comparing isolated nuclei data with 17q results from fresh preparations and LOH studies. We also examined loss at sites on 8p, 10q, and 17q in samples from 36 patients for whom clinical information was available. Loss was found at any of the three loci in 32/36 (89%) of the specimens with specific loss in 53% of the cases at the 8p locus, 33% at the 10q locus, and 61% at the 17q locus. Studies indicate that, as well as providing potential clinical information, isolated nuclei preparations are as reliable as fresh tissue for single-copy FISH studies.