Fluorescence In Situ Hybridization on Tissue Sections

Formalin-fixed paraffin-embedded (FFPE) tissues are typically the specimens available for FISH analysis of solid tissues, particularly of tumor specimens. Occasionally, tissue cores constructed as tissue microarrays from several patients are presented for simultaneous evaluation. FFPE sections can also be prepared from cell blocks derived from cell suspensions. The interphase fluorescence in situ hybridization assay employs specific nucleic acid sequences (probes) that target complementary sequences of interest to detect gains or losses of genes/gene loci or a fusion gene within the tissue. In this chapter, we describe the protocols utilized in our laboratory and include slide deparaffinization, pretreatment, protease treatment, hybridization, washing, and counterstaining. This protocol can be applied to all of the earlier FFPE preparations. In general, the assay takes 3 consecutive days to complete, although a more rapid assay can be performed.