Fluorescence In Situ Hybridization Analysis of Formalin Fixed Paraffin Embedded Tissues, Including Tissue Microarrays

  • Brenda M. Summersgill
  • Janet M. ShipleyEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 659)


Formalin fixed paraffin embedded (FFPE) material is frequently the most convenient readily available source of diseased tissue, including tumors. Multiple cores of FFPE material are being used increasingly to construct tissue microarrays (TMAs) that enable simultaneous analyses of many archival samples. Fluorescence in situ hybridization (FISH) is an important approach to analyze FFPE material for specific genetic aberrations that may be associated with tumor types or subtypes, cellular morphology, and disease prognosis. Annealing, or hybridization of labeled nucleic acid sequences, or probes, to detect and locate one or more complementary nucleic acid sequences within fixed tissue sections allows the detection of structural (translocation/inversion) and numerical (deletion/gain) aberrations and their localization within tissues. The robust protocols described include probe preparation, hybridization, and detection and take 2–3 days to complete. A protocol is also described for the stripping of probes for repeat FISH in order to maximize the use of scarce tissue resources.

Key words

Fluorescence in situ hybridization Formalin fixed paraffin embedded Tissue microarrays Genomic aberrations 



The authors would like to thank Drs. Jeremy Clark and Sian Rizzo for their helpful comments.


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Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  1. 1.Molecular Cytogenetics, Male Urological Cancer Research CentreInstitute of Cancer ResearchSurreyUK

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