Protocol for HER 2 FISH determination on PAX gene‐fixed and paraffin‐embedded tissue in breast cancer

Molecular diagnostics in personalized medicine increasingly relies on the combination of a variety of analytical technologies to characterize individual diseases and to select patients for targeted therapies. The gold standard for tissue‐based diagnostics is fixation in formalin and embedding in paraffin, which results in excellent preservation of morphology but negatively impacts on a variety of molecular assays. The formalin‐free, non‐cross‐linking PAX gene tissue system preserves morphology in a similar way to formalin, but also preserves biomolecules essentially in a similar way to cryopreservation, which markedly widens the spectrum, sensitivity and accuracy of molecular analytics. In this study, we have developed and tested a protocol for PAX gene‐fixed and paraffin‐embedded tissues for fluorescent in situ hybridization ( FISH ). The implementation of a 24‐h formalin postfixation step of slides from PAX gene‐fixed and paraffin‐embedded tissues allowed us to use the assays approved for formalin‐fixed and paraffin‐embedded tissues. The equivalence of the methodologies was demonstrated by FISH analysis of HER 2 amplification in breast cancer cases. The 24‐h postfixation step of the slides used for FISH can be well integrated in the routine diagnostic workflow and allows the remaining PAX gene‐fixed and paraffin‐embedded tissue to be used for further molecular testing.