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Background: Fluorescent in situ hybridization (FISH) equivocal results for Her-2/neu still pose a diagnostic dilemma in oncology practice. In this study, we evaluate if Her-2/neu mRNA expression is an alternative to FISH for detecting Her-2/neu positivity. Patients and Methods: Archival paraffin blocks of 54 breast cancer patients were analyzed for Her-2/neu status using immunohistochemistry (IHC), FISH, and Her-2/neu gene expression using mRNA. Results: There was a 100% positive agreement and 64.7% negative agreement of Her-2/neu mRNA expression with respect to the reference standard (FISH), with the kappa value for agreement being 0.36. mRNA levels correlated positively and strongly with FISH ratio and IHC positivity. For Her-2/neu mRNA expression, Her-2/neu copy number was a significant predictor indicating that mRNA expression is independent of polysomy status. Conclusions: Her-2/neu mRNA expression may help tide over ambiguity posed by polysomy and FISH equivocal samples.

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