| Summary: | Fluorescence<em> </em><em>in situ </em>hybridization (FISH) assay is considered the “gold standard” in evaluating <em>HER2/neu (HER2)</em> gene status. However, FISH detection is costly and time consuming. Thus, we established nuclei microarray with extracted intact nuclei from paraffin embedded breast cancer tissues for FISH detection. The nuclei microarray FISH (NMFISH) technology serves as a useful platform for analyzing <em>HER2</em> gene/chromosome 17 centromere ratio. We examined <em>HER2</em> gene status in 152 cases of invasive ductal carcinomas of the breast that were resected surgically with FISH and NMFISH. <em>HER2</em> gene amplification status was classified according to the guidelines of the American Society of Clinical Oncology and College of American Pathologists (ASCO/CAP). Comparison of the cut-off values for <em>HER2</em>/chromosome 17 centromere copy number ratio obtained by NMFISH and FISH showed that there was almost perfect agreement between the two methods (κ coefficient 0.920). The results of the two methods were almost consistent for the evaluation of <em>HER2</em> gene counts. The present study proved that NMFISH is comparable with FISH for evaluating <em>HER2</em> gene status. The use of nuclei microarray technology is highly efficient, time and reagent conserving and inexpensive.
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