The HER2 gene-protein assay described herein is a significant improvement in the field because: 1) it demonstrates tricolor co-localization of the HER2 protein, HER2 gene, and CEN17 targets on well-preserved breast cancer tissue sections and 2) it automates the entire protocol of a gene-protein assay from deparaffinization to counterstaining. This evidence concerns the gene ERBB2 and breast cancer.