Overall, these data demonstrate that FFPE-smFISH is not only a robust diagnostic assay for assessing the HER2 and ER status, but that unlike standard HER2 and ER diagnostic methods, it can also be used to measure the spatial organization of these two key biomarkers within the tumor, yielding measures of spatial diversity that could in turn be correlated with clinical outcome. Here, ESR1 is linked to neoplasm.