Notably, comparison of the clinical samples with the SKBR3 breast cancer cell line, both by smFISH and RT-PCR, demonstrated that, while smFISH has a relatively broad dynamic range and is capable of detecting high mRNA levels, the expression of HER2 in breast cancer cell lines might not reflect the actual transcript abundance in clinical samples, similarly to what we previously observed for the oncogenic fusion transcript, BCR-ABL1, in chronic myeloid leukemia clinical samples and cell lines [13]. Here, ABL1 is linked to breast carcinoma.