Background: An accurate status determination of breast cancer biomarkers (ER, PR, HER2, Ki67) is crucial for guiding patient management. The “gold standard” for assessing these biomarkers in FFPE tissue is IHC, which faces challenges in standardization and exhibits substantial variability. In this study, we compare the concordance of a new commercial RT-qPCR kit with IHC in determining BC biomarker status. Methods: The performance was evaluated using 634 FFPE specimens, which underwent histological analysis in accordance with standard of care methods. HER2 2+ tumors were referred to ISH testing. An immunoreactive score of ≥2/12 was considered positive for ER/PR and 20% staining was used as a cut-off for Ki67 high/low score. RT-qPCR and results calling were performed according to the manufacturer’s instructions. Results: High concordance with IHC was seen for all markers (93.2% for ER, 87.1% for PR, 93.9% for HER2, 77.9% for Ki67 and 80.1% for proliferative signature (assessed against Ki67 IHC)). Conclusions: By assessing the concordance with the results obtained through IHC, we sought to demonstrate the reliability and utility of the kit for precise BC subtyping. Our findings suggest that the kit provides a highly precise and accurate quantitative assessment of BC biomarkers.

Multigene signatures like Oncotype DX and Prosigna Prediction Analysis of Microarray 50 (PAM50) help estimate distant recurrence risk in patients with luminal breast cancer receiving endocrine therapy. Determining the benefit of adjuvant chemotherapy, tests are costly and not always supported through reimbursement. We aimed to assess the utility of the APIS Breast cancer subtyping kit (BCSK) and its proliferation score (PS), as a potential prognostic assay. We analysed 141 adult patients with early luminal HER2- breast cancer diagnosed between 2020 and 2022 at Cantonal Hospital Basel-Land and Basel University Hospital. All patients had a valid OncotypeDX ^® Recurrence Score (RS) and received at least one line of adjuvant therapy. Molecular subtype and PS were obtained using the APIS BCSK. We performed the Prosigna PAM50 risk of recurrence (ROR) test on a subset of 59 patients. Our findings showed high concordance at the single marker level (estrogen receptor -ESR1, progesterone receptor - PGR, human epidermal growth factor receptor 2 - ERBB2 and marker of proliferation Ki-67 - MKI67), and between the BCSK and PAM50 subtype (overall percent agreement, OPA-71.2%). Notably, BCSK showed stronger agreement with immunohistochemistry (IHC)-based subtypes (OPA: 71.2%) than PAM50 with IHC (OPA: 54.2%). The BCSK PS correlated moderately with Prosigna PAM50 ROR (ρ = 0.4787) and more weakly with Oncotype DX RS (ρ = 0.4006). The correlation between ROR and RS was weak (ρ = 0.2255). In this preliminary comparison, the APIS BCSK and PS demonstrate promising potential as an initial molecular subtyping and risk stratification tool for breast cancer patients.