Comparison of a Novel MRNA-Based Breast Cancer Subtyping Assay with PAM50 and Oncotype DX in Estrogen Receptor-Positive/HER2-Negative Breast Cancer: An Exploratory Age-Stratified Retrospective Cohort Study.

Immunohistochemistry (IHC) of ER, PR, HER2, and Ki67 are established prognostic and predictive markers in breast cancer. Gene expression assays such as PAM50 and Oncotype DX are increasingly used for molecular subtyping and recurrence risk calculation. The APIS Breast Cancer Subtyping Kit (BCSK) quantitatively measures the mRNA expression of these markers (ER, PR, HER2, and Ki67) and includes a novel four-gene BCSK Proliferation Signature (PS) designed for subtype classification and risk stratification. This exploratory retrospective cohort study compares the BCSK with established molecular assays in an age-stratified cohort. We aimed to compare BCSK subtype classification in distinguishing Luminal A versus Luminal B subtypes with IHC and with PAM50. We have also aimed to assess correlations between the BCSK PS and the Oncotype DX Recurrence Score (RS) as well as the PAM50 Risk of Recurrence (ROR) score in patients stratified by age (<65 versus ≥65 years). Formalin-fixed, paraffin-embedded (FFPE) tumor specimens from 59 patients with ER+/HER2- breast cancer (33 < 65 years, 26 ≥ 65 years), diagnosed between 2020 and 2022 at the Cantonal Hospital Baselland and University Hospital Basel, were analyzed using IHC, BCSK, and PAM50 (Prosigna®). All patients received adjuvant therapy and had ODx scores available. Patient, disease and treatment characteristics were compared between age groups using the Fisher exact test. We assessed concordance in luminal subtype classification across IHC, BCSK, and PAM50 assays pairwise and stratified by age groups descriptively. We used Spearman's rank correlation to examine associations between BCSK PS, RS, and ROR. Differences between age groups regarding PS were analyzed using the Mann-Whitney U test. In the ≥65-year cohort, subtype classification concordance between the BCSK and PAM50 was higher (84.6%) than in those aged <65-years (60.6%). In patients aged <65 years, the PS was significantly correlated with both RS (ρ = 0.5745, p < 0.0005) and ROR (ρ = 0.391, p = 0.024), whereas RS and ROR were not significantly correlated. In patients ≥65 years, PS correlated significantly with ROR (ρ = 0.603, p = 0.001), while there were no significant correlations between PS and RS (ρ = 0.134, p = 0.514) and between RS and ROR (ρ = 0.149, p = 0.466). Median PS values did not significantly differ between age groups (0.589 versus 0.602, p = 0.97). In this exploratory retrospective age-stratified analysis, the BCSK demonstrated descriptive concordance with PAM50 subtype classifications, especially in patients aged ≥65 years. PS showed significant but moderate correlation with the established molecular recurrence scores RS and ROR, however these differed across age groups. Our findings should be considered hypothesis-generating because this study did not include outcome metrics and was based on a relatively small cohort. Larger prospective studies incorporating clinical outcomes are necessary to determine the diagnostic and prognostic utility as well as comparative cost-effectiveness of the BCSK and its utility across age groups.