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Life sciences · Preprint
arXiv · October 23, 2026
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Purpose: Human epidermal growth factor receptor 2 (HER2) status is a key biomarker relevant for prognostication and treatment decision making in metastatic breast cancer. Thus, the aim of this work was to explore whether HER2 status can be predicted directly from whole-brain post-contrast T1-weighted (T1w) MRI scans in breast cancer brain metastases (BCBM) using deep learning, and whether providing explicit tumour segmentation information improves prediction. Methods: Using the publicly available BCBM-Radiogenomics dataset, we analysed 135 patients, including 70 HER2+ and 65 HER2- patients. Three approaches were implemented and evaluated: a conventional radiomics model, a simple fully convolutional network (SFCN) using T1w MRI scans alone, and an SFCN using T1w MRI scans with an expert-derived tumour mask as an additional input channel. Results: The radiomics model achieved an area under the receiver operating characteristic curve (ROC-AUC) of 0.602 (95% confidence interval [CI]: 0.528--0.677) while the SFCN achieved a ROC-AUC of 0.667 (95% CI, 0.63--0.71) using T1w MRI scans alone, which increased to 0.692 (95% CI, 0.58--0.81) when an explicit tumour mask was additionally provided. Conclusion: However, the modest performance across all approaches demonstrates the difficulty of predicting HER2 status from structural MRI scans alone. The difference between the segmentation-free and mask-guided SFCN models suggests that much of the predictive signal captured by the deep-learning model may be learned directly from whole-brain T1w MRI without requiring explicit tumour delineation. These findings support further investigation of segmentation-free deep-learning approaches as a potential non-invasive strategy to support HER2 status determination in BCBM.