Determining breast cancer biomarker status and associated morphological features using deep learning

Background Breast cancer management depends on biomarkers including estrogen receptor, progesterone receptor, and human epidermal growth factor receptor 2 (ER/PR/HER2). Though existing scoring systems are widely used and well-validated, they can involve costly preparation and variable interpretation. Additionally, discordances between histology and expected biomarker findings can prompt repeat testing to address biological, interpretative, or technical reasons for unexpected results. Methods We developed three independent deep learning systems (DLS) to directly predict ER/PR/HER2 status for both focal tissue regions (patches) and slides using hematoxylin-and-eosin-stained (H&E) images as input. Models were trained and evaluated using pathologist annotated slides from three data sources. Areas under the receiver operator characteristic curve (AUCs) were calculated for test sets at both a patch-level (>135 million patches, 181 slides) and slide-level ( n = 3274 slides, 1249 cases, 37 sites). Interpretability analyses were performed using Testing with Concept Activation Vectors (TCAV), saliency analysis, and pathologist review of clustered patches. Results The patch-level AUCs are 0.939 (95%CI 0.936–0.941), 0.938 (0.936–0.940), and 0.808 (0.802–0.813) for ER/PR/HER2, respectively. At the slide level, AUCs are 0.86 (95%CI 0.84–0.87), 0.75 (0.73–0.77), and 0.60 (0.56–0.64) for ER/PR/HER2, respectively. Interpretability analyses show known biomarker-histomorphology associations including associations of low-grade and lobular histology with ER/PR positivity, and increased inflammatory infiltrates with triple-negative staining. Conclusions This study presents rapid breast cancer biomarker estimation from routine H&E slides and builds on prior advances by prioritizing interpretability of computationally learned features in the context of existing pathological knowledge.