Data-Efficient Computational Pathology Platform for Faster and Cheaper Breast Cancer Subtype Identifications: Development of a Deep Learning Model

Background: Breast cancer subtyping is a crucial step in determining therapeutic options, but the molecular examination based on immunohistochemical staining is expensive and time-consuming. Deep learning opens up the possibility to predict the subtypes based on the morphological information from hematoxylin and eosin staining, a much cheaper and faster alternative. However, training the predictive model conventionally requires a large number of histology images, which is challenging to collect by a single institute.Objective: We aimed to develop a data-efficient computational pathology platform, 3DHistoNet, which is capable of learning from z-stacked histology images to accurately predict breast cancer subtypes with a small sample size.Methods: We retrospectively examined 401 cases of patients with primary breast carcinoma diagnosed between 2018 and 2020 at the Department of Pathology, National Cancer Center, South Korea. Pathology slides of the patients with breast carcinoma were prepared according to the standard protocols. Age, gender, histologic grade, hormone receptor (estrogen receptor [ER], progesterone receptor [PR], and androgen receptor [AR]) status, erb-B2 receptor tyrosine kinase 2 (HER2) status, and Ki-67 index were evaluated by reviewing medical charts and pathological records.Results: The area under the receiver operating characteristic curve and decision curve were analyzed to evaluate the performance of our 3DHistoNet platform for predicting the ER, PR, AR, HER2, and Ki67 subtype biomarkers with 5-fold cross-validation. We demonstrated that 3DHistoNet can predict all clinically important biomarkers (ER, PR, AR, HER2, and Ki67) with performance exceeding the conventional multiple instance learning models by a considerable margin (area under the receiver operating characteristic curve: 0.75-0.91 vs 0.67-0.8). We further showed that our z-stack histology scanning method can make up for insufficient training data sets without any additional cost incurred. Finally, 3DHistoNet offered an additional capability to generate attention maps that reveal correlations between Ki67 and histomorphological features, which renders the hematoxylin and eosin image in higher fidelity to the pathologist.Conclusions: Our stand-alone, data-efficient pathology platform that can both generate z-stacked images and predict key biomarkers is an appealing tool for breast cancer diagnosis. Its development would encourage morphology-based diagnosis, which is faster, cheaper, and less error-prone compared to the protein quantification method based on immunohistochemical staining.