Enabling large-scale screening of Barrett’s esophagus using weakly supervised deep learning in histopathology

Timely detection of Barrett’s esophagus, the pre-malignant condition of esophageal adenocarcinoma, can improve patient survival rates. The Cytosponge-TFF3 test, a non-endoscopic minimally invasive procedure, has been used for diagnosing intestinal metaplasia in Barrett’s. However, it depends on pathologist’s assessment of two slides stained with H&E and the immunohistochemical biomarker TFF3. This resource-intensive clinical workflow limits large-scale screening in the at-risk population. Deep learning can improve screening capacity by partly automating Barrett’s detection, allowing pathologists to prioritize higher risk cases. We propose a deep learning approach for detecting Barrett’s from routinely stained H&E slides using diagnostic labels, eliminating the need for expensive localized expert annotations. We train and independently validate our approach on two clinical trial datasets, totaling 1,866 patients. We achieve 91.4% and 87.3% AUROCs on discovery and external test datasets for the H&E model, comparable to the TFF3 model. Our proposed semi-automated clinical workflow can reduce pathologists’ workload to 48% without sacrificing diagnostic performance.