A Deep Learning Approach for the Identification of the Molecular Subtypes of Pancreatic Ductal Adenocarcinoma Based on Whole Slide Pathology Images
Pouya Ahmadvand, Hossein Farahani, David Farnell, Amirali Darbandsari, James T. Topham, Joanna M. Karasinska, Jessica Nelson, Julia Naso, Steven J.M. Jones, Daniel J. Renouf, David F. Schaeffer, Ali Bashashati
Abstract
Delayed diagnosis and treatment resistance result in high pancreatic ductal adenocarcinoma (PDAC) mortality rates. Identifying molecular subtypes can improve treatment, but current methods are costly and time-consuming. In this study, deep learning models were used to identify histologic features that classify PDAC molecular subtypes based on routine hematoxylin-eosin-stained histopathologic slides. A total of 97 histopathology slides associated with resectable PDAC from The Cancer Genome Atlas project were used to train a deep learning model and test the performance on 44 needle biopsy material (110 slides) from a local annotated patient cohort. The model achieved balanced accuracy of 96.19% and 83.03% in identifying the classical and basal subtypes of PDAC in The Cancer Genome Atlas and the local cohort, respectively. This study provides a promising method to cost-effectively and rapidly classify PDAC molecular subtypes based on routine hematoxylin-eosin-stained slides, potentially leading to more effective clinical management of this disease.