Classifying non-small cell lung cancer types and transcriptomic subtypes using convolutional neural networks. Journal of the American Medical Informatics Association : JAMIA Yu, K. H., Wang, F. n., Berry, G. J., Ré, C. n., Altman, R. B., Snyder, M. n., Kohane, I. S. 2020; 27 (5): 757–69


Non-small cell lung cancer is a leading cause of cancer death worldwide, and histopathological evaluation plays the primary role in its diagnosis. However, the morphological patterns associated with the molecular subtypes have not been systematically studied. To bridge this gap, we developed a quantitative histopathology analytic framework to identify the types and gene expression subtypes of non-small cell lung cancer objectively.We processed whole-slide histopathology images of lung adenocarcinoma (n?=?427) and lung squamous cell carcinoma patients (n?=?457) in the Cancer Genome Atlas. We built convolutional neural networks to classify histopathology images, evaluated their performance by the areas under the receiver-operating characteristic curves (AUCs), and validated the results in an independent cohort (n?=?125).To establish neural networks for quantitative image analyses, we first built convolutional neural network models to identify tumor regions from adjacent dense benign tissues (AUCs > 0.935) and recapitulated expert pathologists' diagnosis (AUCs > 0.877), with the results validated in an independent cohort (AUCs?=?0.726-0.864). We further demonstrated that quantitative histopathology morphology features identified the major transcriptomic subtypes of both adenocarcinoma and squamous cell carcinoma (P?

View details for DOI 10.1093/jamia/ocz230

View details for PubMedID 32364237