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Triage-driven diagnosis of Barrett’s esophagus for early detection of esophageal adenocarcinoma using deep learning

Abstract

Deep learning methods have been shown to achieve excellent performance on diagnostic tasks, but how to optimally combine them with expert knowledge and existing clinical decision pathways is still an open challenge. This question is particularly important for the early detection of cancer, where high-volume workflows may benefit from (semi-)automated analysis. Here we present a deep learning framework to analyze samples of the Cytosponge-TFF3 test, a minimally invasive alternative to endoscopy, for detecting Barrett’s esophagus, which is the main precursor of esophageal adenocarcinoma. We trained and independently validated the framework on data from two clinical trials, analyzing a combined total of 4,662 pathology slides from 2,331 patients. Our approach exploits decision patterns of gastrointestinal pathologists to define eight triage classes of varying priority for manual expert review. By substituting manual review with automated review in low-priority classes, we can reduce pathologist workload by 57% while matching the diagnostic performance of experienced pathologists.

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Fig. 1: Cytosponge procedure, triage scheme and data summary.
Fig. 2: Tile- and patient-level classification of Cytosponge-TFF3 samples.
Fig. 3: Application of quality control and diagnostic confidence class scheme to the internal validation cohort.
Fig. 4: Triage-driven approach with incremental triage class substitution scheme on internal validation set.
Fig. 5: Triage model applied to the external validation cohort and simulation of cohort variation.

Data availability

The dataset is governed by data usage policies specified by the data controller (University of Cambridge, Cancer Research UK). We are committed to complying with Cancer Research UK’s Data Sharing and Preservation Policy. Whole-slide images used in this study will be available for non-commercial research purposes upon approval by a Data Access Committee according to institutional requirements. Applications for data access should be directed to rcf29@cam.ac.uk. Data derived from the raw images are freely available at a public repository: https://github.com/markowetzlab/cytosponge-triage. The code and included data enable replication of the results and figures in this manuscript.

Code availability

The source code of this work is freely available at a public repository: https://github.com/markowetzlab/cytosponge-triage.

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Acknowledgements

This research was supported by Cancer Research UK (FM: C14303/A17197), the Medical Research Council (RCF: RG84369) and Cambridge University Hospitals NHS Foundation Trust. BEST2 was funded by Cancer Research UK (12088 and 16893). M.G. acknowledges support from an Enrichment Fellowship from the Alan Turing Institute. M.C.O. acknowledges support from a Borysiewicz Fellowship from the University of Cambridge and a Junior Research Fellowship from Trinity College, Cambridge. F.M. is a Royal Society Wolfson Research Merit Award holder. We thank M. Schneider, R. Drews, P. Martinez-Gonzalez and T. Whitmarsh for valuable input on this work. The authors thank the NIHR Cambridge Biomedical Research Centre (BRC-1215-20014) and the Experimental Cancer Medicine Centre for their support and for providing the infrastructure for the research procedures in Cambridge. The views expressed are those of the authors and not necessarily those of the NIHR or the Department of Health and Social Care. In addition, we thank the Human Research Tissue Bank, which is supported by the UK National Institute for Health Research Cambridge Biomedical Research Centre, from Addenbrookes Hospital. Finally, we thank the BEST2 trial team, the Histopathology core facility at the Cancer Research UK Cambridge Institute and Pathognomics Ltd. for their support.

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Authors

Contributions

M.G. conceived and led the analysis. M.C.O. and A.B. contributed to the analysis. M.G. and A.B. wrote the code for analysis. M.O. and R.C.F. were involved in the collection and labeling of the data. R.C.F. conceived the study. R.C.F. and F.M. directed the project. M.G. and F.M. wrote the manuscript with the assistance and feedback of all other co-authors.

Corresponding authors

Correspondence to Rebecca C. Fitzgerald or Florian Markowetz.

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Competing interests

The Cytosponge device technology and the associated TFF3 biomarker are licensed to Covidien GI solutions (now owned by Medtronic) by the Medical Research Council. M.G., M.C.O. and F.M. are named inventors on a patent pertaining to technology applied in this work. R.C.F. and M.O. are named inventors on patents pertaining to the Cytosponge and associated technology. M.G., M.O. and R.C.F. are shareholders of Cyted Ltd., a company working on early detection technology.

Additional information

Peer review information Nature Medicine thanks Marnix Jansen, Nasir Rajpoot and Pratik Shah for their contribution to the peer review of this work. Javier Carmona was the primary editor on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data

Extended Data Fig. 1 Differential increase of training partition size for ResNet-18.

Training subset refers to the relative proportion of the training partition used in the model training phase. Development subset refers to the relative proportion of the training partition used in the model development phase. The peak development weighted recall (a) and precision (b) correspond to the best performing cohort for each training run. The size of the development set was fixed at 15 patients. For each patient, an average of 3,500 tiles was used. For both H&E and TFF3 no substantial increase in performance metrics could be observed after a training subset size of 50 patients. Individual Cytosponge H&E sections are already highly heterogeneous, which means that the value gained by increasing the size of the training dataset is limited. We opted for retaining all the annotated data in the training set, to maximize the chances of capturing the whole spectrum of data variability and therefore the robustness of the model. H&E benefited more from an increased number of patients than the TFF3 model. This difference is associated with the increased complexity of detecting different tissue morphologies on H&E vs. brown goblet cells on TFF3. In TFF3 slides regions were extensively annotated by pathologists and this ground truth served as a comparator for the recall provided in both figures.

Extended Data Fig. 2 Comparison of pathologist landmarks with saliency maps extracted from VGG-16 architectures.

Additional examples of saliency maps for Hematoxylin & Eosin stain (squamous cells and columnar epithelium) and Trefoil factor 3 (positive goblet cells). Landmarks selected by an experienced pathologist are shown as overlays with red borders on pathology tile images. For all classes, there was visual agreement between highlighted areas by the pathologist and saliency map activations.

Extended Data Fig. 3 Determination of probability thresholds in order to obtain number of tiles.

Both plots show the AUC-ROC for individual probability thresholds (after softmax) which are used to decide whether a tile falls into the relevant class. a, AUC-ROC for quality control (QC) ground truth determined by the pathologist compared with number of tiles containing columnar epithelium at individual probability thresholds. b, AUC-ROC for diagnosis ground truth determined by the endoscopy (with confirmed IM on pathology) compared with number of tiles containing positive goblet cells at individual probability thresholds.

Extended Data Fig. 4 Performance of all deep learning architectures on the calibration cohort.

(a) ROC analysis of number of tiles containing columnnar epithelium on H\&E compared with pathologist ground truth from Cytosponge (b) ROC analysis of number of tiles containing positive goblet cells on TFF3 compared with pathologist ground truth from Cytosponge (c) ROC analysis of number of tiles containing positive goblet cells on TFF3 compared with endoscopy (with confirmed IM) ground truth. A weak AUC dependency on architecture complexity can be observed.

Extended Data Fig. 5 Performance of all deep learning architectures on the internal validation cohort.

a, ROC analysis of number of tiles containing columnnar epithelium on H&E compared with pathologist ground truth from Cytosponge (b) ROC analysis of number of tiles containing positive goblet cells on TFF3 compared with pathologist ground truth from Cytosponge (c) ROC analysis of number of tiles containing positive goblet cells on TFF3 compared with endoscopy (with confirmed IM) ground truth. As in the calibration cohort, a weak AUC dependency on architecture complexity can be observed.

Extended Data Fig. 6 Application of quality control and diagnostic confidence class scheme to calibration cohort.

The lines indicate operating points chosen by three different expert observers. a, Quality ground truth by pathologist from Cytosponge (top) compared with number of detected columnar epithelium (CE) tiles on H\&E detected by VGG-16 (bottom). For the first operating point, E#2 and E#3 agreed whereas E#1 selected a higher cut-off. Majority voting resulted in the lower cut-off being chosen. For the second operating point, all thee observers (E#1, E#2, and E#3) agreed on the same threshold. The line drawn by E#1 for the second operating point effectively resulted in the same operating point as E#2 and E#3. b, Diagnosis ground truth by pathologist from Cytosponge (top), Endoscopy (with confirmed IM on biopsy) ground truth (middle) compared with number of detected TFF3-positive tiles on TFF3 detected by ResNet-18 (bottom). For both the first and second operating points E#1, E#2, and E#3 agreed. The line drawn by E#3 for the second operating point effectively resulted in the same operating point as E#1 and E#2.

Extended Data Fig. 7 Performance of semi-automated, triage-driven model on external validation cohort.

a, Cumulative substitution scheme starting with fully manual review, followed by substitution with automated review of class no. 1, then 1 and 2, etc. b, Cumulative substitution scheme starting with fully manual review, followed by substitution with automated review of class no. 8, then 8 and 7, etc.

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Gehrung, M., Crispin-Ortuzar, M., Berman, A.G. et al. Triage-driven diagnosis of Barrett’s esophagus for early detection of esophageal adenocarcinoma using deep learning. Nat Med 27, 833–841 (2021). https://doi.org/10.1038/s41591-021-01287-9

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