A deep learning algorithm to predict risk of pancreatic cancer from disease trajectories

• Published in: Nature medicine Vol. 29; no. 5; pp. 1113 - 1122
• Main Authors: Placido, Davide, Yuan, Bo, Hjaltelin, Jessica X., Zheng, Chunlei, Haue, Amalie D., Chmura, Piotr J., Yuan, Chen, Kim, Jihye, Umeton, Renato, Antell, Gregory, Chowdhury, Alexander, Franz, Alexandra, Brais, Lauren, Andrews, Elizabeth, Marks, Debora S., Regev, Aviv, Ayandeh, Siamack, Brophy, Mary T., Do, Nhan V., Kraft, Peter, Wolpin, Brian M., Rosenthal, Michael H., Fillmore, Nathanael R., Brunak, Søren, Sander, Chris
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.05.2023; Nature Publishing Group
• Subjects: 631/114/1305; 631/67/2322; 631/67/2324; Algorithms; Artificial Intelligence; Biomedical and Life Sciences; Biomedicine; Cancer; Cancer Research; Deep Learning; Electronic health records; Electronic medical records; Humans; Infectious Diseases; Life span; Machine learning; Metabolic Diseases; Middle Aged; Molecular Medicine; Neurosciences; Pancreatic cancer; Pancreatic Neoplasms - diagnosis; Pancreatic Neoplasms - epidemiology; Performance enhancement; Quality of Life; Risk; United States > US
• ISSN: 1078-8956; 1546-170X; 1546-170X
• DOI: 10.1038/s41591-023-02332-5

Pancreatic cancer is an aggressive disease that typically presents late with poor outcomes, indicating a pronounced need for early detection. In this study, we applied artificial intelligence methods to clinical data from 6 million patients (24,000 pancreatic cancer cases) in Denmark (Danish National Patient Registry (DNPR)) and from 3 million patients (3,900 cases) in the United States (US Veterans Affairs (US-VA)). We trained machine learning models on the sequence of disease codes in clinical histories and tested prediction of cancer occurrence within incremental time windows (CancerRiskNet). For cancer occurrence within 36 months, the performance of the best DNPR model has area under the receiver operating characteristic (AUROC) curve = 0.88 and decreases to AUROC (3m) = 0.83 when disease events within 3 months before cancer diagnosis are excluded from training, with an estimated relative risk of 59 for 1,000 highest-risk patients older than age 50 years. Cross-application of the Danish model to US-VA data had lower performance (AUROC = 0.71), and retraining was needed to improve performance (AUROC = 0.78, AUROC (3m) = 0.76). These results improve the ability to design realistic surveillance programs for patients at elevated risk, potentially benefiting lifespan and quality of life by early detection of this aggressive cancer. A deep learning algorithm using electronic health records from two large cohorts of patients predicts the risk of pancreatic cancer from pre-cancer disease trajectories up to 3 years in advance, showing promising performance in retrospective validation.