DNA methylation classifier to diagnose pancreatic ductal adenocarcinoma metastases from different anatomical sites
Permanent link
https://hdl.handle.net/10037/35971Date
2024-11-10Type
Journal articleTidsskriftartikkel
Peer reviewed
Author
Calina, Teodor G.; Perez, Eilís; Grafenhorst, Elena; Benhamida, Jamal; Schallenberg, Simon; Popescu, Adrian; Koch, Ines; Janik, Tobias; Chen, BaoQing; Ihlow, Jana; Roessler, Stephanie; Goeppert, Benjamin; Sinn, Bruno; Bahra, Marcus; Calin, George A.; Taube, Eliane T.; Pelzer, Uwe; Neumann, Christopher C. M.; Horst, David; Knutsen, Erik; Capper, David; Dragomir, Mihnea P.Abstract
Methods - For this scope, the anomaly detection filter of the initial classifier was expanded by 8 additional mimicker carcinomas, amounting to a total of 10 carcinomas in the negative class. We validated the updated version of the classifier on a validation set, which consisted of a biological cohort (n = 3579) and a technical one (n = 15). We then assessed the performance of the classifier on a test set, which included a positive control cohort of 16 PAAD metastases from various sites and a cohort of 124 negative control samples consisting of 96 breast cancer metastases from 18 anatomical sites and 28 carcinoma metastases to the brain.
Results - The updated PAAD-iCCA-Classifier achieved 98.21% accuracy on the biological validation samples, and on the technical validation ones it reached 100%. The classifier also correctly identified 15/16 (93.75%) metastases of the positive control as PAAD, and on the negative control, it correctly classified 122/124 samples (98.39%) for a 97.85% overall accuracy on the test set. We used this DNA methylation dataset to explore the organotropism of PAAD metastases and observed that PAAD liver metastases are distinct from PAAD peritoneal carcinomatosis and primary PAAD, and are characterized by specific copy number alterations and hypomethylation of enhancers involved in epithelial-mesenchymal-transition.
Conclusions - The updated PAAD-iCCA-Classifier (available at https://classifier.tgc-research.de/) can accurately classify PAAD samples from various metastatic sites and it can serve as a diagnostic aid.