A protein-based classifier for differentiating follicular thyroid adenoma and carcinoma

Differentiating follicular thyroid adenoma (FTA) from carcinoma (FTC) remains challenging due to similar histological features separate from invasion. This study developed and validated DNA- and/or protein-based classifiers. A total of 2443 thyroid samples from 1568 patients were obtained from 24 centers in China and Singapore. Next-generation sequencing of a 66-gene panel revealed 41 (62.1%) detectable genes, while 25 were not, showing similar alteration patterns with differing mutation frequencies. Proteomics quantified 10,336 proteins, with 187 dysregulated. A discovery protein-based XGBoost model achieved an AUROC of 0.899 (95% CI, 0.849-0.949), outperforming the gene-based model (AUROC 0.670 [95% CI, 0.612-0.729]). A subsequent 24-protein classifier, developed via targeted mass spectrometry and validated in three independent sets, showed high performance in retrospective cohorts (AUROC 0.871 [95% CI, 0.833-0.910] and 0.853 [95% CI, 0.772-0.934]) and prospective biopsies (AUROC 0.781 [95% CI, 0.563-1.000]). It exhibited a 95.7% negative predictive value for ruling out malignancy. This study presents a promising protein-based approach for the differential diagnosis of FTA and FTC, potentially enhancing diagnostic accuracy and clinical decision-making.