A cfDNA fragmentomics classifier for noninvasive differentiation of benign and malignant renal masses

Noninvasive differentiation of malignant and benign renal masses remains a major clinical challenge, particularly for radiologically indeterminate lesions. Here, we developed and validated a plasma cell-free DNA (cfDNA) fragmentomics-based machine learning classifier for renal mass characterization. The model was trained on 331 participants (171 cancer, 160 benign) and independently validated on 144 participants (73 cancer, 71 benign). Three cfDNA fragmentation features, including copy number variation (CNV), fragmentation-based methylation (FRAGMA), and nucleosome footprint (NF), derived from low-pass whole-genome sequencing, were integrated into an ensemble framework. The model achieved strong discriminative performance, with area under the curve (AUC) values of 0.956 in the training cohort and 0.946 in the validation cohort, outperforming individual feature-based models. At a predefined operating threshold corresponding to 90% sensitivity, specificity reached 0.90 and 0.87, respectively. Notably, most cancer samples exhibited low tumor fraction (TF < 3%), yet the model maintained robust performance in low-TF samples (AUCs: 0.952 and 0.941, respectively). Performance remained consistent across tumor stage, grade, and histological subtypes. The classifier also demonstrated potential clinical utility in diagnostically challenging settings, including lipid-poor angiomyolipoma and oncocytoma, with 12 of 13 oncocytoma samples correctly classified in an independent cohort. In addition, the model correctly identified 85.3% of benign masses > 4 cm, for which surgical intervention is more commonly considered, and 84.6% of malignant tumors ≤ 4 cm, for which management can be challenging. Collectively, these findings support cfDNA fragmentomics as a promising noninvasive liquid biopsy approach for renal mass evaluation and clinical decision-making.