Early detection of renal cell carcinoma: a novel cell-free DNA fragmentomics-based liquid biopsy assay

Renal cell carcinoma (RCC) is a growing global health challenge, with poor survival rates in advanced stages due to the lack of effective early detection methods. This study developed a cell-free DNA (cfDNA) fragmentomics-based liquid biopsy to enable noninvasive RCC diagnosis.

Using low-pass whole-genome sequencing, three cfDNA features-copy number variation, fragment size distribution, and nucleosome footprint-were derived and integrated into a stacked ensemble machine learning model. A total of 280 participants, including 142 RCC patients and 138 noncancer controls, were enrolled for model development. The resultant model was subsequently evaluated using both validation and external cohorts.

The developed model achieved an area under the curve of 0.966 and 0.952 in the validation and external cohorts, respectively. In the validation cohort, the model demonstrated a sensitivity of 90.5% and specificity of 93.8%, while in the external cohort, it exhibited a sensitivity of 76.7% and specificity of 92.9%. Robust performance was observed across different TNM (tumor-node-metastasis) stages, histological subtypes, and Fuhrman grades, with high sensitivity even for early-stage RCC. Furthermore, the assay effectively differentiated malignant tumors from benign renal conditions, thereby potentially reducing unnecessary surgical interventions.

The cfDNA fragmentomics-based liquid biopsy provides a promising, noninvasive, cost-effective, and accurate approach for RCC detection and management, substantiating its potential as a complementary tool to conventional diagnostic techniques. Future research should explore integrating cfDNA fragmentomics with multi-omics approaches to enhance diagnostic precision and broaden clinical utility.