Early detection of colorectal cancer (CRC) is crucial for improving patient survival. This innovative multi-center study aims to develop a non-invasive blood-based assay using cell-free DNA (cfDNA) fragmentomics to differentiate CRC from advanced colorectal adenomas and non-cancerous colorectal and other digestive diseases.

A total of 167 CRC patients and 227 with benign colorectal conditions were divided into training and validation cohorts (1:1 ratio). Plasma cfDNA underwent Low-depth whole-genome sequencing to profile three fragmentomics features, which were integrated into a stacked ensemble model. The model was validated on 69 CRC patients and 96 benign controls, with an additional cohort of 31 advanced adenoma patients included to assess its performance in differentiating advanced adenomas from benign cases.

The model achieved an AUC of 0.926, with sensitivity of 91.3% and specificity of 82.3% in validation. Sensitivities were consistently high across CRC stages (I: 94.4%, II: 86.4%, III: 91.3%, IV: 100%). Notably, the model demonstrated exceptional accuracy in distinguishing advanced adenomas from benign cases, achieving an AUC of 0.846 and sensitivity of 67.7%, outperforming traditional blood tests.

This multi-center study underscores a significant advancement in liquid biopsy technology, offering a highly accurate and non-invasive approach for early CRC detection and differentiation of advanced colorectal adenomas.