Extrachromosomal circular DNA (eccDNA) is gaining substantial attention in basic and clinical research for its contribution to tumor heterogeneity, biogenesis, and evolution. However, its presence and molecular features in peripheral blood from cancer patients are poorly understood. Here, we demonstrated the existence of eccDNA molecules in cancer patients' plasma using atomic-force microscopy and high throughput sequencing technology. We then developed a method named ScanTecc (Screening cancer Types with cell-free eccDNA) that integrates cell-free circular DNA sequencing and machine learning approaches for cancer patient screening and classification. We applied ScanTecc on a total of 413 patients with multiple types of human primary cancers and 52 healthy individuals and found a significantly greater number and more extended size of eccDNAs in patients' peripheral blood. ScanTecc accurately distinguished cancer patients (including early stages I and II) from healthy individuals with an overall prediction rate of 0.85 and identified distinct cancer types with an overall prediction rate of 0.84. Our study provides evidence for a non-invasive approach potentially applicable for early detection of cancer patients in clinics.

Jingwen Fang is the chief executive officer of HanGene Biotech. Kun Qu and Chuang Guo are science advisers of HanGene Biotech. The other authors declare that they have no conflict of interest.

This work was supported by the National Key R&D Program of China (2020YFA0112200 to K.Q.), the National Natural Science Foundation of China grants (T2125012, 91940306, 31970858, and 31771428 to K.Q.; 32100457 to J.F.), CAS Project for Young Scientists in Basic Research YSBR-005 (to K.Q.), Anhui Province Science and Technology Key Program (202003a07020021 to K.Q.) and the Fundamental Research Funds for the Central Universities (YD2070002019, WK9110000141, and WK2070000158 to K.Q.). We thank the USTC supercomputing center and the School of Life Science Bioinformatics Center for providing computing resources for this project.

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