Establishment and validation of circulating cell-free DNA signatures for nasopharyngeal carcinoma detection

Background Early detection of nasopharyngeal carcinoma (NPC) poses a significant fi cant challenge. The absence of highly sensitive and specific fi c diagnostic biomarkers for nasopharyngeal carcinoma contributes to the unfavourable prognosis of NPC patients. Here, we aimed to establish a non-invasive approach for detecting NPC using circulating cell-free DNA (cfDNA). Methods We investigated the potential of next-generation sequencing (NGS) of peripheral blood cells as a diagnostic tool for NPC. We collected data on genome-wide nucleosome footprint (NF), 5 '-end '-end motifs, fragmentation patterns, CNV information, and EBV content from 553 Chinese subjects, including 234 NPC patients and 319 healthy individuals. Through case-control - control analysis, we developed a diagnostic model for NPC, and validated its detection capability. Findings Our fi ndings revealed that the frequencies of NF, fragmentation, and motifs were significantly fi cantly higher in NPC patients compared to healthy controls. We developed an NPC score based on these parameters that accurately distinguished NPC from non-NPC cases according to the American Joint Committee on Cancer staging system from non-NPC (validation set: area under curve (AUC) = 99.9% (95% CI: 99.8%-100%), - 100%), se: 98.15%, sp: 100%). This model showed superior performance over plasma EBV DNA. Additionally, the NPC score effectively differentiated between NPC patients and healthy controls, even after clinical treatment. Furthermore, the NPC score was found to be independent of potential confounders such as age, sex, or TNM stage. Interpretation We have developed and verified fi ed a non-invasive approach with substantial potential for clinical application in detecting NPC. Copyright (c) 2024 Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license creativecommons.org/licenses/by-nc-nd/4.0/).