Better NPC risk stratification with identification of distinct EBV DNA molecular features

A research team from the Faculty of Medicine, Chinese University of Hong Kong (CUHK) has identified molecular features in Epstein-Barr virus (EBV) DNA specifically associated with nasopharyngeal cancer (NPC) that differ significantly from the EBV DNA found in individuals with general EBV infections.

“Our previous research [first-round screening] data showed that some noncancer individuals also tested positive on polymerase chain reaction [PCR] for plasma EBV DNA,” said Dr Jacky Wai-Kei Lam of the Department of Chemical Pathology, CUHK, a member of the research team. “To accurately identify high-risk groups, we conducted in-depth analysis of the positive cases from the first round of screening, using next-generation sequencing technology to profile plasma EBV DNA characteristics. This approach successfully differentiated cancer-associated viral DNA and infection-related viral DNA. These molecular features included size, end motifs, and methylation, analyzed using the fragmentomics-based [FRAGMA] technology previously established by our team.” [N Engl J Med 2017;377:513-522; Cancer Cell 2025;43:1-12] 

“Our research results revealed a distinct plasma DNA profile associated with NPC – individuals with these distinct features were found to have an 87-fold increased risk of developing cancer in second-round screening [current follow-up study, 4 years after the first round] compared with EBV DNA–negative individuals. This finding not only confirms the clinical value of plasma EBV DNA testing, but also establishes a novel molecular biomarker system for precision NPC screening,” Lam reported.

In endemic regions such as Southern China (including Hong Kong), NPC is strongly associated with EBV. According to the Hong Kong Cancer Registry, there were more than 700 new cases of NPC in 2022 and NPC ranked 10^th among top cancers in Hong Kong men.  [https://www.ncbi.nlm.nih.gov/books/NBK459256/; https://www3.ha.org.hk/cancereg/pdf/factsheet/2022/npc_2022.pdf]

Between 2013 and 2016, the CUHK research team conducted plasma EBV DNA screening in 20,174 asymptomatic middle-aged males in Hong Kong and identified 34 with NPC. Between 2017 and 2020, the team performed a second round of NPC screening among 17,838 subjects (88.6 percent) of the original cohort (follow-up study) and identified 24 additional NPC cases. In the follow-up study, the focus was on subjects (n=558) with transiently positive and persistently positive (PCR-positive on second test 4 weeks after first test) plasma EBV DNA results in the first round, and the molecular characteristics of plasma EBV DNA in the first-round blood samples of those subjects who did and did not have NPC identified in the second round were compared and evaluated. [Cancer Cell 2025;43:1-12; N Engl J Med 2017;377:513-522] 

“Plasma DNA-based tests are increasingly adopted for screening of various types of cancer. Our latest research finding confirm that integrating DNA fragmentomics analysis with existing blood tests for cancer can further enhance the accuracy of cancer prediction. This approach not only facilitates early detection for timely treatment initiation, but also optimizes risk management for high-risk groups through refined screening protocols,” noted another member of the research team, Professor Allen Kwan-Chee Chan of the Department of Chemical Pathology, CUHK.