Journal Article

Sequencing-based counting and size profiling of plasma Epstein–Barr virus DNA enhance population screening of nasopharyngeal carcinoma

Tse, O. Y. Olivia, Gai, Wanxia, Hui, Edwin P., Zhang, Haiqiang, Woo, John K. S., Chiu, Rossa W. K., Cheng, Suk H., Zee, Benny C. Y., Ma, Brigette B. Y., Lo, Y. M. Dennis, Chan, Anthony T. C., Tong, Yu K., Jiang, Peiyong, Peng, Wenlei, Chan, K. C. Allen, Lam, W. K. Jacky

2018

Overview

Circulating tumor-derived DNA testing for cancer screening has recently been demonstrated in a prospective study on identification of nasopharyngeal carcinoma (NPC) among 20,174 asymptomatic individuals. Plasma EBV DNA, a marker for NPC, was detected using real-time PCR. While plasma EBV DNA was persistently detectable in 97.1% of the NPCs identified, ∼5% of the general population had transiently detectable plasma EBV DNA. We hypothesized that EBV DNA in plasma of subjects with or without NPC may have different molecular characteristics. We performed target-capture sequencing of plasma EBV DNA and identified differences in the abundance and size profiles of EBV DNA molecules within plasma of NPC and non-NPC subjects. NPC patients had significantly higher amounts of plasma EBV DNA, which showed longer fragment lengths. Cutoff values were established from an exploratory dataset and tested in a validation sample set. Adopting an algorithm that required a sample to concurrently pass cutoffs for EBV DNA counting and size measurements, NPCs were detected at a positive predictive value (PPV) of 19.6%. This represented superior performance compared with the PPV of 11.0% in the prospective screening study, which required participants with an initially detectable plasma EBV DNA result to be retested within 4 weeks. The observed differences in the molecular nature of EBV DNA molecules in plasma of subjects with or without NPC were successfully translated into a sequencing-based test that had a high PPV for NPC screening and achievable through single time-point testing.

• Publisher: National Academy of Sciences
• Subject: Adult / Biological Sciences / Biopsy / Cancer screening / Carcinoma - blood / Carcinoma - diagnosis / Circulating Tumor DNA - blood / Cohort Studies / Deoxyribonucleic acid / Diagnostics / DNA / DNA sequencing / DNA testing / DNA, Viral - blood / DNA, Viral - chemistry / DNA, Viral - genetics / Epstein-Barr virus / Female / Herpesvirus 4, Human - genetics / Humans / Liquid Biopsy - methods / Male / Medical Sciences / Middle Aged / Molecular Diagnostic Techniques - methods / Nasopharyngeal Carcinoma / Nasopharyngeal Neoplasms - blood / Nasopharyngeal Neoplasms - diagnosis / Plasma / PNAS Plus / Reproducibility of Results / Screening / Viral Load - methods / Viruses