Background: Nasopharyngeal carcinoma (NPC) treatment is mainly based on clinical staging. We hypothesize that better understanding of the molecular heterogeneity of NPC can aid in better treatment decisions. Therefore, the purpose of this study was to present our exploration of cancer gene copy-number alterations (CNAs) of Epstein-Barr virus (EBV)-positive and EBV-negative NPC. Methods: Multiplex ligation-dependent probe amplification was applied to detect CNAs of 36 cancer genes (n = 103). Correlation between CNAs, clinicopathological features, and survival were examined. Results: The CNAs occurred significantly more in EBV-negative NPC, with PIK3CA and MCCC1 (P <.001) gain/amplification occurring more frequently. Gain/amplification of cyclin-L1 (CCNL1) and PTK2 (P <.001) predict worse disease-free survival (DFS) in EBV-positive NPC. Conclusion: The EBV-positive and EBV-negative NPC show some similarities in cancer gene CNAs suggesting a common pathogenic route but also important differences possibly indicating divergence in oncogenesis. Copy number gain/amplification of CCNL1 and PTK2 are possibly good predictors of survival in EBV-positive NPC.

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Keywords copy-number alterations, Epstein-Barr virus, gene, multiplex ligation-dependent probe amplification, nasopharyngeal carcinoma
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Journal Head & Neck: journal for the sciences and specialities of the head and neck
Ooft, M.L, van Ipenburg, J. (Jolique), van de Loo, R.J.M. (Rob J. M.), de Jong, R. (Rick), Moelans, C.B, de Bree, R, … Willems, S.M. (2018). Differences in cancer gene copy number alterations between Epstein-Barr virus-positive and Epstein-Barr virus-negative nasopharyngeal carcinoma. Head & Neck: journal for the sciences and specialities of the head and neck, 40(9), 1986–1998. doi:10.1002/hed.25195