Genome sequencing analysis identifies Epstein–Barr virus subtypes associated with high risk of nasopharyngeal carcinoma (original) (raw)

Data availability

The EBV sequencing data are deposited in the US National Center for Biotechnology Information (NCBI) database under BioProject ID PRJNA522388. EBV sequences are released in NCBI database under GenBank IDs MK540241–MK540470.

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Acknowledgements

We thank all of the participants for their generous support of the current study. We would also thank R. Sun, C. Wang, H. Chen, J. Shen and C. Jie for helpful discussions on viral biology and genetic statistical, evolutionary and phylogenetic analyses, W.-S. Liu and X. Zuo for providing code support, Z. Lin (Tulane University) for kindly sharing EBV genome annotation files and J.-Y. Shao from Sun Yat-sen University Cancer Center for providing the MassArray iPlex platform. This work was supported by the National Natural Science Foundation of China (81430059 to Y.-X.Z. and 81872228 to M.X.), the National Key R&D Program of China (2016YF0902000 to Y.-X.Z., and 2018YFC1406902 and 2018YFC0910400 to W.Z.), the National Cancer Institute at the US National Institutes of Health (NIH) (R01CA115873-01 to H.-O.A. and Y.-X.Z., and R35-CA197449, P01-CA134294, U01-HG009088 and U19-CA203654 to X.L.) and the Agency of Science, Technology and Research (A*STAR), Singapore (to J.L.).

Author information

Author notes

  1. These authors contributed equally: Miao Xu,Youyuan Yao,Hui Chen,Shanshan Zhang.

Authors and Affiliations

  1. State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
    Miao Xu, Youyuan Yao, Shanshan Zhang, Su-Mei Cao, Tong Xiang, Guiping He, Qi-Sheng Feng, Li-Zhen Chen, Xiang Guo, Wei-Hua Jia, Ming-Yuan Chen, Xiao Zhang, Shang-Hang Xie, Roujun Peng, Lin Feng, Jin-Xin Bei, Rui-Hua Xu, Mu-Sheng Zeng & Yi-Xin Zeng
  2. Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
    Miao Xu, Zilin Li & Xihong Lin
  3. Department of Comprehensive Medical Oncology, Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang Province, Zhejiang Cancer Hospital, Hangzhou, China
    Youyuan Yao
  4. Human Genetics, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
    Hui Chen, Vincent Pedergnana, Weiwei Zhai & Jianjun Liu
  5. Department of Otolaryngology/Head and Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, China
    Zhe Zhang
  6. Department of Medical Microbiology, Qingdao University Medical College, Qingdao, China
    Bing Luo
  7. Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
    Zhiwei Liu, Weimin Ye & Hans-Olov Adami
  8. Department of Nasopharyngeal Carcinoma, Sun Yat-sen University Cancer Center, Guangzhou, China
    Xiang Guo
  9. Center for Health Sciences, Exponent, Menlo Park, CA, USA
    Ellen T. Chang
  10. Stanford Cancer Institute, Stanford, CA, USA
    Ellen T. Chang
  11. Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
    Hans-Olov Adami
  12. Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
    Weiwei Zhai
  13. Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
    Weiwei Zhai
  14. Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
    Jianjun Liu

Authors

  1. Miao Xu
  2. Youyuan Yao
  3. Hui Chen
  4. Shanshan Zhang
  5. Su-Mei Cao
  6. Zhe Zhang
  7. Bing Luo
  8. Zhiwei Liu
  9. Zilin Li
  10. Tong Xiang
  11. Guiping He
  12. Qi-Sheng Feng
  13. Li-Zhen Chen
  14. Xiang Guo
  15. Wei-Hua Jia
  16. Ming-Yuan Chen
  17. Xiao Zhang
  18. Shang-Hang Xie
  19. Roujun Peng
  20. Ellen T. Chang
  21. Vincent Pedergnana
  22. Lin Feng
  23. Jin-Xin Bei
  24. Rui-Hua Xu
  25. Mu-Sheng Zeng
  26. Weimin Ye
  27. Hans-Olov Adami
  28. Xihong Lin
  29. Weiwei Zhai
  30. Yi-Xin Zeng
  31. Jianjun Liu

Contributions

Y.-X.Z., J.L. and W.Z. were the principal investigators who conceived the study. Y.-X.Z., J.L., W.Z. and M.X. designed and oversaw the study. J.L. and X.L. supervised the viral genome-wide association studies. W.W. supervised phylogenetic analysis. M.X. contributed to sample preparation, sequencing, genotyping, variant calling and genetic statistical analyses. Y.Y. contributed to sequencing, genotyping and variant calling. H.C. contributed to phylogenetic analyses. S.Z. contributed to genotyping and genetic statistical analyses. Z.Li contributed to genetic statistical analyses. Z.Z. contributed to collection of samples from the First Affiliated Hospital of Guangxi Medical College. B.L. contributed to collection of samples from the Affiliated Hospital of the Qingdao University. X.G., M.-Y.C., R.P. and R.-H.X. contributed to collection of samples from Sun Yat-sen University Cancer Center. H.-O.A., W.Y. and Y.-X.Z. supervised the design and implementation of the population-based case–control study in Zhaoqing. W.Y., E.T.C., S.-M.C., S.-H.X. and Z.Liu participated in the case–control study. The manuscript was drafted by M.X., J.L., W.Z. and Y.-X.Z., and revised by V.P. and E.T.C. All authors critically reviewed the article and approved the final manuscript.

Corresponding authors

Correspondence toWeiwei Zhai, Yi-Xin Zeng or Jianjun Liu.

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The authors declare no competing interests.

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Xu, M., Yao, Y., Chen, H. et al. Genome sequencing analysis identifies Epstein–Barr virus subtypes associated with high risk of nasopharyngeal carcinoma.Nat Genet 51, 1131–1136 (2019). https://doi.org/10.1038/s41588-019-0436-5

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