Determination and genome-wide analysis of Epstein-Barr virus (EBV) sequences in EBV-associated gastric carcinoma from Guangdong, an endemic area of nasopharyngeal carcinoma

Journal of Medical Microbiology
Jian-Ning ChenChun-Kui Shao

Abstract

About 10 % of gastric carcinoma worldwide is associated with EBV, which is defined as EBV-associated gastric carcinoma (EBVaGC). To date, EBV sequence data from EBVaGC in Guangdong, China, an endemic area of nasopharyngeal carcinoma (NPC), are not available. In the present study, two EBV genomes from EBVaGC specimens from Guangdong (designated as GDGC1 and GDGC2) were determined by next-generation sequencing, de novo assembly and joining of contigs by Sanger sequencing. In addition, we sequenced EBV from two Korean EBVaGC cell lines, YCCEL1 and SNU-719. Genomic diversity, including single nucleotide polymorphisms (SNPs) and insertions and deletions (indels), phylogenetic analysis and rates of protein evolution, was performed using bioinformatics software. The four gastric carcinoma-derived EBV (GC-EBV) were all type I. Compared with the reference EBV genome, a total of 1815 SNPs (146 indels), 1519 SNPs (106 indels), 1812 SNPs (126 indels) and 1484 SNPs (106 indels) were found in GDGC1, GDGC2, YCCEL1 and SNU-719, respectively. These variations were distributed across the entire genome, especially in latent genes. In contrast, the sequences of promoters and non-coding RNAs were strictly conserved. Phylogenetic analyses suggested ...Continue Reading

References

May 14, 1998·International Journal of Cancer. Journal International Du Cancer·S T CheungD P Huang
Dec 7, 2002·Critical Reviews in Oncology/hematology·Hiroshi Wakiguchi
May 29, 2003·The Journal of General Virology·Orlando de JesusPaul J Farrell
Aug 12, 2003·Oncogene·Lawrence S Young, Paul G Murray
Feb 24, 2006·Virology·Aidan DolanDuncan J McGeoch
Apr 18, 2006·Journal of Clinical Virology : the Official Publication of the Pan American Society for Clinical Virology·Vannarat SaechanTakafumi Ishida
Sep 27, 2006·Acta Crystallographica. Section D, Biological Crystallography·Nicolas TarbouriechWim Pascal Burmeister
Oct 13, 2006·Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association for Cancer Research, Cosponsored by the American Society of Preventive Oncology·Ellen T Chang, Hans-Olov Adami
Apr 27, 2007·Journal of Virology·Lindsey M Hutt-Fletcher
May 8, 2007·Molecular Biology and Evolution·Ziheng Yang
Jun 6, 2009·Bioinformatics·Ruiqiang LiJun Wang
Jun 23, 2009·Genome Research·Martin KrzywinskiMarco A Marra
Aug 25, 2010·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Alexander K Hudek, Daniel G Brown
Dec 15, 2010·Bioinformatics·Samuel V Angiuoli, Steven L Salzberg
Nov 16, 2012·Journal of Virology·Zhen LinErik K Flemington
Nov 24, 2012·The Journal of General Virology·Do Nyun KimSuk Kyeong Lee
Aug 7, 2013·Infectious Agents and Cancer·Ken Kai-Yuen TsoKwok-Wai Lo
Jan 21, 2014·RNA Biology·Walter N MossJoan A Steitz
Sep 25, 2014·The Journal of Pathology·Sai-Wah TsaoKwok-Wai Lo
Feb 6, 2015·CA: a Cancer Journal for Clinicians·Lindsey A TorreAhmedin Jemal
Mar 20, 2015·Journal of Virology·Anne L PalserPaul Kellam
Dec 31, 2016·The Journal of General Virology·Lu ZhouChun-Kui Shao

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Citations

Jul 6, 2019·Molecular Biology and Evolution·Fanny WegnerJudith Breuer
May 14, 2020·Pathogens·Snježana Židovec LepejPetra Korać
May 20, 2021·Analytical Methods : Advancing Methods and Applications·Mengmeng LiuChao Shi

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