Oncotarget

Research Papers:

Detection of nasopharyngeal carcinoma susceptibility with single nucleotide polymorphism analysis using next-generation sequencing technology

Mu-Yun Wu, Shu-Jing Huang, Fan Yang, Xin-Tian Qin, Ying Ding, Shu Yang and Xi-Cheng Wang _

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Oncotarget. 2017; 8:52708-52723. https://doi.org/10.18632/oncotarget.17085

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Abstract

Mu-Yun Wu1,2,*, Shu-Jing Huang1,*, Fan Yang1,*, Xin-Tian Qin1, Dong Liu1, Ying Ding1, Shu Yang1 and Xi-Cheng Wang1

1Department of Oncology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China

2Department of Oncology, The Fifth People’s Hospital of Wuhu, Wuhu, China

*These authors contributed equally to this work and should be considered co-first authors

Correspondence to:

Xi-Cheng Wang, email: 13902400598@126.com

Shu Yang, email: y665925@126.com

Ying Ding, email: dy61321157@163.com

Keywords: nasopharyngeal carcinoma (NPC), next-generation sequencing technology (NGS), susceptibility, single nucleotide polymorphism (SNP)

Received: December 12, 2016    Accepted: March 17, 2017    Published: April 13, 2017

ABSTRACT

Nasopharyngeal carcinoma (NPC) is a head and neck cancer with high incidence in South China and East Asia. To provide a theoretical basis for NPC risk screening and early prevention, we conducted a meta-analysis of relevant literature on the association of single nucleotide polymorphisms (SNP)s with NPC susceptibility. Further, expression of 15 candidate SNPs identified in the meta-analysis was evaluated in a cohort of NPC patients and healthy volunteers using next-generation sequencing technology. Among the 15 SNPs detected in the meta-analysis, miR-146a (rs2910164, C>G), HCG9 (rs3869062, A>G), HCG9 (rs16896923, T>C), MMP2 (rs243865, C>T), GABBR1 (rs2076483, T>C), and TP53 (rs1042522, C>G) were associated with decreased susceptibility to NPC, while GSTM1 (+/DEL), IL-10 (rs1800896, A>G), MDM2 (rs2279744, T>G), MDS1-EVI1 (rs6774494, G>A), XPC (rs2228000, C>T), HLA-F (rs3129055, T>C), SPLUNC1 (rs2752903, T>C; and rs750064, A>G), and GABBR1 (rs29232, G>A) were associated with increased susceptibility to NPC. In our case-control study, an association with increased risk for NPC was found for the AG vs AA genotype in HCG9 (rs3869062, A>G). In addition, heterozygous deletion of the GSTM1 allele was associated with increased susceptibility to NPC, while an SNP in GABBR1 (rs29232, G>A) was associated with decreased risk, and might thus have a protective role on NPC carcinogenesis. This work provides the first comprehensive assessment of SNP expression and its relationship to NPC risk. It suggests the need for well-designed, larger confirmatory studies to validate its findings.


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