Abstract：
Few reports have analyzed the fusion genes involved in carcinogenesis in the oropharynx, where the incidence of human papillomavirus-associated tumors is relatively low. The aim of this study was to identify novel driver fusion genes in patients with oropharyngeal cancer. The study enrolled fifty-seven patients who were diagnosed with oropharyngeal carcinoma. RNA sequencing data from fresh-frozen specimens were used to identify candidate fusion genes via the JAFFA, arriba, and STAR-Fusion pipelines. Candidate fusion genes were confirmed by direct sequencing. The expression level of a candidate fusion gene was compared to that of tumors without fusion genes. Finally, filtering was performed for driver genes using the annoFuse pipeline. In addition, the VIRTUS pipeline was used to analyze the presence of human papillomavirus in the tumors. We identified 5 (8.8 %) novel potential driver in-frame fusion genes, MKNK2::MOB3A, ICMT::RPS6KA3, ATP1B3::GRK7, CSNK2A1::KIF16B, and FGFR3::MAEA, and 1 (1.8 %) known in-frame fusion gene, FGFR3::TACC3, in 57 patients with pharyngeal carcinoma. Our results suggest that sporadic fusion genes may contribute to tumorigenesis in oropharyngeal carcinomas.
摘要：
很少有报道分析口咽癌变中涉及的融合基因，其中人乳头瘤病毒相关肿瘤的发病率相对较低。这项研究的目的是鉴定口咽癌症患者的新型驱动融合基因。该研究纳入了57例被诊断为口鼻咽癌的患者。来自新鲜冷冻标本的RNA测序数据用于通过JAFFA鉴定候选融合基因，arriba,和STAR-Fusion管道。通过直接测序确认候选融合基因。将候选融合基因的表达水平与没有融合基因的肿瘤的表达水平进行比较。最后,使用annoFuse管道对驱动基因进行过滤。此外,VIRTUS管道用于分析肿瘤中是否存在人乳头瘤病毒.我们确定了5个(8.8%)新的潜在驱动框内融合基因，MKNK2::MOB3A,ICMT::RPS6KA3,ATP1B3::GRK7,CSNK2A1::KIF16B,和FGFR3::MAEA，和1个(1.8%)已知的框内融合基因，FGFR3：：TACC3，在57例咽癌患者中。我们的结果表明，零星的融合基因可能有助于口咽癌的肿瘤发生。
