基于高通量测序技术的非小细胞肺癌常见基因位点突变分析

Analysis of common mutations in non-small cell lung cancer by high-throughput sequencing

目的利用高通量测序平台研究非小细胞肺癌(NSCLC)热点基因突变情况,系统性分析突变位点的分布、类型以及频度,评估突变位点致病性。方法本研究共纳入94例NSCLC组织样本,均为2015年7月至2017年4月在山东大学齐鲁医院胸外科收集的非小细胞肺癌(NSCLC)石蜡包埋(FFPE)和新鲜组织样本。患者年龄在35~82岁之间,年龄中位数是61岁。男性63例,女性31例。选择22个基因:KRAS、EGFR、BRAF、PIK3CA、AKT1、ERBB2、PTEN、NRAS、STK11、MAP2K1、ALK、DDR2、CTNNB1、MET、TP53、SMAD4、FBXW7、FGFR3、NOTCH1、ERBB4、FGFR1和FGFR2。用Thermo fisher公司Ion Torrent测序平台的Ion Ampli Seq Colon and Lung Cancer Panel进行测序。Ion Torrent平台测序数据使用Ion torrent suite v4.4.2软件进行分析。结果在NSCLC常见的22个突变基因中,TP53基因突变频率最高,约占所有突变的46.9%,其次是EGFR基因(占28.1%);共检测出89种突变,包括63种热点突变(已报道的位点)和26种新发突变(未见报道的位点),其中检出频率最高的是EGFR基因的19号外显子缺失突变,其次是EGFR基因的Leu858Arg;分析EGFR基因的靶向用药位点的突变情况,结果显示EGFR的19号外显子的缺失突变检出次数最高,其次是21号外显子L858R突变;利用生物信息学软件分析了26种新发突变的致病性,结果显示除ATK1:c.47-12G>A和TP53:c.214C>G这两个位点以外,剩余的24种新发突变位点在基因保守性、氨基酸序列变化、蛋白结构影响三个方面至少有一项会对基因的功能产生重大影响。结论本研究通过NGS对NSCLC多个敏感基因的突变位点进行联合检测,更能全面覆盖基因变异情况,为筛选最适宜靶向治疗的群体提供依据。新发突变的致病性预测以及所涉及的肿瘤相关信号通路的改变,为后续为进一步研究NSCLC致病机制提供参考。

Objective Next Generation Sequencing(NGS) platform was used to study the characteristics of hot gene mutations in non-small cell lung cancer (NSCLC). The distribution, type and frequency of mutation sites were systematically analyzed to evaluate the pathogenicity of mutation sites. Methods A total of 94 NSCLC tissue samples were included in this study including paraffin-embedded (FFPE) samples and fresh tissue samples, which were collected from July 2015 to April 2017 at the Qilu Hospital of Shandong University. The patient′s age ranged from 35 to 82 years with a median age of 61 years. There were 63 males and 31 females. 22 hot genes in NSCLC were selected as the detection panel, including KRAS, EGFR, BRAF, PIK3CA, AKT1, ERBB2, PTEN, NRAS, STK11, MAP2K1, ALK, DDR2, CTNNB1, MET, TP53, SMAD4, FBXW7, NOTCH1, ERBB4, FGFR1 and FGFR2. Mutation detection was performed using the Ion AmpliSeq Colon and Lung Cancer Panel of the Thermo fisher′s Ion Torrent sequencing platform. The sequencing data was analyzed using Ion Torrent suite v4.4.2 software. Results Among the 22 mutant genes commonly found in NSCLC, the mutation frequency of TP53 was the highest, accounting for 46.9% of all mutations, followed by the EGFR mutation (28.1%);A total of 89 mutations were detected, including 63 hot spot mutations (reported mutations) and 26 new mutations (unreported mutations). The most frequently detected mutation was the frameshift deletion of exon 19 of EGFR, followed by the mutation of exon L858R;Analysis of the mutation in targeted drug sites of EGFR showed that the frameshift deletion of exon 19 of EGFR was the most frequently detected, followed by the mutation of exon L858R on chromosome 21. Bioinformatics software was used to analyze the pathogenicity of 26 new mutation sites. Results showed that in addition to ATK1: c. 47-12G>A and TP53: c. 214 C>G, the remaining 24 new mutation sites had at least one major impact on the gene function in three aspects, including gene conservation, amino acid sequence change and protein structure influence. Conclusion In this study, NGS was used to conduct combined detection of mutation sites of multiple hot genes, which might cover more comprehensively genetic variation and provide a basis for screening the most suitable targeted therapy groups. The pathogenicity prediction of new mutations and the changes in tumor-related signaling pathways involved provide a reference for further study of the pathogenesis of NSCLC.