Chen L F, Chen X Y, Lin J, Yu X B, Jin L
Provincial Clinical Medical College of Fujian Medical University; Department of Pathology, Fujian Provincial Hospital, Fuzhou 350001, China.
Zhonghua Bing Li Xue Za Zhi. 2019 Oct 8;48(10):772-778. doi: 10.3760/cma.j.issn.0529-5807.2019.10.005.
To study the characteristics of lung adenocarcinoma driver gene variants detected by next generation sequencing (NGS) and quantitative fluorescence PCR. NGS was performed on 372 surgical resections from primary lung adenocarcinoma patients to detect 10 driver gene mutations, single-nucleotide variants(SNV), insertion/deletion and gene fusions; and quantitative fluorescence PCR were performed on 169 surgical resections from primary lung adenocarcinoma patients to detect nine driver gene hotspot mutations. Variants of VAF (variant allele frequency)≥1.0% were classified into 1 of 4 levels according to the guidelines and the precision oncology knowledge base of OncoKB, and the characteristics were investigated. Sixty seven variants(leve1-4) were found by NGS, the positive rate of total mutations was 86.6% (322/372), in which variants at four levels were detected: levelⅠvariant, which was recognized as biomarker predictive of response to an FDA/NMPA approved drug in non-small cell lung cancer (NSCLC), was 71.2% (265/372);level Ⅱ variant, which was recognized as being standard care by the NCCN or other expert panels, was 3.0% (11/372); levelⅢA, a variant with compelling clinical evidence supports the biomarker as being predictive of response to a drug in this indication 3.0% (11/372); levelⅢB, a variant with compelling clinical evidence supports the biomarker as being predictive of response to a drug in another indication, was 4.3% (16/372); and level Ⅳ, a variant with compelling biological evidence supports the biomarker as being predictive of response to a drug, was 8.1% (30/372). The positive rate of unknown clinical significance and/or benign/likely benign variants was 18.8% (70/372). The positive rate of mutations detected by quantitative fluorescence PCR was 81.7% (138/169). Eighteen of the 20 samples showed concordance between NGS and quantitative fluorescence PCR. The two discordant cases could be due to the lack of coverage of two mutation sites in fluorescence PCR: EGFR c. 2571_2573delinsTCG(p. L858R), and HIP1-ALK_H19:A20 fusion. Lung adenocarcinoma driver gene variants occur mainly in hotspot region, and NGS can comprehensively detect the driver gene variants of significant and potential clinical significance. NGS should be recommended when multiple genes need to be tested.
研究通过下一代测序（NGS）和定量荧光PCR检测的肺腺癌驱动基因变异的特征。对372例原发性肺腺癌患者的手术切除样本进行NGS，以检测10种驱动基因突变、单核苷酸变异（SNV）、插入/缺失和基因融合；对169例原发性肺腺癌患者的手术切除样本进行定量荧光PCR，以检测9种驱动基因热点突变。根据OncoKB的指南和精准肿瘤知识库，将变异等位基因频率（VAF）≥1.0%的变异分为4个级别中的1个，并对其特征进行研究。通过NGS发现67个变异（1-4级），总突变阳性率为86.6%（322/372），其中检测到4个级别的变异：Ⅰ级变异，被认为是预测非小细胞肺癌（NSCLC）对FDA/NMPA批准药物反应的生物标志物，为71.2%（265/372）；Ⅱ级变异，被NCCN或其他专家小组认可为标准治疗，为3.0%（11/372）；ⅢA 级，有令人信服的临床证据支持该生物标志物可预测该适应症药物反应的变异，为3.0%（11/372）；ⅢB级，有令人信服的临床证据支持该生物标志物可预测另一适应症药物反应的变异，为4.3%（16/372）；Ⅳ级，有令人信服的生物学证据支持该生物标志物可预测药物反应的变异，为8.1%（30/372）。临床意义不明和/或良性/可能良性变异的阳性率为18.8%（70/372）。定量荧光PCR检测到的突变阳性率为81.7%（138/169）。20个样本中的18个在NGS和定量荧光PCR之间显示出一致性。两个不一致的病例可能是由于荧光PCR中两个突变位点未覆盖：EGFR c.2571_2573delinsTCG（p.L858R）和HIP1-ALK_H19:A20融合。肺腺癌驱动基因变异主要发生在热点区域，NGS可以全面检测具有显著和潜在临床意义的驱动基因变异。当需要检测多个基因时，建议采用NGS。
