The characteristics of lung adenocarcinoma driver gene variants detected by high-throughput sequencing and quantitative fluorescence PCR
10.3760/cma.j.issn.0529-5807.2019.10.005
- VernacularTitle: 应用高通量测序技术与荧光PCR技术检测肺腺癌驱动基因变异分析
- Author:
Lingfeng CHEN
1
,
2
;
Xiaoyan CHEN
;
Jie LIN
;
Xunbin YU
;
Long JIN
Author Information
1. Provincial Clinical Medical College of Fujian Medical University
2. Department of Pathology, Fujian Provincial Hospital, Fuzhou 350001, China
- Publication Type:Journal Article
- Keywords:
Lung neoplasms;
DNA mutational analysis;
High-throughput nucleotide sequencing;
Polymerase chain reaction
- From:
Chinese Journal of Pathology
2019;48(10):772-778
- CountryChina
- Language:Chinese
-
Abstract:
Objective:To study the characteristics of lung adenocarcinoma driver gene variants detected by next generation sequencing (NGS) and quantitative fluorescence PCR.
Methods: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.
Results: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.
Conclusions: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.
