JOURNAL ARTICLE

Next-Generation Sequencing for Genotyping of Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration Samples in Lung Cancer

Fangfang Xie, Xiaoxuan Zheng, Xiaowei Mao, Ruiying Zhao, Junyi Ye, Yujun Zhang, Jiayuan Sun
Annals of Thoracic Surgery 2019 March 15
30885850

BACKGROUND: Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) can obtain a small amount of specimen. This study aims to evaluate the feasibility and robustness of using EBUS-EBNA samples to perform capture-based targeted next-generation sequencing (NGS).

METHODS: Tissue samples from patients with advanced non-small cell lung cancer (NSCLC) were collected via EBUS-TBNA and formalin-fixed paraffin-embedded. Three representative genes, EGFR, ALK and ROS1, were examined by amplification refractory mutation system polymerase chain reaction (ARMS-PCR), immunohistochemistry and quantitative reverse transcription PCR (RT-qPCR). The remaining samples were processed with NGS assay with a 56 gene panel. Classic driver mutations detected by NGS were verified by conventional methods.

RESULTS: Of the 85 patients diagnosed with advanced NSCLC, 77 successfully performed all assays. Forty-one mutations in EGFR, ALK and ROS1 were detected in both conventional methods and NGS, representing a 100% concordance. In the contrast, four EGFR mutations detected by NGS were not covered in the targeted regions of ARMS-PCR, leading to a negative call in these patients. Altogether, NGS detected 12 additional variants including 6 KRAS mutations, 1 BRAF mutation, 1 RET fusion, 1 MET amplification concurrent with EGFR L858R, 1 KRAS amplification together with EGFR 19del and 1 ERBB2 amplification. The mean number of needle passes per lymph node was 5.2 in samples successfully applied all assays.

CONCLUSIONS: NGS assay can be successfully conducted with limited tissue samples obtained from EBUS-TBNA. Compared to conventional methods, NGS assay provides more comprehensive information on genetic alterations in tumor, which greatly assists therapeutic decision-making for advanced lung cancer.

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