The potential role of next-generation sequencing in identifying amplification and disclosing resistance mechanisms in NSCLC patients with osimertinib resistance.

PURPOSES

Osimertinib, one of the third-generation -tyrosine kinase inhibitors (TKIs) designed to target T790M mutation, significantly improves the prognosis of lung cancer. However, drug resistance still happens and amplification is responsible for one of the main causes. Fluorescence hybridization (FISH) is the gold standard for amplification detection, but fundamentally limited by observer subjectivity. Herein, we assessed the value of next-generation sequencing (NGS) method in amplification detection in non-small cell lung cancer (NSCLC), as well as revealed the mutation profiling of NSCLC patients with osimertinib resistance to provide some valuable clues to the mechanisms of resistance.

METHODS

A total of 317 cancer tissue samples from 317 NSCLC patients at time of progression following osimertinib were submitted to NGS and only 96 tissues were tested by FISH simultaneously. With FISH results as gold standard, enumeration algorithm was applied to establish the optimal model for identifying amplification using gene copy number (GCN) data.

RESULTS

The optimal model for identifying amplification was constructed based on the GCN of , , and , which achieved a 74.0% overall agreement with FISH and performed well in identifying amplification except polysomy with a sensitivity of 85.7% and a specificity of 93.9%. The inconsistency between NGS and FISH occurred mainly in polysomy subtype, while GCN ≥ 5 could be reliably recognized by NGS. Moreover, the most frequently mutated genes in NSCLC patients with osimertinib resistance were (59.94%), followed by (43.85%), (9.46%), (6.31%), and ATM (5.36%). The known resistance mechanisms, including amplification, (C797S, L718Q/R), , , , , , , and mutations were also disclosed in our cohort.

CONCLUSIONS

NGS assay can achieve a high concordance with FISH in amplification detection and has advantages in portraying various genetic alterations, which is of worthy in clinical promotion.