Co-occurring genetic alterations and primary EGFR T790M mutations detected by NGS in pre-TKI-treated NSCLCs
Next-generation sequencing (NGS)-based assays to understand various mutations and co-occurrence of genomic alterations in non-small cell lung cancer (NSCLC) have enabled understanding of treatment impact on clinical outcomes.
This retrospective study was conducted in 1353 formalin-fixed paraffin-embedded (FFPE) tissues from surgically resected, pre-TKI-treated NSCLC patients with identified gene alterations. Genomic DNA and RNA extraction was followed by NGS library preparation and sequencing using the Ion Ampliseq Colon and Lung Cancer Gene Panel V2 and the AmpliSeq RNA Lung Cancer Research Fusion Panel.
A total of 2328 alterations in 25 genes were detected from the 1293 patients. DNA mutations and RNA fusions co-occurred in 27 patients with TP53 being the most common co-occurring DNA mutation (43.8%) with concurrent ALK fusions. Analysis of the 975 patients with EGFR mutations revealed that the incidence of dual EGFR L858R/T790M mutations was higher compared to EGFR 19del/T790M, and the mean allele fraction (MAF) of T790M was lower compared to 19del in dual EGFR 19del/T790M patients.
NSCLC patients represented genetically heterogeneous subgroup with a high frequency of co-occurring mutations in cancer-associated pathways. This diverse mutational profile may have key clinical and research implications for understanding the variability of treatment outcome in pre-TKI-treated NSCLC population. The differences in the MAF of EGFR T790M may determine different responses to TKI therapy in patients harboring dual mutations.
KeywordsNon-small cell lung cancer Co-occurring genetic alterations Next-generation sequencing
Mutant allele frequency
Non-small cell lung cancer
Tyrosine kinase inhibitors
Epidermal growth factor receptor
Anaplastic lymphoma kinase
Amplification refractory mutation system
Fluorescence in situ hybridization
Progression free survival
We acknowledge all other studies that support our work and were not cited due to length limitations. We would like to thank all the patients who have participated in this study. We are also thankful to the doctors from departments of oncology, doctors from departments of pathology for technics and staff of the Novogene Bioinformatics.
Compliance with ethical standards
Conflict of interest
The authors declare no potential conflicts of interest.
Ethics approval and consent to participate
This study was approved by the ethics committee of Peking University Cancer Hospital (2017TW06), and written informed consent was obtained from all patients.
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