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Background  In lung cancer, epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor sensitizing mutations co-existing with rare minor  EGFR  mutations are known as compound mutations. These minor  EGFR  mutations can lead to acquired resistance after  EGFR  tyrosine kinase inhibitor treatment, so determining the mutation status of patients is important. However, using amplicon-based targeted deep sequencing based on next-generation sequencing to characterize mutations is prone to sequencing error. We therefore assessed the benefit of incorporating molecular barcoding with high-throughput sequencing to investigate genomic heterogeneity in treatment-naïve patients who have undergone resection of their non-small cell lung cancer (NSCLC)  EGFR  mutations.    Methods  We performed amplicon-based targeted sequencing with the molecular barcoding system (MBS) to detect major common  EGFR  mutations and uncommon minor mutations at a 0.5% allele frequency in fresh–frozen lung cancer samples.    Results  Profiles of the common mutations of  EGFR  identified by MBS corresponded with the results of clinical testing in 63 (98.4%) out of 64 cases. Uncommon mutations of  EGFR  were detected in seven cases (10.9%). Among the three types of major  EGFR  mutations, patients with the G719X mutation had a significantly higher incidence of compound mutations than those with the L858R mutation or exon 19 deletion ( p  = 0.0052). This was validated in an independent cohort from the Cancer Genome Atlas dataset ( p  = 0.018).    Conclusions  Our findings demonstrate the feasibility of using the MBS to establish an accurate NSCLC patient genotype. This work will help understand the molecular basis of  EGFR  compound mutations in NSCLC, and could aid the development of new treatment modalities.    Electronic supplementary material  The online version of this article (10.1186/s12885-019-5374-1) contains supplementary material, which is available to authorized users.

bmc cancer

Application of amplicon-based targeted sequencing with the molecular barcoding system to detect uncommon minor EGFR mutations in patients with treatment-naïve lung adenocarcinoma