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

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, s...

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Autores principales: Namba, Kei, Tomida, Shuta, Matsubara, Takehiro, Takahashi, Yuta, Kurihara, Eisuke, Ogoshi, Yusuke, Yoshioka, Takahiro, Takeda, Tatsuaki, Torigoe, Hidejiro, Sato, Hiroki, Shien, Kazuhiko, Yamamoto, Hiromasa, Soh, Junichi, Tsukuda, Kazunori, Toyooka, Shinichi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6390598/
https://www.ncbi.nlm.nih.gov/pubmed/30808329
http://dx.doi.org/10.1186/s12885-019-5374-1
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author Namba, Kei
Tomida, Shuta
Matsubara, Takehiro
Takahashi, Yuta
Kurihara, Eisuke
Ogoshi, Yusuke
Yoshioka, Takahiro
Takeda, Tatsuaki
Torigoe, Hidejiro
Sato, Hiroki
Shien, Kazuhiko
Yamamoto, Hiromasa
Soh, Junichi
Tsukuda, Kazunori
Toyooka, Shinichi
author_facet Namba, Kei
Tomida, Shuta
Matsubara, Takehiro
Takahashi, Yuta
Kurihara, Eisuke
Ogoshi, Yusuke
Yoshioka, Takahiro
Takeda, Tatsuaki
Torigoe, Hidejiro
Sato, Hiroki
Shien, Kazuhiko
Yamamoto, Hiromasa
Soh, Junichi
Tsukuda, Kazunori
Toyooka, Shinichi
author_sort Namba, Kei
collection PubMed
description 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.
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spelling pubmed-63905982019-03-11 Application of amplicon-based targeted sequencing with the molecular barcoding system to detect uncommon minor EGFR mutations in patients with treatment-naïve lung adenocarcinoma Namba, Kei Tomida, Shuta Matsubara, Takehiro Takahashi, Yuta Kurihara, Eisuke Ogoshi, Yusuke Yoshioka, Takahiro Takeda, Tatsuaki Torigoe, Hidejiro Sato, Hiroki Shien, Kazuhiko Yamamoto, Hiromasa Soh, Junichi Tsukuda, Kazunori Toyooka, Shinichi BMC Cancer Research Article 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. BioMed Central 2019-02-26 /pmc/articles/PMC6390598/ /pubmed/30808329 http://dx.doi.org/10.1186/s12885-019-5374-1 Text en © The Author(s). 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Namba, Kei
Tomida, Shuta
Matsubara, Takehiro
Takahashi, Yuta
Kurihara, Eisuke
Ogoshi, Yusuke
Yoshioka, Takahiro
Takeda, Tatsuaki
Torigoe, Hidejiro
Sato, Hiroki
Shien, Kazuhiko
Yamamoto, Hiromasa
Soh, Junichi
Tsukuda, Kazunori
Toyooka, Shinichi
Application of amplicon-based targeted sequencing with the molecular barcoding system to detect uncommon minor EGFR mutations in patients with treatment-naïve lung adenocarcinoma
title Application of amplicon-based targeted sequencing with the molecular barcoding system to detect uncommon minor EGFR mutations in patients with treatment-naïve lung adenocarcinoma
title_full Application of amplicon-based targeted sequencing with the molecular barcoding system to detect uncommon minor EGFR mutations in patients with treatment-naïve lung adenocarcinoma
title_fullStr Application of amplicon-based targeted sequencing with the molecular barcoding system to detect uncommon minor EGFR mutations in patients with treatment-naïve lung adenocarcinoma
title_full_unstemmed Application of amplicon-based targeted sequencing with the molecular barcoding system to detect uncommon minor EGFR mutations in patients with treatment-naïve lung adenocarcinoma
title_short Application of amplicon-based targeted sequencing with the molecular barcoding system to detect uncommon minor EGFR mutations in patients with treatment-naïve lung adenocarcinoma
title_sort application of amplicon-based targeted sequencing with the molecular barcoding system to detect uncommon minor egfr mutations in patients with treatment-naïve lung adenocarcinoma
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6390598/
https://www.ncbi.nlm.nih.gov/pubmed/30808329
http://dx.doi.org/10.1186/s12885-019-5374-1
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