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Feasibility study of cancer genome alterations identified by next generation sequencing: ABC study

BACKGROUND: To confirm the feasibility and explore the clinical applicability of amplicon sequencing by next generation sequencing (NGS) of biopsy samples from patients with advanced solid tumors, we conducted a prospective study. METHODS: Patients with unresectable, advanced, or recurrent solid tum...

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Autores principales: Naito, Yoichi, Takahashi, Hideaki, Shitara, Kohei, Okamoto, Wataru, Bando, Hideaki, Kuwata, Takeshi, Kuboki, Yasutoshi, Matsumoto, Shingo, Miki, Izumi, Yamanaka, Takeharu, Watanabe, Atsushi, Kojima, Motohiro
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2018
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Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5974784/
https://www.ncbi.nlm.nih.gov/pubmed/29659903
http://dx.doi.org/10.1093/jjco/hyy052
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author Naito, Yoichi
Takahashi, Hideaki
Shitara, Kohei
Okamoto, Wataru
Bando, Hideaki
Kuwata, Takeshi
Kuboki, Yasutoshi
Matsumoto, Shingo
Miki, Izumi
Yamanaka, Takeharu
Watanabe, Atsushi
Kojima, Motohiro
author_facet Naito, Yoichi
Takahashi, Hideaki
Shitara, Kohei
Okamoto, Wataru
Bando, Hideaki
Kuwata, Takeshi
Kuboki, Yasutoshi
Matsumoto, Shingo
Miki, Izumi
Yamanaka, Takeharu
Watanabe, Atsushi
Kojima, Motohiro
author_sort Naito, Yoichi
collection PubMed
description BACKGROUND: To confirm the feasibility and explore the clinical applicability of amplicon sequencing by next generation sequencing (NGS) of biopsy samples from patients with advanced solid tumors, we conducted a prospective study. METHODS: Patients with unresectable, advanced, or recurrent solid tumors were included. Key eligibility criteria were as follows: 20 years or older, any planned systemic therapy, adequate lesion for biopsy, and written informed consent. Samples were fixed in 10% buffered formalin and embedded in paraffin. Cancer-derived DNA was extracted, and amplicon sequencing was performed using Ion Ampliseq(TM) Cancer Hotspot Panel version 1.0 or version 2.0 by central vendor. We evaluated the success rate of sequencing, and the proportion of the patients with actionable mutations. We organized an expert panel to share the results of targeted sequence, make annotations and reports, and discuss concomitant ethical/legal/social issues. RESULTS: A total of 232 patients were included, and 208 were successfully analyzed (success rate of 89.7%). The biopsy procedures were safe, with only one case of Grade 3 vasovagal reaction. The proportion of actionable/druggable mutations was 38.9% (81/208), which was not significantly different between the cancer panel version 1.0 and version 2.0 (P = 0.476). Expert panel could discuss the findings and make sufficient reports. CONCLUSIONS: We confirmed the feasibility of NGS-based amplicon sequencing using biopsy samples, making the basis for nationwide genome screening for cancer patients using biopsy samples. Our results suggest that focused panel may be sufficient to detect major mutations.
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spelling pubmed-59747842018-06-04 Feasibility study of cancer genome alterations identified by next generation sequencing: ABC study Naito, Yoichi Takahashi, Hideaki Shitara, Kohei Okamoto, Wataru Bando, Hideaki Kuwata, Takeshi Kuboki, Yasutoshi Matsumoto, Shingo Miki, Izumi Yamanaka, Takeharu Watanabe, Atsushi Kojima, Motohiro Jpn J Clin Oncol Original article BACKGROUND: To confirm the feasibility and explore the clinical applicability of amplicon sequencing by next generation sequencing (NGS) of biopsy samples from patients with advanced solid tumors, we conducted a prospective study. METHODS: Patients with unresectable, advanced, or recurrent solid tumors were included. Key eligibility criteria were as follows: 20 years or older, any planned systemic therapy, adequate lesion for biopsy, and written informed consent. Samples were fixed in 10% buffered formalin and embedded in paraffin. Cancer-derived DNA was extracted, and amplicon sequencing was performed using Ion Ampliseq(TM) Cancer Hotspot Panel version 1.0 or version 2.0 by central vendor. We evaluated the success rate of sequencing, and the proportion of the patients with actionable mutations. We organized an expert panel to share the results of targeted sequence, make annotations and reports, and discuss concomitant ethical/legal/social issues. RESULTS: A total of 232 patients were included, and 208 were successfully analyzed (success rate of 89.7%). The biopsy procedures were safe, with only one case of Grade 3 vasovagal reaction. The proportion of actionable/druggable mutations was 38.9% (81/208), which was not significantly different between the cancer panel version 1.0 and version 2.0 (P = 0.476). Expert panel could discuss the findings and make sufficient reports. CONCLUSIONS: We confirmed the feasibility of NGS-based amplicon sequencing using biopsy samples, making the basis for nationwide genome screening for cancer patients using biopsy samples. Our results suggest that focused panel may be sufficient to detect major mutations. Oxford University Press 2018-04-12 /pmc/articles/PMC5974784/ /pubmed/29659903 http://dx.doi.org/10.1093/jjco/hyy052 Text en © The Author(s) 2018. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Original article
Naito, Yoichi
Takahashi, Hideaki
Shitara, Kohei
Okamoto, Wataru
Bando, Hideaki
Kuwata, Takeshi
Kuboki, Yasutoshi
Matsumoto, Shingo
Miki, Izumi
Yamanaka, Takeharu
Watanabe, Atsushi
Kojima, Motohiro
Feasibility study of cancer genome alterations identified by next generation sequencing: ABC study
title Feasibility study of cancer genome alterations identified by next generation sequencing: ABC study
title_full Feasibility study of cancer genome alterations identified by next generation sequencing: ABC study
title_fullStr Feasibility study of cancer genome alterations identified by next generation sequencing: ABC study
title_full_unstemmed Feasibility study of cancer genome alterations identified by next generation sequencing: ABC study
title_short Feasibility study of cancer genome alterations identified by next generation sequencing: ABC study
title_sort feasibility study of cancer genome alterations identified by next generation sequencing: abc study
topic Original article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5974784/
https://www.ncbi.nlm.nih.gov/pubmed/29659903
http://dx.doi.org/10.1093/jjco/hyy052
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