Mutation assay using single-molecule real-time (SMRT) sequencing technology

• Material Type: 記事
• Title: Mutation assay using single-molecule real-time (SMRT) sequencing technology
• Author/Editor: Tomonari Matsuda; Shun Matsuda; Masami Yamada
• Publication, Distribution, etc.: 日本 : Springer Nature
• Publication Date: 2015-09-01
• Publication Date (W3CDTF): 2015-09-01
• Periodical title: Genes and environment
• No. or year of volume/issue: 37(15)
• Volume: 37(15)
• ISSN (Periodical Title): 1880-7062
• ISSN-L (Periodical Title): 1880-7046
• Text Language Code: eng
• DOI: 10.1186/s41021-015-0017-5; https://doi.org/10.1186/s41021-015-0017-5
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• Periodical Title (URI): http://genesenvironment.biomedcentral.com/articles?searchType=journalSearch&sort=PubDate&page=2
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• Summary, etc.: Introduction: We present here a simple, phenotype-independent mutation assay using a PacBio RSII DNA sequencer employing single-molecule real-time (SMRT) sequencing technology. Salmonella typhimurium YG7108 was treated with the alkylating agent N-ethyl-N-nitrosourea (ENU) and grown though several generations to fix the induced mutations, the DNA was extracted and the mutations were analyzed by using the SMRT DNA sequencer. Results: The ENU-induced base-substitution frequency was 15.4 per Megabase pair, which is highly consistent with our previous results based on colony isolation and next-generation sequencing. The induced mutation spectrum (95% G:C→A:T, 5% A:T→G:C) is also consistent with the known ENU signature. The base-substitution frequency of the control was calculated to be less than 0.12 per Megabase pair. A current limitation of the approach is the high frequency of artifactual insertion and deletion mutations it detects. Conclusions: Ultra-low frequency base-substitution mutations can be detected directly by using the SMRT DNA sequencer, and this technology provides a phenotype-independent mutation assay.
• DOI: 10.1186/s41021-015-0017-5; https://doi.org/10.1186/s41021-015-0017-5
• Access Restrictions: インターネット公開
• Rights (production): © 2015 Matsuda et al.; This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://​creativecommons.​org/​licenses/​by/​4.​0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. 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.
• Related Material (URI): http://hdl.handle.net/2433/210413; http://id.ndl.go.jp/digimeta/10224909; https://dl.ndl.go.jp/pid/10224909; http://link.springer.com/content/pdf/10.1186/s41021-015-0017-5.pdf; http://link.springer.com/article/10.1186/s41021-015-0017-5/fulltext.html; http://link.springer.com/content/pdf/10.1186/s41021-015-0017-5
• References: Revised methods for the Salmonella mutagenicity test; https://cir.nii.ac.jp/crid/1360574096464689152; A flexible and efficient template format for circular consensus sequencing and SNP detection; https://cir.nii.ac.jp/crid/1361699993949255936; Real-Time DNA Sequencing from Single Polymerase Molecules; https://cir.nii.ac.jp/crid/1361699995830719488; Detection of ultra-rare mutations by next-generation sequencing; https://cir.nii.ac.jp/crid/1362825893770114688; New tester strains of Salmonella typhimurium lacking O6-methylguanine DNA methyltransferases and highly sensitive to mutagenic alkylating agents; https://cir.nii.ac.jp/crid/1362825894536612096; DNA base changes and alkylation following in vivo exposure of Escherichia coli to N-methyl-N-nitrosourea or N-ethyl-N-nitrosourea.; https://cir.nii.ac.jp/crid/1363388843650247296; A Benchmark Study on Error Assessment and Quality Control of CCS Reads Derived from the PacBio RS; https://cir.nii.ac.jp/crid/1363388843691516288; Detecting ultralow-frequency mutations by Duplex Sequencing; https://cir.nii.ac.jp/crid/1363388845570821376; Anticipated mutation assay using single-molecule real-time (SMRT) sequencing technology; https://cir.nii.ac.jp/crid/1390282680233168768; A Pilot Study for the Mutation Assay Using a High-throughput DNA Sequencer; https://cir.nii.ac.jp/crid/1390282680233647744
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• Bibliographic ID (NDL): 10224909; http://id.ndl.go.jp/bib/10224909
• NAID: 120005749959