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Genome-wide direct quantification of in vivo mutagenesis using high-accuracy paired-end and complementary consensus sequencing

Error-corrected next-generation sequencing (ecNGS) is an emerging technology for accurately measuring somatic mutations. Here, we report paired-end and complementary consensus sequencing (PECC-Seq), a high-accuracy ecNGS approach for genome-wide somatic mutation detection. We characterize a novel 2-...

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Autores principales: You, Xinyue, Cao, Yiyi, Suzuki, Takayoshi, Shao, Jie, Zhu, Benzhan, Masumura, Kenichi, Xi, Jing, Liu, Weiying, Zhang, Xinyu, Luan, Yang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10681716/
https://www.ncbi.nlm.nih.gov/pubmed/37870450
http://dx.doi.org/10.1093/nar/gkad909
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author You, Xinyue
Cao, Yiyi
Suzuki, Takayoshi
Shao, Jie
Zhu, Benzhan
Masumura, Kenichi
Xi, Jing
Liu, Weiying
Zhang, Xinyu
Luan, Yang
author_facet You, Xinyue
Cao, Yiyi
Suzuki, Takayoshi
Shao, Jie
Zhu, Benzhan
Masumura, Kenichi
Xi, Jing
Liu, Weiying
Zhang, Xinyu
Luan, Yang
author_sort You, Xinyue
collection PubMed
description Error-corrected next-generation sequencing (ecNGS) is an emerging technology for accurately measuring somatic mutations. Here, we report paired-end and complementary consensus sequencing (PECC-Seq), a high-accuracy ecNGS approach for genome-wide somatic mutation detection. We characterize a novel 2-aminoimidazolone lesion besides 7,8-dihydro-8-oxoguanine and the resulting end-repair artifacts originating from NGS library preparation that obscure the sequencing accuracy of NGS. We modify library preparation protocol for the enzymatic removal of end-repair artifacts and improve the accuracy of our previously developed duplex consensus sequencing method. Optimized PECC-Seq shows an error rate of <5 × 10(−8) with consensus bases compressed from approximately 25 Gb of raw sequencing data, enabling the accurate detection of low-abundance somatic mutations. We apply PECC-Seq to the quantification of in vivo mutagenesis. Compared with the classic gpt gene mutation assay using gpt delta transgenic mice, PECC-Seq exhibits high sensitivity in quantitatively measuring dose-dependent mutagenesis induced by Aristolochic acid I (AAI). Moreover, PECC-Seq specifically characterizes the distinct genome-wide mutational signatures of AAI, Benzo[a]pyrene, N-Nitroso-N-ethylurea and N-nitrosodiethylamine and reveals the mutational signature of Quinoline in common mouse models. Overall, our findings demonstrate that high-accuracy PECC-Seq is a promising tool for genome-wide somatic mutagenesis quantification and for in vivo mutagenicity testing.
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spelling pubmed-106817162023-10-23 Genome-wide direct quantification of in vivo mutagenesis using high-accuracy paired-end and complementary consensus sequencing You, Xinyue Cao, Yiyi Suzuki, Takayoshi Shao, Jie Zhu, Benzhan Masumura, Kenichi Xi, Jing Liu, Weiying Zhang, Xinyu Luan, Yang Nucleic Acids Res Methods Error-corrected next-generation sequencing (ecNGS) is an emerging technology for accurately measuring somatic mutations. Here, we report paired-end and complementary consensus sequencing (PECC-Seq), a high-accuracy ecNGS approach for genome-wide somatic mutation detection. We characterize a novel 2-aminoimidazolone lesion besides 7,8-dihydro-8-oxoguanine and the resulting end-repair artifacts originating from NGS library preparation that obscure the sequencing accuracy of NGS. We modify library preparation protocol for the enzymatic removal of end-repair artifacts and improve the accuracy of our previously developed duplex consensus sequencing method. Optimized PECC-Seq shows an error rate of <5 × 10(−8) with consensus bases compressed from approximately 25 Gb of raw sequencing data, enabling the accurate detection of low-abundance somatic mutations. We apply PECC-Seq to the quantification of in vivo mutagenesis. Compared with the classic gpt gene mutation assay using gpt delta transgenic mice, PECC-Seq exhibits high sensitivity in quantitatively measuring dose-dependent mutagenesis induced by Aristolochic acid I (AAI). Moreover, PECC-Seq specifically characterizes the distinct genome-wide mutational signatures of AAI, Benzo[a]pyrene, N-Nitroso-N-ethylurea and N-nitrosodiethylamine and reveals the mutational signature of Quinoline in common mouse models. Overall, our findings demonstrate that high-accuracy PECC-Seq is a promising tool for genome-wide somatic mutagenesis quantification and for in vivo mutagenicity testing. Oxford University Press 2023-10-23 /pmc/articles/PMC10681716/ /pubmed/37870450 http://dx.doi.org/10.1093/nar/gkad909 Text en © The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://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 Methods
You, Xinyue
Cao, Yiyi
Suzuki, Takayoshi
Shao, Jie
Zhu, Benzhan
Masumura, Kenichi
Xi, Jing
Liu, Weiying
Zhang, Xinyu
Luan, Yang
Genome-wide direct quantification of in vivo mutagenesis using high-accuracy paired-end and complementary consensus sequencing
title Genome-wide direct quantification of in vivo mutagenesis using high-accuracy paired-end and complementary consensus sequencing
title_full Genome-wide direct quantification of in vivo mutagenesis using high-accuracy paired-end and complementary consensus sequencing
title_fullStr Genome-wide direct quantification of in vivo mutagenesis using high-accuracy paired-end and complementary consensus sequencing
title_full_unstemmed Genome-wide direct quantification of in vivo mutagenesis using high-accuracy paired-end and complementary consensus sequencing
title_short Genome-wide direct quantification of in vivo mutagenesis using high-accuracy paired-end and complementary consensus sequencing
title_sort genome-wide direct quantification of in vivo mutagenesis using high-accuracy paired-end and complementary consensus sequencing
topic Methods
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10681716/
https://www.ncbi.nlm.nih.gov/pubmed/37870450
http://dx.doi.org/10.1093/nar/gkad909
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