Adaptor Template Oligo-Mediated Sequencing (ATOM-Seq) is a new ultra-sensitive UMI-based NGS library preparation technology for use with cfDNA and cfRNA

Abstract Liquid biopsy testing utilising Next Generation Sequencing (NGS) is rapidly moving towards clinical adoption for personalised oncology. However, before NGS can fulfil its potential any novel testing approach must identify ways of reducing errors, allowing separation of true low-frequency mu...

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Autores principales:	Thomas L. Dunwell, Simon C. Dailey, Anine L. Ottestad, Jihang Yu, Philipp W. Becker, Sarah Scaife, Susan D. Richman, Henry M. Wood, Hayley Slaney, Daniel Bottomley, Xiangsheng Yang, Hui Xiao, Sissel G. F. Wahl, Bjørn H. Grønberg, Hongyan Dai, Guoliang Fu
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/fbc2ea58d49a44789ad5beace2c7311d
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spelling	oai:doaj.org-article:fbc2ea58d49a44789ad5beace2c7311d2021-12-02T10:44:21ZAdaptor Template Oligo-Mediated Sequencing (ATOM-Seq) is a new ultra-sensitive UMI-based NGS library preparation technology for use with cfDNA and cfRNA10.1038/s41598-021-82737-92045-2322https://doaj.org/article/fbc2ea58d49a44789ad5beace2c7311d2021-02-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-82737-9https://doaj.org/toc/2045-2322Abstract Liquid biopsy testing utilising Next Generation Sequencing (NGS) is rapidly moving towards clinical adoption for personalised oncology. However, before NGS can fulfil its potential any novel testing approach must identify ways of reducing errors, allowing separation of true low-frequency mutations from procedural artefacts, and be designed to improve upon current technologies. Popular NGS technologies typically utilise two DNA capture approaches; PCR and ligation, which have known limitations and seem to have reached a development plateau with only small, stepwise improvements being made. To maximise the ultimate utility of liquid biopsy testing we have developed a highly versatile approach to NGS: Adaptor Template Oligo Mediated Sequencing (ATOM-Seq). ATOM-Seq's strengths and versatility avoid the major limitations of both PCR- and ligation-based approaches. This technology is ligation free, simple, efficient, flexible, and streamlined, and it offers novel advantages that make it perfectly suited for use on highly challenging clinical material. Using reference and clinical materials, we demonstrate detection of known SNVs down to allele frequencies of 0.1% using as little as 20–25 ng of cfDNA, as well as the ability to detect fusions from RNA. We illustrate ATOM-Seq’s suitability for clinical testing by showing high concordance rates between paired cfDNA and FFPE clinical samples.Thomas L. DunwellSimon C. DaileyAnine L. OttestadJihang YuPhilipp W. BeckerSarah ScaifeSusan D. RichmanHenry M. WoodHayley SlaneyDaniel BottomleyXiangsheng YangHui XiaoSissel G. F. WahlBjørn H. GrønbergHongyan DaiGuoliang FuNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-13 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Thomas L. Dunwell Simon C. Dailey Anine L. Ottestad Jihang Yu Philipp W. Becker Sarah Scaife Susan D. Richman Henry M. Wood Hayley Slaney Daniel Bottomley Xiangsheng Yang Hui Xiao Sissel G. F. Wahl Bjørn H. Grønberg Hongyan Dai Guoliang Fu Adaptor Template Oligo-Mediated Sequencing (ATOM-Seq) is a new ultra-sensitive UMI-based NGS library preparation technology for use with cfDNA and cfRNA
description	Abstract Liquid biopsy testing utilising Next Generation Sequencing (NGS) is rapidly moving towards clinical adoption for personalised oncology. However, before NGS can fulfil its potential any novel testing approach must identify ways of reducing errors, allowing separation of true low-frequency mutations from procedural artefacts, and be designed to improve upon current technologies. Popular NGS technologies typically utilise two DNA capture approaches; PCR and ligation, which have known limitations and seem to have reached a development plateau with only small, stepwise improvements being made. To maximise the ultimate utility of liquid biopsy testing we have developed a highly versatile approach to NGS: Adaptor Template Oligo Mediated Sequencing (ATOM-Seq). ATOM-Seq's strengths and versatility avoid the major limitations of both PCR- and ligation-based approaches. This technology is ligation free, simple, efficient, flexible, and streamlined, and it offers novel advantages that make it perfectly suited for use on highly challenging clinical material. Using reference and clinical materials, we demonstrate detection of known SNVs down to allele frequencies of 0.1% using as little as 20–25 ng of cfDNA, as well as the ability to detect fusions from RNA. We illustrate ATOM-Seq’s suitability for clinical testing by showing high concordance rates between paired cfDNA and FFPE clinical samples.
format	article
author	Thomas L. Dunwell Simon C. Dailey Anine L. Ottestad Jihang Yu Philipp W. Becker Sarah Scaife Susan D. Richman Henry M. Wood Hayley Slaney Daniel Bottomley Xiangsheng Yang Hui Xiao Sissel G. F. Wahl Bjørn H. Grønberg Hongyan Dai Guoliang Fu
author_facet	Thomas L. Dunwell Simon C. Dailey Anine L. Ottestad Jihang Yu Philipp W. Becker Sarah Scaife Susan D. Richman Henry M. Wood Hayley Slaney Daniel Bottomley Xiangsheng Yang Hui Xiao Sissel G. F. Wahl Bjørn H. Grønberg Hongyan Dai Guoliang Fu
author_sort	Thomas L. Dunwell
title	Adaptor Template Oligo-Mediated Sequencing (ATOM-Seq) is a new ultra-sensitive UMI-based NGS library preparation technology for use with cfDNA and cfRNA
title_short	Adaptor Template Oligo-Mediated Sequencing (ATOM-Seq) is a new ultra-sensitive UMI-based NGS library preparation technology for use with cfDNA and cfRNA
title_full	Adaptor Template Oligo-Mediated Sequencing (ATOM-Seq) is a new ultra-sensitive UMI-based NGS library preparation technology for use with cfDNA and cfRNA
title_fullStr	Adaptor Template Oligo-Mediated Sequencing (ATOM-Seq) is a new ultra-sensitive UMI-based NGS library preparation technology for use with cfDNA and cfRNA
title_full_unstemmed	Adaptor Template Oligo-Mediated Sequencing (ATOM-Seq) is a new ultra-sensitive UMI-based NGS library preparation technology for use with cfDNA and cfRNA
title_sort	adaptor template oligo-mediated sequencing (atom-seq) is a new ultra-sensitive umi-based ngs library preparation technology for use with cfdna and cfrna
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/fbc2ea58d49a44789ad5beace2c7311d
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Adaptor Template Oligo-Mediated Sequencing (ATOM-Seq) is a new ultra-sensitive UMI-based NGS library preparation technology for use with cfDNA and cfRNA

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