Reliable and accurate diagnostics from highly multiplexed sequencing assays

Abstract Scalable, inexpensive, and secure testing for SARS-CoV-2 infection is crucial for control of the novel coronavirus pandemic. Recently developed highly multiplexed sequencing assays (HMSAs) that rely on high-throughput sequencing can, in principle, meet these demands, and present promising a...

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Autores principales:	A. Sina Booeshaghi, Nathan B. Lubock, Aaron R. Cooper, Scott W. Simpkins, Joshua S. Bloom, Jase Gehring, Laura Luebbert, Sri Kosuri, Lior Pachter
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2020
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/fd9d2f00173b429397dc016800968d3a
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spelling	oai:doaj.org-article:fd9d2f00173b429397dc016800968d3a2021-12-02T15:11:50ZReliable and accurate diagnostics from highly multiplexed sequencing assays10.1038/s41598-020-78942-72045-2322https://doaj.org/article/fd9d2f00173b429397dc016800968d3a2020-12-01T00:00:00Zhttps://doi.org/10.1038/s41598-020-78942-7https://doaj.org/toc/2045-2322Abstract Scalable, inexpensive, and secure testing for SARS-CoV-2 infection is crucial for control of the novel coronavirus pandemic. Recently developed highly multiplexed sequencing assays (HMSAs) that rely on high-throughput sequencing can, in principle, meet these demands, and present promising alternatives to currently used RT-qPCR-based tests. However, reliable analysis, interpretation, and clinical use of HMSAs requires overcoming several computational, statistical and engineering challenges. Using recently acquired experimental data, we present and validate a computational workflow based on kallisto and bustools, that utilizes robust statistical methods and fast, memory efficient algorithms, to quickly, accurately and reliably process high-throughput sequencing data. We show that our workflow is effective at processing data from all recently proposed SARS-CoV-2 sequencing based diagnostic tests, and is generally applicable to any diagnostic HMSA.A. Sina BooeshaghiNathan B. LubockAaron R. CooperScott W. SimpkinsJoshua S. BloomJase GehringLaura LuebbertSri KosuriLior PachterNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 10, Iss 1, Pp 1-7 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q A. Sina Booeshaghi Nathan B. Lubock Aaron R. Cooper Scott W. Simpkins Joshua S. Bloom Jase Gehring Laura Luebbert Sri Kosuri Lior Pachter Reliable and accurate diagnostics from highly multiplexed sequencing assays
description	Abstract Scalable, inexpensive, and secure testing for SARS-CoV-2 infection is crucial for control of the novel coronavirus pandemic. Recently developed highly multiplexed sequencing assays (HMSAs) that rely on high-throughput sequencing can, in principle, meet these demands, and present promising alternatives to currently used RT-qPCR-based tests. However, reliable analysis, interpretation, and clinical use of HMSAs requires overcoming several computational, statistical and engineering challenges. Using recently acquired experimental data, we present and validate a computational workflow based on kallisto and bustools, that utilizes robust statistical methods and fast, memory efficient algorithms, to quickly, accurately and reliably process high-throughput sequencing data. We show that our workflow is effective at processing data from all recently proposed SARS-CoV-2 sequencing based diagnostic tests, and is generally applicable to any diagnostic HMSA.
format	article
author	A. Sina Booeshaghi Nathan B. Lubock Aaron R. Cooper Scott W. Simpkins Joshua S. Bloom Jase Gehring Laura Luebbert Sri Kosuri Lior Pachter
author_facet	A. Sina Booeshaghi Nathan B. Lubock Aaron R. Cooper Scott W. Simpkins Joshua S. Bloom Jase Gehring Laura Luebbert Sri Kosuri Lior Pachter
author_sort	A. Sina Booeshaghi
title	Reliable and accurate diagnostics from highly multiplexed sequencing assays
title_short	Reliable and accurate diagnostics from highly multiplexed sequencing assays
title_full	Reliable and accurate diagnostics from highly multiplexed sequencing assays
title_fullStr	Reliable and accurate diagnostics from highly multiplexed sequencing assays
title_full_unstemmed	Reliable and accurate diagnostics from highly multiplexed sequencing assays
title_sort	reliable and accurate diagnostics from highly multiplexed sequencing assays
publisher	Nature Portfolio
publishDate	2020
url	https://doaj.org/article/fd9d2f00173b429397dc016800968d3a
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Reliable and accurate diagnostics from highly multiplexed sequencing assays

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