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Reliable and accurate diagnostics from highly multiplexed sequencing assays

Booeshaghi, A. Sina and Lubock, Nathan B. and Cooper, Aaron R. and Simpkins, Scott W. and Bloom, Joshua S. and Gehring, Jase and Luebbert, Laura and Kosuri, Sriram and Pachter, Lior (2020) Reliable and accurate diagnostics from highly multiplexed sequencing assays. Scientific Reports, 10 . Art. No. 21759. ISSN 2045-2322. PMCID PMC7730459. https://resolver.caltech.edu/CaltechAUTHORS:20200601-101849395

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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.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1038/s41598-020-78942-7DOIArticle
https://doi.org/10.1101/2020.05.13.20100131DOIDiscussion Paper
https://github.com/pachterlab/BLCSBGLKP_2020Related ItemData/Code
http://www.ncbi.nlm.nih.gov/pmc/articles/pmc7730459/PubMed CentralArticle
ORCID:
AuthorORCID
Booeshaghi, A. Sina0000-0002-6442-4502
Lubock, Nathan B.0000-0001-8064-2465
Cooper, Aaron R.0000-0003-4588-2513
Simpkins, Scott W.0000-0002-5997-2838
Bloom, Joshua S.0000-0002-7241-1648
Gehring, Jase0000-0002-3894-9495
Luebbert, Laura0000-0003-1379-2927
Kosuri, Sriram0000-0002-4661-0600
Pachter, Lior0000-0002-9164-6231
Alternate Title:Fast and accurate diagnostics from highly multiplexed sequencing assays
Additional Information:© 2020 The Author(s). This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. Received 02 November 2020; Accepted 24 November 2020; Published 10 December 2020. We thank Páll Melsted for assistance with bustools. Author Contributions: A.S.B. and L.P. developed the kallisto|bustools approach to processing and analyzing HMSA data. A.S.B. adapted kallisto and bustools to process SwabSeq, LAMP-seq, covE-seq, and TRB-seq data. A.S.B. performed the analyses and collected results for the paper. N.L. developed the bcl2fastq + starcode processing approach with assistance from A.R.C., S.W.S., and J.S.B. J.G. assisted with technical aspects of the SwabSeq assay and in assessing the kallisto|bustools workflow results. L.L. created Fig. 1 and explored the sample index structures of LAMP-seq, TRB-seq, and SwabSeq. S.K., N.L.B., A.R.C., S.W.S. and J.S.B. developed SwabSeq. A.S.B., L.L., and L.P. wrote the manuscript. Competing interests: A.S.B., J.G., L.L., and L.P. declare no conflicts of interest. S.K., N.L.B., A.R.C., S.W.S. and J.S.B. are employees of Ocant, which developed SwabSeq. SwabSeq is released under the terms of the Octant Covid License20.
Group:COVID-19
Subject Keywords:Computational biology and bioinformatics; Infectious diseases
PubMed Central ID:PMC7730459
Record Number:CaltechAUTHORS:20200601-101849395
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20200601-101849395
Official Citation:Booeshaghi, A.S., Lubock, N.B., Cooper, A.R. et al. Reliable and accurate diagnostics from highly multiplexed sequencing assays. Sci Rep 10, 21759 (2020). https://doi.org/10.1038/s41598-020-78942-7
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:103585
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:01 Jun 2020 17:29
Last Modified:02 Feb 2021 20:16

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