Sensitivity, specificity, and accuracy of a liquid biopsy approach utilizing molecular amplification pools

Abstract Circulating cell-free DNA (cfDNA) has the potential to be a specific biomarker for the therapeutic management of lung cancer patients. Here, a new sequencing error-reduction method based on molecular amplification pools (MAPs) was utilized to analyze cfDNA in lung cancer patients. We determ...

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Autores principales:	Jessica Garcia, Nick Kamps-Hughes, Florence Geiguer, Sébastien Couraud, Brice Sarver, Léa Payen, Cristian Ionescu-Zanetti
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/da8aee7bdc1c403a8d63c53a6d8142ba
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spelling	oai:doaj.org-article:da8aee7bdc1c403a8d63c53a6d8142ba2021-12-02T15:49:28ZSensitivity, specificity, and accuracy of a liquid biopsy approach utilizing molecular amplification pools10.1038/s41598-021-89592-82045-2322https://doaj.org/article/da8aee7bdc1c403a8d63c53a6d8142ba2021-05-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-89592-8https://doaj.org/toc/2045-2322Abstract Circulating cell-free DNA (cfDNA) has the potential to be a specific biomarker for the therapeutic management of lung cancer patients. Here, a new sequencing error-reduction method based on molecular amplification pools (MAPs) was utilized to analyze cfDNA in lung cancer patients. We determined the accuracy of MAPs plasma sequencing with respect to droplet digital polymerase chain reaction assays (ddPCR), and tested whether actionable mutation discovery is improved by next-generation sequencing (NGS) in a clinical setting. This study reports data from 356 lung cancer patients receiving plasma testing as part of routine clinical management. Sequencing of cfDNA via MAPs had a sensitivity of 98.5% and specificity 98.9%. The ddPCR assay was used as the reference, since it is an established, accurate assay that can be performed contemporaneously on the same plasma sample. MAPs sequencing detected somatic variants in 261 of 356 samples (73%). Non-actionable clonal hematopoiesis-associated variants were identified via sequencing in 21% of samples. The accuracy of this cfDNA sequencing approach was similar to that of ddPCR assays in a clinical setting, down to an allele frequency of 0.1%. Due to broader coverage and high sensitivity for insertions and deletions, sequencing via MAPs afforded important detection of additional actionable mutations.Jessica GarciaNick Kamps-HughesFlorence GeiguerSébastien CouraudBrice SarverLéa PayenCristian Ionescu-ZanettiNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Jessica Garcia Nick Kamps-Hughes Florence Geiguer Sébastien Couraud Brice Sarver Léa Payen Cristian Ionescu-Zanetti Sensitivity, specificity, and accuracy of a liquid biopsy approach utilizing molecular amplification pools
description	Abstract Circulating cell-free DNA (cfDNA) has the potential to be a specific biomarker for the therapeutic management of lung cancer patients. Here, a new sequencing error-reduction method based on molecular amplification pools (MAPs) was utilized to analyze cfDNA in lung cancer patients. We determined the accuracy of MAPs plasma sequencing with respect to droplet digital polymerase chain reaction assays (ddPCR), and tested whether actionable mutation discovery is improved by next-generation sequencing (NGS) in a clinical setting. This study reports data from 356 lung cancer patients receiving plasma testing as part of routine clinical management. Sequencing of cfDNA via MAPs had a sensitivity of 98.5% and specificity 98.9%. The ddPCR assay was used as the reference, since it is an established, accurate assay that can be performed contemporaneously on the same plasma sample. MAPs sequencing detected somatic variants in 261 of 356 samples (73%). Non-actionable clonal hematopoiesis-associated variants were identified via sequencing in 21% of samples. The accuracy of this cfDNA sequencing approach was similar to that of ddPCR assays in a clinical setting, down to an allele frequency of 0.1%. Due to broader coverage and high sensitivity for insertions and deletions, sequencing via MAPs afforded important detection of additional actionable mutations.
format	article
author	Jessica Garcia Nick Kamps-Hughes Florence Geiguer Sébastien Couraud Brice Sarver Léa Payen Cristian Ionescu-Zanetti
author_facet	Jessica Garcia Nick Kamps-Hughes Florence Geiguer Sébastien Couraud Brice Sarver Léa Payen Cristian Ionescu-Zanetti
author_sort	Jessica Garcia
title	Sensitivity, specificity, and accuracy of a liquid biopsy approach utilizing molecular amplification pools
title_short	Sensitivity, specificity, and accuracy of a liquid biopsy approach utilizing molecular amplification pools
title_full	Sensitivity, specificity, and accuracy of a liquid biopsy approach utilizing molecular amplification pools
title_fullStr	Sensitivity, specificity, and accuracy of a liquid biopsy approach utilizing molecular amplification pools
title_full_unstemmed	Sensitivity, specificity, and accuracy of a liquid biopsy approach utilizing molecular amplification pools
title_sort	sensitivity, specificity, and accuracy of a liquid biopsy approach utilizing molecular amplification pools
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/da8aee7bdc1c403a8d63c53a6d8142ba
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Sensitivity, specificity, and accuracy of a liquid biopsy approach utilizing molecular amplification pools

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