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Analytical Validation of a Pan-Cancer Panel for Cell-Free Assay for the Detection of EGFR Mutations

Liquid biopsies have increasingly shown clinical utility. Although next-generation sequencing has been widely used for the detection of somatic mutations from plasma, performance characteristics vary by platform. Therefore, thorough validation is mandatory for clinical use. This study aimed to evalu...

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Autores principales: So, Min-Kyung, Park, Jong-Ho, Kim, Jong-Won, Jang, Ja-Hyun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8227964/
https://www.ncbi.nlm.nih.gov/pubmed/34199654
http://dx.doi.org/10.3390/diagnostics11061022
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author So, Min-Kyung
Park, Jong-Ho
Kim, Jong-Won
Jang, Ja-Hyun
author_facet So, Min-Kyung
Park, Jong-Ho
Kim, Jong-Won
Jang, Ja-Hyun
author_sort So, Min-Kyung
collection PubMed
description Liquid biopsies have increasingly shown clinical utility. Although next-generation sequencing has been widely used for the detection of somatic mutations from plasma, performance characteristics vary by platform. Therefore, thorough validation is mandatory for clinical use. This study aimed to evaluate the analytical validity of the Oncomine Pan-Cancer Cell-Free Assay. A massively parallel sequencing for the assay was performed using the Ion S5 XL System with Ion 540 kit. The analytical sensitivity and precision were evaluated using pre-characterized reference materials. The specificity was evaluated using plasma from healthy subjects. A comparison with the Cobas EGFR Mutation Test v2 was performed using reference materials and plasma from lung cancer patients. For SNVs and short indels, the analytical sensitivities at variant allele frequencies (VAFs) of 0.1%, 0.5%, and 1% were 50%, 93.4%, and 100% with 20 ng of input, respectively. The overall precision of the true positive variants was 98% at a VAF of 1% with 20 ng input. The assay showed a similar sensitivity to that of the Cobas EGFR Mutation Test v2 at a VAF of 0.5% with 20 ng of input and 100% concordance on clinical samples. The Pan-Cancer Cell-Free Assay can be applied to detect EGFR mutations in advanced lung cancer patients, although follow-up studies will be needed to evaluate the analytical validity for other types of genes and aberrations using clinical samples.
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spelling pubmed-82279642021-06-26 Analytical Validation of a Pan-Cancer Panel for Cell-Free Assay for the Detection of EGFR Mutations So, Min-Kyung Park, Jong-Ho Kim, Jong-Won Jang, Ja-Hyun Diagnostics (Basel) Article Liquid biopsies have increasingly shown clinical utility. Although next-generation sequencing has been widely used for the detection of somatic mutations from plasma, performance characteristics vary by platform. Therefore, thorough validation is mandatory for clinical use. This study aimed to evaluate the analytical validity of the Oncomine Pan-Cancer Cell-Free Assay. A massively parallel sequencing for the assay was performed using the Ion S5 XL System with Ion 540 kit. The analytical sensitivity and precision were evaluated using pre-characterized reference materials. The specificity was evaluated using plasma from healthy subjects. A comparison with the Cobas EGFR Mutation Test v2 was performed using reference materials and plasma from lung cancer patients. For SNVs and short indels, the analytical sensitivities at variant allele frequencies (VAFs) of 0.1%, 0.5%, and 1% were 50%, 93.4%, and 100% with 20 ng of input, respectively. The overall precision of the true positive variants was 98% at a VAF of 1% with 20 ng input. The assay showed a similar sensitivity to that of the Cobas EGFR Mutation Test v2 at a VAF of 0.5% with 20 ng of input and 100% concordance on clinical samples. The Pan-Cancer Cell-Free Assay can be applied to detect EGFR mutations in advanced lung cancer patients, although follow-up studies will be needed to evaluate the analytical validity for other types of genes and aberrations using clinical samples. MDPI 2021-06-02 /pmc/articles/PMC8227964/ /pubmed/34199654 http://dx.doi.org/10.3390/diagnostics11061022 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
So, Min-Kyung
Park, Jong-Ho
Kim, Jong-Won
Jang, Ja-Hyun
Analytical Validation of a Pan-Cancer Panel for Cell-Free Assay for the Detection of EGFR Mutations
title Analytical Validation of a Pan-Cancer Panel for Cell-Free Assay for the Detection of EGFR Mutations
title_full Analytical Validation of a Pan-Cancer Panel for Cell-Free Assay for the Detection of EGFR Mutations
title_fullStr Analytical Validation of a Pan-Cancer Panel for Cell-Free Assay for the Detection of EGFR Mutations
title_full_unstemmed Analytical Validation of a Pan-Cancer Panel for Cell-Free Assay for the Detection of EGFR Mutations
title_short Analytical Validation of a Pan-Cancer Panel for Cell-Free Assay for the Detection of EGFR Mutations
title_sort analytical validation of a pan-cancer panel for cell-free assay for the detection of egfr mutations
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8227964/
https://www.ncbi.nlm.nih.gov/pubmed/34199654
http://dx.doi.org/10.3390/diagnostics11061022
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