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Detection of EGFR mutations in non-small cell lung cancer by droplet digital PCR

Activating mutations in EGFR predict benefit from tyrosine kinase inhibitor therapy for patients with advanced non-small cell lung cancer. Directing patients to appropriate therapy depends on accurate and timely EGFR assessment in the molecular pathology laboratory. This article describes the analyt...

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Autores principales: Williamson, Drew F. K., Marris, Sean R. N., Rojas-Rudilla, Vanesa, Bruce, Jacqueline L., Paweletz, Cloud P., Oxnard, Geoffrey R., Sholl, Lynette M., Dong, Fei
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8870499/
https://www.ncbi.nlm.nih.gov/pubmed/35202431
http://dx.doi.org/10.1371/journal.pone.0264201
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author Williamson, Drew F. K.
Marris, Sean R. N.
Rojas-Rudilla, Vanesa
Bruce, Jacqueline L.
Paweletz, Cloud P.
Oxnard, Geoffrey R.
Sholl, Lynette M.
Dong, Fei
author_facet Williamson, Drew F. K.
Marris, Sean R. N.
Rojas-Rudilla, Vanesa
Bruce, Jacqueline L.
Paweletz, Cloud P.
Oxnard, Geoffrey R.
Sholl, Lynette M.
Dong, Fei
author_sort Williamson, Drew F. K.
collection PubMed
description Activating mutations in EGFR predict benefit from tyrosine kinase inhibitor therapy for patients with advanced non-small cell lung cancer. Directing patients to appropriate therapy depends on accurate and timely EGFR assessment in the molecular pathology laboratory. This article describes the analytical design, performance characteristics, and clinical implementation of an assay for the rapid detection of EGFR L858R and exon 19 deletion mutations. A droplet digital polymerase chain reaction (ddPCR) assay was implemented with probe hydrolysis-dependent signal detection. A mutation-specific probe was used to detect EGFR L858R. A loss of signal design was used to detect EGFR exon 19 deletion mutations. Analytical sensitivity was dependent on DNA input and was as low as 0.01% variant allele fraction for the EGFR L858R assay and 0.1% variant allele fraction for the EGFR exon 19 deletion assay. Correlation of 20 clinical specimens tested by ddPCR and next generation sequencing showed 100% concordance. ddPCR showed 53% clinical sensitivity in the detection of EGFR mutations in plasma cell-free DNA from patients with lung cancer. The median clinical turnaround time was 5 days for ddPCR compared to 13 days for next generation sequencing. The findings show that ddPCR is an accurate and rapid method for detecting EGFR mutations in patients with non-small cell lung cancer.
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spelling pubmed-88704992022-02-25 Detection of EGFR mutations in non-small cell lung cancer by droplet digital PCR Williamson, Drew F. K. Marris, Sean R. N. Rojas-Rudilla, Vanesa Bruce, Jacqueline L. Paweletz, Cloud P. Oxnard, Geoffrey R. Sholl, Lynette M. Dong, Fei PLoS One Research Article Activating mutations in EGFR predict benefit from tyrosine kinase inhibitor therapy for patients with advanced non-small cell lung cancer. Directing patients to appropriate therapy depends on accurate and timely EGFR assessment in the molecular pathology laboratory. This article describes the analytical design, performance characteristics, and clinical implementation of an assay for the rapid detection of EGFR L858R and exon 19 deletion mutations. A droplet digital polymerase chain reaction (ddPCR) assay was implemented with probe hydrolysis-dependent signal detection. A mutation-specific probe was used to detect EGFR L858R. A loss of signal design was used to detect EGFR exon 19 deletion mutations. Analytical sensitivity was dependent on DNA input and was as low as 0.01% variant allele fraction for the EGFR L858R assay and 0.1% variant allele fraction for the EGFR exon 19 deletion assay. Correlation of 20 clinical specimens tested by ddPCR and next generation sequencing showed 100% concordance. ddPCR showed 53% clinical sensitivity in the detection of EGFR mutations in plasma cell-free DNA from patients with lung cancer. The median clinical turnaround time was 5 days for ddPCR compared to 13 days for next generation sequencing. The findings show that ddPCR is an accurate and rapid method for detecting EGFR mutations in patients with non-small cell lung cancer. Public Library of Science 2022-02-24 /pmc/articles/PMC8870499/ /pubmed/35202431 http://dx.doi.org/10.1371/journal.pone.0264201 Text en © 2022 Williamson et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Williamson, Drew F. K.
Marris, Sean R. N.
Rojas-Rudilla, Vanesa
Bruce, Jacqueline L.
Paweletz, Cloud P.
Oxnard, Geoffrey R.
Sholl, Lynette M.
Dong, Fei
Detection of EGFR mutations in non-small cell lung cancer by droplet digital PCR
title Detection of EGFR mutations in non-small cell lung cancer by droplet digital PCR
title_full Detection of EGFR mutations in non-small cell lung cancer by droplet digital PCR
title_fullStr Detection of EGFR mutations in non-small cell lung cancer by droplet digital PCR
title_full_unstemmed Detection of EGFR mutations in non-small cell lung cancer by droplet digital PCR
title_short Detection of EGFR mutations in non-small cell lung cancer by droplet digital PCR
title_sort detection of egfr mutations in non-small cell lung cancer by droplet digital pcr
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8870499/
https://www.ncbi.nlm.nih.gov/pubmed/35202431
http://dx.doi.org/10.1371/journal.pone.0264201
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