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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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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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.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0264201</identifier><identifier>PMID: 35202431</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Alleles ; Assaying ; Cancer ; Carcinoma, Non-Small-Cell Lung - genetics ; Deletion ; Deoxyribonucleic acid ; Design ; Diagnosis ; DNA ; DNA Mutational Analysis - methods ; Droplets ; Enzyme inhibitors ; Epidermal growth factor receptors ; ErbB Receptors - genetics ; Flow cytometry ; Gene deletion ; Gene mutations ; Genetic aspects ; Humans ; Kinases ; Laboratories ; Lung cancer ; Lung cancer, Non-small cell ; Lung diseases ; Lung Neoplasms - genetics ; Mutation ; Next-generation sequencing ; Non-small cell lung carcinoma ; Oncology, Experimental ; Pathology ; Patients ; Polymerase chain reaction ; Polymerase Chain Reaction - methods ; Protein-tyrosine kinase ; Sensitivity analysis ; Sensitivity and Specificity ; Severe acute respiratory syndrome coronavirus 2 ; Signal detection ; Small cell lung carcinoma ; Tyrosine ; Women</subject><ispartof>PloS one, 2022-02, Vol.17 (2), p.e0264201-e0264201</ispartof><rights>COPYRIGHT 2022 Public Library of Science</rights><rights>2022 Williamson et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2022 Williamson et al 2022 Williamson et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c692t-f8ce493106331eb30629daa07563995f3cf8edbc8724f4ef30151b19732585fb3</citedby><cites>FETCH-LOGICAL-c692t-f8ce493106331eb30629daa07563995f3cf8edbc8724f4ef30151b19732585fb3</cites><orcidid>0000-0003-3769-0247 ; 0000-0003-1745-8846</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8870499/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8870499/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2096,2915,23845,27901,27902,53766,53768,79343,79344</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/35202431$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Williamson, Drew F K</creatorcontrib><creatorcontrib>Marris, Sean R N</creatorcontrib><creatorcontrib>Rojas-Rudilla, Vanesa</creatorcontrib><creatorcontrib>Bruce, Jacqueline L</creatorcontrib><creatorcontrib>Paweletz, Cloud P</creatorcontrib><creatorcontrib>Oxnard, Geoffrey R</creatorcontrib><creatorcontrib>Sholl, Lynette M</creatorcontrib><creatorcontrib>Dong, Fei</creatorcontrib><title>Detection of EGFR mutations in non-small cell lung cancer by droplet digital PCR</title><title>PloS one</title><addtitle>PLoS One</addtitle><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. 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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.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>35202431</pmid><doi>10.1371/journal.pone.0264201</doi><tpages>e0264201</tpages><orcidid>https://orcid.org/0000-0003-3769-0247</orcidid><orcidid>https://orcid.org/0000-0003-1745-8846</orcidid><oa>free_for_read</oa></addata></record> |
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subjects | Alleles Assaying Cancer Carcinoma, Non-Small-Cell Lung - genetics Deletion Deoxyribonucleic acid Design Diagnosis DNA DNA Mutational Analysis - methods Droplets Enzyme inhibitors Epidermal growth factor receptors ErbB Receptors - genetics Flow cytometry Gene deletion Gene mutations Genetic aspects Humans Kinases Laboratories Lung cancer Lung cancer, Non-small cell Lung diseases Lung Neoplasms - genetics Mutation Next-generation sequencing Non-small cell lung carcinoma Oncology, Experimental Pathology Patients Polymerase chain reaction Polymerase Chain Reaction - methods Protein-tyrosine kinase Sensitivity analysis Sensitivity and Specificity Severe acute respiratory syndrome coronavirus 2 Signal detection Small cell lung carcinoma Tyrosine Women |
title | Detection of EGFR mutations in non-small cell lung cancer by droplet digital PCR |
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