Cargando…

Effects of Different Centrifugation Protocols on the Detection of EGFR Mutations in Plasma Cell-Free DNA

OBJECTIVES: Various preanalytical factors, including the collection tube, storage conditions, and centrifugation, affect the detection results of plasma cell-free DNA (cfDNA). We compared the effect of different centrifugation protocols on the detection of EGFR mutations in cfDNA. METHODS: We analyz...

Descripción completa

Detalles Bibliográficos
Autores principales: Shin, Kyung-Hwa, Lee, Sun Min, Park, Kongkyoung, Choi, Hyunji, Kim, In-suk, Yoon, Seong Hoon, Oh, Seung Hwan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9350828/
https://www.ncbi.nlm.nih.gov/pubmed/35285877
http://dx.doi.org/10.1093/ajcp/aqac024
_version_ 1784762311495385088
author Shin, Kyung-Hwa
Lee, Sun Min
Park, Kongkyoung
Choi, Hyunji
Kim, In-suk
Yoon, Seong Hoon
Oh, Seung Hwan
author_facet Shin, Kyung-Hwa
Lee, Sun Min
Park, Kongkyoung
Choi, Hyunji
Kim, In-suk
Yoon, Seong Hoon
Oh, Seung Hwan
author_sort Shin, Kyung-Hwa
collection PubMed
description OBJECTIVES: Various preanalytical factors, including the collection tube, storage conditions, and centrifugation, affect the detection results of plasma cell-free DNA (cfDNA). We compared the effect of different centrifugation protocols on the detection of EGFR mutations in cfDNA. METHODS: We analyzed 117 plasma specimens from 110 patients with non–small cell lung cancer using the cobas EGFR Mutation Test v2 (Roche Diagnostics). We compared the identified EGFR mutations and semiquantitative index values from the 1- and 2-step centrifugation groups and confirmed the clinical impact of differences in the results after further high-speed centrifugation. RESULTS: We detected EGFR mutations in 44 (37.6%) and 47 (40.2%) samples that were centrifuged once and twice, respectively; the 2 groups showed an 89.7% (105/117) concordance and a strong correlation in their semiquantitative index values (r = 0.929). Among the 12 inconsistent result pairs, 9 samples of 2-step centrifugation (75%) were consistent with the results of a recent tissue biopsy. CONCLUSIONS: Additional high-speed centrifugation has been shown to increase the sensitivity of EGFR mutation detection in a commercial in vitro diagnostic real-time polymerase chain reaction device and is an optimal preanalytical factor for detecting low-allele frequency gene mutations using low concentrations of cfDNA.
format Online
Article
Text
id pubmed-9350828
institution National Center for Biotechnology Information
language English
publishDate 2022
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-93508282022-08-05 Effects of Different Centrifugation Protocols on the Detection of EGFR Mutations in Plasma Cell-Free DNA Shin, Kyung-Hwa Lee, Sun Min Park, Kongkyoung Choi, Hyunji Kim, In-suk Yoon, Seong Hoon Oh, Seung Hwan Am J Clin Pathol Original Articles OBJECTIVES: Various preanalytical factors, including the collection tube, storage conditions, and centrifugation, affect the detection results of plasma cell-free DNA (cfDNA). We compared the effect of different centrifugation protocols on the detection of EGFR mutations in cfDNA. METHODS: We analyzed 117 plasma specimens from 110 patients with non–small cell lung cancer using the cobas EGFR Mutation Test v2 (Roche Diagnostics). We compared the identified EGFR mutations and semiquantitative index values from the 1- and 2-step centrifugation groups and confirmed the clinical impact of differences in the results after further high-speed centrifugation. RESULTS: We detected EGFR mutations in 44 (37.6%) and 47 (40.2%) samples that were centrifuged once and twice, respectively; the 2 groups showed an 89.7% (105/117) concordance and a strong correlation in their semiquantitative index values (r = 0.929). Among the 12 inconsistent result pairs, 9 samples of 2-step centrifugation (75%) were consistent with the results of a recent tissue biopsy. CONCLUSIONS: Additional high-speed centrifugation has been shown to increase the sensitivity of EGFR mutation detection in a commercial in vitro diagnostic real-time polymerase chain reaction device and is an optimal preanalytical factor for detecting low-allele frequency gene mutations using low concentrations of cfDNA. Oxford University Press 2022-03-14 /pmc/articles/PMC9350828/ /pubmed/35285877 http://dx.doi.org/10.1093/ajcp/aqac024 Text en © American Society for Clinical Pathology, 2022. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Original Articles
Shin, Kyung-Hwa
Lee, Sun Min
Park, Kongkyoung
Choi, Hyunji
Kim, In-suk
Yoon, Seong Hoon
Oh, Seung Hwan
Effects of Different Centrifugation Protocols on the Detection of EGFR Mutations in Plasma Cell-Free DNA
title Effects of Different Centrifugation Protocols on the Detection of EGFR Mutations in Plasma Cell-Free DNA
title_full Effects of Different Centrifugation Protocols on the Detection of EGFR Mutations in Plasma Cell-Free DNA
title_fullStr Effects of Different Centrifugation Protocols on the Detection of EGFR Mutations in Plasma Cell-Free DNA
title_full_unstemmed Effects of Different Centrifugation Protocols on the Detection of EGFR Mutations in Plasma Cell-Free DNA
title_short Effects of Different Centrifugation Protocols on the Detection of EGFR Mutations in Plasma Cell-Free DNA
title_sort effects of different centrifugation protocols on the detection of egfr mutations in plasma cell-free dna
topic Original Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9350828/
https://www.ncbi.nlm.nih.gov/pubmed/35285877
http://dx.doi.org/10.1093/ajcp/aqac024
work_keys_str_mv AT shinkyunghwa effectsofdifferentcentrifugationprotocolsonthedetectionofegfrmutationsinplasmacellfreedna
AT leesunmin effectsofdifferentcentrifugationprotocolsonthedetectionofegfrmutationsinplasmacellfreedna
AT parkkongkyoung effectsofdifferentcentrifugationprotocolsonthedetectionofegfrmutationsinplasmacellfreedna
AT choihyunji effectsofdifferentcentrifugationprotocolsonthedetectionofegfrmutationsinplasmacellfreedna
AT kiminsuk effectsofdifferentcentrifugationprotocolsonthedetectionofegfrmutationsinplasmacellfreedna
AT yoonseonghoon effectsofdifferentcentrifugationprotocolsonthedetectionofegfrmutationsinplasmacellfreedna
AT ohseunghwan effectsofdifferentcentrifugationprotocolsonthedetectionofegfrmutationsinplasmacellfreedna