Evaluation of the Analytical Performance of Oncomine Lung cfDNA Assay for Detection of Plasma <i>EGFR</i> Mutations
Background: The clinical utility of circulating tumor DNA (ctDNA) in the early detection of tumor mutations for targeted therapy and the monitoring of tumor recurrence has been reported. However, the analytical validation of ctDNA assays is required for clinical application. Methods: This study eval...
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| Format: | Article |
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MDPI AG
2023-06-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/14/6/1219 |
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| author | Yong Gon Cho Joonhong Park Ji Yoon Han Tae Yun Kim |
| author_facet | Yong Gon Cho Joonhong Park Ji Yoon Han Tae Yun Kim |
| author_sort | Yong Gon Cho |
| collection | DOAJ |
| description | Background: The clinical utility of circulating tumor DNA (ctDNA) in the early detection of tumor mutations for targeted therapy and the monitoring of tumor recurrence has been reported. However, the analytical validation of ctDNA assays is required for clinical application. Methods: This study evaluated the analytical performance of the Oncomine Lung cfDNA Assay compared with the cobas<sup>®</sup> <i>EGFR</i> Mutation Test v2. The analytical specificity and sensitivity were estimated using commercially pre-certified reference materials. The comparative evaluation of the two assays was carried out using reference materials and plasma derived from patients diagnosed with lung cancer. Results: Using 20 ng of input cell-free DNA (cfDNA), the analytical sensitivities for <i>EGFR</i> mutations with variant allele frequencies (VAFs) of 1% and 0.1% were 100% and 100%, respectively. With VAFs of 1.2% and 0.1% using 20 ng of input cfDNA, seven out of nine different mutations in six driver genes were identified in the Oncomine Lung cfDNA Assay. The two assays showed 100% concordance in 16 plasma samples clinically. Furthermore, various <i>PIK3CA</i> and/or <i>TP53</i> mutations were identified only in the Oncomine Lung cfDNA Assay. Conclusions: The Oncomine Lung cfDNA Assay can be used to identify plasma <i>EGFR</i> mutations in patients with lung cancer, although further large-scale studies are required to evaluate the analytical validity for other types of aberrations and genes using clinical samples. |
| first_indexed | 2024-03-11T02:25:49Z |
| format | Article |
| id | doaj.art-da631180cfb1461fb3ff92b1dd306c01 |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-11T02:25:49Z |
| publishDate | 2023-06-01 |
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| series | Genes |
| spelling | doaj.art-da631180cfb1461fb3ff92b1dd306c012023-11-18T10:34:26ZengMDPI AGGenes2073-44252023-06-01146121910.3390/genes14061219Evaluation of the Analytical Performance of Oncomine Lung cfDNA Assay for Detection of Plasma <i>EGFR</i> MutationsYong Gon Cho0Joonhong Park1Ji Yoon Han2Tae Yun Kim3Department of Laboratory Medicine, Jeonbuk National University Medical School and Hospital, Jeonju 54907, Republic of KoreaDepartment of Laboratory Medicine, Jeonbuk National University Medical School and Hospital, Jeonju 54907, Republic of KoreaDepartment of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of KoreaDepartment of Thoracic and Cardiovascular Surgery, Jeonbuk National University Medical School and Hospital, Jeonju 54907, Republic of KoreaBackground: The clinical utility of circulating tumor DNA (ctDNA) in the early detection of tumor mutations for targeted therapy and the monitoring of tumor recurrence has been reported. However, the analytical validation of ctDNA assays is required for clinical application. Methods: This study evaluated the analytical performance of the Oncomine Lung cfDNA Assay compared with the cobas<sup>®</sup> <i>EGFR</i> Mutation Test v2. The analytical specificity and sensitivity were estimated using commercially pre-certified reference materials. The comparative evaluation of the two assays was carried out using reference materials and plasma derived from patients diagnosed with lung cancer. Results: Using 20 ng of input cell-free DNA (cfDNA), the analytical sensitivities for <i>EGFR</i> mutations with variant allele frequencies (VAFs) of 1% and 0.1% were 100% and 100%, respectively. With VAFs of 1.2% and 0.1% using 20 ng of input cfDNA, seven out of nine different mutations in six driver genes were identified in the Oncomine Lung cfDNA Assay. The two assays showed 100% concordance in 16 plasma samples clinically. Furthermore, various <i>PIK3CA</i> and/or <i>TP53</i> mutations were identified only in the Oncomine Lung cfDNA Assay. Conclusions: The Oncomine Lung cfDNA Assay can be used to identify plasma <i>EGFR</i> mutations in patients with lung cancer, although further large-scale studies are required to evaluate the analytical validity for other types of aberrations and genes using clinical samples.https://www.mdpi.com/2073-4425/14/6/1219analytical performanceOncomine Lung cfDNA Assayplasma <i>EGFR</i> mutationsnext-generation sequencingcobas<sup>®</sup> <i>EGFR</i> Mutation Test v2 |
| spellingShingle | Yong Gon Cho Joonhong Park Ji Yoon Han Tae Yun Kim Evaluation of the Analytical Performance of Oncomine Lung cfDNA Assay for Detection of Plasma <i>EGFR</i> Mutations Genes analytical performance Oncomine Lung cfDNA Assay plasma <i>EGFR</i> mutations next-generation sequencing cobas<sup>®</sup> <i>EGFR</i> Mutation Test v2 |
| title | Evaluation of the Analytical Performance of Oncomine Lung cfDNA Assay for Detection of Plasma <i>EGFR</i> Mutations |
| title_full | Evaluation of the Analytical Performance of Oncomine Lung cfDNA Assay for Detection of Plasma <i>EGFR</i> Mutations |
| title_fullStr | Evaluation of the Analytical Performance of Oncomine Lung cfDNA Assay for Detection of Plasma <i>EGFR</i> Mutations |
| title_full_unstemmed | Evaluation of the Analytical Performance of Oncomine Lung cfDNA Assay for Detection of Plasma <i>EGFR</i> Mutations |
| title_short | Evaluation of the Analytical Performance of Oncomine Lung cfDNA Assay for Detection of Plasma <i>EGFR</i> Mutations |
| title_sort | evaluation of the analytical performance of oncomine lung cfdna assay for detection of plasma i egfr i mutations |
| topic | analytical performance Oncomine Lung cfDNA Assay plasma <i>EGFR</i> mutations next-generation sequencing cobas<sup>®</sup> <i>EGFR</i> Mutation Test v2 |
| url | https://www.mdpi.com/2073-4425/14/6/1219 |
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