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Validation and Clinical Application of ONCOaccuPanel for Targeted Next-Generation Sequencing of Solid Tumors
PURPOSE: Targeted next-generation sequencing (NGS) is widely used for simultaneously detecting clinically informative genetic alterations in a single assay. Its application in clinical settings requires the validation of NGS gene panels. In this study, we aimed to validate a targeted hybridization c...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Korean Cancer Association
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10101781/ https://www.ncbi.nlm.nih.gov/pubmed/36470260 http://dx.doi.org/10.4143/crt.2022.891 |
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author | Kim, Moonsik Lee, Changseon Hong, Juyeon Kim, Juhee Jeong, Ji Yun Park, Nora Jee-Young Kim, Ji-Eun Park, Ji Young |
author_facet | Kim, Moonsik Lee, Changseon Hong, Juyeon Kim, Juhee Jeong, Ji Yun Park, Nora Jee-Young Kim, Ji-Eun Park, Ji Young |
author_sort | Kim, Moonsik |
collection | PubMed |
description | PURPOSE: Targeted next-generation sequencing (NGS) is widely used for simultaneously detecting clinically informative genetic alterations in a single assay. Its application in clinical settings requires the validation of NGS gene panels. In this study, we aimed to validate a targeted hybridization capture-based DNA panel (ONCOaccuPanel) using the Illumina MiSeq sequencing platform. The panel allows the simultaneous detection of single-nucleotide variants (SNVs), insertions, deletions, and copy number changes of 323 genes and fusions of 17 genes in solid tumors. MATERIALS AND METHODS: We used 16 formalin-fixed paraffin-embedded (FFPE) tumor samples with previously known genetic mutations and one reference material (HD827) for validation. Moreover, we sequenced an additional 117 FFPE tumor samples to demonstrate the clinical utility of this panel. RESULTS: Validation revealed a 100% positive percentage agreement and positive predictive value for the detection of SNVs, insertions, deletions, copy number changes, fusion genes, and microsatellite instability–high types. We observed high levels of reproducibility and repeatability (R(2) correlation coefficients=0.96–0.98). In the limit of detection assessment, we identified all clinically relevant genes with allele frequencies > 3%. Furthermore, the clinical application of ONCOaccuPanel using 117 FFPE samples demonstrated robust detection of oncogenic alterations. Oncogenic alterations and targetable genetic alterations were detected in 98.2% and 27.4% cases, respectively. CONCLUSION: ONCOaccuPanel demonstrated high analytical sensitivity, reproducibility, and repeatability and is feasible for the detection of clinically relevant mutations in clinical settings. |
format | Online Article Text |
id | pubmed-10101781 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Korean Cancer Association |
record_format | MEDLINE/PubMed |
spelling | pubmed-101017812023-04-15 Validation and Clinical Application of ONCOaccuPanel for Targeted Next-Generation Sequencing of Solid Tumors Kim, Moonsik Lee, Changseon Hong, Juyeon Kim, Juhee Jeong, Ji Yun Park, Nora Jee-Young Kim, Ji-Eun Park, Ji Young Cancer Res Treat Original Article PURPOSE: Targeted next-generation sequencing (NGS) is widely used for simultaneously detecting clinically informative genetic alterations in a single assay. Its application in clinical settings requires the validation of NGS gene panels. In this study, we aimed to validate a targeted hybridization capture-based DNA panel (ONCOaccuPanel) using the Illumina MiSeq sequencing platform. The panel allows the simultaneous detection of single-nucleotide variants (SNVs), insertions, deletions, and copy number changes of 323 genes and fusions of 17 genes in solid tumors. MATERIALS AND METHODS: We used 16 formalin-fixed paraffin-embedded (FFPE) tumor samples with previously known genetic mutations and one reference material (HD827) for validation. Moreover, we sequenced an additional 117 FFPE tumor samples to demonstrate the clinical utility of this panel. RESULTS: Validation revealed a 100% positive percentage agreement and positive predictive value for the detection of SNVs, insertions, deletions, copy number changes, fusion genes, and microsatellite instability–high types. We observed high levels of reproducibility and repeatability (R(2) correlation coefficients=0.96–0.98). In the limit of detection assessment, we identified all clinically relevant genes with allele frequencies > 3%. Furthermore, the clinical application of ONCOaccuPanel using 117 FFPE samples demonstrated robust detection of oncogenic alterations. Oncogenic alterations and targetable genetic alterations were detected in 98.2% and 27.4% cases, respectively. CONCLUSION: ONCOaccuPanel demonstrated high analytical sensitivity, reproducibility, and repeatability and is feasible for the detection of clinically relevant mutations in clinical settings. Korean Cancer Association 2023-04 2022-11-25 /pmc/articles/PMC10101781/ /pubmed/36470260 http://dx.doi.org/10.4143/crt.2022.891 Text en Copyright © 2023 by the Korean Cancer Association https://creativecommons.org/licenses/by-nc/4.0/This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/ (https://creativecommons.org/licenses/by-nc/4.0/) ) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Original Article Kim, Moonsik Lee, Changseon Hong, Juyeon Kim, Juhee Jeong, Ji Yun Park, Nora Jee-Young Kim, Ji-Eun Park, Ji Young Validation and Clinical Application of ONCOaccuPanel for Targeted Next-Generation Sequencing of Solid Tumors |
title | Validation and Clinical Application of ONCOaccuPanel for Targeted Next-Generation Sequencing of Solid Tumors |
title_full | Validation and Clinical Application of ONCOaccuPanel for Targeted Next-Generation Sequencing of Solid Tumors |
title_fullStr | Validation and Clinical Application of ONCOaccuPanel for Targeted Next-Generation Sequencing of Solid Tumors |
title_full_unstemmed | Validation and Clinical Application of ONCOaccuPanel for Targeted Next-Generation Sequencing of Solid Tumors |
title_short | Validation and Clinical Application of ONCOaccuPanel for Targeted Next-Generation Sequencing of Solid Tumors |
title_sort | validation and clinical application of oncoaccupanel for targeted next-generation sequencing of solid tumors |
topic | Original Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10101781/ https://www.ncbi.nlm.nih.gov/pubmed/36470260 http://dx.doi.org/10.4143/crt.2022.891 |
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