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Updated: Aug 18, 2025
Next Generation Sequencing for the Detection of Actionable Mutations in Solid and Liquid Tumors
Published on: September 20, 2016
Validation and Clinical Application of ONCOaccuPanel for Targeted Next-Generation Sequencing of Solid Tumors
Moonsik Kim1, Changseon Lee2, Juyeon Hong2
1Department of Pathology, Kyungpook National University Chilgok Hospital, School of Medicine, Kyungpook National University, Daegu, Korea.
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 (R2 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.
Insights
This study validates the ONCOaccuPanel, a next-generation sequencing (NGS) assay for detecting genetic mutations in solid tumors. The panel shows high accuracy and reproducibility, proving its clinical utility for identifying oncogenic alterations.
Area of Science:
- Oncology
- Genomics
- Molecular Diagnostics
Background:
- Targeted next-generation sequencing (NGS) panels are crucial for simultaneous genetic alteration detection in clinical oncology.
- Validation of these NGS panels is essential before clinical implementation.
- ONCOaccuPanel is a targeted hybridization capture-based DNA panel designed for solid tumor analysis.
Purpose of the Study:
- To validate the ONCOaccuPanel for detecting single-nucleotide variants (SNVs), insertions, deletions, copy number changes, and gene fusions.
- To assess the panel's performance using Illumina MiSeq sequencing platform.
- To demonstrate the clinical utility of the panel in a cohort of solid tumor samples.
Main Methods:
- Validation was performed using 16 formalin-fixed paraffin-embedded (FFPE) tumor samples with known mutations and one reference material.
- Analytical performance was assessed for SNVs, insertions, deletions, copy number changes, and fusion genes.
- Clinical utility was evaluated by sequencing an additional 117 FFPE tumor samples.
Main Results:
- The ONCOaccuPanel achieved 100% positive percentage agreement and positive predictive value for all tested mutation types.
- High reproducibility and repeatability were observed, with R2 correlation coefficients ranging from 0.96 to 0.98.
- Clinically relevant genes were detected with allele frequencies > 3%, and oncogenic alterations were found in 98.2% of clinical samples.
Conclusions:
- ONCOaccuPanel demonstrates high analytical sensitivity, reproducibility, and repeatability.
- The panel is feasible for detecting clinically relevant mutations in solid tumors within clinical settings.
- The study confirms the robust detection of oncogenic and targetable genetic alterations.
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