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Updated: Jul 22, 2025
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Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies
Published on: April 11, 2016
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Validation and benchmarking of targeted panel sequencing for cancer genomic profiling
Duo Wang1,2,3, Sizhen Wang4, Yuanfeng Zhang1,2,3
1National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China.
American Journal of Clinical Pathology
|July 21, 2023
Summary
This study validates the OncoPanScan next-generation sequencing (NGS) panel for comprehensive genomic profiling, demonstrating high sensitivity and specificity for detecting cancer-related gene alterations to enhance precision oncology.
Area of Science:
- Genomics
- Oncology
- Molecular Diagnostics
Background:
- Precision oncology relies on comprehensive genomic profiling to guide treatment decisions.
- Next-generation sequencing (NGS) panels are crucial for identifying actionable genomic alterations in cancer.
Purpose of the Study:
- To validate the OncoPanScan, an 825-gene NGS panel for comprehensive genomic profiling.
- To assess the analytical performance of the panel for detecting diverse genomic alterations.
- To improve patient access to effective precision oncology treatments.
Main Methods:
- A practical validation strategy was employed using 97 tumor specimens, 25 paired blood specimens, 10 cell lines, and 121 artificial DNA samples.
- Analytical performance was evaluated across various genomic alteration classes.
- Sequencing was performed on 1107 libraries, with a low failure rate of 0.18%.
Main Results:
- High sensitivity (>0.938), specificity (>0.889), positive predictive value (>0.867), repeatability (>0.908), and reproducibility (>0.832) were achieved across alteration types.
- Established limits of detection for variants, tumor mutation burden, and microsatellite instability.
- Benchmarking identified dry-bench processes as the primary source of discordant variant calls.
Conclusions:
- The OncoPanScan panel is analytically validated for comprehensive genomic profiling.
- The study provides a robust validation framework and recommendations for large NGS panel implementation.
- Understanding sources of discordance is key for reliable genomic profiling in precision oncology.
