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Updated: May 12, 2026
Next Generation Sequencing for the Detection of Actionable Mutations in Solid and Liquid Tumors
Published on: September 20, 2016
A targeted next-generation sequencing panel for identification of clinically relevant mutation profiles in solid
Kakoli Das1, Mandy Li Ian Tay2, Elena Yaqing Yong2
1Department of Pathology, Tan Tock Seng Hospital, 11 Jalan Tan Tock Seng, Singapore, 308433, Singapore. kaks23@yahoo.com.
Abstract:
Targeted next generation sequencing (NGS) using multigene panels has become an effective tool for comprehensive genomic analysis in cancer, overcoming limitations of single gene assays. Nonetheless, outsourcing these assays to external laboratories and the extended turnaround time (~ 3 weeks) required for obtaining results may impede timely clinical management of cancer patients. We developed an oncopanel targeting 61 cancer-associated genes and validated its efficacy by performing NGS on 43 unique samples including clinical tissues, external quality assessment samples, and reference controls. The assay detected 794 mutations including all 92 known variants from orthogonal methods. Overall performance measures of the assay showed 99.99% repeatability and 99.98% reproducibility. Likewise, sensitivity to detect unique variants was 98.23%, with specificity at 99.99%, precision at 97.14% and accuracy at 99.99% all at 95% CI. Notably, clinically actionable mutations were observed in key genes such as KRAS, EGFR, ERBB2, PIK3CA, TP53 and BRCA1. The average turnaround time from sample processing to results was reduced to 4 days. These findings demonstrate a sensitive, high throughput oncopanel that is suitable for use in routine clinical testing. The shorter turnaround time of the assay has the potential to significantly improve patient care by facilitating more timely and personalized clinical interventions.
Insights
A new oncopanel test for cancer genes offers high accuracy and speed. This targeted next-generation sequencing assay significantly reduces turnaround time for genomic analysis, improving timely patient care.
Area of Science:
- Oncology
- Genomics
- Molecular Diagnostics
Background:
- Targeted next-generation sequencing (NGS) with multigene panels is crucial for cancer genomic analysis.
- Outsourcing NGS assays leads to long turnaround times (approx. 3 weeks), delaying clinical decisions.
Purpose of the Study:
- To develop and validate an efficient oncopanel for comprehensive cancer gene analysis.
- To reduce the turnaround time for genomic profiling in cancer patients.
Main Methods:
- Developed an oncopanel targeting 61 cancer-associated genes.
- Validated the assay using next-generation sequencing on 43 diverse samples.
- Evaluated performance metrics including repeatability, reproducibility, sensitivity, specificity, precision, and accuracy.
Main Results:
- The assay detected 794 mutations, including all 92 known variants.
- Achieved high performance: 99.99% repeatability, 99.98% reproducibility, 98.23% sensitivity, and 99.99% specificity.
- Reduced average turnaround time to 4 days, identifying actionable mutations in key cancer genes.
Conclusions:
- The developed oncopanel is a sensitive, high-throughput assay suitable for routine clinical testing.
- The significantly shorter turnaround time can enhance patient care through timely, personalized interventions.
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