Rapid targeted somatic mutation analysis of solid tumors in routine clinical diagnostics

Area of Science:

• Oncology
• Molecular Diagnostics
• Mass Spectrometry

Background:

• Tumor genotyping is crucial for targeted therapy selection in clinical practice.
• Pathology labs require rapid, sensitive, and updated molecular testing methods.
• Existing methods may not meet the demand for high-throughput, comprehensive mutation analysis.

Purpose of the Study:

• To develop and validate a novel mass spectrometry multiplexed genotyping platform, PentaPanel.
• To concurrently assess single nucleotide polymorphisms in 56 hotspots across five key cancer genes (KRAS, NRAS, BRAF, EGFR, PIK3CA).
• To evaluate the platform's performance, including sensitivity, specificity, and reproducibility, for clinical application.

Main Methods:

• Development of the PentaPanel mass spectrometry multiplexed genotyping platform.
• Analysis of 1025 tumor specimens from six cancer types (colon, lung, breast, pancreas, biliary tract, melanoma).
• Validation using Sanger sequencing and assessment of sensitivity, specificity, and reproducibility.

Main Results:

• PentaPanel successfully genotyped 221 mutations across 56 hotspots in five clinically relevant cancer genes.
• The platform demonstrated high throughput, robustness, sensitivity, specificity, and reproducibility.
• A turnaround time of two working days was achieved, enabling genotyping for 10 patients per run.
• PentaPanel effectively analyzed DNA from various routinely processed specimens (FFPE, frozen, cytological).

Conclusions:

• PentaPanel provides an immediate, accurate, and cost-effective multiplex approach for clinically relevant gene mutation analysis in solid tumors.
• The platform meets the requirements for clinical molecular testing, offering rapid turnaround and broad applicability.
• PentaPanel is valuable for targeted therapy selection and can support clinical trials, including basket trials for drug combination strategies.