Comparison of real-time PCR and nCounter NanoString techniques to validate copy number alterations in oral cancer
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View abstract on PubMed
Summary
This summary is machine-generated.Real-time PCR is a robust method for validating genomic biomarkers in oral cancer. nCounter NanoString showed moderate agreement but identified different prognostic gene associations compared to PCR.
Area Of Science
- Genomics
- Cancer Research
- Molecular Biology
Background
- Copy number alterations (CNAs) are crucial for cancer prognosis and treatment prediction.
- Real-time polymerase chain reaction (PCR) is a standard for validating genomic profiling results.
- The nCounter NanoString platform's utility for CNA analysis requires further evaluation.
Purpose Of The Study
- To comprehensively compare real-time PCR and nCounter NanoString for copy number analysis in oral cancer.
- To assess the prognostic implications of specific gene CNAs identified by both methods.
- To evaluate the concordance between the two techniques.
Main Methods
- Analysis of 24 genes across 119 oral cancer samples.
- Comparison of real-time PCR and nCounter NanoString techniques.
- Statistical analysis using Spearman's rank correlation and Cohen's Kappa.
- Prognostic evaluation using Kaplan-Meier curves and Log-rank tests for RFS, DSS, and OS.
Main Results
- Spearman's rank correlation (r=0.188 to 0.517) and moderate to substantial agreement (Cohen's Kappa) were observed between the methods.
- Real-time PCR identified ISG15 as a favorable prognostic marker for RFS, DSS, and OS, and ATM, CASP4, CYB5A for poor RFS.
- nCounter NanoString indicated ISG15 as a poor prognostic marker for RFS, DSS, and OS, and CDK11A for poor RFS.
Conclusions
- Real-time PCR is a reliable method for validating genomic biomarkers in oral cancer.
- Discrepancies in prognostic gene associations between real-time PCR and nCounter NanoString warrant further investigation.
- Independent studies are needed to validate these findings.
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