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Implementation of a High-Accuracy Targeted Gene Expression Panel for Clinical Care
Aileen Y Alontaga1, Pedro Cano2, Hilal Ozakinci1
1Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida.
The Journal of Molecular Diagnostics : JMD
|May 22, 2024
Summary
This study validates the RNA Salah Targeted Expression Panel (RNA STEP) for clinical gene expression analysis. RNA STEP shows high repeatability and reproducibility, complementing next-generation sequencing (NGS) for trial prescreening.
Area of Science:
- Molecular Biology
- Oncology
- Genomics
Background:
- Clinical trials require accurate gene expression profiling for patient selection.
- Next-generation sequencing (NGS) is a validated method for detecting gene copy number gain.
- RNA expression panels offer complementary data for therapeutic decisions.
Purpose of the Study:
- To validate the RNA Salah Targeted Expression Panel (RNA STEP) for clinical use.
- To evaluate the concordance between RNA STEP gene expression and NGS-based gene copy gain.
- To assess the utility of RNA STEP for clinical trial prescreening and therapy selection.
Main Methods:
- Validation of the 204-gene RNA STEP using the nanoString platform.
- Analysis of remnant formalin-fixed, paraffin-embedded RNA from 102 patients.
- Comparison of RNA STEP results with a validated clinical NGS panel.
- Evaluation of repeatability, reproducibility, and concordance between assays.
Main Results:
- RNA STEP demonstrated high repeatability and reproducibility (r > 0.97).
- Concordance between high gene expression (RNA STEP) and gene copy gain (NGS) was 93.0% accurate.
- Moderate correlation (r = 0.53) was observed between the RNA and NGS platforms.
Conclusions:
- RNA STEP is a validated tool for clinical gene expression analysis.
- RNA STEP provides complementary data to NGS, aiding in therapy selection.
- The panel is suitable for prescreening patients for clinical trials.
