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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.
Abstract:
This study describes the validation of a clinical RNA expression panel with evaluation of concordance between gene copy gain by a next-generation sequencing (NGS) assay and high gene expression by an RNA expression panel. The RNA Salah Targeted Expression Panel (RNA STEP) was designed with input from oncologists to include 204 genes with utility for clinical trial prescreening and therapy selection. RNA STEP was validated with the nanoString platform using remnant formalin-fixed, paraffin-embedded-derived RNA from 102 patients previously tested with a validated clinical NGS panel. The repeatability, reproducibility, and concordance of RNA STEP results with NGS results were evaluated. RNA STEP demonstrated high repeatability and reproducibility, with excellent correlation (r > 0.97, P < 0.0001) for all comparisons. Comparison of RNA STEP high gene expression (log2 ratio ≥ 2) versus NGS DNA-based gene copy number gain (copies ≥ 5) for 38 mutually covered genes revealed an accuracy of 93.0% with a positive percentage agreement of 69.4% and negative percentage agreement of 93.8%. Moderate correlation was observed between platforms (r = 0.53, P < 0.0001). Concordance between high gene expression and gene copy number gain varied by specific gene, and some genes had higher accuracy between assays. Clinical implementation of RNA STEP provides gene expression data complementary to NGS and offers a tool for prescreening patients for clinical trials.
Insights
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.
