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Comparison of Results from Two Commercially Available In-House Tissue-Based Comprehensive Genomic Profiling
Hans-Peter Adams1, Matthew C Hiemenz2, Kay Hertel3
1Signature Diagnostics GmbH, Potsdam, Germany.
The Journal of Molecular Diagnostics : JMD
|September 13, 2024
Summary
Comparing two comprehensive genomic profiling (CGP) assays revealed good agreement for some biomarkers but significant differences in tumor mutational burden, copy number alterations, and clinical trial matching. These discrepancies highlight challenges in standardizing CGP testing.
Area of Science:
- Genomic Medicine
- Molecular Diagnostics
- Bioinformatics
Background:
- Personalized medicine relies on comprehensive genomic profiling (CGP) for treatment decisions.
- Variability in CGP assay, bioinformatics, and reporting hinders implementation and uniformity.
Purpose of the Study:
- To compare two commercial tissue-based CGP assays (AVENIO and TruSight Oncology 500) with tertiary analysis solutions.
- To assess agreement and differences in variant detection, biomarker scoring, and clinical trial matching (CTM).
Main Methods:
- Comparative analysis of two research-use-only (RUO) CGP assays.
- Evaluation of short variants, copy number alterations, rearrangements, tumor mutational burden, and microsatellite instability.
- Assessment of variant categorization and CTM recommendations.
Main Results:
- Good overall agreement for short variants, gene fusions, and microsatellite instability.
- Significant differences observed in tumor mutational burden scoring, copy number alteration detection, and CTM.
- Discrepancies attributed to bioinformatic pipelines and system parameters.
Conclusions:
- Differences in CGP assay and analysis pipelines can lead to inconsistent results.
- Standardization of variant calling, filtering, and interpretation is crucial for high-quality CGP.
- Addressing these complexities is key to achieving uniformity in genomic profiling.
