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Updated: Jan 9, 2026
Next Generation Sequencing for the Detection of Actionable Mutations in Solid and Liquid Tumors
Published on: September 20, 2016
Validation and clinical evaluation of a comprehensive circulating tumor DNA assay for genomic profiling in solid
Lisa Schöpfer1, Lucia Zisser2, Felicitas Oberndorfer1
1Department of Pathology, Medical University of Vienna, Vienna, Austria.
Background:
Since 2023, the Department of Pathology at Vienna General Hospital has implemented comprehensive genomic profiling (CGP) of circulating tumor DNA (ctDNA) using the AmoyDx® Comprehensive Assay. Initially intended for cases where tissue biopsy was unfeasible, this study summarizes our experience including analytical validation, biomarker yield, and retrospective clinical utility of this assay.
Methods:
Analytical validation was performed using commercial reference standards with variant allele frequencies between 0% and 5%. Cell-free DNA (cfDNA) was extracted from routine plasma samples and analyzed according to the manufacturer's protocol and optimized filtering thresholds. A total of 559 samples from 501 patients were included in the biomarker yield analysis. Clinical utility was assessed in a subset of 126 patients. Biomarker annotation was retrospectively performed using the Cancer Genome Interpreter. Clinical data were retrospectively obtained via electronic medical record review.
Results:
The assay demonstrated 98% analytical sensitivity for small variants at 0.5% variant allele frequency (VAF), with a limit of detection (95%) at 0.37% VAF and a limit of blank of 0.06% VAF, while demonstrating lower sensitivity for fusions (66% at 0.5% VAF). Mutations corresponding to actionable biomarkers (ASCO Tier 1/A) were identified in 28.6% of samples. CtDNA findings contributed to a documented change in therapy in 11.7% of patients, either by establishing first-line therapy in 6.2% or change in management based on detected actionable alterations in 5.5%. Only 15% of results were explicitly acknowledged in tumor board documentation. Clinical requisitions lacked legible diagnoses in 16% of cases, and an explicit clinical question in 75%.
Conclusion:
The assay demonstrates high analytical validity for small variants at VAF > 0.5% and yields actionable biomarkers in a substantial proportion of cases. However, inconsistent clinical documentation and poor integration into care workflows limit the assessment of its clinical impact. We recommend that the implementation of ctDNA-based CGP in public health settings be accompanied by standardized requisition protocols and mandatory clinical data capture.
