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.

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.

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%.

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.