Validation and clinical evaluation of a comprehensive circulating tumor DNA assay for genomic profiling in solid tumors

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 the analytical validation, biomarker yield, and retrospective clinical utility of this assay. Methods Cell-free DNA (cfDNA) was extracted from routine plasma samples and analyzed according to the manufacturer’s protocol. A total of 485 samples from 438 patients were included in the biomarker yield analysis. Clinical utility was assessed in a subset of 126 patients. Biomarker annotation was performed using the Cancer Genome Interpreter. Clinical data were 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 blank of 0.06% VAF. Actionable biomarkers (ASCO Tier 1/A, including pertinent negative findings) were identified in 27.4% of samples. In regard to clinical utility, 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 molecular tumor board (MTB) documentation. Clinical requisitions lacked legible diagnoses in 16% of cases, and an explicit clinical question in 75%. Conclusion The assay demonstrates high analytical validity 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.