Analytical validation of a rapid next generation sequencing-based liquid biopsy assay using fine needle aspiration supernatants for clinical use

Introduction: Genomic profiling for patients with solid tumors using conventional tissue-based next-generation sequencing (NGS) usually takes several weeks and can delay timely initiation of targeted therapies. Further, patients may often lack adequate tissue for NGS that is needed to guide therapeutic decisions. Fine needle aspiration supernatants (FNA-Sup), a routinely discarded component of cytology specimen processing, contains tumor-derived cell-free nucleic acids and offers an alternative liquid biopsy source that bypasses these limitations. This study validates a rapid NGS assay using FNA-Sup for clinical use. Materials and methods: We extended a previously validated plasma-based liquid biopsy assay to FNA-Sup samples (N = 22) utilizing the Oncomine Precision Assay on the Genexus Integrated Sequencer. For accuracy studies, results were compared to the patient’s known tissue-based NGS profiling performed on the paired specimen. Performance metrics including sensitivity, specificity, accuracy, and precision for the detection of single-nucleotide variants, insertions/deletions, and gene fusions were evaluated. Results: The assay demonstrated 100% sensitivity, specificity, and accuracy for single-nucleotide variants and insertions/deletions (variant allele frequencies ≥0.5%) and for gene fusions. All inter-run, intrarun, interinstrument, and interoperator precision studies met the acceptance criteria (≥90% concordance with reference method). Specimen stability of FNA-Sup was established up to day 7 postcollection. Conclusions: Our study shows FNA-Sup, a routinely discarded cytology substrate, are analytically suitable for NGS-based testing. Integration of cytology-derived liquid biopsy into the clinical workflow expands access to molecular testing when tissue is limited and when rapid test results are needed. The automated workflow of the platform can support rapid molecular diagnostics within a single day from specimen receipt to test results.