A rapid turnaround time workflow for a cytological liquid biopsy assay using FNA supernatant specimens

Background

Genomic profiling is essential in the management of non–small cell lung cancer. However, this may often be challenging because of limited cytological tissue and extended turnaround time (TAT) for next-generation sequencing (NGS). This study aims to describe a rapid TAT workflow for molecular profiling using fine-needle aspiration (FNA) supernatants.

Methods

A fully automated total nucleic acid extraction using the Genexus Integrated System was compared to a manual extraction using FNA supernatants from 50 patients with non–small cell lung cancer. Molecular profiling using the 50 gene Oncomine Precision Assay GX panel was performed and NGS results were compared with those of paired tissue samples.

Results

The FNA samples processed using the automated Genexus purification system (n = 42) and the manual extraction method (n = 8) showed comparable quality control metrics with a median total nucleic acid yield of 1230 ng (18–17720 ng) and 1068 ng (777–1740 ng), respectively. The Genexus purification system reduced the hands-on time from 120 to 30 minutes, enhancing workflow efficiency and decreasing the overall TAT. Of the 50 samples extracted, NGS was performed on 26 samples: seven via manual extraction and 19 using automated extraction. NGS quality control metrics were also comparable between both extraction methods. The overall TAT of the automated NGS workflow from specimen received to test result was 24 hours, providing rapid and reliable molecular results for timely clinical decision-making and improved patient outcomes.