Key Clinical Summary:

• Cell-free nucleic acid (cfNA) sequencing via Ion Torrent platforms successfully identified DNA variants across all NSCLC stages (I–IV).
• Among 5668 samples, 1940 (34%) harbored detectable variants—most frequently TP53 and KRAS, followed by EGFR exon 19 deletions.
• The AmpliSeq HD and Genexus workflow enabled high-throughput, low-input, and precise cfNA analysis for clinical applications.

Researchers using Ion Torrent next-generation sequencing (NGS) technology have demonstrated the feasibility of detecting clinically relevant DNA variants from cell-free nucleic acids (cfNA) in non-small cell lung cancer (NSCLC). The study, conducted using Genexus purification and sequencing systems, highlights the potential of liquid biopsy approaches for noninvasive tumor profiling and monitoring across disease stages.

In this large-scale retrospective analysis, cfNA was isolated from plasma samples collected in K₂-EDTA tubes from NSCLC patients spanning stages I through IV. Using the Genexus Cell-Free Total Nucleic Acid Purification Kit and sequenced via Ion Torrent AmpliSeq HD target amplification assays, investigators evaluated two gene panels: the Oncomine Precision Assay (OPA) covering 50 genes and 2769 variants, and a new developmental panel targeting 49 genes and 2159 variants—including ALK, BRAF, EGFR, KRAS, and ROS1.

The study analyzed 5668 plasma specimens, with 1940 (34%) demonstrating detectable DNA variants. Among these, 42.5% originated from stage IV, 33% from stage III, 19% from stage II, and 14% from stage I disease. The cohort was 69% male and 31% female. The average mapped read depth ranged from 7–13 million reads, with an average read length of 93 base pairs, confirming high sequencing fidelity.

The most frequently detected variants were TP53 and KRAS, followed by EGFR exon 19 deletions and EGFR single nucleotide variants. Serial whole blood samples collected from the same donors over time revealed an increase in variant allele frequencies, suggesting the potential of cfNA monitoring for tracking disease progression or therapeutic response.

The findings support the clinical viability of cfNA-based NGS for real-time molecular profiling in NSCLC. Compared with tissue biopsy, cfNA sequencing offers advantages including reduced invasiveness, improved representation of tumor heterogeneity, and the ability to monitor molecular evolution through serial sampling.

By integrating AmpliSeq HD assays with the Genexus sequencing platform, laboratories can achieve high-throughput, automated analysis with minimal manual input—reducing turnaround time while maintaining analytical sensitivity and specificity. This workflow could enhance precision oncology, enabling clinicians to detect actionable mutations such as EGFR, KRAS, and ALK variants earlier and guide targeted therapy decisions more efficiently.

This large-scale evaluation confirms that cfNA sequencing using AmpliSeq HD and Genexus systems is a rapid, accurate, and scalable approach for variant detection in NSCLC. The results strengthen the role of liquid biopsy in advancing personalized cancer care and improving early detection and treatment monitoring.

Source:

Jasti M, Hassell D, Bigley A, et al. The Genomic Landscape of Non-Small Cell Lung Cancer Plasma Samples, Determined by Cell-Free Nucleic Acid Analysis Using AmpliSeq HD Assays. Presented at the 2025 AMP Annual Meeting & Expo. November 11-15, 2025; Boston, Massachusetts. ST148