Rapid genomic profiling of circulating tumor DNA in non-small cell lung cancer using Oncomine Precision Assay with Genexus™ integrated sequencer

Abstract

Background: Genomic profiling of tumors from cancer patients facilitates molecular-guided therapy. The turnaround time is one of important issues to deliver results timely for clinical decisions. The Ion Torrent™ Genexus™ Integrated Sequencer automates all next generation sequencing (NGS) workflows and delivers results within a day.

Methods: In this study, we conducted a feasibility study to evaluate the detection rate of genomic alterations from cell-free total nucleic acid (cfTNA, containing cfDNA and cfRNA) of 119 non-small cell lung cancer using Oncomine Precision Assay on Genexus™ Integrated Sequencer. Oncomine Precision Assay (OPA) covers actionable mutations, copy number variations and fusion genes and that are applicable for the selection of targeted therapy. cfTNA isolated from plasma (derived from 14 ml of blood) were subjected to the Genexus system for library construction, templating, sequencing, and data analyses.

Results: The sequencing resulted in median overall depth of 35,773× and median molecular coverage of 2,192× with cfTNA input ranged from 11 to 36 ng. Among the 119 samples evaluated, we detected at least one genomic alteration in plasma cfTNA of 79 cases (66%). When comparing to standard-of-care testing, the sensitivity and specificity of mutation detection in non-small cell lung cancer related genes using liquid biopsy with Genexus-OPA ranged between 49-67% and 93-100%, respectively. 59% of actionable mutations, which were present in tumor tissues, were detected by the Genexus- Oncomine Precision Assay using plasma cfTNA. Among the 5 mutations detected from liquid biopsy only, three mutations are of level 1 evidence according to OncoKB database, highlighting the clinical utilities of liquid biopsy in addressing tumor heterogeneity. Extrathoracic metastasis and levels of lactate dehydrogenase (LDH), C-reactive protein (CRP) and Carcinoembryonic Antigen (CEA) are found to be associated with increased circulating tumor DNA detection.

Conclusions: The Genexus™ Integrated Sequencer system is an automated, accurate NGS system with short turnaround time (TAT) that could assist clinicians to make more timely decision.

Keywords: Non-small cell lung cancer (NSCLC); actionable mutation; circulating tumor DNA; liquid biopsy; next generation sequencing (NGS).

Figure 1

Genomic landscape of ctDNA analysis with Genexus-OPA system in 119 NSCLC patients. (A) Heatmap showing SNV, CNV and fusions detected; (B) frequencies (%) of ctDNA detection in individual genes. Ad, adenocarcinoma; ctDNA, circulating tumor DNA; Sq, squamous cell carcinoma; NSCLC, non-small cell lung carcinoma, not otherwise specified; LCNEC, large cell neuroendocrine carcinoma; p-Stage, pathological stage; Rec, recurrence; SNV, single nucleotide variant; CNV, copy number variations; VAF, variant allele frequency; NOS, XXXX.

Figure 2

The concordance of genomic alteration detected from Genexus-Oncomine Precision Assay (Genexus-OPA) and standard-of-care (SOC) tumor tissue testing. cfTNA, cell-free total nucleic acids.

Figure 3

Various parameters that are associated ctDNA detection rate (A) Level of cfDNA concentration (ng/mL of plasma) and (B) white blood cell (WBC), lactate dehydrogenase (LDH), C-reactive protein (CRP) and carcinoembryonic antigen (CEA) levels. ctDNA, circulating tumor DNA; cfTNA, cell-free total nucleic acids.