Rapid genomic profiling of circulating tumor DNA in non-small cell lung cancer using Oncomine Precision Assay with GenexusTM 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.

Circulating Tumor DNA correlates with Lactate Dehydrogenase, CYFRA 21-1, and CRP levels in patients with advanced NSCLC

“…Their study included only 14 patients (just 7 of which were adenocarcinomas), however, and therefore, although they observed a certain trend in the relationship between elevated CEA and ctDNA, their results did not reach statistical significance. The largest study we have found is the aforementioned study by Low et al, who describe the correlation between ctDNA positivity and CEA 27 . In their study, they found ctDNA in 79 patients, the majority of whom had adenocarcinomas.…”

“…A similar relationship between LDH and ctDNA also has been described for Hodgkin's lymphoma and colorectal cancer 25 , 26 . However, the relationship between laboratory parameters and ctDNA in NSCLC had not been investigated until a recent study by Low et al brought the first results on this topic 27 . Using a similar number of patients as did we (n = 79), they investigated the relationship between ctDNA and LDH, CRP, or white blood cells (WBC).…”

Circulating Tumor DNA-Based Genomic Profiling Assays in Adult Solid Tumors for Precision Oncology: Recent Advancements and Future Challenges

“…The expected TAT for the currently commercially available ctDNA CGP assays is within 7-10 days [87,88], which coincides with the current observations. However, the current TAT can potentially be further shortened with a more flexible and decentralized sequencing system, which can be placed at the point of care and operated with minimal technical supervision [89][90][91]. Such an automated NGS system would need further analytical and clinical validation for its use in clinical settings.…”

Liquid biopsies come of age in lung cancer

“…In the current issue of Translational Lung Cancer Research, Low et al offer us another glimpse of how wonderful a LBdominated world of non-small-cell lung cancer (NSCLC) management could become in the near future (1). "Rapid genomic profiling of circulating tumor DNA" would ensure molecular results before treatment start for every single lung cancer patient, including those 25% with insufficient tissue samples (2), as well as many others hampered by high procedural risk, hardly accessible tumors, and lack of local expertise.…”

“…Of note, technical failures were infrequent in this study, i.e., <10% (11/119) at first sequencing attempt, and could all be "salvaged" by resequencing on Ion 540 chips, which have equivalent reads with GX5 chips on the Ion S5 Prime system (1). However, an important problem of most current LB platforms, including that employed by Low et al, is limited sensitivity, with a minimum detectable variant allelic fraction (VAF) of 0.1-0.01%, which will miss up to approximately 1/3 of mutations found in tissue NGS (1). Therefore, an optimal strategy to maximize diagnostic yield today would be the complementary use of both tissue and LB (7).…”