Mass Spectrometry as a Highly Sensitive Method for Specific Circulating Tumor DNA Analysis in NSCLC: A Comparison Study

Abstract

Plasma-based tumor mutational profiling is arising as a reliable approach to detect primary and therapy-induced resistance mutations required for accurate treatment decision making. Here, we compared the FDA-approved Cobas® EGFR Mutation Test v2 with the UltraSEEK™ Lung Panel on the MassARRAY® System on detection of EGFR mutations, accompanied with preanalytical sample assessment using the novel Liquid IQ® Panel. 137 cancer patient-derived cell-free plasma samples were analyzed with the Cobas® and UltraSEEK™ tests. Liquid IQ® analysis was initially validated (n = 84) and used to determine ccfDNA input for all samples. Subsequently, Liquid IQ® results were applied to harmonize ccfDNA input for the Cobas® and UltraSEEK™ tests for 63 NSCLC patients. The overall concordance between the Cobas® and UltraSEEK™ tests was 86%. The Cobas® test detected more EGFR exon19 deletions and L858R mutations, while the UltraSEEK™ test detected more T790M mutations. A 100% concordance in both the clinical (n = 137) and harmonized (n = 63) cohorts was observed when >10 ng of ccfDNA was used as determined by the Liquid IQ® Panel. The Cobas® and UltraSEEK™ tests showed similar sensitivity in EGFR mutation detection, particularly when ccfDNA input was sufficient. It is recommended to preanalytically determine the ccfDNA concentration accurately to ensure sufficient input for reliable interpretation and treatment decision making.

Current status of ctDNA in precision oncology for hepatocellular carcinoma

“…Plasmonic nanoparticles are used in surface-enhanced Raman scattering (SERS) nanosensors for signal-amplification and mutations are identified based on specific Raman spectroscopy [47,48]. For matrixassisted laser desorption/ ionization time of flight mass spectrometry (MALDI-TOF-MS), biotin-labeled extended products are captured and eluted, then dispensed onto bioarrays for spectrum profiles [49]. Relatively, the electrochemical biosensors are more widespread and easier to fabricate, time-and cost-effective, rapidly responsive, and portable.…”

The identification of circulating tumour DNA using MassARRAY technology in non-small-cell lung cancer (NSCLC)

“…Recent work by Lamy et al, 2020 have demonstrated the parallel use of the Cobas® EGFR mutation test. The study highlighted a 86% concordance between the UltraSEEK lung and Cobas® assays with similar sensitivity in EGFR mutation detected, in particular when cfDNA input was similar [20]. Another study performed in melanoma, using the UltraSEEK melanoma panel and digital droplet PCR for the detection of BRAF V600E showed that the UltraSEEK assay was as sensitive as digital droplet PCR [23].…”

“…However, the Qubit was found to detect higher concentrations of cfDNA compared to the Liquid IQ™. Studies have shown strong correlations between the two assays [20].…”

cfDNA Sequencing: Technological Approaches and Bioinformatic Issues

“…The use of a 68 mutations panel on cfDNA from melanoma patients showed the same sensitivity as ddPCR [ 63 ]. In NSCLC, the limit of detection of the UltraSEEK Lung Panel, consists of 73 variants, was 0.125–1% with low input of specific tumoral cfDNA fragments beforehand measured with the LiquidIQ Panel [ 64 ]. Of note, this study showed the importance of preanalytical cfDNA quality control and input amount for the accuracy of liquid biopsy testing.…”