Abstract
Cell‐free plasma DNA (cfDNA) and mimicking circulating tumor cells (mCTCs) have demonstrated tremendous potential for molecular diagnosis of cancer and have been rapidly implemented in specific settings. However, widespread clinical adoption still faces some obstacles. The purpose was to compare the performance of a BEAMing (beads, emulsion, amplification, and magnetics) assay (OncoBEAM™‐epidermal growth factor receptor [EGFR] [Sysmex Inostics]) and a next‐generation sequencing assay (NGS; 56G Oncology panel kit, Swift Bioscience) to detect the p.T790M EGFR mutation in cfDNA of non‐small cell lung cancer (NSCLC) patients. CfDNA samples (n = 183) were collected within our hospital from patients having a known EGFR sensitizing mutation, and presenting disease progression while under first‐line therapy. EGFR mutations were detected using NGS in 42.1% of samples during progression in cfDNA. Testing using the OncoBEAM™‐EGFR assay enabled detection of the p.T790M EGFR mutation in 40/183 NSCLC patients (21.8%) versus 20/183 (10.9%), using the NGS assay. Samples that were only positive with the OncoBEAM™‐EGFR assay had lower mutant allelic fractions (Mean = 0.1304%; SD ± 0.1463%). In addition, we investigated the detection of p.T790M in mCTCs using H1975 cells. These cells spiked into whole blood were enriched using the ClearCellFX1 microfluidic device. Using the OncoBEAM™‐EGFR assay, p.T790M was detected in as few as 1.33 tumoral cells/mL. Overall, these findings highlight the value of using the OncoBEAM™‐EGFR to optimize detection of the p.T790M mutation, as well as the complementary clinical value that each of the mutation detection assay offers: NGS enabled the detection of mutations in other oncogenes that may be relevant to secondary resistance mechanisms, whereas the OncoBEAM™‐EGFR assay achieved higher sensitivity for detection of clinically actionable mutations.
Highlights
Knowledge of the molecular complexity of cancers and the role of oncogenic drivers such as mutations in genes encoding the Epidermal Growth Factor Receptor (EGFR) has flourished in the era of targeted therapies.[1,2] Molecular profiling of a cancer patient's tumor to reveal targetable alterations is an important first step in the personalization of cancer treatment plans
The objective of the present study was to assess the utility of detecting mutations in circulating tumor DNA (ctDNA) and in mimicking circulating tumor cells using the digital polymerase chain reaction (PCR) OncoBEAMTM‐EGFR assay compared to next‐generation sequencing (NGS)‐56G to detect the p.T790M EGFR mutation in paired samples
To assess the specificity and sensitivity of the OncoBEAMTM‐EGFR assay for p.T790M detection, WT and mutated p.T790M EGFR Horizon Cell‐free plasma DNA (cfDNA) controls were used at different allelic frequencies (0.1% and 1% mutant allele fraction (MAF)) (Figure 1)
Summary
Knowledge of the molecular complexity of cancers and the role of oncogenic drivers such as mutations in genes encoding the Epidermal Growth Factor Receptor (EGFR) has flourished in the era of targeted therapies.[1,2] Molecular profiling of a cancer patient's tumor to reveal targetable alterations is an important first step in the personalization of cancer treatment plans. The proportion of patients with detectable ctDNA varies by indication,[14] stage of disease,[15] tumor burden, tumor location and other biological characteristics that may be unrelated to the tumor.[16,17] In EGFR‐ mutated NSCLC patients who progress during first‐line TKI treatment, the frequency of false‐negative results for p.T790M detection in ctDNA remains high (approximately 20%‐30%) This is in part due to limited levels of ctDNA and is highly dependent on the method used for mutational analysis.[18,19] Given these considerations, the objective of the present study was to assess the utility of detecting mutations in ctDNA and in mimicking circulating tumor cells (mCTCs) using the digital PCR OncoBEAMTM‐EGFR assay compared to NGS‐56G to detect the p.T790M EGFR mutation in paired samples. | 3687 using the ClearCell FX device (Biolidics Limited, Science Park, Singapore 118257)
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