Detection of EGFR mutations in non-small cell lung cancer by droplet digital PCR.
Drew F K WilliamsonSean R N MarrisVanesa Rojas-RudillaJacqueline L BruceCloud P PaweletzGeoffrey R OxnardLynette M ShollFei DongPublished in: PloS one (2022)
Activating mutations in EGFR predict benefit from tyrosine kinase inhibitor therapy for patients with advanced non-small cell lung cancer. Directing patients to appropriate therapy depends on accurate and timely EGFR assessment in the molecular pathology laboratory. This article describes the analytical design, performance characteristics, and clinical implementation of an assay for the rapid detection of EGFR L858R and exon 19 deletion mutations. A droplet digital polymerase chain reaction (ddPCR) assay was implemented with probe hydrolysis-dependent signal detection. A mutation-specific probe was used to detect EGFR L858R. A loss of signal design was used to detect EGFR exon 19 deletion mutations. Analytical sensitivity was dependent on DNA input and was as low as 0.01% variant allele fraction for the EGFR L858R assay and 0.1% variant allele fraction for the EGFR exon 19 deletion assay. Correlation of 20 clinical specimens tested by ddPCR and next generation sequencing showed 100% concordance. ddPCR showed 53% clinical sensitivity in the detection of EGFR mutations in plasma cell-free DNA from patients with lung cancer. The median clinical turnaround time was 5 days for ddPCR compared to 13 days for next generation sequencing. The findings show that ddPCR is an accurate and rapid method for detecting EGFR mutations in patients with non-small cell lung cancer.
Keyphrases
- epidermal growth factor receptor
- small cell lung cancer
- tyrosine kinase
- advanced non small cell lung cancer
- high throughput
- loop mediated isothermal amplification
- primary care
- stem cells
- circulating tumor
- single cell
- gene expression
- newly diagnosed
- mesenchymal stem cells
- single molecule
- cell therapy
- prognostic factors
- quality improvement
- patient reported
- smoking cessation
- peritoneal dialysis