Developing Ultrasensitive Library-Aliquot-Based Droplet Digital PCR for Detecting T790M in Plasma-Circulating Tumor...

A T790M secondary mutation in epidermal-growth-factor receptor (EGFR) is the most well-established EGFR-tyrosine-kinase-inhibitor (TKI) resistance marker in non-small-cell lung cancer (NSCLC). The current methods to rapidly and accurately detect T790M in clinical practice are not satisfactory because of several obstacles, including the unavailability of tumor-tissue rebiopsies and the low DNA copy number of T790M in circulating tumor DNA (ctDNA). Here, we develop library-aliquot-based droplet digital PCR (LAB-ddPCR) to increase detection sensitivity without affecting accuracy. This new LAB-ddPCR method is performed using aliquots of the ctDNA precapture next-generation-sequencing (NGS) library, in which the isolated ctDNA was amplified and enriched. We show that the LAB-ddPCR can precisely distinguish between T790M wild-type and mutation alleles without introducing extra false-positive signals. In a cohort of 70 post-TKI NSCLC patients, the LAB-ddPCR identified 41 T790M-positive cases (sensitivity 58.57%), but ddPCR only detected T790M in 27 cases (sensitivity 38.57%). Taking the ARMS-PCR result from matched tumor rebiopsies into consideration, the LAB-ddPCR method is better than ddPCR. In conclusion, the LAB-ddPCR ctDNA test offers a feasible and flexible option for the rapid and accurate detection of the T790M secondary mutation, which is helpful in dynamically monitoring drug response and disease progression throughout the therapeutic regimen.