A comparative study of ddPCR and sanger sequencing for quantitative detection of low-frequency mutation rate

Abstract

Mutation detection has been applied to the entire diagnostic system of prevention, diagnosis, treatment, monitoring, and prognosis. However, owing to the limit of the technology, the low-frequency mutations are often identified as the false negative. Hence, this study focused on the comparison of Sanger sequencing and droplet digital PCR (ddPCR) in the quantitative detection of low-frequency mutation rate. The drug-induced deafness was chosen as the target for comparison, and the simulated samples and 15 clinical samples were detected respectively. The difference between the two methods was comprehensively analyzed in terms of repeatability, accuracy, dynamic detection range and concordance. The results showed that Sanger sequencing took advantage of acceptable cost, new mutations' discovery, and high-Throughput detection, while ddPCR performed better, especially in the detection of low-frequency mutations. In summary, this study compares in detail the merits and demerits of Sanger sequencing and ddPCR in the quantitative detection of low-frequency mutations, offering the potential to promote the further development of technology.