A multiplex droplet digital PCR assay for non-invasive prenatal testing of fetal aneuploidies

Higher multiplexing in droplet digital PCR (ddPCR) can simplify the detection process of ddPCR-based non-invasive prenatal testing (NIPT) and improve its reliability, making it a practical approach in clinical practice. However, a high level of multiplex ddPCR-based NIPT has rarely been reported. In this study, we developed a multiplex ddPCR assay using universal locked nucleic acid (LNA) probes to reliably identify fetal aneuploidies. We first performed statistical analysis based on the Poisson distribution to evaluate the required number of target DNA molecules and the total number of droplets for a ddPCR assay. Next, we designed two sets of primers and probes to quantify cfDNA from chromosomes 21 and 18 and then determined the disease status of a sample. Finally, we evaluated our multiplex ddPCR assay with 60 clinical plasma samples. All of the 60 clinical samples were correctly identified. The accessibility and cost-effectiveness of our multiplex ddPCR-based NIPT make it a competitive prenatal testing method in clinical use.