Assessment and clinical utility of a non-Next-Generation Sequencing based Non-Invasive Prenatal Testing technology

Background Rolling circle replication (RCR) is a novel technology that has not been applied to cell-free DNA (cfDNA) testing until recently. Given the cost and simplicity advantages of this technology compared to other platforms currently used in cfDNA analysis, an assessment of RCR in clinical laboratories was performed. Here, we present the first validation study from clinical laboratories utilizing RCR technology. Methods 831 samples from spontaneously pregnant women carrying a singleton fetus and 25 synthetic samples were analyzed for the fetal risk of Trisomy 21, Trisomy 18 and Trisomy 13 by three laboratories on three continents. All women who provided the samples were followed to birth, where evaluation for fetal aneuploidies was performed using newborn examinations and any suspected aneuploidies were confirmed with karyotyping. Results The study found rolling circle replication to be a highly viable technology for clinical assessment of fetal aneuploidies with 100% sensitivity for T21 (95% CI:82.35% - 100.00%); 100.00% sensitivity for T18 (71.51% - 100.00%) and 100.00% sensitivity for T13 analyses (66.37% - 100.00%). The specificities were >99% for each trisomies [99.7% (99.01% - 99.97%) for T21; 99.5% (98.62% - 99.85%) for T18; 99.7% (99.03% - 99.97%) for T13], along with a first pass no-call rate of 0.93%. Conclusions The study showed that using a rolling circle replication-based cfDNA system for the evaluation of the common aneuploidies would provide greater accuracy and clinical utility compared to conventional biochemical screening and comparable results to other reported cfDNA methodologies.