Comparative Evaluation of Three Next Generation Sequencing - Based Non-Invasive Prenatal Testing Platforms in a Private South African Laboratory

The demand for non-invasive prenatal testing (NIPT) has increased significantly over the past decade. Numerous next-generation sequencing (NGS)-based platforms, including YourGene IONA®, Medicover VERACITY™, and Illumina VeriSeq™, have been developed. This study aimed to evaluate and compare the clinical utility, performance, and operational experience of these three NIPT platforms implemented at the Genetics Department, National Reference Laboratory, Ampath Laboratories, South Africa, between 2017 and 2024. A retrospective analysis of 3,000 anonymised NIPT samples, comprising 1,000 samples per platform, was undertaken to compare performance. Separately, demographic and clinical data were collected for an additional 2,000 samples, irrespective of platform. Descriptive statistics and chi-squared analyses were used to assess significance. All three platforms reliably detected the common trisomies. The overall dataset showed an average gestational age of 16.3 weeks and an average maternal age of 34.7 ± 4.8 years. Of the 58 high-risk pregnancy results identified, 42 (72%) occurred in women aged 35 years and older. Trisomy 21 accounted for 35 (60%) of these cases. This comparative analysis of three NIPT platforms within a single South African diagnostic laboratory highlight both the strengths and operational challenges of implementing NGS-based prenatal screening in a private healthcare setting. All platforms demonstrated reliable detection of common trisomies; however, variations in workflow efficiency, failure rates, cost-effectiveness, workflow logistics and clinical performance were observed. The results reinforce the influence of AMA on the risk of fetal aneuploidy, while also emphasising the need for accessible, cost-effective solutions in resource-limited environments. These findings provide important guidance for selecting NIPT platforms suited to varying clinical and socioeconomic environments, particularly in resource-limited settings