Expanded noninvasive prenatal screening for dominant single-gene disorders: proof-of-concept, performance, and challenges

Non-invasive prenatal screening for single-gene disorders is an emerging tool that might complement traditional aneuploidy screening by providing earlier, safer insights to invasive diagnostic methods, such as amniocentesis and chorionic villus sampling. However, previous studies were limited by small gene panels and incomplete follow-up data, hindering the accurate assessment of screening performance. This study aimed to demonstrate the technical feasibility and evaluate the potential clinical performance of non-invasive prenatal screening for 202 dominant single-gene disorders using an expanded 155-genes panel in high-risk pregnancies, while also addressing limitations of prior studies, particularly in the calculation of positive predictive value and negative predictive value. We conducted non-invasive prenatal screening for 202 dominant single-gene disorders on 750 maternal plasma samples from pregnant women with definitive ultrasound abnormalities. Unique Molecular Identifiers were used for sequencing error correction. All participants underwent confirmatory prenatal diagnostic testing via whole-genome sequencing or whole-exome sequencing of amniotic fluid samples. Variants identified through non-invasive prenatal screening for single-gene disorders were classified based on allele frequencies, and performance metrics (sensitivity, specificity, positive predictive value, and negative predictive value) were calculated to evaluate the efficacy of the screening approach. Among 750 high-risk pregnancies, non-invasive prenatal screening for 202 dominant single-gene disorders identified 32 positive cases. Subsequent prenatal diagnosis confirmed one false positive and no false negatives, yielding a sensitivity of 100.0% (95% CI, 100.0%-100.0%) and a specificity of 99.9% (95% CI, 99.6%-100.1%). The PPV and NPV were 96.9% and 100.0%, respectively. Notably, 7 (22.6%) confirmed positive cases involved genes not covered in previous screening panels. Variant with a variant allele frequency (VAF) >20% required maternal carrier verification to rule out potential false-positive result. A negative case initially classified as a variant of uncertain significance was reclassified as likely pathogenic following trio WGS/WES analysis. This study demonstrated the technical feasibility and clinical performance of an expanded non-invasive prenatal screening for 202 dominant single-gene disorders in the high-risk cohort. However, this screening panel does not replace the need for invasive diagnostic procedures, particularly for high VAF variants, and confirmatory trio WGS/WES enhanced variant interpretation. Further studies in low-risk populations are needed to assess the clinical utility of this screening and to guide its appropriate integration with existing prenatal screening strategies.