Non-invasive prenatal testing for dominant single-gene disorders using targeted next-generation sequencing

Current noninvasive prenatal testing (NIPT) based on cell-free DNA (cfDNA) mainly targets the detection of chromosome aberrations but not dominant single-gene disorders (dSGDs). This prospective pilot study aims to evaluate the clinical utility of a plasma cfDNA and targeted next-generation sequencing-based NIPT approach for dSGDs (NIPT-dSGD), with a particular focus on neurodevelopmental disorders (NDDs). The NIPT-dSGD method targeted 34 genes, including 25 correlated to NDDs and nine correlated to Noonan spectrum, skeletal, craniosynostosis, and other syndromic disorders. Retrospective samples first validated NIPT-dSGD and then performed for a prospective cohort of 567 pregnant women seeking NIPT-dSGD. The testing results were compared to invasive prenatal or postnatal genetic diagnosis by whole-exome sequencing and Sanger sequencing. Of the 535 samples with qualified NIPT-dSGD analysis, 11 (2.1%) had one pathogenic or likely pathogenic variant in one of the 34 genes. Three of the 11 variants were paternally inherited, and eight were de novo. Five positive cases had normal ultrasound parameters, and three of them had disease-causing variants in NDD genes. Particularly, one family had two pregnancies with de novo variants of two different genes (GRIN2B: c.1606G>A and ARID1B: c.6100A>G). NIPT-dSGD did not generate any false-positive or negative results, achieving 100% of sensitivity (95% CI, 71.7%-100%) and 100% of specificity (95% CI, 99.0%-100%). NIPT-dSGD provides accurate genetic testing for de novo and paternally inherited variants of dominant genes, including those that do not cause any ultrasound abnormalities, which could assist clinicians and families in better pregnancy management.