Real-World Application of Trio-Based Exome Sequencing in Prenatal Genetic Diagnosis

Whole exome sequencing (WES) is increasingly employed in the prenatal setting to identify genetic causes of fetal anomalies, particularly when cytogenetic tests such as karyotyping and chromosomal microarray (CMA) return normal results. In this prospective study, we assessed the diagnostic yield of trio-based WES (fetus and both parents) in 249 pregnancies with sonographic findings and prior negative results from quantitative fluorescent PCR (QF-PCR), conducted in parallel with CMA. A molecular diagnosis was established in 26.9% (67/249) of cases. Among these, 58.2% were de novo autosomal-dominant variants, 29.9% were autosomal-recessive (compound heterozygous or homozygous), 9.0% were inherited dominant, and 3.0% were X-linked. Diagnostic yield varied by anomaly category, ranging from 37.5% in growth disorders to 6.3% in gastrointestinal anomalies. The median turnaround time was 12 days, notably shorter than the average turnaround time of 20 days typically of other reports. Identification of a pathogenic variant had a direct impact on clinical management, with pregnancy termination occurring in 54.7% of diagnosed cases compared to 18.1% among those without a diagnosis. Prenatal parallel trio-based WES and CMA following negative QF-PCR results could represent an appropriate and actionable strategy in the current prenatal diagnostic landscape. This approach provides a significantly improved diagnostic yield and faster turnaround time, especially in structurally anomalous pregnancies, thereby delivering meaningful support to families facing complex prenatal decision-making.