Application of chromosomal microarray analysis and trio whole-exome sequencing in first-trimester prenatal diagnosis for high-risk pregnancies

This study aimed to evaluate and compare the clinical utility of chromosomal microarray analysis (CMA) and trio whole-exome sequencing (trio-WES) in a consecutive cohort of high-risk pregnant women who underwent chorionic villus sampling (CVS), as well as to develop a stratified diagnostic strategy based on first-trimester pregnancy indications. This single-center retrospective cohort study included 338 singleton pregnancies that underwent CVS during the first trimester (11+ 0-13+ 6 weeks of gestation) between December 2023 and April 2025. High-risk pregnancies were defined by the presence of at least one of the following criteria: (1) advanced maternal age (AMA); (2) ultrasound detection of one or more soft markers or structural fetal anomalies; (3) abnormal first-trimester serum screening results; or (4) a history of adverse obstetric outcomes. Each chorionic villus sample underwent CMA using the Affymetrix CytoScan 750 K chip following DNA extraction, and 25 cases presenting with ultrasound abnormalities were subsequently analyzed using trio-WES on the MGISEQ-2000/DNBSEQ-T7 platform. Pregnancy outcomes and management decisions were prospectively monitored. Among the 338 patients, CMA identified chromosomal abnormalities in 56 cases (16.6%), including 23 cases of aneuploidy and 33 cases of copy number variation (CNV). The detection rate was significantly higher in the ultrasound abnormality group compared to the high-risk group identified through first-trimester serum screening (25.3% vs. 7.1%, p < 0.001). Within the ultrasound abnormality group, chromosomal abnormalities were most frequently observed in fetuses exhibiting both soft markers and structural anomalies (9/20, 45%). Moreover, the incidence of chromosomal abnormalities was higher among fetuses with nuchal translucency (NT) ≥ 4.5 mm and choroid plexus cystic hygroma (CH) (42.9% and 35.7%, respectively), though these differences were not statistically significant. Among CMA-negative cases with abnormal ultrasound findings, trio-WES identified an additional 5 of 22 (22.7%) genetic abnormalities, with a single-gene disease detection rate of 37.5% (3/8) in cases of multisystem malformations. The likelihood of single-gene disorders was significantly increased in pregnancies with NT ≥ 4.5 mm or multisystem malformations. Genetic findings had a substantial impact on clinical decision-making: termination rates were 95.7% (22/23) for aneuploidy, 50.0% (6/12) for pathogenic/likely pathogenic (P/LP) CNVs, and 100% (5/5) for P/LP monogenic variants identified by WES. Conversely, pregnancies with normal results had an 80.4% live birth rate, representing 94.4% of followed-up cases with normal findings. CMA remains essential for first-trimester prenatal diagnosis, while trio-WES provides a significant advantage in detecting single-gene disorders, particularly in fetuses with severe ultrasound anomalies. The strong association between genetic results and clinical decision-making highlights the clinical value of the proposed stratified diagnostic approach, offering evidence-based recommendations for optimizing first-trimester prenatal diagnostic strategies.