Prenatal genetic diagnosis of fetal ventricular septal defects: diagnostic yield, genomic hotspots and pregnancy outcomes

Ventricular septal defects (VSDs) are the most prevalent congenital cardiovascular anomalies, with genetic factors playing a significant role in the pathogenesis. This study aimed to investigate chromosomal copy number variants (CNVs) in fetal VSDs and explore the genotype-phenotype correlation. A cohort of 258 fetuses with prenatally diagnosed VSDs were enrolled between October 2018 and June 2022. All cases underwent simultaneous karyotyping and chromosomal microarray analysis (CMA). According to the presence/absence of other ultrasound abnormalities, VSDs were divided into isolated VSDs, VSDs with other cardiac/great vessel anomalies, VSDs with extra-cardiac structural anomalies, and VSDs with both cardiac and extra-cardiac anomalies; and into advanced maternal age (AMA, ≥ 35 years) and non-AMA groups based on maternal age for subgroup analysis. A pooled analysis of chromosomal numerical abnormality and likely pathogenic/pathogenic CNVs in fetal VSDs was also performed. Functional enrichment and pathway analysis for genes in LP/P CNVs from isolated VSDs cases were performed using clusterProfiler package in R 3.6.3. Then pregnancy and postnatal outcomes were followed up. The detection rate of chromosomal abnormalities by karyotyping was 5.0% (13/258), whereas CMA identified likely pathogenic/pathogenic CNVs in 7.0% (18/258) of cases. The total detection rate by both methods was 7.8% (20/258). The detection rate of genomic abnormalities was significantly different across VSDs subgroups ( P <0.001), with the highest rate observed in VSDs combined with both cardiac and extra-cardiac anomalies (37.5%). The advanced maternal age (AMA) group showed a higher detection rate than the non-AMA group, but without statistical significance ( P > 0.05). Among 253 cases with follow-up, 44 were terminated and 209 were delivered. Cases with positive results from both CMA and karyotyping had a higher termination rate than those with single positive or negative results ( P < 0.001). Pooled analysis identified 22q11.21 deletion, 16p12.2 deletion and 22q11.21 duplication as the top three hotspot CNVs in fetal isolated VSDs. Functional enrichment analysis showed that these genes were significantly enriched in cGMP‑PKG, calcium signaling, and circulatory system development pathways. CMA yields an additional 2.7% incremental diagnostic yield over karyotyping in fetuses with VSDs. Combined CMA and karyotyping is effective for identifying the genetic etiology of VSDs. The identified CNVs hotspots enable more precise genetic counseling for VSDs pregnancies. VSDs pathogenesis may involve multiple cardiac‑related signaling pathways, which provides a theoretical basis for understanding the genotype-phenotype correlation for VSDs.