Genetic diagnosis in fetal hydronephrosis: assessment using chromosomal microarray analysis and whole-genome sequencing

Abstract Background Antenatal hydronephrosis (AHN) is a common urological abnormality identified during prenatal ultrasound examination, with heterogeneous underlying causes. This study aimed to investigate the genetic etiologies of AHN using chromosomal microarray analysis (CMA) and whole-genome sequencing (WGS), and to identify the relationship between changes in AHN severity and genetic abnormalities. Methods Fetuses with AHN underwent CMA, followed by retrospective WGS. Detection rates of chromosomal abnormalities and monogenic variants were compared among different AHN types and between fetuses with downgraded versus persistent or upgraded hydronephrosis. A variant of uncertain significance (VUS) affecting a splice site was functionally validated using a minigene-splicing assay, leading to reclassification. Results Chromosomal abnormalities were detected in five of 54 fetuses (9.26%) using CMA, while WGS identified monogenic variants and chromosomal abnormalities in 10 of 54 (18.52%). The detection rate was significantly higher in AHN with extrarenal system malformations than in isolated AHN or AHN with renal tract malformations (p < 0.05). Fetuses with downgraded AHN had a lower detection rate (6.25%) than those with persistent or upgraded hydronephrosis (23.68%, p = 0.249). A novel GREB1L splice-site variant (c.2557G > A) caused aberrant splicing and was reclassified as likely pathogenic. Conclusions WGS demonstrates higher diagnostic efficiency over CMA for AHN. Persistent or worsening AHN warrants timely genetic testing, and functional assays are critical for resolving VUS in prenatal diagnosis.