Objective:To investigate genetic findings and pregnancy outcomes in fetuses with omphalocele.Methods:This retrospective study analyzed data from 502 fetuses with prenatally diagnosed omphalocele who underwent genetic testing at Guangzhou Women and Children's Medical Center and Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region between January 2014 and March 2024. Testing methods included karyotyping, chromosomal microarray analysis (CMA), methylation-specific multiplex ligation-dependent probe amplification, and whole-exome sequencing (WES). Cases were categorized as non-isolated ( n=340) or isolated ( n=162) based on ultrasound findings. Differences in genetic abnormality detection rates and pregnancy outcomes were analyzed using Mann-Whitney U test, independent samples t-test, and Chi-square test (or Fisher's exact test). Results:Among 502 fetuses, karyotyping plus CMA detected chromosomal abnormalities in 223 cases (44.4%, 223/502), including trisomy 18 (57.0%, 127/223) and trisomy 13 (23.3%, 52/223). CMA additionally identified nine pathogenic copy number variations (1.8%, 9/502) and five uniparental disomies (1.0%, 5/502), increasing the total diagnostic yield from 44.4% to 47.2%. The genetic abnormality rate was significantly lower in isolated (14.8%, 24/162) versus non-isolated omphalocele (64.7%, 220/340) ( χ2=109.34, P<0.001). WES detected variants in nine of 16 karyotype/CMA-negative cases, including five pathogenic variants involving PIK3CA and CDKN1C. Eight imprinting disorders (1.6%, 8/502) were identified, including five Beckwith-Wiedemann syndrome cases. Among 499 cases with follow-up, 401 (80.4%, 401/499) underwent pregnancy termination. Live birth rate was higher in isolated versus non-isolated groups [42.5% (69/162) vs. 8.5% (29/340), χ2=77.67, P<0.001]. Three cases were lost to follow-up. The one-year survival rate was 93.9% (92/98) in live-born infants. Conclusion:Aneuploidy (particularly trisomy 18) is the primary genetic etiology of omphalocele. CMA and WES significantly improve diagnostic yield. Isolated omphalocele has a more favorable prognosis, while non-isolated cases show significantly higher genetic abnormality rates. A stratified testing strategy is recommended: karyotyping plus CMA for isolated cases and prioritization of WES for multiple anomalies.

Objective:To investigate genetic findings and pregnancy outcomes in fetuses with omphalocele.Methods:This retrospective study analyzed data from 502 fetuses with prenatally diagnosed omphalocele who underwent genetic testing at Guangzhou Women and Children's Medical Center and Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region between January 2014 and March 2024. Testing methods included karyotyping, chromosomal microarray analysis (CMA), methylation-specific multiplex ligation-dependent probe amplification, and whole-exome sequencing (WES). Cases were categorized as non-isolated ( n=340) or isolated ( n=162) based on ultrasound findings. Differences in genetic abnormality detection rates and pregnancy outcomes were analyzed using Mann-Whitney U test, independent samples t-test, and Chi-square test (or Fisher's exact test). Results:Among 502 fetuses, karyotyping plus CMA detected chromosomal abnormalities in 223 cases (44.4%, 223/502), including trisomy 18 (57.0%, 127/223) and trisomy 13 (23.3%, 52/223). CMA additionally identified nine pathogenic copy number variations (1.8%, 9/502) and five uniparental disomies (1.0%, 5/502), increasing the total diagnostic yield from 44.4% to 47.2%. The genetic abnormality rate was significantly lower in isolated (14.8%, 24/162) versus non-isolated omphalocele (64.7%, 220/340) ( χ2=109.34, P<0.001). WES detected variants in nine of 16 karyotype/CMA-negative cases, including five pathogenic variants involving PIK3CA and CDKN1C. Eight imprinting disorders (1.6%, 8/502) were identified, including five Beckwith-Wiedemann syndrome cases. Among 499 cases with follow-up, 401 (80.4%, 401/499) underwent pregnancy termination. Live birth rate was higher in isolated versus non-isolated groups [42.5% (69/162) vs. 8.5% (29/340), χ2=77.67, P<0.001]. Three cases were lost to follow-up. The one-year survival rate was 93.9% (92/98) in live-born infants. Conclusion:Aneuploidy (particularly trisomy 18) is the primary genetic etiology of omphalocele. CMA and WES significantly improve diagnostic yield. Isolated omphalocele has a more favorable prognosis, while non-isolated cases show significantly higher genetic abnormality rates. A stratified testing strategy is recommended: karyotyping plus CMA for isolated cases and prioritization of WES for multiple anomalies.