| Test modality | When to use in prenatal omphalocele | Diagnostic yield / typical findings | Example abnormalities detected or targeted | Supporting sources |
|---|---|---|---|---|
| Conventional karyotype | Recommended routinely once fetal omphalocele is diagnosed prenatally, especially for non-isolated cases or when additional ultrasound abnormalities are present | Detects aneuploidy and large structural chromosome abnormalities; in one 2023 cohort, 35 patients underwent karyotype+CMA and 5/35 (14.3%) had chromosomal abnormalities; all abnormal karyotypes were in non-isolated cases | Trisomy 18 (3 cases), trisomy 13 (1 case), trisomy 21 is a recognized recurrent association, chromosome 8;11 translocation (1 case) (pqac-00000012, pqac-00000013, pqac-00000027) | (pqac-00000012, pqac-00000013, pqac-00000027) |
| Chromosomal microarray (CMA) | Recommended together with karyotype as first-line prenatal genetic testing for omphalocele; useful when ultrasound suggests associated anomalies and for clarifying submicroscopic CNVs | Adds genome-wide CNV detection beyond karyotype; in the Que et al. cohort, CMA was performed with karyotype in 35 cases and was normal in 6 selected non-isolated cases later escalated to WES; parental blood/pedigree analysis is recommended when CMA yields VUS | Can detect pathogenic/likely pathogenic CNVs not visible on karyotype; examples in the cohort were mainly normal CMA followed by WES escalation rather than specific recurrent CNVs reported in the excerpt (pqac-00000012, pqac-00000014, pqac-00000015) | (pqac-00000012, pqac-00000014, pqac-00000015) |
| QF-PCR | Rapid adjunct test when rapid confirmation of common aneuploidies is needed, particularly if trisomy is strongly suspected on ultrasound | Fast targeted confirmation rather than genome-wide discovery; highlighted as useful for rapid confirmation of trisomy 13 in review evidence | Trisomy 13, and by standard panel use also common autosomal trisomies such as T18/T21 when suspected (pqac-00000000) | (pqac-00000000) |
| Whole exome sequencing (WES) | Consider when karyotype and CMA are normal, especially in non-isolated omphalocele or persistent suspicion of syndromic/genetic disease | In Que et al., 6 non-isolated cases with normal karyotype/CMA underwent WES and 3/6 had abnormal findings (1 pathogenic, 2 suspected pathogenic); review evidence notes WES may increase diagnostic yield by ~8–10% after normal karyotype/CMA | COL2A1 c.2759C>A (p.Pro920His), SCP2 c.674+1G>C, SDHB c.725G>A (p.R242H); review also notes WES is an option after normal karyotype/CMA and may improve yield (pqac-00000012, pqac-00000013, pqac-00000014, pqac-00000015, pqac-00000000) | (pqac-00000012, pqac-00000013, pqac-00000014, pqac-00000015, pqac-00000000) |
| Stepwise prenatal testing strategy | Practical recommendation for current care pathways in prenatally diagnosed omphalocele | Start with karyotype + CMA because aneuploidy risk is elevated; escalate to WES if first-line testing is normal; if all are normal but phenotype remains suggestive, additional syndrome-specific testing may be needed | Common prenatal genetic associations include T13, T18, T21; structural rearrangements such as t(8;11); monogenic findings by WES may include COL2A1, SCP2, SDHB; if karyotype/CMA/WES are normal, additional testing may be required to evaluate disorders such as Beckwith-Wiedemann syndrome (pqac-00000012, pqac-00000015, pqac-00000000) | (pqac-00000012, pqac-00000015, pqac-00000000) |


*Table: This table summarizes the main prenatal genetic testing modalities used for omphalocele, when each is recommended, and the kinds of abnormalities they can detect. It is useful for structuring a diagnostic workflow from aneuploidy testing through exome sequencing in isolated and non-isolated cases.*