Congenital heart disease (CHD) is the most common congenital malformation, and its incidence is approximately 5–8 per 1000 live births [1, 2]. This malformation not only affects the quality of life of patients but also leads to severe cardiovascular complications; it may even become life-threatening. In prenatal diagnosis, fetal CHD can be primarily detected by traditional ultrasound examination. Simple CHD can be cured through surgery, thereby allowing patients to achieve a normal and healthy life. For complex CHD, a small portion of cases with poor prognosis may not respond well to surgery, but most patients can attain a good quality of life after surgery and live as healthily as individuals without a heart disease. However, genetic abnormalities frequently result in poor outcomes [3, 4], thereby highlighting the importance of genetic testing. Recently, with advancements in genomic technologies, the use of chromosomal microarray analysis (CMA) and exome sequencing (ES) in prenatal diagnosis has increased [5, 6, 7, 8]. CMA offers significantly enhanced resolution for detecting copy number variations (CNVs), enabling the identification of even submicroscopic alterations that are typically under 5–10 Mb in size [9]. CMA has been established as a gold standard in prenatal genetic testing, offering unrivaled sensitivity for detecting CNVs underlying fetal developmental delay and structural malformations [10]. The diagnostic value of CMA for CHDs with different cardiac phenotypes and extracardiac abnormalities has been evaluated [11]. ES has revolutionized diagnostic protocols by providing comprehensive analysis of the protein-coding genome in fetuses with CHDs [12]. These techniques can efficiently detect microvariations and single-gene mutations in the genome; thus, they can enhance the diagnostic accuracy and molecular genetic understanding of fetal CHD.

Despite the existence of numerous studies in this area, simple and complex CHD remain poorly understood. Previous studies focused on different aspects or did not employ essential methodologies to answer the research questions posed in this study. Our study aims to compare complex cardiac malformations, which have two or more cardiovascular structural abnormalities, with simple cardiac malformations, which have only one cardiovascular structural abnormality, to help provide the appropriate prenatal genetic testing.

CHD refers to a range of structural heart defects that develop during fetal growth and can substantially affect health outcomes. CHD includes various conditions, including simple anomalies (such as ASD and VSD) and complex malformations. These complex cases often involve multiple cardiac structures and may be associated with genetic syndromes or extracardiac anomalies [16]. Our study investigated the genetic findings in the prenatal diagnosis of CHDs and focused on the differences between simple and complex cardiac malformations.

Of the 211 fetuses diagnosed with CHD, 62.6% and 37.4% had simple and complex malformations, respectively. The proportion of different types of CHD was similar to that reported in relevant literature [17]. The overall rate of chromosomal abnormalities was 12.3%. Numerous studies have reported the detection rate of CMA in fetuses with CHD although rates vary depending on the array types used [18, 19]. The positive rate of prenatal CMA testing ranges from 6.6% to 38.7% [19, 20, 21]. In our study, the yield of the CMA test was generally consistent with previously published findings.

Our results indicated a significant distinction between the two groups; specifically, the rate of chromosomal abnormalities of complex CHD was markedly higher than that of simple CHD (22.8% vs. 6.1%). This finding was consistent with existing literature that suggests a stronger association between complex CHD and genetic factors, particularly in cases with structural anomalies and soft markers; therefore, these complex conditions likely exhibit a multifactorial etiology [18].

Our study revealed that the detection rates of chromosomal abnormalities significantly differed between isolated and non-isolated CHDs (8.7% vs. 23.5%). Previous studies reported similar findings in both groups of CHD [18, 22]. In isolated CHDs, the rate of chromosomal abnormalities in complex malformations was higher than that in simple malformations (20.0% vs. 2.9%). Furthermore, the presence of extracardiac anomalies or soft markers increased the likelihood of chromosomal abnormalities in simple and complex CHDs. Specifically, the detection rate in these cases increased to 23.5%. However, in non-isolated CHDs, the lack of a statistically significant difference suggested that extracardiac anomalies had a similar effect on genetic abnormalities in simple and complex CHDs. Therefore, non-cardiac anomalies may be important indicators for genetic testing regardless of the complexity of the heart defect [18, 23, 24, 25].

CMA is recommended as the first-line test. When CMA results are negative, ES is performed as a follow-up. However, the evidence supporting the use of ES in straightforward cases remains debated among experts. In our study, 32 fetuses with cardiac anomalies underwent ES when negative CMA results were obtained. The cohort comprised 7 cases of simple cardiac malformations and 25 cases of complex cardiac malformations. Among them, the proportion of fetuses with complex cardiac malformations was significantly higher; as such, ES evaluation was subsequently performed. Of the 7 cases with simple cardiac malformations in our study, 1 had a P/LP variant identified and only had one structural cardiac abnormality, which was VSD; however, it was combined with extracardiac abnormalities, which were cleft lip and palate and pyelectasis. Of the 25 cases with complex cardiac malformations in our study, 2 had P/LP variants identified, and 1 had multiple cardiac structural anomalies combined with fetal growth restriction (FGR). Our findings suggested that ES should be offered to the simple CHD group, particularly when extracardiac abnormalities are detected. Our diagnostic yield of 9.4% for ES was consistent with the established 10% yield reported in larger cohorts (n = 260) of fetuses with CHD [12]. This consistency remained despite our smaller sample size and was independent of CHD complexity or syndromic status. ES is necessary regardless of which cohort. Another study has also shown that approximately 10% of cases are attributable to de novo variants [26]. Therefore, ES should be offered to all pregnant women carrying a fetus with CHD that does not show chromosomal abnormalities or P/LP CNVs identified by CMA. This recommendation applies regardless of the classification of CHD.

A considerable limitation of this study was its relatively small sample size, especially the ES cases, which may limit the statistical power and generalizability of the findings. Larger prospective studies are warranted to validate our findings and obtain more precise estimates. The selection bias from patients retrospectively included with various degrees of cardiac and extracardiac anomalies could further distort the detection rates of chromosomal abnormalities. These issues highlighted the need for larger studies that not only include genetic testing but also involve clinical follow-up to evaluate the influence of genetic findings on patient management and outcomes. Furthermore, the retrospective nature of this study might hinder our ability to establish causal relationships between genetic factors and the complexity of cardiac malformations. Future research should address these limitations by incorporating comprehensive clinical data and investigating the functional implications of the identified genetic anomalies.

Our findings reveal notable differences in chromosomal abnormality detection rates between simple and complex cardiac malformations. Specifically, complex cases showed a stronger link to genetic anomalies. The higher prevalence of chromosomal abnormalities in CHD with extracardiac issues highlights the need for thorough genetic evaluation. Additionally, advanced genomic techniques such as ES should be integrated to further reveal genetic factors associated with all forms of CHD. Therefore, further research should clarify the complex relationship between genetic factors and structural heart abnormalities to improve prenatal diagnosis and management strategies.

The datasets used and analyzed during the current study are available from the corresponding authors on reasonable request.

JG, PT, and SL designed the research study and manuscript writing. WZ performed data curation for the study. XW analyzed the data. All authors contributed to critical revision of the manuscript for important intellectual content. All authors read and approved the final manuscript. All authors have participated sufficiently in the work and agreed to be accountable for all aspects of the work.

The research protocol was approved by the Ethics Committee of Jiaxing Maternity and Children Health Care Hospital (Ethics No. 2024-Y-87). Informed consent was waived for this retrospective study due to the exclusive use of de-identified patient data, which posed no potential harm or impact on patient care. The study was carried out in accordance with the guidelines of the Declaration of Helsinki.

This research was funded by the project of Science and Technology Bureau of Jiaxing, Zhejiang Province (2022AD30093), the Medical and Health Technology Project of Zhejiang Province (2023KY1220), and the Natural Science Foundation of Zhejiang Province (LTGY24H040001).

The authors declare no conflict of interest.

During the preparation of this manuscript, the author(s) utilized DeepSeek-R1 exclusively for language polishing purposes. This tool assisted in improving grammatical accuracy, sentence structure, and overall readability of the text. The authors take full responsibility for the content integrity and have thoroughly reviewed and edited all AI-modified sections to ensure alignment with the original scientific intent.