Prenatal diagnosis of congenital heart defect by genome-wide high-resolution SNP array.

Objective: This study aimed to detect genomic imbalances in fetuses with congenital heart defect (CHD) by high-resolution single-nucleotide polymorphism (SNP) array.

Methods: A total of 99 fetuses with CHDs with or without other ultrasound anomalies (including structural anomalies and soft markers) but normal karyotypes were investigated using Affymetrix CytoScan HD array.

Results: Clinical significant copy number variations (CNVs) were detected in 19 fetuses (19.2%). The proportion for variants of unknown significance was 3% after parental analysis. Five known microdeletion/microduplication syndromes were identified. The detection rate in CHD plus structural anomaly (27.8%) or soft marker (25%) group was higher than but not statistically different from isolated CHD group (15.9%). There was no significant difference between the detection rates in simple and complex CHD groups (20.7% vs. 16.7%). The detection rate in fetuses with CHD and neurologic defect was significantly higher than those with other types of structural anomaly (75% vs. 14.3%, P < 0.05).

Conclusions: Our results demonstrated the value of high-resolution SNP arrays in prenatal diagnosis of CHD; it should become an integral aspect in clinically molecular diagnosis and genetic counseling. The complexity of the cardiac defect was not related to the frequency of clinical significant CNV, but the presence of neurologic defect was related.