Copy Number Variation Test In Prenatal Genetic Diagnosis Of Congenital Heart Defects

BackgroundCongenital heart disease (CHD) is a common birth defect, affecting 0.5-1.2% of newborns. With the availability of advanced surgical techniques, normal or near normal heart function can be restored after cardiovascular surgery for most types of CHDs ranging from simple ventricular septal defects (VSD) to more complex cardiovascular abnormalities. However, the long-term prognosis of a small, but significant number of CHD fetuses is usually complicated by severe extracardiac problems, such as mental retardation and developmental delay. In a prenatal setting, even with significant advances in the sensitivity of ultrasound technologies and well-trained sonographers,43-96% of CHDs are not detectable and, of those that are detected, it is not known whether there is a secondary chromosomal disease that manifests with CHD. Consequently, from ultrasound it is extremely difficult for physicians to make a comprehensive assessment of a CHD fetus and manage the course of the established pregnancy. Therefore, genetic testing is now highly recommended for any woman diagnosed with a CHD fetus.Cytogenetic analysis using techniques such as karyotyping and fluorescence in situ hybridization (FISH) have been the mainstream diagnostic technologies for identifying chromosomal abnormalities associated with CHD. At the level of prenatal diagnosis, chromosomal anomalies are estimated to be as high as 18-22% for CHD cases. Chromosome microarray array (CMA) has now become the first tier technique for genetic follow up of fetal structural anomalies identified by ultrasonography. More recently, next generation sequencing (NGS) is emerging as high-resolution tehchnology for genome-wide CNV detection and may represent another comprehensive approach for detecting pathogenic CNVs associated with CHD and extra cardiac abnormalities.ObjectiveTo determine the type and frequency of pathogenic chromosomal abnormalities in fetuses diagnosed with congenital heart defect using chromosomal microarray analysis (CMA) and by analyzing the genotype-phenotype relation in CHD fetuses, we are trying to find out a cost-effective way for prenatal genetic testing in CHD fetuses. We also tired to validate NGS as an alternative diagnostic method of CMA.Materials and MethodRoutine fetal ultrasound anatomy scans were performed for pregnant women presenting at the Prenatal Diagnosis Center of Jiangsu Province. The anatomy scans were conducted between 20-28 weeks gestational age by senior sonographers on either GE E8 or ALOKA a 10 ultrasound machines. If CHD was suspected, echocardiography was subsequently performed. According to recommended guidelines, genetic testing was also performed after an informed consent form was signed by the couple. Amniotic fluid was obtained after the fetal diagnosis of CHD. CMA was conducted with DNA from amniotic cells. CNV sequencing (CNV-Seq) was applied on 38 selected DNA samples.ResultsAn interpretable CMA profile was obtained for all 115 test genomic DNA samples. Clinically significant chromosomal abnormalities were found in 21 of 115 samples (18.3%), including six whole chromosome aneuploidies (28.6%), three partial chromosome aneuploidies (14.3%), two other chromosomal structural abnormalities (9.5%), four 22q11.2 microdeletions or duplications (19.0%) and six with submicroscopic CNVs (28.6%) related to known chromosomal disease syndromes.In addition, five of 115 samples (4.3%) had CNVs of unknown significance (VOUS). In the 73 isolated CHD fetuses, CMA identified six CNVs (8.2%) involving duplication of 22q11.2 (n=1) and deletions of 22q11.2 (n=2), 1q21.1 (n=1),16p11.2 (n=1) and 15q11.2ql3.1 (n=1) (Table 2). In the 42 CHD fetuses with extra cardiac defects, CMA identified 6 trisomies (14.3%) associated with Down (n=3), Edward (n=2) and Patau (n=1) syndromes and two unusual partial aneuploidies, namely monosomy 13 and a trisomy 22 with one chromosome exhibiting a 22q11.2 microdeletion. Additionally, CMA identified seven CNVs (11.9%) involving duplication of17ql2 and deletions of 22q11.2,2ql4.3q22.3,3q22.1q23,4p16.3p15.32, 5p15.33pl5.2 and 17p13.3p13.2 one case each. Overall, there was a 100% diagnostic concordance between CMA and CNV-Seq for detecting all 21 pathogenic chromosomal abnormalities associated with CHD.ConclusiosnManagement of CHD pregnancies to achieve the best possible outcomes is a challenging and complex issue and requires an interactive multi-discipline team. This study demonstrates the importance of having both ultrasound and CMA information available for genetic counselling so that the couple can make an informed decision on whether to terminate or continue the CHD pregnancy. CMA and CNV-Seq are both valuable diagnostic technologies that help support and extrapolate on the prenatal ultrasound CHD findings.