Genome-Wide Association Study Identifies Novel Risk Loci in Patients with Transposition of the Great Arteries and Anomalies of the Thoracic Arteries and Veins

Objectives: Congenital heart disease (CHD) represents about one-third of all congenital anomalies. While genetic factors undisputably contribute to CHD no causal genes have been identified in most of the cases. We performed a genome-wide association study to characterize genetic risk factors possibly associated with CHD.

Methods: Genotyping was performed using affymetrix axiom genome-wide human array and illumina 660wQUAD arrays. The cohort comprised 4,034 CHD patients, 1,440 elective patients of the German Heart Center Munich and 2,594 from multiple centers together with 3,554 and 4,932 control persons, respectively. Genomic DNA from blood samples was purified using the QIAamp DNA purification kit.

Results: We have classified the clinical pathotype of the patients according to the recognized guidelines of the Society of Thoracic Surgeons (STS) and analyzed the five largest clinical categories. The analysis across all patients identified one single nucleotide polymorphism (SNP) which reached genome-wide significance (rs185531658, p = 5.28 × 10⁻⁹) which also occurred in patients with septal defects (p = 6.15 × 10⁻⁸). In ASD patients a cluster with multiple variants was evident on chromosome 4p16 and two loci on chromosome 18 and one on chromosome 3 (p < 3 × 10⁻⁸) were associated with a risk for ASDII. In the subgroups of patients with left or right heart lesions four different SNPs were detected which showed genome-wide significance (p < 5 × 10⁻⁸). Regrettably, these SNPs were located in intergenic regions or close to genes without known cardiac function. Four SNPs within the MACROD2 locus and two SNPs close to ZBTB10 were associated with a risk for transposition of the great arteries (p between 5 × 10⁻⁸ and 1.27 × 10⁻¹⁰). Finally, patients with anomalies of thoracic arteries and veins were carriers of three variants within the GOSR2 locus (p between 6.64 × 10⁻⁸ and 9.95 × 10⁻⁸). This region can possibly interact with the WNT3 locus which is open early during cardiogenesis. Differentiation of human induced pluripotent stem cells into cardiomyocytes confirmed WNT3 expression peaking at early time-points of direct cardiac differentiation.

Conclusion: Our results have identified genetic risk factors in CHD patients with transposition of the great arteries or anomalies of the thoracic arteries and veins which have not been reported yet. The associated variants may affect the development of mesodermal cells at an early time-point of cardiogenesis.