Genome-wide association study in European patients with congenital heart disease identifies risk loci for transposition of the great arteries and anomalies of the thoracic arteries and veins and expression of discovered candidate genes in the developing heart

Rationale Genetic factors undoubtedly contribute to the development of congenital heart disease (CHD), but still remain mostly ill-defined. Objective Identification of genetic risk factors associated with CHD and functional analysis of SNP-carrying genes. Methods and Results Genetic association study of 1,440 Caucasian CHD patients from the German Heart Center Munich collected from March 2009 to June 2016, 2,594 patients of previous studies provided by the Newcastle University and 8,486 controls underwent meta-analysis to detect single nucleotide polymorphisms (SNPs) associated with CHD. Results 4,034 Caucasian CHD patients strictly classified according to the Society of Thoracic Surgeons nomenclature and 8,486 controls were included. One SNP on chromosome 5 reached genome-wide significance across all CHD phenotypes (rs185531658,OR:2.16, p =5.28×10−9) and was also indicative for septal defects (OR:2.16, p =6.15×10−8). One region on chromosome 20 pointing to the MACROD2 locus, identified four SNPs (rs150246290,OR:3.78, p =1.27×10−10; rs149890280,OR:3.74, p =1.8×10−10; rs149467721,OR:3.53; p =1.39×10−9, rs77094733,OR:3.53, p =1.73×10−9) in patients with transposition of the great arteries (TGA). A second region was detected on chromosome 8 located at ZBTB10 (rs148563140,OR:3.42, p =3.28×10−8; rs143638934,OR:3.42, p =3.51×10−8) in the same subgroup. Three highly significant risk variants on chromosome 17 (rs76774446,OR:1.60, p =9.95×10−8; rs11874,OR:1.60, p =6.64×10−8; rs17677363,OR:1.60, p =9.81×10−8) within the GOSR2 locus were identified in patients with anomalies of thoracic arteries and veins (ATAV). Genetic variants associated with ATAV are suggested to influence expression of WNT3 , and variant rs870142 related to septal defects is proposed to influence expression of MSX1 . Cardiac differentiation of human and murine induced pluripotent stem cells and single cell RNAseq analyses of developing murine and human hearts show essential functional roles for MACROD2, GOSR2, WNT3 and MSX1 at all developmental stages. Conclusions For the first time genetic risk factors in CHD patients with TGA and ATAV were identified. Several candidate genes play an essential functional role in heart development at the embryonic, newborn and adult stage. ### Competing Interest Statement The authors have declared no competing interest. * ASD : atrial septal defect ASDII : atrial septal defect type II ATAV : anomalies of thoracic arteries and veins CHD : congenital heart disease CHSD : Congenital Heart Surgery Database CE : cardiac enhancer CM : cardiomyocyte CPC : cardiac progenitor cells ESC : embryonic stem cell GO : gene ontology GSEA : gene set enrichment analysis GWAS : genome-wide association study iPS : induced pluripotent stem cell KORA : Cooperative Health Research in the Region of Augsburg RVOT : right ventricular outflow tract scRNAseq : single cell RNA sequencing SHF : second heart field SNP : single nucleotide polymorphism STS : Society of Thoracic Surgeons TGA : transposition of the great arteries TOF : Tetralogy of Fallot VSD : ventricular septal defect