Ciliary genes contribute to a complex genetic model of congenital heart disease

Congenital heart disease (CHD) is the most common birth defect, affecting ~1% of infants born each year. While a genetic etiology is strongly supported for CHD, the majority of cases remain unsolved. The genetic heterogeneity, variable expressivity, and incomplete penetrance of CHD suggests that a more complex or non-Mendelian genetic model is involved. A large-scale mouse mutagenesis screen in our lab previously showed an enrichment for cilia related genes among genes causing CHD, including many involved in the ciliogenesis and planar cell polarity network, as well as cilia-transduced cell signaling pathways known to play important roles in cardiovascular development. Importantly, these genes were shown to be part of a tight protein- protein interaction network, and CHD in some mouse lines was observed to have a multigenic etiology. Hence, we hypothesized that a complex genetic model comprising interactions between ciliary genes can contribute to CHD pathogenesis. Here, we investigated the role of protein truncating variants in known CHD genes that are cilia-related in a cohort of 1932 CHD patients and 2602 controls without structural cardiac defects. We show that there is a significantly greater number of CHD cases with variants in more than one cilia-CHD gene than controls. When considering specific subtypes, this is true for patients with left ventricular outflow tract obstructions and laterality defect patients, suggesting that in the context of ciliary variants, a digenic model drives disease in these subtypes. Conversely, there are significantly more conotruncal defect patients with variants in only one cilia-CHD gene compared to controls, suggesting that in ciliary genes, a monogenic model of disease drives this phenotype. We then identify gene-gene interactions between genes in the cilia-CHD interactome that are statistically significant in cases, but not controls, and use these to identify candidate CHD genes, including ciliary genes that interact or cluster with known CHD genes. Overall, these studies provide evidence for a complex genetic model of CHD involving ciliary genes, identify gene-gene interactions between known CHD genes that may contribute to pathogenesis, and use these interactions to identify novel candidate CHD genes for future study