De novo mutations in congenital heart disease with neurodevelopmental and other congenital anomalies

Abstract

Congenital heart disease (CHD) patients have an increased prevalence of extracardiac congenital anomalies (CAs) and risk of neurodevelopmental disabilities (NDDs). Exome sequencing of 1213 CHD parent-offspring trios identified an excess of protein-damaging de novo mutations, especially in genes highly expressed in the developing heart and brain. These mutations accounted for 20% of patients with CHD, NDD, and CA but only 2% of patients with isolated CHD. Mutations altered genes involved in morphogenesis, chromatin modification, and transcriptional regulation, including multiple mutations in RBFOX2, a regulator of mRNA splicing. Genes mutated in other cohorts examined for NDD were enriched in CHD cases, particularly those with coexisting NDD. These findings reveal shared genetic contributions to CHD, NDD, and CA and provide opportunities for improved prognostic assessment and early therapeutic intervention in CHD patients.

Fig. 1

Genes with multiple de novo mutations are candidate CHD risk genes. A: Histograms show the expected distribution of the number of genes containing multiple de novo mutations (empirically derived using 1M permutations, black), and the observed number of genes with multiple mutations in cases (red line) for each class. P-values were calculated by permutation. B: Twenty-one genes with multiple damaging de novo mutations in cases. P-values are from Poisson test against expectation, with significance threshold < 9×10⁻⁷. Further details are shown in Table S6.

Fig. 2

Burden of damaging de novo mutations in HHE genes among CHD cases with extra-cardiac phenotypes. A: The enrichment (ratio of observed/expected) of damaging de novo mutations in HHE genes is shown for each phenotype (± 95% confidence interval). Case probands were excluded if they carried de novo mutations in known CHD syndrome genes (n=19), had unknown extracardiac phenotype for both NDD and CA (n=6), or had one unknown phenotype and were negative for the other (n=273). Cases with either CA or NDD and unknown status for the other phenotype (n=97) were included in the “Extra” category but excluded from the “only” categories. B: Percent excess of individuals carrying damaging de novo mutations in HHE genes by indicated phenotype (± 95% confidence interval). Explanation of calculation is provided (12). C: Table of observed and expected de novo rates for the indicated variant classes by phenotype.

Fig. 3

Genes containing de novo mutations in CHD cases show pleotropic developmental effects. A: Individuals with CHD carry an excess of damaging de novo mutations among 1,161 genes identified by containing damaging de novo mutations in 7 published studies of NDD (P-NDD cohort) (, –23). All CHD cases were subdivided by NDD status (CHD + NDD, n=417 subjects, CHD – NDD n=440, Unknown NDD, n=363). P-values ≤ 0.005 as indicated (stars) were calculated from Poisson test against model-derived distribution (values in Table S11). P-NDD gene set (blue) was further filtered for HHE genes (P-NDD/HHE, red, 564 genes). Enrichments are shown ± 95% confidence intervals. B: Percentile gene expression ranks (100=high) are shown for all genes (grey) in the developing brain and heart, highlighting 69 genes with damaging de novo mutations in both CHD cases and the P-NDD cohort (blue or purple). Genes with multiple de novo mutations in CHD (red or purple) are shown. Point size represents numbers of de novo events.