Genomic analysis of 11,555 probands identifies 60 dominant congenital heart disease genes

Abstract

Congenital heart disease (CHD) is a leading cause of infant mortality. We analyzed de novo mutations (DNMs) and very rare transmitted/unphased damaging variants in 248 prespecified genes in 11,555 CHD probands. The results identified 60 genes with a significant burden of heterozygous damaging variants. Variants in these genes accounted for CHD in 10.1% of probands with similar contributions from de novo and transmitted variants in parent-offspring trios that showed incomplete penetrance. DNMs in these genes accounted for 58% of the signal from DNMs. Thirty-three genes were linked to a single CHD subtype while 12 genes were associated with 2 to 4 subtypes. Seven genes were only associated with isolated CHD, while 37 were associated with 1 or more extracardiac abnormalities. Genes selectively expressed in the cardiomyocyte lineage were associated with isolated CHD, while those widely expressed in the brain were also associated with neurodevelopmental delay (NDD). Missense variants introducing or removing cysteines in epidermal growth factor (EGF)-like domains of NOTCH1 were enriched in tetralogy of Fallot and conotruncal defects, unlike the broader CHD spectrum seen with loss of function variants. Transmitted damaging missense variants in MYH6 were enriched in multiple CHD phenotypes and account for ~1% of all probands. Probands with characteristic mutations causing syndromic CHD were frequently not diagnosed clinically, often due to missing cardinal phenotypes. CHD genes that were positively or negatively associated with development of NDD suggest clinical value of genetic testing. These findings expand the understanding of CHD genetics and support the use of molecular diagnostics in CHD.

Keywords: congenital heart disease; exome sequencing; genomics; human genetics; molecular inversion probes.

Fig. 1.

Quantile–quantile plots of meta-analysis using DNMs and TUVs in 248 genes in 11,555 probands. For indicated variant classes, Q–Q plot is shown. Genes surpassing genome-wide significance (P-value < 2.6 × 10⁻⁶) and those with FDR < 0.05 are shown in red and blue, respectively. The y-axis has been truncated at –logP = 10. Red arrows denote genes that have P < 10⁻¹⁰. The genomic inflation factor, λ, adjusted per 1,000 samples is shown for syn and T-Mis variants. In Damaging variant results, the boxed Inset shows genes with observed −logP from 1.5 to 3.0.

Fig. 2.

Single-cell expression during mouse gastrulation of genes enriched in probands with isolated CHD or NDD & EC. (A) Single-cell RNA-seq from mouse gastrulation (24) for 28 genes associated with isolated CHD probands (in pink) or NDD & EC (in purple) are shown. On the vertical axis, cell types are sorted for heart (red), brain (blue), and other tissues (green). Expression levels are scaled to the greatest TPM (Transcripts per Million Reads) for each gene across all tissues. Chromatin genes are annotated with a white dot in the purple bar. (B) Quantitation of expression of genes expressed in heart, brain, and other tissues comparing genes associated with isolated CHD and NDD & EC. Median values are shown on each boxplot. A Wilcoxon rank-sum P-value comparing expression levels in heart/brain/other tissues is shown for genes associated with isolated vs. NDD & EC probands.

Fig. 3.

Frequent cysteine-altering mutations in NOTCH1 EGF domain #5 in TOF/CTD probands. (A) NOTCH1 protein domain structure derived from Prosite and PFAM databases is shown, with EGF-like domains in green; amino acid positions in NOTCH1 are numbered on the x-axis. Lollipops show location of very rare D-mis variants in CHD probands; those in CTD/TOF probands are shown above the protein diagram and non-CTD-TOF probands are shown below. Variants that introduce or remove a cysteine are shown in yellow; all others are in green. Height of lollipops corresponds to number of independent occurrences of specific variants. “DUF” denotes “Domain of unknown function DUF3454.” (B) Crystal structure of NOTCH1 EGF domain. Amino acids altered to or from cysteine in CTD/TOF probands (blue text), and other mutations in EGF #5 in CTD/TOF probands are in red; disulfide bridges in canonical protein are shown as black lines. Structure from ref. .