Congenital Heart Disease Gene Research Articles

Genetics and etiology of congenital heart disease.

Congenital heart disease (CHD) is the most common severe birth anomaly, affecting almost 1% of infants. Most CHD is genetic, but only 40% of patients have an identifiable genetic risk factor for CHD. Chromosomal variation contributes significantly to CHD but is not readily amenable to biological follow-up due to the number of affected genes and lack of evolutionary synteny. The first CHD genes were implicated in extended families with syndromic CHD based on the segregation of risk alleles in affected family members. These have been complemented by more CHD gene discoveries in large-scale cohort studies. However, fewer than half of the 440 estimated human CHD risk genes have been identified, and the molecular mechanisms underlying CHD genetics remains incompletely understood. Therefore, model organisms and cell-based models are essential tools for improving our understanding of cardiac development and CHD genetic risk. Recent advances in genome editing, cell-specific genetic manipulation of model organisms, and differentiation of human induced pluripotent stem cells have recently enabled the characterization of developmental stages. In this chapter, we will summarize the latest studies in CHD genetics and the strengths of various study methodologies. We identify opportunities for future work that will continue to further CHD knowledge and ultimately enable better diagnosis, prognosis, treatment, and prevention of CHD.

Single-Cell Reconstruction and Mutation Enrichment Analysis Identifies Dysregulated Cardiomyocyte and Endothelial Cells in Congenital Heart Disease.

Congenital heart disease (CHD) is one of the most prevalent neonatal congenital anomalies. To catalog the putative candidate CHD risk, we collected 16,349 variants (single nucleotide variants (SNVs) and Indels) impacting 8,308 genes in 3,166 CHD cases for a comprehensive meta-analysis. Using ACMG guidelines we excluded the 0.1% of benign/likely benign variants and resulting data set consisted of 83% predicted loss of function variants and 17% missense variants. Seventeen percent were de novo variants. A stepwise analysis identified 90 variant-enriched CHD genes, of which six (GPATCH1, NYNRIN, TCLD2, CEP95, MAP3K19 and TTC36) were novel candidate CHD genes. Single cell transcriptome cluster reconstruction analysis on six CHD tissues and four controls revealed upregulation of top 10 frequently mutated genes primarily in cardiomyocytes. NOTCH1 (highest number of variants) and MYH6 (highest number of recurrent variants) expression was elevated in endocardial cells and cardiomyocytes, respectively, and 60% of these gene variants were associated with tetralogy of Fallot and coarctation of the aorta, respectively. Pseudobulk analysis using single cell transcriptome, revealed significant (p<0.05) upregulation of both NOTCH1 (endocardial cells) and MYH6 (cardiomyocytes) in the control heart data. We observed nine different subpopulations of CHD heart cardiomyocytes of which only four were observed in the control heart. This is the first comprehensive meta-analysis combining genomics and CHD single cell transcriptomics, identifying the most frequently mutated CHD genes, and demonstrating CHD gene heterogeneity, suggesting that multiple genes contribute to the phenotypic heterogeneity of CHD. Cardiomyocytes and endocardial cells are identified as major CHD-related cell types.

Abstract 18657: Diagnostic Yield of Whole Genome Sequencing in Congenital Heart Disease: Data From the UK 100,000 Genomes Project

Congenital heart disease (CHD) is the most common birth defect affecting around 1% global live births. The aetiology of CHD is poorly understood: while a number genetic loci have already been identified, the majority of cases remain unexplained. Many CHD cases occur with additional abnormalities, or as part of a defined syndrome (eg. Noonan or CHARGE syndromes). The 100,000 Genomes Project conducted whole genome sequencing for patients with a range of rare diseases and cancers in partnership with the UK National Health Service. We analysed clinical and genetic data from the project in 2638 participants with CHD, including both primary CHD cases and secondary cases who have CHD as part of a syndromic presentation but were recruited under other disease categories. Both cohorts are primarily composed of patients with CHD accompanied by additional extra-cardiac abnormalities without a prior diagnosis of a defined syndrome. We found that families recruited as primary CHD cases were significantly less likely to have been classed as “solved cases” (indicating a pathogenic variant has been identified) than phenotypically similar secondary CHD cases (5.4% primary, 16.2% secondary; p = 6.78х -11 ). This is primarily due to differences in the gene lists used in analysis, with the majority of diagnoses in both groups due to genes not included in the CHD gene panel (83% primary and 97% secondary cases). Expanding standard CHD screening to include a wider range of syndromic CHD genes is likely to increase the diagnostic yield for the primary CHD cohort by more than two-fold. Copy number variants (CNVs) also contribute to CHD, especially in cases with additional abnormalities. CHD cases have a significantly higher burden of both deletions (p = 1.00х10 -5 ) and duplications (p = 0.009) than an ethnically-matched control cohort. However, only 7 of 2638 participants have CNVs in known CHD-causative regions such as the 22q11.2 or Williams-Beuren syndrome regions indicating novel CNVs are likely to contribute to a significant number of cases. Wider screening of syndromic CHD genes and novel copy number variants is likely significantly increase the diagnostic yield for CHD both within the 100,000 Genomes Project and in healthcare settings, and potentially yield novel CHD-associated loci.

Abstract P1009: Investigating The Effect Of Patient Missense Variants In CHD7 Using An Induced Pluripotent Stem Cell Model

Congenital heart disease (CHD) is a phenotypically diverse and genetically heterogenous disease. While monogenic causes of familial CHD and damaging de novo variants are known contributors to CHD risk, novel variants of uncertain significance (VUS) detected among CHD probands remain under characterized. In particular, the effect of missense variants in CHD7 (chromodomain helicase DNA binding protein 7), remain poorly explored. CHD7 is an established CHD gene with variants associated with CHARGE syndrome (Coloboma, Heart defects, Atresia of the choanae, Retardation of growth and development, Genital/urinary abnormalities, and Ear abnormalities) and incomplete syndromic phenotypes. We hypothesized that some CHD7 missense variants in genetically engineered human-induced pluripotent stem cells (iPSCs) perturb essential cardiac developmental pathways. CHD7 is highly expressed in iPSCs and during differentiation to iPSC-cardiomyocytes. Out of seventy rare patient missense variants in CHD7 reported by the Pediatric Cardiac Genetics Consortium (PCGC), six were chosen for genomic editing. To investigate the functional effects of missense variants in CHD7, we first predicted pathogenicity using AlphaFold, an algorithm which models variant impact on the three-dimensional structure of proteins. We then introduced six patient missense variants (Q161R, R286G, I1500V, T262A, T894A, L2299P) into an iPSC line using adenine base editors. Heterozygous and homozygous loss-of-function CHD7 lines were generated for comparison. RNA expression profiles of edited iPSCs were analyzed using single cell gene expression with multiplexing to assess the impact of the missense variants on transcriptional profiles. Bulk RNA sequencing was performed in parallel to better characterize transcriptional changes. These results further our understanding of how CHD7 missense variants may contribute to CHD risk. In the future, these approaches could be applied to a broader list of genes, as rare patient missense variants in definitive and candidate CHD genes require further investigation to determine pathogenicity. Developing iPSC models to investigate functional effects of missense variants can aid in understanding the complex genetic architecture of CHD.

Contribution of Previously Unrecognized RNA Splice-Altering Variants to Congenital Heart Disease.

Known genetic causes of congenital heart disease (CHD) explain <40% of CHD cases, and interpreting the clinical significance of variants with uncertain functional impact remains challenging. We aim to improve diagnostic classification of variants in patients with CHD by assessing the impact of noncanonical splice region variants on RNA splicing. We tested de novo variants from trio studies of 2649 CHD probands and their parents, as well as rare (allele frequency, <2×10-6) variants from 4472 CHD probands in the Pediatric Cardiac Genetics Consortium through a combined computational and in vitro approach. We identified 53 de novo and 74 rare variants in CHD cases that alter splicing and thus are loss of function. Of these, 77 variants are in known dominant, recessive, and candidate CHD genes, including KMT2D and RBFOX2. In 1 case, we confirmed the variant's predicted impact on RNA splicing in RNA transcripts from the proband's cardiac tissue. Two probands were found to have 2 loss-of-function variants for recessive CHD genes HECTD1 and DYNC2H1. In addition, SpliceAI-a predictive algorithm for altered RNA splicing-has a positive predictive value of ≈93% in our cohort. Through assessment of RNA splicing, we identified a new loss-of-function variant within a CHD gene in 78 probands, of whom 69 (1.5%; n=4472) did not have a previously established genetic explanation for CHD. Identification of splice-altering variants improves diagnostic classification and genetic diagnoses for CHD. URL: https://clinicaltrials.gov; Unique identifier: NCT01196182.

Evidence-Based Assessment of Congenital Heart Disease Genes to Enable Returning Results in a Genomic Study.

Congenital heart disease (CHD) is the most common major congenital anomaly and causes significant morbidity and mortality. Epidemiologic evidence supports a role of genetics in the development of CHD. Genetic diagnoses can inform prognosis and clinical management. However, genetic testing is not standardized among individuals with CHD. We sought to develop a list of validated CHD genes using established methods and to evaluate the process of returning genetic results to research participants in a large genomic study. Two-hundred ninety-five candidate CHD genes were evaluated using a ClinGen framework. Sequence and copy number variants involving genes in the CHD gene list were analyzed in Pediatric Cardiac Genomics Consortium participants. Pathogenic/likely pathogenic results were confirmed on a new sample in a clinical laboratory improvement amendments-certified laboratory and disclosed to eligible participants. Adult probands and parents of probands who received results were asked to complete a post-disclosure survey. A total of 99 genes had a strong or definitive clinical validity classification. Diagnostic yields for copy number variants and exome sequencing were 1.8% and 3.8%, respectively. Thirty-one probands completed clinical laboratory improvement amendments-confirmation and received results. Participants who completed postdisclosure surveys reported high personal utility and no decision regret after receiving genetic results. The application of ClinGen criteria to CHD candidate genes yielded a list that can be used to interpret clinical genetic testing for CHD. Applying this gene list to one of the largest research cohorts of CHD participants provides a lower bound for the yield of genetic testing in CHD.

Modeling Human TBX5 Haploinsufficiency Predicts Regulatory Networks for Congenital Heart Disease.

Haploinsufficiency of transcriptional regulators causes human congenital heart disease (CHD); however, the underlying CHD gene regulatory network (GRN) imbalances are unknown. Here, we define transcriptional consequences of reduced dosage of the CHD transcription factor, TBX5, in individual cells during cardiomyocyte differentiation from human induced pluripotent stem cells (iPSCs). We discovered highly sensitive dysregulation of TBX5-dependent pathways-including lineage decisions and genes associated with heart development, cardiomyocyte function, and CHD genetics-in discrete subpopulations of cardiomyocytes. Spatial transcriptomic mapping revealed chamber-restricted expression for many TBX5-sensitive transcripts. GRN analysis indicated that cardiac network stability, including vulnerable CHD-linked nodes, is sensitive to TBX5 dosage. A GRN-predicted genetic interaction between Tbx5 and Mef2c, manifesting as ventricular septation defects, was validated in mice. These results demonstrate exquisite and diverse sensitivity to TBX5 dosage in heterogeneous subsets of iPSC-derived cardiomyocytes and predicts candidate GRNs for human CHDs, with implications for quantitative transcriptional regulation in disease.

Abstract 16552: Chromosomal Microarray Abnormalities in More Than 1300 Patients With Congenital Heart Disease Provide Novel Clinical and Etiological Insights

Introduction: The genetic basis of congenital heart disease (CHD) is incompletely understood. Approximately 10-20% of infants with CHD have abnormal chromosome microarray (CMA) results, however, the spectrum of genomic and phenotypic abnormalities remains incompletely characterized. Methods: All study patients had abnormal CMA on clinical testing and abnormal cardiac findings on echocardiogram, as identified at 9 pediatric cardiac centers. Clinical genetic testing results, diagnoses, and echocardiogram reports for detailed cardiac phenotyping were collected. CMA results were denoted as abnormal for any reported findings that included copy number variants (CNVs) and/or regions of homozygosity. Cardiac classification was performed with minor modification to National Birth Defect Prevention Study methods. Recurrent CNVs were identified algorithmically. Functional enrichment analysis of genes predicted to be intolerant of loss-of-function (LOF) in CNVs and genes located in monogenic CNVs was performed using ToppGene. Results: The study included 1369 patients. Genetic syndromes highly associated with CHD such as Trisomy 21, Turner syndrome, and 22q11.2 deletion syndrome among others were identified in 401 patients and elucidated less recognized cardiac phenotypes in these groups. Analyzing genes known to be causative of CHD in the remaining patients (N=968) showed enrichment in CNVs &lt; 5 megabases (N=51; 7%). Common recurrent loci included duplications in 15q13.2-13.3 (N=16 patients) and 16p11.13 (N=12; 8 with left-sided cardiac lesion), and deletions in 15q11.2 (N=14; 6 with total anomalous pulmonary venous return) and 2q13 (N=10; 8 with conotruncal defect). Genes predicted to be intolerant of LOF (495 genes) or located in monogenic CNVs (137 genes) were enriched for neuronal processes. Conclusions: The consortium provides the largest data set of abnormal clinical CMA results in patients with detailed CHD phenotyping to our knowledge. The findings provide novel understanding of CHD phenotypes, a roadmap of recurrent loci, and pathways and candidate genes in CNV-associated CHD. The consortium’s data will lead to improved genetic understanding and clinical care of patients with CHD.

Genetic Basis of Human Congenital Heart Disease.

Congenital heart disease (CHD) is the most common major congenital anomaly with an incidence of ∼1% of live births and is a significant cause of birth defect-related mortality. The genetic mechanisms underlying the development of CHD are complex and remain incompletely understood. Known genetic causes include all classes of genetic variation including chromosomal aneuploidies, copy number variants, and rare and common single-nucleotide variants, which can be either de novo or inherited. Among patients with CHD, ∼8%-12% have a chromosomal abnormality or aneuploidy, between 3% and 25% have a copy number variation, and 3%-5% have a single-gene defect in an established CHD gene with higher likelihood of identifying a genetic cause in patients with nonisolated CHD. These genetic variants disrupt or alter genes that play an important role in normal cardiac development and in some cases have pleiotropic effects on other organs. This work reviews some of the most common genetic causes of CHD as well as what is currently known about the underlying mechanisms.

A Screening Approach to Identify Clinically Actionable Variants Causing Congenital Heart Disease in Exome Data

Congenital heart disease (CHD)-structural abnormalities of the heart that arise during embryonic development-is the most common inborn malformation, affecting ≤1% of the population. However, currently, only a minority of cases can be explained by genetic abnormalities. The goal of this study was to identify disease-causal genetic variants in 30 families affected by CHD. Whole-exome sequencing was performed with the DNA of multiple family members. We utilized a 2-tiered whole-exome variant screening and interpretation procedure. First, we manually curated a high-confidence list of 90 genes known to cause CHD in humans, identified predicted damaging variants in genes on this list, and rated their pathogenicity using American College of Medical Genetics and Genomics-Association for Molecular Pathology guidelines. In 3 families (10%), we found pathogenic variants in known CHD genes TBX5, TFAP2B, and PTPN11, explaining the cardiac lesions. Second, exomes were comprehensively analyzed to identify additional predicted damaging variants that segregate with disease in CHD candidate genes. In 10 additional families (33%), likely disease-causal variants were uncovered in PBX1, CNOT1, ZFP36L2, TEK, USP34, UPF2, KDM5A, KMT2C, TIE1, TEAD2, and FLT4. The pathogenesis of CHD could be explained using our high-confidence CHD gene list for variant filtering in a subset of cases. Furthermore, our unbiased screening procedure of family exomes implicates additional genes and variants in the pathogenesis of CHD, which suggest themselves for functional validation. This 2-tiered approach provides a means of (1) identifying clinically actionable variants and (2) identifying additional disease-causal genes, both of which are essential for improving the molecular diagnosis of CHD.

The promises and challenges of exome sequencing in familial, non-syndromic congenital heart disease

BackgroundExome sequencing is an established strategy to identify causal variants in families with two or more members affected by congenital heart disease (CHD). This unbiased approach, in which both rare and common variants are identified, makes it suitable to research complex, heterogeneous diseases such as CHD. Methods and resultsExome sequencing was performed on two affected members of a three generation family with atrial septal defects (ASD), suggesting a dominant inheritance pattern. Variants were filtered using two bioinformatics pipelines and prioritised according to in silico prediction programs. Segregation studies and functional analyses were used to assess co-segregation with disease and effects on protein function, respectively. Following the data and in silico analyses, ten candidate variants were prioritised. Of these, SRPK2 (c.2044C>T[p.Arg682Trp]) and NOTCH1 (c.3835C>T[p.Arg1279Cys]), co-segregated with disease in the family; however, previous functional analyses on SRPK2 make this an unlikely candidate. Functional analyses in the variant (c.3835C>T[p.Arg1279Cys]) of the known CHD gene NOTCH1 demonstrated a non-significant decrease in signalling activity. ConclusionThis study demonstrates both the potential, as well as the challenges, of applying exome sequencing to complex diseases such as CHD. While in silico evidence and segregation analyses in the NOTCH1 p.Arg1279Cys variant are highly suggestive of pathogenicity, the minimal change in signalling capacity suggests that other variants may be required for CHD development. This study highlights the difficulties of applying exome sequencing in familial, non-syndromic CHD in the clinical environment and a cautionary note in the interpretation of apparently causal abnormalities in silico without supportive functional data.

Abstract 12295: Utilization of Whole-Exome Sequencing to Identify Causative Mutations in Familial Congenital Heart Disease

Congenital heart disease (CHD) is the most common type of birth defect, affecting ~8 out of every 1,000 live births, but there remains a limited understanding of the etiology for the majority of cases of CHD. Familial and population based studies have identified a strong genetic component to CHD, and familial cases of almost every type of CHD have been reported. The goal of this study was to identify pathogenic segregating variants in multiplex CHD families by whole-exome sequencing (WES). Target capture was performed using the Agilent SureSelectXT Target Enrichment kit, followed by WES on an Illumina HiSeq2500, on members from 9 families with Mendelian inherited CHD. Sequence alignment, post alignment processing, variant calling, and genotyping was performed with the Churchill pipeline. Tertiary analysis and annotation consisted of identifying rare (&lt;1% mean allele frequency in the population) segregating variants, prioritizing by matching to a CHD gene list, and predicting pathogenicity via 12 different utilities. This strategy utilized a list of 69 CHD genes selected under strict criteria and allowed for prioritization of the variants. Predicted pathogenic mutations were identified in 3 of the 9 families. A splice donor site mutation was identified in MYH11 (c.4599+1delC) in a family with autosomal dominant patent ductus arteriosus that is predicted to cause a 71 amino acid deletion, affecting functionality of the coiled-coil tail domain. A GATA4 mutation, p.G115W , was identified in a family with autosomal dominant atrial septal defects (ASD) and is predicted to affect the transactivation ability of GATA4 . A p.I263V mutation in TLL1 was identified in a family with autosomal dominant ASD; as this mutation was located in the astacin-like metalloprotease catalytic domain it is predicted to affect the enzymatic efficacy of TLL1 . In summary, our findings demonstrate the clinical utility of WES to successfully identify causative mutations in familial CHD and support the use of a CHD candidate gene list to allow for a more streamlined approach that enables rapid prioritization and identification of pathogenic variants from large WES data sets.

Genetic Pathways in Congenital Heart Development

Congenital heart disease (CHD) is the most common birth defect in newborns. Although insights into the genes and pathways involved that cause CHD have been identified by targeted perturbations of molecules that function in the developmental pathways involved in myocyte specification, differentiation or cardiac morphogenesis, the direct role of these or other perturbations in humans has remained poorly understood. Researchers have tried to bridge this knowledge gap through conventional genome‐wide analyses of rare Mendelian CHD families and by sequencing candidate genes in CHD cohorts. While these discoveries have yield highly penetrant inherited mutations in families with mild to moderately severe CHD, analyses of these genes rarely defines a pathogenic mutation in severe forms of CHD that occurs as a sporadic event, the most common presentation of CHD. The advent of contemporary genomic technologies including SNP arrays, next‐generation sequencing, and CNV analyses are accelerating the discovery of genetic causes of severe and sporadic CHD. Remarkably, emerging genomic data have validated and extended earlier observations leaned from the experimental CHD models and monogenic CHD families. Together these dataset have begun to define the genetic architecture of CHD: CHD gene encode molecules that orchestrate cardiac development; CHD mutations alter gene/protein dosage; comparable CHD mutations yield many distinct malformations, implying that higher order interactions account for particular CHD phenotypes.

Essential Role of the Zinc Finger Transcription Factor Casz1 for Mammalian Cardiac Morphogenesis and Development

Chromosome 1p36 deletion syndrome is one of the most common terminal deletions observed in humans and is related to congenital heart disease (CHD). However, the 1p36 genes that contribute to heart disease have not been clearly delineated. Human CASZ1 gene localizes to 1p36 and encodes a zinc finger transcription factor. Casz1 is required for Xenopus heart ventral midline progenitor cell differentiation. Whether Casz1 plays a role during mammalian heart development is unknown. Our aim is to determine 1p36 gene CASZ1 function at regulating heart development in mammals. We generated a Casz1 knock-out mouse using Casz1-trapped embryonic stem cells. Casz1 deletion in mice resulted in abnormal heart development including hypoplasia of myocardium, ventricular septal defect, and disorganized morphology. Hypoplasia of myocardium was caused by decreased cardiomyocyte proliferation. Comparative genome-wide RNA transcriptome analysis of Casz1 depleted embryonic hearts identifies abnormal expression of genes that are critical for muscular system development and function, such as muscle contraction genes TNNI2, TNNT1, and CKM; contractile fiber gene ACTA1; and cardiac arrhythmia associated ion channel coding genes ABCC9 and CACNA1D. The transcriptional regulation of some of these genes by Casz1 was also found in cellular models. Our results showed that loss of Casz1 during mouse development led to heart defect including cardiac noncompaction and ventricular septal defect, which phenocopies 1p36 deletion syndrome related CHD. This suggests that CASZ1 is a novel 1p36 CHD gene and that the abnormal expression of cardiac morphogenesis and contraction genes induced by loss of Casz1 contributes to the heart defect.

Insights into the genetic structure of congenital heart disease from human and murine studies on monogenic disorders.

Study of monogenic congenital heart disease (CHD) has provided entry points to gain new understanding of heart development and the molecular pathogenesis of CHD. In this review, we discuss monogenic CHD caused by mutations of the cardiac transcription factor genes NKX2-5 and GATA4. Detailed investigation of these genes in mice and humans has expanded our understanding of heart development, shedding light on the complex genetic and environmental factors that influence expression and penetrance of CHD gene mutations.

Detailed mapping of a congenital heart disease gene in chromosome 3p25

Distal deletion of chromosome 3p25-pter (3p− syndrome) produces a distinct clinical syndrome characterised by low birth weight, mental retardation, telecanthus, ptosis, and micrognathia. Congenital heart disease (CHD), typically atrioventricular septal...