Advances in the Genetics of Congenital Heart Disease: A Clinician's Guide

Outcomes and experiences of genetic testing in children with congenital heart disease

BACKGROUND

Following genomic advances, genetic testing options for paediatric patients with congenital heart disease (CHD) have evolved significantly. A single-site audit was conducted to assess testing outcomes and a survey created to explore family experiences and preferences.

METHOD

All genetic tests ordered in postcardiac surgery patients with CHD at The Children's Hospital at Westmead between January 2017 and December 2021 were reviewed. Diagnostic yield, clinical and demographic factors, and testing trends over time were evaluated. Surveys were sent to parents of children who had met a clinical geneticist (n=112).

RESULTS

Genetic testing was completed in 607 individuals (74 molecular testing; 533 cytogenetic testing only). The diagnostic rate was 36% and 9%, respectively. Use of molecular testing significantly increased over time (p=0.033), but yield did not (p=0.288). Molecular testing yield was high in neonates (64%), and patients with extracardiac anomalies (40%) or relevant family history (40%). Brain (p=0.022), haematological/cancer (p≤0.001), immune (p≤0.001), endocrine (p≤0.001) anomalies and intellectual disability (p=0.027) were associated with a diagnosis following cytogenetic testing. Short stature was significantly associated with diagnostic yield following molecular testing (p=0.012). Survey respondents (n=28) reported a positive experience (p=0.013) with minimal decisional regret (p=0.322).

CONCLUSION

Cytogenetic testing remains an important first-tier test in CHD. Furthermore, molecular testing guided by a clinical geneticist generates a high rate of genetic diagnoses. Parents of children with CHD value genetic testing with little regret.

Foetal cortical expansion is associated with neurodevelopmental outcome at 2-years in congenital heart disease: a longitudinal follow-up study

BACKGROUND

In adolescents and adults with complex congenital heart disease (CHD), abnormal cortical folding is a putative predictor of poor neurodevelopmental outcome. However, it is unknown when this relationship first emerges. We test the hypothesis that it begins in utero, when the brain starts to gyrify and folding patterns first become established.

METHODS

We carried out a prospective, longitudinal case-control study, acquiring foetal MRIs at two timepoints in utero, (Scan 1 = 20-30 Gestational Weeks (GW) and Scan 2 = 30-39 GW), then followed up participants at two years of age to assess neurodevelopmental outcomes. We used normative modelling to chart growth trajectories of surface features across 60 cortical regions in a control population (n = 157), then quantified the deviance of each foetus with CHD (n = 135) and explored the association with neurodevelopmental outcomes at two years of age.

FINDINGS

Differences in cortical development between CHD and Control foetuses only emerged after 30 GW, and lower regional cortical surface area growth was correlated with poorer neurodevelopmental outcomes at two years of age in the CHD group.

INTERPRETATION

This work highlights the third trimester specifically as a critical period in brain development for foetuses with CHD, where the reduced surface area expansion in specific cortical regions becomes consequential in later life, and predictive of neurodevelopmental outcome in toddlerhood.

FUNDING

This research was supported by the NINDS (R01NS114087, K23NS101120) and NIBIB (R01EB031170) of the NIH, PHN Scholar Award, AAN Clinical Research Training Fellowship, BBRF Young Investigator Awards, and the Farb Family Fund.

Molecular genetics of congenital heart disease

Congenital heart disease (CHD) is the most prevalent human birth defect and remains a leading cause of mortality in childhood. Although advancements in surgical and medical interventions have significantly reduced mortality rates among infants with critical CHDs, many survivors experience substantial cardiac and extracardiac comorbidities that affect their quality of life. The etiology of CHD is multifactorial, involving both genetic and environmental factors, yet a definitive cause remains unidentified in many cases. Recent advancements in genetic testing technologies have improved our ability to identify the genetic causes of CHD. This review presents an updated summary of the established genetic contributions to CHD, including chromosomal aberrations and mutations in genes associated with transcription factors, cardiac structural proteins, chromatin modifiers, cilia-related proteins, and cell signaling pathways. Furthermore, we discuss recent findings that support the roles of non-coding mutations and complex inheritance in the etiology of CHD.

Congenital heart disease presentations in the 15q11.2 microdeletion syndrome

Congenital heart disease (CHD) is the most common type of birth defect and results from anomalies in the cardiogenesis process. There are multiple genetic mechanisms contributing to CHD, including copy number variants (CNVs). One such CNV is the 15q11.2 (BP1-BP2) microdeletion, which contains four evolutionarily conserved genes: NIPA1, NIPA2, CYFIP1, and TUBGCP5. The deletion causes a syndrome which includes developmental delays and multiple anatomical malformations including CHD. The link between the 15q11.2 (BP1-BP2) microdeletion and CHD has been previously described in the literature but not explored in terms of mechanistic investigations. The characteristics of the BP1-BP2 deletion also prove challenging in the context of genetic counselling. Here we discuss the 15q11.2 (BP1-BP2) microdeletion syndrome with a focus on CHD.

Computational analysis of congenital heart disease associated SNPs: unveiling their impact on the gene regulatory system

Congenital heart disease (CHD) is a prevalent condition characterized by defective heart development, causing premature death and stillbirths among infants. Genome-wide association studies (GWASs) have provided insights into the role of genetic variants in CHD pathogenesis through the identification of a comprehensive set of single-nucleotide polymorphisms (SNPs). Notably, 90-95% of these variants reside in the noncoding genome, complicating the understanding of their underlying mechanisms. Here, we developed a systematic computational pipeline for the identification and analysis of CHD-associated SNPs spanning both coding and noncoding regions of the genome. Initially, we curated a thorough dataset of SNPs from GWAS-catalog and ClinVar database and filtered them based on CHD-related traits. Subsequently, these CHD-SNPs were annotated and categorized into noncoding and coding regions based on their location. To study the functional implications of noncoding CHD-SNPs, we cross-validated them with enhancer-specific histone modification marks from developing human heart across 9 Carnegie stages and identified potential cardiac enhancers. This approach led to the identification of 2,056 CHD-associated putative enhancers (CHD-enhancers), 38.9% of them overlapping with known enhancers catalogued in human enhancer disease database. We identified heart-related transcription factor binding sites within these CHD-enhancers, offering insights into the impact of SNPs on TF binding. Conservation analysis further revealed that many of these CHD-enhancers were highly conserved across vertebrates, suggesting their evolutionary significance. Utilizing heart-specific expression quantitative trait loci data, we further identified a subset of 63 CHD-SNPs with regulatory potential distributed across various cardiac tissues. Concurrently, coding CHD-SNPs were represented as a protein interaction network and its subsequent binding energy analysis focused on a pair of proteins within this network, pinpointed a deleterious coding CHD-SNP, rs770030288, located in C2 domain of MYBPC3 protein. Overall, our findings demonstrate that SNPs have the potential to disrupt gene regulatory systems, either by affecting enhancer sequences or modulating protein-protein interactions, which can lead to abnormal developmental processes contributing to CHD pathogenesis.

Structural Covariance Networks in the Fetal Brain Reveal Altered Neurodevelopment for Specific Subtypes of Congenital Heart Disease

BACKGROUND

Altered structural brain development has been identified in fetuses with congenital heart disease (CHD), suggesting that the neurodevelopmental impairment observed later in life might originate in utero. There are many interacting factors that may perturb neurodevelopment during the fetal period and manifest as structural brain alterations, such as altered cerebral substrate delivery and aberrant fetal hemodynamics.

METHODS AND RESULTS

We extracted structural covariance networks from the log Jacobian determinants of 435 in utero T2 weighted image magnetic resonance imaging scans, (n=67 controls, 368 with CHD) acquired during the third trimester. We fit general linear models to test whether age, sex, expected cerebral substrate delivery, and CHD diagnosis were significant predictors of structural covariance. We identified significant effects of age, sex, cerebral substrate delivery, and specific CHD diagnosis across a variety of structural covariance networks, including primary motor and sensory cortices, cerebellar regions, frontal cortex, extra-axial cerebrospinal fluid, thalamus, brainstem, and insula, consistent with widespread coordinated aberrant maturation of specific brain regions over the third trimester.

CONCLUSIONS

Structural covariance networks offer a sensitive, data-driven approach to explore whole-brain structural changes without anatomical priors. We used them to stratify a heterogenous patient cohort with CHD, highlighting similarities and differences between diagnoses during fetal neurodevelopment. Although there was a clear effect of abnormal fetal hemodynamics on structural brain maturation, our results suggest that this alone does not explain all the variation in brain development between individuals with CHD.

The global, regional, and national patterns of change in the burden of congenital birth defects, 1990-2021: an analysis of the global burden of disease study 2021 and forecast to 2040

Background

Congenital birth defects (CBDs) present enormous challenges to global healthcare systems. These conditions severely impact patients' health and underscore issues related to socioeconomic development and healthcare accessibility and efficiency. Previous studies have been geographically limited and lacked comprehensive global analysis. This study provides global, regional, and national disability-adjusted life years (DALYs) data for four major congenital birth defects-congenital heart defects (CHD), neural tube defects (NTDs), digestive congenital anomalies (DCAs), and Down syndrome (DS) from 1990 to 2021, emphasizing health inequalities. The goal is to offer scientific evidence for optimizing resource allocation, focusing on high-burden populations, and reducing disease burden.

Methods

This study systematically evaluated the global, regional, and national burden of CBDs and their changes from 1990 to 2021 using the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2021. To conduct a more focused analysis, four specific CBDs were selected: CHD, NTDs, DCAs, and DS. DALYs were used as the metric, combined with the sociodemographic index (SDI). Analyses included the slope index of inequality and concentration index to measure health inequalities, frontier analysis to estimate achievable outcomes based on development levels, decomposition analysis to identify drivers of disease burden changes, Joinpoint regression analysis to assess temporal trends, and the Bayesian age-period-cohort (BAPC) model to predict future disease burden trends.

Findings

Compared to 1990, the global burden of the CBDs in 2021 showed a downward trend. Males had a higher burden than females, with the highest burden observed in low-SDI regions. When examining CHD, NTDs, DCAs, and DS specifically, trends in burden changes varied across different CBDs at the global, regional, and national levels. Frontier analysis revealed potential for burden improvement in various countries and territories. Decomposition analysis highlighted differences in disease burden drivers across SDI regions, showing the greatest improvement observed in low-SDI regions. Joinpoint regression analysis indicated a downward trend in DALYs burden across SDI regions, and BAPC model predictions suggested that the burden of CBDs will continue to decline in the future.

Interpretation

CBDs pose a major challenge to global public health. Despite an overall decline in disease burden, health inequalities remain prominent, particularly in countries and territories with lower levels of development. Future public health interventions should focus on countries and territories with low levels of development by optimizing healthcare resource allocation, improving basic health infrastructure, enhancing health education, and reducing disease burden inequalities. Global collaboration and data sharing are essential to promote a lifecycle management model for CBDs research and treatment, advancing global health development.

Funding

This study was supported by the National Natural Science Foundation of China (No. 82270310) and the Jiangsu Provincial Key Research and Development Program (No. BE2023662).

Performance of Dysmorphology-Based Screening for Genetic Disorders in Pediatric Congenital Heart Disease Supports Wider Genetic Testing

BACKGROUND

Dysmorphology evaluation is important for congenital heart disease (CHD) assessment, but there are no prior investigations quantifying the screening performance compared to standardized genetics evaluations. We investigated this through systematic dysmorphology assessment in CHD patients with standardized genetic testing in primarily pediatric patients with CHD.

METHODS

Dysmorphology evaluations preceding genetic testing results allowed us to test for associations between dysmorphic status and genetic diagnoses while adjusting for extracardiac anomalies (ECAs). We use a test-negative case-control design on a pediatric inpatient CHD cohort for our study.

RESULTS

Of 568 patients, nearly 96% of patients completed genetic testing, primarily chromosome microarray (CMA) ± exome sequencing-based genetic testing (493/568, 86.8%). Overall, 115 patients (20.2%) were found to have genetic diagnoses, and dysmorphic patients had doubled risk of genetic diagnoses, after ECA adjustment (OR = 2.10, p = 0.0030). We found that 7.9% (14/178) of ECA-/nondysmorphic patients had genetic diagnoses, which increased to 13.5% (26/192) in the ECA-/dysmorphic patients. Nearly 43% of ECA+/dysmorphic patients had genetic diagnoses (63/147). The positive predictive value of dysmorphic status was only 26.3%, and the negative predictive value of nondysmorphic status was 88.7%.

CONCLUSIONS

Dysmorphology-based prediction of genetic disorders is limited because of diagnoses found in apparently isolated CHD. Our findings represent one of the only assessments of phenotype-based screening for genetic disorders in CHD and should inform clinical genetics evaluation practices for pediatric CHD.

Global research landscape on the genetics of congenital heart disease: A bibliometric and visualized analysis via VOSviewer and CiteSpace

Genetic factors play a significant role in the development of congenital heart disease (CHD). Many studies on the genetics of CHD have been published worldwide; however, no research has assessed and mapped the global research landscape of these studies. This bibliometric and visualized study aimed to delineate research hotspots and trends in the field of CHD genetics. Scientific papers on the genetics of CHD from January 1, 1950, to December 31, 2023, were obtained by searching the Web of Science Core Collection. The bibliometric metadata of each chosen research paper were extracted, analyzed, and visualized using tools such as Microsoft Excel 2021, VOSviewer, and CiteSpace. The final analysis included 5317 papers discussing the genetics of CHD. The countries and journals that published the highest number of papers were the United States (n = 2118), and American Journal of Medical Genetics Part A (n = 332), respectively. In addition to CHD and genetics, keywords such as tetralogy of Fallot, ventricular septal defect, and atrial septal defect appeared most frequently among 8365 keywords. Eight clusters were formed to categorize the keywords. Keywords such as case-control study, whole genome sequencing, and whole exome sequencing in clusters 6, 7, and 8, respectively, had the latest average publication year among all clusters. To the best of our knowledge, this is the first bibliometric analysis of CHD genetics studies. Tetralogy of Fallot, ventricular septal defect, and atrial septal defect are global research topics. The interactions between environmental and genetic factors in the pathogenesis of CHD, genetic etiology of CHD-associated pulmonary arterial hypertension, and molecular genetics of CHD via high-throughput genomic technology are possible areas of future research on the genetics of CHD.

A validated heart-specific model for splice-disrupting variants in childhood heart disease

BACKGROUND

Congenital heart disease (CHD) is the most common congenital anomaly. Almost 90% of isolated cases have an unexplained genetic etiology after clinical testing. Non-canonical splice variants that disrupt mRNA splicing through the loss or creation of exon boundaries are not routinely captured and/or evaluated by standard clinical genetic tests. Recent computational algorithms such as SpliceAI have shown an ability to predict such variants, but are not specific to cardiac-expressed genes and transcriptional isoforms.

METHODS

We used genome sequencing (GS) (n = 1101 CHD probands) and myocardial RNA-Sequencing (RNA-Seq) (n = 154 CHD and n = 43 cardiomyopathy probands) to identify and validate splice disrupting variants, and to develop a heart-specific model for canonical and non-canonical splice variants that can be applied to patients with CHD and cardiomyopathy. Two thousand five hundred seventy GS samples from the Medical Genome Reference Bank were analyzed as healthy controls.

RESULTS

Of 8583 rare DNA splice-disrupting variants initially identified using SpliceAI, 100 were associated with altered splice junctions in the corresponding patient myocardium affecting 95 genes. Using strength of myocardial gene expression and genome-wide DNA variant features that were confirmed to affect splicing in myocardial RNA, we trained a machine learning model for predicting cardiac-specific splice-disrupting variants (AUC 0.86 on internal validation). In a validation set of 48 CHD probands, the cardiac-specific model outperformed a SpliceAI model alone (AUC 0.94 vs 0.67 respectively). Application of this model to an additional 947 CHD probands with only GS data identified 1% patients with canonical and 11% patients with non-canonical splice-disrupting variants in CHD genes. Forty-nine percent of predicted splice-disrupting variants were intronic and > 10 bp from existing splice junctions. The burden of high-confidence splice-disrupting variants in CHD genes was 1.28-fold higher in CHD cases compared with healthy controls.

CONCLUSIONS

A new cardiac-specific in silico model was developed using complementary GS and RNA-Seq data that improved genetic yield by identifying a significant burden of non-canonical splice variants associated with CHD that would not be detectable through panel or exome sequencing.

From genes to therapy: A comprehensive exploration of congenital heart disease through the lens of genetics and emerging technologies

Congenital heart disease (CHD) affects approximately 1 % of live births worldwide, making it the most common congenital anomaly in newborns. Recent advancements in genetics and genomics have significantly deepened our understanding of the genetics of CHDs. While the majority of CHD etiology remains unclear, evidence consistently indicates that genetics play a significant role in its development. CHD etiology holds promise for enhancing diagnosis and developing novel therapies to improve patient outcomes. In this review, we explore the contributions of both monogenic and polygenic factors of CHDs and highlight the transformative impact of emerging technologies on these fields. We also summarized the state-of-the-art techniques, including targeted next-generation sequencing (NGS), whole genome and whole exome sequencing (WGS, WES), single-cell RNA sequencing (scRNA-seq), human induced pluripotent stem cells (hiPSCs) and others, that have revolutionized our understanding of cardiovascular disease genetics both from diagnosis perspective and from disease mechanism perspective in children and young adults. These molecular diagnostic techniques have identified new genes and chromosomal regions involved in syndromic and non-syndromic CHD, enabling a more defined explanation of the underlying pathogenetic mechanisms. As our knowledge and technologies continue to evolve, they promise to enhance clinical outcomes and reduce the CHD burden worldwide.

Cardiomyocyte proliferation and regeneration in congenital heart disease

Despite advances in prenatal screening and a notable decrease in mortality rates, congenital heart disease (CHD) remains the most prevalent congenital disorder in newborns globally. Current therapeutic surgical approaches face challenges due to the significant rise in complications and disabilities. Emerging cardiac regenerative therapies offer promising adjuncts for CHD treatment. One novel avenue involves investigating methods to stimulate cardiomyocyte proliferation. However, the mechanism of altered cardiomyocyte proliferation in CHD is not fully understood, and there are few feasible approaches to stimulate cardiomyocyte cell cycling for optimal healing in CHD patients. In this review, we explore recent progress in understanding genetic and epigenetic mechanisms underlying defective cardiomyocyte proliferation in CHD from development through birth. Targeting cell cycle pathways shows promise for enhancing cardiomyocyte cytokinesis, division, and regeneration to repair heart defects. Advancements in human disease modeling techniques, CRISPR-based genome and epigenome editing, and next-generation sequencing technologies will expedite the exploration of abnormal machinery governing cardiomyocyte differentiation, proliferation, and maturation across diverse genetic backgrounds of CHD. Ongoing studies on screening drugs that regulate cell cycling are poised to translate this nascent technology of enhancing cardiomyocyte proliferation into a new therapeutic paradigm for CHD surgical interventions.

ENU-based dominant genetic screen identifies contractile and neuronal gene mutations in congenital heart disease

BACKGROUND

Congenital heart disease (CHD) is the most prevalent congenital anomaly, but its underlying causes are still not fully understood. It is believed that multiple rare genetic mutations may contribute to the development of CHD.

METHODS

In this study, we aimed to identify novel genetic risk factors for CHD using an ENU-based dominant genetic screen in mice. We analyzed fetuses with malformed hearts and compared them to control littermates by whole exome or whole genome sequencing (WES/WGS). The differences in mutation rates between observed and expected values were tested using the Poisson and Binomial distribution. Additionally, we compared WES data from human CHD probands obtained from the Pediatric Cardiac Genomics Consortium with control subjects from the 1000 Genomes Project using Fisher's exact test to evaluate the burden of rare inherited damaging mutations in patients.

RESULTS

By screening 10,285 fetuses, we identified 1109 cases with various heart defects, with ventricular septal defects and bicuspid aortic valves being the most common types. WES/WGS analysis of 598 cases and 532 control littermates revealed a higher number of ENU-induced damaging mutations in cases compared to controls. GO term and KEGG pathway enrichment analysis showed that pathways related to cardiac contraction and neuronal development and functions were enriched in cases. Further analysis of 1457 human CHD probands and 2675 control subjects also revealed an enrichment of genes associated with muscle and nervous system development in patients. By combining the mice and human data, we identified a list of 101 candidate digenic genesets, from which each geneset was co-mutated in at least one mouse and two human probands with CHD but not in control mouse and control human subjects.

CONCLUSIONS

Our findings suggest that gene mutations affecting early hemodynamic perturbations in the developing heart may play a significant role as a genetic risk factor for CHD. Further validation of the candidate gene set identified in this study could enhance our understanding of the complex genetics underlying CHD and potentially lead to the development of new diagnostic and therapeutic approaches.

The Kids Heart BioBank: supporting 20 years of patient care and research into CHD

INTRODUCTION

The cause of most CHD is unknown and considered complex, implicating genetic and environmental factors in disease causation. The Kids Heart BioBank was established in 2003 to accelerate genetic investigations into CHD.

METHODS

Recruitment includes patients undergoing interventions for CHD at The Children's Hospital at Westmead. Informed consent is obtained from parents/guardians, and blood is collected at the time of cardiac intervention from which DNA is extracted and stored. Associated detailed clinical information and a family history are stored in the purpose-designed database.

RESULTS

To date, the Kids Heart BioBank contains biospecimens and associated clinical information from over 4,900 patients with CHD and their families. Two-thirds (64.1%) of probands have been included in research studies with 28.9% of participants who underwent genomic sequencing receiving a molecular diagnosis with direct clinical utility. The value of this resource to patients and families is highlighted by the high consent rate (94.6%) and the low withdrawal of consent rate (0.4%). The Kids Heart BioBank has supported many large national and international collaborations and contributed significantly to CHD research.

CONCLUSIONS

The Kids Heart BioBank is an invaluable resource and, together with other similar resources, the resulting research has paved the way for clinical genetic testing options for CHD patients, previously not possible. With research in the field moving away from diagnosing monogenic disease, the Kids Heart BioBank is ideally placed to support the next chapter of research efforts into complex disease mechanisms, requiring large patient cohorts with detailed phenotypic information.

Conotruncal Heart Defects: A Narrative Review of Molecular Genetics, Genomics Research and Innovation

Congenital heart defects (CHDs) are most prevalent cardiac defects that occur at birth, leading to significant neonatal mortality and morbidity, especially in the developing nations. Among the CHDs, conotruncal heart defects (CTDs) are particularly noteworthy, comprising a significant portion of congenital cardiac anomalies. While advances in imaging and surgical techniques have improved the diagnosis, prognosis, and management of CTDs, their molecular genetics and genomic substrates remain incompletely understood. This expert review covers the recent advances from January 2016 onward and examines the complexities surrounding the genetic etiologies, prevalence, embryology, diagnosis, and clinical management of CTDs. We also emphasize the known copy number variants and single nucleotide variants associated with CTDs, along with the current planetary health research efforts aimed at CTDs in large cohort studies. In all, this comprehensive narrative review of molecular genetics and genomics research and innovation on CTDs draws from and highlights selected works from around the world and offers new ideas for advances in CTD diagnosis, precision medicine interventions, and accurate assessment of prognosis and recurrence risks.

Cardiac Development and Factors Influencing the Development of Congenital Heart Defects (CHDs): Part I

The traditional description of cardiac development involves progression from a cardiac crescent to a linear heart tube, which in the phase of transformation into a mature heart forms a cardiac loop and is divided with the septa into individual cavities. Cardiac morphogenesis involves numerous types of cells originating outside the initial cardiac crescent, including neural crest cells, cells of the second heart field origin, and epicardial progenitor cells. The development of the fetal heart and circulatory system is subject to regulatation by both genetic and environmental processes. The etiology for cases with congenital heart defects (CHDs) is largely unknown, but several genetic anomalies, some maternal illnesses, and prenatal exposures to specific therapeutic and non-therapeutic drugs are generally accepted as risk factors. New techniques for studying heart development have revealed many aspects of cardiac morphogenesis that are important in the development of CHDs, in particular transposition of the great arteries.

Congenital heart diseases (CHDs) and forensic investigations: Searching for the cause of death

Congenital Heart Diseases (CHDs) are a group of structural abnormalities or defects of the heart that are present at birth. CHDs could be connected to sudden death (SD), defined by the WHO (World Health Organization) as "death occurring within 24 h after the onset of the symptoms" in an apparently "healthy" subject. These conditions can range from relatively mild defects to severe, life-threatening anomalies. The prevalence of CHDs varies across populations, but they affect millions of individuals worldwide. This article aims to discuss the post-mortem investigation of death related to CHDs, exploring the forensic approach, current methodologies, challenges, and potential advancements in this challenging field. A further goal of this article is to provide a guide for understanding these complex diseases, highlighting the pivotal role of autopsy, histopathology, and genetic investigations in defining the cause of death, and providing evidence about the translational use of autopsy reports. Forensic investigations play a crucial role in understanding the complexities of CHDs and determining the cause of death accurately. Through collaboration between medical professionals and forensic experts, meticulous examinations, and analysis of evidence, valuable insights can be gained. These insights not only provide closure to the families affected but also contribute to the prevention of future tragedies.

Potential Impact of a Pregnant Woman's Microbiota on the Development of Fetal Heart Defects: A Review of the Literature

Developments in medicine and biology in recent decades have led to a significant increase in our knowledge of the complex interactions between the microbiota and human health. In the context of perinatal medicine and neonatology, particular attention is being paid to the potential impact of the maternal microbiota on fetal development. Among the many aspects of this relationship, the question of the impact of dysbiosis on the development of fetal heart defects is an important one. In this article, we present an analysis of recent research and scientific evidence on the relationship between a pregnant woman's microbiota and the development of fetal heart defects. We also discuss potential intervention strategies, including the role of probiotics and diet in optimising the maternal microbiota.

Co-Occurrence of Sensorineural Hearing Loss and Congenital Heart Disease: Etiologies and Management

OBJECTIVES/HYPOTHESIS

The co-occurrence of sensorineural hearing loss (SNHL) and congenital heart disease (CHD) is a rare condition with complex etiologies. The purpose of this study is to assess the etiologies, clinical features, and outcomes of cochlear implant (CI) in this patient population.

STUDY DESIGN

Case series and literature review.

METHODS

Clinical data of children who were diagnosed with SNHL and CHD and received CIs at a tertiary hospital from 2016 to 2021 were retrospectively analyzed. A literature review was performed to identify patients with SNHL and CHD.

FINDINGS

Of the 382 children who underwent cochlear implantation at our center, eight (2.1%) were diagnosed with SNHL and CHD. A literature review identified 1525 patients from 254 studies; the database therefore consisted of 1533 patients. The most common genetic etiologies of co-occurring SNHL and CHD were CHARGE syndrome (36.3%), Turner syndrome (8.4%), 22q11.2 deletion (3.0%), Noonan syndrome (2.9%), and Down syndrome (2.5%), whereas the most common non-genetic etiologies were congenital rubella syndrome (22.9%) and SNHL after early cardiac surgery (5.5%). Most of the patients presented with congenital, bilateral, severe-profound SNHL requiring early rehabilitation. Of the 126 children who received CIs at a median age of 2.5 years, half showed delayed speech development at last follow-up.

CONCLUSIONS

Co-occurring SNHL and CHD is a rare condition with complex etiologies. Timely hearing intervention with long-term follow-up and proper timing of heart surgery is essential for these children.

LEVEL OF EVIDENCE

4, case series Laryngoscope, 134:400-409, 2024.

Human Genetics of Ventricular Septal Defect

Ventricular septal defects (VSDs) are recognized as one of the commonest congenital heart diseases (CHD), accounting for up to 40% of all cardiac malformations, and occur as isolated CHDs as well as together with other cardiac and extracardiac congenital malformations in individual patients and families. The genetic etiology of VSD is complex and extraordinarily heterogeneous. Chromosomal abnormalities such as aneuploidy and structural variations as well as rare point mutations in various genes have been reported to be associated with this cardiac defect. This includes both well-defined syndromes with known genetic cause (e.g., DiGeorge syndrome and Holt-Oram syndrome) and so far undefined syndromic forms characterized by unspecific symptoms. Mutations in genes encoding cardiac transcription factors (e.g., NKX2-5 and GATA4) and signaling molecules (e.g., CFC1) have been most frequently found in VSD cases. Moreover, new high-resolution methods such as comparative genomic hybridization enabled the discovery of a high number of different copy number variations, leading to gain or loss of chromosomal regions often containing multiple genes, in patients with VSD. In this chapter, we will describe the broad genetic heterogeneity observed in VSD patients considering recent advances in this field.

Human Genetics of Congenital Heart Defects

Congenital heart diseases (or congenital heart defects/disorders; CHDs) are structural abnormalities of the heart and/or great vessels that are present at birth. CHDs include an extensive range of defects that may be minor and require no intervention or may be life-limiting and require complex surgery shortly after birth. This chapter reviews the current knowledge on the genetic causes of CHD.

SMC5 Plays Independent Roles in Congenital Heart Disease and Neurodevelopmental Disability

Up to 50% of patients with severe congenital heart disease (CHD) develop life-altering neurodevelopmental disability (NDD). It has been presumed that NDD arises in CHD cases because of hypoxia before, during, or after cardiac surgery. Recent studies detected an enrichment in de novo mutations in CHD and NDD, as well as significant overlap between CHD and NDD candidate genes. However, there is limited evidence demonstrating that genes causing CHD can produce NDD independent of hypoxia. A patient with hypoplastic left heart syndrome and gross motor delay presented with a de novo mutation in SMC5. Modeling mutation of smc5 in Xenopus tropicalis embryos resulted in reduced heart size, decreased brain length, and disrupted pax6 patterning. To evaluate the cardiac development, we induced the conditional knockout (cKO) of Smc5 in mouse cardiomyocytes, which led to the depletion of mature cardiomyocytes and abnormal contractility. To test a role for Smc5 specifically in the brain, we induced cKO in the mouse central nervous system, which resulted in decreased brain volume, and diminished connectivity between areas related to motor function but did not affect vascular or brain ventricular volume. We propose that genetic factors, rather than hypoxia alone, can contribute when NDD and CHD cases occur concurrently.

Case-control association study of congenital heart disease from a tertiary paediatric cardiac centre from North India

BACKGROUND

Congenital Heart diseases (CHDs) account for 1/3rd of all congenital birth defects. Etiopathogenesis of CHDs remain elusive despite extensive investigations globally. Phenotypic heterogeneity witnessed in this developmental disorder reiterate gene-environment interactions with periconceptional factors as risk conferring; and genetic analysis of both sporadic and familial forms of CHD suggest its multigenic basis. Significant association of de novo and inherited variants have been observed. Approximately 1/5th of CHDs are documented in the ethnically distinct Indian population but genetic insights have been very limited. This pilot case-control based association study was undertaken to investigate the status of Caucasian SNPs in a north Indian cohort.

METHOD

A total of 306 CHD cases sub-classified into n = 198 acyanotic and n = 108 cyanotic types were recruited from a dedicated tertiary paediatric cardiac centre in Palwal, Haryana. 23 SNPs primarily prioritized from Genome-wide association studies (GWAS) on Caucasians were genotyped using Agena MassARRAY Technology and test of association was performed with adequately numbered controls.

RESULTS

Fifty percent of the studied SNPs were substantially associated in either allelic, genotypic or sub-phenotype categories validating their strong correlation with disease manifestation. Of note, strongest allelic association was observed for rs73118372 in CRELD1 (p < 0.0001) on Chr3, rs28711516 in MYH6 (p = 0.00083) and rs735712 in MYH7 (p = 0.0009) both on Chr 14 and were also significantly associated with acyanotic, and cyanotic categories separately. rs28711516 (p = 0.003) and rs735712 (p = 0.002) also showed genotypic association. Strongest association was observed with rs735712(p = 0.003) in VSD and maximum association was observed for ASD sub-phenotypes.

CONCLUSIONS

Caucasian findings were partly replicated in the north Indian population. The findings suggest the contribution of genetic, environmental and sociodemographic factors, warranting continued investigations in this study population.

Association of MTR gene polymorphisms with the occurrence of non-syndromic congenital heart disease: a case-control study

To exhaustively explore the association of infant genetic polymorphisms of methionine synthase (MTR) gene with the risk of non-syndromic congenital heart disease (CHD). A hospital-based case-control study involving 620 CHD cases and 620 health controls was conducted from November 2017 to March 2020. Eighteen SNPs were detected and analyzed. Our date suggested that the genetic polymorphisms of MTR gene at rs1805087 (GG vs. AA: aOR = 6.85, 95% CI 2.94-15.96; the dominant model: aOR = 1.77, 95% CI 1.35-2.32; the recessive model: aOR = 6.26, 95% CI 2.69-14.54; the addictive model: aOR = 1.81, 95% CI 1.44-2.29) and rs2275565 (GT vs. GG: aOR = 1.52, 95% CI 1.15-1.20; TT vs. GG: aOR = 4.93, 95% CI 1.93-12.58; the dominant model: aOR = 1.66, 95% CI 1.27-2.17; the recessive model: aOR = 4.41, 95% CI 1.73-11.22; the addictive model: aOR = 1.68, 95% CI 1.32-2.13) were significantly associated with the higher risk of CHD. And three haplotypes of G-A-T (involving rs4659724, rs95516 and rs4077829; OR = 5.48, 95% CI 2.58-11.66), G-C-A-T-T-G (involving rs2275565, rs1266164, rs2229276, rs4659743, rs3820571 and rs1050993; OR = 0.78, 95% CI 0.63-0.97) and T-C-A-T-T-G (involving rs2275565, rs1266164, rs2229276, rs4659743, rs3820571 and rs1050993; OR = 1.60, 95% CI 1.26-2.04) were observed to be significantly associated with risk of CHD. Our study found that genetic polymorphisms of MTR gene at rs1805087 and rs2275565 were significantly associated with higher risk of CHD. Additionally, our study revealed a significant association of three haplotypes with risk of CHD. However, the limitations in this study should be carefully taken into account. In the future, more specific studies in different ethnic populations are required to refine and confirm our findings.Trial registration: Registration number: ChiCTR1800016635; Date of first registration: 14/06/2018.

Genetic Alterations of Transcription Factors and Signaling Molecules Involved in the Development of Congenital Heart Defects-A Narrative Review

Congenital heart defects (CHD) are the most common congenital abnormality, with an overall global birth prevalence of 9.41 per 1000 live births. The etiology of CHDs is complex and still poorly understood. Environmental factors account for about 10% of all cases, while the rest are likely explained by a genetic component that is still under intense research. Transcription factors and signaling molecules are promising candidates for studies regarding the genetic burden of CHDs. The present narrative review provides an overview of the current knowledge regarding some of the genetic mechanisms involved in the embryological development of the cardiovascular system. In addition, we reviewed the association between the genetic variation in transcription factors and signaling molecules involved in heart development, including TBX5, GATA4, NKX2-5 and CRELD1, and congenital heart defects, providing insight into the complex pathogenesis of this heterogeneous group of diseases. Further research is needed in order to uncover their downstream targets and the complex network of interactions with non-genetic risk factors for a better molecular-phenotype correlation.

CHD-associated enhancers shape human cardiomyocyte lineage commitment

Enhancers orchestrate gene expression programs that drive multicellular development and lineage commitment. Thus, genetic variants at enhancers are thought to contribute to developmental diseases by altering cell fate commitment. However, while many variant-containing enhancers have been identified, studies to endogenously test the impact of these enhancers on lineage commitment have been lacking. We perform a single-cell CRISPRi screen to assess the endogenous roles of 25 enhancers and putative cardiac target genes implicated in genetic studies of congenital heart defects (CHDs). We identify 16 enhancers whose repression leads to deficient differentiation of human cardiomyocytes (CMs). A focused CRISPRi validation screen shows that repression of TBX5 enhancers delays the transcriptional switch from mid- to late-stage CM states. Endogenous genetic deletions of two TBX5 enhancers phenocopy epigenetic perturbations. Together, these results identify critical enhancers of cardiac development and suggest that misregulation of these enhancers could contribute to cardiac defects in human patients.

Evaluating High-Confidence Genes in Conotruncal Cardiac Defects by Gene Burden Analyses

Background In nonsyndromic conotruncal cardiac defects, the use of next-generation sequencing for clinical diagnosis is increasingly adopted, but gene-disease associations in research are only partially translated to diagnostic panels, suggesting a need for evidence-based consensus. Methods and Results In an exome data set of 245 patients with conotruncal cardiac defects, we performed burden analysis on a high-confidence congenital heart disease gene list (n=132) with rare (<0.01%) and ultrarare (absent in the Genome Aggregation Database) protein-altering variants. Overall, we confirmed an excess of rare variants compared with ethnicity-matched controls and identified 2 known genes (GATA6, NOTCH1) and 4 candidate genes supported by the literature (ANKRD11, DOCK6, NPHP4, and STRA6). Ultrarare variant analysis was performed in combination with 3 other published studies (n=1451) and identified 3 genes (FLT4, NOTCH1, TBX1) to be significant, whereas a subgroup analysis involving 391 Chinese subjects identified only GATA6 as significant. Conclusions We suggest that these significant genes in our rare and ultrarare burden analyses warrant prioritization for clinical testing implied for rare inherited and de novo variants. Additionally, associations on ClinVar for these genes were predominantly variants of uncertain significance. Therefore, a more stringent assessment of gene-disease associations in a larger and ethnically diverse cohort is required to be prudent for future curation of conotruncal cardiac defect genes.

Maternal Serum tRNA-Derived Fragments (tRFs) as Potential Candidates for Diagnosis of Fetal Congenital Heart Disease

BACKGROUND

Congenital heart disease (CHD) is one of the most predominant birth defects that causes infant death worldwide. The timely and successful surgical treatment of CHD on newborns after delivery requires accurate detection and reliable diagnosis during pregnancy. However, there are no biomarkers that can serve as an early diagnostic factor for CHD patients. tRNA-derived fragments (tRFs) have been reported to play an important role in the occurrence and progression of numerous diseases, but their roles in CHD remains unknown.

METHODS

High-throughput sequencing was performed on the peripheral blood of pregnant women with an abnormal fetal heart and a normal fetal heart, and 728 differentially expressed tRFs/tiRNAs were identified, among which the top 18 tRFs/tiRNAs were selected as predictive biomarkers of CHD. Then, a quantitative reverse transcriptase polymerase chain reaction verified the expression of tRFs/tiRNAs in more clinical samples, and the correlation between tRFs/tiRNAs abnormalities and CHD was analyzed.

RESULTS

tRF-58:74-Gly-GCC-1 and tiRNA-1:35-Leu-CAG-1-M2 may be promising biomarkers. Through further bioinformatics analysis, we predicted that TRF-58:744-GLy-GCC-1 could induce CHD by influencing biological metabolic processes.

CONCLUSIONS

Our results provide a theoretical basis for the abnormally expressed tRF-58:74-Gly-GCC-1 in maternal peripheral blood as a new potential biomarker for the accurate diagnosis of CHD during pregnancy.

Epigenetic Evaluation of the TBX20 Gene and Environmental Risk Factors in Mexican Paediatric Patients with Congenital Septal Defects

The TBX20 gene has a key role during cardiogenesis, and it has been related to epigenetic mechanisms in congenital heart disease (CHD). The purpose of this study was to assess the association between DNA methylation status and congenital septal defects. The DNA methylation of seven CpG sites in the TBX20 gene promoter was analyzed through pyrosequencing as a quantitative method in 48 patients with congenital septal defects and 104 individuals with patent ductus arteriosus (PDA). The average methylation was higher in patients than in PDA (p < 0.001). High methylation levels were associated with a higher risk of congenital septal defects (OR = 4.59, 95% CI = 1.57-13.44, p = 0.005). The ROC curve analysis indicated that methylation of the TBX20 gene could be considered a risk marker for congenital septal defects (AUC = 0.682; 95% CI = 0.58-0.77; p < 0.001). The analysis of environmental risk factors in patients with septal defects and PDA showed an association between the consumption of vitamins (OR = 0.10; 95% CI = 0.01-0.98; p = 0.048) and maternal infections (OR = 3.10; 95% CI = 1.26-7.60; p = 0.013). These results suggest that differences in DNA methylation of the TBX20 gene can be associated with septal defects.

The Genetics of Neurodevelopment in Congenital Heart Disease

Congenital heart disease (CHD) is the most common birth anomaly, affecting almost 1% of infants. Neurodevelopmental delay is the most common extracardiac feature in people with CHD. Many factors may contribute to neurodevelopmental risk, including genetic factors, CHD physiology, and the prenatal/postnatal environment. Damaging variants are most highly enriched among individuals with extracardiac anomalies or neurodevelopmental delay in addition to CHD, indicating that genetic factors have an impact beyond cardiac tissues in people with CHD. Potential sources of genetic risk include large deletions or duplications that affect multiple genes, such as 22q11 deletion syndrome, single genes that alter both heart and brain development, such as CHD7, and common variants that affect neurodevelopmental resiliency, such as APOE. Increased use of genome-sequencing technologies in studies of neurodevelopmental outcomes in people with CHD will improve our ability to detect relevant genes and variants. Ultimately, such knowledge can lead to improved and more timely intervention of learning support for affected children.

A guide to prenatal counseling regarding neurodevelopment in congenital heart disease

Advances in cardiac surgical techniques taking place over the past 50 years have resulted in the vast majority of children born with congenital cardiac malformations now surviving into adulthood. As the focus shifts from survival to the functional outcomes of our patients, it is increasingly being recognized that a significant proportion of patients undergoing infant cardiac repair experience adverse neurodevelopmental (ND) outcomes. The etiology of abnormal brain development in the setting of congenital heart disease is poorly understood, complex, and likely multifactorial. Furthermore, the efficacy of therapies available for the learning disabilities, attention deficit, and hyperactivity disorders and other ND deficits complicating congenital heart disease is currently uncertain. This situation presents a challenge for prenatal counseling as current antenatal testing does not usually provide prognostic information regarding the likely ND trajectories of individual patients. However, we believe it is important for parents to be informed about potential issues with child development when a new diagnosis of congenital heart disease is disclosed. Parents deserve a comprehensive and thoughtful approach to this subject, which conveys the uncertainties involved in predicting the severity of any developmental disorders encountered, while emphasizing the improvements in outcomes that have already been achieved in infants with congenital heart disease. A balanced approach to counseling should also discuss what local arrangements are in place for ND follow-up. This review presents an up-to-date overview of ND outcomes in patients with congenital heart disease, providing possible approaches to communicating this information to parents during prenatal counseling in a sensitive and accurate manner.

Insights into the genetic architecture underlying complex, critical congenital heart disease

Congenital heart disease (CHD) has a multifactorial aetiology, raising the possibility of an underlying genetic burden, predisposing to disease but also variable expression, including variation in disease severity, and incomplete penetrance. Using whole genome sequencing (WGS), the findings of this study, indicate that complex, critical CHD is distinct from other types of disease due to increased genetic burden in common variation, specifically among established CHD genes. Additionally, these findings highlight associations with regulatory genes and environmental "stressors" in the final presentation of disease.

Investigation of Copy Number Variation in South African Patients With Congenital Heart Defects

BACKGROUND

Congenital heart disease (CHD) is a leading non-infectious cause of pediatric morbidity and mortality worldwide. Although the etiology of CHD is poorly understood, genetic factors including copy number variants (CNVs) contribute to the risk of CHD in individuals of European ancestry. The presence of rare CNVs in African CHD populations is unknown. This study aimed to identify pathogenic and likely pathogenic CNVs in South African patients with CHD.

METHODS

Genotyping was performed on 90 patients with nonsyndromic CHD using the Affymetrix CytoScan HD platform. These data were used to identify large, rare CNVs in known CHD-associated genes and candidate genes.

RESULTS

We identified eight CNVs overlapping known CHD-associated genes (GATA4, CRKL, TBX1, FLT4, B3GAT3, NSD1) in six patients. The analysis also revealed CNVs encompassing five candidate genes likely to play a role in the development of CHD (DGCR8, KDM2A, JARID2, FSTL1, CYFIP1) in five patients. One patient was found to have 47, XXY karyotype. We report a total discovery yield of 6.7%, with 5.6% of the cohort carrying pathogenic or likely pathogenic CNVs expected to cause the observed phenotypes.

CONCLUSIONS

In this study, we show that chromosomal microarray is an effective technique for identifying CNVs in African patients diagnosed with CHD and have demonstrated results similar to previous CHD genetic studies in Europeans. Novel potential CHD genes were also identified, indicating the value of genetic studies of CHD in ancestrally diverse populations.

WDR62 variants contribute to congenital heart disease by inhibiting cardiomyocyte proliferation

Background

Congenital heart disease (CHD) is the most common birth defect and has high heritability. Although some susceptibility genes have been identified, the genetic basis underlying the majority of CHD cases is still undefined.

Methods

A total of 1320 unrelated CHD patients were enrolled in our study. Exome‐wide association analysis between 37 tetralogy of Fallot (TOF) patients and 208 Han Chinese controls from the 1000 Genomes Project was performed to identify the novel candidate gene WD repeat‐containing protein 62 (WDR62). WDR62 variants were searched in another expanded set of 200 TOF patients by Sanger sequencing. Rescue experiments in zebrafish were conducted to observe the effects of WDR62 variants. The roles of WDR62 in heart development were examined in mouse models with Wdr62 deficiency. WDR62 variants were investigated in an additional 1083 CHD patients with similar heart phenotypes to knockout mice by multiplex PCR‐targeting sequencing. The cellular phenotypes of WDR62 deficiency and variants were tested in cardiomyocytes, and the molecular mechanisms were preliminarily explored by RNA‐seq and co‐immunoprecipitation.

Results

Seven WDR62 coding variants were identified in the 237 TOF patients and all were indicated to be loss of function variants. A total of 25 coding and 22 non‐coding WDR62 variants were identified in 80 (6%) of the 1320 CHD cases sequenced, with a higher proportion of WDR62 variation (8%) found in the ventricular septal defect (VSD) cohort. WDR62 deficiency resulted in a series of heart defects affecting the outflow tract and right ventricle in mouse models, including VSD as the major abnormality. Cell cycle arrest and an increased number of cells with multipolar spindles that inhibited proliferation were observed in cardiomyocytes with variants or knockdown of WDR62. WDR62 deficiency weakened the association between WDR62 and the cell cycle‐regulated kinase AURKA on spindle poles, reduced the phosphorylation of AURKA, and decreased expression of target genes related to cell cycle and spindle assembly shared by WDR62 and AURKA.

Conclusions

WDR62 was identified as a novel susceptibility gene for CHD with high variant frequency. WDR62 was shown to participate in the cardiac development by affecting spindle assembly and cell cycle pathway in cardiomyocytes.

Risk of cancer in young and older patients with congenital heart disease and the excess risk of cancer by syndromes, organ transplantation and cardiac surgery: Swedish health registry study (1930-2017)

Background

Increasing survival of patients with congenital heart disease (CHD) will result in an increased risk of age-dependent acquired diseases later in life. We aimed to investigate the risk of cancer in young and older patients with CHD and to evaluate the excess risk of cancer by syndromes, organ transplantation and cardiac surgery.

Methods

Patients with CHD born between 1930 and 2017 were identified using Swedish Health Registers. Each patient with CHD (n = 89,542) was matched by sex and birth year with ten controls without CHD (n = 890,472) from the Swedish Total Population Register.

Findings

4012 patients with CHD (4·5%) and 35,218 controls (4·0%) developed cancer. The median follow-up time was 58·8 (IQR 42·4-69·0) years. The overall cancer risk was 1·23 times higher (95% confidence interval (CI) 1·19-1·27) in patients with CHD compared with matched controls, and remained significant when patients with syndromes and organ transplant recipients were excluded. The risk of cancer was higher in all CHD age groups, and in patients that underwent cardiac surgery during the first year after birth (Hazard Ratio 1·83; 95% CI 1·32-2·54). The highest risk was found in children (0-17 years), HR 3·21 (95% CI 2·90-3·56).

Interpretation

The cancer risk in patients with CHD was 23% higher than in matched controls without CHD. The highest risk was found in children and in the latest birth cohort (1990-2017).

Funding

Funding by the Swedish state (Grant Number: 236611), the Swedish Research Council (Grant Number: 2019-00193), the Swedish Childhood Cancer Fund (Grant Number: SP2017-0012) and the Swedish Heart-Lung Foundation (Grant Number: 20190724).

Mutation spectrum of congenital heart disease in a consanguineous Turkish population

BACKGROUNDS

While many studies agree that consanguinity increases the rate of congenital heart disease (CHD), few genome analyses have been conducted with consanguineous CHD cohorts.

METHODS

We recruited 73 CHD probands from consanguineous families in Turkey and used whole-exome sequencing (WES) to identify genetic lesions in these patients.

RESULTS

On average, each patient had 6.95 rare damaging homozygous variants, 0.68 of which are loss-of-function (LoF) variants. Seven patients (9.6%) carried damaging homozygous variants in five causal CHD genes. Six of those patients exhibited laterality defects (six HTX and one D-TGA). Three additional patients (4.1%) harbored other types of CHD-associated genomic alterations, which overall explained 13.7% (10/73) of the cohort. The contribution from recessive variants in our cohort is higher than 1.8% reported from a cohort of 2871 CHD subjects where 5.6% of subjects met the criteria for consanguinity.

CONCLUSIONS

Our WES screen of a Turkish consanguineous population with structural CHD revealed its unique genetic architecture. Six of seven damaging homozygous variants in CHD causal genes occur in the setting of laterality defects implies a strong contribution from consanguinity to these defects specifically. Our study thus provided valuable information about the genetic landscape of CHD in consanguineous families in Turkey.

MLPA analysis of 32 foetuses with a congenital heart defect and 1 foetus with renal defects - pilot study. The significant frequency rate of presented pathological CNV

AIMS

The aim of this retrospective study was to determine the detection rate of the pathogenic copy number variants (CNVs) in a cohort of 33 foetuses - 32 with CHD (congenital heart defects) and 1 with kidney defect, after exclusion of common aneuploidies (trisomy 13, 18, 21, and monosomy X) by karyotyping, Multiplex ligation - dependent probe amplification (MLPA) and chromosomal microarray analysis (CMA). We also assess the effectivity of MLPA as a method of the first tier for quick and inexpensive detection of mutations, causing congenital malformations in foetuses.

METHODS

MLPA with probe mixes P070, P036 - Telomere 3 and 5, P245 - microdeletions, P250 - DiGeorge syndrome, and P311 - CHD (Congenital heart defects) was performed in 33 samples of amniotic fluid and chorionic villi. CMA was performed in 10 relevant cases.

RESULTS

Pathogenic CNVs were found in 5 samples: microdeletions in region 22q11.2 (≈2 Mb) in two foetuses, one distal microdeletion of the 22q11.2 region containing genes LZTR1, CRKL, AIFM3 and SNAP29 (≈416 kb) in the foetus with bilateral renal agenesis, 8p23.1 (3.8 Mb) microdeletion syndrome and microdeletion in area 9q34.3 (1.7 Mb, Kleefstra syndrome). MLPA as an initial screening method revealed unambiguously pathogenic CNVs in 15.2 % of samples.

CONCLUSION

Our study suggests that MLPA and CMA are a reliable and high-resolution technology and should be used as the first-tier test for prenatal diagnosis of congenital heart disease. Determination of the cause of the abnormality is crucial for genetic counselling and further management of the pregnancy.

NKX2-5 variants screening in patients with atrial septal defect in Indonesia

Background

NKX2-5 variant in atrial septal defect patients has been reported. However, it is not yet been described in the Southeast Asian population. Here, we screened the NKX2-5 variants in patients with atrial septal defect (ASD) in the Indonesian population.

Method

We recruited 97 patients with ASD for genetic screening of the NKX2-5 variant using Sanger sequencing.

Results

We identified three variants of NKX2-5: NM_004387.4:c.63A>G at exon 1, NM_004387.4:c.413G>A, and NM_004387.4:c.561G>C at exon 2. The first variant is commonly found (85.6%) and benign. The last two variants are heterozygous at the same locus. These variants are rare (3.1%) and novel. Interestingly, these variants were discovered in familial atrial septal defects with a spectrum of arrhythmia and severe pulmonary hypertension.

Conclusion

Our study is the first report of the NKX2-5 variant in ASD patients in the Southeast Asian population, including a novel heterozygous variant: NM_004387.4:c.413G>A and NM_004387.4:c.561G>C. These variants might contribute to familial ASD risk with arrhythmia and severe pulmonary hypertension. Functional studies are necessary to prove our findings.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12920-022-01242-8.

Diagnostic yield of whole exome data in fetuses aborted for conotruncal malformations

OBJECTIVE

We investigated a custom congenital heart disease (CHD) geneset to assess the diagnostic value of whole-exome sequencing (WES) in karyotype- and copy number variation (CNV)-negative aborted fetuses with conotruncal defects (CTD), and to explore the impact of postnatal phenotyping on genetic diagnosis.

METHODS

We sequentially analyzed CNV-seq and WES data from 47 CTD fetuses detected by prenatal ultrasonography. Fetuses with either a confirmed aneuploidy or pathogenic CNV were excluded from the WES analyses, which were performed following the American College of Medical Genetics and Genomics recommendations and a custom CHD-geneset. Imaging and autopsy were applied to obtain postnatal phenotypic information about aborted fetuses.

RESULTS

CNV-seq identified aneuploidy in 7/47 cases while 13/47 fetuses were CNV-positive. Eighty-five rare deleterious variants in 61 genes (from custom geneset) were identified by WES in the remaining fetuses. Of these, five (likely) pathogenic variants (LPV/PV) were identified in five fetuses, revealing a 10.6% incremental diagnostic yield. Furthermore, RERE:c.2461_2472delGGGATGTGGCGA was reclassified as LPV based on postnatal phenotypic data.

CONCLUSION

We have developed and defined a CHD gene panel that can be utilized in a subset of fetuses with CTDs. We demonstrate the utility of incorporating both prenatal and postnatal phenotypic information may facilitate WES diagnostics. This article is protected by copyright. All rights reserved.

PTPN11 Gene Mutations and Its Association with the Risk of Congenital Heart Disease

Congenital heart disease (CHD) is the most common congenital birth defect, with a prevalence of 8.98‰ of all live births in China. PTPN11 has been known to be closely involved in heart developments. In this research, we carried out whole-exome sequencing in nine CHD families and identified eight rare deleterious missense variants of PTPN11 gene in nine probands by stringently filtering criteria. Sanger sequencing of these probands and their unaffected familiar members revealed that six damaging variants were de novo in seven CHD families. Then, targeted sequencing was used to assess the PTPN11 exon variants in 672 sporadic CHD cases and 399 unrelated controls and identified 7 deleterious missense variants in 8 patients. Fisher's exact test reveals a significant association of PTPN11 variations with CHD (P = 0.0289). We observed the distribution of different subtypes in CHD patients with PTPN11 variants and found atrial septal defect (ASD) is a prominent phenotype (58.8%, 10/17). In vitro functional assays revealed that the predicted PTPN11 variants disturb RAS-mitogen-activated protein kinase signaling activity by influencing the phosphorylation level of pathway proteins and increasing the proliferation and migration abilities of cardiomyocytes to different extents. Our findings demonstrated that PTPN11 variants were associated with increased risk of CHD development and may be served as an important susceptible genetic event for CHD, especially the ASD subphenotype.

Deleterious Rare Mutations of GLI1 Dysregulate Sonic Hedgehog Signaling in Human Congenital Heart Disease

The Glioma-associated oncogene (Gli) family members of zinc finger DNA-binding proteins are core effectors of Sonic hedgehog (SHH) signaling pathway. Studies in model organisms have identified that the Gli genes play critical roles during organ development, including the heart, brain, kidneys, etc. Deleterious mutations in GLI genes have previously been revealed in several human developmental disorders, but few in congenital heart disease (CHD). In this study, the mutations in GLI1-3 genes were captured by next generation sequencing in human cohorts composed of 412 individuals with CHD and 213 ethnically matched normal controls. A total of 20 patient-specific nonsynonymous rare mutations in coding regions of human GLI1-3 genes were identified. Functional analyses showed that GLI1 c.820G> T (p.G274C) is a gain-of-function mutation, while GLI1 c.878G>A (p.R293H) and c.1442T>A (p.L481X) are loss-of-function mutations. Our findings suggested that deleterious rare mutations in GLI1 gene broke the balance of the SHH signaling pathway regulation and may constitute a great contribution to human CHD, which shed new light on understanding genetic mechanism of embryo cardiogenesis regulated by SHH signaling.

Whole genome sequencing in transposition of the great arteries and associations with clinically relevant heart, brain and laterality genes

BACKGROUND

The most common cyanotic congenital heart disease (CHD) requiring management as a neonate is transposition of great arteries (TGA). Clinically, up to 50% of TGA patients develop some form of neurodevelopmental disability (NDD), thought to have a significant genetic component. A "ciliopathy" and links with laterality disorders have been proposed. This first report of whole genome sequencing in TGA, sought to identify clinically relevant variants contributing to heart, brain and laterality defects.

METHODS

Initial whole genome sequencing analyses on 100 TGA patients focussed on established disease genes related to CHD (n = 107), NDD (n = 659) and heterotaxy (n = 74). Single variant as well as copy number variant analyses were conducted. Variant pathogenicity was assessed using the American College of Medical Genetics and Genomics-Association for Molecular Pathology guidelines.

RESULTS

Fifty-five putatively damaging variants were identified in established disease genes associated with CHD, NDD and heterotaxy; however, no clinically relevant variants could be attributed to disease. Notably, case-control analyses identified significantly more predicted-damaging, silent and total variants in TGA cases than healthy controls in established CHD genes (P < .001), NDD genes (P < .001) as well as across the three gene panels (P < .001).

CONCLUSION

We present compelling evidence that the majority of TGA is not caused by monogenic rare variants and is most likely oligogenic and/or polygenic in nature, highlighting the complex genetic architecture and multifactorial influences on this CHD sub-type and its long-term sequelae. Assessment of variant burden in key heart, brain and/or laterality genes may be required to unravel the genetic contributions to TGA and related disabilities.

Socioeconomic inequality in congenital heart diseases in Iran

INTRODUCTION

Social-economic factors have an important role in shaping inequality in congenital heart diseases. The current study aimed to assess and decompose the socio-economic inequality in Congenital Heart Diseases (CHDs) in Iran.

METHODS

This is a cross-sectional research conducted at Shahid Rajaie Cardiovascular Medical and Research Center in Tehran, Iran, as one of the largest referral heart hospitals in Asia. Data were collected primarily from 600 mothers who attended in pediatric cardiology department in 2020. The polychoric principal component analysis (PCA) and Errygers corrected CI (ECI) were used to construct household socioeconomic status and to assess inequality in CHDs, respectively. A regression-based decomposition analysis was also applied to explain socioeconomic-related inequalities. To select the explanatory social, medical/biological, and lifestyle variables, the chi-square test was first used.

RESULTS

There was a significant pro-rich inequality in CHDs (ECI = -0.65, 95% CI, - 0.72 to - 0.58). The social, medical/biological, and lifestyle variables accounted for 51.47, 43.25, and 3.92% of inequality in CHDs, respectively. Among the social variables, family SES (about 50%) and mother's occupation (21.05%) contributed the most to CHDs' inequality. Besides, in the medical/biological group, receiving pregnancy care (22.06%) and using acid folic (15.70%) had the highest contribution.

CONCLUSION

We concluded that Iran suffers from substantial socioeconomic inequality in CHDs that can be predominantly explained by social and medical/biological variables. It seems that distributional policies aim to reduce income inequality while increasing access of prenatal care and folic acid for disadvantaged mothers could address this inequality much more strongly in Iran.

Deep Learning-Based Analysis of Face Images as a Screening Tool for Genetic Syndromes

Approximately 4% of the world’s population suffers from rare diseases. A vast majority of these disorders have a genetic background. The number of genes that have been linked to human diseases is constantly growing, but there are still genetic syndromes that remain to be discovered. The diagnostic yield of genetic testing is continuously developing, and the need for testing is becoming more significant. Due to limited resources, including trained clinical geneticists, patients referred to clinical genetics units must be accurately selected. Around 30–40% of genetic disorders are associated with specific facial characteristics called dysmorphic features. As part of our research, we analyzed the performance of classifiers based on deep learning face recognition models in detecting dysmorphic features. We tested two classification problems: a multiclass problem (15 genetic disorders vs. controls) and a two-class problem (disease vs. controls). In the multiclass task, the best result reached an accuracy level of 84%. The best accuracy result in the two-class problem reached 96%. More importantly, the binary classifier detected disease features in patients with diseases that were not previously present in the training dataset. The classifier was able to generalize differences between patients and controls, and to detect abnormalities without information about the specific disorder. This indicates that a screening tool based on deep learning and facial recognition could not only detect known diseases, but also detect patients with diseases that were not previously known. In the future, this tool could help in screening patients before they are referred to the genetic unit.