Clinical Genetic and Genomic Testing in Congenital Heart Disease and Cardiomyopathy.

Congenital heart disease (CHD) and cardiomyopathies are the leading cause of morbidity and mortality worldwide. These conditions are often caused by genetic factors, and recent research has shown that genetic and genomic testing can provide valuable information for patient care. By identifying genetic causes, healthcare providers can screen for other related health conditions, offer early interventions, estimate prognosis, select appropriate treatments, and assess the risk for family members. Genetic and genomic testing is now the standard of care in patients with CHD and cardiomyopathy. However, rapid advances in technology and greater availability of testing options have led to changes in recommendations for the most appropriate testing method. Several recent studies have investigated the utility of genetic testing in this changing landscape. This review summarizes the literature surrounding the clinical utility of genetic evaluation in patients with CHD and cardiomyopathy.

Rapid Genome Sequencing Shows Diagnostic Utility In Infants With Congenital Heart Defects.

Congenital heart disease (CHD) is the most common birth defect and a leading cause of infant mortality. CHD often has a genetic etiology and recent studies demonstrate utility in genetic testing. In clinical practice, decisions around genetic testing choices continue to evolve, and the incorporation of rapid genome sequencing (rGS) in CHD has not been well studied. Though smaller studies demonstrate the value of rGS, they also highlight the burden of results interpretation. We analyze genetic testing in CHD at two time-points, in 2018 and 2022-2023, across a change in clinical testing guidelines from chromosome microarray (CMA) to rGS. Analysis of 421 hospitalized infants with CHD demonstrated consistent genetic testing across time. Overall, after incorporation of rGS in 2022-2023, the diagnostic yield was 6.8% higher compared to 2018, and this pattern was consistent across all patient subtypes analyzed. In 2018, CMA was the most common test performed, with diagnostic results for CHD in 14.3%, while in 2022-2023, rGS was the most frequent test performed, with results diagnostic for CHD in 16.9%. Additionally, rGS identified 44% more unique genetic diagnoses than CMA. This is the largest study to highlight the value of rGS in CHD and has important implications for management.

A Multicenter Analysis of Abnormal Chromosomal Microarray Findings in Congenital Heart Disease.

Background Chromosomal microarray analysis (CMA) provides an opportunity to understand genetic causes of congenital heart disease (CHD). The methods for describing cardiac phenotypes in patients with CMA abnormalities have been inconsistent, which may complicate clinical interpretation of abnormal testing results and hinder a more complete understanding of genotype-phenotype relationships. Methods and Results Patients with CHD and abnormal clinical CMA were accrued from 9 pediatric cardiac centers. Highly detailed cardiac phenotypes were systematically classified and analyzed for their association with CMA abnormality. Hierarchical classification of each patient into 1 CHD category facilitated broad analyses. Inclusive classification allowing multiple CHD types per patient provided sensitive descriptions. In 1363 registry patients, 28% had genomic disorders with well-recognized CHD association, 67% had clinically reported copy number variants (CNVs) with rare or no prior CHD association, and 5% had regions of homozygosity without CNV. Hierarchical classification identified expected CHD categories in genomic disorders, as well as uncharacteristic CHDs. Inclusive phenotyping provided sensitive descriptions of patients with multiple CHD types, which occurred commonly. Among CNVs with rare or no prior CHD association, submicroscopic CNVs were enriched for more complex types of CHD compared with large CNVs. The submicroscopic CNVs that contained a curated CHD gene were enriched for left ventricular obstruction or septal defects, whereas CNVs containing a single gene were enriched for conotruncal defects. Neuronal-related pathways were over-represented in single-gene CNVs, including top candidate causative genes NRXN3, ADCY2, and HCN1. Conclusions Intensive cardiac phenotyping in multisite registry data identifies genotype-phenotype associations in CHD patients with abnormal CMA.

Clinical exome sequencing efficacy and phenotypic expansions involving anomalous pulmonary venous return.

Anomalous pulmonary venous return (APVR) frequently occurs with other congenital heart defects (CHDs) or extra-cardiac anomalies. While some genetic causes have been identified, the optimal approach to genetic testing in individuals with APVR remains uncertain, and the etiology of most cases of APVR is unclear. Here, we analyzed molecular data from 49 individuals to determine the diagnostic yield of clinical exome sequencing (ES) for non-isolated APVR. A definitive or probable diagnosis was made for 8 of those individuals yielding a diagnostic efficacy rate of 16.3%. We then analyzed molecular data from 62 individuals with APVR accrued from three databases to identify novel APVR genes. Based on data from this analysis, published case reports, mouse models, and/or similarity to known APVR genes as revealed by a machine learning algorithm, we identified 3 genes-EFTUD2, NAA15, and NKX2-1-for which there is sufficient evidence to support phenotypic expansion to include APVR. We also provide evidence that 3 recurrent copy number variants contribute to the development of APVR: proximal 1q21.1 microdeletions involving RBM8A and PDZK1, recurrent BP1-BP2 15q11.2 deletions, and central 22q11.2 deletions involving CRKL. Our results suggest that ES and chromosomal microarray analysis (or genome sequencing) should be considered for individuals with non-isolated APVR for whom a genetic etiology has not been identified, and that genetic testing to identify an independent genetic etiology of APVR is not warranted in individuals with EFTUD2-, NAA15-, and NKX2-1-related disorders.

Genetic Testing Guidelines Impact Care in Newborns with Congenital Heart Defects.

OBJECTIVE: To evaluate genetic evaluation practices in newborns with the most common birth defect, congenital heart defects (CHD), we determined the prevalence and the yield of genetic evaluation across time and across patient subtypes, before and after implementation of institutional genetic testing guidelines. STUDY DESIGN: This was a retrospective, cross-sectional study of 664 hospitalized newborns with CHD using multivariate analyses of genetic evaluation practices across time and patient subtypes. RESULTS: Genetic testing guidelines for hospitalized newborns with CHD were implemented in 2014, and subsequently genetic testing increased (40% in 2013 and 75% in 2018, OR 5.02, 95% CI 2.84-8.88, P < .001) as did medical geneticists' involvement (24% in 2013 and 64% in 2018, P < .001). In 2018, there was an increased use of chromosomal microarray (P < .001), gene panels (P = .016), and exome sequencing (P = .001). The testing yield was high (42%) and consistent across years and patient subtypes analyzed. Increased testing prevalence (P < .001) concomitant with consistent testing yield (P = .139) added an estimated 10 additional genetic diagnoses per year, reflecting a 29% increase. CONCLUSIONS: In patients with CHD, yield of genetic testing was high. After implementing guidelines, genetic testing increased significantly and shifted to newer sequence-based methods. Increased use of genetic testing identified more patients with clinically important results with potential to impact patient care.

Surgical History and Outcomes in Trisomy 13 and 18: A Thirty-year Review.

BACKGROUND: Patients with Trisomy 13(T13) and 18(T18) have many comorbidities that may require surgical intervention. However, surgical care and outcomes are not well described, making patient selection and family counseling difficult. Here the surgical history and outcomes of T13/ T18 patients are explored. METHODS: A retrospective review of patients with T13 or T18 born between 1990 and 2020 and cared for at a tertiary children's hospital (Riley Hospital for Children, Indianapolis IN) was conducted, excluding those with insufficient records. Primary outcomes of interest were rates of mortality overall and after surgery. Factors that could predict mortality outcomes were also assessed. RESULTS: One-hundred-seventeen patients were included, with 65% T18 and 35% T13. More than half of patients(65%) had four or more comorbidities. Most deaths occurred by three months at median 42.0 days. Variants of classic trisomies (mosaicism, translocation, partial duplication; p = 0.001), higher birth weight(p = 0.002), and higher gestational age(p = 0.01) were associated with lower overall mortality, while cardiac(p = 0.002) disease was associated with higher mortality. Over half(n = 64) underwent surgery at median age 65 days at time of first procedure. The most common surgical procedures were general surgical. Median survival times were longer in surgical rather than nonsurgical patients(p<0.001). Variant trisomy genetics(p = 0.002) was associated with lower mortality after surgery, while general surgical comorbidities(p = 0.02), particularly tracheoesophageal fistula/esophageal atresia(p = 0.02), were associated with increased mortality after surgery. CONCLUSIONS: Trisomy 13 and 18 patients have vast surgical needs. Variant trisomy was associated with lower mortality after surgery while general surgical comorbidities were associated with increased mortality after surgery. Those who survived to undergo surgery survived longer overall. LEVEL OF EVIDENCE: III.

A multi-disciplinary, comprehensive approach to management of children with heterotaxy.

Heterotaxy (HTX) is a rare condition of abnormal thoraco-abdominal organ arrangement across the left-right axis of the body. The pathogenesis of HTX includes a derangement of the complex signaling at the left-right organizer early in embryogenesis involving motile and non-motile cilia. It can be inherited as a single-gene disorder, a phenotypic feature of a known genetic syndrome or without any clear genetic etiology. Most patients with HTX have complex cardiovascular malformations requiring surgical intervention. Surgical risks are relatively high due to several serious comorbidities often seen in patients with HTX. Asplenia or functional hyposplenism significantly increase the risk for sepsis and therefore require antimicrobial prophylaxis and immediate medical attention with fever. Intestinal rotation abnormalities are common among patients with HTX, although volvulus is rare and surgical correction carries substantial risk. While routine screening for intestinal malrotation is not recommended, providers and families should promptly address symptoms concerning for volvulus and biliary atresia, another serious morbidity more common among patients with HTX. Many patients with HTX have chronic lung disease and should be screened for primary ciliary dyskinesia, a condition of respiratory cilia impairment leading to bronchiectasis. Mental health and neurodevelopmental conditions need to be carefully considered among this population of patients living with a substantial medical burden. Optimal care of children with HTX requires a cohesive team of primary care providers and experienced subspecialists collaborating to provide compassionate, standardized and evidence-based care. In this statement, subspecialty experts experienced in HTX care and research collaborated to provide expert- and evidence-based suggestions addressing the numerous medical issues affecting children living with HTX.

Learning to Crawl: Determining the Role of Genetic Abnormalities on Postoperative Outcomes in Congenital Heart Disease.

Background Our cardiac center established a systematic approach for inpatient cardiovascular genetics evaluations of infants with congenital heart disease, including routine chromosomal microarray (CMA) testing. This provides a new opportunity to investigate correlation between genetic abnormalities and postoperative course. Methods and Results Infants who underwent congenital heart disease surgery as neonates (aged ≤28 days) from 2015 to 2020 were identified. Cases with trisomy 21 or 18 were excluded. Diagnostic genetic results or CMA with variant of uncertain significance were considered abnormal. We compared postoperative outcomes following initial congenital heart disease surgery in patients found to have genetic abnormality to those who had negative CMA. Among 355 eligible patients, genetics consultations or CMA were completed in 88%. A genetic abnormality was identified in 73 patients (21%), whereas 221 had negative CMA results. Genetic abnormality was associated with prematurity, extracardiac anomaly, and lower weight at surgery. Operative mortality rate was 9.6% in patients with a genetic abnormality versus 4.1% in patients without an identified genetic abnormality (P=0.080). Mortality was similar when genetic evaluations were diagnostic (9.3%) or identified a variant of uncertain significance on CMA (10.0%). Among 14 patients with 22q11.2 deletion, the 2 mortality cases had additional CMA findings. In patients without extracardiac anomaly, genetic abnormality was independently associated with increased mortality (P=0.019). CMA abnormality was not associated with postoperative length of hospitalization, extracorporeal membrane oxygenation, or >7 days to initial extubation. Conclusions Routine genetic evaluations and CMA may help to stratify mortality risk in severe congenital heart disease with syndromic or nonsyndromic presentations.

OBGYN providers' lack of knowledge and management of genetic risks due to advanced paternal age underscore the need for updated practice guidance.

The objective of this pilot study was to characterize healthcare professionals' knowledge of advanced paternal age (APA), the associated risks, as well as current clinical practices regarding APA. Our study utilized an online survey that questioned providers who see children with genetic conditions and patients who are or may become pregnant regarding demographic information, APA knowledge, APA guideline familiarity, and their clinical practices. A total of 67 providers responded to the survey. We had responses from 54 physician participants in the specialties of medical genetics (GEN), maternal fetal medicine (MFM), and obstetrics and gynecology (OBGYN). OBGYN, but not MFM, reported significantly lower agreement that current data supports an association between APA and certain genetic diseases compared to GEN. Furthermore, OBGYN were less likely to identify established risks associated with APA and more likely to incorrectly identify unestablished risks compared to GEN and MFM. Regardless of specialty, the majority of physicians were unfamiliar with the most recently published APA guidelines. This study revealed a desire for more information regarding APA risks and management among our participants. Our data suggest that GEN, MFM, and OBGYN would benefit from updated and more visible guidelines regarding APA. Additionally, OBGYN consistently showed knowledge gaps and misconceptions regarding the risks of APA. Targeted educational or guidance materials regarding APA may also be beneficial for OBGYNs.

Pathogenic variants in MRPL44 cause infantile cardiomyopathy due to a mitochondrial translation defect.

Cardiac dysfunction is a common phenotypic manifestation of primary mitochondrial disease with multiple nuclear and mitochondrial DNA pathogenic variants as a cause, including disorders of mitochondrial translation. To date, five patients have been described with pathogenic variants in MRPL44, encoding the ml44 protein which is part of the large subunit of the mitochondrial ribosome (mitoribosome). Three presented as infants with hypertrophic cardiomyopathy, mild lactic acidosis, and easy fatigue and muscle weakness, whereas two presented in adolescence with myopathy and neurological symptoms. We describe two infants who presented with cardiomyopathy from the neonatal period, failure to thrive, hypoglycemia and in one infant lactic acidosis. A decompensation of the cardiac function in the first year resulted in demise. Exome sequencing identified compound heterozygous variants in the MRPL44 gene including the known pathogenic variant c.467 T > G and two novel pathogenic variants. We document a combined respiratory chain enzyme deficiency with emphasis on complex I and IV, affecting heart muscle tissue more than skeletal muscle or fibroblasts. We show this to be caused by reduced mitochondrial DNA encoded protein synthesis affecting all subunits, and resulting in dysfunction of complex I and IV assembly. The degree of oxidative phosphorylation dysfunction correlated with the impairment of mitochondrial protein synthesis due to different pathogenic variants. These functional studies allow for improved understanding of the pathogenesis of MRPL44-associated mitochondrial disorder.

Variants of significance: medical genetics and surgical outcomes in congenital heart disease.

PURPOSE OF REVIEW: This article reviews the current understanding and limitations in knowledge of the effect genetics and genetic diagnoses have on perioperative and postoperative surgical outcomes in patients with congenital heart disease (CHD). RECENT FINDINGS: Presence of a known genetic diagnosis seems to effect multiple significant outcome metrics in CHD surgery including length of stay, need for extracorporeal membrane oxygenation, mortality, bleeding, and heart failure. Data regarding the effects of genetics in CHD is complicated by lack of standard genetic assessment resulting in inaccurate risk stratification of patients when analyzing data. Only 30% of variation in CHD surgical outcomes are explained by currently measured variables, with 2.5% being attributed to diagnosed genetic disorders, it is thought a significant amount of the remaining outcome variation is because of unmeasured genetic factors. SUMMARY: Genetic diagnoses clearly have a significant effect on surgical outcomes in patients with CHD. Our current understanding is limited by lack of consistent genetic evaluation and assessment as well as evolving knowledge and discovery regarding the genetics of CHD. Standardizing genetic assessment of patients with CHD will allow for the best risk stratification and ultimate understanding of these effects.

Language regression, hemichorea and focal subclinical seizures in a 6-year-old girl with GLUT-1 deficiency.

•A 6 year old girl with progressive speech difficulties, new abnormal movements, olfactory hallucinations•Choreiform movement of her right hemibody along with her face and tongue•Seizures were noted during sleep without clinical correlate, progressing to awake subclinical seizures.

Neonatal Assessment of Infants with Heterotaxy.

Heterotaxy is a generalized term for patients who have an abnormality of laterality that cannot be described as situs inversus. Infants with heterotaxy can have significant anatomic and medical complexity and require personalized, specialized care, including comprehensive anatomic assessment. Common and rare anatomic findings are reviewed by system to help guide a thorough phenotypic evaluation. General care guidelines and considerations unique to this patient population are included. Future directions for this unique patient population, particularly in light of improved neonatal survival, are discussed.

Novel KLHL26 variant associated with a familial case of Ebstein's anomaly and left ventricular noncompaction.

BACKGROUND: Ebstein's anomaly (EA) is a rare congenital heart disease of the tricuspid valve and right ventricle. Patients with EA often manifest with left ventricular noncompaction (LVNC), a cardiomyopathy. Despite implication of cardiac sarcomere genes in some cases, very little is understood regarding the genetic etiology of EA/LVNC. Our study describes a multigenerational family with at least 10 of 17 members affected by EA/LVNC. METHODS: We performed echocardiography on all family members and conducted exome sequencing of six individuals. After identifying candidate variants using two different bioinformatic strategies, we confirmed segregation with phenotype using Sanger sequencing. We investigated structural implications of candidate variants using protein prediction models. RESULTS: Exome sequencing analysis of four affected and two unaffected members identified a novel, rare, and damaging coding variant in the Kelch-like family member 26 (KLHL26) gene located on chromosome 19 at position 237 of the protein (GRCh37). This variant region was confirmed by Sanger sequencing in the remaining family members. KLHL26 (c.709C > T p.R237C) segregates only with EA/LVNC-affected individuals (FBAT p < .05). Investigating structural implications of the candidate variant using protein prediction models suggested that the KLHL26 variant disrupts electrostatic interactions when binding to part of the ubiquitin proteasome, specifically Cullin3 (CUL3), a component of E3 ubiquitin ligase. CONCLUSION: In this familial case of EA/LVNC, we have identified a candidate gene variant, KLHL26 (p.R237C), which may have an important role in ubiquitin-mediated protein degradation during cardiac development.

Three year experience of a clinical cardiovascular genetics program for infants with congenital heart disease.

OBJECTIVE: To describe the first 3 years of experience of having an inpatient "cardiogenetics" program which involves medical geneticist assessment of infants with major congenital heart disease (CHD) requiring surgical intervention in the first year of life. PATIENTS: Patients less than a year of age admitted to Children's Hospital of Wisconsin's Herma Heart Institute for surgical intervention for CHD seen by the cardiogenetics program. Patients with major trisomies (13, 18, and 21) were excluded. OUTCOME MEASURES: Utilization and yield of genetic testing, and diagnostic rate were assessed as outcome measures and compared to a baseline time period and a genetic testing protocol time period. RESULTS: There were 201 infants with CHD evaluated by the cardiogenetics program over 3 years. A total of patients 46 patients of the 196 who underwent genetic testing had multiple tests completed. This is a significant decrease from the baseline (247/329, P < .0001) and from the genetic testing protocol (29/81, P < .0387) time periods. The diagnostic rate was 33% which is significantly increased compared to the baseline rate of 15% (80/524, P < .0001) and trends toward a significant increase during the testing protocol rate (25/113, P = .0520). The number of dual diagnosis increased to 9 of 201 compared to the baseline (2/524) and the genetic testing protocol (1/113) time periods. The rate of incidental diagnoses altering care increased to 6 of 201 from the baseline (1/524) and the genetic testing protocol (1/113) time periods. CONCLUSION: An inpatient cardiogenetics program significantly increases the diagnostic rate, the detection of complex phenotypes with dual diagnoses, the identification of incidental genetic diagnoses associated with changes in care, and significantly decreases the likelihood of multiple tests being completed on an individual patient. Increased medical geneticist involvement in programs that care for infants with CHD should be encouraged to improve patient care and genetic testing utilization.

A case of Coffin-Siris syndrome with severe congenital heart disease and a novel SMARCA4 variant.

Coffin-Siris syndrome (CSS) is a developmental disability, caused by genomic variants in the gene SMARCA4, in addition to other known genes, but the full spectrum of SMARCA4 variants that can cause CSS is unknown with 40% of cases not having molecular confirmation. In this report, we identify a patient with CSS, a severe cardiac phenotype, and a novel SMARCA4 variant. There is no experimental structure of human SMARCA4, so we use molecular modeling techniques to generate a structural model of human SMARCA4. We then map known SMARCA4 variants causative of CSS and our novel variant to the model. We use the resulting information to support the interpretation that the novel variant is causative of disease in our patient. Modeling demonstrates that the variant found in our patient is in a region of SMARCA4 associated with DNA binding, as are the other known pathogenic SMARCA4 variants mapped. Because of this structural information, we discuss how these variants may be disease-causing through a dominant negative effect of disrupting DNA binding.

Genetic evaluation of patients with congenital heart disease.

PURPOSE OF REVIEW: The aim of this study is to review genetics of congenital heart disease (CHD) with a focus on clinical applications, genetic testing and clinical challenges. RECENT FINDINGS: With improved clinical care, there is a rapidly expanding population of adults, especially women, with CHD who have not undergone contemporary genetic assessment and do not understand their risk for having a child with CHD. Many patients have never undergone assessment or had genetic testing. A major barrier is medical geneticist availability, resulting in this burden of care shifting to providers outside of genetics. Even with current understanding, the cause for the majority of cases of CHD is still not known. There are significant gaps in knowledge in the realms of more complex causes such as noncoding variants, multigenic contribution and small structural chromosomal anomalies. SUMMARY: Standard assessment of patients with CHD, including adult survivors, is indicated. The best first-line genetic assessment for most patients with CHD is a chromosomal microarray, and this will soon evolve to be genomic sequencing with copy number variant analysis. Due to lack of medical geneticists, creative solutions to maximize the number of patients with CHD who undergo assessment with standard protocols and plans for support with result interpretation need to be explored.