Identification of a novel hypertrophic cardiomyopathy-associated mutation using targeted next-generation sequencing

Clinical Interpretation of Sequence Variants

Clinical interpretation of DNA sequence variants is a critical step in reporting clinical genetic testing results. Application of next-generation sequencing technology in molecular genetic testing has facilitated diagnoses of genetic disorders in clinical practice. However, the large number of DNA sequence variants detected in clinical specimens, many of which have never been seen before, make clinical interpretation challenging. Recommendations by the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP) have been widely adopted by clinical laboratories around the world to guide clinical interpretation of sequence variants. The ClinGen Sequence Variant Interpretation Working Group and various disease-specific variant curation expert panels have also developed specifications for the ACMG/AMP recommendations. Despite these efforts to standardize variant interpretation in clinical practice, different laboratories may subjectively use professional judgment to determine which criteria are applicable when classifying a variant. In addition, clinicians and researchers who are not familiar with the variant interpretation process may have difficulty understanding clinical genetic reports and communicating the clinical significance of genetic testing results. Here we provide a step-by-step protocol for clinical interpretation of sequence variants, including practical examples. By following this protocol, clinical laboratory geneticists can interpret the clinical significance of sequence variants according to the ACMG/AMP recommendations and ClinGen framework. Furthermore, this article will help clinicians and researchers to understand variant classification in clinical genetic testing reports and evaluate the quality of the reports. © 2020 by John Wiley & Sons, Inc. Basic Protocol: Interpreting the clinical significance of sequence variants Support Protocol: Reevaluating the clinical significance of sequence variants.

Novel frameshift variant in MYL2 reveals molecular differences between dominant and recessive forms of hypertrophic cardiomyopathy

Hypertrophic cardiomyopathy (HCM) is characterized by thickening of the ventricular muscle without dilation and is often associated with dominant pathogenic variants in cardiac sarcomeric protein genes. Here, we report a family with two infants diagnosed with infantile-onset HCM and mitral valve dysplasia that led to death before one year of age. Using exome sequencing, we discovered that one of the affected children had a homozygous frameshift variant in Myosin light chain 2 (MYL2:NM_000432.3:c.431_432delCT: p.Pro144Argfs*57;MYL2-fs), which alters the last 20 amino acids of the protein and is predicted to impact the most C-terminal of the three EF-hand domains in MYL2. The parents are unaffected heterozygous carriers of the variant and the variant is absent in control cohorts from gnomAD. The absence of the phenotype in carriers and the infantile presentation of severe HCM is in contrast to HCM associated with dominant MYL2 variants. Immunohistochemical analysis of the ventricular muscle of the deceased patient with the MYL2-fs variant showed a marked reduction of MYL2 expression compared to an unaffected control. In vitro overexpression studies further indicate that the MYL2-fs variant is actively degraded. In contrast, an HCM-associated missense variant (MYL2:p.Gly162Arg) and three other MYL2 stop-gain variants (p.E22*, p.K62*, p.E97*) that result in loss of the EF domains are stably expressed but show impaired localization. The degradation of the MYL2-fs can be rescued by inhibiting the cell’s proteasome function supporting a post-translational effect of the variant. In vivo rescue experiments with a Drosophila MYL2-homolog (Mlc2) knockdown model indicate that neither the MYL2-fs nor the MYL2:p.Gly162Arg variant supports normal cardiac function. The tools that we have generated provide a rapid screening platform for functional assessment of variants of unknown significance in MYL2. Our study supports an autosomal recessive model of inheritance for MYL2 loss-of-function variants in infantile HCM and highlights the variant-specific molecular differences found in MYL2-associated cardiomyopathy.

We report a novel frameshift variant in MYL2 that is associated with a severe form of infantile-onset hypertrophic cardiomyopathy. The impact of the variant is only observed in the recessive form of the disease found in the proband and not in the parents who are carriers of the variant. This contrasts with other dominant variants in MYL2 that are associated with cardiomyopathies. We compared the stability of this variant to that of other cardiomyopathy associated MYL2 variants and found molecular differences that correlated with disease pathology. We also show different protein domain requirements for stability and localization of MYL2 in cardiomyocytes. Furthermore, we used a fly model to demonstrate functional deficits due to the variant in the developing heart. Overall, our study shows a molecular mechanism by which loss-of-function variants in MYL2 are recessive while missense variants are dominant. We highlight the use of exome sequencing and functional testing to assist in the diagnosis of rare forms of disease where pathogenicity of the variant is not obvious. The new tools we developed for in vitro functional study and the fly fluorescent reporter analysis will permit rapid analysis of MYL2 variants of unknown significance.

A Bayesian Analysis to Determine the Prevalence of Barth Syndrome in the Pediatric Population

OBJECTIVE

To determine the prevalence of Barth syndrome in the pediatric population.

STUDY DESIGN

Data were collected from the Barth Syndrome Foundation Registry and relevant literature. With the advent of genetic testing and whole-exome sequencing, a multipronged Bayesian analysis was used to estimate the prevalence of Barth syndrome based on published data on the incidence and prevalence of cardiomyopathy and neutropenia, and the respective subpopulations of patients with Barth syndrome indicated in these publications.

RESULTS

Based on 7 published studies of cardiomyopathy and 2 published studies of neutropenia, the estimated prevalence of Barth syndrome is approximately 1 case per million male population. This contrasts with 99 cases in the Barth Syndrome Foundation Registry, 58 of which indicate a US location, and only 230-250 cases known worldwide.

CONCLUSIONS

It appears that Barth syndrome is greatly underdiagnosed. There is a need for better education and awareness of this rare disease to move toward early diagnosis and treatment.

[Hypertrophic cardiomyopathy. Cardiomyocyte ultrastructure, the specific or stereotypic signs]

Hypertrophic cardiomyopathy (HCM) is a congenital disease caused by mutations in a number of sarcomere proteins. According to the type of mutation, clinical observations record similar clinical manifestations, myocardial pathological changes, and the timing of manifestation of the disease in HCM patients.

OBJECTIVE

To study cardiomyocyte (CMC) ultrastructural changes in the interventricular septum (IVS) of patients with HCM and evaluate their specificity for this pathology.

MATERIAL AND METHODS

IVS myocardial samples taken from 44 HCM patients aged 18-59 years at IVS myoectomy underwent an electron microscopic study. The diameter of CMCs and their nuclei was measured in semithin sections.

RESULTS

A morphometric examination of the IVS myocardium in HCM patients revealed moderate hypertrophy of CMCs and their nuclei, the diameters of which averaged 23.7±4.4 and 5.2±0.9 μm, respectively. The IVS CMCs were characterized by the ultrastructural signs of hypertrophy: the larger size and number of structures ensuring contractile and synthetic functions; the myocytes contained higher amounts of myofibrils, intermyofibrillar mitochondria, granular endoplasmic reticulum cisterns, and free ribosomes. On the contrary, some CMCs had fewer myofibrils in the perinuclear region, which is an adaptive change under hemodynamic overload conditions. In addition, a number of myocytes displayed signs of dystrophic changes: the appearance of lipofuscin granules, myelin figures, phagosomes, lipid droplets, and vacuoles, which can fill all free sarcoplasmic zones.

CONCLUSION

Ultrastructural changes characteristic of hypertrophy were found in IVS CMCs in HCM patients. In addition, there was partial myofibrillar loss and dystrophic changes in a number of myocytes, which are stereotypic compensatory-adaptive changes under hemodynamic overload conditions. All the above-mentioned changes in the CMC ultrastructure are characteristic of myocardial hypertrophy, but not specific for hypertrophic cardiomyopathy.

Genetics and pharmacogenetics in the diagnosis and therapy of cardiovascular diseases

Cardiovascular diseases are the main cause of death worldwide. The ability to accurately define individual susceptibility to these disorders is therefore of strategic importance. Linkage analysis and genome-wide association studies have been useful for the identification of genes related to cardiovascular diseases. The identification of variants predisposing to cardiovascular diseases contributes to the risk profile and the possibility of tailored preventive or therapeutic strategies. Molecular genetics and pharmacogenetics are playing an increasingly important role in the correct clinical management of patients. For instance, genetic testing can identify variants that influence how patients metabolize medications, making it possible to prescribe personalized, safer and more efficient treatments, reducing medical costs and improving clinical outcomes. In the near future we can expect a great increment in information and genetic testing, which should be acknowledged as a true branch of diagnostics in cardiology, like hemodynamics and electrophysiology. In this review we summarize the genetics and pharmacogenetics of the main cardiovascular diseases, showing the role played by genetic information in the identification of cardiovascular risk factors and in the diagnosis and therapy of these conditions. (www.actabiomedica.it)

Heart rate variability as predictive factor for sudden cardiac death

Sudden cardiac death (SCD) represents about 25% of deaths in clinical cardiology. The identification of risk factors for SCD is the philosopher's stone of cardiology and the identification of non-invasive markers of risk of SCD remains one of the most important goals for the scientific community.

The aim of this review is to analyze the state of the art around the heart rate variability (HRV) as a predictor factor for SCD.

HRV is probably the most analyzed index in cardiovascular risk stratification technical literature, therefore an important number of models and methods have been developed.

Nowadays, low HRV has been shown to be independently predictive of increased mortality in post- myocardial infarction patients, heart failure patients, in contrast with the data of the general population.

Contrariwise, the relationship between HRV and SCD has received scarce attention in low-risk cohorts. Furthermore, in general population the attributable risk is modest and the cost/benefit ratio is not always convenient.

The HRV evaluation could become an important tool for health status in risks population, even though the use of HRV alone for risk stratification of SCD is limited and further studies are needed.

Presence of Hypertrophic Cardiomyopathy Related Gene Mutations and Clinical Manifestations in Vietnamese Patients With Hypertrophic Cardiomyopathy

BACKGROUND

Hypertrophic cardiomyopathy (HCM) is associated primarily with pathogenic mutations in sarcomeric genes. The aim of this study was to identify the prevalence and distribution of disease-causing mutations in HCM-associated genes and the genotype-phenotype relationship in Vietnamese patients with HCM.Methods and Results:Genetic testing was performed by next-generation sequencing in 104 unrelated probands for 23 HCM-related genes and in 57 family members for the mutation(s) detected. Clinical manifestations were recorded for genotype-phenotype correlation analysis. Mutation detection rate was 43.4%. Mutations inMYBPC3accounted for 38.6%, followed byTPM1(20.5%),MYH7(18.2%),TNNT2(9.1%),TNNI3(4.5%) andMYL2(2.3%). A mutation inGLAassociated with Fabry disease was found in 1 patient. A mutation inTPM1(c.842T>C, p.Met281Thr) was identified in 8 unrelated probands (18.2%) and 8 family members from 5 probands. Genotype-positive status related toMYH7,TPM1, andTNNT2mutations was associated with severe clinical manifestations.MYH7-positive patients displayed worse prognosis compared withMYBPC3-positive patients. Interestingly,TPM1c.842T>C mutation was associated with high penetrance and severe HCM phenotype.

CONCLUSIONS

We report for the first time the prevalence of HCM-related gene variants in Vietnamese patients with HCM.MYH7,TPM1, andTNNT2mutations were associated with unfavorable prognosis.