Phenotype guided characterization and molecular analysis of Indian patients with long QT syndromes

Whole genome sequencing of families diagnosed with cardiac channelopathies reveals structural variants missed by whole exome sequencing

Cardiac channelopathies are a group of heritable disorders that affect the heart's electrical activity due to genetic variations present in genes coding for ion channels. With the advent of new sequencing technologies, molecular diagnosis of these disorders in patients has paved the way for early identification, therapeutic management and family screening. The objective of this retrospective study was to understand the efficacy of whole-genome sequencing in diagnosing patients with suspected cardiac channelopathies who were reported negative after whole exome sequencing and analysis. We employed a 3-tier analysis approach to identify nonsynonymous variations and loss-of-function variations missed by exome sequencing, and structural variations that are better resolved only by sequencing whole genomes. By performing whole genome sequencing and analyzing 25 exome-negative cardiac channelopathy patients, we identified 3 pathogenic variations. These include a heterozygous likely pathogenic nonsynonymous variation, CACNA1C:NM_000719:exon19:c.C2570G:p. P857R, which causes autosomal dominant long QT syndrome in the absence of Timothy syndrome, a heterozygous loss-of-function variation CASQ2:NM_001232.4:c.420+2T>C classified as pathogenic, and a 9.2 kb structural variation that spans exon 2 of the KCNQ1 gene, which is likely to cause Jervell-Lange-Nielssen syndrome. In addition, we also identified a loss-of-function variation and 16 structural variations of unknown significance (VUS). Further studies are required to elucidate the role of these identified VUS in gene regulation and decipher the underlying genetic and molecular mechanisms of these disorders. Our present study serves as a pilot for understanding the utility of WGS over clinical exomes in diagnosing cardiac channelopathy disorders.

Results of comprehensive genetic testing in patients presenting to a multidisciplinary inherited heart disease clinic in India

OBJECTIVES

This study aims to analyze the results of comprehensive genetic testing in patients presenting to a dedicated multidisciplinary inherited heart disease clinic in India.

METHODS

All patients presenting to our clinic from August 2017 to October 2023 with a suspected inherited heart disease and consenting for genetic testing were included. The probands were grouped into familial cardiomyopathies namely hypertrophic cardiomyopathy (HCM), dilated cardiomyopathy (DCM), arrhythmogenic cardiomyopathy (ACM) and peripartum cardiomyopathy (PPCM), channelopathies namely congenital long QT syndrome (LQTS) and Brugada syndrome (BrS), and heritable connective tissue disorder namely Marfan Syndrome (MFS). Next generation sequencing (NGS) was used, and pre-test and post-test counseling were provided to probands and cascade screening offered to relatives.

RESULTS

Mean age of the subjects (n = 77; 48 probands, 29 relatives) was 43 ± 18 years, 68 % male and 44 % symptomatic, with 36 HCM, 3 DCM, 3 ACM, 1 PPCM, 3 LQTS, 1 BrS and 1 MFS probands. The diagnostic yield of NGS-based genetic testing was 31 %; variants of uncertain significance (VUS) were identified in 54 %; and 15 % were genotype-negative. Twenty-nine relatives from 18 families with HCM (n = 12), DCM (n = 3), ACM (n = 2) and MFS (n = 1) underwent genetic testing. The genotype positive probands/relatives and VUS carriers with strong disease phenotype and/or high risk variant were advised periodic follow-up; the remaining probands/relatives were discharged from further clinical surveillance.

CONCLUSIONS

Genetic testing guides treatment and follow-up of patients with inherited heart diseases and should be carried out in dedicated multidisciplinary clinics with expertise for counseling and cascade screening of family members.

Next-Generation Sequencing in Unexplained Intellectual Disability

OBJECTIVES

To determine the diagnostic yield of next generation sequencing (NGS) in patients with moderate/severe/profound intellectual disability (ID) unexplained by conventional tests and to assess the impact of definitive diagnosis on the clinical management and genetic counselling of these families.

METHODS

This was a ambi-directional study conducted at Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi. The study comprised 227 patients (prospective cohort - 126, retrospective cohort - 101) in whom NGS based tests were performed.

RESULTS

The mean age of study cohort was 4.5 ± 4.4 y (2.5 mo to 37.3 y). The male: female ratio was 1.6:1. The overall diagnostic yield of NGS was 53.3% (121/227) with causative variants identified in 84 known ID genes. Autosomal recessive intellectual disability (ARID) (23.3%, 53/227) was the most common followed by autosomal dominant intellectual disability (ADID) (20.7%, 47/227) and X-linked intellectual disability (XLID) (9.2%, 21/227). The diagnostic yield was notably higher for ID plus associated condition group (55.6% vs. 20%) (p = 0.0075, Fisher's exact test) compared to isolated ID group. The impact of diagnosis on active or long-term management was observed in 17/121 (14%) and on reproductive outcomes in 26/121 (21.4%) families.

CONCLUSIONS

There is paucity of data on molecular genetic spectrum of ID from India. The current study identifies extensive genetic heterogeneity and the impact of NGS in patients with ID unexplained by standard genetic tests. The study identified ARID as the most common cause of ID with additional implications for reproductive outcomes. It reiterates the importance of phenotype in genetic testing.

Institutionalization of personalized medicine in India: analysis of research trends and government interventions

The biggest challenges that any country faces are affordability and accessibility of quality healthcare. Technological advancements can address these challenges. One such advancement is personalized medicine (PM). This paper discusses the implementation and institutionalization of PM. Using the sectoral innovation system framework, this work describes government interventions with research trends in PM in India. The Web of Science database was used to analyze research trends. Indian government-funded interventions to institutionalize PM were compiled and analyzed. Results suggest that India's healthcare sector is dynamic. The framework discusses some specifics, including the research network, boundaries and government initiatives to promote PM adoption. Based on the policy gaps, this paper further proposes an integrated policy framework for incorporating PM into India's healthcare system.

Mutational spectrum of congenital long QT syndrome in Turkey; identification of 12 novel mutations across KCNQ1, KCNH2, SCN5A, KCNJ2, CACNA1C, and CALM1

INTRODUCTION

Long QT syndrome (LQTS) is of great importance as it is the most common cause of sudden cardiac death in childhood. The diagnosis is made by the prolongation of the QTc interval on the electrocardiography. However, clinical heterogeneity and nondiagnostic QTc intervals may cause a delay in the diagnosis. In such cases, genetic tests such as next-generation sequencing (NGS) panel analysis enable a definitive diagnosis. We present the first study that aimed to expand the LQTS's mutational spectrum by NGS panel analysis from Turkey.

METHODS

Fifty-seven unrelated patients with clinically diagnosed LQTS were investigated using an NGS panel that includes six LQTS-related genes. Clinical aspects, outcome, and molecular analysis results were reviewed.

RESULTS

Pathogenic (53%)/likely pathogenic (23%)/variant of unknown significance (4%) variants were detected in any of the genes examined in 79% of the patients. Among all detected variants, KCNQ1(71%) was the most common gene, followed by SCN5A (11%), KCNH2 (10%), CALM1 (5%), and CACNA1C (3%). Twelve novel variants were detected. Among the variants in KCNQ1, the c.1097G>A variant was present in 42% of patients. This variant also composed 31% of the variants detected in all of the genes.

CONCLUSION

Our study expands the spectrum of the variations associated with LQTS with twelve novel variants in five genes. And also it draws attention to the frequency of the KCNQ1 c.1097G>A variant and forms the basis for new studies to determine the possible founder effect in the Turkish population. Furthermore, identifying new variants and clinical findings has importance in elaborating the roles of related genes in pathophysiology and determining the variable expression and incomplete penetration rates in this syndrome.

Long QT syndrome with potassium voltage-gated channel subfamily H member 2 gene mutation mimicking refractory epilepsy: case report

BACKGROUND

Epileptic seizures can be difficult to distinguish from other etiologies that cause cerebral hypoxia, especially cardiac diseases. Long QT syndrome (LQTS), especially LQTS type 2 (LQT2), frequently masquerades as seizures because of the transient cerebral hypoxia caused by ventricular arrhythmia. The high rate of sudden death in LQTS highlights the importance of accurate and early diagnosis; correct diagnosis of LQTS also prevents inappropriate treatment with anti-epileptic drugs (AEDs).

CASE PRESENTATION

We report a case of congenital LQT2 with potassium voltage-gated channel subfamily H member 2 gene (KCNH2) mutation misdiagnosed as refractory epilepsy and treated with various AEDs for 22 years. The possibility of cardiac arrhythmia was suspected after the patient presented to the emergency room and the electrocardiograph (ECG) monitor showed paroxysmal ventricular tachycardia during attacks. Atypical seizure like attacks with prodromal uncomfortable chest sensation and palpitation, triggered by auditory stimulation, and typical ventricular tachycardia monitored by ECG raised suspicion for LQT2, which was confirmed by exome sequencing and epileptic seizure was ruled out by 24-h EEG monitoring. Although the patient rejected implantation of an implantable cardioverter defibrillator, β blocker was given and the syncope only attacked 1-2 per year when there was an incentive during the 5 years follow up.

CONCLUSIONS

Our case illustrates how long LQTS can masquerade convincingly as epilepsy and can be treated wrongly with AEDs, putting the patient at high risk of sudden cardiac death. Careful ECG evaluation is recommend for both patients with first seizure and those with refractory epilepsy.

Modeling genetic cardiac channelopathies using induced pluripotent stem cells - Status quo from an electrophysiological perspective

Long QT syndrome (LQTS), Brugada syndrome (BrS), and catecholaminergic polymorphic ventricular tachycardia (CPVT) are genetic diseases of the heart caused by mutations in specific cardiac ion channels and are characterized by paroxysmal arrhythmias, which can deteriorate into ventricular fibrillation. In LQTS3 and BrS different mutations in the SCN5A gene lead to a gain-or a loss-of-function of the voltage-gated sodium channel Nav1.5, respectively. Although sharing the same gene mutation, these syndromes are characterized by different clinical manifestations and functional perturbations and in some cases even present an overlapping clinical phenotype. Several studies have shown that Na⁺ current abnormalities in LQTS3 and BrS can also cause Ca²⁺-signaling aberrancies in cardiomyocytes (CMs). Abnormal Ca²⁺ homeostasis is also the main feature of CPVT which is mostly caused by heterozygous mutations in the RyR2 gene. Large numbers of disease-causing mutations were identified in RyR2 and SCN5A but it is not clear how different variants in the SCN5A gene produce different clinical syndromes and if in CPVT Ca²⁺ abnormalities and drug sensitivities vary depending on the mutation site in the RyR2. These questions can now be addressed by using patient-specific in vitro models of these diseases based on induced pluripotent stem cells (iPSCs). In this review, we summarize different insights gained from these models with a focus on electrophysiological perturbations caused by different ion channel mutations and discuss how will this knowledge help develop better stratification and more efficient personalized therapies for these patients.

An NGS-based genotyping in LQTS; minor genes are no longer minor

Mutations in KCNQ1, KCNH2, and SCN5A are the major cause of long QT syndrome (LQTS). More than 90% of the genotyped patients have been reported to carry mutations in any of these three genes. Thanks to increasing popularity of next generation sequencer (NGS), novel CACNA1C mutations have been identified among LQTS patients without extra-cardiac phenotypes. We aimed to clarify the frequency of genotypes in LQTS patients in the era of NGS. The study comprised 160 congenital LQTS patients (71 males) registered from November 2015 to September 2018. Inclusion criteria was QTc > 460 ms and Schwartz score ≥ 3. We performed genetic analysis using target gene method by NGS and confirmed the mutations by Sanger method. The median age for genetic screening was 13 (0-68) years. Sixteen patients suffered cardiac arrest, 47 syncope, and 97 were asymptomatic. We identified genetic mutations in 111 (69.4%) patients including 6 CACNA1C (5.4% of the genotyped patients) with 4 asymptomatic patients. Five (3.1%) patients carried double mutations; three out of them with RYR2 and KCNQ1 or KCNH2. In conclusion, CACNA1C screening would be recommended even if the patient is asymptomatic to elucidate the genetic background of the LQTS patients.

Genotype and clinical characteristics of congenital long QT syndrome in Thailand

Background

Congenital long QT syndrome (LQTS) is an inheritable arrhythmic disorder which is linked to at least 17 genes. The clinical characteristics and genetic mutations may be variable among different population groups and they have not yet been studied in Thai population.

Methods

Clinical characteristics were retrospectively reviewed from children and young adults with congenital long QT syndrome whose blood samples were sent for genotyping during 1998–2017. Sangers sequencing was used to sequentially identify KCNQ1 or KCNH2 genetic variants. Whole exome sequencing (WES) was used to identify variants in all other known LQTS genes.

Results

Of the 20 subjects (17 families), 45% were male, mean QTc was 550.3 ± 68.8 msec (range 470–731 msec) and total Schwartz's score was 5.6 ± 1.2 points (range 3–8 points). Fifty percent of patients had events at rest, 30% had symptoms after adrenergic mediated events, and 20% were asymptomatic. We discovered pathogenic and likely pathogenic genetic variants in KCNQ1, KCNH2, and SCN5A in 6 (35%), 4 (24%), and 2 (12%) families, respectively. One additional patient had variance of unknown significance (VUS) in KCNH2 and another one in ANK2. No pathogenic genetic variant was found in 3 patients (18%). Most patients received beta-blocker and 9 (45%) had ICD implanted. LQT1 patients were either asymptomatic or had stress-induced arrhythmia. Most of the LQT2 and LQT3 patients developed symptoms at rest or during sleep.

Conclusions

Our patients with LQTS were mostly symptomatic at presentation. The genetic mutations were predominantly in LQT1, LQT2, and LQT3 genes.

Fatty acid analogue N-arachidonoyl taurine restores function of IKs channels with diverse long QT mutations

About 300 loss-of-function mutations in the I_Ks channel have been identified in patients with Long QT syndrome and cardiac arrhythmia. How specific mutations cause arrhythmia is largely unknown and there are no approved I_Ks channel activators for treatment of these arrhythmias. We find that several Long QT syndrome-associated I_Ks channel mutations shift channel voltage dependence and accelerate channel closing. Voltage-clamp fluorometry experiments and kinetic modeling suggest that similar mutation-induced alterations in I_Ks channel currents may be caused by different molecular mechanisms. Finally, we find that the fatty acid analogue N-arachidonoyl taurine restores channel gating of many different mutant channels, even though the mutations are in different domains of the I_Ks channel and affect the channel by different molecular mechanisms. N-arachidonoyl taurine is therefore an interesting prototype compound that may inspire development of future I_Ks channel activators to treat Long QT syndrome caused by diverse I_Ks channel mutations.

DOI:http://dx.doi.org/10.7554/eLife.20272.001

Every heartbeat relies on an electric wave that travels through the heart. This wave must reach different parts of the heart in a specific sequence to ensure that the heart muscle cells contract in a coordinated manner. Such coordinated contractions enable the heart to pump enough blood around the body. By allowing specific ions to flow into or out of the heart muscle cell, proteins called ion channels in the cell membrane generate the electric wave, keep it going and stop it. One such protein called the I_Ks channel controls the flow of potassium ions, and in doing so stops the electric wave in heart muscle cells.

About 300 different mutations in the I_Ks channel have been shown to cause abnormal heart rhythms in individuals with a disorder called long QT syndrome. People with this condition may suddenly black out because their heart develops prolonged electric waves that prevent blood from being pumped properly.

To investigate how mutations in the I_Ks channel produce heart rhythm abnormalities, Liin et al. genetically engineered the egg cells of African clawed frogs to have one of eight mutant forms of the human I_Ks channel. Studying these channels revealed that the mutations reduce how well the channels work in a wide variety of ways. However, treating the cells with a particular fatty acid helped to normalize how each of the mutant channels worked. Therefore, variants of the fatty acid could potentially form a useful treatment for people with heart rhythm problems caused by mutations in the I_Ks channel.

More studies are needed to confirm whether the fatty acid is as effective at combating the effects of the mutations in whole hearts and animals. As ion channels related to the I_Ks channel are found in many types of cells, it is also important to investigate whether treatment with the fatty acid could cause any side effects that affect other organs.

DOI:http://dx.doi.org/10.7554/eLife.20272.002