Gene-Targeted Analysis of Clinically Diagnosed Long QT Russian Families

Identifying the Pathogenic Variants in Heart Genes in Vietnamese Sudden Unexplained Death Victims by Next-Generation Sequencing

In forensics, one-third of sudden deaths remain unexplained after a forensic autopsy. A majority of these sudden unexplained deaths (SUDs) are considered to be caused by inherited cardiovascular diseases. In this study, we investigated 40 young SUD cases (<40 years), with non-diagnostic structural cardiac abnormalities, using Targeted NGS (next-generation sequencing) for 167 genes previously associated with inherited cardiomyopathies and channelopathies. Fifteen cases identified 17 variants on related genes including the following: AKAP9, CSRP3, GSN, HTRA1, KCNA5, LAMA4, MYBPC3, MYH6, MYLK, RYR2, SCN5A, SCN10A, SLC4A3, TNNI3, TNNI3K, and TNNT2. Of these, eight variants were novel, and nine variants were reported in the ClinVar database. Five were determined to be pathogenic and four were not evaluated. The novel and unevaluated variants were predicted by using in silico tools, which revealed that four novel variants (c.5187_5188dup, p.Arg1730llefsTer4 in the AKAP9 gene; c.1454A>T, p.Lys485Met in the MYH6 gene; c.2535+1G>A in the SLC4A3 gene; and c.10498G>T, p.Asp3500Tyr in the RYR2 gene) were pathogenic and three variants (c.292C>G, p.Arg98Gly in the TNNI3 gene; c.683C>A, p.Pro228His in the KCN5A gene; and c.2275G>A, p.Glu759Lys in the MYBPC3 gene) still need to be further verified experimentally. The results of our study contributed to the general understanding of the causes of SUDs. They provided a scientific basis for screening the risk of sudden death in family members of victims. They also suggested that the Targeted NGS method may be used to identify the pathogenic variants in SUD victims.

Retinitis Pigmentosa Associated with EYS Gene Mutations: Disease Severity Staging and Central Retina Atrophy

BACKGROUND

Eyes shut homolog (EYS) gene mutations are estimated to affect at least 5% of patients with autosomal recessive retinitis pigmentosa. Since there is no mammalian model of human EYS disease, it is important to investigate its age-related changes and the degree of central retinal impairment.

METHODS

A cohort of EYS patients was studied. They underwent full ophthalmic examination as well as assessment of retinal function and structure, by full-field and focal electroretinograms (ERGs) and spectral domain optical coherence tomography (OCT), respectively. The disease severity stage was determined by the RP stage scoring system (RP-SSS). Central retina atrophy (CRA) was estimated from the automatically calculated area of the sub-retinal pigment epithelium (RPE) illumination (SRI).

RESULTS

The RP-SSS was positively correlated with age, showing an advanced severity score (≥8) at an age of 45 and a disease duration of 15 years. The RP-SSS was positively correlated with the CRA area. LogMAR visual acuity and ellipsoid zone width, but not ERG, were correlated with CRA.

CONCLUSIONS

In EYS-related disease, the RP-SSS showed advanced severity at a relative early age and was correlated with the central area of the RPE/photoreceptor atrophy. These correlations may be relevant in view of therapeutic interventions aimed at rescuing rods and cones in EYS-retinopathy.

AKAP9-Related Channelopathy: Novel Pathogenic Variant and Review of the Literature

Disease-associated pathogenic variants in the A-Kinase Anchor Protein 9 (AKAP9) (MIM *604001) have been recently identified in patients with autosomal dominant long QT syndrome 11 (MIM #611820), lethal arrhythmia (ventricular fibrillation, polymorphic ventricular tachycardia), Brugada syndrome, and sudden unexpected death. However, AKAP9 sequence variations were rarely reported and AKAP9 was classified as a "disputed evidence" gene to support disease causation due to the insufficient genetic evidence and a limited number of reported AKAP9-mutated patients. Here, we describe a 47-year-old male carrying a novel frameshift AKAP9 pathogenic variant who presented recurrent syncopal attacks and sudden cardiac arrest that required a semi-automatic external defibrillator implant and an electric shock treatment of ventricular arrhythmia. This study provides insight into the mechanism underlying cardiac arrest and confirms that AKAP9 loss-of-function variants predispose to serious, life-threatening ventricular arrhythmias.

Variable Clinical Appearance of the Kir2.1 Rare Variants in Russian Patients with Long QT Syndrome

Background: The KCNJ2 gene encodes inward rectifier Kir2.1 channels, maintaining resting potential and cell excitability. Presumably, clinical phenotypes of mutation carriers correlate with ion permeability defects. Loss-of-function mutations lead to QTc prolongation with variable dysmorphic features, whereas gain-of-function mutations cause short QT syndrome and/or atrial fibrillation. Methods: We screened 210 probands with Long QT syndrome for mutations in the KCNJ2 gene. The electrophysiological study was performed for the p.Val93Ile variant in the transfected CHO-K1 cells. Results: We found three rare genetic variants, p.Arg67Trp, p.Val93Ile, and p.R218Q, in three unrelated LQTS probands. Probands with p.Arg67Trp and p.R218Q had a phenotype typical for Andersen-Tawil (ATS), and the p.Val93Ile carrier had lone QTc prolongation. Variant p.Val93Ile was initially described as a gain-of-function pathogenic mutation causing familial atrial fibrillation. We validated electrophysiological features of this variant in CHO-K1 cells, but no family members of these patients had atrial fibrillation. Using ACMG (2015) criteria, we re-assessed this variant as a variant of unknown significance (class III). Conclusions: LQT7 is a rare form of LQTS in Russia, and accounts for 1% of the LQTS cohort. Variant p.Val93Ile leads to a gain-of-function effect in the different cell lines, but its clinical appearance is not so consistent. The clinical significance of this variant might be overestimated.

Genetic characteristics of 234 Italian patients with macular and cone/cone-rod dystrophy

Two-hundred and thirty-four Italian patients with a clinical diagnosis of macular, cone and cone-rod dystrophies (MD, CD, and CRD) were examined using next-generation sequencing (NGS) and gene sequencing panels targeting a specific set of genes, Sanger sequencing and—when necessary—multiplex ligation-dependent probe amplification (MLPA) to diagnose the molecular cause of the aforementioned diseases. When possible, segregation analysis was performed in order to confirm unsolved cases. Each patient’s retinal phenotypic characteristics were determined using focal and full-field ERGs, perimetry, spectral domain optical coherence tomography and fundus autofluorescence. We identified 236 potentially causative variants in 136 patients representing the 58.1% of the total cohort, 43 of which were unpublished. After stratifying the patients according to their clinical suspicion, the diagnostic yield was 62.5% and 53.8% for patients with MD and for those with CD/CRD, respectively. The mode of inheritance of all cases confirmed by genetic analysis was 70% autosomal recessive, 26% dominant, and 4% X-linked. The main cause (59%) of both MD and CD/CRD cases was the presence of variants in the ABCA4 gene, followed by variants in PRPH2 (9%) and BEST1 (6%). A careful morpho-functional evaluation of the phenotype, together with genetic counselling, resulted in an acceptable diagnostic yield in a large cohort of Italian patients. Our study emphasizes the role of targeted NGS to diagnose MDs, CDs, and CRDs, as well as the clinical usefulness of segregation analysis for patients with unsolved diagnosis.

Targeted Sequencing of 242 Clinically Important Genes in the Russian Population From the Ivanovo Region

We performed a targeted sequencing of 242 clinically important genes mostly associated with cardiovascular diseases in a representative population sample of 1,658 individuals from the Ivanovo region northeast of Moscow. Approximately 11% of 11,876 detected variants were not found in the Single Nucleotide Polymorphism Database (dbSNP) or reported earlier in the Russian population. Most novel variants were singletons and doubletons in our sample, and virtually no novel alleles presumably specific for the Russian population were able to reach the frequencies above 0.1-0.2%. The overwhelming majority (99.3%) of variants detected in this study in three or more copies were shared with other populations. We found two dominant and seven recessive known pathogenic variants with allele frequencies significantly increased compared to those in the gnomAD non-Finnish Europeans. Of the 242 targeted genes, 28 were in the list of 59 genes for which the American College of Medical Genetics and Genomics (ACMG) recommended the reporting of incidental findings. Based on the number of variants detected in the sequenced subset of ACMG59 genes, we approximated the prevalence of known pathogenic and novel or rare protein-truncating variants in the complete set of ACMG59 genes in the Ivanovo population at 1.4 and 2.8%, respectively. We analyzed the available clinical data and observed the incomplete penetrance of known pathogenic variants in the 28 ACMG59 genes: only 1 individual out of 12 with such variants had the phenotype most likely related to the variant. When known pathogenic and novel or rare protein-truncating variants were considered together, the overall rate of confirmed phenotypes was about 19%, with maximum in the subset of novel protein-truncating variants. We report three novel protein truncating variants in APOB and one in MYH7 observed in individuals with hypobetalipoproteinemia and hypertrophic cardiomyopathy, respectively. Our results provide a valuable reference for the clinical interpretation of gene sequencing in Russian and other populations.

Molecular Epidemiology in 591 Italian Probands With Nonsyndromic Retinitis Pigmentosa and Usher Syndrome

Purpose

To describe the molecular epidemiology of nonsyndromic retinitis pigmentosa (RP) and Usher syndrome (US) in Italian patients.

Methods

A total of 591 probands (315 with family history and 276 sporadics) were analyzed. For 155 of them, we performed a family segregation study, considering a total of 382 relatives. Probands were analyzed by a customized multigene panel approach. Sanger sequencing was used to validate all genetic variants and to perform family segregation studies. Copy number variants of selected genes were analyzed by multiplex ligation-dependent probe amplification. Four patients who tested negative to targeted next-generation sequencing analysis underwent clinical exome sequencing.

Results

The mean diagnostic yield of molecular testing among patients with a family history of retinal disorders was 55.2% while the diagnostic yield including sporadic cases was 37.4%. We found 468 potentially pathogenic variants, 147 of which were unpublished, in 308 probands and 66 relatives. Mean ages of onset of the different classes of RP were autosomal dominant RP, 19.3 ± 12.6 years; autosomal recessive RP, 23.2 ± 16.6 years; X-linked RP, 13.9 ± 9.9 years; and Usher syndrome, 18.9 ± 9.5 years. We reported potential new genotype-phenotype correlations in three probands, two revealed by TruSight One testing. All three probands showed isolated RP caused by biallelic variants in genes usually associated with syndromes such as PERCHING and Senior-Loken or with retinal dystrophy, iris coloboma, and comedogenic acne syndrome.

Conclusions

This is the largest molecular study of Italian patients with RP in the literature, thus reflecting the epidemiology of the disease in Italy with reasonable accuracy.

Impaired Ca2+ Sensitivity of a Novel GCAP1 Variant Causes Cone Dystrophy and Leads to Abnormal Synaptic Transmission Between Photoreceptors and Bipolar Cells

Guanylate cyclase-activating protein 1 (GCAP1) is involved in the shutdown of the phototransduction cascade by regulating the enzymatic activity of retinal guanylate cyclase via a Ca²⁺/cGMP negative feedback. While the phototransduction-associated role of GCAP1 in the photoreceptor outer segment is widely established, its implication in synaptic transmission to downstream neurons remains to be clarified. Here, we present clinical and biochemical data on a novel isolate GCAP1 variant leading to a double amino acid substitution (p.N104K and p.G105R) and associated with cone dystrophy (COD) with an unusual phenotype. Severe alterations of the electroretinogram were observed under both scotopic and photopic conditions, with a negative pattern and abnormally attenuated b-wave component. The biochemical and biophysical analysis of the heterologously expressed N104K-G105R variant corroborated by molecular dynamics simulations highlighted a severely compromised Ca²⁺-sensitivity, accompanied by minor structural and stability alterations. Such differences reflected on the dysregulation of both guanylate cyclase isoforms (RetGC1 and RetGC2), resulting in the constitutive activation of both enzymes at physiological levels of Ca²⁺. As observed with other GCAP1-associated COD, perturbation of the homeostasis of Ca²⁺ and cGMP may lead to the toxic accumulation of second messengers, ultimately triggering cell death. However, the abnormal electroretinogram recorded in this patient also suggested that the dysregulation of the GCAP1–cyclase complex further propagates to the synaptic terminal, thereby altering the ON-pathway related to the b-wave generation. In conclusion, the pathological phenotype may rise from a combination of second messengers’ accumulation and dysfunctional synaptic communication with bipolar cells, whose molecular mechanisms remain to be clarified.

appMAGI: A complete laboratory information management system for clinical diagnostics

Background:

The increasing demand for genetic testing for clinical diagnosis and research challenges genetic laboratory capacity to track an increasing number of patient samples through all steps of analysis, from sample collection to report generation. This task is usually performed with the help of a laboratory information management system (LIMS), software that makes it possible to collect, store and retrieve laboratory and sample data. To date there are no open-source options that can manage the entire analytical flow of a genetic laboratory. appMAGI seeks to include all the management aspects of a clinical diagnostic laboratory, making it simpler to process many samples while maintaining the high security and quality standards required in clinical diagnostic practice.

Methods:

appMAGI is written in python using Django. It is a web application that does not require local installation, making development, updates and maintenance a much easier task. appMAGI runs on the Ubuntu server and uses SQLite as engine database.

Results:

In this work we describe an innovative LIMS called appMAGI designed to support all aspects of a clinical diagnostic laboratory. appMAGI can track samples throughout the diagnostic workflow and NGS analysis by virtue of a customizable bioinformatics pipeline. It can handle sample non-compliance, manage laboratory stocks, help generate reports and provide insights into sample data by means of special tools.

Conclusions:

appMAGI is a LIMS endowed with all the features required to manage thousands of samples. Allowing efficient management of patient samples from sample collection to diagnostic report generation. (www.actabiomedica.it)

Cardiac Arrest Associated with Both an Anomalous Left Coronary Artery and KCNE1 Polymorphism

A 14-year-old boy collapsed suddenly after a basketball game and was transported to our hospital after recovering from ventricular fibrillation by an automated external defibrillator. He had experienced loss of consciousness twice and has been examined for suspected long-QT syndrome at another hospital. The 12-lead electrocardiogram on admission revealed a prolonged QTc interval of 480 milliseconds. After the patient recovered without any sequelae, computed tomography revealed an anomalous left coronary artery arising from the opposite sinus of Valsalva and coursing between the aorta and the pulmonary artery. Furthermore, genetic testing identified a KCNE1-D85N abnormality. An anomalous coronary artery is one of the major causes of sudden death in young people; therefore, surgical revascularization is recommended for left coronary arteries arising from the contralateral sinus and coursing between the aorta and the pulmonary artery, regardless of myocardial ischemia. Transient myocardial ischemia may have exaggerated the instability from the arrhythmic substrate, even though KCNE1-D85N abnormalities alone are not thought to cause fatal arrhythmias. Besides routine electrocardiography, further examinations, including imaging and genetic testing, can characterize the pathophysiology of fatal cardiac disease.

Central Retina Functional Damage in Usher Syndrome Type 2: 22 Years of Focal Macular ERG Analysis in a Patient Population From Central and Southern Italy

Purpose

Recent studies show that patients with Usher syndrome type 2 (USH2) have abnormal cone structure and density in the central retina. This occurs in the presence of normal acuity, opening the quest for additional sensitive functional measures of central cone function in USH. We tested here whether focal macular cone electroretinogram (fERG) could be such a tool.

Methods

This retrospective study of central cone function loss was based on data from 47 patients with USH2 from the Ophthalmology Department of the Policlinico Gemelli/Catholic University in Rome. The analysis focused on the decrease of the fERG, obtained in response to a 41-Hz sinusoidal modulation of a uniform field presented to the central 18°, generated by red light-emitting diodes (LEDs) and superimposed on an equiluminant steady adapting background. fERG decrease was compared with the decrease of best-corrected visual acuity and Goldmann kinetic perimetry V4E field.

Results

fERG follow-up data document a severe and precocious loss of central cone function in USH2 patients, preceding losses in other measures of cone function. fERG is already reduced to 40% of control at the beginning of the second decade of life, and by 25 years of age, all USH2 patients have fERGs less than 30% of control values.

Conclusions

fERG represents a sensitive tool to evaluate central cone function in USH2, anticipating the decline of other central cone function measures, such as visual acuity and Goldmann perimetry.

Persistent QT Prolongation in a Child with Gitelman Syndrome and SCN5A H558R Polymorphism

Gitelman syndrome (GS) is an inherited renal tubular disorder characterized by hypokalemic metabolic alkalosis, hypomagnesemia, and low urinary calcium excretion. While it is considered a benign disease, severe ventricular arrhythmia and sudden cardiac death related to the prolongation of the QT interval have been reported in rare cases. Herein we report a 13-year-old girl with GS who presented with persistent prolongation of the QT interval, even after being treated for hypokalemia and hypomagnesemia. Genetic analysis identified SCN5A H558R polymorphism, which modulates the function of myocardial sodium channel, and SLC12A3 A588V mutation, which causes GS. The SCN5A polymorphism and GS-related electrolyte disturbance might have contributed to the persistent QT prolongation in this patient. Although no ventricular arrhythmias were recorded in this case, careful cardiac surveillance should be applied for avoiding life-threatening cardiac events.

Early impairment of the full-field photopic negative response in patients with Stargardt disease and pathogenic variants of the ABCA4 gene

BACKGROUND

To study the photopic negative response of the full-field photopic electroretinography (ERG) in Stargardt patients with pathogenic variants in the ABCA4 gene.

METHODS

A retrospective analysis of 35 Stargardt patients with ABCA4 gene pathogenic variants, compared to normal age-matched controls. Patients were clinically followed at the Ophthalmology Department of Fondazione Policlinico Universitario A. Gemelli/Università Cattolica del Sacro Cuore, Rome, Italy.

RESULTS

The photopic negative response of the full-field photopic ERG was compromised in most Stargardt patients. In the presence of a normal B-wave, the amplitude ratio between the photopic negative response and the B-wave displayed a 97% accuracy in detecting diseased eyes (receiver operating characteristic curves).

CONCLUSIONS

In Stargardt patients with ABCA4 pathogenic mutations, the photopic negative response of the full-field photopic ERG is a very sensitive disease read-out. Its inclusion in standard ERG analysis would be a no-cost addition of practical consequence in the follow-up of Stargardt disease. The early impairment of the photopic negative response suggests that inner retinal function might be affected in Stargardt disease earlier than previously acknowledged.

Endurance Exercise Ability in the Horse: A Trait with Complex Polygenic Determinism

Endurance horses are able to run at more than 20 km/h for 160 km (in bouts of 30-40 km). This level of performance is based on intense aerobic metabolism, effective body heat dissipation and the ability to endure painful exercise. The known heritabilities of endurance performance and exercise-related physiological traits in Arabian horses suggest that adaptation to extreme endurance exercise is influenced by genetic factors. The objective of the present genome-wide association study (GWAS) was to identify single nucleotide polymorphisms (SNPs) related to endurance racing performance in 597 Arabian horses. The performance traits studied were the total race distance, average race speed and finishing status (qualified, eliminated or retired). We used three mixed models that included a fixed allele or genotype effect and a random, polygenic effect. Quantile-quantile plots were acceptable, and the regression coefficients for actual vs. expected log10p-values ranged from 0.865 to 1.055. The GWAS revealed five significant quantitative trait loci (QTL) corresponding to 6 SNPs on chromosomes 6, 1, 7, 16, and 29 (two SNPs) with corrected p-values from 1.7 × 10-6 to 1.8 × 10-5. Annotation of these 5 QTL revealed two genes: sortilin-related VPS10-domain-containing receptor 3 (SORCS3) on chromosome 1 is involved in protein trafficking, and solute carrier family 39 member 12 (SLC39A12) on chromosome 29 is active in zinc transport and cell homeostasis. These two coding genes could be involved in neuronal tissues (CNS). The other QTL on chromosomes 6, 7, and 16 may be involved in the regulation of the gene expression through non-coding RNAs, CpG islands and transcription factor binding sites. On chromosome 6, a new candidate equine long non-coding RNA (KCNQ1OT1 ortholog: opposite antisense transcript 1 of potassium voltage-gated channel subfamily Q member 1 gene) was predicted in silico and validated by RT-qPCR in primary cultures of equine myoblasts and fibroblasts. This lncRNA could be one element of the cardiac rhythm regulation. Our GWAS revealed that equine performance during endurance races is a complex polygenic trait, and is partially governed by at least 5 QTL: two coding genes involved in neuronal tissues and three other loci with many regulatory functions such as slowing down heart rate.