Genetic variant interpretation for the neurologist - A pragmatic approach in the next-generation sequencing era in childhood epilepsy.

Genetic advances over the past decade have enhanced our understanding of the genetic landscape of childhood epilepsy. However a major challenge for clinicians ha been understanding the rationale and systematic approach towards interpretation of the clinical significance of variant(s) detected in their patients. As the clinical paradigm evolves from gene panels to whole exome or whole genome testing including rapid genome sequencing, the number of patients tested and variants identified per patient will only increase. Each step in the process of variant interpretation has limitations and there is no single criterion which enables the clinician to draw reliable conclusions on a causal relationship between the variant and disease without robust clinical phenotyping. Although many automated online analysis software tools are available, these carry a risk of misinterpretation. This guideline provides a pragmatic, real-world approach to variant interpretation for the child neurologist. The focus will be on ascertaining aspects such as variant frequency, subtype, inheritance pattern, structural and functional consequence with regard to genotype-phenotype correlations, while refraining from mere interpretation of the classification provided in a genetic test report. It will not replace the expert advice of colleagues in clinical genetics, however as genomic investigations become a first-line test for epilepsy, it is vital that neurologists and epileptologists are equipped to navigate this landscape.

Metabolic causes of pediatric developmental & epileptic encephalopathies (DEE)- genetic variant analysis in a south Indian cohort.

PURPOSE: Drug-resistant epilepsy is seen in patients with inborn errors of metabolism and metabolic dysfunction in neurons is crucial to brain disorders associated with psychomotor impairment. Diagnostic rates of metabolic causes of developmental and epileptic encephalopathy (DEE) using next generation sequencing have been rarely studied in literature. METHODS: A prospective hospital study was carried out in 384 children with DEE, who underwent genetic testing. Metabolic disorders were evaluated with biochemical blood/urine assays and when required CSF estimations performed. RESULTS: A total of 154 pathogenic/likely pathogenic variants in 384 children were identified. Out of 384 children, 89 were clinically suspected to have probable or possible metabolic disorders. Pathogenic/likely pathogenic variants in metabolic genes were identified in 39 out of 89 (43.8 %) and promising VUS in 28 (31.4 %). These included variants for progressive myoclonus epilepsies (21; 53.8 %), DEE with focal/multifocal seizures (8; 20.5 %), generalized epilepsy (5;12.8 %), early myoclonic encephalopathy (2; 5.1 %), LGS (1; 2.6 %) and West syndrome (2; 5.1 %). CONCLUSION: Our cohort demonstrates for the first time from the Indian subcontinent that identification of metabolic variants can guide investigations and has therapeutic implications in patients with variable DEE phenotypes. A high utility is noted with regard to diagnosis and prognostication, given the low yield of available biochemical tests, indicating cost-effectiveness of this approach.

Impact of variant subtype on electro-clinical phenotype of Dravet syndrome- a South Indian cohort study.

OBJECTIVE: We aimed to compare the electroclinical correlates of truncating and missense variants of SCN1A variants in children with Dravet syndrome (DS) and to determine phenotypic features in relation to variants identified and seizure outcomes. METHODS: A single center prospective study was carried out on a South Indian cohort. Patients below 18 years of age who met the clinical criteria for DS who had undergone genetic testing and completed a minimum of one year follow up were included. We compared the differences in clinical profile, seizure outcome, developmental characteristics and anti-seizure medication (ASM) responsiveness profiles between patients with missense and truncating variants. RESULTS: Out of a total of 3967 children with drug-resistant epilepsy during the period 2015-2021, 49 patients who fulfilled the inclusion criteria were studied. Thirty-seven had positive genetic tests, out of which 29 were SCN1A variants and 9 were other novel variants. The proportion of missense (14; 48.3%) and truncating SCN1A variants (15; 51.7%) was similar. A significant trend for developing multiple seizure types was noted among children with truncating variants (p = 0.035) and seizure freedom was more likely among children with missense variants (p = 0.042). All patients with truncating variants had ASM resistant epilepsy (p = 0.020). Developmental outcomes did not differ between the variant subtypes. CONCLUSION: Our results show that children harbouring missense variants demonstrated a significantly lower propensity for multiple seizure subtypes and a higher proportion with seizure freedom. However developmental implications appear to be independent of variant subtype.

Clinical Utility of Proband Only Clinical Exome Sequencing in Neurodevelopmental Disorders.

Chromosomal microarray is recommended as the first line of investigation in neurodevelopmental disorders (NDDs). However, advances in next-generation sequencing have unraveled more than 900 genes associated with NDDs, thus improving the genetic diagnosis. Therefore, this study was conducted to explore the utility of clinical exome sequencing (CES) in NDDs from a tertiary care centre in India. A retrospective observational analysis of 78 children with NDDs for whom CES was performed between 2017 and 2021 was conducted. The American College of Medical Genetics and Genomics (ACMG) criteria were used to classify the variants. The mean age was 5.8 ± 3.6 y, and 42 (53%) were male. Pathogenic, likely pathogenic, and variants of uncertain significance (VUS) were observed in 22 (28.2%), 10 (12.8%), and 26 (33.3%) patients, respectively, which included five copy number variants. The diagnostic yield for pathogenic and likely pathogenic variants in NDDs by CES was 41%, which was reasonably high.

Paediatric quality of life in toddlers and children who underwent arterial switch operation beyond early neonatal period.

OBJECTIVES: The aim of this study was to evaluate the quality of life (QOL) of children who underwent the arterial switch operation (ASO) for Transposition of Great Arteries in our population and, specifically, to explore early modifiable factors and the influence of parental and socioeconomic factors on the QOL of these children. METHODS: Cross-sectional study using Paediatric Quality of Life Inventory™ 3.0 Cardiac Module was carried out on 3- to 12-year-old children who had undergone ASO between the years 2012-2018. Socioeconomic status was calculated using the modified Kuppuswamy scale (2019). Other clinical factors with possible bearing on the outcome were also analysed. RESULTS: Immediate survival after surgery was 196 out of 208 (94.2%) with an attrition of 19 patients (9.6%) over the follow-up period. Most surviving children (98.9%) had started formal schooling in age-appropriate classes. Two children had severe neuromotor impairment. The median cumulative health-related QOL score of the children was 97.9 (interquartile range 4.2) at 5.6 ± 1.27 years of life. The median scores each of the health-related QOL parameters, viz, heart problem symptoms, treatment compliance, perceived physical appearance, treatment-related anxiety, cognitive problems, and communication was 100 with negative skewing. CONCLUSIONS: Excellent QOL was observed in most children after ASO with the median total paediatric QOL scores in all domains of 97.9. Social factors did not show a statistically significant influence on the QOL parameters in the current cohort. The gradually declining trend across the age groups emphasizes the need for continued follow-up for early identification of possible correctable factors and initiating intervention to ensure good QOL into teenage and adulthood.

Diagnostic Classification of ASD Using Fractal Functional Connectivity of fMRI and Logistic Regression.

Our study used functional magnetic resonance imaging and fractal functional connectivity (FC) methods to analyze the brain networks of Autism Spectrum Disorder (ASD) and typically developing participants using data available on ABIDE databases. Blood-Oxygen-Level-Dependent time series were extracted from 236 regions of interest of cortical, subcortical, and cerebellar regions using Gordon's, Harvard Oxford, and Diedrichsen atlases respectively. We computed the fractal FC matrices which resulted in 27,730 features, ranked using XGBoost feature ranking. Logistic regression classifiers were used to analyze the performance of the top 0.1%, 0.3%, 0.5%, 0.7%, 1%, 2%, and 3% of FC metrics. Results showed that 0.5% percentile features performed better, with average 5-fold accuracy of 94%. The study identified significant contributions from dorsal attention (14.75%), cingulo-opercular task control (14.39%), and visual networks (12.59%). This study could be used as an essential brain FC method to diagnose ASD.

Arginase deficiency-An unheralded cause of developmental epileptic encephalopathy.

Arginase deficiency, which leads to hyperargininaemia is a rare urea cycle disorder caused by a mutation in the ARG1 gene. It is an under-recognized cause of pediatric developmental epileptic encephalopathy, with the key coexistent clinical features being developmental delay or regression and spasticity. Detection of ARG1 gene mutation on genetic testing is the confirmatory diagnostic test. However, elevated levels of plasma arginine and low plasma arginase level can be considered as biochemical markers for diagnosis. We present two cases of arginase deficiency with genetically confirmed ARG1 mutation in one and biochemical confirmation in both. As the spectrum of epilepsy in arginase deficiency has been less explored, we attempted to elucidate the novel electroclinical features and syndromic presentations in these patients. Informed consent was obtained from families of patients. Electroclinical diagnosis was consistent with Lennox Gastaut syndrome (LGS) in the first patient while the second patient had refractory atonic seizures with electrophysiological features consistent with developmental and epileptic encephalopathy. Though primary hyperammonaemia is not a consistent feature, secondary hyperammonaemia in the setting of infectious triggers and drugs like valproate (valproate sensitivity) has been well described as also observed in our patient. In the absence of an overt antecedent in a child with spasticity and seizure disorder, with a progressive course consistent with a developmental epileptic encephalopathy, arginase deficiency merits consideration. Diagnosis often has important therapeutic implications with respect to dietary management and choice of the appropriate antiseizure medications.

Autism Spectrum Disorders: Barriers to Implementing Parent-Based Home Programs.

An exploratory survey to identify the barriers experienced by caregivers of children with autism spectrum disorders (ASD) when implementing home programs (HP) was conducted with a newly developed questionnaire, 'barriers in the parent-based home program for ASD (BHPQ-ASD)' in English and Malayalam. The questionnaire has 25 items in Likert scale response format and underwent face validation and cognitive debriefing. It was administered to 50 caregivers of ASD children for factor extraction and reliability analysis. Seven questions under service provider-related barriers emerged to have good psychometric properties in the principal axis factoring method and were grouped to form the 'service provider-related BHPQ-ASD' scale, which has very good internal consistency (Cronbach alpha 0.903). In regression analysis, parents of children not receiving occupational therapy (OT) reported 6.6 times more barriers when compared to those undergoing OT (OR 6.6, CI 1.5-29.7, p = 0.014). BHPQ-ASD is a useful valid tool for detecting the barriers to implementing HPs.

C12orf57 pathogenic variants: a unique cause of developmental encephalopathy in a south Indian child.

Open reading frame variants which lack stop codons such as C12orf57 variants are known to cause Temtamy syndrome, an extremely rare disorder characterized by intellectual disability, seizures, facial dysmorphism and agenesis of corpus callosum. C12orf57 was initially reported to be required for human corpus callosum development. We report the first child who is of Indian origin with developmental and epileptic encephalopathy (DEE) with a unique phenotypic evolution as focal onset reflex seizures. We performed whole exome sequencing of genomic DNA isolated from peripheral blood samples of proband and his parents. Two pathogenic compound heterozygous variants, a start loss variant (Chr12:7053285:c.1A>G) and a premature stop gain variant (Chr12:7053327:c.43C>T), involving the C12orf57 gene were identified in the proband. Our case report which details genotyping in this rare syndromic developmental encephalopathy, with no prior cases reported from India, expands the ethnic spectrum of patients.