Genomic testing in pediatric epilepsy

Study on the Economic Burden of Neurodevelopmental Diseases on Patients With Genetic Diagnosis

Objective

To study the burden of neurodevelopmental diseases (NDDs) via cost-of-illness analysis of Chinese patients with genetic diagnosis.

Methods

We recruited NDD patients (0–18 years old) with genetic diagnosis (GD) from September 1, 2020 to January 30, 2021. We gathered basic information on the details of diagnosis, as well as the direct medical cost, direct non-healthcare cost and indirect cost before and after receiving GD. We corrected the cost for time biases by calculating the cost per day for each patient.

Results

For the 502 patients with NDDs, the mean age was 4.08 ± 3.47. The household income was 0.6 (0.4, 1.0) 10,000 CNY per-month on average. The direct medical cost, direct non-healthcare cost and indirect cost were 12.27 (7.36, 22.23) 10,000 CNY, 1.45 (0.73, 2.69)10,000 CNY and 14.14(4.80, 28.25) 10,000 CNY per patient, respectively. Every patient received 1.20 (0.34, 3.60) 10,000 CNY on average (15.91%) from insurance. The daily total cost after receiving GD were ~62.48% lower than those before GD (191.59 CNY vs. 71.45 CNY). The descend range of lab cost (95.77%, P < 0.05) was the largest, followed by drugs (91.39%, P < 0.05), hospitalization (90.85%, P < 0.05), and consultation (57.41%, P < 0.05). The cost of rehabilitation kept slightly increasing but there were no significant differences (P > 0.05). The daily direct medical cost of each patient fell by 75.26% (P < 0.05) from 311.79 CNY to 77.14 CNY when the diagnostic age was younger than 1, and declined by 49.30% (P < 0.05) and 8.97% (P > 0.05) when the diagnostic age was 1–3 and older than 3, respectively.

Conclusions

Early genetic diagnosis is crucial for to reducing the burden of disease because of the amount of money spent was lower when they are diagnosed at younger age. Patients with NDDs can incur a heavy economic burden, especially in rehabilitation cost and indirect cost, because the insurance coverage for patients is low, so it is urgent for governments to pay more attention to these issues.

A Review of the Prevalence, Etiology, Diagnosis, and Management of Pediatric Epilepsies in India

Pediatric seizures are one of the most common neurological manifestations seen in pediatrics. Unravelling the etiology, timely and appropriate investigations followed by suitable therapies are essential for improving quality of life. During the pandemic, focused group discussions were conducted among 50 pediatric neurologists across five cities in India to gather insights on treatment practices in pediatric epilepsy and to optimize therapeutic strategies and alternative approaches for rational use of antiepileptic medications. These discussions were mainly aimed at reviewing current literature on prevalence, etiology, diagnosis, and management of epilepsy in children and subsequently rationalizing diagnostic and treatment approaches in routine clinical practice. Epileptic encephalopathies comprise of childhood epilepsy with progressive cerebral dysfunction. Genomics plays a vital role in identifying the underlying genetic associations, empowering precision therapy. Currently, the ketogenic diet has become a well-recognized modality for reducing severity of seizures. To overcome the high incidence of adverse effects due to older antiepileptic drugs, newer drugs are being developed to improve ease of use, diminish drug interactions, decrease adverse effects, and identify drugs with unique mechanisms of action. Common lacunae in practice include information gaps, educating parents, or caregivers about rational drug use and ensuring compliance to antiepileptic medications. This article discussed the consensus clinical viewpoint of expert clinicians, as well as insights on optimized treatment of pediatric epilepsies in both infancy and childhood. It also discusses aspects, like reducing drug burden, emerging therapies in the identification of the genetic basis of epilepsies, and targeted therapy alternatives, for pediatric populations in the Indian scenario.

Transcriptome Analysis Reveals Higher Levels of Mobile Element-Associated Abnormal Gene Transcripts in Temporal Lobe Epilepsy Patients

Mesial temporal lobe epilepsy (MTLE) is the most common form of epilepsy, and temporal lobe epilepsy patients with hippocampal sclerosis (TLE-HS) show worse drug treatment effects and prognosis. TLE has been shown to have a genetic component, but its genetic research has been mostly limited to coding sequences of genes with known association to epilepsy. Representing a major component of the genome, mobile elements (MEs) are believed to contribute to the genetic etiology of epilepsy despite limited research. We analyzed publicly available human RNA-seq-based transcriptome data to determine the role of mobile elements in epilepsy by performing de novo transcriptome assembly, followed by identification of spliced gene transcripts containing mobile element (ME) sequences (ME-transcripts), to compare their frequency across different sample groups. Significantly higher levels of ME-transcripts in hippocampal tissues of epileptic patients, particularly in TLE-HS, were observed. Among ME classes, short interspersed nuclear elements (SINEs) were shown to be the most frequent contributor to ME-transcripts, followed by long interspersed nuclear elements (LINEs) and DNA transposons. These ME sequences almost in all cases represent older MEs normally located in the intron sequences. For protein coding genes, ME sequences were mostly found in the 3'-UTR regions, with a significant portion also in the coding sequences (CDSs), leading to reading frame disruption. Genes associated with ME-transcripts showed enrichment for the mRNA splicing process and an apparent bias in epileptic transcriptomes toward neural- and epilepsy-associated genes. The findings of this study suggest that abnormal splicing involving MEs, leading to loss of functions in critical genes, plays a role in epilepsy, particularly in TLE-HS, thus providing a novel insight into the molecular mechanisms underlying epileptogenesis.

Genetics in Epilepsy

The presence of unprovoked, recurrent seizures, particularly when drug resistant and associated with cognitive and behavioral deficits, warrants investigation for an underlying genetic cause. This article provides an overview of the major classes of genes associated with epilepsy phenotypes divided into functional categories along with the recommended work-up and therapeutic considerations. Gene discovery in epilepsy supports counseling and anticipatory guidance but also opens the door for precision medicine guiding therapy with a focus on those with disease-modifying effects.

Genetic Testing in Neurodevelopmental Disorders

Neurodevelopmental disorders are the most prevalent chronic medical conditions encountered in pediatric primary care. In addition to identifying appropriate descriptive diagnoses and guiding families to evidence-based treatments and supports, comprehensive care for individuals with neurodevelopmental disorders includes a search for an underlying etiologic diagnosis, primarily through a genetic evaluation. Identification of an underlying genetic etiology can inform prognosis, clarify recurrence risk, shape clinical management, and direct patients and families to condition-specific resources and supports. Here we review the utility of genetic testing in patients with neurodevelopmental disorders and describe the three major testing modalities and their yields - chromosomal microarray, exome sequencing (with/without copy number variant calling), and FMR1 CGG repeat analysis for fragile X syndrome. Given the diagnostic yield of genetic testing and the potential for clinical and personal utility, there is consensus that genetic testing should be offered to all patients with global developmental delay, intellectual disability, and/or autism spectrum disorder. Despite this recommendation, data suggest that a minority of children with autism spectrum disorder and intellectual disability have undergone genetic testing. To address this gap in care, we describe a structured but flexible approach to facilitate integration of genetic testing into clinical practice across pediatric specialties and discuss future considerations for genetic testing in neurodevelopmental disorders to prepare pediatric providers to care for patients with such diagnoses today and tomorrow.

[Genetics of epilepsy: successes, problems and development prospects]

The authors present a detailed review of current advances in the field of genetics of epilepsy. Separately, new views on the etiology and pathogenesis of genetic epileptic encephalopathies, focal epilepsy and idiopathic generalized epilepsies are examined. The authors emphasize the importance of genetic discoveries for the clinical practice, including the prospects in the development of patients' personalized treatment. A comparative analysis of the value of various methods of genetic research in the diagnosis of epilepsy, methods of integrating molecular genetic analyses into everyday practical medicine is presented.

Assessment of Interlaboratory Variation in the Interpretation of Genomic Test Results in Patients With Epilepsy

IMPORTANCE

Discordance in the interpretations of genetic test results has occurred with the increased number of laboratories that are performing testing. Differences in diagnostic interpretations may have implications for the treatment of patients.

OBJECTIVE

To assess the interlaboratory variation in the interpretations of genetic test results with potential therapeutic implications.

DESIGN, SETTING, AND PARTICIPANTS

In this cross-sectional study, 70 genes that are commonly tested in patients with epilepsy were examined to identify 22 676 genetic variants from an unknown number of patients using the ClinVar public database of clinically annotated variants. Variant annotations submitted to ClinVar (data set version 2019-05) between November 16, 2012, and May 3, 2019, were included in the analysis. Conflicting interpretations of the genetic variants associated with epilepsy were analyzed for clinically substantial discrepancies between May 7 and June 29, 2019. Variants were examined only if they had been interpreted by 2 or more clinical laboratories. A variant with a clinically substantial difference in interpretation was defined as a variant that crossed the threshold between a likely pathogenic variant and a variant of uncertain significance.

MAIN OUTCOMES AND MEASURES

The frequency and types of variant interpretation conflicts were analyzed when a conflict was identified.

RESULTS

A total of 6292 of 22 676 variants related to epilepsy (27.7%) were interpreted by 2 or more clinical laboratories. Many variants (3307 of 6292 [52.6%]) had interpretations that were fully concordant. However, 2985 variants (47.4%) had conflicting interpretations. A clinically substantial conflict was identified in 201 of 6292 variants (3.2%). Furthermore, 117 of 201 variants (58.2%) with differences in interpretation occurred in genes with therapeutic implications.

CONCLUSIONS AND RELEVANCE

In this cross-sectional study, most interpretations of genetic variants associated with epilepsy were concordant among laboratories, but more than half of the variants with conflicting interpretations occurred in genes that have therapeutic implications. It would be helpful for genetic laboratories to report known diagnostic discordance with other clinical laboratories.