A Model Program for Translational Medicine in Epilepsy Genetics

Utility of Exome Sequencing for Diagnosis in Unexplained Pediatric-Onset Epilepsy

Importance

Genomic advances inform our understanding of epilepsy and can be translated to patients as precision diagnoses that influence clinical treatment, prognosis, and counseling.

Objective

To delineate the genetic landscape of pediatric epilepsy and clinical utility of genetic diagnoses for patients with epilepsy.

Design, Setting, and Participants

This cohort study used phenotypic data from medical records and treating clinicians at a pediatric hospital to identify patients with unexplained pediatric-onset epilepsy. Exome sequencing was performed for 522 patients and available biological parents, and sequencing data were analyzed for single nucleotide variants (SNVs) and copy number variants (CNVs). Variant pathogenicity was assessed, patients were provided with their diagnostic results, and clinical utility was evaluated. Patients were enrolled from August 2018 to October 2021, and data were analyzed through December 2022.

Exposures

Phenotypic features associated with diagnostic genetic results.

Main Outcomes and Measures

Main outcomes included diagnostic yield and clinical utility. Diagnostic findings included variants curated as pathogenic, likely pathogenic (PLP), or diagnostic variants of uncertain significance (VUS) with clinical features consistent with the involved gene's associated phenotype. The proportion of the cohort with diagnostic findings, the genes involved, and their clinical utility, defined as impact on clinical treatment, prognosis, or surveillance, are reported.

Results

A total of 522 children (269 [51.5%] male; mean [SD] age at seizure onset, 1.2 [1.4] years) were enrolled, including 142 children (27%) with developmental epileptic encephalopathy and 263 children (50.4%) with intellectual disability. Of these, 100 participants (19.2%) had identifiable genetic explanations for their seizures: 89 participants had SNVs (87 germline, 2 somatic mosaic) involving 69 genes, and 11 participants had CNVs. The likelihood of identifying a genetic diagnosis was highest in patients with intellectual disability (adjusted odds ratio [aOR], 2.44; 95% CI, 1.40-4.26), early onset seizures (aOR, 0.93; 95% CI, 0.88-0.98), and motor impairment (aOR, 2.19; 95% CI 1.34-3.58). Among 43 patients with apparently de novo variants, 2 were subsequently determined to have asymptomatic parents harboring mosaic variants. Of 71 patients who received diagnostic results and were followed clinically, 29 (41%) had documented clinical utility resulting from their genetic diagnoses.

Conclusions and Relevance

These findings suggest that pediatric-onset epilepsy is genetically heterogeneous and that some patients with previously unexplained pediatric-onset epilepsy had genetic diagnoses with direct clinical implications.

Genetic testing and counseling for the unexplained epilepsies: An evidence‐based practice guideline of the National Society of Genetic Counselors

Epilepsy, defined by the occurrence of two or more unprovoked seizures or one unprovoked seizure with a propensity for others, affects 0.64% of the population and can lead to significant morbidity and mortality. A majority of unexplained epilepsy (seizures not attributed to an acquired etiology, such as trauma or infection) is estimated to have an underlying genetic etiology. Despite rapid progress in understanding of the genetic underpinnings of the epilepsies, there are no recent evidence-based guidelines for genetic testing and counseling for this population. This practice guideline provides evidence-based recommendations for approaching genetic testing in the epilepsies using the Grading of Recommendations Assessment, Development and Evaluation (GRADE) Evidence to Decision framework. We used evidence from a recent systematic evidence review and meta-analysis of diagnostic yield of genetic tests in patients with epilepsy. We also compiled data from other sources, including recently submitted conference abstracts and peer-reviewed journal articles. We identified and prioritized outcomes of genetic testing as critical, important or not important and based our recommendations on outcomes deemed critical and important. We considered the desirable and undesirable effects, value and acceptability to relevant stakeholders, impact on health equity, cost-effectiveness, certainty of evidence, and feasibility of the interventions in individuals with epilepsy. Taken together, we generated two clinical recommendations: (1) Genetic testing is strongly recommended for all individuals with unexplained epilepsy, without limitation of age, with exome/genome sequencing and/or a multi-gene panel (>25 genes) as first-tier testing followed by chromosomal microarray, with exome/genome sequencing conditionally recommended over multi-gene panel. (2) It is strongly recommended that genetic tests be selected, ordered, and interpreted by a qualified healthcare provider in the setting of appropriate pre-test and post-test genetic counseling. Incorporation of genetic counselors into neurology practices and/or referral to genetics specialists are both useful models for supporting providers without genetics expertise to implement these recommendations.

Possible precision medicine implications from genetic testing using combined detection of sequence and intragenic copy number variants in a large cohort with childhood epilepsy

OBJECTIVE

Molecular genetic etiologies in epilepsy have become better understood in recent years, creating important opportunities for precision medicine. Building on these advances, detailed studies of the complexities and outcomes of genetic testing for epilepsy can provide useful insights that inform and refine diagnostic approaches and illuminate the potential for precision medicine in epilepsy.

METHODS

We used a multi-gene next-generation sequencing (NGS) panel with simultaneous sequence and exonic copy number variant detection to investigate up to 183 epilepsy-related genes in 9769 individuals. Clinical variant interpretation was performed using a semi-quantitative scoring system based on existing professional practice guidelines.

RESULTS

Molecular genetic testing provided a diagnosis in 14.9%-24.4% of individuals with epilepsy, depending on the NGS panel used. More than half of these diagnoses were in children younger than 5 years. Notably, the testing had possible precision medicine implications in 33% of individuals who received definitive diagnostic results. Only 30 genes provided 80% of molecular diagnoses. While most clinically significant findings were single-nucleotide variants, ~15% were other types that are often challenging to detect with traditional methods. In addition to clinically significant variants, there were many others that initially had uncertain significance; reclassification of 1612 such variants with parental testing or other evidence contributed to 18.5% of diagnostic results overall and 6.1% of results with precision medicine implications.

SIGNIFICANCE

Using an NGS gene panel with key high-yield genes and robust analytic sensitivity as a first-tier test early in the diagnostic process, especially for children younger than 5 years, can possibly enable precision medicine approaches in a significant number of individuals with epilepsy.

Neonatal epilepsy genetics

Neonatal epilepsy genetics is a rapidly expanding field with recent technological advances in genomics leading to an expanding list of genetic disorders associated with neonatal-onset epilepsy. The genetic causes of neonatal epilepsy can be grouped into the following categories: (i) malformations of cortical development, (ii) genetic-metabolic, (iii) genetic-vascular, (iv) genetic-syndromic, and (v) genetic-cellular. Clinically, epilepsy in the neonate shows phenotypic overlap with pathogenic variants in unrelated genes causing similar clinical presentation (locus heterogeneity) and variants in the same gene leading to a wide clinical spectrum ranging from benign familial neonatal seizures to more severe epileptic encephalopathies (variable expressivity). We suggest a diagnostic approach to obtaining a genetic diagnosis with emphasis on clinical features such as electro-clinical phenotype and magnetic resonance imaging findings. Rapid identification of genetic disorders with targeted treatments should be a clinical priority. Achieving a genetic diagnosis can be challenging in a rapidly changing genetic landscape, but is increasingly possible.

Genetic Testing in Pediatric Epilepsy

PURPOSE OF REVIEW

This article summarizes the emerging landscape of pediatric epilepsy, highlighting genetic contributions, and reviews approaches to genetic evaluation for pediatric epilepsy in this context.

RECENT FINDINGS

Advances in understanding the genetic basis for epilepsy over the last several years have been due in large part to the identification of de novo genetic variation underlying sporadic severe epilepsy in children; the genetic underpinnings of the more common epilepsies remain largely unknown. Next-generation sequencing approaches have been added to the repertoire of clinical tests for the evaluation of pediatric epilepsy, improving our ability to make positive diagnoses. Yields of over 50% are now being reported in selected groups of patients. Genetic variation contributing to the risk for pediatric epilepsy spans continua of scale and influence. The highest yield of genetic testing is currently in children with sporadic severe epilepsy caused by de novo variation. The approach to genetic evaluation and interpretation of results requires an understanding of (1) the epilepsy phenotype and (2) the particular advantages and limitations of the different genetic tests available. Our understanding of genetic variation will continue to improve over time and "negative" results are best conceptualized as "unresolved" or "negative for now."