Next-generation sequencing in children with epilepsy: The importance of precise genotype–phenotype correlation

Highlights

• Multidisciplinary approach is important while interpreting epilepsy genetic results.

• Precise genotype–phenotype correlation can increase the yield of NGS panel by 53.33%.

• Proposed approach allowed the yield of next-generation sequencing to reach 26.28%.

Abstract

Aim

The primary goal was to determine the yield of next-generation sequencing (NGS) epilepsy gene panels used for epilepsy etiology diagnosing using a multidisciplinary approach and to demonstrate the importance of genotype–phenotype correlations. The secondary goal was to evaluate the application of precision medicine in selected patients.

Methods

This single-center retrospective study included a total of 175 patients (95 males and 80 females) aged 0–19 years. They were examined between 2015 and 2020 using an NGS epilepsy gene panel (270 genes). A bioinformatic analysis was performed including copy number variation identification. Thorough genotype–phenotype correlation was performed.

Results

Out of 175 patients, described pathogenic variants or novel variants with clear pathogenic impact were identified in 30 patients (17.14%). Genotype–phenotype correlations and parental DNA analysis were performed, and genetic diagnosis was confirmed on the basis of the results in another 16 out of 175 patients (9.14%). The diagnostic yield of our study increased from 30 to 46 patients (by 53.33%) by the precise genotype–phenotype correlation.

Interpretation

We emphasize a complex genotype–phenotype correlation and a multidisciplinary approach in evaluating the results of the NGS epilepsy gene panel, which enables the most accurate genetic diagnosis and correct interpretation of results.

Introduction

Epilepsy affects 0.5% to 1% of children and is the most frequent chronic neurologic condition in childhood [1]. The underlying etiology is unknown in 40–50% of cases of epilepsy, although it has been estimated that approximately 30% of epilepsy is genetic [2].

Clinical genetic diagnosis methods have become popular in recent years and include various technologies and strategies. Next generation sequencing (NGS) is revolutionary especially in terms of the possibility of simultaneously examining many genes. NGS testing includes not only specific gene panels, but a methodology that can encompass the entire exome (whole exome sequencing, WES) or genome (whole genome sequencing, WGS), methods that have the potential to further increase the yield of genetic testing in patients with epilepsy. The yield of NGS epilepsy gene panels ranges from 20 to 40% depending on the sample investigated [3], [4], [5]. Geneticists interpret and report detected sequence variants on the basis of currently valid recommendations according to the American College of Medical Genetics and Genomics (ACMG) [6]. Thus, each sequence variant is included in the group of pathogenic (P), likely pathogenic (LP), benign (B), likely benign (LB), or with uncertain significance (VUS). The thorough genotypic–phenotypic correlation and interpretation of genetic results from the neurological-epileptological point of view, taking into account other anamnestic data, are an integral and crucial part of the process of interpreting the result of NGS; it importantly increases the diagnostic yield of NGS examination.

Knowing the genetic cause of epilepsy in a patient opens new horizons in terms of understanding the pathophysiology of the epileptological process, and it also creates a space for the study of pharmacological models of antiepileptic drugs. The definition of precision medicine thus takes on real proportions in some patients with epilepsy.

We present our single-center experience of using targeted gene-panel sequencing to diagnose the genetic etiology of epilepsy in children and we focus on the precise multidisciplinary genotype–phenotype correlation of each patient in order to maximize the yield of this examination method.