Targeted re-sequencing for early diagnosis of genetic causes of childhood epilepsy: the Italian experience from the 'beyond epilepsy' project

Abstract

Background: Childhood epilepsies are a heterogeneous group of conditions differing in diagnostic criteria, management, and outcome. Late-infantile neuronal ceroid lipofuscinosis type 2 (CLN2) is a neurodegenerative condition caused by biallelic TPP1 variants. This disorder presents with subtle and relatively non-specific symptoms, mimicking those observed in more common paediatric epilepsies and followed by rapid psychomotor deterioration and drug-resistant epilepsy. A prompt diagnosis is essential to adopt appropriate treatment and disease management strategies.

Methods: This is a prospective, multicentre study on the efficiency of targeted re-sequencing in the early identification of the genetic causes of childhood epilepsy, with particular regard to CLN2. After phenotypic characterization, a 283-gene Next Generation Sequencing panel was performed in 21 Italian children with neurodevelopmental abnormalities, aged between 24 and 60 months, experiencing first unprovoked seizure after 2 years of age.

Results: The average age at enrolment was 39.9 months, with a mean age at seizure onset of 30.9 months and a mean time interval between seizure onset and targeted resequencing of 9 months. Genetic confirmation was achieved in 4 out of 21 patients, with a diagnostic yield of 19%. In one case, the homozygous splice acceptor variant c.509-1G > C in TPP1 was identified, leading to a CLN2 diagnosis. Three pathogenic variants in MECP2 were also detected in three patients, including the frameshift variant c.1157_1186delinsA (p.Leu386Hisfs*9) in a girl with negative single gene sequencing. Variants of unknown significance (VUS) were found in 11 out of 21 (52.4%) individuals, whereas no clinically significant variants were observed in the remaining 6 subjects.

Conclusions: Our findings support the efficacy of target re-sequencing in the identification of the genetic causes of childhood epilepsy and suggest that this technique might prove successful in the early detection of CLN2 as well as other neurodevelopmental conditions.

Keywords: CLN2; Early diagnosis; Epilepsy; Next generation sequencing (NGS); TPP1; Targeted re-sequencing.

Fig. 1

Phenotypic features of this cohort. a Seizure types recorded in our cohort. b Distribution of the most relevant associated clinical features

Fig. 2

Brain magnetic resonance imaging (MRI) of patient #21. a Axial T2-weighted image showing mild hyperintensity in the periventricular deep white matter (thin arrow). b Axial fluid attenuated inversion recovery (FLAIR) scan demonstrating hyperintensity in the periventricular white matter, especially in the posterior regions (thin arrow), with preserved myelination in the subcortical white matter (thick arrow). c Coronal T2-weighted scan demonstrating mild hyperintensity in the posterior periventricular white matter (thin arrow) and moderate cerebellar atrophy (thick arrow). d Sagittal T1-weighted scan showing moderate cerebellar atrophy (thick arrow) with enlarged IV ventricle (star) and cisterna magna (thin arrow). The time from the first seizure to MRI was one month