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Genotype-phenotype analysis of pathogenic copy number variations in pediatric epilepsy

Hao Zheng1, JiaLi Dai1, Miao Xiong1

  • 1Department of Neurology, Children's Hospital of Chongqing Medical University, China; National Clinical Research Center for Child Health and Disorders, China; Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing 400014, China; Chongqing Key Laboratory of Child Neurodevelopment and Cognitive Disorders, Chongqing 400014, China.

Epilepsy & Behavior : E&B
|December 4, 2025
PubMed

Insights

Pathogenic copy number variations (CNVs) are a significant cause of pediatric epilepsy, impacting brain development. Identifying these genetic variations is crucial, especially when epilepsy presents with comorbidities.

Area of Science:

  • Genetics
  • Neuroscience
  • Pediatrics

Background:

  • Pediatric epilepsy is a complex neurological disorder with diverse genetic underpinnings.
  • Copy number variations (CNVs) are increasingly recognized as important genetic contributors to epilepsy.
  • Understanding the genotype-phenotype correlations of pathogenic CNVs in children is essential for diagnosis and treatment.

Purpose of the Study:

  • To characterize genotype-phenotype features of pediatric epilepsy associated with pathogenic CNVs.
  • To investigate the pathogenic mechanisms of these CNVs using functional enrichment and network analysis.

Main Methods:

  • A cohort of 418 pediatric epilepsy patients (0-18 years) underwent CNV sequencing (CNV-seq).
  • Functional enrichment analysis (ClusterProfiler) and protein-protein interaction (PPI) network analysis (STRING) were performed on identified dosage-sensitive genes.

Main Results:

  • Pathogenic CNVs were detected in 9.57% (40/418) of patients, including 39 microdeletions and 5 microduplications.
  • The 16p11.2 microdeletion was the most frequent CNV.
  • Enriched genes were associated with forebrain and telencephalon development, and neuronal cell bodies, forming extensive interaction networks. Comorbidities like congenital heart disease and facial dysmorphism were noted in 30 patients.

Conclusions:

  • CNVs are a significant cause of pediatric epilepsy, potentially by disrupting cortical development and neuronal cell function through dosage-sensitive genes.
  • The likelihood of detecting pathogenic CNVs increases when epilepsy is accompanied by intellectual disability or systemic diseases.

Keywords:
Copy number variationEpilepsyMicrodeletionsMicroduplicationsWhole-genome Low-coverage sequencing

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