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Genetic Diagnosis in Children with Epilepsy and Developmental Delay/Mental Retardation Using Targeted Gene Panel Analysis

Author(s): Jao-Shwann Liang, Jinn-Shyan Wang, Li-Ju Lin, Ming-Tao Yang, Kun-Long Hung, Jyh-Feng Lu


Epileptic encephalopathies (EEs) are the severe form of childhood epilepsy and phenotypically heterogeneous disorders with different underlying genetic defects. EEs are always accompanied with developmental delay/mental retardation and behavior problems. Finding the genetic basis of epileptic encephalopathies with developmental delay/mental retardation can be valuable not only for diagnosis but also for guiding treatment and providing disease prognosis.

Methods and Results

A customized panel of 90 genes related to epileptic encephalopathies was utilized to screen for potential genetic variants via targeted next generation sequencing (NGS). A total of 78 children with epilepsy and developmental delay/mental retardation were analyzed with an average read depth of 265.3 ± 68.3X. Mutations were found in 23 (9 boys and 14 girls) probands, and the overall mutation identification rate was 29.5% (25.0% for males and 33.3% for females). Fifteen (65.2%) mutations involve ion channels, including SCN1A, KCNT1, SCN2A, SCN8, KCNB1 and KCNQ2. The other (34.8%) mutations involve CDKL5, ALG13, GFAP, SNAP25, STXBP1 and SYNGAP1. Sixteen (69.6%) of the identified mutations were confirmed to be de novo and one (4.3%) was found to be paternal mosaicism. Channelopathies were found to be the major cause of both early onset (≤6 months) and later onset of unclassified EE as well as febrile seizure cases. On the contrary, patients with infantile spasms or West syndrome were mainly caused by mutations in non-ion channel proteins, whereas patients of epilepsy with developmental delays and/or mental retardation were caused by mutations in both channel and non-channel genes.


NGS is a valuable and reliable diagnostic tool to detect the gene mutation in epileptic children with developmental delay/mental retardation. This cost-effective method shortens the course from seizure onset to genetic diagnosis. By understanding the gene mutations and genotypephenotype correlation better, clinical practitioners could provide the optimal anticonvulsant and treatment.

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