The clinical utility of array-CGH and targeted NGS in idiopathic intellectual disabilities and developmental delays: a case report of SCN2A p.Ala263Val variant

Introduction: Next-generation sequencing (NGS) techniques have become a powerful tool for the identification of the genetic causes of the heterogeneous conditions such as intellectual disabilities, multiple congenital anomalies and autism spectrum disorders. Material and methods: We present our first experience with targeted NGS approach using commercially available design SureSelect Inherited Disease (Agilent Technologies) containing more than 2700 genes known to cause inherited disorders. We report on a case of 9-year-old boy with a diagnosis of severe intellectual disability related to early myoclonic encephalopathy. This patient was examined according to our investigatory algorithm, from G-banding karyotype (46,XY) to array-CGH on oligonucleotide DNA microarrays (Agilent Technologies) followed by confirmative targeted quantitative PCR and FISH. Results: We detected a de novo copy-number gain of 18q21.23 (539 kb) classified as probably benign. Consequently this patient was included in our pilot study using targeted NGS with pre-designed gene panel SureSelect Inherited disease and Illumina MiSeq. We detected de novo heterozygous missense genetic variant in SCN2A gene, resulting in the amino acid residue change from alanine to valine at position 263 (p.Ala263Val). This variant had been previously described as definitely pathogenic in patients with Otahara syndrome. Conclusions: This case has proved the usefulness and effectivity of our molecular diagnostics algorithm enhanced by NGS approaches leading to higher diagnostic yield of heterogeneous genetic conditions. This study was supported by Ministry of Health, Czech Republic [[unable to display character: –]] conceptual development of research organization (FNBr, 65269705).