Exome sequencing reveals new causal mutations in children with epileptic encephalopathies

Abstract

Summary Purpose The management of epilepsy in children is particularly challenging when seizures are resistant to anti-epileptic medications, or undergo many changes in seizure type over time, or have comorbid cognitive, behavioral, or motor deficits. Despite efforts to classify such epilepsies based on clinical and electroencephalographic criteria, many children never receive a definitive etiological diagnosis. Whole exome sequencing (WES) is proving to be a highly effective method for identifying de novo variants that cause neurological disorders, especially those associated with abnormal brain development. Here we explore the utility of WES for identifying candidate causal de novo variants in a cohort of children with heterogeneous sporadic epilepsies without etiological diagnoses. Methods We performed WES (mean coverage ~40X) on 10 trios comprised of unaffected parents and a child with sporadic epilepsy characterized by difficult-to-control seizures and some combination of developmental delay, epileptic encephalopathy, autistic features, cognitive impairment, or motor deficits. Sequence processing and variant calling were performed using standard bioinformatics tools. A custom filtering system was used to prioritize de novo variants of possible functional significance for validation by Sanger sequencing. Key Findings In nine of ten probands, we identified one or more de novo variants predicted to alter protein function, for a total of 15. Four probands had de novo mutations in genes previously shown to harbor heterozygous mutations in patients with severe, early-onset epilepsies (two in SCN1A, and one each in CDKL5 and EEF1A2). In three children, the de novo variants were in genes with functional roles that are plausibly relevant to epilepsy (KCNH5, CLCN4 and ARHGEF15). The variant in KCNH5 alters one of the highly conserved arginine residues of the voltage sensor of the encoded voltage-gated potassium channel. In vitro analyses using cell-based assays revealed that the CLCN4 mutation greatly impaired ion transport by the ClC-4 2Cl−/H+-exchanger and that the mutation in ARHGEF15 reduced GEF exchange activity of the gene product, Ephexin5, by about 50%. Interestingly, these seven probands all presented with seizures within the first six months of life, and six of these have intractable seizures. Significance The finding that seven of ten children carried de novo mutations in genes of known or plausible clinical significance to neuronal excitability suggests that WES will be of use for the molecular genetic diagnosis of sporadic epilepsies in children, especially when seizures are of early onset and difficult to control.

Diagnostic exome sequencing provides a molecular diagnosis for a significant proportion of patients with epilepsy

“…8,9,23 Data from small cohorts of patients with severe epilepsies also highlight the utility of DES for improving molecular diagnoses. [24][25][26] However, these studies rely on data from small, highly selected patient cohorts and may not reflect the diagnostic yield in an unselected sample of patients with epilepsy.…”

Exome Sequencing Fails to Identify the Genetic Cause of Aicardi Syndrome

“…Massively parallel sequencing has been used in several studies to identify mutations underlying rare Mendelian disorders [Ng et al, 2010;Guerreiro et al, 2014]. In particular, analysis of trios has been successful in finding de novo mutations in sporadic neurodevelopmental disorders [Epi4K Consortium et al, 2013;Veeramah et al, 2013].…”

Epileptic encephalopathies – next generation diagnostics

“…Nie chodzi tu tylko o różnicę WES vs. sekwencjonowanie panelowe, ale także o różnice w stosowanych panelach. Niemniej jednak doniesienia te, szczególnie obejmujące większe grupy pacjentów z encefalopatiami padaczkowymi i/lub chorobami neurorozwojowymi z padaczką [18][19][20][21][22][23], pozwoliły wstępnie oszacować skuteczność diagnostyczną z zastosowaniem NGS, oraz określić grupę genów, któ-rych mutacje najczęściej identyfikowane są u pacjentów z ciężkimi padaczkami o wczesnym początku i poważny-mi chorobami neurorozwojowymi. W przypadku badań dla populacji europejskich (angielskiej i włoskiej) identyfikowano najczęściej mutacje w genie SCN2A a także SCN1A, KCNQ2, STXBP1, CDKL5 i MECP2 [19,20].…”