Rare coding variants in genes encoding GABAA receptors in genetic generalised epilepsies: an exome-based case-control study.

BACKGROUND: Genetic generalised epilepsy is the most common type of inherited epilepsy. Despite a high concordance rate of 80% in monozygotic twins, the genetic background is still poorly understood. We aimed to investigate the burden of rare genetic variants in genetic generalised epilepsy. METHODS: For this exome-based case-control study, we used three different genetic generalised epilepsy case cohorts and three independent control cohorts, all of European descent. Cases included in the study were clinically evaluated for genetic generalised epilepsy. Whole-exome sequencing was done for the discovery case cohort, a validation case cohort, and two independent control cohorts. The replication case cohort underwent targeted next-generation sequencing of the 19 known genes encoding subunits of GABAA receptors and was compared to the respective GABAA receptor variants of a third independent control cohort. Functional investigations were done with automated two-microelectrode voltage clamping in Xenopus laevis oocytes. FINDINGS: Statistical comparison of 152 familial index cases with genetic generalised epilepsy in the discovery cohort to 549 ethnically matched controls suggested an enrichment of rare missense (Nonsyn) variants in the ensemble of 19 genes encoding GABAA receptors in cases (odds ratio [OR] 2·40 [95% CI 1·41-4·10]; pNonsyn=0·0014, adjusted pNonsyn=0·019). Enrichment for these genes was validated in a whole-exome sequencing cohort of 357 sporadic and familial genetic generalised epilepsy cases and 1485 independent controls (OR 1·46 [95% CI 1·05-2·03]; pNonsyn=0·0081, adjusted pNonsyn=0·016). Comparison of genes encoding GABAA receptors in the independent replication cohort of 583 familial and sporadic genetic generalised epilepsy index cases, based on candidate-gene panel sequencing, with a third independent control cohort of 635 controls confirmed the overall enrichment of rare missense variants for 15 GABAA receptor genes in cases compared with controls (OR 1·46 [95% CI 1·02-2·08]; pNonsyn=0·013, adjusted pNonsyn=0·027). Functional studies for two selected genes (GABRB2 and GABRA5) showed significant loss-of-function effects with reduced current amplitudes in four of seven tested variants compared with wild-type receptors. INTERPRETATION: Functionally relevant variants in genes encoding GABAA receptor subunits constitute a significant risk factor for genetic generalised epilepsy. Examination of the role of specific gene groups and pathways can disentangle the complex genetic architecture of genetic generalised epilepsy. FUNDING: EuroEPINOMICS (European Science Foundation through national funding organisations), Epicure and EpiPGX (Sixth Framework Programme and Seventh Framework Programme of the European Commission), Research Unit FOR2715 (German Research Foundation and Luxembourg National Research Fund).

Global characterization of copy number variants in epilepsy patients from whole genome sequencing.

Epilepsy will affect nearly 3% of people at some point during their lifetime. Previous copy number variants (CNVs) studies of epilepsy have used array-based technology and were restricted to the detection of large or exonic events. In contrast, whole-genome sequencing (WGS) has the potential to more comprehensively profile CNVs but existing analytic methods suffer from limited accuracy. We show that this is in part due to the non-uniformity of read coverage, even after intra-sample normalization. To improve on this, we developed PopSV, an algorithm that uses multiple samples to control for technical variation and enables the robust detection of CNVs. Using WGS and PopSV, we performed a comprehensive characterization of CNVs in 198 individuals affected with epilepsy and 301 controls. For both large and small variants, we found an enrichment of rare exonic events in epilepsy patients, especially in genes with predicted loss-of-function intolerance. Notably, this genome-wide survey also revealed an enrichment of rare non-coding CNVs near previously known epilepsy genes. This enrichment was strongest for non-coding CNVs located within 100 Kbp of an epilepsy gene and in regions associated with changes in the gene expression, such as expression QTLs or DNase I hypersensitive sites. Finally, we report on 21 potentially damaging events that could be associated with known or new candidate epilepsy genes. Our results suggest that comprehensive sequence-based profiling of CNVs could help explain a larger fraction of epilepsy cases.

X-linked focal epilepsy with reflex bathing seizures: Characterization of a distinct epileptic syndrome.

OBJECTIVE: We recently reported a Q555X mutation of synapsin 1 (SYN1) on chromosome Xp11-q21 in a family segregating partial epilepsy and autistic spectrum disorder. Herein, we provide a detailed description of the epileptic syndrome in the original family. METHODS: A total of 34 members from a large French-Canadian family were evaluated. Family members with seizures or epilepsy underwent (when possible) clinical, neuropsychological, electrophysiologic, and neuroimaging assessments. RESULTS: Epilepsy was diagnosed in 10 family members (4 deceased, 6 living). In addition to occasional spontaneous complex partial seizures, seven family members clearly had reflex seizures triggered by bathing or showering. Hippocampal atrophy was found in two of five epileptic family members family members who underwent magnetic resonance (MR) imaging. Video-electroencephalography (EEG) recordings of three triggered seizures in two affected members showed rhythmic theta activity over temporal head regions. Ictal single-photon emission computed tomography (SPECT) showed temporoinsular perfusion changes. Detailed neuropsychological assessments revealed that SYN1 Q555X male mutation carriers showed specific language impairment and mild autistic spectrum disorder. Female carriers also exhibited reading impairments and febrile seizures but no chronic epilepsy. SIGNIFICANCE: Available evidence suggests that impaired SYN1 function is associated with hyperexcitability of the temporoinsular network and disturbance of high mental functions such as language and social interaction. The presence of reflex bathing seizures, a most peculiar clinical feature, could be helpful in identifying other patients with this syndrome.

Expanding the clinical phenotype associated with ELOVL4 mutation: study of a large French-Canadian family with autosomal dominant spinocerebellar ataxia and erythrokeratodermia.

IMPORTANCE: The autosomal dominant spinocerebellar ataxias (SCAs) are a complex group of neurodegenerative disorders with significant genetic heterogeneity. Despite the identification of 20 SCA genes, the cause of the disorder in a significant proportion of families with SCA remains unexplained. In 1972, a French-Canadian family segregating a combination of SCA and erythrokeratodermia variabilis (EKV) in an autosomal dominant fashion was described. OBJECTIVE: To map and identify the causative gene in this large family with SCA and EKV using a combination of linkage analysis and whole-exome sequencing. DESIGN, SETTING, AND PARTICIPANTS: A total of 32 individuals from the family have undergone complete neurologic and dermatologic examinations. MAIN OUTCOMES AND MEASURES: Mutations in ELOVL4 have been reported in families with macular degeneration. Recently, homozygous mutations were found in patients with ichthyosis, spastic paraplegia, and severe neurodevelopmental defects. In the present study, we report on a heterozygote mutation in ELOVL4 in affected individuals from the family with SCA and EKV. The mutation segregates with a milder phenotype consisting of early-onset patches of erythema and hyperkeratosis, as well as SCA manifesting in the fourth or fifth decade of life. RESULTS: We describe the mapping and the identification of a c.504G>C transversion in ELOVL4 resulting in the p.L168F substitution. We also provide clinical characterization of the phenotypes in 19 mutation carriers. CONCLUSIONS AND RELEVANCE: We report, to our knowledge, the first mutation in ELOVL4 that is associated with SCA and EKV. This gene encodes a member of the elongase family, which is responsible for the elongation of very long-chain fatty acids (at least 26 carbons). These fatty acids participate in a wide variety of physiological functions, including skin barrier formation and peroxisome ß-oxidation. Overall, these results provide additional insight into the pathogenesis of these complex neurodegenerative disorders.

Retrospective analysis of phone queries to an epilepsy clinic hotline.

We undertook a retrospective study of 5,189 telephone calls made between January 2004 and June 2011 through our adult epilepsy clinic hotline to a single epileptologist initially and two epileptologists from June 2010 onwards. The majority of calls were made by patients themselves (72%), followed by family members (16%) and health care providers (11%). Half of the calls originated from outside the city limits. Most were related to medication (25%), notification of seizures (23%), appointments or tests (12%), and side effects (9%). Half of the workload was generated by 10% of patients. The hotline service appears to respond to needs, with most calls requiring rapid intervention. It is desirable to develop novel approaches to address the needs of high-frequency callers.

Screening of GABRB3 in French-Canadian families with idiopathic generalized epilepsy.

Mutations in the GABRB3 have been recently associated with childhood absence epilepsy (CAE) in families from Honduras and Mexico. In this study, we aimed to determine the frequency of mutation in this gene in our cohort of families with CAE and other related idiopathic generalized epilepsy (IGE) syndromes. We screened the open reading frame of GABRB3 in 183 French-Canadian individuals with IGE, including 88 with CAE. A total of nine single nucleotide polymorphisms (SNPs) have been identified,five of which are novel. The previously described P11S missense mutation was found in three affected and one unaffected individuals from a French-Canadian family. However, the P11S variant was also found in one of our 190 control individuals of French-Canadian origin, suggesting that this variant is rather a rare polymorphism in this population. Further screening of other IGE cohorts from various ethnic origins would help to confirm the association between this rare functional variant and epilepsy.

Phenotypic concordance in 70 families with IGE-implications for genetic studies of epilepsy.

INTRODUCTION: A crucial issue in the genetic analysis of idiopathic generalized epilepsy (IGE) is deciding on the phenotypes that are likely to give the greatest power to detect predisposing variants. A complex inheritance pattern and unclear nature of the genotype-phenotype correlation makes this task difficult. In the absence of much definitive genetic information to clarify this correlation, we inferred the putative effects of predisposing genes by studying the clustering of various phenotypic features, both clinical and electrophysiological, within families. METHODS: We examined the distribution of clinical features among relatives of a proband in 70 French-Canadian families with a minimum of two affected individuals with a clear diagnosis of IGE and then, using concordance analysis, identified the relative genetic influences on IGE syndrome, seizure type, age-at-onset, and EEG features. RESULTS: The mean number of affected individuals with IGE per family was three. One-third of relatives had the same syndrome as the proband. 16-22.5% of relatives of a proband with one of the absence syndromes had juvenile myoclonic epilepsy (JME). Conversely, 27% of relatives of probands with JME had an absence syndrome. 15% of relatives displayed the exact constellation of seizure types as the proband. Concordance analysis demonstrated greater clustering within families of IGE syndrome, seizure type, and age-at-onset than would be expected by chance. Significant concordance was not evident for EEG features. DISCUSSION: There was a large degree of clinical heterogeneity present within families. However we found evidence for clustering of a number of clinical features. Further refinement of the phenotypes used in genetic studies of complex IGE is necessary for progress to be made.