Genetic analysis of human absence epilepsy

Idiopathic Mendelian epilepsies have been typically identified as channelopathies. Evidence suggests that mutations in genes encoding GABAA receptors, GABAB receptors or voltage-dependent calcium channels (VDCCs) may underlie childhood absence epilepsy (CAE), an idiopathic generalised epilepsy with complex inheritance. The aims of this project were: i) Ascertainment of a patient resource ii) Investigation of candidate genes by linkage analysis iii) Mutation analysis by direct sequencing iv) Construction of single nucleotide polymorphism (SNP) based haplotypes in candidate genes v) Intra-familial association analysis using SNP based haplotypes DNA and clinical data were obtained from: 53 nuclear CAE pedigrees; 29 families including individuals with CAE and a broader „absence‟ epilepsy phenotype; 217 parent-child trios; a North American family in which absence epilepsy segregates with episodic ataxia type 2 (EA2) Sixteen calcium channel genes and seven GABAA and two GABAB receptor subunit genes were excluded by linkage analysis. Significant linkage was demonstrated for CACNG3 on chromosome 16p12-p13.1 for both CAE and the broader absence phenotype. Positive linkage was also obtained at the GABRA5, GABRB3, GABRG3 cluster on chromosome 15q11-q13. Non-parametric linkage analysis was significant at both the 16p and 15q loci. Two-locus analysis supported a digenic effect from these two loci. Sequencing of CACNG3 revealed 34 sequence variants, none clearly causal, although bioinformatic analysis provided supportive functional evidence. Association analysis showed significant transmission disequilibrium both for individual single nucleotide polymorphisms (SNPs) and SNP based haplotypes spanning CACNG3. This work has provided genetic evidence that CACNG3 and at least one of the three GABAA receptor genes are susceptibility loci for absence epilepsy. Linkage analysis performed in the family with absence epilepsy and EA2 was suggestive that the VDCC CACNA1A was the causative gene. This was subsequently confirmed by sequence analysis in collaboration with the Institute of Neurology, UCL. This is the first reported family in which a CACNA1A mutation that impairs calcium channel function cosegregates with typical absence seizures and 3Hz spike-wave discharges on EEG