Abstracts

Rationale: Quantitative trait loci mapping (QTL) in DBA/2 (relatively seizure sensitive) and C57BL6 (relatively seizure resistant) strains of mice identified several chromosomal regions linked to seizure phenotypes. One of these is on chromosome 5, a region which is homologous to a segment of human chromosome 4p12, and that contains a cluster of four GABA receptor subunit genes (GABRG1, GABRA2, GABRA4, and GABRB1). We have begun to study variation in these genes systematically using DNA samples from a cohort of human epilepsy patients and controls collected in the US and Canada. We report preliminary findings on the GABRA4 gene as prior literature suggests a role for this receptor in Temporal Lobe Epilepsy (TLE).Methods: Single nucleotide polymorphisms (SNPs) rs1512132 and rs2229940 (http://www.ncbi.nlm.nih.gov/SNP/) were genotyped using TaqMan assays in patients with common forms of epilepsy (n=572), including both idiopathic generalized (IGE, n=309) and focal (TLE, n=263) and in unrelated healthy control individuals (n= 203). All subjects were of European ancestry. Hardy-Weinberg equilibrium (HWE) was tested and alleles were studied for disease associations using chi square analysis. Linkage disequilibrium (LD) between SNPs was tested using likelihood ratio analysis. Haplotype estimation and association analysis were performed using HAPSTAT and Plink software. Results: Markers were in HWE for all controls and IGE patients; however, the TLE group did not exhibit HWE: rs1512132 p=0.007, rs2229940 p=0.01. The two markers do not exhibit strong LD in IGE patients or controls with r2 values of 0.39 and 0.54, respectively. In TLE patients, however, the LD is strong (r2 = 0.85). In addition, minor allele frequencies (MAF) for controls and IGE patients are in agreement with data published by Applied Biosystems and the International HAPMAP project, but MAF for the TLE group is significantly different for rs1512132 (0.36 compared to 0.47) leading to a positive association with single marker analysis p=0.0007. Haplotype analysis shows a less significant result (p=0.02, dominant model) as the markers are separated by 40KB in the locus. Conclusions: Results suggest that variation at SNP rs1512132 may be associated with susceptibility to TLE. Lack of HWE in the TLE group could have occured because of genotyping errors, non random mating, genetic drift or other geographical considerations. However, this result can also indicate the presence of a skewed allelic distribution consistent with a mutation or susceptibility allele. Preliminary examination of data files does not indicate the presence of genotyping errors and it is improbable that non random mating occured in our cohort. Since the MAF for controls and IGE patients are in agreement with published figures, but the MAF for rs1512132 is significantly different in the TLE group, we hypothesize that variation in this SNP is in fact associated with susceptibility to TLE. Further studies at this locus are required to confirm this association. Support: R01NS40396 to RJB; UPenn Ctr for Neuro and Behav; Dept Veteran Affairs; Neurosci Inst, U Cincinnati.