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Partial epilepsies have a substantial heritability. However, the actual genetic causes are largely unknown. In contrast to many other common diseases for which genetic association-studies have successfully revealed common variants associated with disease risk, the role of common variation in partial epilepsies has not yet been explored in a well-powered study. We undertook a genome-wide association-study to identify common variants which influence risk for epilepsy shared amongst partial epilepsy syndromes, in 3445 patients and 6935 controls of European ancestry. We did not identify any genome-wide significant association. A few single nucleotide polymorphisms may warrant further investigation. We exclude common genetic variants with effect sizes above a modest 1.3 odds ratio for a single variant as contributors to genetic susceptibility shared across the partial epilepsies. We show that, at best, common genetic variation can only have a modest role in predisposition to the partial epilepsies when considered across syndromes in Europeans. The genetic architecture of the partial epilepsies is likely to be very complex, reflecting genotypic and phenotypic heterogeneity. Larger meta-analyses are required to identify variants of smaller effect sizes (odds ratio

Summary Background The Epilepsy Genetics (EPIGEN) Consortium was established to undertake genetic mapping analyses with augmented statistical power to detect variants that influence the development and treatment of common forms of epilepsy. Methods We examined common variations across 279 prime candidate genes in 2717 case and 1118 control samples collected at four independent research centres (in the UK, Ireland, Finland, and Australia). Single nucleotide polymorphism (SNP) and combined set-association analyses were used to examine the contribution of genetic variation in the candidate genes to various forms of epilepsy. Findings We did not identify clear, indisputable common genetic risk factors that contribute to selected epilepsy subphenotypes across multiple populations. Nor did we identify risk factors for the general all-epilepsy phenotype. However, set-association analysis on the most significant p values, assessed under permutation, suggested the contribution of numerous SNPs to disease predisposition in an apparent population-specific manner. Variations in the genes KCNAB1, GABRR2, KCNMB4, SYN2 , and ALDH5A1 were most notable. Interpretation The underlying genetic component to sporadic epilepsy is clearly complex. Results suggest that many SNPs contribute to disease predisposition in an apparently population-specific manner. However, subtle differences in phenotyping across cohorts, combined with a poor understanding of how the underlying genetic component to epilepsy aligns with current phenotypic classifications, might also account for apparent population-specific genetic risk factors. Variations across five genes warrant further study in independent cohorts to clarify the tentative association.

Throughout much of the world, 'race' and 'ethnicity' are key determinants of health. For example, African Americans have, by some estimates, a twofold higher incidence of fatal heart attacks and a 10% higher incidence of cancer than European Americans, and South Asian- or Caribbean-born British are approximately 3.5 times as likely to die as a direct result of diabetes than are British of European ancestry. The health care that people receive also depends on 'race' and 'ethnicity'. African Americans are less likely to receive cancer-screening services and more likely to have late-stage cancer when diagnosed than European Americans. Health disparities such as these are one of the greatest social injustices in the developed world and one of the most important scientific and political challenges.

Most people in the developed world will sooner or later be given prescription drugs to treat common diseases or to reduce the risk of getting them. Almost everyone who takes medicines will, at some stage, encounter those that do not work as well as they do in other people or even that cause an adverse reaction. Pharmacogenetics seeks to reduce the variation in how people respond to medicines by tailoring therapy to individual genetic make-up. It seems increasingly likely that investment in this field might be the most effective strategy for rapidly delivering the public health benefits that are promised by the Human Genome Project and related endeavours.

Deletions at 16p13.11 are associated with schizophrenia, mental retardation, and most recently idiopathic generalized epilepsy. To evaluate the role of 16p13.11 deletions, as well as other structural variation, in epilepsy disorders, we used genome-wide screens to identify copy number variation in 3812 patients with a diverse spectrum of epilepsy syndromes and in 1299 neurologically-normal controls. Large deletions (> 100 kb) at 16p13.11 were observed in 23 patients, whereas no control had a deletion greater than 16 kb. Patients, even those with identically sized 16p13.11 deletions, presented with highly variable epilepsy phenotypes. For a subset of patients with a 16p13.11 deletion, we show a consistent reduction of expression for included genes, suggesting that haploinsufficiency might contribute to pathogenicity. We also investigated another possible mechanism of pathogenicity by using hybridization-based capture and next-generation sequencing of the homologous chromosome for ten 16p13.11-deletion patients to look for unmasked recessive mutations. Follow-up genotyping of suggestive polymorphisms failed to identify any convincing recessive-acting mutations in the homologous interval corresponding to the deletion. The observation that two of the 16p13.11 deletions were larger than 2 Mb in size led us to screen for other large deletions. We found 12 additional genomic regions harboring deletions > 2 Mb in epilepsy patients, and none in controls. Additional evaluation is needed to characterize the role of these exceedingly large, non-locus-specific deletions in epilepsy. Collectively, these data implicate 16p13.11 and possibly other large deletions as risk factors for a wide range of epilepsy disorders, and they appear to point toward haploinsufficiency as a contributor to the pathogenicity of deletions., Journal Article, Research Support, Non-U.S. Gov't, SCOPUS: ar.j, info:eu-repo/semantics/published

Levetiracetam (LEV), a newer antiepileptic drug (AED) useful for several epilepsy syndromes, binds to SV2A. Identifying genetic variants that influence response to LEV may allow more tailored use of LEV. Obvious candidate genes are SV2A, SV2B and SV2C, which encode the only known binding site, synaptic vesicle protein 2 (SV2), with LEV binding to the SV2A isoform. SV2A is an essential protein as homozygous SV2A knockout mice appear normal at birth but fail to grow, experience severe seizures and die by 3 weeks. We addressed characterising AED response issues in pharmacogenetics and whether variation in these genes associates with response to LEV in two independent cohorts with epilepsy. We also investigated whether variation in these three genes associated with epilepsy predisposition in two larger cohorts of patients with various epilepsy phenotypes. Common genetic variation in SV2A, encoding the actual binding site of LEV, was fully represented in this study whereas SV2B and SV2C were not fully covered. None of the polymorphisms tested in SV2A, SV2B or SV2C influence LEV response or predisposition to epilepsy. We found no association between genetic variation in SV2A, SV2B or SV2C and response to LEV or epilepsy predisposition. We suggest this study design may be used in future pharmacogenetic work examining AED or LEV efficacy. However, different study designs would be needed to examine common variation with minor effect sizes, or rare variation, influencing AED or LEV response or epilepsy predisposition.

Multidrug resistance is one of the most serious problems in the treatment of epilepsy and is likely to have a complex genetic and environmental basis. Various experimental data support the hypothesis that overexpression of antiepileptic drug transporters may be important. However, key questions concerning their functionality remain unanswered. The first study reporting a positive association – between genetic variation in a putative antiepileptic drug transporter (P-glycoprotein, encoded by ABCB1) and multidrug resistant epilepsy was published in 2003. Since then, several other association genetics studies have sought to confirm this result, but, taken overall, do not support a major role for this polymorphism. Lessons learnt from the ABCB1 studies can help guide future association genetics studies, both for multidrug resistance in epilepsy, and for other epilepsy phenotypes.

The pregnane X receptor gene (PXR/NR1I2) regulates an array of genes involved in the response to xenobiotics.1,2 Dysregulation of this gene may critically influence intestinal barrier defence and susceptibility to inflammatory bowel disease (IBD).3 Recent data from Ireland have suggested strong associations between polymorphisms within the PXR/NR1I2 gene and IBD. Dring et al performed a case control study involving 422 patients with IBD (185 ulcerative colitis (UC) and 237 (Crohn’s disease (CD)) and 350 healthy controls, using eight candidate polymorphisms in this gene.4 Highly significant associations were demonstrated with UC, CD, and IBD as a whole. This effect was most significant for the two individual single nucleotide polymorphisms (SNPs) in the promoter region of this gene; compared between the IBD cohort and controls, rs3814055/−23585 (p = 0.000008; odds ratio (OR) 1.62 (95% confidence interval (CI) 1.31–2.00)) and rs1523127/−24381 (p = 0.0002; OR 1.50 (95% CI 1.21–1.84)). We have critically re-evaluated the contribution of these allelic …

A broad range of phenytoin doses is used in clinical practice, with the final 'maintenance' dose normally determined by trial and error. A common functional polymorphism in the SCN1A gene (one of the genes encoding the drug target) has been previously associated with maximum dose of phenytoin used clinically, and also maximum dose of carbamazepine, another antiepileptic drug with the same drug target.We have related variation at the SCN1A IVS5-91 GA polymorphism to maximum dose and to maintenance dose of phenytoin in 168 patients with epilepsy treated with phenytoin. We also related genotype to phenytoin serum levels at maximum dose and at maintenance dose of phenytoin. We genotyped the polymorphism using an Applied Biosystems Taqman assay.The polymorphism is associated with phenytoin serum concentration at maintenance dose (P=0.03). In a reduced cohort of 71 patients receiving phenytoin monotherapy this association is also significant (P=0.03). Neither association remains significant after Bonferroni correction for multiple testing.These results are not a replication of the original study. They do, however, support the hypothesis that this polymorphism influences the clinical use of phenytoin. They also demonstrate the utility of using multiple phenotypes in pharmacogenetics studies, particularly when attempting to separate pharmacokinetic and pharmacodynamic effects. As the SCN1A polymorphism affects phenytoin pharmacodynamics, it is particularly useful to obtain data on serum levels in addition to dose because association of a pharmacodynamic variant may be stronger with serum levels than dose as the serum level may eliminate or reduce pharmacokinetic variability.

Phenytoin and carbamazepine are effective and inexpensive anti-epileptic drugs (AEDs). As with many AEDs, a broad range of doses is used, with the final “maintenance” dose normally determined by trial and error. Although many genes could influence response to these medicines, there are obvious candidates. Both drugs target the α-subunit of the sodium channel, encoded by the SCN family of genes. Phenytoin is principally metabolized by CYP2C9, and both are probable substrates of the drug transporter P-glycoprotein. We therefore assessed whether variation in these genes associates with the clinical use of carbamazepine and phenytoin in cohorts of 425 and 281 patients, respectively. We report that a known functional polymorphism in CYP2C9 is highly associated with the maximum dose of phenytoin ( P = 0.0066). We also show that an intronic polymorphism in the SCN1A gene shows significant association with maximum doses in regular usage of both carbamazepine and phenytoin ( P = 0.0051 and P = 0.014, respectively). This polymorphism disrupts the consensus sequence of the 5′ splice donor site of a highly conserved alternative exon (5N), and it significantly affects the proportions of the alternative transcripts in individuals with a history of epilepsy. These results provide evidence of a drug target polymorphism associated with the clinical use of AEDs and set the stage for a prospective evaluation of how pharmacogenetic diagnostics can be used to improve dosing decisions in the use of phenytoin and carbamazepine. Although the case made here is compelling, our results cannot be considered definitive or ready for clinical application until they are confirmed by independent replication.

Nature Reviews Genetics 4, 937–947 (2003); doi: 10.1038/nrg1229 The glossary definitions for 'Map-based' and 'Sequence-based' were incorrect. The correct definitions should have read: MAP BASED An approach to genetic-association studies that is focused on a set of genetic markers, often now called tagging SNPs, which are statistically associated with whichever variants influence the phenotype.

An intronic polymorphism in the SCN1A gene, which encodes a neuronal sodium-channel alpha subunit, has been previously associated with the dosing of two commonly used antiepileptic drugs that elicit their pharmacologic action primarily at this ion-channel subunit. This study sought to characterize the functional effects of this polymorphism on alternative splicing of SCN1A and to explore the potential for modulating the drug response in the pharmacologically unfavorable genotype by identification of a splice modifier acting on SCN1A. The effects of the genotype at the SCN1A IVS5N+5 G-->A polymorphism on SCN1A splice-variant proportions and the consequences of increased expression of splice modifiers were investigated both in human temporal neocortex tissue and in a cellular minigene expression system. Quantitative real-time polymerase chain reaction was used to quantify the amounts of SCN1A transcripts forms. We show that the polymorphism has a dramatic effect on the proportions of neonate and adult alternative transcripts of SCN1A in adult brain tissue and that the effect of the polymorphism also appears to be modified by Nova2 expression levels. A minigene expression system confirms both the effect of the polymorphism on transcript proportions and the role of Nova2 in the regulation of splicing, with higher Nova2 expression increasing the proportion of the neonate form. A larger Nova2-mediated effect was detected in the AA genotype that is associated with increased dose requirements. The effects of Nova2 on modulation of the alternative splicing of 17 other neuronally expressed genes were investigated, and no effect was observed. These findings emphasize the emerging role of genetic polymorphisms in modulation of drug effect and illustrate both alternative splicing as a potential therapeutic target and the importance of considering the activity of compounds at alternative splice forms of drug targets in screening programs.