Mark Gardiner

Genome-wide association analysis of genetic generalized epilepsies implicates susceptibility loci at 1q43, 2p16.1, 2q22.3 and 17q21.32

Genetic generalized epilepsies (GGEs) have a lifetime prevalence of 0.3% and account for 20-30% of all epilepsies. Despite their high heritability of 80%, the genetic factors predisposing to GGEs remain elusive. To identify susceptibility variants shared across common GGE syndromes, we carried out a two-stage genome-wide association study (GWAS) including 3020 patients with GGEs and 3954 controls of European ancestry. To dissect out syndrome-related variants, we also explored two distinct GGE subgroups comprising 1434 patients with genetic absence epilepsies (GAEs) and 1134 patients with juvenile myoclonic epilepsy (JME). Joint Stage-1 and 2 analyses revealed genome-wide significant associations for GGEs at 2p16.1 (rs13026414, P(meta) = 2.5 × 10(-9), OR[T] = 0.81) and 17q21.32 (rs72823592, P(meta) = 9.3 × 10(-9), OR[A] = 0.77). The search for syndrome-related susceptibility alleles identified significant associations for GAEs at 2q22.3 (rs10496964, P(meta) = 9.1 × 10(-9), OR[T] = 0.68) and at 1q43 for JME (rs12059546, P(meta) = 4.1 × 10(-8), OR[G] = 1.42). Suggestive evidence for an association with GGEs was found in the region 2q24.3 (rs11890028, P(meta) = 4.0 × 10(-6)) nearby the SCN1A gene, which is currently the gene with the largest number of known epilepsy-related mutations. The associated regions harbor high-ranking candidate genes: CHRM3 at 1q43, VRK2 at 2p16.1, ZEB2 at 2q22.3, SCN1A at 2q24.3 and PNPO at 17q21.32. Further replication efforts are necessary to elucidate whether these positional candidate genes contribute to the heritability of the common GGE syndromes.

Genetics of idiopathic generalized epilepsies.

Summary:  The idiopathic generalized epilepsies (IGEs) are considered to be primarily genetic in origin. They encompass a number of rare mendelian or monogenic epilepsies and more common forms which are familial but manifest as complex, non‐mendelian traits. Recent advances have demonstrated that many monogenic IGEs are ion channelopathies. These include benign familial neonatal convulsions due to mutations in KCNQ2 or KCNQ3, generalized epilepsy with febrile seizures plus due to mutations in SCN1A, SCN2A, SCN1B, and GABRG2, autosomal‐dominant juvenile myoclonic epilepsy (JME) due to a mutation in GABRA1 and mutations in CLCN2 associated with several IGE sub‐types. There has also been progress in understanding the non‐mendelian IGEs. A haplotype in the Malic Enzyme 2 gene, ME2, increases the risk for IGE in the homozygous state. Five missense mutations have been identified in EFHC1 in 6 of 44 families with JME. Rare sequence variants have been identified in CACNA1H in sporadic patients with childhood absence epilepsy in the Chinese Han population. These advances should lead to new approaches to diagnosis and treatment.

Linkage and mutational analysis of CLCN2 in childhood absence epilepsy

In order to assess the chloride channel gene CLCN2 as a candidate susceptibility gene for childhood absence epilepsy, parametric and non-parametric linkage analysis was performed in 65 nuclear pedigrees. This provided suggestive evidence for linkage with heterogeneity: NPL score=2.3, p<0.009; HLOD=1.5, alpha=0.44. Mutational analysis of the entire genomic sequence of CLCN2 was performed in 24 unrelated patients from pedigrees consistent with linkage, identifying 45 sequence variants including the known non-synonymous polymorphism rs2228292 (G2154C, Glu718Asp) and a novel variant IVS4+12G>A. Intra-familial association analysis using the pedigrees and a further 308 parent-child trios showed suggestive evidence for transmission disequilibrium of the G2154C minor allele: AVE-PDT chi(1)2 = 5.17, p<0.03. Case-control analysis provided evidence for a protective effect of the IVS4+12G>A minor allele: chi(1)2 = 7.27, p<0.008. The 65 nuclear pedigrees were screened for three previously identified mutations shown to segregate with a variety of idiopathic generalised epilepsy phenotypes (597insG, IVS2-14del11 and G2144A) but none were found. We conclude that CLCN2 may be a susceptibility locus in a subset of cases of childhood absence epilepsy.

Linkage and association analysis of CACNG3 in childhood absence epilepsy.

Childhood absence epilepsy (CAE) is an idiopathic generalised epilepsy characterised by absence seizures manifested by transitory loss of awareness with 2.5–4 Hz spike–wave complexes on ictal EEG. A genetic component to aetiology is established but the mechanism of inheritance and the genes involved are not fully defined. Available evidence suggests that genes encoding brain expressed voltage-gated calcium channels, including CACNG3 on chromosome 16p12–p13.1, may represent susceptibility loci for CAE. The aim of this work was to further evaluate CACNG3 as a susceptibility locus by linkage and association analysis. Assuming locus heterogeneity, a significant HLOD score (HLOD=3.54, α=0.62) was obtained for markers encompassing CACNG3 in 65 nuclear families with a proband with CAE. The maximum non-parametric linkage score was 2.87 (P<0.002). Re-sequencing of the coding exons in 59 patients did not identify any putative causal variants. A linkage disequilibrium (LD) map of CACNG3 was constructed using 23 single nucleotide polymorphisms (SNPs). Transmission disequilibrium was sought using individual SNPs and SNP-based haplotypes with the pedigree disequilibrium test in 217 CAE trios and the 65 nuclear pedigrees. Evidence for transmission disequilibrium (P≤0.01) was found for SNPs within a ∼35 kb region of high LD encompassing the 5’UTR, exon 1 and part of intron 1 of CACNG3. Re-sequencing of this interval was undertaken in 24 affected individuals. Seventy-two variants were identified: 45 upstream; two 5’UTR; and 25 intronic SNPs. No coding sequence variants were identified, although four variants are predicted to affect exonic splicing. This evidence supports CACNG3 as a susceptibility locus in a subset of CAE patients.

Genome-wide linkage meta-analysis identifies susceptibility loci at 2q34 and 13q31.3 for genetic generalized epilepsies

Purpose:  Genetic generalized epilepsies (GGEs) have a lifetime prevalence of 0.3% with heritability estimates of 80%. A considerable proportion of families with siblings affected by GGEs presumably display an oligogenic inheritance. The present genome‐wide linkage meta‐analysis aimed to map: (1) susceptibility loci shared by a broad spectrum of GGEs, and (2) seizure type–related genetic factors preferentially predisposing to either typical absence or myoclonic seizures, respectively.

Molecular Genetics of the Neuronal Ceroid Lipofuscinoses

The neuronal ceroid lipofuscinoses (NCLs) are a group of inherited neurodegenerative disorders characterised by the accumulation of autofluorescent storage material in neurons and other cell types. The clinical features include visual impairment, progressive myoclonic epilepsy, and cognitive decline reflecting progressive neurodegeneration. The NCLs are subdivided into several subtypes according to age of onset, clinical course, and ultrastructure of the storage material. The molecular genetic basis of this group of disorders has recently been clarified. Mutations in the gene encoding a lysosomal enzyme, palmitoyl protein thioesterase (PPT), cause infantile NCL (locus CLN1 on chromosome 1p32) or Haltia‐Santavuori disease. This Finnish disease is characterised ultrastructurally by granular osmiophilic deposits (GRODs). Juvenile‐onset NCL with GRODs also is caused by mutations in PPT. Classic late‐infantile NCL (Jansky‐Bielschowsky disease) is caused by mutations in a gene encoding a pepstatin‐insensitive lysosomal peptidase (CLN2 on chromosome 11p15), and juvenile‐onset NCL (Batten disease) is caused by mutations in a gene encoding a 438‐amino‐acid membrane protein (CLN3 on chromosome 16p12) of unknown function. A locus for Finnish variant late‐infantile NCL, CLN5, has been mapped to chromosome 13q22 and a locus for variant late‐infantile NCL, CLN6, to chromosome 15q21–23. These and further advances will allow the molecular basis of the NCLs to be elucidated and may lead to new strategies for diagnosis and treatment.

Genetics of the epilepsies.

The epilepsy gene map has been refined and extended with new information concerning benign familial neonatal convulsions, benign familial infantile convulsions, Unverricht-Lundborg disease, epilepsy with progressive mental retardation and juvenile myoclonic epilepsy. Understanding of the molecular basis of paroxysmal disorders affecting the central nervous system has been revolutionalized with the identification of mutations in genes for the neurotransmitter receptors, GLRA1 and CHRNA4, and a voltage-gated potassium channel, KCNA1, as causes of inherited neurological disease.

Pyloric stenosis a 100 years after Ramstedt

Conrad Ramstedt performed the first pyloromyotomy for what is now called idiopathic hypertrophic pyloric stenosis 100 years ago. The intervening century has seen the management of this condition transformed but the underlying cause remains a mystery. This article reviews the treatment of this condition before and after the introduction of pyloromyotomy and the advances made subsequently towards understanding its cause.

Molecular basis of Mendelian idiopathic epilepsies

A genetic aetiology is estimated to be present in about 40% of patients with epilepsy. Significant progress has been made in understanding the molecular genetic basis of Mendelian epilepsies. Fourteen genes have been identified which underlie a group of rare, autosomal dominant Mendelian idiopathic epilepsies. All but two of these genes encode subunits of ion‐channels, revealing that idiopathic Mendelian human epilepsies are predominantly channelopathies. The two non‐ion‐channel genes, LGI1 causing autosomal dominant lateral temporal lobe epilepsy and MASS1 causing febrile and afebrile seizures, both contain a novel repeat motif variously called the epilepsy‐associated repeat (EAR) and epitempin (EPTP) repeat. This motif defines a subfamily of genes, some of which have also been implicated in epilepsy in mice and humans. Progress in dissecting the more common ‘complex’ genetic epilepsies remains slow, but ion channels represent the most biologically plausible candidates. Characterization of common population sequence variants for the entire cohort of ion channel genes and the development of high‐throughput techniques should enable rapid advances in the understanding of the common idiopathic familial epilepsies.

Genetics of childhood epilepsy

The epilepsies are a heterogeneous group of disorders with many causes. However, a genetic aetiology may be present in up to 40% of patients, and this proportion is even higher in epilepsy of childhood onset.1 The past decade has seen spectacular advances in our understanding of the genetics of epilepsy at a molecular level, and several comprehensive reviews are available.2 3 It is apparent that epilepsy genes fall into several quite distinct classes including those in which mutations cause abnormal brain development, progressive neurodegeneration, disturbed energy metabolism, or dysfunction of ion channels. The discovery that several idiopathic mendelian epilepsies are caused by mutations in ion channels, including voltage gated potassium and sodium channels, is the most exciting advance because this might provide a clue to the cause of the more common idiopathic familial epilepsies. In this short review, the focus is on those mendelian childhood epilepsies for which genes have recently been identified, and non-mendelian epilepsies for which mapping data are available. It is helpful to categorise genetic epilepsies according to the mechanism of inheritance involved and according to whether they are idiopathic (primary) or symptomatic. Three major groups can be recognised according to the mechanism of inheritance: (1) : Mendelian epilepsies, in which a single major locus accounts for segregation of the disease trait in a family. (2) : Non-mendelian or “complex” epilepsies, in which the pattern of familial clustering can be accounted for by the interaction of several susceptibility loci together with environmental factors (or by the maternal inheritance pattern of mitochondrial DNA). (3) : Chromosomal disorders, in which a gross cytogenetic abnormality is present. In the idiopathic (primary) epilepsies, recurrent seizures occur in individuals who are otherwise neurologically and cognitively intact, whereas in symptomatic epilepsies the seizures are usually one component of a complex neurological phenotype and a detectable anatomical or metabolic abnormality is present. Over 160 mendelian phenotypes include epilepsy as a component of the phenotype. Although numerous, they are individually rare and probably account for no more than 1% of patients. Most are “symptomatic” and associated with major central nervous system abnormalities or recognisable metabolic disturbances. These include such major disorders as tuberous sclerosis, fragile X syndrome, neurofibromatosis, Angelman syndrome, and the …