Association mapping of genomic microdeletions and common susceptibility variants predisposing to genetic generalized epilepsies

Approximately 3% of the general population is affected by epilepsy during lifetime, making epilepsy one of the most common neurological diseases. Genetic generalized epilepsies (GGE) are the most common of genetic epilepsies and account for 20-30% of all epilepsies. GGE is subdivided into genetically determined subgroups with gradual transition, including genetic absence epilepsies (GAE), juvenile myoclonic epilepsy (JME), and epilepsy with generalized tonic-clonic seizures (EGTCS). In spite of a high heritability rate of 80% and a predominant genetic etiology, the genetic factors predisposing to GGE are still mostly unknown. In the present study, we carried out association studies to investigate whether genomic microdeletions and common susceptibility variants increase risk for GGE. To test the common disease/common variant hypothesis, genome-wide association studies (GWAS) were performed in several GGE cohorts using case-control and family-based study designs. For analysis, all patients were either pooled or stratified according to the subgroup they belong to in order to detect common or subgroupspecific risk factors, respectively. The GWAS comprised a case-control cohort of 1,523 European GGE patients and 2,454 German controls and a sample cohort of 566 European parent-offspring trios. Meta-GWAS analyses revealed significant association (P < 5.0 × 10-8) with GGE at 2p16.1 (rs35577149, meta-analysis P = 1.65E-08, OR[C] = 0.78, 95% CI 0.71 - 0.86). Significant association with JME was detected at 1q43 (rs12059546, meta-analysis P = 2.27E-08, OR[G] = 1.53, 95% CI 1.33 - 1.78). Suggestive evidence for association (P < 1.0E-05) was found for GGE at 8q12.2 (rs6999304, meta-analysis P= 1.77E-06, OR[G] = 1.33, 95% CI 1.17 - 1.51) and for GAE at 2q22.3 (rs75917352, meta-analysis P = 1.41E-07, OR[T] = 0.67, 95% CI 0.58 - 0.79). The associated regions harbor high-ranking candidate genes: CHRM3 at 1q43, VRK2 at 2p16.1, and ZEB2 at 2q22.3. Further replication efforts are necessary to elucidate whether these positional candidate genes contribute to the heritability of the common GGE syndromes. Exploring the rare variant/common disease hypothesis, we investigated the impact of six recurrent microdeletions on the genetic risk of GGE at the genomic hotspot regions 1q21.1, 15q11.2, 15q13.3, 16p11.2, 16p13.11, and 22q11.2, which had been implicated as rare genetic risk factors in a wide range of neurodevelopmental disorders. Recurrent microdeletions were assessed in 1,497 European GGE patients, 5,374 controls, and 566 GGE trios using high-resolution SNP microarrays. Considering all six microdeletion hot spots together, we found a significant excess of these microdeletions in 2,563 GGE patients versus 5,940 controls (P < 2.20E-16, OR = 7.65, 95% CI 4.59 - 13.18). Individually, significant associations with GGE were observed for the microdeletions at 15q11.2 (P = 1.12E-4, OR = 3.59, 95% CI 1.80 - 7.25), 15q13.3 (P = 5.48× 10−9) and 16p13.11 (P = 4.42E-06, OR = 17.39, 95% CI 3.86 - 159.88). In a candidate-gene approach, we tested whether exon-disrupting/removing microdeletions in the genes encoding NRXN1 and RBFOX1 confer susceptibility for GGE. We found a significant association with GGE at both loci (NRXN1: P = 0.0049; RBFOX1: P = 0.0083). However, high phenotypic variability and incomplete penetrance, resulting in apparently imperfect segregation, indicate that partial NRXN1 and RBFOX1 deletions represent susceptibility factors rather than highly penetrant mutations. The present study substantiates a role of both genomic microdeletions and common susceptibility variants in the genetic predisposition of common GGE syndromes. We strengthened the statistical evidence for associations of genetic variants at 1q43, 2p16.1, and 2q23.2 with GGE syndromes and identified a novel susceptibility locus at 8q12.2. Although individually rare, the associations of all microdeletions at 15q11.2, 15q13.3, 16p13.3, NRXN1, and RBFOX1 taken together contribute significantly to the genetic variance of GGE

Mutations in FKBP10 can cause a severe form of isolated Osteogenesis imperfecta

<p>Abstract</p> <p>Background</p> <p>Mutations in the <it>FKBP10 </it>gene were first described in patients with Osteogenesis imperfecta type III. Two follow up reports found <it>FKBP10 </it>mutations to be associated with Bruck syndrome type 1, a rare disorder characterized by congenital contractures and bone fragility. This raised the question if the patients in the first report indeed had isolated Osteogenesis imperfecta or if Bruck syndrome would have been the better diagnosis.</p> <p>Methods</p> <p>The patients described here are affected by severe autosomal recessive Osteogenesis imperfecta without contractures.</p> <p>Results</p> <p>Homozygosity mapping identified <it>FKBP10 </it>as a candidate gene, and sequencing revealed a base pair exchange that causes a C-terminal premature stop codon in this gene.</p> <p>Conclusions</p> <p>Our study demonstrates that <it>FKBP10 </it>mutations not only cause Bruck syndrome or Osteogenesis imperfecta type III but can result in a severe type of isolated Osteogenesis imperfecta type IV with prenatal onset. Furthermore, it adds dentinogenesis imperfecta to the spectrum of clinical symptoms associated with <it>FKBP10 </it>mutations.</p

Методы и механизмы геттерирования кремниевых структур в производстве интегральных микросхем

Увеличение степени интеграции элементной базы предъявляет все более жесткие требования к уменьшению концентрации загрязняющих примесей и окислительных дефектов упаковки в исходных кремниевых пластинах с ее сохранением в технологическом цикле изготовления ИМС. Это обуславливает высокую актуальность применения геттерирования в современной технологии микроэлектроники. В статье рассмотрены существующие методы геттерирования кремниевых пластин и механизмы их протекания.Збільшення ступеня інтеграції елементної бази пред'являє все більш жорсткі вимоги до зменшення концентрації забруднюючих домішок та окислювальних дефектів упаковки у вихідних кремнієвих пластинах за її збереження у технологічному циклі виготовлення ІМС. Це обумовлює високу актуальність застосування гетерування в сучасній технології мікроелектроніки. Розглянуто існуючі методи гетерування кремнієвих пластин та розглянуто механізми їх перебігу.Increasing the degree of integration of hardware components imposes more stringent requirements for the reduction of the concentration of contaminants and oxidation stacking faults in the original silicon wafers with its preservation in the IC manufacturing process cycle. This causes high relevance of the application of gettering in modern microelectronic technology. The existing methods of silicon wafers gettering and the mechanisms of their occurrence are considered

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, Pmeta = 2.5 × 10−9, OR[T] = 0.81) and 17q21.32 (rs72823592, Pmeta = 9.3 × 10−9, OR[A] = 0.77). The search for syndrome-related susceptibility alleles identified significant associations for GAEs at 2q22.3 (rs10496964, Pmeta = 9.1 × 10−9, OR[T] = 0.68) and at 1q43 for JME (rs12059546, Pmeta = 4.1 × 10−8, OR[G] = 1.42). Suggestive evidence for an association with GGEs was found in the region 2q24.3 (rs11890028, Pmeta = 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 syndrome

16p11.2 600 kb Duplications confer risk for typical and atypical Rolandic epilepsy

Rolandic epilepsy (RE) is the most common idiopathic focal childhood epilepsy. Its molecular basis is largely unknown and a complex genetic etiology is assumed in the majority of affected individuals. The present study tested whether six large recurrent copy number variants at 1q21, 15q11.2, 15q13.3, 16p11.2, 16p13.11 and 22q11.2 previously associated with neurodevelopmental disorders also increase risk of RE. Our association analyses revealed a significant excess of the 600 kb genomic duplication at the 16p11.2 locus (chr16: 29.5-30.1 Mb) in 393 unrelated patients with typical (n = 339) and atypical (ARE; n = 54) RE compared with the prevalence in 65 046 European population controls (5/393 cases versus 32/65 046 controls; Fisher's exact test P = 2.83 × 10−6, odds ratio = 26.2, 95% confidence interval: 7.9-68.2). In contrast, the 16p11.2 duplication was not detected in 1738 European epilepsy patients with either temporal lobe epilepsy (n = 330) and genetic generalized epilepsies (n = 1408), suggesting a selective enrichment of the 16p11.2 duplication in idiopathic focal childhood epilepsies (Fisher's exact test P = 2.1 × 10−4). In a subsequent screen among children carrying the 16p11.2 600 kb rearrangement we identified three patients with RE-spectrum epilepsies in 117 duplication carriers (2.6%) but none in 202 carriers of the reciprocal deletion. Our results suggest that the 16p11.2 duplication represents a significant genetic risk factor for typical and atypical R

Exonic microdeletions of the gephyrin gene impair GABAergic synaptic inhibition in patients with idiopathic generalized epilepsy

Gephyrin is a postsynaptic scaffolding protein, essential for the clustering of glycine and gamma-aminobutyric acid type-A receptors (GABA(A)Rs) at inhibitory synapses. An impairment of GABAergic synaptic inhibition represents a key pathway of epileptogenesis. Recently, exonic microdeletions in the gephyrin (GPHN) gene have been associated with neurodevelopmental disorders including autism spectrum disorder, schizophrenia and epileptic seizures. Here we report the identification of novel exonic GPHN microdeletions in two patients with idiopathic generalized epilepsy (ICE), representing the most common group of genetically determined epilepsies. The identified GPHN microdeletions involve exons 5-9 (Delta 5-9) and 2-3 (Delta 2-3), both affecting the gephyrin G-domain. Molecular characterization of the GPHN Delta 5-9 variant demonstrated that it perturbs the clustering of regular gephyrin at inhibitory synapses in cultured mouse hippocampal neurons in a dominant-negative manner, resulting in a significant loss of gamma(2)-subunit containing GABAARs. GPHN Delta 2-3 causes a frameshift resulting in a premature stop codon (p.V22Gfs*7) leading to haplo-insufficiency of the gene. Our results demonstrate that structural exonic microdeletions affecting the GPHN gene constitute a rare genetic risk factor for IGE and other neuropsychiatric disorders by an impairment of the GABAergic inhibitory synaptic transmission. (C) 2014 Published by Elsevier Inc

Exonic microdeletions of the gephyrin gene impair GABAergic synaptic inhibition in patients with idiopathic generalized epilepsy

Gephyrin is a postsynaptic scaffolding protein, essential for the clustering of glycine and gamma-aminobutyric acid type-A receptors (GABA(A)Rs) at inhibitory synapses. An impairment of GABAergic synaptic inhibition represents a key pathway of epileptogenesis. Recently, exonic microdeletions in the gephyrin (GPHN) gene have been associated with neurodevelopmental disorders including autism spectrum disorder, schizophrenia and epileptic seizures. Here we report the identification of novel exonic GPHN microdeletions in two patients with idiopathic generalized epilepsy (ICE), representing the most common group of genetically determined epilepsies. The identified GPHN microdeletions involve exons 5-9 (Delta 5-9) and 2-3 (Delta 2-3), both affecting the gephyrin G-domain. Molecular characterization of the GPHN Delta 5-9 variant demonstrated that it perturbs the clustering of regular gephyrin at inhibitory synapses in cultured mouse hippocampal neurons in a dominant-negative manner, resulting in a significant loss of gamma(2)-subunit containing GABAARs. GPHN Delta 2-3 causes a frameshift resulting in a premature stop codon (p.V22Gfs*7) leading to haplo-insufficiency of the gene. Our results demonstrate that structural exonic microdeletions affecting the GPHN gene constitute a rare genetic risk factor for IGE and other neuropsychiatric disorders by an impairment of the GABAergic inhibitory synaptic transmission. (C) 2014 Published by Elsevier Inc

Familial and sporadic 15q13.3 microdeletions in idiopathic generalized epilepsy: precedent for disorders with complex inheritance

Microdeletion at chromosomal position 15q13.3 has been described in intellectual disability, autism spectrum disorders, schizophrenia and recently in idiopathic generalized epilepsy (IGE). Using independent IGE cohorts, we first aimed to confirm the association of 15q13.3 deletions and IGE. We then set out to determine the relative occurrence of sporadic and familial cases and to examine the likelihood of having seizures for individuals with the microdeletion in familial cases. The 15q13.3 microdeletion was identified in 7 of 539 (1.3%) unrelated cases of IGE using quantitative PCR or SNP arrays and confirmed by array comparative genomic hybridization analysis using probes specific to the 15q13.3 region. The inheritance of this lesion was tracked using family studies. Of the seven microdeletions identified in probands, three were de novo, two were transmitted from an unaffected parent and in two cases the parents were unavailable. Non-penetrance of the microdeletion was identified in 4/7 pedigrees and three pedigrees included other family members with IGE who lacked the 15q13.3 deletion. The odds ratio is 68 (95% confidence interval 29–181), indicating a pathogenic lesion predisposing to epilepsy with complex inheritance and incomplete penetrance for the IGE component of the phenotype in multiplex families.Leanne M. Dibbens, Saul Mullen, Ingo Helbig, Heather C. Mefford, Marta A. Bayly, Susannah Bellows, Costin Leu, Holger Trucks, Tanja Obermeier, Michael Wittig, Andre Franke, Hande Caglayan, Zuhal Yapici, EPICURE Consortium, Thomas Sander, Evan E. Eichler, Ingrid E. Scheffer, John C. Mulley and Samuel F. Berkovi