Publications by authors named "Karen L Oliver"

28 Publications

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Progressive myoclonus epilepsies-Residual unsolved cases have marked genetic heterogeneity including dolichol-dependent protein glycosylation pathway genes.

Am J Hum Genet 2021 04;108(4):722-738

Neurology - Neurophysiology Unit, ASST dei Sette Laghi, Galmarini Tradate Hospital, Tradate 21049, Italy.

Progressive myoclonus epilepsies (PMEs) comprise a group of clinically and genetically heterogeneous rare diseases. Over 70% of PME cases can now be molecularly solved. Known PME genes encode a variety of proteins, many involved in lysosomal and endosomal function. We performed whole-exome sequencing (WES) in 84 (78 unrelated) unsolved PME-affected individuals, with or without additional family members, to discover novel causes. We identified likely disease-causing variants in 24 out of 78 (31%) unrelated individuals, despite previous genetic analyses. The diagnostic yield was significantly higher for individuals studied as trios or families (14/28) versus singletons (10/50) (OR = 3.9, p value = 0.01, Fisher's exact test). The 24 likely solved cases of PME involved 18 genes. First, we found and functionally validated five heterozygous variants in NUS1 and DHDDS and a homozygous variant in ALG10, with no previous disease associations. All three genes are involved in dolichol-dependent protein glycosylation, a pathway not previously implicated in PME. Second, we independently validate SEMA6B as a dominant PME gene in two unrelated individuals. Third, in five families, we identified variants in established PME genes; three with intronic or copy-number changes (CLN6, GBA, NEU1) and two very rare causes (ASAH1, CERS1). Fourth, we found a group of genes usually associated with developmental and epileptic encephalopathies, but here, remarkably, presenting as PME, with or without prior developmental delay. Our systematic analysis of these cases suggests that the small residuum of unsolved cases will most likely be a collection of very rare, genetically heterogeneous etiologies.
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http://dx.doi.org/10.1016/j.ajhg.2021.03.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8059372PMC
April 2021

Progressive Myoclonus Epilepsy Caused by a Homozygous Splicing Variant of SLC7A6OS.

Ann Neurol 2021 02 5;89(2):402-407. Epub 2020 Nov 5.

Genetics Department, Lyon Civil Hospices, Lyon, France.

Exome sequencing was performed in 2 unrelated families with progressive myoclonus epilepsy. Affected individuals from both families shared a rare, homozygous c.191A > G variant affecting a splice site in SLC7A6OS. Analysis of cDNA from lymphoblastoid cells demonstrated partial splice site abolition and the creation of an abnormal isoform. Quantitative reverse transcriptase polymerase chain reaction and Western blot showed a marked reduction of protein expression. Haplotype analysis identified a ~0.85cM shared genomic region on chromosome 16q encompassing the c.191A > G variant, consistent with a distant ancestor common to both families. Our results suggest that biallelic loss-of-function variants in SLC7A6OS are a novel genetic cause of progressive myoclonus epilepsy. ANN NEUROL 2021;89:402-407.
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http://dx.doi.org/10.1002/ana.25941DOI Listing
February 2021

Familial adult myoclonic epilepsy type 1 SAMD12 TTTCA repeat expansion arose 17,000 years ago and is present in Sri Lankan and Indian families.

Eur J Hum Genet 2020 07 16;28(7):973-978. Epub 2020 Mar 16.

Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.

Familial adult myoclonic epilepsy 1 (FAME1), first recognised in Japanese families, was recently shown to be caused by a TTTCA repeat insertion in intron 4 of SAMD12 on chromosome 8. We performed whole genome sequencing on two families with FAME, one of Sri Lankan origin and the other of Indian origin, and identified a TTTCA repeat insertion in SAMD12 in both families. Haplotype analysis revealed that both families shared the same core ancestral haplotype reported in Japanese and Chinese families with FAME1. Mutation dating, based on the length of shared haplotypes, estimated the age of the ancestral haplotype to be ~670 generations, or 17,000 years old. Our data extend the geographic range of this repeat expansion to Southern Asia and potentially implicate an even broader regional distribution given the age of the variant. This finding suggests patients of Asian ancestry with suspected FAME should be screened for the SAMD12 TTTCA expansion.
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http://dx.doi.org/10.1038/s41431-020-0606-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7316749PMC
July 2020

No evidence for a BRD2 promoter hypermethylation in blood leukocytes of Europeans with juvenile myoclonic epilepsy.

Epilepsia 2019 05 4;60(5):e31-e36. Epub 2019 Feb 4.

Translational Epilepsy Research, Department of Neuropathology, University of Bonn Medical Center, Bonn, Germany.

Juvenile myoclonic epilepsy (JME) is a common syndrome of genetic generalized epilepsies (GGEs). Linkage and association studies suggest that the gene encoding the bromodomain-containing protein 2 (BRD2) may increase risk of JME. The present methylation and association study followed up a recent report highlighting that the BRD2 promoter CpG island (CpG76) is differentially hypermethylated in lymphoblastoid cells from Caucasian patients with JME compared to patients with other GGE subtypes and unaffected relatives. In contrast, we found a uniform low average percentage of methylation (<4.5%) for 13 CpG76-CpGs in whole blood cells from 782 unrelated European Caucasians, including 116 JME patients, 196 patients with genetic absence epilepsies, and 470 control subjects. We also failed to confirm an allelic association of the BRD2 promoter single nucleotide polymorphism (SNP) rs3918149 with JME (Armitage trend test, P = 0.98), and we did not detect a substantial impact of SNP rs3918149 on CpG76 methylation in either 116 JME patients (methylation quantitative trait loci [meQTL], P = 0.29) or 470 German control subjects (meQTL, P = 0.55). Our results do not support the previous observation that a high DNA methylation level of the BRD2 promoter CpG76 island is a prevalent epigenetic motif associated with JME in Caucasians.
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http://dx.doi.org/10.1111/epi.14657DOI Listing
May 2019

Kufs disease due to mutation of CLN6: clinical, pathological and molecular genetic features.

Brain 2019 01;142(1):59-69

Department of Neurophysiology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy.

Kufs disease is the major adult form of neuronal ceroid lipofuscinosis, but is rare and difficult to diagnose. Diagnosis was traditionally dependent on the demonstration of characteristic storage material, but distinction from normal age-related accumulation of lipofuscin can be challenging. Mutation of CLN6 has emerged as the most important cause of recessive Kufs disease but, remarkably, is also responsible for variant late infantile ceroid lipofuscinosis. Here we provide a detailed description of Kufs disease due to CLN6 pathogenic variants. We studied 20 cases of Kufs disease with CLN6 pathogenic variants from 13 unrelated families. Mean age of onset was 28 years (range 12-51) with bimodal peaks in teenage and early adult life. The typical presentation was of progressive myoclonus epilepsy with debilitating myoclonic seizures and relatively infrequent tonic-clonic seizures. Patients became wheelchair-bound with a mean 12 years post-onset. Ataxia was the most prominent motor feature. Dementia appeared to be an invariable accompaniment, although it could take a number of years to manifest and occasionally cognitive impairment preceded myoclonic seizures. Patients were usually highly photosensitive on EEG. MRI showed progressive cerebral and cerebellar atrophy. The median survival time was 26 years from disease onset. Ultrastructural examination of the pathology revealed fingerprint profiles as the characteristic inclusions, but they were not reliably seen in tissues other than brain. Curvilinear profiles, which are seen in the late infantile form, were not a feature. Of the 13 unrelated families we observed homozygous CLN6 pathogenic variants in four and compound heterozygous variants in nine. Compared to the variant late infantile form, there was a lower proportion of variants that predicted protein truncation. Certain heterozygous missense variants in the same amino acid position were found in both variant late infantile and Kufs disease. There was a predominance of cases from Italy and surrounding regions; this was partially explained by the discovery of three founder pathogenic variants. Clinical distinction of type A (progressive myoclonus epilepsy) and type B (dementia with motor disturbance) Kufs disease was supported by molecular diagnoses. Type A is usually caused by recessive pathogenic variants in CLN6 or dominant variants in DNAJC5. Type B Kufs is usually associated with recessive CTSF pathogenic variants. The diagnosis of Kufs remains challenging but, with the availability of genetic diagnosis, this will largely supersede the use of diagnostic biopsies, particularly as biopsies of peripheral tissues has unsatisfactory sensitivity and specificity.
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http://dx.doi.org/10.1093/brain/awy297DOI Listing
January 2019

Reanalysis and optimisation of bioinformatic pipelines is critical for mutation detection.

Hum Mutat 2019 04 31;40(4):374-379. Epub 2019 Jan 31.

Centre for Clinical Genetics, Sydney Children's Hospital, Randwick, Australia.

Rapid advances in genomic technologies have facilitated the identification pathogenic variants causing human disease. We report siblings with developmental and epileptic encephalopathy due to a novel, shared heterozygous pathogenic 13 bp duplication in SYNGAP1 (c.435_447dup, p.(L150Vfs*6)) that was identified by whole genome sequencing (WGS). The pathogenic variant had escaped earlier detection via two methodologies: whole exome sequencing and high-depth targeted sequencing. Both technologies had produced reads carrying the variant, however, they were either not aligned due to the size of the insertion or aligned to multiple major histocompatibility complex (MHC) regions in the hg19 reference genome, making the critical reads unavailable for variant calling. The WGS pipeline followed different protocols, including alignment of reads to the GRCh37 reference genome, which lacks the additional MHC contigs. Our findings highlight the benefit of using orthogonal clinical bioinformatic pipelines and all relevant inheritance patterns to re-analyze genomic data in undiagnosed patients.
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http://dx.doi.org/10.1002/humu.23699DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6492103PMC
April 2019

Evidence of linkage to chromosome 5p13.2-q11.1 in a large inbred family with genetic generalized epilepsy.

Epilepsia 2018 08 4;59(8):e125-e129. Epub 2018 Jul 4.

Epilepsy Research Centre, Austin Health, University of Melbourne, Heidelberg, Victoria, Australia.

The clinical genetics of genetic generalized epilepsy suggests complex inheritance; large pedigrees, with multiple affected individuals, are rare exceptions. We studied a large consanguineous family from Turkey where extensive electroclinical phenotyping revealed a familial phenotype most closely resembling juvenile myoclonic epilepsy. For a subject to be considered affected (n = 14), a diagnostic electroencephalogram was required. Seizure onset ranged between 6 and 19 years (mean = 12 years). Thirteen of 14 experienced myoclonic jerks; in 11, this was associated with eyelid blinking, and in 10 it was interspersed with absences. Generalized tonic-clonic seizures were seen in 11. One individual had generalized tonic-clonic seizures alone. Electroencephalograms demonstrated generalized polyspike and wave discharges that were not associated with photoparoxysmal response. Intellect was normal. Nineteen family members were subsequently chosen for nonparametric multipoint linkage analyses, which identified a 39.5 Mb region on chromosome 5 (P < 0.0001). Iterative analysis, including discovery of a subtly affected individual, narrowed the critical region to 15.4 Mb and possibly to 5.5 Mb. Homozygous versus heterozygous state of the refined 5p13.2-q11.1 haplotype was not associated with phenotypic severity or onset age, suggesting that one versus two pathogenic variants may result in similar phenotypes. Whole exome sequencing (n = 3) failed to detect any rare, protein-coding variants within the highly significant linkage region that includes HCN1 as a promising candidate.
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http://dx.doi.org/10.1111/epi.14506DOI Listing
August 2018

De Novo Mutations in PPP3CA Cause Severe Neurodevelopmental Disease with Seizures.

Am J Hum Genet 2017 Oct 21;101(4):516-524. Epub 2017 Sep 21.

Institute for Genomic Medicine, Columbia University Medical Center, New York, NY 10032, USA; Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA. Electronic address:

Exome sequencing has readily enabled the discovery of the genetic mutations responsible for a wide range of diseases. This success has been particularly remarkable in the severe epilepsies and other neurodevelopmental diseases for which rare, often de novo, mutations play a significant role in disease risk. Despite significant progress, the high genetic heterogeneity of these disorders often requires large sample sizes to identify a critical mass of individuals with disease-causing mutations in a single gene. By pooling genetic findings across multiple studies, we have identified six individuals with severe developmental delay (6/6), refractory seizures (5/6), and similar dysmorphic features (3/6), each harboring a de novo mutation in PPP3CA. PPP3CA encodes the alpha isoform of a subunit of calcineurin. Calcineurin encodes a calcium- and calmodulin-dependent serine/threonine protein phosphatase that plays a role in a wide range of biological processes, including being a key regulator of synaptic vesicle recycling at nerve terminals. Five individuals with de novo PPP3CA mutations were identified among 4,760 trio probands with neurodevelopmental diseases; this is highly unlikely to occur by chance (p = 1.2 × 10) given the size and mutability of the gene. Additionally, a sixth individual with a de novo mutation in PPP3CA was connected to this study through GeneMatcher. Based on these findings, we securely implicate PPP3CA in early-onset refractory epilepsy and further support the emerging role for synaptic dysregulation in epilepsy.
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http://dx.doi.org/10.1016/j.ajhg.2017.08.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5630160PMC
October 2017

ExACtly zero or once: A clinically helpful guide to assessing genetic variants in mild epilepsies.

Neurol Genet 2017 Aug 6;3(4):e163. Epub 2017 Jul 6.

Department of Medicine (C.A.B., S.P., K.L.O., S.F.B.), Epilepsy Research Centre; and Department of Medicine (S.P.), Royal Melbourne Hospital, University of Melbourne, Victoria, Australia.

Objective: To assist the interpretation of genomic data for common epilepsies, we asked whether variants implicated in mild epilepsies in autosomal dominant families are present in the general population.

Methods: We studied 12 genes for the milder epilepsies and identified published variants with strong segregation support (de novo germline mutation or ≥4 affected family members). These variants were checked in the Exome Aggregation Consortium (ExAC), a database of genetic variation in over 60,000 individuals. We subsequently evaluated variants in these epilepsy genes that lacked strong segregation support. To determine whether the findings in epilepsies were representative of other diseases, we also assessed the presence of variants in other dominant neurologic disorders (e.g., CADASIL).

Results: Published epilepsy variants with strong segregation support (n = 65) were absent (n = 61) or present once (n = 4) in ExAC. By contrast, of 46 published epilepsy variants without strong segregation support, 8 occurred recurrently (2-186 times). Similarly, none of the 45 disease-associated variants from other neurologic disorders with strong segregation support occurred more than once in ExAC. Reanalysis using the larger ExAC V2 plus gnomAD reference cohort showed consistent results.

Conclusions: Variants causing autosomal dominant epilepsies are ultra-rare in the general population. Variants observed more than once in ExAC were only found among reports without strong segregation support, suggesting that they may be benign. Clinicians are increasingly faced with the interpretation of genetic variants of unknown significance. These data illustrate that variants present more than once in ExAC are less likely to be pathogenic, reinforcing the valuable clinical role of ExAC.
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http://dx.doi.org/10.1212/NXG.0000000000000163DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5503456PMC
August 2017

brain-coX: investigating and visualising gene co-expression in seven human brain transcriptomic datasets.

Genome Med 2017 06 8;9(1):55. Epub 2017 Jun 8.

Population Health and Immunity Divison, The Walter and Eliza Hall Institute of Medical Research, 1G Royale Parade, 3052, Parkville, Australia.

Background: The pathogenesis of neurological and mental health disorders often involves multiple genes, complex interactions, as well as brain- and development-specific biological mechanisms. These characteristics make identification of disease genes for such disorders challenging, as conventional prioritisation tools are not specifically tailored to deal with the complexity of the human brain. Thus, we developed a novel web-application-brain-coX-that offers gene prioritisation with accompanying visualisations based on seven gene expression datasets in the post-mortem human brain, the largest such resource ever assembled.

Results: We tested whether our tool can correctly prioritise known genes from 37 brain-specific KEGG pathways and 17 psychiatric conditions. We achieved average sensitivity of nearly 50%, at the same time reaching a specificity of approximately 75%. We also compared brain-coX's performance to that of its main competitors, Endeavour and ToppGene, focusing on the ability to discover novel associations. Using a subset of the curated SFARI autism gene collection we show that brain-coX's prioritisations are most similar to SFARI's own curated gene classifications.

Conclusions: brain-coX is the first prioritisation and visualisation web-tool targeted to the human brain and can be freely accessed via http://shiny.bioinf.wehi.edu.au/freytag.s/ .
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http://dx.doi.org/10.1186/s13073-017-0444-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5465565PMC
June 2017

Myoclonus epilepsy and ataxia due to KCNC1 mutation: Analysis of 20 cases and K channel properties.

Ann Neurol 2017 May;81(5):677-689

Department of Neurology and Epileptology, Epilepsy Center Hamburg-Alsterdorf, Hamburg, Germany.

Objective: To comprehensively describe the new syndrome of myoclonus epilepsy and ataxia due to potassium channel mutation (MEAK), including cellular electrophysiological characterization of observed clinical improvement with fever.

Methods: We analyzed clinical, electroclinical, and neuroimaging data for 20 patients with MEAK due to recurrent KCNC1 p.R320H mutation. In vitro electrophysiological studies were conducted using whole cell patch-clamp to explore biophysical properties of wild-type and mutant K 3.1 channels.

Results: Symptoms began at between 3 and 15 years of age (median = 9.5), with progressively severe myoclonus and rare tonic-clonic seizures. Ataxia was present early, but quickly became overshadowed by myoclonus; 10 patients were wheelchair-bound by their late teenage years. Mild cognitive decline occurred in half. Early death was not observed. Electroencephalogram (EEG) showed generalized spike and polyspike wave discharges, with documented photosensitivity in most. Polygraphic EEG-electromyographic studies demonstrated a cortical origin for myoclonus and striking coactivation of agonist and antagonist muscles. Magnetic resonance imaging revealed symmetrical cerebellar atrophy, which appeared progressive, and a prominent corpus callosum. Unexpectedly, transient clinical improvement with fever was noted in 6 patients. To explore this, we performed high-temperature in vitro recordings. At elevated temperatures, there was a robust leftward shift in activation of wild-type K 3.1, increasing channel availability.

Interpretation: MEAK has a relatively homogeneous presentation, resembling Unverricht-Lundborg disease, despite the genetic and biological basis being quite different. A remarkable improvement with fever may be explained by the temperature-dependent leftward shift in activation of wild-type K 3.1 subunit-containing channels, which would counter the loss of function observed for mutant channels, highlighting KCNC1 as a potential target for precision therapeutics. Ann Neurol 2017;81:677-689.
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http://dx.doi.org/10.1002/ana.24929DOI Listing
May 2017

SCN1A clinical spectrum includes the self-limited focal epilepsies of childhood.

Epilepsy Res 2017 03 4;131:9-14. Epub 2017 Feb 4.

Epilepsy Research Centre, University of Melbourne, Austin Health, Heidelberg, Australia. Electronic address:

Introduction: Amongst autosomal dominant genetic epilepsy with febrile seizures plus (GEFS+) families, SCN1A variants are the most common genetic cause. Initially regarded as a generalized form of epilepsy, the GEFS+ spectrum is now known to include some focal epilepsies, but it is generally not conceptualized as extending to the self-limited focal epilepsies of childhood, such as Panayiotopoulos syndrome. There are, however, three reports of SCN1A variants in Panayiotopoulos syndrome. We describe the variable clinical phenotypes that include the self-limited focal epilepsies of childhood, present in a large GEFS+ family, segregating a heterozygous SCN1A missense variant.

Material And Methods: Electro-clinical details on all putatively affected family members were sought and blood samples were taken for genetic analysis. Two individuals were chosen for SCN1A testing. All 26 exons and exon-intron junctions were amplified, sequenced and analyzed. This was followed by pedigree segregation analysis of the variant identified.

Results: A pathogenic heterozygous SCN1A (c.2624C>A; p.Thr875Lys) variant was identified. Sixteen of the 18 variant positive family members were affected (88% penetrance): 8 with febrile seizures, 2 febrile seizures plus, 1 unclassified seizures and 5 with self-limited focal epilepsy of childhood. Of these, one was diagnosed with atypical childhood epilepsy with centrotemporal spikes and four with Panayiotopoulos syndrome.

Discussion: By characterizing the heterogeneous clinical phenotypes in a large, SCN1A mutation positive GEFS+ family, we conclude that the GEFS+ spectrum can extend to the self-limited focal epilepsies of childhood, including Panayiotopoulos syndrome, and in turn highlight the complex genotype-phenotype correlations associated with SCN1A-related epilepsies.
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http://dx.doi.org/10.1016/j.eplepsyres.2017.01.012DOI Listing
March 2017

Diagnosis and misdiagnosis of adult neuronal ceroid lipofuscinosis (Kufs disease).

Neurology 2016 Aug 13;87(6):579-84. Epub 2016 Jul 13.

From the Epilepsy Research Centre, Department of Medicine (S.F.B., K.L.O., J.A.D., M.S.H.), University of Melbourne, Austin Health, Heidelberg, Australia; Biogen, Inc. (J.F.S.), Cambridge, MA; Department of Pathology (S.C.), Centro Hospitalar São João, Porto, Portugal; Institute of Inherited Metabolic Disorders (S.K., I.J., A.P.), First Faculty of Medicine, Charles University in Prague; General University Hospital in Prague (S.K.), Czech Republic; Great Ormond Street Hospital for Children NHS Foundation Trust (G.W.A.), London, UK; Center for Human Genetic Research and Department of Neurology (K.B.S., S.L.C.), Harvard Medical School, Massachusetts General Hospital, Boston; Population Health and Immunity Division (M.B., K.R.S.), The Walter and Eliza Hall Institute of Medical Research; Departments of Mathematics and Statistics and Medical Biology (M.B.), University of Melbourne, Australia; Centre de Recherche du Centre Hospitalier de l'Université de Montréal (M.C.-D., P.C.), University of Montreal, Canada; and MRC Laboratory for Cell Biology (S.E.M.), Department of Genetics, Evolution & Environment and UCL Institute of Child Health, University College London, UK.

Objective: To critically re-evaluate cases diagnosed as adult neuronal ceroid lipofuscinosis (ANCL) in order to aid clinicopathologic diagnosis as a route to further gene discovery.

Methods: Through establishment of an international consortium we pooled 47 unsolved cases regarded by referring centers as ANCL. Clinical and neuropathologic experts within the Consortium established diagnostic criteria for ANCL based on the literature to assess each case. A panel of 3 neuropathologists independently reviewed source pathologic data. Cases were given a final clinicopathologic classification of definite ANCL, probable ANCL, possible ANCL, or not ANCL.

Results: Of the 47 cases, only 16 fulfilled the Consortium's criteria of ANCL (5 definite, 2 probable, 9 possible). Definitive alternate diagnoses were made in 10, including Huntington disease, early-onset Alzheimer disease, Niemann-Pick disease, neuroserpinopathy, prion disease, and neurodegeneration with brain iron accumulation. Six cases had features suggesting an alternate diagnosis, but no specific condition was identified; in 15, the data were inadequate for classification. Misinterpretation of normal lipofuscin as abnormal storage material was the commonest cause of misdiagnosis.

Conclusions: Diagnosis of ANCL remains challenging; expert pathologic analysis and recent molecular genetic advances revealed misdiagnoses in >1/3 of cases. We now have a refined group of cases that will facilitate identification of new causative genes.
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http://dx.doi.org/10.1212/WNL.0000000000002943DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4977374PMC
August 2016

TBC1D24 genotype-phenotype correlation: Epilepsies and other neurologic features.

Neurology 2016 07 8;87(1):77-85. Epub 2016 Jun 8.

Objective: To evaluate the phenotypic spectrum associated with mutations in TBC1D24.

Methods: We acquired new clinical, EEG, and neuroimaging data of 11 previously unreported and 37 published patients. TBC1D24 mutations, identified through various sequencing methods, can be found online (http://lovd.nl/TBC1D24).

Results: Forty-eight patients were included (28 men, 20 women, average age 21 years) from 30 independent families. Eighteen patients (38%) had myoclonic epilepsies. The other patients carried diagnoses of focal (25%), multifocal (2%), generalized (4%), and unclassified epilepsy (6%), and early-onset epileptic encephalopathy (25%). Most patients had drug-resistant epilepsy. We detail EEG, neuroimaging, developmental, and cognitive features, treatment responsiveness, and physical examination. In silico evaluation revealed 7 different highly conserved motifs, with the most common pathogenic mutation located in the first. Neuronal outgrowth assays showed that some TBC1D24 mutations, associated with the most severe TBC1D24-associated disorders, are not necessarily the most disruptive to this gene function.

Conclusions: TBC1D24-related epilepsy syndromes show marked phenotypic pleiotropy, with multisystem involvement and severity spectrum ranging from isolated deafness (not studied here), benign myoclonic epilepsy restricted to childhood with complete seizure control and normal intellect, to early-onset epileptic encephalopathy with severe developmental delay and early death. There is no distinct correlation with mutation type or location yet, but patterns are emerging. Given the phenotypic breadth observed, TBC1D24 mutation screening is indicated in a wide variety of epilepsies. A TBC1D24 consortium was formed to develop further research on this gene and its associated phenotypes.
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http://dx.doi.org/10.1212/WNL.0000000000002807DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4932231PMC
July 2016

In silico prioritization based on coexpression can aid epileptic encephalopathy gene discovery.

Neurol Genet 2016 Feb 14;2(1):e51. Epub 2016 Jan 14.

Epilepsy Research Centre (K.L.O., I.E.S., S.F.B.), Department of Medicine, Austin Health, University of Melbourne, Heidelberg, Australia; Population Health and Immunity Division (V.L., S.F., M.B.), The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia; Florey Institute (I.E.S.), Melbourne, Australia; Department of Paediatrics (I.E.S.), University of Melbourne, Royal Children's Hospital, Melbourne, Australia; and Department of Mathematics and Statistics (M.B.) and Department of Medical Biology (M.B.), University of Melbourne, Australia.

Objective: To evaluate the performance of an in silico prioritization approach that was applied to 179 epileptic encephalopathy candidate genes in 2013 and to expand the application of this approach to the whole genome based on expression data from the Allen Human Brain Atlas.

Methods: PubMed searches determined which of the 179 epileptic encephalopathy candidate genes had been validated. For validated genes, it was noted whether they were 1 of the 19 of 179 candidates prioritized in 2013. The in silico prioritization approach was applied genome-wide; all genes were ranked according to their coexpression strength with a reference set (i.e., 51 established epileptic encephalopathy genes) in both adult and developing human brain expression data sets. Candidate genes ranked in the top 10% for both data sets were cross-referenced with genes previously implicated in the epileptic encephalopathies due to a de novo variant.

Results: Five of 6 validated epileptic encephalopathy candidate genes were among the 19 prioritized in 2013 (odds ratio = 54, 95% confidence interval [7,∞], p = 4.5 × 10(-5), Fisher exact test); one gene was false negative. A total of 297 genes ranked in the top 10% for both the adult and developing brain data sets based on coexpression with the reference set. Of these, 9 had been previously implicated in the epileptic encephalopathies (FBXO41, PLXNA1, ACOT4, PAK6, GABBR2, YWHAG, NBEA, KNDC1, and SELRC1).

Conclusions: We conclude that brain gene coexpression data can be used to assist epileptic encephalopathy gene discovery and propose 9 genes as strong epileptic encephalopathy candidates worthy of further investigation.
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http://dx.doi.org/10.1212/NXG.0000000000000051DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4817907PMC
February 2016

Seizures as presenting and prominent symptom in chorea-acanthocytosis with c.2343del VPS13A gene mutation.

Epilepsia 2016 Apr 27;57(4):549-56. Epub 2016 Jan 27.

Department of Neurology, Sheba Medical Center, Tel Hashomer, Israel.

Objective: The aim of the study was to characterize the clinical features of nine patients in three families with chorea-acanthocytosis (ChAc) sharing the same rare c.2343del mutation in the VPS13A gene.

Methods: Genetic test results, clinical description, magnetic resonance imaging (MRI), and electroencephalography (EEG), as well as laboratory results are summarized.

Results: ChAc is a rare genetic disorder characterized by hyperkinetic movements, seizures, cognitive decline, neuropsychiatric symptoms, and acanthocytes on peripheral blood smear. This unique cohort of nine patients is characterized by seizures as a first and prominent symptom. In our patients, other features of ChAc appeared later, including tics, other movement disorders, dysarthria, and mild to moderate cognitive decline.

Significance: Patients with chorea-acanthocytosis carrying the described rare mutation can present with focal, treatment-resistant seizures.
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http://dx.doi.org/10.1111/epi.13318DOI Listing
April 2016

Multiplex families with epilepsy: Success of clinical and molecular genetic characterization.

Neurology 2016 Feb 22;86(8):713-22. Epub 2016 Jan 22.

From the Sackler School of Medicine (Z.A., I.B., M.Y.N., T.L.-S., A.D.K.), Tel Aviv University, Ramat Aviv, Israel; Epilepsy Research Centre (K.L.O., K.L.H., I.E.S., S.F.B.), University of Melbourne, Austin Health, Heidelberg, Australia; Epilepsy Unit (S.K., H.G.-S., R.S.), Schneider Children's Medical Center of Israel, Petach Tikvah; Department of Neurology (A.M., M.Y.N.), Tel Aviv Sourasky Medical Center; Department of Neurology (I.B.), The Chaim Sheba Medical Center, Tel Hashomer; Shaare Zedek Medical Center (A.J.M.), Jerusalem; Department of Neurology (S.W.), Western Galilee Hospital, Nahariya; Pediatric Neurology and Child Development Center (M. Mahajnah), Hillel Yaffe Medical Center, Hadera; Ruth and Bruce Rappaport Faculty of Medicine (M. Mahajnah), Technion, Haifa; Pediatric Neurology Unit (T.L.-S.), Wolfson Medical Center, Holon; The Edmond and Lily Safra Children's Hospital (B.B.-Z.), Sheba Medical Center, Ramat Gan; Department of Neurology (E.K.), Barzilai Medical Center, Ashkelon; Faculty of Health Sciences (E.K., R.M., Z.S.), Ben-Gurion University of the Negev, Beer-Sheva; Department of Neurology (R.M.) and Pediatric Neurology Unit (Z.S.), Soroka University Medical Center, Beer-Sheva; Pediatric Neurology Unit (U.K.), Dana Children's Hospital, Tel Aviv; Department of Neurology (D.E.), Agnes Ginges Center of Neurogenetics, Hadassah-Hebrew University Medical Center, Jerusalem, Israel; School of Biomedical Sciences (R.H.W.), Charles Sturt University, NSW; Queensland Brain Institute (M. Mangelsdorf), University of Queensland, Brisbane, Australia; Wessex Regional Genetics Laboratory (J.N.M.), Salisbury NHS Foundation Trust, Salisbury, UK; Division of Genetic Medicine (G.L.C., H.C.M.), Department of Pediatrics, University of Washington, Seattle; Florey Institute (G.D.J., I.E.S.), Melbourne; Department of Pediatrics (I.E.S.), University of Melbourne, Royal Children's Hospital; Population Health and Immunity Division (M.B.), The Walter and Eliza Hall Institute o

Objective: To analyze the clinical syndromes and inheritance patterns of multiplex families with epilepsy toward the ultimate aim of uncovering the underlying molecular genetic basis.

Methods: Following the referral of families with 2 or more relatives with epilepsy, individuals were classified into epilepsy syndromes. Families were classified into syndromes where at least 2 family members had a specific diagnosis. Pedigrees were analyzed and molecular genetic studies were performed as appropriate.

Results: A total of 211 families were ascertained over an 11-year period in Israel. A total of 169 were classified into broad familial epilepsy syndrome groups: 61 generalized, 22 focal, 24 febrile seizure syndromes, 33 special syndromes, and 29 mixed. A total of 42 families remained unclassified. Pathogenic variants were identified in 49/211 families (23%). The majority were found in established epilepsy genes (e.g., SCN1A, KCNQ2, CSTB), but in 11 families, this cohort contributed to the initial discovery (e.g., KCNT1, PCDH19, TBC1D24). We expand the phenotypic spectrum of established epilepsy genes by reporting a familial LAMC3 homozygous variant, where the predominant phenotype was epilepsy with myoclonic-atonic seizures, and a pathogenic SCN1A variant in a family where in 5 siblings the phenotype was broadly consistent with Dravet syndrome, a disorder that usually occurs sporadically.

Conclusion: A total of 80% of families were successfully classified, with pathogenic variants identified in 23%. The successful characterization of familial electroclinical and inheritance patterns has highlighted the value of studying multiplex families and their contribution towards uncovering the genetic basis of the epilepsies.
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http://dx.doi.org/10.1212/WNL.0000000000002404DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4763801PMC
February 2016

Mutation of the nuclear lamin gene LMNB2 in progressive myoclonus epilepsy with early ataxia.

Hum Mol Genet 2015 Aug 7;24(16):4483-90. Epub 2015 May 7.

Department of Medicine, Epilepsy Research Centre, University of Melbourne, Austin Health, Melbourne, VIC, Australia,

We studied a consanguineous Palestinian Arab family segregating an autosomal recessive progressive myoclonus epilepsy (PME) with early ataxia. PME is a rare, often fatal syndrome, initially responsive to antiepileptic drugs which over time becomes refractory and can be associated with cognitive decline. Linkage analysis was performed and the disease locus narrowed to chromosome 19p13.3. Fourteen candidate genes were screened by conventional Sanger sequencing and in one, LMNB2, a novel homozygous missense mutation was identified that segregated with the PME in the family. Whole exome sequencing excluded other likely pathogenic coding variants in the linked interval. The p.His157Tyr mutation is located in an evolutionarily highly conserved region of the alpha-helical rod of the lamin B2 protein. In vitro assembly analysis of mutant lamin B2 protein revealed a distinct defect in the assembly of the highly ordered fibrous arrays typically formed by wild-type lamin B2. Our data suggests that disruption of the organisation of the nuclear lamina in neurons, perhaps through abnormal neuronal migration, causes the epilepsy and early ataxia syndrome and extends the aetiology of PMEs to include dysfunction in nuclear lamin proteins.
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http://dx.doi.org/10.1093/hmg/ddv171DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6281347PMC
August 2015

A recurrent de novo mutation in KCNC1 causes progressive myoclonus epilepsy.

Nat Genet 2015 Jan 17;47(1):39-46. Epub 2014 Nov 17.

Department of Neurology, Cerrahpasa Medical Faculty, Istanbul University, Istanbul, Turkey.

Progressive myoclonus epilepsies (PMEs) are a group of rare, inherited disorders manifesting with action myoclonus, tonic-clonic seizures and ataxia. We sequenced the exomes of 84 unrelated individuals with PME of unknown cause and molecularly solved 26 cases (31%). Remarkably, a recurrent de novo mutation, c.959G>A (p.Arg320His), in KCNC1 was identified as a new major cause for PME. Eleven unrelated exome-sequenced (13%) and two affected individuals in a secondary cohort (7%) had this mutation. KCNC1 encodes KV3.1, a subunit of the KV3 voltage-gated potassium ion channels, which are major determinants of high-frequency neuronal firing. Functional analysis of the Arg320His mutant channel showed a dominant-negative loss-of-function effect. Ten cases had pathogenic mutations in known PME-associated genes (NEU1, NHLRC1, AFG3L2, EPM2A, CLN6 and SERPINI1). Identification of mutations in PRNP, SACS and TBC1D24 expand their phenotypic spectra to PME. These findings provide insights into the molecular genetic basis of PME and show the role of de novo mutations in this disease entity.
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http://dx.doi.org/10.1038/ng.3144DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4281260PMC
January 2015

Using familial information for variant filtering in high-throughput sequencing studies.

Hum Genet 2014 Nov 17;133(11):1331-41. Epub 2014 Aug 17.

The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia,

High-throughput sequencing studies (HTS) have been highly successful in identifying the genetic causes of human disease, particularly those following Mendelian inheritance. Many HTS studies to date have been performed without utilizing available family relationships between samples. Here, we discuss the many merits and occasional pitfalls of using identity by descent information in conjunction with HTS studies. These methods are not only applicable to family studies but are also useful in cohorts of apparently unrelated, 'sporadic' cases and small families underpowered for linkage and allow inference of relationships between individuals. Incorporating familial/pedigree information not only provides powerful filtering options for the extensive variant lists that are usually produced by HTS but also allows valuable quality control checks, insights into the genetic model and the genotypic status of individuals of interest. In particular, these methods are valuable for challenging discovery scenarios in HTS analysis, such as in the study of populations poorly represented in variant databases typically used for filtering, and in the case of poor-quality HTS data.
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http://dx.doi.org/10.1007/s00439-014-1479-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4185103PMC
November 2014

Harnessing gene expression networks to prioritize candidate epileptic encephalopathy genes.

PLoS One 2014 9;9(7):e102079. Epub 2014 Jul 9.

Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia; Department of Mathematics and Statistics, University of Melbourne, Melbourne, Victoria, Australia.

We apply a novel gene expression network analysis to a cohort of 182 recently reported candidate Epileptic Encephalopathy genes to identify those most likely to be true Epileptic Encephalopathy genes. These candidate genes were identified as having single variants of likely pathogenic significance discovered in a large-scale massively parallel sequencing study. Candidate Epileptic Encephalopathy genes were prioritized according to their co-expression with 29 known Epileptic Encephalopathy genes. We utilized developing brain and adult brain gene expression data from the Allen Human Brain Atlas (AHBA) and compared this to data from Celsius: a large, heterogeneous gene expression data warehouse. We show replicable prioritization results using these three independent gene expression resources, two of which are brain-specific, with small sample size, and the third derived from a heterogeneous collection of tissues with large sample size. Of the nineteen genes that we predicted with the highest likelihood to be true Epileptic Encephalopathy genes, two (GNAO1 and GRIN2B) have recently been independently reported and confirmed. We compare our results to those produced by an established in silico prioritization approach called Endeavour, and finally present gene expression networks for the known and candidate Epileptic Encephalopathy genes. This highlights sub-networks of gene expression, particularly in the network derived from the adult AHBA gene expression dataset. These networks give clues to the likely biological interactions between Epileptic Encephalopathy genes, potentially highlighting underlying mechanisms and avenues for therapeutic targets.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0102079PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4090166PMC
December 2015

A variant of KCC2 from patients with febrile seizures impairs neuronal Cl- extrusion and dendritic spine formation.

EMBO Rep 2014 Jun 24;15(6):723-9. Epub 2014 Mar 24.

Department of Biosciences, University of Helsinki, Helsinki, Finland Neuroscience Center, University of Helsinki, Helsinki, Finland

Genetic variation in SLC12A5 which encodes KCC2, the neuron-specific cation-chloride cotransporter that is essential for hyperpolarizing GABAergic signaling and formation of cortical dendritic spines, has not been reported in human disease. Screening of SLC12A5 revealed a co-segregating variant (KCC2-R952H) in an Australian family with febrile seizures. We show that KCC2-R952H reduces neuronal Cl(-) extrusion and has a compromised ability to induce dendritic spines in vivo and in vitro. Biochemical analyses indicate a reduced surface expression of KCC2-R952H which likely contributes to the functional deficits. Our data suggest that KCC2-R952H is a bona fide susceptibility variant for febrile seizures.
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http://dx.doi.org/10.1002/embr.201438749DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4197883PMC
June 2014

Glucose metabolism transporters and epilepsy: only GLUT1 has an established role.

Epilepsia 2014 Feb 31;55(2):e18-21. Epub 2014 Jan 31.

Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, Victoria, Australia.

The availability of glucose, and its glycolytic product lactate, for cerebral energy metabolism is regulated by specific brain transporters. Inadequate energy delivery leads to neurologic impairment. Haploinsufficiency of the glucose transporter GLUT1 causes a characteristic early onset encephalopathy, and has recently emerged as an important cause of a variety of childhood or later-onset generalized epilepsies and paroxysmal exercise-induced dyskinesia. We explored whether mutations in the genes encoding the other major glucose (GLUT3) or lactate (MCT1/2/3/4) transporters involved in cerebral energy metabolism also cause generalized epilepsies. A cohort of 119 cases with myoclonic astatic epilepsy or early onset absence epilepsy was screened for nucleotide variants in these five candidate genes. No epilepsy-causing mutations were identified, indicating that of the major energetic fuel transporters in the brain, only GLUT1 is clearly associated with generalized epilepsy.
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http://dx.doi.org/10.1111/epi.12519DOI Listing
February 2014

TBC1D24 mutation associated with focal epilepsy, cognitive impairment and a distinctive cerebro-cerebellar malformation.

Epilepsy Res 2013 Jul 19;105(1-2):240-4. Epub 2013 Mar 19.

Tel-Aviv University Medical School, Tel-Aviv 61999, Israel.

We describe the clinical and radiological features of a family with a homozygous mutation in TBC1D24. The phenotype comprised onset of focal seizures at 2 months with prominent eye-blinking, facial and limb jerking with an oral sensory aura. These were controllable with medication but persisted into adult life. Associated features were mild to moderate intellectual disability and cerebellar features. MRI showed subtle cortical thickening with cerebellar atrophy and high signal confined to the ansiform lobule. The disorder is allelic with familial infantile myoclonic epilepsy, where intellect and neurologic examination are normal, highlighting the phenotypic variation with mutations of TBC1D24.
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http://dx.doi.org/10.1016/j.eplepsyres.2013.02.005DOI Listing
July 2013

Missense mutations in the sodium-gated potassium channel gene KCNT1 cause severe autosomal dominant nocturnal frontal lobe epilepsy.

Nat Genet 2012 Nov 21;44(11):1188-90. Epub 2012 Oct 21.

Epilepsy Research Program, School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, Australia.

We performed genomic mapping of a family with autosomal dominant nocturnal frontal lobe epilepsy (ADNFLE) and intellectual and psychiatric problems, identifying a disease-associated region on chromosome 9q34.3. Whole-exome sequencing identified a mutation in KCNT1, encoding a sodium-gated potassium channel subunit. KCNT1 mutations were identified in two additional families and a sporadic case with severe ADNFLE and psychiatric features. These findings implicate the sodium-gated potassium channel complex in ADNFLE and, more broadly, in the pathogenesis of focal epilepsies.
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http://dx.doi.org/10.1038/ng.2440DOI Listing
November 2012

Rare protein sequence variation in SV2A gene does not affect response to levetiracetam.

Epilepsy Res 2012 Sep 30;101(3):277-9. Epub 2012 Apr 30.

Epilepsy Research Program, School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia, Australia.

Levetiracetam, a broad spectrum antiepileptic drug, binds to membrane protein SV2A. The protein coding region of SV2A was sequenced in 158 patients with focal or generalized epilepsies divided into three groups based on their response to levetiracetam: responders (>75% decrease), exacerbators (50% increase) and non-responders. Nonsynonymous coding variation within SV2A was extremely rare, suggesting that rare variation is not likely to account for the individual differences in response to levetiracetam.
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http://dx.doi.org/10.1016/j.eplepsyres.2012.04.007DOI Listing
September 2012

A focal epilepsy and intellectual disability syndrome is due to a mutation in TBC1D24.

Am J Hum Genet 2010 Sep;87(3):371-5

Genetics and Molecular Pathology, SA Pathology, Adelaide, Australia.

We characterized an autosomal-recessive syndrome of focal epilepsy, dysarthria, and mild to moderate intellectual disability in a consanguineous Arab-Israeli family associated with subtle cortical thickening. We used multipoint linkage analysis to map the causative mutation to a 3.2 Mb interval within 16p13.3 with a LOD score of 3.86. The linked interval contained 160 genes, many of which were considered to be plausible candidates to harbor the disease-causing mutation. To interrogate the interval in an efficient and unbiased manner, we used targeted sequence enrichment and massively parallel sequencing. By prioritizing unique variants that affected protein translation, a pathogenic mutation was identified in TBC1D24 (p.F251L), a gene of unknown function. It is a member of a large gene family encoding TBC domain proteins with predicted function as Rab GTPase activators. We show that TBC1D24 is expressed early in mouse brain and that TBC1D24 protein is a potent modulator of primary axonal arborization and specification in neuronal cells, consistent with the phenotypic abnormality described.
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http://dx.doi.org/10.1016/j.ajhg.2010.08.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2933342PMC
September 2010

Familial neonatal seizures with intellectual disability caused by a microduplication of chromosome 2q24.3.

Epilepsia 2010 Sep;51(9):1865-9

SA Pathology at Women's and Children's Hospital, Adelaide, South Australia, Australia.

A family with dominantly inherited neonatal seizures and intellectual disability was atypical for neonatal and infantile seizure syndromes associated with potassium (KCNQ2 and KCNQ3) and sodium (SCN2A) channel mutations. Microsatellite markers linked to KCNQ2, KCNQ3, and SCN2A were examined to exclude candidate locations, but instead revealed a duplication detected by observation of three alleles for two markers flanking SCN2A. Characterization revealed a 1.57 Mb duplication at 2q24.3 containing eight genes including SCN2A, SCN3A, and the 3¢ end of SCN1A. The duplication was partially inverted and inserted within or near SCN1A, probably affecting the expression levels of associated genes, including sodium channels. Rare or unique microchromosomal copy number mutations might underlie familial epilepsies that do not fit within the clinical criteria for the established syndromes.
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http://dx.doi.org/10.1111/j.1528-1167.2010.02558.xDOI Listing
September 2010
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