Semantic Similarity Analysis Reveals Robust Gene-Disease Relationships in Developmental and Epileptic Encephalopathies.

More than 100 genetic etiologies have been identified in developmental and epileptic encephalopathies (DEEs), but correlating genetic findings with clinical features at scale has remained a hurdle because of a lack of frameworks for analyzing heterogenous clinical data. Here, we analyzed 31,742 Human Phenotype Ontology (HPO) terms in 846 individuals with existing whole-exome trio data and assessed associated clinical features and phenotypic relatedness by using HPO-based semantic similarity analysis for individuals with de novo variants in the same gene. Gene-specific phenotypic signatures included associations of SCN1A with "complex febrile seizures" (HP: 0011172; p = 2.1 × 10-5) and "focal clonic seizures" (HP: 0002266; p = 8.9 × 10-6), STXBP1 with "absent speech" (HP: 0001344; p = 1.3 × 10-11), and SLC6A1 with "EEG with generalized slow activity" (HP: 0010845; p = 0.018). Of 41 genes with de novo variants in two or more individuals, 11 genes showed significant phenotypic similarity, including SCN1A (n = 16, p < 0.0001), STXBP1 (n = 14, p = 0.0021), and KCNB1 (n = 6, p = 0.011). Including genetic and phenotypic data of control subjects increased phenotypic similarity for all genetic etiologies, whereas the probability of observing de novo variants decreased, emphasizing the conceptual differences between semantic similarity analysis and approaches based on the expected number of de novo events. We demonstrate that HPO-based phenotype analysis captures unique profiles for distinct genetic etiologies, reflecting the breadth of the phenotypic spectrum in genetic epilepsies. Semantic similarity can be used to generate statistical evidence for disease causation analogous to the traditional approach of primarily defining disease entities through similar clinical features.

The landscape of early infantile epileptic encephalopathy in a consanguineous population.

PURPOSE: Epileptic encephalopathies (EE), are a group of age-related disorders characterized by intractable seizures and electroencephalogram (EEG) abnormalities that may result in cognitive and motor delay. Early infantile epileptic encephalopathies (EIEE) manifest in the first year of life. EIEE are highly heterogeneous genetically but a genetic etiology is only identified in half of the cases, typically in the form of de novo dominant mutations. METHOD: This is a descriptive retrospective study of a consecutive series of patients diagnosed with EIEE from the participating hospitals. A chart review was performed for all patients. The diagnosis of epileptic encephalopathy was confirmed by molecular investigations in commercial labs. In silico study was done for all novel mutations. A systematic search was done for all the types of EIEE and their correlated genes in the literature using the Online Mendelian Inheritance In Man and PubMed databases. RESULTS: In this case series, we report 72 molecularly characterized EIEE from a highly consanguineous population, and review their clinical course. We identified 50 variants, 26 of which are novel, causing 26 different types of EIEE. Unlike outbred populations, autosomal recessive EIEE accounted for half the cases. The phenotypes ranged from self-limiting and drug-responsive to severe refractory seizures or even death. CONCLUSIONS: We reported the largest EIEE case series in the region with confirmed molecular testing and detailed clinical phenotyping. The number autosomal recessive predominance could be explained by the society's high consanguinity. We reviewed all the EIEE registered causative genes in the literature and proposed a functional classification.

Epileptic spasms without hypsarrhythmia in infancy and childhood: tonic spasms as a seizure type.

Epileptic spasms were defined by the International League Against Epilepsy Task Force on Classification and Terminology in 2001 as a specific seizure type. Epileptic spasms without hypsarrhythmia have been described in some series of patients, occurring either in infancy or childhood. More prolonged epileptic spasms without hypsarrhythmia were previously defined as a different seizure type, and referred to as "tonic spasm seizures". Here, we present a 5-year-old boy who started having epileptic spasms without hypsarrhythmia at 8 months of age, effectively treated with oxcarbazepine. With the withdrawal of medication, epileptic spasms returned. Video-EEG monitoring revealed high-voltage slow waves superimposed by low-voltage fast activity, followed by an electrodecremental phase and a burst of asymmetric fast activity, time-locked to clinical tonic spasm seizures. Brain MRI showed left temporal atrophy with temporal pole grey/white matter junction blurring and ictal PET-CT showed left basal frontal hypermetabolism. Seizures were refractory to several AEDs and vigabatrin was introduced with seizure cessation. Despite efforts to classify epileptic spasms, these are still considered as part of the group of unknown seizure types. In some cases, a focal origin has been suggested, leading to the term "periodic spasms" and "focal spasms". In this case, epileptic spasms without hypsarrhythmia, associated with tonic spasms, may be a variant of focal spasms and might be considered as an epileptic syndrome. [Published with video sequence].

PIGA mutations cause early-onset epileptic encephalopathies and distinctive features.

OBJECTIVE: To investigate the clinical spectrum caused by mutations in PIGA at Xp22.2, which is involved in the biosynthesis of the glycosylphosphatidylinositol (GPI) anchor, among patients with early-onset epileptic encephalopathies (EOEEs). METHODS: Whole-exome sequencing was performed as a comprehensive genetic analysis for a cohort of 172 patients with EOEEs including early myoclonic encephalopathy, Ohtahara syndrome, and West syndrome, and PIGA mutations were carefully investigated. RESULTS: We identified 4 PIGA mutations in probands showing early myoclonic encephalopathy, West syndrome, or unclassified EOEE. Flow cytometry of blood granulocytes from patients demonstrated reduced expression of GPI-anchored proteins. Expression of GPI-anchored proteins in PIGA-deficient JY5 cells was only partially or hardly restored by transient expression of PIGA mutants with a weak TATA box promoter, indicating a variable loss of PIGA activity. The phenotypic consequences of PIGA mutations can be classified into 2 types, severe and less severe, which correlate with the degree of PIGA activity reduction caused by the mutations. Severe forms involved myoclonus and asymmetrical suppression bursts on EEG, multiple anomalies with a dysmorphic face, and delayed myelination with restricted diffusion patterns in specific areas. The less severe form presented with intellectual disability and treatable seizures without facial dysmorphism. CONCLUSIONS: Our study confirmed that PIGA mutations are one genetic cause of EOEE, suggesting that GPI-anchor deficiencies may be an underlying cause of EOEE.

Ictal electroencephalography and electromyography features in symptomatic infantile epileptic encephalopathy with late-onset spasms.

AIM: Recently, epilepsy with late-onset epileptic spasms (ES) has been reported to be distinct from West syndrome and Lennox-Gastaut syndrome. We identified the characteristics of this clinical entity by analyzing clinical data, including ictal electroencephalography (EEG) and electromyography (EMG) in symptomatic patients. METHODS: We evaluated retrospectively eight symptomatic patients with epilepsy with late-onset ES. All patients underwent video-EEG analysis for more than 24 hours and have been followed up for at least 1 year. Interictal EEG, ictal EEG, ictal EMG, coexistence seizures, response to treatment, and intellectual or daily activity level were assessed. Ictal EMG was evaluated by spectral analysis. RESULTS: All patients exhibited neurological deterioration and had multiple seizure types; seven of them had intractable seizures. Interictal EEG showed no typical hypsarrhythmia in any case. Ictal EMG analysis revealed that the predominant seizure types presenting with the tonic component were distributed among ES, spasms followed by tonic seizures (SFT), and tonic seizures. CONCLUSIONS: The clinical characteristics of our patients were identical to infantile epileptic encephalopathy with late-onset spasms. Our patients had ES, SFT, and tonic seizures as the core seizure types, developed ES beyond the age of 1 year, and showed neurological deterioration. These may be essential symptoms of this clinical entity.

Text Classification towards Detecting Misdiagnosis of an Epilepsy Syndrome in a Pediatric Population.

When attempting to identify a specific epilepsy syndrome, physicians are often unable to make or agree upon a diagnosis. This is further complicated by the fact that the current classification and diagnosis of epilepsy requires specialized training and the use of resources not typically available to the average clinician, such as training to recognize specific seizure types and electroencephalography (EEG). Even when training and resources are available, expert epileptologists often find it challenging to identify seizure types and to distinguish between specific epilepsy syndromes. Information relevant to the diagnosis is present in narrative form in the medical record across several visits for an individual patient. Our ultimate goal is to create a system that will assist physicians in the diagnosis of epilepsy. This paper explores, as a baseline, text classification methods that attempt to correlate the narrative text features to the diagnosis of West syndrome (Infantile Spasms), using data from Phoenix Children's Hospital (PCH). We tested these methods against a dataset containing known (coded) diagnosis of West Syndrome, and found the best performing method to have a precision / recall / f-measure of 76.8 / 66.7 / 71.4 when evaluated with 10-fold cross validation.

Latest American and European updates on infantile spasms.

Infantile spasms remain a challenging condition to study and treat, and although they form the commonest epilepsy syndrome with onset in infancy, the challenge is broadened by the wide range of potential underlying causes. The field of study remains dynamic, with debates relating to case definitions and organising structures for classification of seizures and epilepsies in general, and a newly proposed genetic and biologic classification specifically for infantile spasms. There have been recent consensus statements, a Delphi process eliciting prioritised quality-of-care indicators, systematic reviews of treatment, and a survey of clinical practice in the USA. There is increasing evidence that longer duration of spasms is associated with poorer neurodevelopmental outcomes. It has taken many years to develop an animal model that reasonably represents infantile spasms, but there are now several animal models, and they are leading to innovative and valuable studies that suggest novel treatments.

Genetic testing of epileptic encephalopathies of infancy: an approach.

The epileptic encephalopathies of infancy are a group of disorders characterized by intractable seizures, persistent abnormality of cortical function documented on EEG, and consequently impaired neuro-developmental outcomes. The etiologies vary and include; structural brain malformations, acquired brain insults, and inborn errors of metabolism in the majority of the affected patients. In a proportion of these cases no obvious etiology is identifiable on investigation. Recent advances in molecular diagnostics have led to the discovery of a number of gene defects that may be causal in many epileptic encephalopathies. Identification of the causative mutation is important for prognostic and genetic counseling, and may also carry treatment implications. The recently described genes include; Cyclin-Dependent Kinase-Like 5 gene (CDKL5), Protocadherin 19 (PCDH19), Sodium channel neuronal type 1a subunit gene (SCN1A), Aristaless-Related Homeobox Gene (ARX), and Syntaxin binding protein 1 gene (STXBP1), amongst others. Distinct electro-clinical syndromes are increasingly being identified amongst patients carrying the various mutations. In this review, we outline the approach to clinical evaluation and genetic testing of epileptic encephalopathies in infancy.

Pediatric focal epilepsy syndromes.

Benign epilepsy with centrotemporal spikes, early-onset childhood occipital epilepsy (Panayiotopoulos syndrome [PS]) and late-onset childhood occipital epilepsy (Gastaut type [LOCE-G]) are the principal pediatric focal epilepsy syndromes. They share major common characteristics: the appearance and resolution of electroclinical features are age related, there is a strong genetic predisposition, the clinical course is often mild with infrequent and easy to control seizures, interictal epileptiform activity is disproportionately abundant when compared with the clinical correlate, and tends to potentiate and generalize during sleep. In this review, we outline the relevant pathophysiology underlying this electroclinical spectrum. Then, the initial description of individual syndromes is followed by a summary of overlapping features and intermediate presentations that question the boundaries between these entities and provide the basis for the concept of a childhood seizure susceptibility syndrome. Additionally, we outline the main features of the related epileptic encephalopathies. An outlook on potential future lines of research completes this review.

Epileptic encephalopathies in infants and children.

The term epileptic encephalopathy is used to describe diffuse brain dysfunction that is caused, at least in part, by some aspect of epilepsy. Early-infantile epileptic encephalopathy (EIEE), West syndrome, late infantile epileptic encephalopathy, and Lennox-Gastaut are four epilepsy syndromes. These epilepsies are also among the most severe with dire consequences including intractable seizures and severe cognitive dysfunction. These epilepsies share several important characteristics: diverse causes; severe and frequent seizures; diffusely abnormal background activity on electroencephalograms that is often profound; medical intractability; and severe consequences for a normal development. Ohtahara proposed that these epilepsies exist on an electroclinical spectrum and that the clinical and electroencephalogram features are dependent on the maturation of the nervous system. One can now add Late Infantile Epileptogenic Encephalopathy (LIEE) or epilepsy with late-onset of epileptic spasms. Recently, similar gene mutations have been found in several different epilepsy syndromes, reinforcing the notion that these epilepsies are not likely to be distinguished based on cause alone. Recognition and accurate classification of these severe epilepsies is important as the first step toward improving treatment and outcomes.

Estudio clínico-genético de pacientes cubanos con síndrome de West / Clinical and genetic studies in Cuban patients suffering from West syndrome

El síndrome de West constituye una encefalopatía epiléptica asociada a una amplia diversidad de factores causales, cuyas bases genéticas hasta el momento no se han estudiado en Cuba. Con el objetivo de describir las principales características clínicas y genéticas del trastorno, se realizó un estudio descriptivo, transversal en los pacientes con el síndrome de West, atendidos en dos hospitales pediátricos de La Habana desde enero de 2005 a diciembre del año 2009. Predominaron los pacientes masculinos. Inicialmente los casos sintomáticos representaron solo el 53,5 por ciento del total. Se identificó la historia familiar positiva de epilepsia en el 51,92 por ciento y hubo una recurrencia del diagnóstico de síndrome West en tres familias; lo que orienta hacia la participación del componente genético en el desarrollo de este síndrome epiléptico. El 82,69 por ciento presentó hallazgos positivos al examen físico, de ellos, el 11,63 por ciento mostró anomalías cromosómicas. Las pruebas metabólicas aportaron diagnóstico en el 17,39 por ciento de los casos con antecedentes familiares positivos y/o defectos congénitos. Finalmente se modificó la frecuencia de clasificación del síndrome epiléptico concluyendo el estudio con un 78,85 por ciento de casos sintomáticos lo que apoya la utilidad del enfoque genético en la evaluación de los pacientes con síndrome de West(AU)

West Syndrome, which is classified as an epileptic encephalopathy, is associated with an ample variety of etiological factors. Up to this moment, the molecular bases of this entity have not been studied in Cuba. A cross-sectional, descriptive study of West Syndrome was conducted with the purpose of describing the main clinical and genetic characteristics of this syndrome. It included the patients diagnosed in two pediatric hospitals in Havana between January 2005 and December 2009. The study showed a high prevalence of male patients. Initially, symptomatic cases represented only 53,85 per cent of the sample. A positive family history of epilepsy was detected in 51,92 per cent of the cases and recurrence of the disease was identified in three of all families included in the study. These two results pointed to a strong genetic component in association with the development of West Syndrome. The 82,69 per cent was found to have positive physical examination findings; among them 11,63 per cent presented chromosomal anomalies. Metabolic studies confirmed 17,39 per cent of the cases with family history and/or congenital defects. At the end, the frequency of classification for the epileptic syndrome was modified to conclude the study with a 78,85 per cent out of the symptomatic cases. Results corroborate the importance of a genetic assessment in the evaluation and diagnosis of patients with suspected West Syndrome(AU)

Genetic and biologic classification of infantile spasms.

Infantile spasms constitute an age-dependent epilepsy, highly associated with cognitive impairment, autism, and movement disorders. Previous classification systems focused on a distinction between symptomatic and cryptogenic etiologies, and have not kept pace with recent discoveries of mutations in genes in key pathways of central nervous system development in patients with infantile spasms. Children with certain genetic syndromes are much likelier to manifest infantile spasms, and we review the literature to propose a genetic classification of these disorders. Children demonstrating genetic associations with infantile spasms also manifest phenotypes beyond epilepsy that may be explained by recent advances in the understanding of underlying biological mechanisms. Therefore we propose a biologic classification of genes highly associated with infantile spasms, and articulate models for infantile spasms pathogenesis based on those data. The two best described pathways of pathogenesis involve abnormalities in the gene regulatory network of gamma-aminobutyric acidergic forebrain development and abnormalities in molecules expressed at the synapse. These genetic and biologic classifications are flexible, and they should encourage much needed progress in syndrome recognition, clinical genetic testing, and the development of new therapies targeting specific pathways of pathogenesis.

Electroencephalography features of primary epileptogenic regions in surgically treated MRI-negative infantile spasms.

OBJECTIVE: To evaluate the surgical outcome for intractable, MRI-negative infantile spasms (IS), and to identify diagnostic targets in the focal epileptogenic area by methods other than MRI. METHODS: We retrospectively studied 9 patients who had had surgery for intractable IS, and whose lesions did not appear on MRI. We analyzed video/electroencephalography (EEG), single photon emission computed tomography (SPECT) and positron emission tomography (PET) findings and their surgical outcomes. In 7 patients who were seizure free after surgery, we analyzed the EEG parameters for characteristics expected in the primary epileptogenic region. RESULTS: All patients underwent resective surgery including frontal lobectomy and multilobar resection. Seven patients showed an Engel class I outcome, and 2 patients showed a class III outcome. Interictal SPECT results showed 66.7% concordance for the hemisphere affected (lateralization), and 55.6% for lesion location (localization). Ictal SPECT showed 71.4% concordance for lateralization and localization. PET showed 66.7% concordance for lateralization, and 55.6% for localization. EEG parameters, including localized paroxysmal fast activities, spindle-shaped fast activities, repetitive or rhythmic sharp/spike wave discharges, and subclinical seizures showed highly localized specificity, and may serve to identify the epileptogenic lesion. CONCLUSION: Surgical treatment of MRI-negative IS should be justified using a combination of diagnostic methods.

West syndrome with periventricular leukomalacia: ten-year clinical study.

The aim of the study was to evaluate magnetic resonance imaging (MRI) findings in infants with periventricular leukomalacia (PVL) and West syndrome (WS) and determine the neurodevelopmental outcome in children with West syndrome and PVL. Ultrasound and brain MRI were performed in 37 infants with recognized PVL. PVL was categorized according to De Vries, whereas West syndrome was categorized according to International League Against Epilepsy 1989. West syndrome in our patients developed during the first 2 years of life. The most common interictal abnormality was hypsarrhythmia. All, except two patients had delayed development and various degrees of mental retardation. The most characteristic neuroimaging findings were major reduction in cerebral cortical gray matter volume, reduction in the volume of brain myelin, and delayed myelination. These findings may explain the anatomical association between the West syndrome onset and PVL and intellectual and cognitive deficit in premature infants with PVL.

Is hypsarrhythmia a form of non-convulsive status epilepticus in infants?

BACKGROUND: Hypsarrhythmia is generally associated with infantile spasms, a combination referred to as West syndrome. It is debatable whether hypsarrhythmia is usefully regarded as a form of non-convulsive status epilepticus (NCSE). SUMMARY POINTS: The earliest English language description of hypsarrhythmia reported an almost continuous EEG pattern, although later studies showed a degree of state dependence. Its principal features are very high amplitude and irregular slow waves with superimposed multifocal epileptiform discharges. Paroxysms of spasms are clearly overt seizure events, and there are variable EEG patterns associated with this ictus. There remains a debate about the definitional boundaries of hypsarrhythmia, and about the defining characteristics of NCSE. There is evidence that hypsarrhythmia is an age-dependent EEG pattern that evolves, sometimes independently of clinical features. Frequently, hypsarrhythmia is associated with delay in or regression of neuro-developmental skills, and recent studies have reported that a longer lead time to diagnosis and effective treatment is associated with poorer long-term neuro-developmental outcomes. Recent consensus definitions and classifications of NCSE have suggested boundaries that permit inclusion of hypsarrhythmia as an EEG pattern of NCSE. In practice, adopting the idea that hypsarrhythmia is a form of NCSE might lead to earlier appropriate investigation of infants with subtle developmental delay or regression, hence avoiding treatment delays and potentially preserving developmental potential.

Analysis of single nucleotide polymorphisms in the melanocortin-4 receptor promoter in infantile spasms.

OBJECTIVES: Infantile spasms is a severe epileptic encephalopathy of infancy. ACTH that ameliorates infantile spasms might act through activating the central melanocortin-4 receptor (MC4R) to suppress excessive production of corticotrophin-releasing hormone (CRH). This study aimed to elucidate an association between the genetic variants of the MC4R gene and infantile spasms. METHODS: The study population comprised 96 patients with infantile spasms and 118 controls. All subjects were screened for variations in the promoter and coding region of the MC4R gene using a direct sequencing method. ATCH responses in patients carrying different genotypes were also assessed. RESULTS: The distributions of genotypes and alleles of rs11872992 in the MC4R promoter were significantly different between cases and controls. The frequencies of heterozygous carriers (TC genotype) were significantly lower in cases (10%) than in controls (27%) (p=0.003). The distributions of rs11872992 TC and CC genotypes were significantly different between ACTH responders and non-responders (OR, 0.14; 95% C.I, 0.03-0.69; p=0.007). The T-allele carriers (83.3%) had a higher responsiveness to ACTH than non-carriers (41.7%). CONCLUSIONS: The present study shows that genetic variants in the MC4R promoter are associated with the development of infantile spasms. The rs11872992 polymorphism influences ACTH treatment responses in patients with infantile spasms.

Extremely low-dose ACTH step-up protocol for West syndrome: maximum therapeutic effect with minimal side effects.

We studied the effectiveness of our new ACTH treatment strategy for West syndrome (WS), which was based on the results of our previous extremely low-dose ACTH study. The subjects were 31 infants with WS (cryptogenic WS in nine; symptomatic WS in 22). Synthetic ACTH-Z in a dose of 0.005 mg (= 0.2 IU)/kg/day was injected once every morning for at least 2 weeks, up to a maximum of 3 weeks. When this first treatment course achieved full seizure and EEG control, ACTH was tapered to zero over the subsequent 1 or 2 weeks. In the absence of a documented response, the dosage was increased to 0.025 mg (= 1.0 IU)/kg/day for the next 2 weeks (second treatment course). We analyzed the short-term as well as long-term effects, and the incidence of side effects. The first treatment course successfully controlled both spasms and hypsarrhythmia in 17 patients (55%), only spasms in one, and hypsarrhythmia in two. The second treatment course was then introduced in eight of the remaining 14 patients, providing complete suppression of WS in an additional two patients. Regarding the long-term effects, 13 patients (48%), with excellent short-term results and a longer than 1-year follow-up, remained seizure-free. Side effects of a mild degree were seen in 13 patients during ACTH treatment. Our new ACTH step-up method brought 61 and 48% of the patients into short-term and long-term remission, respectively, without significant side effects. The dose of ACTH required to control WS appears to be unexpectedly smaller than the dose we previously used.