Phenotype definition in epilepsy

Pathogenic variants of human GABRA1 gene associated with epilepsy: A computational approach

Critical for brain development, neurodevelopmental and network disorders, the GABRA1 gene encodes for the α1 subunit, an abundantly and developmentally expressed subunit of heteropentameric gamma-aminobutyric acid A receptors (GABAARs) mediating primary inhibition in the brain. Mutations of the GABAAR subunit genes including GABRA1 gene are associated with epilepsy, a group of syndromes, characterized by unprovoked seizures and diagnosed by integrative approach, that involves genetic testing. Despite the diagnostic use of genetic testing, a large fraction of the GABAAR subunit gene variants including the variants of GABRA1 gene is not known in terms of their molecular consequence, a challenge for precision and personalized medicine. Addressing this, one hundred thirty-seven GABRA1 gene variants of unknown clinical significance have been extracted from the ClinVar database and computationally analyzed for pathogenicity. Eight variants (L49H, P59L, W97R, D99G, G152S, V270G, T294R, P305L) are predicted as pathogenic and mapped to the α1 subunit's extracellular domain (ECD), transmembrane domains (TMDs) and extracellular linker. This is followed by the integration with relevant data for cellular pathology and severity of the epilepsy syndromes retrieved from the literature. Our results suggest that the pathogenic variants in the ECD of GABRA1 (L49H, P59L, W97R, D99G, G152S) will probably manifest decreased surface expression and reduced current with mild epilepsy phenotypes while V270G, T294R in the TMDs and P305L in the linker between the second and the third TMDs will likely cause reduced cell current with severe epilepsy phenotypes. The results presented in this study provides insights for clinical genetics and wet lab experimentation.

Translational veterinary epilepsy: A win-win situation for human and veterinary neurology

Epilepsy is a challenging multifactorial disorder with a complex genetic background. Our current understanding of the pathophysiology and treatment of epilepsy has substantially increased due to animal model studies, including canine studies, but additional basic and clinical research is required. Drug-resistant epilepsy is an important problem in both dogs and humans, since seizure freedom is not achieved with the available antiseizure medications. The evaluation and exploration of pharmacological and particularly non-pharmacological therapeutic options need to remain a priority in epilepsy research. Combined efforts and sharing knowledge and expertise between human medical and veterinary neurologists are important for improving the treatment outcomes or even curing epilepsy in dogs. Such interactions could offer an exciting approach to translate the knowledge gained from people and rodents to dogs and vice versa. In this article, a panel of experts discusses the similarities and knowledge gaps in human and animal epileptology, with the aim of establishing a common framework and the basis for future translational epilepsy research.

Chronic Central Vestibulopathies for the Otolaryngologist

Central vestibulopathies involve disorders of the central nervous system that lead to problems with balance, often manifested as dizziness, vertigo, and gait difficulty. Central vestibulopathies can be distinguished from peripheral vestibulopathies with the use of certain tests, including nystagmography and posturography. The neuroanatomy of individuals with central vestibulopathies can reveal structural abnormalities in the posterior cerebrum or cerebellum. Various medications can be used to manage central vestibulopathies, including vestibular migraine.

Sharp decrease in the Laplacian matrix rank of phase-space graphs: a potential biomarker in epilepsy

In this paper, phase space reconstruction from stereo-electroencephalography data of ten patients with focal epilepsy forms a series of graphs. Those obtained graphs reflect the transition characteristics of brain dynamical system from pre-seizure to seizure of epilepsy. Interestingly, it is found that the rank of Laplacian matrix of these graphs has a sharp decrease when a seizure is close to happen, which thus might be viewed as a new potential biomarker in epilepsy. In addition, the reliability of this method is numerically verified with a coupled mass neural model. In particular, our simulation suggests that this potential biomarker can play the roles of predictive effect or delayed awareness, depending on the bias current of the Gaussian noise. These results may give new insights into the seizure detection.

Improving cognitive task in kindled rats by using low frequency stimulation during epileptogenesis

Numerous studies indicate that one of the bad effects of epilepsy is cognitive impairment. In this study we focused on the effect of LFS as a potential anticonvulsant agent, during epileptogenesis on cognitive impairments induced by amygdala kindling in rat. Twenty-one adult rats were divided into 3 groups including control (n = 7), kindled (n = 7), and Kindled+LFS (KLFS) (n = 7). Animals in the kindled group received kindling stimulation in a rapid kindling manner (a 3 s train of 50 Hz monophasic pulses of 1 ms duration, 12 times a day) in amygdala whereas control animals had no stimulation. Four packages of LFS (each package consisting of 200 monophasic square pulses, 0.1 ms pulse duration at 1 Hz) were applied daily after termination of kindling stimulation in KLFS group. Spatial memory of all animals was tested using radial arm maze after termination of stimulation on acquisition trial days and 14 days after the final acquisition trial test. Epileptogenesis process significantly increased working and reference memory error compared to control groups whereas application of LFS immediately after kindling stimulation prevented this impairment in 8 arm radial maze and there was no significant difference between KLS and control groups. Our results indicated that application of LFS during kindling acquisition suppresses memory impairment in epileptogenesis by kindling stimulation.

Understanding Personalized Training Responses: Can Genetic Assessment Help?

Background:

Traditional exercise prescription is based on the assumption that exercise adaptation is predictable and standardised across individuals. However, evidence has emerged in the past two decades demonstrating that large inter-individual variation exists regarding the magnitude and direction of adaption following exercise.

Objective:

The aim of this paper was to discuss the key factors influencing this personalized response to exercise in a narrative review format.

Findings:

Genetic variation contributes significantly to the personalized training response, with specific polymorphisms associated with differences in exercise adaptation. These polymorphisms exist in a number of pathways controlling exercise adaptation. Environmental factors such as nutrition, psycho-emotional response, individual history and training programme design also modify the inter-individual adaptation following training. Within the emerging field of epigenetics, DNA methylation, histone modifications and non-coding RNA allow environmental and lifestyle factors to impact genetic expression. These epigenetic mechanisms are themselves modified by genetic and non-genetic factors, illustrating the complex interplay between variables in determining the adaptive response. Given that genetic factors are such a fundamental modulator of the inter-individual response to exercise, genetic testing may provide a useful and affordable addition to those looking to maximise exercise adaption, including elite athletes. However, there are ethical issues regarding the use of genetic tests, and further work is needed to provide evidence based guidelines for their use.

Conclusion:

There is considerable inter-individual variation in the adaptive response to exercise. Genetic assessments may provide an additional layer of information allowing personalization of training programmes to an individual’s unique biology.

Familial aggregation of focal seizure semiology in the Epilepsy Phenome/Genome Project

OBJECTIVE

To improve phenotype definition in genetic studies of epilepsy, we assessed the familial aggregation of focal seizure types and of specific seizure symptoms within the focal epilepsies in families from the Epilepsy Phenome/Genome Project.

METHODS

We studied 302 individuals with nonacquired focal epilepsy from 149 families. Familial aggregation was assessed by logistic regression analysis of relatives' traits (dependent variable) by probands' traits (independent variable), estimating the odds ratio for each symptom in a relative given presence vs absence of the symptom in the proband.

RESULTS

In families containing multiple individuals with nonacquired focal epilepsy, we found significant evidence for familial aggregation of ictal motor, autonomic, psychic, and aphasic symptoms. Within these categories, ictal whole body posturing, diaphoresis, dyspnea, fear/anxiety, and déjà vu/jamais vu showed significant familial aggregation. Focal seizure type aggregated as well, including complex partial, simple partial, and secondarily generalized tonic-clonic seizures.

CONCLUSION

Our results provide insight into genotype-phenotype correlation in the nonacquired focal epilepsies and a framework for identifying subgroups of patients likely to share susceptibility genes.

Complex epilepsy phenotype extraction from narrative clinical discharge summaries

Epilepsy is a common serious neurological disorder with a complex set of possible phenotypes ranging from pathologic abnormalities to variations in electroencephalogram. This paper presents a system called Phenotype Exaction in Epilepsy (PEEP) for extracting complex epilepsy phenotypes and their correlated anatomical locations from clinical discharge summaries, a primary data source for this purpose. PEEP generates candidate phenotype and anatomical location pairs by embedding a named entity recognition method, based on the Epilepsy and Seizure Ontology, into the National Library of Medicine's MetaMap program. Such candidate pairs are further processed using a correlation algorithm. The derived phenotypes and correlated locations have been used for cohort identification with an integrated ontology-driven visual query interface. To evaluate the performance of PEEP, 400 de-identified discharge summaries were used for development and an additional 262 were used as test data. PEEP achieved a micro-averaged precision of 0.924, recall of 0.931, and F1-measure of 0.927 for extracting epilepsy phenotypes. The performance on the extraction of correlated phenotypes and anatomical locations shows a micro-averaged F1-measure of 0.856 (Precision: 0.852, Recall: 0.859). The evaluation demonstrates that PEEP is an effective approach to extracting complex epilepsy phenotypes for cohort identification.

Familial risk of epilepsy: a population-based study

Almost all previous studies of familial risk of epilepsy have had potentially serious methodological limitations. Our goal was to address these limitations and provide more rigorous estimates of familial risk in a population-based study. We used the unique resources of the Rochester Epidemiology Project to identify all 660 Rochester, Minnesota residents born in 1920 or later with incidence of epilepsy from 1935-94 (probands) and their 2439 first-degree relatives who resided in Olmsted County. We assessed incidence of epilepsy in relatives by comprehensive review of the relatives' medical records, and estimated age-specific cumulative incidence and standardized incidence ratios for epilepsy in relatives compared with the general population, according to proband and relative characteristics. Among relatives of all probands, cumulative incidence of epilepsy to age 40 was 4.7%, and risk was increased 3.3-fold (95% confidence interval 2.75-5.99) compared with population incidence. Risk was increased to the greatest extent in relatives of probands with idiopathic generalized epilepsies (standardized incidence ratio 6.0) and epilepsies associated with intellectual or motor disability presumed present from birth, which we denoted 'prenatal/developmental cause' (standardized incidence ratio 4.3). Among relatives of probands with epilepsy without identified cause (including epilepsies classified as 'idiopathic' or 'unknown cause'), risk was significantly increased for epilepsy of prenatal/developmental cause (standardized incidence ratio 4.1). Similarly, among relatives of probands with prenatal/developmental cause, risk was significantly increased for epilepsies without identified cause (standardized incidence ratio 3.8). In relatives of probands with generalized epilepsy, standardized incidence ratios were 8.3 (95% confidence interval 2.93-15.31) for generalized epilepsy and 2.5 (95% confidence interval 0.92-4.00) for focal epilepsy. In relatives of probands with focal epilepsy, standardized incidence ratios were 1.0 (95% confidence interval 0.00-2.19) for generalized epilepsy and 2.6 (95% confidence interval 1.19-4.26) for focal epilepsy. Epilepsy incidence was greater in offspring of female probands than in offspring of male probands, and this maternal effect was restricted to offspring of probands with focal epilepsy. The results suggest that risks for epilepsies of unknown and prenatal/developmental cause may be influenced by shared genetic mechanisms. They also suggest that some of the genetic influences on generalized and focal epilepsies are distinct. However, the similar increase in risk for focal epilepsy among relatives of probands with either generalized (2.5-fold) or focal epilepsy (2.6-fold) may reflect some coexisting shared genetic influences.

Recruitment for genetic studies of epilepsy

Virtually nothing has been published about recruitment of adults with sporadic temporal lobe epilepsy (TLE) for genetic studies. We examined eligibility, recruitment, participation rates, and reasons for exclusion in a genetic study of TLE. Participants with non-acquired TLE with onset ≤35 were recruited through review of records and screening of incoming patients at Columbia University Medical Center (CUMC). Eligible patients were asked to participate in an interview about seizures and give a blood sample for DNA extraction. Medical records were sought for each participant. Of 2974 patients screened 252 (8.5%) were eligible, and 40 (15.9% of eligible) participated. Leading reasons for ineligibility included an antecedent cause of epilepsy, syndrome other than TLE, and seizure onset after age 35. Those declining participation cited concerns about confidentiality, lack of compensation, and fear of phlebotomy. Although TLE is common and patients were recruited from a major surgical epilepsy center, a small proportion of potential participants participated. Large numbers need to be screened to reach the target sample size. Obtaining permission from treating physicians to contact their patients directly can improve recruitment. Saliva DNA collection, monetary incentives and patient education can improve participation. This information can facilitate study design in epilepsy genetics.

Autism and epilepsy: historical perspective

Autism spectrum disorders (ASD) and epilepsy co-occur in approximately 30% of individuals with either ASD or epilepsy. While there is no single unifying ASD-epilepsy phenotype, understanding potential commonalities in subgroups of children with an ASD-epilepsy phenotype will help us disentangle the pathophysiology of both ASD and epilepsy. Throughout this brief historical perspective we selectively review critical trends in ASD-epilepsy research and highlight challenges to clinical and research efforts including terminology, heterogeneity of both ASD and epilepsy, and lack of careful characterization of children affected with both ASD and epilepsy. These complex issues continue to burden research on the diagnosis, neurobiology and management of children with ASD and epilepsy. A key concept that has emerged during the past 40 years is the strong association between intellectual disability and a higher prevalence of epilepsy in individuals with ASD. In addition, the two peaks of seizure onset, one in early childhood and one in adolescence and continuing through adulthood may be unique to individuals with ASD. The overlap of language and autistic regression to epilepsy, EEG epileptiform activity, sleep, and to epileptic encephalopathies such as Landau-Kleffner syndrome continue to be controversial areas of research and of clinical interest. An emerging consensus is that shared developmental genetic, molecular and pathophysiological mechanisms exist and account for the common co-occurrence of ASD and epilepsy.

Variable selection in canonical discriminant analysis for family studies

In family studies, canonical discriminant analysis can be used to find linear combinations of phenotypes that exhibit high ratios of between-family to within-family variabilities. But with large numbers of phenotypes, canonical discriminant analysis may overfit. To estimate the predicted ratios associated with the coefficients obtained from canonical discriminant analysis, two methods are developed; one is based on bias correction and the other based on cross-validation. Because the cross-validation is computationally intensive, an approximation to the cross-validation is also developed. Furthermore, these methods can be applied to perform variable selection in canonical discriminant analysis. The proposed methods are illustrated with simulation studies and applications to two real examples.

Definition of phenotype

Definition of the phenotype is crucial in designing any genetic study, especially an association study, intended to detect the disease predisposing genes. In this chapter, we review the different types of phenotypes such as discrete or continuous and discuss the issues impacting on the phenotype definition related to study design, specifically, the impact of diagnostic error (misclassification) in case-control studies and measurement error in continuous traits. We show that the power of a study depends heavily on the phenotype measured and that misclassification or measurement error can dramatically reduce the power. We also suggest some possible responses to these challenges.