Dataset Information

Assessment of genetic variant burden in epilepsy-associated brain lesions.

ABSTRACT: It is challenging to estimate genetic variant burden across different subtypes of epilepsy. Herein, we used a comparative approach to assess the genetic variant burden and genotype-phenotype correlations in four most common brain lesions in patients with drug-resistant focal epilepsy. Targeted sequencing analysis was performed for a panel of 161 genes with a mean coverage of >400×. Lesional tissue was histopathologically reviewed and dissected from hippocampal sclerosis (n?=?15), ganglioglioma (n?=?16), dysembryoplastic neuroepithelial tumors (n?=?8), and focal cortical dysplasia type II (n?=?15). Peripheral blood (n?=?12) or surgical tissue samples histopathologically classified as lesion-free (n?=?42) were available for comparison. Variants were classified as pathogenic or likely pathogenic according to American College of Medical Genetics and Genomics guidelines. Overall, we identified pathogenic and likely pathogenic variants in 25.9% of patients with a mean coverage of 383×. The highest number of pathogenic/likely pathogenic variants was observed in patients with ganglioglioma (43.75%; all somatic) and dysembryoplastic neuroepithelial tumors (37.5%; all somatic), and in 20% of cases with focal cortical dysplasia type II (13.33% somatic, 6.67% germline). Pathogenic/likely pathogenic positive genes were disorder specific and BRAF V600E the only recurrent pathogenic variant. This study represents a reference for the genetic variant burden across the four most common lesion entities in patients with drug-resistant focal epilepsy. The observed large variability in variant burden by epileptic lesion type calls for whole exome sequencing of histopathologically well-characterized tissue in a diagnostic setting and in research to discover novel disease-associated genes.

SUBMITTER: Niestroj LM

PROVIDER: S-EPMC6871528 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

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Assessment of genetic variant burden in epilepsy-associated brain lesions.

Niestroj Lisa-Marie LM May Patrick P Artomov Mykyta M Kobow Katja K Coras Roland R Pérez-Palma Eduardo E Altmüller Janine J Thiele Holger H Nürnberg Peter P Leu Costin C Palotie Aarno A Daly Mark J MJ Klein Karl Martin KM Beschorner Rudi R Weber Yvonne G YG Blümcke Ingmar I Lal Dennis D

European journal of human genetics : EJHG 20190729 11

It is challenging to estimate genetic variant burden across different subtypes of epilepsy. Herein, we used a comparative approach to assess the genetic variant burden and genotype-phenotype correlations in four most common brain lesions in patients with drug-resistant focal epilepsy. Targeted sequencing analysis was performed for a panel of 161 genes with a mean coverage of >400×. Lesional tissue was histopathologically reviewed and dissected from hippocampal sclerosis (n = 15), ganglioglioma ( ...[more]

PMID: 31358956

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Project description:BackgroundSudden unexpected death in children is a tragic event. Understanding the genetics of sudden death in the young (SDY) enables family counseling and cascade screening. The objective of this study was to characterize genetic variation in an SDY cohort using whole genome sequencing.MethodsThe SDY Case Registry is a National Institutes of Health/Centers for Disease Control and Prevention surveillance effort to discern the prevalence, causes, and risk factors for SDY. The SDY Case Registry prospectively collected clinical data and DNA biospecimens from SDY cases < 20 years of age. SDY cases were collected from medical examiner and coroner offices spanning 13 US jurisdictions from 2015 to 2019. The cohort included 211 children (median age 0.33 year; range 0-20 years), determined to have died suddenly and unexpectedly and from whom DNA biospecimens for DNA extractions and next-of-kin consent were ascertained. A control cohort consisted of 211 randomly sampled, sex- and ancestry-matched individuals from the 1000 Genomes Project. Genetic variation was evaluated in epilepsy, cardiomyopathy, and arrhythmia genes in the SDY and control cohorts. American College of Medical Genetics/Genomics guidelines were used to classify variants as pathogenic or likely pathogenic. Additionally, pathogenic and likely pathogenic genetic variation was identified using a Bayesian-based artificial intelligence (AI) tool.ResultsThe SDY cohort was 43% European, 29% African, 3% Asian, 16% Hispanic, and 9% with mixed ancestries and 39% female. Six percent of the cohort was found to harbor a pathogenic or likely pathogenic genetic variant in an epilepsy, cardiomyopathy, or arrhythmia gene. The genomes of SDY cases, but not controls, were enriched for rare, potentially damaging variants in epilepsy, cardiomyopathy, and arrhythmia-related genes. A greater number of rare epilepsy genetic variants correlated with younger age at death.ConclusionsWhile damaging cardiomyopathy and arrhythmia genes are recognized contributors to SDY, we also observed an enrichment in epilepsy-related genes in the SDY cohort and a correlation between rare epilepsy variation and younger age at death. These findings emphasize the importance of considering epilepsy genes when evaluating SDY.

Project description:BackgroundPrevious genetic research in pediatric cardiomyopathy (CM) has focused on pathogenic variants for diagnostic purposes, with limited data evaluating genotype-outcome correlations. We explored whether greater genetic variant burden (pathogenic or variants of unknown significance, VUS) correlates with worse outcomes.MethodsChildren with dilated CM (DCM) and hypertrophic CM (HCM) who underwent multigene testing between 2010 and 2018 were included. Composite endpoint was freedom from major adverse cardiac event (MACE).ResultsThree hundred and thirty-eight subjects were included [49% DCM, median age 5.7 (interquartile range (IQR) 0.2-13.4) years, 51% HCM, median age 3.0 (IQR 0.1-12.5) years]. Pathogenic variants alone were not associated with MACE in either cohort (DCM p = 0.44; HCM p = 0.46). In DCM, VUS alone [odds ratio (OR) 4.0, 95% confidence interval (CI) 1.9-8.3] and in addition to pathogenic variants (OR 5.2, 95% CI 1.7-15.9) was associated with MACE. The presence of VUS alone or in addition to pathogenic variants were not associated with MACE in HCM (p = 0.22 and p = 0.33, respectively).ConclusionIncreased genetic variant burden (pathogenic variants and VUS) is associated with worse clinical outcomes in DCM but not HCM. Genomic variants that influence DCM onset may be distinct from those driving disease progression, highlighting the potential value of universal genetic testing to improve risk stratification.ImpactIn pediatric CM, inconsistent findings historically have been shown between genotype and phenotype severity when only pathogenic variants have been considered. Increased genetic variant burden (including both pathogenic variants and VUS) is associated with worse clinical outcomes in DCM but not HCM. Genomic variants that influence CM onset may be distinct from those variants that drive disease progression and influence outcomes in phenotype-positive individuals. Incorporation of both pathogenic variants and VUS may improve risk stratification models in pediatric CM.

Project description:BackgroundSince the 1990s, evidence has accumulated of an increased prevalence of epilepsy in onchocerciasis-endemic areas in Africa as compared to onchocerciasis-free areas. Although the causal relationship between onchocerciasis and epilepsy has yet to be proven, there is likely an association. Here we discuss the need for disease burden estimates of onchocerciasis-associated epilepsy (OAE), provide them, detail how such estimates should be refined, and discuss the socioeconomic impact of OAE, including a cost-estimate for anti-epileptic drugs.Main bodyProviding OAE burden estimates may aid prevention of epilepsy in onchocerciasis- endemic areas by inciting and informing collaboration between onchocerciasis control programmes and mental health services. Epilepsy not only massively impacts the health of those affected, but it also carries a high socioeconomic burden for the households and communities involved. We used previously published geospatial estimates of onchocerciasis in Africa and a separately published logistic regression model quantifying the association between onchocerciasis and epilepsy to estimate the number of OAE cases. We then applied disability weights for epilepsy to quantify the burden in terms of years of life lived with disability (YLD) and estimate the cost of treatment. We estimate that in 2015 roughly 117 000 people were affected by OAE across onchocerciasis-endemic areas previously under the African Programme for Onchocerciases control (APOC) mandate where OAE has ever been reported or suspected, and another 264 000 persons in onchocerciasis-endemic areas where OAE has never been investigated before. The total number of YLDs due to OAE was 39 300 and 88 700 in these areas respectively, based on a weighted mean disability weight of 0.336. The burden of OAE is approximately 13% of the total YLDs attributable to onchocerciasis and 10% of total YLDs attributable to epilepsy. We estimated that by 2015 the total costs of treatment with anti-epileptic drug for OAE cases would have been a minimum of 12.4 million US$.ConclusionsThese estimates suggest a considerable health, social and economic burden of OAE in Africa. The treatment and care for people with epilepsy, especially in hyperendemic onchocerciasis areas with high epilepsy prevalence thus requires more financial and human resources.

Dataset Information

Assessment of genetic variant burden in epilepsy-associated brain lesions.

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Assessment of genetic variant burden in epilepsy-associated brain lesions.

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