1. Identification of epilepsy related pathways using genome-wide DNA methylation measures: A trio-based approach
- Author
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Ugur Ozbek, Sibel Aylin Ugur Iseri, Nerses Bebek, Ozkan Ozdemir, Osman Ugur Sezerman, Betül Baykan, Ece Egemen, and Acibadem University Dspace
- Subjects
Male ,0301 basic medicine ,Inheritance Patterns ,Genome-wide association study ,Biochemistry ,Genome ,Epigenesis, Genetic ,0302 clinical medicine ,Cell Signaling ,Medicine and Health Sciences ,Child ,DNA methylation ,Multidisciplinary ,Chemical Reactions ,Electroencephalography ,Gene Pool ,Methylation ,Chromatin ,Nucleic acids ,Chemistry ,Phenotype ,Neurology ,Physical Sciences ,Medicine ,Epigenetics ,Epilepsy, Generalized ,Female ,DNA modification ,Genomic Signal Processing ,Chromatin modification ,Metabolic Networks and Pathways ,Research Article ,Chromosome biology ,Signal Transduction ,Adult ,Cell biology ,Genotype ,Science ,Locus (genetics) ,Computational biology ,Biology ,Nuclear Family ,03 medical and health sciences ,Genetics ,Humans ,Genetic Predisposition to Disease ,Nerve Growth Factors ,Gene ,Evolutionary Biology ,Epilepsy ,Biology and life sciences ,Population Biology ,Genome, Human ,Gene Expression Profiling ,Human Genetics ,DNA ,Gene expression profiling ,030104 developmental biology ,Genetic Loci ,Gene expression ,Population Genetics ,030217 neurology & neurosurgery ,Genome-Wide Association Study - Abstract
Genetic generalized epilepsies (GGE) are genetically determined, as their name implies and they are clinically characterized by generalized seizures involving both sides of the brain in the absence of detectable brain lesions or other known causes. GGEs are yet complex and are influenced by many different genetic and environmental factors. Methylation specific epigenetic marks are one of the players of the complex epileptogenesis scenario leading to GGE. In this study, we have set out to perform genome-wide methylation profiling to analyze GGE trios each consisting of an affected parent-offspring couple along with an unaffected parent. We have developed a novel scoring scheme within trios to categorize each locus analyzed as hypo or hypermethylated. This stringent approach classified differentially methylated genes in each trio and helped us to produce trio specific and pooled gene lists with inherited and aberrant methylation levels. In order to analyze the methylation differences from a boarder perspective, we performed enrichment analysis with these lists using the PANOGA software. This collective effort has led us to detect pathways associated with the GGE phenotype, including the neurotrophin signaling pathway. We have demonstrated a trio based approach to genome-wide DNA methylation analysis that identified individual and possibly minor changes in methylation marks that could be involved in epileptogenesis leading to GGE.
- Published
- 2019
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