Abstracts

Rationale: The developmental and epileptic encephalopathies (DEEs) are a group of severe disorders characterized by developmental delay and intractable seizures. Advances in genomic testing technology have accelerated the discovery of genetic causes of DEEs; in the clinical setting, a genetic diagnosis can now be made in up to 40% of patients. However, more than 50% of patients with DEEs remain without a genetic diagnosis despite state-of-the-art genetic testing. Methylation represents an epigenetic modification of DNA that does not change the underlying DNA sequence but can impact gene expression. We hypothesize that a subset of DEEs, where the cause remains unknown using conventional sequence-based analysis, harbors rare DNA methylation abnormalities that affect gene expression and cause DEE. We predict that pathogenic aberrant methylation will be due to an underlying DNA defect. Methods: We are using Illumina Infinium MethylationEPIC Kit in 400 probands to perform methylation chip analysis and identify differentially methylated regions (DMRs) compared to controls. Bioconductor tools are used for DMR analysis using a sliding window approach to identify rare regions with extreme methylation. We will perform validation studies and segregation analysis to determine inheritance, prioritizing DMRs that occurred de novo. For de novo DMRs, we will perform follow-up studies including regional or genome sequence analysis, repeat analysis and copy number studies to identify underlying DNA defects, prioritizing DMRs near known DEE genes. Results: We have phenotyped 400 individuals with DEEs for whom a molecular diagnosis has not been found after sequencing at least 104 DEE genes. We have completed methylation arrays for 96 samples and developed a pipeline to identify outlier individuals with putative DMRs. Analysis and downstream testing are ongoing. Conclusions: Based on studies in a similarly sized cohort of individuals with neurodevelopmental disorders, we predict that 5-10% of unsolved DEEs will be due to rare methylation abnormalities. Though there are rare examples of epilepsy-related disorders due to methylation defects, to our knowledge, this will be the first genome-wide screen for methylation abnormalities in a cohort of individuals with DEE. This study will enhance our understanding of the molecular and genetic mechanisms of epilepsy, improve diagnostics and provide new avenues for therapies for people and families living with DEEs. Funding: NIH grant 2R01NS069605