Unraveling the role of non-coding rare variants in epilepsy

Importance Despite the use of very large cohorts, the discovery of new variants has leveled off in recent years in epilepsy studies and consequently, most of the heritability is still unexplained. Rare non-coding variants have been largely ignored in studies on epilepsy, although non-coding single nucleotide variants can have a significant impact on gene expression. Objective To determine if rare non-coding deleterious variants are associated with epilepsy. Design This is a case-control study made possible by the CENet cohort. Setting This was initially a multicenter study (families and trios), although the sequencing was processed at the same facility and for the present case-control study, only unrelated individuals were drawn. Participants Patients used in this study are affected either by genetic generalized epilepsy (GGE), non-acquired focal epilepsy (NAFE) or are called ‘mixed’ (phenotype that differs from other affected relatives). Controls are unaffected parents from developmental and epileptic encephalopathy trios. Main Outcomes and Measures To assess the functional impact of non-coding variants, ExPecto, a deep learning algorithm was used. A binomial logistic regression was performed to compare the burden of rare non-coding deleterious variants between cases and controls. Results We had access to WGS from 123 GGE, 112 NAFE and 12 mixed for a total of 247 patients, as well as 377 controls. Rare non-coding highly deleterious variants were associated with GGE (OR 2.74; 95% CI 1.20-6.22), but not with NAFE (OR 0.85; 95% CI 0.27-2.67) or all epilepsy cases (OR 1.54; 95% CI 0.77-3.11) when compared with controls. Conclusion and Relevance In this study we showed that rare non-coding deleterious variants are associated with epilepsy, specifically with GGE. Larger WGS epilepsy cohort will be needed to investigate those effects at a greater resolution. Nevertheless, we demonstrated the importance of studying non-coding regions in epilepsy, a disease where new discoveries are scarce, and a high proportion of the heritability is yet to be explained. Question Are non-coding single nucleotide variants (SNV) associated with epilepsy? Findings In this study we showed that patients with generalized genetic epilepsy (GGE) had significantly more rare non-coding deleterious variants than controls and non-acquired focal epilepsy (NAFE) patients. The study included 247 epilepsy patients and 377 controls who were sequenced for the whole genome. Meaning Rare non-coding SNV are associated with epilepsy, more specifically with GGE. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This study was funded by the Institute for Data Valorization and the Canadian Institutes of Health Research ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Commité d'Éthique à la Recherche of Centre Hospitalier de l'Université de Montréal gave ethical approval for this work I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes Raw whole genome sequences of a subset of the epilepsy patients for which we have appropriate consent have been deposited in the European Genome-phenome Archive, under the accession code EGAS00001002825. The rest of the data are available upon request to the authors.