Exome Sequencing of 963 Chinese Families Identifies Novel Epilepsy Candidate Genes

Epilepsy, a prevalent neurodevelopmental disorder in children, is often accompanied by detrimental psychological consequences and other comorbidities. We performed exome sequencing on 963 patient-parent trios, revealing differences in genetic epidemiology between Chinese and European epilepsy cohorts. The diagnostic yield for known epilepsy genes was 40%. Pathogenic variants were most commonly found in SCN1A, KCNQ2, and DEPDC5. Additionally, we identified 15 novel monogenic epilepsy candidates in at least two patients diagnosed with developmental and epileptic encephalopathy, non-acquired focal epilepsy, or genetic generalized epilepsy, including ADCY2, BCAR3, CDC45, CHRNG, CRTC2, CSMD1, CSMD2, KDM6B, KIF1B, PLEKHM3, PPP4R1, RASGRP2, SGSM2, SYNE1, and ZFHX3. Aside from ADCY2, which was implicated in the GABAergic synapse pathway based on KEGG analysis, these candidates do not belong to known epilepsy pathways. Local field potential recordings in zebrafish and calcium imaging experiments validated associations for 11 of these genes, excluding those unsuitable for functional analyses. Furthermore, we found that CRTC2 overexpression leads to hippocampal neuronal hyperactivity using multi-electrode arrays and electrophysiology. We have documented the first-line medications prescribed for patients harboring variants in the novel candidate genes. This study expands our understanding of the genetic underpinnings of epilepsy and provides opportunities for early diagnosis and personalized medicine approaches. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement The authors thank for participants who donated samples. This work was supported by the National Key Research and Development Program of China (2020YFE0201600 and 2021YFC2500202 to S.F., 2018YFA0801000 to G.P.), National Natural Science Foundation of China (grant No. 31970563 to S.F., grant No. 82101486 to Q.W.), the 111 Project (B13016 to S.F.), and Shanghai Municipal Science and Technology (grant No. 2017SHZDZX01, grant No. 2023SHZDZX02 to S.F. and Y.W., and grant No. 19410741100 to S.F.), the Science and Technology Innovation Plan of Shanghai Science and Technology Commission (22ZR1414000 to G.P.), Shanghai Municipal Science and Technology Major Project (No.2018SHZDZX01 to G.P.), ZJ Lab, Shanghai Center for Brain Science and Brain-Inspired Technology, the Shanghai Fourth People's Hospital affiliated to Tongji University School of Medicine (sykyqd02301 to Q.W.), the Fundamental Research Funds for the Central Universities, the Shanghai Pujiang Program (21PJ1412100 to Q.W.), the Ningxia Hui Autonomous Region Key Research and Development Project (2022BFH02012 to Q.W.), and the Science and Technology Commission of Shanghai Municipality (STCSM) grant (23ZR1467900 to Q.W.). ### 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: The study was approved by the ethics committee of the Children's Hospital of Fudan University, and written informed consent was obtained from all parents or legal guardians according to the Declaration of Helsinki principles. 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, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes Data supporting this study are available from at the National Genomics Data Center (https://ngdc.cncb.ac.cn) with accession number HRA006570. Access to the data is subject to approval and a data sharing agreement due to IRB restrictions.