Identification of Susceptibility Variants to BECTS in Chinese Han Population

Benign Childhood Epilepsy with Centro-temporal Spikes (BECTS) is the most common form of idiopathic epilepsy in children. To explore the genetic susceptibility loci in children with BECTS, we conducted 2stage genome-wide association study (GWAS) in over 1,800 Chinese Han patients with BECTS, and 7,090 healthy controls. We combined the datasets of the two stages by meta-analysis to identify the SNPs associated to BECTS. Significant common variant heritability of BECTS was observed. Heritability in the combined phase 1 and 2 datasets was > 10% even for assumed prevalence as low as 0.00025 on the liability scale. Twelve loci achieved suggestive evidence of association (5x10-8 < P < 10-5). In addition, the intersection between the GWAS findings and gene expression in brain tissue was analyzed by Summary-data-based Mendelian Randomization (SMR). We found association of t3603436 transcripts in CHRNA5 gene with SNP rs1948, which is suggestively associated with BECTS (Peqtl = 2.10x10-12, Psmr = 7.9x10-5), suggesting that rs1948 is significantly associated with BECTS through effects on expression of CHRNA5 in brain tissue. These findings suggest involvements of KALRN and CHRNA5-A3-B4 cluster in BECTS, give new directions to biological understanding of pediatric epilepsy, and opens avenues for investigation of prognostic factors and possible prevention of epilepsy in children. Funding: The study was funded by the National Key R&D Program of China (No. 2016YFC1000707), the National Natural Science Foundation of China (No. 81771389 and No. 81471329), and China Ministry of Science and technology (973 Program of China 2014CB541800). The study was also funded by Australian Research Council grant LPl10200926, and by the Queensland Premier’s Fellowship for Science (awarded to MAB, 2013). MAB was funded by Electronic copy available at: https://ssrn.com/abstract=3384897 a National Health and Medical Research Council Senior Principal Research Fellowship (APP1024879). Declaration of Interest: The authors have no conflict of interest. Ethical Approval: Written informed consent was obtained from all the parents or guardians, and the study was approved by the relevant ethics committees of the hospitals and institutions involved.