Genome Wide Association Study Of Benign Childhood Epilepsy With Centrotemporal Spikes And Bone Metabolism In Pediatric Patients

Benigh Childhood Epilepsy with Centrotemporal Spikes（BECTS）is the most common form of idiopathic epilepsy in children.The age of onset is between 3 to 14 years old.BECTS accounts for 8 to 23%of epilepsy in children under 16 years old.The incidence in boys is higher than girls.BECTS can lead to varying degrees of neuropsychological damage in children,and can result in sociological and behavior problems after the patiens grow into adults.In addition,children with epilepsy often have different degrees of abnormal bone metabolism which cause growth and development abnormalities.These abnormalities may be due to epilepsy itself or by lifestyle or lack of outdoor activities caused by the disease.Therefore,the pathogenesis of BECTS and the occurrence of abnormal bone metabolism should be taken seriously.BECTS is a complex disease involving multiple susceptibility genes.By now,the Genome-wide association study（GWAS）method has been widely used to explore the pathogenesis of various complex diseases and pharmacogenomics research.GWAS is an important method to explore the genetic mechanism of complex trait.Objective:To explore the genetic susceptibility loci in children with BECTS by GWAS.Then use the bone metabolism index as quantitative trait to explore SNPs associated with bone metabolism in children with BECTS.Finally,the latest SMR technique was used to combine the expression quantity trait loci（eQTL）database and our GWAS results to find out SNPs associated with BECTS and gene expression in brain.Methods:We collected 1800 cases of BECTS from multi centre of children’s Neurology department.The first stage included 997 cases,and the second stage included803 cases.We also collected 7090 controls.The first phase included 3115 controls;the second phase included 3975 controls.The first phase of 997 cases of BECTS and 3115healthy controls were tested by Omni Zhonghua chip.Corexome was used for gene detection at the second stage.After quality control,973 cases and 2926 controls in the first stage and 781 cases and 3779 controls in the second stage were included in further analysis.HRC1.1 and 1000G databases were used for the imputation of the data gained from two stages.Then we combined the data of the two stages for meta analysis to find out the SNPs associated with BECTS.In the second part,the bone metabolic index of 650 BECTS cases was obtained as the quantitative trait,and the whole genome association study was carried out to explore the single nucleotide polymorphisms（SNPs）related to the quantitative traits of bone metabolism index in BECTS children.In the third part,the data of the previous GWAS study were combined with the European brain tissue eQTL database,and the SNP locus related to brain tissue gene expression and BECTS was analyzed by SMR software.Results:The first part:After quality control,973cases of BECTS and 2926 healthy controls were analyzed by Omni Zhonghua chip scanning and genome-wide association analysis,and gene imputation was performed according to HRC1.1 and 1000G databases.We did not find significant genome-wide associated loci.781 cases and 3779 healthy subjects were scaned by corexome chip and imputed according to HRC1.1 and 1000G databases.We also did not find significant genome-wide associated loci.After the meta-analysis of the two-stage data,no significant correlation level was found in the whole genome,but we found four SNPs,which were rs609313,rs1948,rs28405640,and rs1561578 had a trend to be associated with BECTS(5×10^-8<P<5×10^-6).In the second part,we used nine bone metabolism index including calcium,phosphorus,magnesium,parathyroid hormone,osteocalcin,type I procollagen amino terminal peptide,C-terminal crosslinking telopeptides of type 1 collagen,vitamin D,alkaline phosphatase as a quantitative trait for genome-wide association analysis,only found that rs1352846 SNP was significant associated with vitamin D metabolism.In the third part,we combined the GWAS data with the European brain tissue eQTL database.We found two positive probes which are t3603436 and t3634656.The result indicates that rs1948 loci or linkage disequilibrium（LD）polymorphism is associated with gene expression and BECTS.Conclusion:We used two kinds of chips to carry out gene scanning and genome-wide association analysis of all the 1800 cases and 7090 controls.After quality control,1754cases and 6705 controls were included in further analysis.Then we imputed the SNPs according to the HRC1.1 and 1000G databases.Because the phenotype of BECTS is strict,the sample is difficult to obtain and the sample size is limited.Although the genome-wide association level is not reached,the four SNPs we found were closely related to neurotransmitters and brain development.Then we used bone metabolism index as quantitive trait to detect SNPs associating with bone metabolism in BECTS patients.Our result suggested rs1352846 SNP might be associated with Vitamin D in children with BECTS.Combining our GWAS data with the European brain tissue eQTL database,we found that rs1948 loci or linkage disequilibrium（LD）polymorphism is associated with gene expression and BECTS.However,due to the lack of published BECTS genome-wide association study data and only the European adult brain tissue eQTL database can be analyzed,the results may still have some limitations.