Analysis Of The Relationship Between EPHA3 Gene Polymorphism And Non-syndromic Cleft Of Lip With Or Without Palate

Objective The aim of this study was to investigate the relationship between SNPs of EPHA3 gene and non-syndromic cleft of lip with or without palate(NSCL/P)by detecting single nucleotide polymorphism of EPHA3 gene through SNa PShot.We also performed bioinformatics analysis of potential functional SNPs and preliminarily analyzed its potential functional significance by online software of SNPinfo and mi RN ASNP.Methods The samples of 180 patients with NSCL/P and 167 normal controls were collected.We detected 5 SNPs of EPHA3 gene(rs7650466,rs1398197,rs17801309,rs1054750 and rs7632427)by SNa PShot technology.To analyze whether the genotype frequencies of different loci were in accordance with the Hardy-Weinberg Equilibrium(HWE)by Plink.And the relationship between the alleles and genotypes of 5 loci and the incidence of NSCL/P were analyzed.We also used Haplo View software for linkage disequilibrium(LD)and haplotype analysis.Bioinformaticsanalysis was performed by SNPinfo and mi RNASNP software.Results The genotype frequencies of the 5 SNPs were in accordance with HWE.LD and haplotype analysis revealed that there is no LD between the 5 loci.They did not constitute haplotypes.The allele frequencies of rs7650466 T in NSCL/P(OR=0.245,95%CI=0.159-0.379,Pχ2=2.803×10-11,Adjusted Pχ2=1.401×10-10)and C L/P(O R=0.205,95%CI=0.126-0.333,Pχ2=9.138×10-12,Adjusted Pχ2=4.569×10-11)groups were statistically different.And rs7650466 T allele was extremely associated with incidence of NSCL/P(OR=0.211,95%CI=0.131-0.338,P=9.763×10-11,Adjusted P=4.881×10-10)and CL/P(OR=0.176,95%CI=0.104-0.297,P=7.234×10-11,Adjusted P=3.617×10-10).We also found rs7650466 T allele had a protective effect.In the logistic regression of dominant inheritance model,the rs7650466 T allele was dominant effect both in NSCL/P(Adjusted P=8.18×10-10)and CL/P(Adjusted P=3.139×10-10).The other 4 SNPs alleles were not statistically significant in each group.And there was no significant difference of the 5 SNPs genotypes in each group.In bioinformatics analysis,we found the potential matching sites of EPHA3 gene(mi R-1255 a,mi R-125a-3p,mi R-143 and mi R-552)by SNPinfo software.In mi RNASNP software analysis,we also found that under normal circumstances,the rs7650466 allele of C was associated with the G allele of the mi R-2052 seed region.When rs7650466 allele of C became T,the binding ability between 3’-UTR of EPHA3 gene and mi R-2052 may be decreased.EPHA3 gene expression levels maybe alter.Conclusions EPHA3 gene polymorphism(rs7650466)is associated with the incidence of NSCL/P in Chinese Han population.And rs7650466 is associated with the incidence of C L/P in stratified analysis,but not with ICP.