MAFs and haplotype frequencies for SNPs in ROR2 gene among parents of Han Chinese NSCL/P patients in China

ObjectiveTo analyze minor allele frequencies(MAFs) and haplotype frequencies for single neucleotide polymorphisms(SNPs) in receptor tyrosine kinase-like orphan receptor 2(ROR2) gene among parents of patients with non-syndromic cleft lip with or without cleft palate(NSCL/P) trios recruited from Shandong province and Wuhan city in China.MethodsMAF and its frequency distribution were analyzed for SNPs in ROR2 gene according to Hardy-Weinberg equilibrium of recruitment site with Haploview program.The difference in relative ratio of MAF was used to identify the MAF difference between two sites.Haplotype blocks and frequencies were analyzed and compared for SNPs of MAF>0.01 and genotyping rate>80%.ResultsAmong 89 non-homogenous SNPs with same minor allele in 101 SNPs genotyped,the proportions for those with different relative ratio less than 20% and equal or greater than 50% were 76.4% and 4.5%,respectively.The four SNPs with different relative ratio of MAF ≥50% were located in the first intron region.Compared with that of Shandong,the 94 non-homogenous SNPs with genotyping call rate >80% formed an independent haplotype block in the first intron region in Wuhan.ConclusionThe SNPs for ROR2 genotyped in Shandong and Wuhan present similar distribution,with the four SNPs with different relative ratios equal or greater than 50% in the two areas and one independent haplotype block locating in the first intron region identified in Wuhan.