title: [Analysis of the HapMap data on SNPs in SUMO1 and association study of rs7599810 in trios with non-syndromic cleft lip with or without cleft palate].
abstract: OBJECTIVE
  To analyze the minor allele frequencies (MAFs), haplotype block and haplotype frequencies for single nucleotide polymorphisms (SNPs) in SUMO1 using HapMap data and perform association analysis between SNPs in SUMO1 and non-syndromic cleft lip with or without cleft palate (NSCL/P) using 183 trios recruited from Shandong Province.
  
  
  METHODS
  SNPs with MAF>0.01 and Hardy-Weinberg equilibrium (P>0.01) were identified as qualified SNPs by Haploview. The MAFs of qualified SNPs were analyzed and the relative range ratios of the MAFs were developed to measure the differences in MAFs for common qualified SNPs with mutual minor allele among the samples. Haplotype blocks and haplotype frequencies for common qualified SNPs in four samples were analyzed and compared among the samples. Transmission disequilibrium test (TDT) was carried out to identify the association between rs7599810 and NSCL/P using 183 NSCL/P case-parent trios.
  
  
  RESULTS
  Among the 24 SNPs released by HapMap project, the number of monotonic SNPs was 9 in Han Chinese in Beijing, China (CHB) and Japanese in Tokyo, Japan (JPT) samples, 8 in Utah residents with Northern and Western European ancestry from the CEPH collection (CEU) sample, and 6 in Yoruban in Ibadan, Nigeria (YRI) sample. The 12 common qualified SNPs in the four samples formed one haplotype in each sample. There were 3, 3, 5, and 6 forms of haplotypes in the CHB, JPT, CEU, and YRI samples respectively, and the cumulative frequencies for the 2 most common haplotypes ranged from 0.634 to 0.922. Significant transmission disequilibrium of G allele at rs7599810 from parents to offspring was not shown (χ(2)=0.485, P=0.486, OR=0.898, 95% CI: 0.663-1.021) for rs7599810 in Shandong Han sample.
  
  
  CONCLUSIONS
  SNPs in SUMO1 mainly showed common features in minor alleles, MAFs and haplotype blocks among CHB, JPT and CEU samples, but unique features in YRI compared with those for the other three samples. Although no association was established between the markers in SUMO1 and NSCL/P using data from Shandong Han population, our analysis suggests further studies are warranted.
authors.affiliation: Department of Epidemiology and Biostatistics, Peking University School of Public Health, Beijing 100191, China.
authors.forename: Qing
authors.initials: Q
authors.lastname: Yue
authors.affiliation: Department of Epidemiology and Biostatistics, Peking University School of Public Health, Beijing 100191, China.
authors.forename: Hong
authors.initials: H
authors.lastname: Wang
authors.affiliation: Department of Biomedical Engineering, Xi'an Jiaotong University, Xi'an 710049, China.
authors.forename: Bo
authors.initials: B
authors.lastname: Zhang
authors.affiliation: Department of Medical Records and Statistics, Beijing Jishuitan Hospital, Beijing 100035, China.
authors.forename: Kai-ping
authors.initials: KP
authors.lastname: Zhao
mesh_terms: D000483:Alleles; D044466:Asian People; D002681:China; D002971:Cleft Lip / Q000235:genetics*; D002972:Cleft Palate / Q000235:genetics*; D005787:Gene Frequency; D056726:Genetic Association Studies; D060148:HapMap Project; D006239:Haplotypes; D006801:Humans; D020641:Polymorphism, Single Nucleotide; D025842:SUMO-1 Protein / Q000235:genetics*
chemical_list: D025842:SUMO-1 Protein; C495501:SUMO1 protein, human