SUMO1基因单核苷酸多态性分析及rs7599810多态性与非综合征型唇/腭裂的关联研究

摘要/Abstract

摘要： 目的：对HapMap数据库四个不同人群SUMO1基因的单核苷酸多态性(single nucleotide polymorphisms，SNPs)进行分析和比较，并探讨山东汉族人群rs7599810位点多态性与非综合征型唇/腭裂（non-syndromic cleft lip with or without cleft palate，NSCL/P）的关联。方法：首先用Haploview软件确定HapMap四个人群，分别为：中国北京汉族（Han Chinese in Beijing，China，CHB）、日本东京（Japanese in Tokyo，Japan，JPT）、西北欧后裔（Utah residents with Northern and Western European ancestry from the CEPH collection，CEU）和尼日利亚约鲁巴（Yoruban in Ibadan，Nigeria，YRI），四个人群中SUMO1基因SNPs中最小等位基因频率(minor allele frequency， MAF)>0.01且符合HardyWeinberg平衡的SNPs为合格SNPs，用MAF全距相对比指标衡量人群间最小等位基因相同的共有合格SNPs的MAFs差异；然后对四个人群共有合格SNPs进行单体域和单体型的分析及比较；最后对本研究所测该基因中的rs7599810在山东地区183个NSCL/P核心家系中进行传递不平衡检验（transmission/disequilibrium test，TDT）。结果：HapMap提供的24个SNPs中，纯合SNPs在CHB和JPT均为9个，在CEU为8个，在YRI为6个，四个人群共有合格SNPs为12个。这些SNPs在四个人群均形成了一个单体域，其中CHB、JPT、CEU人群的单体域包括全部12个SNPs，YRI人群的单体域包括第3~11个SNPs。CHB、JPT、CEU和YRI人群的单体域分别确定了3、3、5、6种单体型，且均以前两种单体型为主，频率为0.634~0.922。TDT结果显示SUMO1基因 rs7599810多态性与NSCL/P未见统计学关联(χ²=0.485，P=0.486，OR=0.898，95% CI：0.663~1.021）。结论：CHB、JPT和CEU人群SUMO1基因SNPs在等位基因组成、MAF、单体域及单体型构成等方面以共性特征为主，与之相比，YRI人群SNPs表现出较大的独特性。山东汉族人群中SUMO1基因rs7599810多态性与NSCL/P未见统计学关联。

关键词: SUMO1, 基因关联研究, 多态性, 单核苷酸, 唇裂, 腭裂

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 (χ²=0.485, P=0.486, OR=0.898, 95% CI: 0.663-1.021) for rs7599810 in Shandong Han sample. Conclusion: 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.

Key words: SUMO1, Genetic association studies, Polymorphism, single nucleotide, Cleft lip, Cleft palate

岳青, 王红, 张博, 赵凯平. SUMO1基因单核苷酸多态性分析及rs7599810多态性与非综合征型唇/腭裂的关联研究[J]. 北京大学学报（医学版）, 2014, 46(2): 258-263.

YUE Qing, WANG Hong, ZHANG Bo, ZHAO Kai-Ping. 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[J]. Journal of Peking University(Health Sciences), 2014, 46(2): 258-263.

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