应用Hapmap数据库分析HBG1-HBD基因间序列单倍型及标签SNP的挑选

Haplotypes and tagSNPs selected in the HBG1-HBD intergenic region: Analysis based on the Hapmap database

目的 HBG1-HBD基因间序列在γ珠蛋白基因表达有重要作用,文中分析中国北京汉族人群HBG1-HBD基因间序列的单倍型并挑选标签SNP(tag SNP)。方法从Hapmap数据库中下载HBG1-HBD基因间序列上中国北京汉族人群的所有SNP数据。应用Haploview 4.0软件对HBG1-HBD基因间序列的SNP位点进行连锁不平衡分析,在此基础上构建HBG1-HBD基因间序列范围的单倍域及单倍型。用MEGA5.10软件对单倍型进行聚类分析,根据SNP之间的r2值挑选出可代表不同类型单倍型的tag SNP。结果在中国北京汉族人群中,HBG1-HBD基因间序列中共有2个单倍域(Block1和Block2),分别有7种和3种单倍型,发生频率均>1%。通过聚类分析将Block1的单倍型分为2组,可通过相互代表的11个tag SNP进行分组,11个SNP依次为:rs3813727、rs10837643、rs4320977、rs4283007、rs4402323、rs4910543、rs4910736、rs2105819、rs968857、rs968856、rs10768687。结论获得了中国北京汉族人群中HBG1-HBD基因间序列的单倍型及tag SNP,为研究HBG1-HBD基因间序列的单倍型与γ珠蛋白基因表达的相关性打下了基础。

Objective The HBG1-HBD intergenic region plays an important role in the expression of the gamma globin gene. This study aimed to analyze haplotypes and select tagSNPs in the HBG1-HBD intergenic region in the Chinese Han population of Bei-jing. Methods We downloaded from the Hapmap database the literature on the genotype of SNPs in the HBG1-HBD intergenic re-gion in the Chinese Han population of Beijing. Based on the results of linkage disequilibrium analysis between SNPs in the HBG1-HBD intergenic region with the Haploview 4 .0 software, we constructedanalysis of the haplotypes using the MEGA5.10 software, and selected tagSNPs to represent different haplotype types according to the r2 val-ues between the SNPs. Results There were two haplotype blocks （ block 1 and block2） in the HBG1-HBD intergenic region in the Chi-nese Han population of Beijing, with 7 and 3 haplotypes respectively, and the frequency of each haplotype was 〉1%. Through clustering a-nalysis, the haplotypes in block 1 were divided into two groupshaplotype blocks and haplotypes in this region, performed a clustering （M and N） by 11 tagSNP that represented one another. Conclusion Haplotypes and tagSNPs in the HBG1-HBD intergenetic region were obtained in the Chinese Han population of Beijing, which has laid a basis for studying the correlation between the haplotypes in the HBG1-HBD intergenetic region and the expression of the , globin gene.