应用人群中HLA-DRB1单核苷酸多态性推算氨基酸单倍型的研究

Using the HLA-DRB1 SNPs data of population to impute the amino acid haplotypes

目的评估应用人群中HLA-DRB1基因的SNPs数据结合ELB算法来推算氨基酸及氨基酸单倍型的准确度,探索一种在群体研究中简便快捷的获得HLA-DRB1氨基酸类型及氨基酸单倍型的分布情况的方法。方法 144例样本采用传统的组特异性引物多次测序法获得HLA-DRB1基因的第11、13、57、67、71、74位氨基酸类型及氨基酸单倍型的分布情况,并与单次测序获得的SNPs数据结合ELB算法推算法的结果进行比较。结果用人群中HLA-DRB1基因的SNPs数据结合ELB算法推算HLADRB1单个位点的氨基酸类型与多次测序法之间的吻合率为100%,推算HLA-DRB1基因3个位点氨基酸单倍型(11-71-74)的吻合率为96.5%,推算6个位点氨基酸单倍型(11-13-57-67-71-74)的吻合率为93.7%。结论应用人群中HLA-DRB1的SNPs结合ELB算法可获得HLA-DRB1的氨基酸类型及氨基酸单倍型,其准确率与包含的氨基酸位点数相关。该方法具有准确性高和简便、快速的优点。

Objective：To Evaluate the accuracy of HLA-DRB1 amino acid haplotypes imputed by ELB algorithm from single nucleotide polymorphisms data of population,and to explore a quick method to get the amino acid haplotypes distribution of HLA-DRB1 in population studies.Methods：In total of 144 human genomic DNA samples,HLA-DRB1 amino acid types and haplotypes on positions 11,13,57,67,71 and 74 were determined by using mutiple DNA sequencing and group specific primers. Meanwhile,HLA-DRB1 SNPs data of the amino acid obtaining from single DNA sequencing were analyzed using the ELB algorithm in order to impute the amino acid types and haplotypes distribution. The output results were compared between mutiple sequencing and ELB algorithm based on population SNPs. Results：When a single amino acid of HLA-DRB1 was imputed by ELB algorithm,the coincident rate was 100%,comparing with that of mutiple sequencing method. When haplotypes from three amino acid,11,71 and 74,were imputed by ELB,the coincident rate of amino acid haplotypes was 96.5%. Moreover,When haplotypes from six amino acid positions of 11,13,57,67,71 and 74 were inferred by ELB,the coincident rate was 93.7%. Conclusion：SNPs based ELB algorithm is a accurate,cost effective and high throughput method for imputing HLA-DRB1 amino acid haplotypes in given populations. The accuracy of the ELB method is associated with the number of amino acid analyzed.