基于靶基因捕获测序法对海南省汉族寻常型银屑病与维生素D受体基因关系的研究

Analysis of relationship between psoriasis vulgaris and vitamin D receptor gene in a Han population in Hainan Province based on targeted capture sequencing

目的探讨维生素D受体(VDR)基因多态性与寻常型银屑病的关系。方法2018年3月至2020年2月在海南医学院第二附属医院皮肤性病科和体检中心分别收集101例海南籍汉族寻常型银屑病患者与79例海南籍健康对照。采用靶基因捕获测序法对VDR基因及其上、下游各2 kb进行全长测序,对于最小等位基因频率大于1%的单核苷酸多态性(SNP)进行基于SNP和单倍型的关联分析。采用生物信息学方法预测风险位点对基因功能的影响。结果基于SNP的关联分析显示,40个SNP(29个位于内含子区、1个位于外显子区及10个位于基因间区)为银屑病的易感位点,其OR值为0.148(95%CI:0.016~1.294)~2.779(95%CI:1.260~6.130),P<0.001~0.976。生物信息学预测显示位于外显子2上的rs2228570可引起氨基酸改变(蛋氨酸→苏氨酸),继而导致基因功能改变。基于单倍型的关联分析显示,10个单倍型为寻常型银屑病的保护性单倍型,在健康对照组和银屑病患者组中的频率分别为5.150%~45.570%、1.110%~33.170%,其OR值为0.198(95%CI:0.040~0.985)~0.630(95%CI:0.419~0.947),P值0.002~0.048。结论在海南籍汉族人群中,发现40个寻常型银屑病相关的风险SNP,分别位于内含子区、外显子区及基因间区域,同时发现10个保护性单倍型。

Objective To investigate the relationship between vitamin D receptor(VDR)gene polymorphisms and psoriasis vulgaris.Methods From March 2018 to February 2020,a total of 101 patients with psoriasis vulgaris were collected from Department of Dermatology and Venereology,the Second Affiliated Hospital of Hainan Medical University,and 79 healthy controls from the health examination center in this hospital.All the subjects were of Han nationality from Hainan province.Targeted capture sequencing was performed to sequence the full length of the VDR gene and its 2-kb upstream and downstream regions.Single-nucleotide polymorphism(SNP)-and haplotype-based association analyses were performed for SNPs with minor allele frequency greater than 1%.Bioinformatics methods were used to predict the impact of risk SNPs on gene functions.Results The SNP-based association analysis showed that 40 SNPs,including 29 in the intron region,1 in the exon region and 10 in the intergenic region,conferred susceptibility to psoriasis vulgaris,with the odds ratio ranging from 0.148(95%CI:0.016-1.294)to 2.779(95%CI:1.260-6.130),and P value ranging from<0.001 to 0.976.Bioinformatics analysis indicated that rs2228570 in exon 2 could cause the substitution of methionine by threonine,leading to changes in gene functions.The haplotype-based association analysis showed that 10 haplotypes were protective haplotypes for psoriasis vulgaris,and their frequencies were 5.150%-45.570%in the healthy control group and 1.110%-33.170%in the psoriasis group,with the odds ratio ranging from 0.198(95%CI:0.040-0.985)to 0.630(95%CI:0.419-0.947),and the P value ranging from 0.002 to 0.048.Conclusion Among the Han population in Hainan Province,40 risk SNPs for psoriasis vulgaris were identified in intron,exon and intergenic regions of the VDR gene,and 10 protective haplotypes were identified as well.