Selecting the tag SNPs of TLR2 gene with bioinformatics techniques
- VernacularTitle:利用生物信息学技术挑选TLR2基因标签单核苷酸多态性位点
- Author:
Kehong CHEN
;
Ling ZENG
;
Wei GU
;
Shuna HUANG
;
Qing LIU
;
Jianxin JIANG
- Publication Type:Journal Article
- Keywords:
TLR2;
haplotype block;
tag SNP;
haplotype
- From:
Basic & Clinical Medicine
2010;30(3):242-245
- CountryChina
- Language:Chinese
-
Abstract:
Objective To select the tag SNPs of TLR2 gene in the Chinese population with bioinformatics techniques.Methods We ascertained the assayed scope of the TLR2 gene with the aid of NCBI database and downloaded SNP genotype data of TLR2 gene in the Chinese population from Hapmap database.Then Haploview (version 4.0) was used to calculate linkage disequilibrium (LD) statistics.Haplotype blocks were constructed throughout the TLR2 gene according to the upper and lower 95% confidence bound of the D'value.Meanwhile,we selected the tag SNPs based on r~2 values and the LOD value between SNPs and picked up the representative haplotypes in accordance with the proportion of each haplotype in the haplotype blocks,respectively.Results We constructed 2 haplotype blocks within the TLR2 gene and selected 3 tag SNPs containing 3013 A/G,19216 T/C and 22215 G/T in the Chinese population.Meanwhile,we identified the representative haplotypes of which the tag SNP would be on behalf of every haplotype block.Conclusion The SNPs of 3013 A/G,19216 T/C and 22215 G/T,the most representative SNPs in the whole TLR2 gene in the Chinese population,could be selected as tag SNPs to guide their association studies between the TLR2 gene and sepsis.
