Effects of Single Nucleotide Polymorphism Marker Density on Haplotype Block Partition

Many researchers have found that one of the most important characteristics of the structure of linkage disequilibrium is that the human genome can be divided into non-overlapping block partitions in which only a small number of haplotypes are observed. The location and distribution of haplotype blocks can be seen as a population property influenced by population genetic events such as selection, mutation, recombination and population structure. In this study, we investigate the effects of the density of markers relative to the full set of all polymorphisms in the region on the results of haplotype partitioning for five popular haplotype block partition methods: three methods in Haploview (confidence interval, four gamete test, and solid spine), MIG++ implemented in PLINK 1.9 and S-MIG++. We used several experimental datasets obtained by sampling subsets of single nucleotide polymorphism (SNP) markers of chromosome 22 region in the 1000 Genomes Project data and also the HapMap phase 3 data to compare the results of haplotype block partitions by five methods. With decreasing sampling ratio down to 20% of the original SNP markers, the total number of haplotype blocks decreases and the length of haplotype blocks increases for all algorithms. When we examined the marker-independence of the haplotype block locations constructed from the datasets of different density, the results using below 50% of the entire SNP markers were very different from the results using the entire SNP markers. We conclude that the haplotype block construction results should be used and interpreted carefully depending on the selection of markers and the purpose of the study.

Selecting the tag SNPs of TLR2 gene with bioinformatics techniques / 基础医学与临床

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.

HapAnalyzer: Minimum Haplotype Analysis System for Association Studies

SUMMARY: HapAnalyzer is an analysis system that provides minimum analysis methods for the SNP-based association studies. It consists of Hardy-Weinberg equilibrium (HWE) test, linkage disequilibrium (LD) computation, haplotype reconstruction, and SNP (or haplotype)-phenotype association assessment. It is well suited to a case-control association study for the unrelated population.