Article

[Linkage disequilibrium analysis of -1516, -574 and 4259 single nucleotide polymorphisms in TIM-3 gene].

Department of Laboratory Medicine, Huazhong University of Science and Technology, Wuhan, Hubei, 430022 People's Republic of China.
Zhonghua yi xue yi chuan xue za zhi = Zhonghua yixue yichuanxue zazhi = Chinese journal of medical genetics 03/2008; 25(1):101-4. pp.101-4
Source: PubMed

ABSTRACT To investigate the frequencies of -1516,-574 and 4259 single nucleotide polymorphisms (SNPs) of T cells immunoglobulin mucin -3(TIM-3) gene in Hubei population and address the question whether they are in linkage disequilibrium(LD) .
Genotypes and allele frequencies of TIM-3 gene were examined by allele-specific polymerase chain reaction (AS-PCR) methods in 147 healthy Hubei Han individuals. Hardy-Weinberg equilibrium and Two-point LD analyses and haplotype frequencies were evaluated with Arlequin v3.1 software.
The allele frequencies of the 3 SNPs were in agreement with Hardy-Weinberg equilibrium. Minor allelic frequencies of TIM-3 -1516G/T,-574T/G and 4259G/T were 8.5%,1.0% and 2.0%,respectively. The dominant haplotypes comprising the three loci were G-G-G(2.0%),G-G-T(88.4%), T-G-T(8.5%) and G-T-T(1.0%). LD analyses revealed that all of the coefficient of linkage disequilibrium (D') were 1.
The -1516,-574 and 4259 loci of TIM-3 gene are in complete linkage disequilibrium. Our study has provided population genetic data on TIM-3 gene in Chinese Hubei Han population and a basis for searching immune-mediated disease-related TIM-3 haplotype.

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Keywords

147 healthy Hubei Han individuals
 
3 SNPs
 
4259 single nucleotide polymorphisms
 
allele frequencies
 
allele-specific polymerase chain reaction
 
Arlequin v3.1 software
 
AS-PCR
 
Chinese Hubei Han population
 
dominant haplotypes
 
frequencies
 
haplotype frequencies
 
Hubei population
 
immune-mediated disease-related TIM-3 haplotype
 
linkage disequilibrium(LD)
 
Minor allelic frequencies
 
SNPs
 
T cells immunoglobulin mucin -3(TIM-3)
 
three loci
 
TIM-3 gene
 
Two-point LD analyses