Linkage disequilibrium analysis of -1516, -574 and 4259 single nucleotide polymorphisms in TIM-3 gene.
- Author:
Zhi-zhong CHEN
1
;
Lin WANG
;
Hong LI
;
Tian-pen CUI
;
Yi-rong LI
;
Li-hua HU
Author Information
- Publication Type:Journal Article
- MeSH: Adult; Alleles; Base Sequence; China; Electrophoresis; Ethnic Groups; genetics; Haplotypes; Hepatitis A Virus Cellular Receptor 2; Humans; Linkage Disequilibrium; genetics; Male; Membrane Proteins; genetics; Molecular Sequence Data; Polymerase Chain Reaction; Polymorphism, Single Nucleotide; Sequence Analysis, DNA
- From: Chinese Journal of Medical Genetics 2008;25(1):101-104
- CountryChina
- Language:Chinese
-
Abstract:
OBJECTIVETo 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) .
METHODSGenotypes 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.
RESULTSThe 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.
CONCLUSIONThe -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.