Dataset Information

Single nucleotide polymorphisms of ER? and coronary atherosclerotic disease in Chinese Han women.

ABSTRACT: Growing evidence has shown that with the increase of age, the incidence of coronary atherosclerotic disease (CAD) in women increases to equal that of men. Several studies on the single nucleotide polymorphisms [SNPs] seem to provide evidence in support of the protective role estrogen receptor ? (ER?) has in reducing the risk of CAD.To determine the association of ER? SNPs rs1256049 RsaI 1082 A > G and rs4986938 AluI 1730 G > A with coronary atherosclerotic disease in Chinese Han women.We designed a nested case-control research, in which 120 case women and 30 control women were selected from the Forensic Medicine Department of Tongji Medical College, HUST. We isolated DNA from their lung paraffin blocks, and then screened for these two SNPs for each DNA sample. Post-statistical analysis of their genotypes and haplotypes was used to figure out the targeted association.We found no significant difference between the genotypes or haplotypes of the two SNPs and the risk of CAD. However, the rs4986938 heterozygote AG variant was correlated with a significantly lower risk for CAD than did homozygote GG variant in the group of less than 40 years old. Haplotype AA of the two SNPs was correlated with a higher risk for CAD in the same group.The rs4986938 AluI 1730 G > A seems to be quite involved in the genetic basis of the disease and needs more attention in future studies. Meanwhile, this very association made between CAD and the mentioned SNP seems to be affected quite a bit by age.

SUBMITTER: Shen C

PROVIDER: S-EPMC4396251 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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Publications

Single nucleotide polymorphisms of ERβ and coronary atherosclerotic disease in Chinese Han women.

Shen Chunyu C Chen Zhenglian Z Mahmoodurrahman Mohammed M Chen Xinshan X

International journal of clinical and experimental pathology 20150201 2

<h4>Background</h4>Growing evidence has shown that with the increase of age, the incidence of coronary atherosclerotic disease (CAD) in women increases to equal that of men. Several studies on the single nucleotide polymorphisms [SNPs] seem to provide evidence in support of the protective role estrogen receptor β (ERβ) has in reducing the risk of CAD.<h4>Objective</h4>To determine the association of ERβ SNPs rs1256049 RsaI 1082 A > G and rs4986938 AluI 1730 G > A with coronary atherosclerotic di ...[more]

PMID: 25973102

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Project description:BACKGROUND: Genetic variation associated with human leukocyte antigen (HLA) genes has immunological functions and is associated with autoimmune diseases. To date, large-scale studies involving classical HLA genes have been limited by time-consuming and expensive HLA-typing technologies. To reduce these costs, single-nucleotide polymorphisms (SNPs) have been used to predict HLA-allele types. Although HLA allelic distributions differ among populations, most prediction model of HLA genes are based on Caucasian samples, with few reported studies involving non-Caucasians. RESULTS: Our sample consisted of 437 Han Chinese with Affymetrix 5.0 and Illumina 550 K SNPs, of whom 214 also had data on Affymetrix 6.0 SNPs. All individuals had HLA typings at a 4-digit resolution. Using these data, we have built prediction model of HLA genes that are specific for a Han Chinese population. To optimize our prediction model of HLA genes, we analyzed a number of critical parameters, including flanking-region size, genotyping platform, and imputation. Predictive accuracies generally increased both with sample size and SNP density. CONCLUSIONS: SNP data from the HapMap Project are about five times more dense than commercially available genotype chip data. Using chips to genotype our samples, however, only reduced the accuracy of our HLA predictions by only ~3%, while saving a great deal of time and expense. We demonstrated that classical HLA alleles can be predicted from SNP genotype data with a high level of accuracy (80.37% (HLA-B) ~95.79% (HLA-DQB1)) in a Han Chinese population. This finding offers new opportunities for researchers in obtaining HLA genotypes via prediction using their already existing chip datasets. Since the genetic variation structure (e.g. SNP, HLA, Linkage disequilibrium) is different between Han Chinese and Caucasians, and has strong impact in building prediction models for HLA genes, our findings emphasize the importance of building ethnic-specific models when analyzing human populations.

Dataset Information

Single nucleotide polymorphisms of ER? and coronary atherosclerotic disease in Chinese Han women.

Publications

Single nucleotide polymorphisms of ERβ and coronary atherosclerotic disease in Chinese Han women.

Similar Datasets

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