Dataset Information

Association Between Single Nucleotide Polymorphisms in the Vitamin D Receptor and Incidence of Dry Eye Disease in Chinese Han Population.

ABSTRACT: BACKGROUND Dry eye disease (DED) is a chronic dysfunction of the ocular surface and has become an important public problem. Vitamin D receptor (VDR) gene polymorphism has been found to be associated with different kinds of diseases. The relationship between single nucleotide polymorphisms (SNPs) in the VDR gene should be studied. MATERIAL AND METHODS In the present case-control study, we investigated the association of VDR gene polymorphism with DED risk. Clinical data including age, gender, body mass index (BMI, kg/m²), smoking history, diabetes, and blood pressure were recorded. Serum 25-hydroxy vitamin D (25[OH]D) was chosen as the main parameter that reflected the level of vitamin D. We identified SNPs of VDR gene Apa-1, Bsm-1, Fok-1, and Taq-1 in both DED cases and healthy controls. RESULTS A total of 124 DED cases and 135 healthy controls were included in this study. It was reported that aa in Apa-1 (OR=2.803, 95% CI, 1.350-5.820) and tt in Taq-1 (OR=0.362, 95% CI, 0.141-0.930) were associated with increased the risk of DED. Analysis of the allele frequencies of VDR gene polymorphisms among DED patients and healthy controls showed that allele differences in Apa-1 were significantly associated with higher risk. CONCLUSIONS SNPs of VDR gene (Apa-1 and Taq-1) were associated with the risk of DED. No significant association of Bsm-1 and Fok-1 in VDR gene demonstrated significant effect in the incidence of DED. Thus, we found that several SNPs of VDR gene could provide significant pathogenic effects in the risk of DED.

SUBMITTER: Meng YF

PROVIDER: S-EPMC6611217 | biostudies-literature | 2019 Jun

REPOSITORIES: biostudies-literature

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Association Between Single Nucleotide Polymorphisms in the Vitamin D Receptor and Incidence of Dry Eye Disease in Chinese Han Population.

Meng Yi-Fang YF Xin Qian Q Lu Jiong J Xiao Pan P Li Jian J

Medical science monitor : international medical journal of experimental and clinical research 20190627

BACKGROUND Dry eye disease (DED) is a chronic dysfunction of the ocular surface and has become an important public problem. Vitamin D receptor (VDR) gene polymorphism has been found to be associated with different kinds of diseases. The relationship between single nucleotide polymorphisms (SNPs) in the VDR gene should be studied. MATERIAL AND METHODS In the present case-control study, we investigated the association of VDR gene polymorphism with DED risk. Clinical data including age, gender, bod ...[more]

PMID: 31243261

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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

Association Between Single Nucleotide Polymorphisms in the Vitamin D Receptor and Incidence of Dry Eye Disease in Chinese Han Population.

Publications

Association Between Single Nucleotide Polymorphisms in the Vitamin D Receptor and Incidence of Dry Eye Disease in Chinese Han Population.

Similar Datasets

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