Dataset Information

Single-nucleotide Polymorphism of CTLA-4 (rs5742909) in Correlation with Schizophrenia Risk Factor.

ABSTRACT: Background:Cytotoxic T protein lymphocyte antigen-4 (CTLA-4) plays a key role in regulating the T-cell system, where occurrence of disturbances in the system seen by imbalances in Th1 and Th2 levels is believed to be one of the etiologies of schizophrenia. Single-nucleotide polymorphisms (SNPs) at rs5742909 in the CTLA-4 gene (C?T) might affect the expression level of CTLA-4 protein. Aims and Objectives:The aim of this study was to determine the genotype distribution of the CTLA-4 gene (rs5742909) in patients with schizophrenia at Rumah Sakit Jiwa Prof. Dr. Soerojo Magelang and identify the correlation of these genetic polymorphisms as the risk factors of schizophrenia. Materials and Methods:This research was conducted through the stage of submitting ethical approval, primer design, chromosomal DNA isolation, optimization of polymerase chain reaction conditions, and data analysis. Results:Based on the results of the study, the CC genotype was shown in 36 patients (78.26%), TT genotype in 10 patients (21.73%), and no TT genotypes. However, statistical analysis using Fisher's exact and binary logistic regression statistical test showed no significant relationship between genetic polymorphism of the CTLA-4 rs5742909 against risk factors for schizophrenia (P = 0.05; ? = 5%). Conclusion:SNP at rs5742909, C-to-T-allele transition, was not significant associated with the risk of schizophrenia.

SUBMITTER: Sumirtanurdin R

PROVIDER: S-EPMC7020830 | biostudies-literature | 2019 Dec

REPOSITORIES: biostudies-literature

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Single-nucleotide Polymorphism of CTLA-4 (rs5742909) in Correlation with Schizophrenia Risk Factor.

Sumirtanurdin Riyadi R Laksono James P JP Dania Haafizah H Ramadhani Fitri N FN Perwitasari Dyah A DA Abdulah Rizky R Barliana Melisa I MI

Journal of pharmacy & bioallied sciences 20191230 Suppl 4

<h4>Background</h4>Cytotoxic T protein lymphocyte antigen-4 (CTLA-4) plays a key role in regulating the T-cell system, where occurrence of disturbances in the system seen by imbalances in Th1 and Th2 levels is believed to be one of the etiologies of schizophrenia. Single-nucleotide polymorphisms (SNPs) at rs5742909 in the <i>CTLA</i>-4 gene (C→T) might affect the expression level of CTLA-4 protein.<h4>Aims and objectives</h4>The aim of this study was to determine the genotype distribution of the ...[more]

PMID: 32148371

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Project description:BACKGROUND:Schizophrenia is a severe mental disorder affecting >21 million people worldwide. Some genetic studies reported that single nucleotide polymorphism (SNP) involving variant rs1344706 from the ZNF804A gene in human beings is associated with the risk of schizophrenia in several populations. Similar results tend to conflict with other reports in literature, indicating that no true significant association exists between rs1344706 and schizophrenia. We seek to determine the level of association of this SNP with schizophrenia in the Asian population using more recent genome-wide association study (GWAS) datasets. METHODS:Applying a computational approach with inclusion of more recent GWAS datasets, we conducted a meta-analysis to examine the level of association of SNP rs1344706 and the risk of schizophrenia disorder among the Asian population constituting Chinese, Indonesians, Japanese, Kazakhs and Singaporeans. For a total of 21 genetic studies, including a total of 28,842 cases and 35,630 controls, regression analysis, publication bias, Cochran's Q and I2 tests were performed. The DerSimonian and Laird random-effects model was used to assess the association of the genetic variant to schizophrenia. Leave-one-out sensitivity analysis was also conducted to determine the influence of each study on the final outcome of the association study. RESULTS:Our summarized analysis for Asian population revealed a pooled odds ratio of 1.06, 95% confidence interval of 1.01-1.11 and two-tailed P-value of 0.0228. Our test for heterogeneity showed the presence of large heterogeneity (I2=53.44%, P =0.00207) and Egger's regression test (P =0.8763) and Begg's test (P =0.8347), indicating no presence of publication bias among our selected studies. In our sensitivity analysis, 10 different studies comprising of ~50% of the entire study had an impact on our final results as each leave-one-out test became insignificant. Our result suggests that genetic variant rs1344706 might be associated with the development of schizophrenia in Asians.

Project description:Risk prediction for a particular disease in a population through SNP genotyping exploits tests whose primary goal is to rank the SNPs on the basis of their disease association. This manuscript reveals a different approach of predicting the risk through network representation by using combined genotypic data (instead of a single allele/haplotype). The aim of this study is to classify diseased group and prediction of disease risk by identifying the responsible genotype. Genotypic combination is chosen from five independent loci present on platelet receptor genes P2RY1 and P2RY12. Genotype-sets constructed from combinations of genotypes served as a network input, the network architecture constituting super-nodes (e.g., case and control) and nodes representing individuals, each individual is described by a set of genotypes containing M markers (M = number of SNP). The analysis becomes further enriched when we consider a set of networks derived from the parent network. By maintaining the super-nodes identical, each network is carrying an independent combination of M-1 markers taken from M markers. For each of the network, the ratio of case specific and control specific connections vary and the ratio of super-node specific connection shows variability. This method of network has also been applied in another case-control study which includes oral cancer, precancer and control individuals to check whether it improves presentation and interpretation of data. The analyses reveal a perfect segregation between super-nodes, only a fraction of mixed state being connected to both the super-nodes (i.e. common genotype set). This kind of approach is favorable for a population to classify whether an individual with a particular genotypic combination can be in a risk group to develop disease. In addition with that we can identify the most important polymorphism whose presence or absence in a population can make a large difference in the number of case and control individuals.

Dataset Information

Single-nucleotide Polymorphism of CTLA-4 (rs5742909) in Correlation with Schizophrenia Risk Factor.

Publications

Single-nucleotide Polymorphism of CTLA-4 (rs5742909) in Correlation with Schizophrenia Risk Factor.

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