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Association of Single-Nucleotide Polymorphisms of Gab1 Gene with Susceptibility to Meningioma in a Northern Chinese Han Population.

ABSTRACT: BACKGROUND The Gab1 gene has an important role in cell proliferation in meningioma via various signaling pathways. However, the relationship between polymorphisms of the Gab1 gene and meningioma remains unknown. In this study, we aimed to investigate the plausible association of single-nucleotide polymorphisms (SNPs) of the Gab1 gene and meningioma risk in a northern Chinese Han population. MATERIAL AND METHODS This case-control study included 205 patients with meningioma and 297 healthy controls. Four loci of the Gab1 gene were genotyped using the multiplex snapshot technique. The odds ratio (OR) and 95% confidence interval (CI) were calculated by chi-squared and logistic regression analysis. The distributions of Gab1 SNP genotypes and allele frequencies were compared between patients with meningioma and healthy controls and among patients stratified by clinical phenotypes. RESULTS The allelic frequency distributions of G at rs3805236 and C at rs1397529 were significantly higher in patients with meningioma than in healthy controls. The frequency of the rs3805236-GG and rs1397529-AC genotypes were significantly higher in patients with meningioma than in controls. Furthermore, there was a statistically significant difference between the genotypes of patients versus healthy individuals at rs1397529, according to stratification by dural invasion. The allelic frequency distributions of alleles or genotypes at rs3805246 and rs3828512 were not different in patients with meningioma and healthy controls. CONCLUSIONS The Gab1 gene rs3805236A>G and rs1397529A>C SNPs increased the risk of meningioma in the northern Chinese Han population. Furthermore, rs1397529A>C may be related to enhanced dural invasion in patients with meningioma.

SUBMITTER: Chen W

PROVIDER: S-EPMC8577039 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundRheumatoid arthritis (RA) is a systemic autoimmune disease characterized by chronic destructive inflammation in synovial joints. It is well known that genetic and environmental risk factors and their interaction contribute to RA pathogenesis. This study aimed to investigate the association between the critical polymorphisms in the tumor necrosis factor α (TNFα)-induced protein 3(TNFAIP3) gene and the risk of RA in a large northern Chinese Han population.MethodsA case-control study of 1280 RA patients and 1280 matched healthy controls was conducted.ResultsThis study showed that carriers of the rs2230926 TG genotype or rs10499194 CT genotype had an increased risk for RA compared with those carrying the wild genotype (rs2230926: OR = 1.48, 95% CI = 1.17-1.86, p = 0.001; rs10499194: OR = 2.00, 95% CI = 1.46-2.74, p < 0.001). The combined rs2230926TG/GG or rs10499194 CT/TT were associated with an increased risk of RA (ORs were 1.50 and 2.01, 95% CIs were 1.19-1.88 and 1.47-2.74, respectively, both p < 0.001). There was not significant association between rs13207033 polymorphism and RA risk. Subset analysis stratified to gender showed that the increased risks were significant among the genotypes TG, TG/GG of rs2230926 and CT, CT/TT of rs10499194 and the corresponding ORs were 1.42 (95% CI = 1.10-1.83, p = 0.006), 1.44(95% CI = 1.12-1.85, p = 0.004), 1.52(95% CI = 1.05-2.20, p = 0.026) and 1.52(95% CI = 1.06-2.19, p = 0.023) in the female population. Stratified analyses by age found that rs2230926(TG, TG/GG) and rs10499194(CT, CT/TT) polymorphisms were associated with RA risks in population ≤53 years old and among >53 years old only rs10499194(CT, TT, CT/TT) polymorphism had significant results. The interaction analysis suggested that individuals with both risk genotypes of the two SNPs have a higher elevated risk of RA than those with only one of them (ORs were 3.44 compared to 1.74 and 1.35). The haplotype results showed that individuals with the rs2230926G-rs13207033G-rs10499194C haplotype were associated with increased risks of RA (OR = 1.37, 95% CI = 1.08-1.74, p = 0.010).ConclusionsRs10499194 and rs2230926 polymorphisms in the TNFAIP3 gene region may be susceptibility factors for rheumatoid arthritis in the northern Chinese Han population.

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.

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Association of Single-Nucleotide Polymorphisms of Gab1 Gene with Susceptibility to Meningioma in a Northern Chinese Han Population.

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