Browse
Submit Data
Databases
API
Help

Dataset Information

42 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Association of PTPN22 polymorphsims and ankylosing spondylitis susceptibility.

ABSTRACT: As a susceptibility gene for AS, the polymorphsims of PTPN22 associated with disease susceptibility.We selected two SNPs of rs1217406 and rs1217414 within PTPN22 with Haploview software and investigated the relationship between the SNPs of PTPN22 gene and AS susceptibility. 120 AS patients and 100 healthy people were enrolled from Qilu Hospital of Shandong University. And we genotyped the SNPs of PTPN22 with PCR-RFLP method.The results showed that C allele (rs1217406) and T allele (rs1217414) both were risk factors for AS (OR: 3.12, 2.13). The persons with A-T, C-C or C-T haplotypes were more likely to suffer AS (OR: 3.17, 3.66, 4.011).Due to the close relationship of PTPN22 and AS, the study may be helpful for the early diagnosis and differential diagnosis.

SUBMITTER: Meng Q

PROVIDER: S-EPMC4348882 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Association of PTPN22 polymorphsims and ankylosing spondylitis susceptibility.

Meng Qingxi Q Zhang Xiaojun X Liu Xin X Wang Weiguo W Yu Peng P Shan Qunqun Q Mao Zhaohu Z Zhao Tingbao T

International journal of clinical and experimental pathology 20150101 1

<h4>Background</h4>As a susceptibility gene for AS, the polymorphsims of PTPN22 associated with disease susceptibility.<h4>Methods</h4>We selected two SNPs of rs1217406 and rs1217414 within PTPN22 with Haploview software and investigated the relationship between the SNPs of PTPN22 gene and AS susceptibility. 120 AS patients and 100 healthy people were enrolled from Qilu Hospital of Shandong University. And we genotyped the SNPs of PTPN22 with PCR-RFLP method.<h4>Results</h4>The results showed th ...[more]

PMID: 25755798

Similar Datasets

Association between HRH4 polymorphisms and ankylosing spondylitis susceptibility.

Project description:The purpose of the study was to investigate the association between the histamine H4 receptor (HRH4) polymorphisms and the susceptibility to ankylosing spondylitis (AS).Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was used to analyze the HRH4 rs8088140 and rs657132 polymorphisms. Linkage disequilibrium and haplotype analyses were conducted with Haploview software. The genotypes distributions of HRH4 polymorphisms in the control group were tested by Hardy-Weinberg equilibrium (HWE), allele, genotype and haplotype frequencies between the cases and control groups were compared by ?(2) test. The controls were matched with cases by age and gender. The relative risk of AS with HRH4 polymorphisms was represented by odds ratio (OR) with 95% confidence interval (CI) calculated by ?(2) test.The genotypes distributions of HRH4 rs8088140, rs657132 polymorphisms in controls conformed to HWE. The frequency of rs657132 AA genotype in the case group was obviously higher than that in the control group (P=0.040), and so was the A allele (OR=2.572, 95% CI=1.475-4.486, P=0.022). The frequency differences of A-A haplotype between two groups had statistical significance (P=0.011, OR=2.071, 95% CI=1.172-3.660) through haplotype analysis, indicating A-A might be the susceptible haplotype to AS.The AA genotypes of HRH4 rs657132 polymorphism may be the susceptible factors for AS, and rs657132 plays a role in generation of AS. In addition, A-A haplotype in rs8088140-rs657132 is also increased the risk of AS.

| S-EPMC4713664 | biostudies-literature

Genome-wide association study of ankylosing spondylitis identifies non-MHC susceptibility loci.

Project description:To identify susceptibility loci for ankylosing spondylitis, we undertook a genome-wide association study in 2,053 unrelated ankylosing spondylitis cases among people of European descent and 5,140 ethnically matched controls, with replication in an independent cohort of 898 ankylosing spondylitis cases and 1,518 controls. Cases were genotyped with Illumina HumHap370 genotyping chips. In addition to strong association with the major histocompatibility complex (MHC; P < 10(-800)), we found association with SNPs in two gene deserts at 2p15 (rs10865331; combined P = 1.9 x 10(-19)) and 21q22 (rs2242944; P = 8.3 x 10(-20)), as well as in the genes ANTXR2 (rs4333130; P = 9.3 x 10(-8)) and IL1R2 (rs2310173; P = 4.8 x 10(-7)). We also replicated previously reported associations at IL23R (rs11209026; P = 9.1 x 10(-14)) and ERAP1 (rs27434; P = 5.3 x 10(-12)). This study reports four genetic loci associated with ankylosing spondylitis risk and identifies a major role for the interleukin (IL)-23 and IL-1 cytokine pathways in disease susceptibility.

| S-EPMC3224997 | biostudies-literature

Association between ERAP1 gene polymorphisms and ankylosing spondylitis susceptibility in Han population.

Project description:The present study was designed to investigate the relationship between endoplasmic reticulum amino peptidase 1 (ERAP1) gene polymorphisms and ankylosing spondylitis (AS) in Han population of Shaanxi province.100 AS patients and 100 healthy people were enrolled in present study as case and control groups respectively, and the control group was matched with the case group by age and gender. ERAP1 gene rs27434 and rs7711564 polymorphisms were test by TaqMan probe genotyping method. SHEsis software was used to operate linkage disequilibrium (LD) and haplotype analysis between the two single nucleotide polymorphisms (SNPs). ?(2) test was employed to compare the differences of the genotype, allele and haplotype frequencies between the case and control groups. Relative risk of AS was represented by odds ratios (ORs) and 95% confidence intervals (95% CIs).In ERAP1 rs27434 and rs7711564 polymorphisms, the frequencies of AA and CC genotypes in case group were significantly higher compared to those in control group (P=0.036; P=0.039), and so were the frequencies of A and C alleles (OR=1.589, 95% CI=1.070-2.359, P=0.028; OR=1.535, 95% CI=1.021-2.308, P=0.050). Linkage disequilibrium test and haplotype analysis of the alleles of the two SNPs showed that the frequency of A-C haplotype was higher in case group than that in control group (P=0.005), which indicated that A-C might be the susceptible haplotype to AS.ERAP1 gene rs27434 and rs7711564 polymorphisms may increase the risk of AS.

| S-EPMC4637719 | biostudies-literature

Chromosomal Distribution of Ankylosing Spondylitis Susceptibility Loci.

Project description:ObjectivesPrevious studies have been indicated that susceptible loci of several multifactorial diseases were non-randomly distributed on human genome. There is no published data on chromosomal distribution of genes associated with risk of ankylosing spondylitis. Therefore, the present study was carried out.MethodsPublished meta-analyses indexed in the PubMed database were used in the present study. Non-randomness chromosomal distribution of these loci was evaluated by the statistical method of Tai et al.ResultsA total of 88 articles were obtained. There was 32 ankylosing spondylitis associated genes. The present study revealed that the human chromosome segments 6p11.2-p21.33, 19q13.2-q13.42, and 2q11.2-q14.1 were ankylosing spondylitis associated-rich regions by bearing 7, 6 and 4 susceptible loci, respectively.ConclusionAnkylosing spondylitis associated-genes non-randomly have been distributed non-randomly on human chromosomes.

| S-EPMC10466362 | biostudies-literature

Association study between matrix metalloproteinase-3 gene (MMP3) polymorphisms and ankylosing spondylitis susceptibility.

Project description:BackgroundAnkylosing spondylitis (AS) is the second most common cause of inflammatory arthritis worldwide affecting the axial skeleton. Single nucleotide polymorphisms (SNPs) of matrix metalloproteinase-3 (MMP3) in the development of AS has few been investigated in Chinese population.MethodsA total of 362 patients with AS and 362 healthy controls were enrolled in the study. Five SNPs in MMP3 genotypes were identified by Agena MassARRAY. Chi-squared tests and genetic model were used to evaluate associations.Resultsrs522616 had a significant risk of AS development compared to those with the TT genotype (p = 0.008). By multiple logistic regression models analysis, in codominant model, rs522616 CT genotypes also had a 1.44-fold risk (95% CI = 1.06-1.96, p = 0.008) for AS development compared to those with TT genotypes. In recessive model, the CC genotypes was a significantly reduced AS risk for individuals with TT/CT genotype (OR = 0.64; 95% CI = 0.41-0.99, p = 0.040).ConclusionThe present study suggests that MMP3 rs522616 polymorphism is associated with AS susceptibility and MMP3 might be a potential diagnostic biomarker for AS. Further independent studies with larger cohorts are warranted to validate our findings in different populations.

| S-EPMC6625098 | biostudies-literature

Association Between Protein Tyrosine Phosphatase Non-Receptor Type 22 (PTPN22) Polymorphisms and Risk of Ankylosing Spondylitis: A Meta-analysis.

Project description:BACKGROUND Ankylosing spondylitis (AS) is a chronic autoimmune disease that involves the imbalance of peripheral tolerance possibly caused by the negative signal of activated T cells. The polymorphisms in the human protein tyrosine phosphatase non-receptor type 22 (PTPN22) gene have been pointed out to be related to the pathogenesis of AS, but conclusions over this issue remain contradictory. We attempted to give a more precise conclusion about the effects of PTPN22 polymorphisms on AS risk by means of a meta-analysis. MATERIAL AND METHODS PubMed, Embase, Wanfang, and Chinese National Knowledge Infrastructure (CNKI) were searched for relevant studies published in the English or Chinese language. Odds ratios (ORs) and 95% confidence intervals (95% CIs) were calculated with a fixed- or random-effects model to evaluate the correlation between PTPN22 rs2488457, rs1217414, and rs2476601 polymorphisms and AS susceptibility. Sensitivity analysis was also carried out to detect the stability of the results. RESULTS The present meta-analysis showed a positive correlation of both PTPN22 rs2488457 and rs1217414 polymorphisms with AS risk under CC vs. GG, CC + GC vs. GG, CC vs. GC + GG, allele C vs. allele G (OR=1.39, 95% CI=1.04-1.85, P=0.646; OR=1.29, 95% CI=1.03-1.62, P=0.426; OR=1.26, 95% CI=1.02-1.56, P=0.971; OR=1.20, 95% CI=1.05-1.38, P=0.571), and TT vs. CC and TT vs. CT + CC models (OR=3.83, 95% CI=1.11-13.24, P=0.196; OR=3.83, 95% CI=1.09-13.42, P=0.244), respectively. CONCLUSIONS PTPN22 rs2488457 and rs1217414 polymorphisms may be risk factors for AS occurrence.

| S-EPMC5461884 | biostudies-literature

Association Study of IL-12B Polymorphisms Susceptibility with Ankylosing Spondylitis in Mainland Han Population.

Project description:ObjectiveThis study aims to determine whether the genetic polymorphisms of IL-12B gene is a susceptibility factor to Ankylosing spondylitis (AS) in mainland Han Chinese population.MethodEight single-nucleotide polymorphisms (SNPs) (rs10045431, rs11167764, rs3212227, rs6556412, rs6556416, rs6871626, rs6887695 and rs7709212) in the IL-12B gene were genotyped by iMLDR Assay technology in 400 patients [96% (384/400) HLA-B27(+)] and 395 geographically and ethnically matched healthy controls in mainland Han Chinese population. The correlation between IL-12B genetic polymorphisms and AS activity index (BASDAI, BASFI) were tested.ResultsThe significant difference was found in genotype distribution between AS and healthy controls (χ2 = 6.942, P-value = 0.031) of the SNP rs6871626. Furthermore, significant evidence was also detected under the recessive model for minor allele A. The AA genotype carrier had 1.830 fold risk compared with C allele carrier (with CC and AC genotypes) [OR (95% CI) = 1.830 (1.131-2.961), P-value = 0.014]. Nevertheless, the difference was no longer significant after Bonferroni correction. Subset analysis on cases with HLA-B27(+) did find the same results. Three genotypic groups (AA, CC and CA) in rs6871626 site was highly associated with the BASDAI and BASFI (P-value = 0.012 and P-value = 0.023, respectively), after adjustment for effect of age, sex, and disease duration, the P-value was 0.031 and 0.041, respectively. The AA genotype of rs6871626 was also significantly correlated with an increased BASDAI and BASFI compared to the AC and CC genotypes in AS patients.ConclusionOur findings suggest that rs6871626 may be associated AS susceptibility and with disease activity (BASDAI, BASFI) in mainland Han Chinese population.

| S-EPMC4477880 | biostudies-literature

MICA, a gene contributing strong susceptibility to ankylosing spondylitis.

Project description:ObjectiveThe human major histocompatibility complex class I chain-related gene A (MICA) controls the immune process by balancing activities of natural killer cells, γδ T cells and αβ CD8 T cells, and immunosuppressive CD4 T cells. MICA is located near HLA-B on chromosome 6. Recent genomewide association studies indicate that genes most strongly linked to ankylosing spondylitis (AS) susceptibility come from the region containing HLA-B and MICA. While HLA-B27 is a well-known risk genetic marker for AS, the potential effect of linkage disequilibrium (LD) shields any associations of genes around HLA-B with AS. The aim of this study was to investigate a novel independent genetic association of MICA to AS.MethodsWe examined 1543 AS patients and 1539 controls from two ethnic populations by sequencing MICA and genotyping HLA-B alleles. Initially, 1070 AS patients and 1003 controls of European ancestry were used as a discovery cohort, followed by a confirmation cohort of 473 Han Chinese AS patients and 536 controls. We performed a stratified analysis based on HLA-B27 carrier status. We also conducted logistic regression with a formal interaction term.ResultsSequencing of MICA identified that MICA*007:01 is a significant risk allele for AS in both Caucasian and Han Chinese populations, and that MICA*019 is a major risk allele in Chinese AS patients. Conditional analysis of MICA alleles on HLA-B27 that unshielded LD effect confirmed associations of the MICA alleles with AS.ConclusionsParallel with HLA-B27, MICA confers strong susceptibility to AS in US white and Han Chinese populations.

| S-EPMC3874076 | biostudies-literature

ETS1 variants confer susceptibility to ankylosing spondylitis in Han Chinese.

Project description:INTRODUCTION: ETS1 is a negative regulator of the Th17 differentiation gene and plays a central role in the pathogenesis of autoimmune diseases. We aimed to investigate whether polymorphisms in ETS1 confer susceptibility to ankylosing spondylitis (AS) in Han Chinese. METHODS: We selected seven single nucleotide polymorphisms (SNPs) within ETS1 based on HapMap data and previous genome-wide association study. Genotyping involved the TaqMan method in 1,015 patients with AS and 1,132 healthy controls from Shandong Province, and 352 AS patients and 400 healthy controls from Ningxia, a northwest region in China. Gene expression was determined by real-time PCR. RESULTS: The SNP rs1128334 was strongly associated with AS (odds ratio 1.204, 95% confidence interval 1.06-1.37; P?=?0.005). This association was confiexrmed in the Ningxia population (P?=?0.015). Carriers of the haplotype TAT for rs12574073, rs1128334 and rs4937333 were associated with increased risk of AS and haplotype CGC with reduced risk as compared to controls. In addition, ETS1 expression was lower in AS patients than controls. The risk allele A of rs1128334 and haplotype A-T of rs1128334 and rs4937333 were associated with decreased expression of ETS1. CONCLUSIONS: Common variants in ETS1 may contribute to AS susceptibility in Han Chinese people.

| S-EPMC4060494 | biostudies-literature

A functional variant of PTPN22 confers risk for Vogt-Koyanagi-Harada syndrome but not for ankylosing spondylitis.

Project description:BackgroundProtein tyrosine phosphatase non-receptor 22 (PTPN22) is a key negative regulator of T lymphocytes and has emerged as an important candidate susceptibility factor for a number of immune-related diseases. This study aimed to examine the predisposition of PTPN22 SNPs to Vogt-Koyanagi-Harada (VKH) syndrome and acute anterior uveitis (AAU) associated with ankylosing spondylitis (AS).MethodsA total of 1005 VKH syndrome, 302 AAU+AS+ patients and 2010 normal controls among the Chinese Han population were enrolled in the study. Genotyping, PTPN22 expression, cell proliferation, cytokine production and cell activation were examined by PCR-RFLP, Real-time PCR, CCK8, ELISA and Flow cytometry.ResultsThe results showed significantly increased frequencies of the rs2488457 CC genotype and C allele but a decreased frequency of the GG genotype in VKH syndrome patients (PBonferroni correction (Pc) = 3.47×10(-7), OR = 1.54; Pc = 3.83×10(-8), OR = 1.40; Pc = 6.35×10(-4), OR = 0.62; respectively). No significant association of the tested SNPs with AAU+AS+ patients was observed. Functional studies showed a decreased PTPN22 expression, impaired cell proliferation and lower production of IL-10 in rs2488457 CC cases compared to GG cases (Pc = 0.009, Pc = 0.015 and Pc = 0.048 respectively). No significant association was observed concerning T cell activation and rs2488457 genotype.ConclusionsThe study showed that a functional variant of PTPN22 confers risk for VKH syndrome but not for AAU+AS+ in a Chinese Han population, which may be due to a modulation of the PTPN22 expression, PBMC proliferation and IL-10 production.

| S-EPMC4016172 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data