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A novel gene variation of TNFalpha associated with ankylosing spondylitis: a reconfirmed study.

ABSTRACT: BACKGROUND: A great deal of evidence has shown that non-human leucocyte antigen (HLA)-B27 genes may play crucial roles in the aetiology of ankylosing spondylitis (AS), but there is little evidence of a relationship with tumour necrosis factor (TNF)alpha gene variation. One functional single-nucleotide polymorphism (SNP), -850 C-->T, on the TNFalpha gene promoter region was identified and confirmed to be significantly associated with AS by our recent study. OBJECTIVE: To investigate whether the -850 C-->T SNP is a susceptibility locus for AS or is only a marker linked to potential disease gene loci in a Chinese population. METHODS: Ten common SNPs were selected from nine inflammatory genes covering the right and left flanking regions of the TNFalpha gene, which span a region of about 100 kb on chromosome 6p21.31, and a tag SNP in HCP5 gene was used to examine the linkage between the HLA-B27 and TNFalpha genes. SNPs were genotyped by PCR restriction-fragment length polymorphism (RFLP), allele-specific PCR and restriction site-generating PCR-RFLP for single-base association and linkage disequilibrium (LD). RESULTS: The prevalence of TNFalpha-850 C-->T SNP was significantly different between case and control groups. A specific haplotype covering TNFalpha gene mutant was strongly associated with AS. An LD test showed that a recombination between HLA-B27 and TNFalpha might have taken place. CONCLUSION: The TNFalpha locus was reconfirmed and showed association with susceptibility to AS. It may be independent of HLA-B27. A range of 58 kb covering TNFalpha had strong LD to AS.

SUBMITTER: Zhu X

PROVIDER: S-EPMC2111619 | biostudies-literature | 2007 Nov

REPOSITORIES: biostudies-literature

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A novel gene variation of TNFalpha associated with ankylosing spondylitis: a reconfirmed study.

Zhu Xiaoquan X Wang Yawen Y Sun Liang L Song Yuguo Y Sun Fei F Tang Lei L Huo Zhenghao Z Li Jianxin J Yang Ze Z

Annals of the rheumatic diseases 20070501 11

<h4>Background</h4>A great deal of evidence has shown that non-human leucocyte antigen (HLA)-B27 genes may play crucial roles in the aetiology of ankylosing spondylitis (AS), but there is little evidence of a relationship with tumour necrosis factor (TNF)alpha gene variation. One functional single-nucleotide polymorphism (SNP), -850 C-->T, on the TNFalpha gene promoter region was identified and confirmed to be significantly associated with AS by our recent study.<h4>Objective</h4>To investigate ...[more]

PMID: 17472990

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Project description:Genotyping was performed using a custom-designed Illumina 384-SNP VeraCode microarray (Illumina) to determine possible associations of genes encoding PADI1, PADI2, PADI3, PADI4, PADI6, PRKD3, Gc, GLRX,CDSN, PSORS1C1, TXNDC5, CA1, bub3, SORBS1, VDR,SERPNA1, PCSK6, DNAH9 to rheumatoid arthrities (RA) and ankylosing spondylitis (AS). We previously found that encoding genes of PADI1, PADI2, PADI3, PADI4, PADI6, PRKD3, Gc, GLRX,CDSN, PSORS1C1, TXNDC5, CA1, bub3, SORBS1, VDR, SERPNA1, PCSK6 and DNAH9 could be associated with rheumatoid arthritis (RA) and ankylosing spondylitis (AS). We used illumina customer designed microarray to verify the above finding with an increased numbers of samples. Genotyping was performed using a custom-designed Illumina 384-SNP VeraCode microarray (Illumina) to determine possible associations of genes encoding PADI1, PADI2, PADI3, PADI4, PADI6, PRKD3, Gc, GLRX,CDSN, PSORS1C1, TXNDC5, CA1, bub3, SORBS1, VDR, SERPNA1, PCSK6, DNAH9 to RA and AS. A case-control study was performed with 51 AS patients, 266 rheumatoid arthritis (RA) and 163 health controls. Tag single nucleotide polymorphisms (tag SNPs) across the above genes were determined by searching the HapMap database. The tag SNPs were selected on the basis of linkage disequilibrium patterns observed in the Han Chinese in Beijing (CHB) samples that were genotyped as a part of the International HapMap Project. Only SNPs with a minor allele frequency of greater than 5% with a pair-wise r2 ≥ 0.8 in the HapMap were considered. SNPs that were in exons and untranslated regions (UTR), as well as promoters and introns within 500 bp of exons were also selected. Candidate SNPs were submitted to Illumina for a design score. The Illumina Assay Design Tool filtered out SNPs that were not suitable for the Illumina platform. Finally, 382 SNPs with a design score of “1” were selected. 382 SNPs within PADI1, PADI2, PADI3, PADI4, PADI6, PRKD3, Gc, GLRX,CDSN, PSORS1C1, TXNDC5, CA1, bub3, SORBS1, VDR,SERPNA1, PCSK6, DNAH9 encoding genes were selected. Genotyping was performed using Illumina VeraCode microarray in a case-control study including 51 AS patients, 266 rheumatoid arthritis (RA) and 163 health controls We performed genotyping using a custom-designed Illumina 384-SNP VeraCode microarray (Illumina). Peripheral blood samples were collected from patients with RA (n=266, 183 female) and AS (n=51, 10 female). RA patients had a mean age of 51.7 years, while AS patients had a mean age of 35.9 years. A total of 163 (60 female) healthy individuals with a mean age of 48.0 years were blood donors. Blood samples were put into Monovette tubes containing 3.8% sodium citrate. The genotyping was conducted with the BeadXpress Reader using the Illumina VeraCode GoldenGate Assay kit. 500 ng of sample DNA were used per assay. Genotype clustering and calling were performed using BeadStudio software (Genomestudio V2010.2 Genotyping module V1.6) (Illumina). This work was completed at the Beijing Institute of Genomics.

Project description:ObjectivesThis study aimed to investigate the potential effect of the mevalonate kinase (MVK) gene polymorphisms on the pathogenesis and clinical findings in ankylosing spondylitis (AS) patients.Patients and methodsThis cross-sectional study was conducted with 103 participants (63 males, 40 females) between January 2013 and January 2014. Of these, 51 (32 males, 19 females; mean age: 37.3±10.2 years; range, 19 to 60 years) were adult AS patients who met the 1984 Modified New York Criteria, and 52 (31 males, 21 females; mean age: 33.8±12 years; range, 19 to 60 years) were healthy volunteers with similar demographics. MVK gene analysis was performed using polymerase chain reaction sequencing by isolating deoxyribonucleic acids from peripheral blood samples. We determined serum immunoglobulin (Ig)D levels using radial immunodiffusion. We performed physical examinations on the AS patients. The Bath Ankylosing Spondylitis Disease Activity Index and the Bath Ankylosing Spondylitis Functional Index forms were filled and erythrocyte sedimentation rate, C-reactive protein, and IgD levels were recorded.ResultsThere was no statistically significant difference in the mean age between the groups (p=0.121). The frequency of symptomatic single nucleotide polymorphisms (SNPs), c.769-38 C>T heterozygous, c.769-7 T>G heterozygous, and c.769-38 C>T homozygous were similar between the groups (15/15; p=0.646). Nonsymptomatic SNPs were more common in the patient group, but the difference was not significant (83/58; p>0.05). The rate of having an MVK gene polymorphism was 36 (70.6%) in the AS compared to the 33 (63.4%) in the control group (p>0.05). There were no associations in clinical findings between the AS patients with or without MVK gene polymorphisms. New heterozygous SNPs, I56V A>G, E281D G>D, V80I G>A, and C173Y G>A, were present in four AS patients.ConclusionThe frequency of MVK gene polymorphisms was higher in AS patients than in healthy controls. But there was no statistically significant difference. We determined no effect of the present polymorphisms on AS clinical and laboratory findings.

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A novel gene variation of TNFalpha associated with ankylosing spondylitis: a reconfirmed study.

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A novel gene variation of TNFalpha associated with ankylosing spondylitis: a reconfirmed study.

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