Protective association of tumor necrosis factor superfamily 15 (TNFSF15) polymorphic haplotype with Ulcerative Colitis and Crohn's disease in an Indian population.

BACKGROUND: Tumor necrosis factor superfamily (TNFSF) proteins are involved in the genesis of inflammatory bowel disease (IBD). We examined the association of seven single nucleotide polymorphisms (SNP) in the TNFSF15 gene with Crohn's disease (CD) and ulcerative colitis (UC) in the Indian population. METHODS: Seven SNPs in the TNFSF15 gene (rs10114470, rs3810936, rs6478108, rs4263839, rs6478109, rs7848647 and rs7869487) were genotyped in 309 CD patients, 330 UC patients and 437 healthy controls using the Sequenom iPLEX MassArray platform. Disease associations were evaluated for allelotypes and for genotypes. RESULTS: The minor T alleles and the TT genotypes of rs10114470 and rs3810936 were significantly protectively associated with both CD and UC. The CC genotype of rs6478108, AA genotype of rs4263839, the AA genotype of rs6478109, the TT genotype of rs7848647 and the CC genotype of rs7869487 were all protectively associated with CD but not with UC. Two haplotype blocks could be discerned, one where SNPs rs10114470 and rs3810936 were in tight LD (D' = 0.8) and the other where rs6478108, rs4263839, rs6478109, rs7848647 and rs7869487 were in tight LD (D' 0.92-1.00). The second block of haplotypes were not associated with CD or with UC. The first block of haplotypes was very significantly associated with both CD and UC. CONCLUSIONS: Strong associations exist between TNFSF15 gene polymorphisms and IBD (both CD and UC) in the Indian population

Association of ATG16L1 gene haplotype with inflammatory bowel disease in Indians.

Inflammatory bowel disease (IBD) is characterized by multigenic inheritance. Defects in autophagy related genes are considered to show genetic heterogeneity between populations. We evaluated the association of several single nucleotide polymorphisms (SNPs) in the autophagy related 16 like 1 (ATG16L1) gene with IBD in Indians. The ATG16L1 gene was genotyped for ten different SNPs using DNA extracted from peripheral blood of 234 patients with Crohn's disease (CD), 249 patients with ulcerative colitis (UC) and 393 healthy controls The SNPs rs2241880, rs4663396, rs3792106, rs10210302, rs3792109, rs2241877, rs6737398, rs11682898, rs4663402 and rs4663421 were genotyped using the Sequenom MassArray platform. PLINK was used for the association analysis and pairwise linkage disequilibrium (LD) values. Haplotype analysis was done using Haploview. All SNPs were in Hardy Weinberg equilibrium in cases and controls. The G allele at rs6737398 exhibited a protective association with both CD and UC. The T allele at rs4663402 and C allele at rs4663421 were positively associated with CD and UC. The T allele at rs2241877 exhibited protective association with UC only. The AA genotype at rs4663402 and the GG genotype at rs4663421 were protectively associated with both CD and UC. Haplotype analysis revealed that all the SNPs in tight LD (D' = 0.76-1.0) and organized in a single haplotype block. Haplotype D was positively associated with IBD (P = 5.8 x 10-6 for CD and 0.002 for UC). SNPs in ATG16L1 were associated with IBD in Indian patients. The relevance to management of individual patients requires further study

Association of <i>IRGM</i> Gene Mutations with Inflammatory Bowel Disease in the Indian Population

<div><p>Background</p><p>Mutations in the <i>IRGM</i> gene have been associated with Crohn's disease in several populations but have not been explored in Indian patients with this disease. This study examined the association of <i>IRGM</i> mutations with ulcerative colitis and Crohn's disease in Indian patients with inflammatory bowel disease.</p><p>Methods</p><p>The <i>IRGM</i> gene was amplified in four segments and Sanger-sequenced in 101 participants (42 Crohn's disease, 39 ulcerative colitis, and 20 healthy controls). Ten single nucleotide polymorphisms (SNP) were genotyped in 1200 participants (352 Crohn's disease, 400 ulcerative colitis, and 448 healthy controls) using Sequenom MassARRAY iPLEX. Disease associations were evaluated for each of the ten SNPs.</p><p>Results</p><p>Thirty one mutations were identified in the <i>IRGM</i> gene, of which two had not hitherto been reported (150226250- ss947429272 & 150227858- ss947429273). Ten SNPs (6 from the above and 4 from the literature) were evaluated. Significant associations with Crohn's disease were noted with the T allele of rs1000113 (OR 1.46, 95% CI 1.12–1.90), T allele of rs9637876 (OR 1.25, 95% CI 1.005–1.561) and C allele of rs 13361189 (OR 1.33, 95% CI 1.07–1.669). Two SNPs – rs11747270 and rs180802994 – did not exhibit Hardy-Weinberg equilibrium but were associated with both Crohn's disease and ulcerative colitis in this population. The remaining SNPs did not show significant associations with either Crohn's disease or ulcerative colitis.</p><p>Conclusions</p><p>Association of <i>IRGM</i> gene SNPs with Crohn's disease is reported for the first time in Indian patients. We also report, for the first time, an association of rs 9637876 in the <i>IRGM</i> gene with Crohn's disease.</p></div

Haplotype A-F frequency estimates in controls and IBD patients.

<p>*Indicates significant P value.</p><p>Haplotype A-F frequency estimates in controls and IBD patients.</p

SNPs identified by sequencing of the <i>IRGM</i> gene in Indians.

<p>SNPs identified by sequencing of the <i>IRGM</i> gene in Indians.</p

Haplotype frequency in cases and controls.

<p>Haplotypes indicated in Bold exhibited plausible association with CD. Rest of the haplotypes did not show any association with CD. None of these haplotypes was associated with UC.</p><p>Haplotype frequency in cases and controls.</p

Structure of haplotypes G-N constructed using LD among all 7 TNFSF15 SNPs examined in the study.

<p>Structure of haplotypes G-N constructed using LD among all 7 TNFSF15 SNPs examined in the study.</p

Clinical characteristics of the study population.

<p>Clinical characteristics of the study population.</p

Linkage pattern between IRGM SNPs.

<p>rs13361189, rs10059011, rs9637876, rs72553867, rs4958847 and rs1000113 were in tight linkage dysequilibrium and were organised in a single haplotype block (D′ = 1).</p

Primers and products in PCR amplification of <i>IRGM</i> gene.

<p>52°C was the annealing temperature for all four overlapping PCRs. Primers 2 & 3 were chosen from a previously published article (17) and primers 1 & 4 were newly designed using GeneFisher2 (20).</p><p>Primers and products in PCR amplification of <i>IRGM</i> gene.</p