High‐throughput single‐nucleotide polymorphism analysis of the IL1RN locus in patients with ankylosing spondylitis by matrix‐assisted laser desorption ionization‐time‐of‐flight mass spectrometry

Open Access
Publisher Website
Google Scholar
Abstract
Objective To examine single‐nucleotide polymorphisms (SNPs) in the 3′ region of the IL1RN gene in a large Caucasoid case–control series and in ankylosing spondylitis (AS) families from Western Canada by use of high‐throughput MassArray matrix‐assisted laser desorption ionization–time‐of‐flight (MALDI‐TOF) mass spectrometry SNP typing. Methods An association analysis was performed in a case–control cohort of 394 AS cases and 500 controls. Family‐based association analysis was performed in 58 simplex and 13 multiplex families. Three SNPs located in the 3′ region of the IL1RN gene (T/C at position 27810 in exon 4, T/C at position 30735 in exon 6, and G/C at position 31017 in exon 6) were examined by high‐throughput MassArray MALDI‐TOF mass spectrometry. Haplotype inference software programs were used to infer the most likely haplotypes and to compare haplotype frequencies, which were then further analyzed in family‐based association studies by transmission disequilibrium tests. Results The frequency of allele C at SNP position 30735 in exon 6 was significantly increased in AS cases (35.1%) versus controls (27.8%), as was the phenotype frequency (61.7% versus 48.6%). A significantly increased frequency of SNP allele G at position 31017 in exon 6 in cases (32.9%) versus controls (28.3%) was also noted. A highly significant difference in the overall distribution of haplotype frequencies was evident between cases and controls, with significant increases in the frequencies of the 27810C/30735C/31017C and 27810C/30735T/31017G haplotypes, but a significant reduction in the estimated frequency of the 27810C/30735T/31017C haplotype, in the AS cases. Estimation of haplotype frequencies based on 2 SNP markers indicated a highly significant increase in the 30735C/31017C haplotype and a highly significant decrease in the 30735T/31017C haplotype in cases compared with controls. Preliminary evidence for reduced transmission of the 27810C/30735T/31017C 3‐marker haplotype was also found in family‐based association analyses. Conclusion Our data establish a highly significant disease association with markers in the IL1RN gene. In the absence of nonsynonymous coding sequence substitutions, it is possible that the primary disease‐associated locus regulates gene expression. Association with specific haplotypes raises the possibility that the primary disease locus is in linkage disequilibrium with a specific combination(s) of markers in the IL1RN gene.