Dataset Information

The -590C/TIL4 single-nucleotide polymorphism as a genetic factor of atopic allergy.

ABSTRACT: Elevated IgE levels in individuals with asthma, allergic rhinitis, and atopic dermatitis represents a situation in that increased IL4 production seems to occur because of the genetic component of the disease. In this study, one-hundred two matched-pairs of allergic and non-allergic individuals were phenotyped for total serum IgE level using enzyme-linked immunosorbent assay (ELISA). Atopic status was defined by serum IgE concentration ?100 IU/mL The -590C/T IL4 (rs2243250) was screened by polymerase chain reaction-restriction fragment-length polymorphism (PCR-RFLP) analysis. An association between the IL4 -590 TT genotype and levels of IgE was confirmed in the study population (ANOVA p=0.017). Furthermore, the IL4 T allele was significantly increased in allergic (0.299) compared with non-allergic subjects (0.172) (OR=2.060, 95% 01 = 1.285-3.301, ?(2) uncorrected p=0.002) at total serum IgE cut-off of 100 IU/mL. A significant relationship between IL4 -590 TT genotype and very high IgE levels (>1000 IU/mL) (OR=3.968, 95% CI = 1.499-10.5, ?(2) uncorrected p=0.01624) was also established. The -590C/T IL4 polymorphism is a potential risk factor to and correlates with atopic allergy.

SUBMITTER: de Guia RM

PROVIDER: S-EPMC3076745 | biostudies-literature | 2010

REPOSITORIES: biostudies-literature

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The -590C/TIL4 single-nucleotide polymorphism as a genetic factor of atopic allergy.

de Guia Roldan M RM Ramos John Donnie A JD

International journal of molecular epidemiology and genetics 20091125 1

Elevated IgE levels in individuals with asthma, allergic rhinitis, and atopic dermatitis represents a situation in that increased IL4 production seems to occur because of the genetic component of the disease. In this study, one-hundred two matched-pairs of allergic and non-allergic individuals were phenotyped for total serum IgE level using enzyme-linked immunosorbent assay (ELISA). Atopic status was defined by serum IgE concentration ≥100 IU/mL The -590C/T IL4 (rs2243250) was screened by polyme ...[more]

PMID: 21537454

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Project description:BackgroundGenome-wide association studies (GWAS) identify disease-associations for single-nucleotide-polymorphisms (SNPs) from scattered genomic-locations. However, SNPs frequently reside on several different SNP-haplotypes, only some of which may be disease-associated. This circumstance lowers the observed odds-ratio for disease-association.Methodology/principal findingsHere we develop a method to identify the two SNP-haplotypes, which combine to produce each person's SNP-genotype over specified chromosomal segments. Two multiple sclerosis (MS)-associated genetic regions were modeled; DRB1 (a Class II molecule of the major histocompatibility complex) and MMEL1 (an endopeptidase that degrades both neuropeptides and β-amyloid). For each locus, we considered sets of eleven adjacent SNPs, surrounding the putative disease-associated gene and spanning ∼200 kb of DNA. The SNP-information was converted into an ordered-set of eleven-numbers (subject-vectors) based on whether a person had zero, one, or two copies of particular SNP-variant at each sequential SNP-location. SNP-strings were defined as those ordered-combinations of eleven-numbers (0 or 1), representing a haplotype, two of which combined to form the observed subject-vector. Subject-vectors were resolved using probabilistic methods. In both regions, only a small number of SNP-strings were present. We compared our method to the SHAPEIT-2 phasing-algorithm. When the SNP-information spanning 200 kb was used, SHAPEIT-2 was inaccurate. When the SHAPEIT-2 window was increased to 2,000 kb, the concordance between the two methods, in both of these eleven-SNP regions, was over 99%, suggesting that, in these regions, both methods were quite accurate. Nevertheless, correspondence was not uniformly high over the entire DNA-span but, rather, was characterized by alternating peaks and valleys of concordance. Moreover, in the valleys of poor-correspondence, SHAPEIT-2 was also inconsistent with itself, suggesting that the SNP-string method is more accurate across the entire region.Conclusions/significanceAccurate haplotype identification will enhance the detection of genetic-associations. The SNP-string method provides a simple means to accomplish this and can be extended to cover larger genomic regions, thereby improving a GWAS's power, even for those published previously.

Dataset Information

The -590C/TIL4 single-nucleotide polymorphism as a genetic factor of atopic allergy.

Publications

The -590C/TIL4 single-nucleotide polymorphism as a genetic factor of atopic allergy.

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