Computational protocol: A Nonsynonymous FCER1B SNP is Associated with Risk of Developing Allergic Rhinitis and with IgE Levels

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Protocol publication

[…] Statistical analyses were carried out by using the Statistical Package for the Social Sciences (SPSS) version 19.0 for Windows (SPSS Inc., Chicago, Ill. USA). Genotype, allelic and Hardy-Weinberg equilibrium analyses were performed by using the software PLINK.The comparison of the frequencies for alleles and genotypes between patients and control individuals was performed with the χ2 statistics or Fisher exact test, as appropriate. The putative association between the SNPs and the risk of developing rhinitis was estimated by determining the odds ratio (OR) and the 95% confidence interval (CI). Multiple comparison adjustments were done by using the False Discover Rate (FDR) correction. The statistical significance of the differences in analytical or clinical parameters were calculated by using the non-parametric Kruskall-Wallis test for independent samples. The gene-dose effect was analyzed by using the test for trend (Cochran-Armitage test). Potential confounders considered in this study were the type of allergic rhinitis, age, gender, familial antecedents of the disease, smoking habits, the presence of asthma and asthma severity step. Multiple analyses were performed by using logistic regression. Differences in the parameters determined were considered to be statistically significant when adjusted p values were lower than 0.05.In order to calculate the statistical power of the study, we evaluated the sample size with a genetic model based on the frequency for carriers of the risk SNP with an OR value = 2 (α = 0.05). According to the sample size in this study, the statistical power (two-sided associations) for the risk related to the presence of the variant alleles was higher than 99.8% for all SNPs except for the SNPs rs569108 (power = 93.2%) and rs512555 (power = 92.6%). […]

Pipeline specifications

Software tools SPSS, PLINK
Applications Miscellaneous, GWAS
Organisms Homo sapiens
Diseases Asthma, Rhinitis, Allergic, Seasonal