Computational protocol: Variable number of tandem repeat polymorphisms of the interleukin-1 receptor antagonist gene IL-1RN: a novel association with the athlete status

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Protocol publication

[…] The genotype frequencies for each polymorphism were compared by 2-sided Pearson chi-square or Fisher's exact test as appropriate, using STATA statistical software version 10, College Station, TX, USA and Powermarker []. The odds ratio (OR) and the 95% confidence interval (CI) were calculated to evaluate the genotype effects of each genotype against all others. Tests for deviations from Hardy-Weinberg equilibrium (HWE) were performed in Powermarker, using a chi-square distribution in cases and controls separately for each SNP. Haplotype analysis was performed with the program Unphased []. Haplotypes estimated to be below 1% in frequency were not reported. Due to the low allele frequencies of the 3, 4 and 5 allele of IL-1RN, the intron 2 VNTR genotypes were grouped into the short allele (S, allele 2) and the long alleles (L, alleles 1, 3, 4, and 5) according to Machado et al. []. Linkage disequilibrium (LD) between the two SNPs in IL-1B and the VNTR short and long alleles in IL-1RN was determined using Haploview []. Differences in the haplotype distributions between cases and controls were determined by likelihood ratio tests. The reference distribution for which all the other haplotypes were compared against was the most common haplotype. The OR was considered significant if the CI did not cross unity. The P-value for each haplotype was determined by comparing the haplotype against all others. Therefore, a P-value may be slightly significant even if the OR is not. […]

Pipeline specifications

Software tools PowerMarker, UNPHASED, Haploview
Application GWAS
Organisms Homo sapiens
Diseases Athletic Injuries