Computational protocol: Micro-RNA Binding Site Polymorphisms in the WFS1 Gene Are Risk Factors of Diabetes Mellitus

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Protocol publication

[…] The Hardy–Weinberg equilibrium (HWE) for genotype distributions was assessed by χ 2-test. No significant difference (p > 0.1) could be observed between the measured and expected genotype frequencies in the control group for any of the investigated SNPs. The frequency of both T1DM and T2DM is similar in females and males, and both disease types can develop at any age, although T1DM is more characteristic in juveniles, whereas symptoms of T2DM usually appear in patients older than 40. Despite, age- and sex-matched study design was used in each analysis to rule out any spurious association. Allele-wise association analysis and genotype-wise tests using dominant and recessive models were carried out by comparing the allele or genotype frequency values of each polymorphism in the patient and control group using SPSS v17.0 and HaploView v4.2[]. GWASpi[] was applied to perform Cochran–Armitage trend test[]. Correction for multiple testing was carried out to avoid false positive results using two different approaches. False Discovery Rate (FDR) was calculated by Microsoft Excel, results were verified using a web-based tool ( []. The more stringent Bonferroni correction was also applied, the accepted level of statistical significance was 0.05 / 84 = 5.95 · 10−4, as 7 loci and 3 patient categories (T1DM, T2DM and combined) were analyzed in 4 different approaches. Haplotype analysis was carried out by HaploView v4.2[]. The same software package was used to linkage disequilibrium analysis. ANOVA of the luciferase assays was carried out using GraphPad InStat (version 3.05). […]

Pipeline specifications

Software tools Haploview, GWASpi
Application GWAS
Organisms Homo sapiens
Diseases Diabetes Mellitus, Wolfram Syndrome