Computational protocol: The contribution of FTO and UCP-1 SNPs to extreme obesity, diabetes and cardiovascular risk in Brazilian individuals

Similar protocols

Protocol publication

[…] Allele and genotype frequencies were compared between case and control groups with the χ2 test using the Unphased software program v.3.0.13. Deviation of allele frequency from Hardy-Weinberg equilibrium (HWE) was tested for all SNPs using the Haploview software. In addition, linkage disequilibrium (LD) pattern between the three studied SNPs near the UCP-1 was tested also using Haploview. One thousand permutation tests were done for the SNPs near the UCP-1. We performed 1,000 permutations in each test to estimate the global significance of the results for all analyses and to validate the expectation-maximization values. Putative associations with the FTO and UCP-1 loci, including suitable adjustment for age, were assessed via regression analysis. In table , the p-value was calculated using Mann–Whitney U test to compare continuous variables, and chi-square analysis was performed to compare categorical variables. We used the Structure software to estimate the proportion of European, African and Amerindian biogeographical ancestry of each group and the Unphased software to analyze the polymorphisms and their association with obesity, diabetes, lipids, hypertension and metabolic syndrome. Nonparametric analysis was performed by the GraphPad Prism 5 to analyze a significant synergistic effect between FTO and UCP-1 SNPs with obesity. Difference in BMI between genotypes was analyzed using a multiple linear regression, with BMI as the dependent variable and genotype as the independent variable, and with gender as covariate for BMI. Statistical significance was taken at a p- value <0.05 for all comparisons. […]

Pipeline specifications

Software tools UNPHASED, Haploview
Application GWAS
Organisms Homo sapiens
Diseases Diabetes Mellitus, Hyperlipidemias, Hypertension
Chemicals Glucose