Computational protocol: The RS4939827 polymorphism in the SMAD7 GENE and its association with Mediterranean diet in colorectal carcinogenesis

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Protocol publication

[…] First, a descriptive statistical analysis was performed to determine the characteristics of our study population. For age, mean and standard deviation were calculated. For the rest of variables, we calculate frequencies of cases and controls using STATA. Table  show variables used in analysis and how they were classified. Then multivariate logistic mixed models, including the study region as a random effect term, were performed to evaluate the association between genotypes of selected polymorphisms and the risk of CRC. The same analysis was made in order to show the association of the component of the Mediterranean diet with the colorectal cancer. Adjusted odds ratios and confidence intervals at 95% were calculated by reference to the homozygous genotype of the most common allele (T allele). The minimally adjusted odds ratio was calculated by adjusting by sex, age and educational background. The adjusted odds ratios were calculated taking into account the variables mentioned before and BMI, total energy intake, family history first degree, race and METS.Finally, linear regression was used for associations between polymorphisms and the study variables. For this, the online software used was SNPstats, by the log-additive model mainly, although we also observed the results of other models (dominant, codominant, recessive and overdominant) []. By using STATA, the rs4939827 SNP association with the Mediterranean diet pattern was evaluated with logistic regression. For that, we stratified the variable of adherence to the Mediterranean diet and the genotype was also taken into account. […]

Pipeline specifications

Software tools Stata, snpStats
Application GWAS