Computational protocol: CEACAM6 Gene Variants in Inflammatory Bowel Disease

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Protocol publication

[…] Each genetic marker was tested for Hardy-Weinberg equilibrium in the three subgroups of the study population. Fisher's exact test was used for comparison between categorical variables, while Student's t test was applied for quantitative variables. Single-marker allelic tests were performed with Pearson's χ2 test. All tests were two-tailed, considering p-values<0.05 as significant. Odds ratios were calculated for the minor allele at each SNP. For multiple comparisons, Bonferroni correction was applied where indicated. Interactions between different polymorphisms were tested using logistic regression in R using the number of minor alleles as predictor variable, therefore implementing an Armitage test of trend. Data were evaluated by using the SPSS 13.0 software (SPSS Inc., Chicago, IL, USA) and R-2.4.1. (http://cran.r-project.org). For haplotype analysis, PLINK v 1.06 (http://pngu.mgh.harvard.edu/~purcell/plink/) was used running a sliding window approach with variation of the window size from 2 to 8 included markers and using the option “hap-logistic”. Linkage disequilibrium (LD) was also analyzed using PLINK. […]

Pipeline specifications

Software tools SPSS, PLINK
Applications Miscellaneous, GWAS
Organisms Escherichia coli, Homo sapiens
Diseases Colitis, Ulcerative, Crohn Disease, Inflammatory Bowel Diseases