Computational protocol: Association of SNPs of CD40 Gene with Multiple Sclerosis in Russians

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Protocol publication

[…] Tests for the Hardy-Weinberg equilibrium were performed using the DeFinetti program available from the website of the Institute of Human Genetics (Munich, Germany; http://ihg2.helmholtz-muenchen.de/cgi-bin/hw/hwa1.pl). Associations of genotype with the disease was studied using logistic regression analysis, as implemented in “glm” function of the R package for statistical analysis (www.r-project.org). The likelihood ratio test (LRT) was used to test the statistical hypotheses and the Akaike Information Criterion (AIC) was used to decide on “best model” describing the association of MS with SNPs. Meta-analysis and Q-test were carried out using the ‘rmeta' package for R (http://cran.r-project.org/web/packages/rmeta/rmeta.pdf). Haplotype analysis was carried out using the ‘haplo.stats' package for R (http://cran.r-project.org/web/packages/haplo.stats/haplo.stats.pdf). Results were considered statistically significant for all statistical calculations if P<0.05. […]

Pipeline specifications

Software tools rmeta, haplo.stats
Application GWAS
Organisms Homo sapiens
Diseases Multiple Sclerosis, Nervous System Diseases