Computational protocol: Associations of common polymorphisms in GCKR with type 2 diabetes and related traits in a Han Chinese population: a case-control study

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Protocol publication

[…] Continuous variables are expressed as the means ± SEM. Comparisons between groups were performed with T testing and χ2 testing for normally distributed continuous and categorical variables, respectively. Deviations from the Hardy-Weinberg equilibrium were assessed by means of χ2 testing. SNPs that were not in Hardy-Weinberg equilibrium were excluded from further analysis. Pairwise linkage disequilibrium including D' and r2 was estimated using Haploview. Haplotypes estimating from the population genotype data were performed in Haplo. Stats (R2.8.1). We did allelic analysis for the association of GCKR polymorphisms with type 2 diabetes using logistic regression. We did genotypic analysis for the association of GCKR polymorphisms with quantitative traits using a general linear model, assuming an additive model. We tested the association of haplotypes with type 2 diabetes and quantitative traits by using logistic regression and a general linear model. Non-normally distributed values were log-transformed before analysis. All models were adjusted for year of birth and sex. Additional models were adjusted for BMI. Analysis was performed using SPSS software version 13.0. We used Bonferroni correction for multiple testing. […]

Pipeline specifications

Software tools Haploview, haplo.stats, SPSS
Applications Miscellaneous, GWAS
Diseases Diabetes Mellitus, Machado-Joseph Disease, Dyslipidemias