Computational protocol: Case-Control Analysis of SNPs in GLUT4, RBP4 and STRA6: Association of SNPs in STRA6 with Type 2 Diabetes in a South Indian Population

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Protocol publication

[…] Hardy Weinberg equilibrium (HWE) test was done for each SNP by Pearson's Goodness of fit Chi square test before further analysis. Association analysis of each SNP with type 2 diabetes was done by Chi-square test, for difference in allele frequency between cases and controls. Association of SNPs with type 2 diabetes was also confirmed by logistic regression analysis after adjustment for age, sex and BMI. An additive model was used for logistic regression where homozygotes for the major allele (1_1), heterozygotes (1_2) and homozygotes for the minor allele (2_2) were coded to a continuous numeric variable for the genotype as 0, 1 and 2 respectively. Linkage disequilibrium was estimated for combined data of cases and controls using Haploview version 4.1. Haplotype analysis was done by using the software SNP and Variation Suite Ver-7 from Golden Helix, Inc. Haplotype analysis was done by using all the markers in a gene as a single block. Quantitative traits were analyzed for association with type 2 diabetes by ANCOVA (available at http://faculty.vassar.edu/lowry/VassarStats.html) and multivariate regression analysis after adjustment for age, sex and BMI. Correction for multiple testing was done by Bonferroni's inequality method wherever applicable and was defined as P value (single tests) × number of tests. Bonferroni correction was not done for multiple traits due to lack of any significant association. Multiallelic analysis with sentinel SNPs in STRA6 (rs736118), RBP4 (rs3758539) and GLUT4 (rs5435) was done by ANOVA after categorizing the participants into groups according to the number of risk alleles they carried. All association analysis was performed using the software SNP and Variation Suite Ver-7 from Golden Helix, Inc. […]

Pipeline specifications

Software tools Haploview, SVS, VassarStats
Applications Miscellaneous, GWAS
Diseases Diabetes Mellitus