Computational protocol: Association of the Adiponectin Gene Variations with Risk of Ischemic Stroke in a South Korean Population

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Protocol publication

[…] In the preliminary experiment with 320 Affymetrix 250 k NSP chips, SNPs in genes that were associated with the combined phenotype of ischemic stroke were identified (p < 0.01), and we selected several SNPs within the 100-kb upstream and downstream regions (using the Affymetrix annotation file; Mapping205K_Nsp.na22.annot.csv). We searched the GeneCards, OMIM, and PubMed databases and found 768 stroke-related genes compared with the SNPs in the preliminary experiment.In a follow-up association analysis (the Illumina Golden Gate experiment), we selected 10 tag SNPs in the AdipoQ gene, which was one of the candidate genes related to ischemic stroke. The 10 tag SNPs were selected if they had an efficiency of more than 80% using Haploview and HapMap Japanese data (http://www.hapmap.org). [...] Differences in clinical characteristics between the 2 groups were determined by a Student's t-test for continuous variables [age, body-mass index (BMI)] and a Chi-squared test for categorical variables (sex, hypertension, diabetes mellitus, and hypercholesterolemia). The Chi-squared test was used to measure Hardy-Weinberg equilibrium (HWE) for comparing allele and genotype frequencies between cases and controls. The relative risk for stroke associated with genotype in the case-control analysis was calculated with odds ratios (ORs) [95% confidence interval (CI)] using logistic regression models and corresponding p values, while controlling for age and sex as covariates [software: PLINK (v1.03, http://pngu.mgh.harvard.edu/~purcell/plink/)].Three alternative models for the minor alleles-codominant, dominant, and recessive-were applied in our analyses. For each OR, we calculated 95% CIs. Association analysis of the haplotypes was performed using Haploview (v 4.1). Logistic regression models were used to estimate odds ratios that assessed the association between AdipoQ haplotypes and stroke, adjusting for sex and age [software: PLINK (v1.03)]. A 2-tailed p value < 0.05 was significant. […]

Pipeline specifications

Software tools Haploview, PLINK
Databases OMIM GeneCards
Application GWAS
Organisms Homo sapiens
Diseases Cerebral Infarction, Death, Ischemia, Stroke