Computational protocol: Genetic polymorphisms in the ALDH2 gene and the risk of ischemic stroke in a Chinese han population

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Protocol publication

[…] We used SPSS version 17.0 statistical software (SPSS Inc., Chicago, IL, United States) and Excel (Microsoft Corp., Redmond, WA, United States) for statistical analyses. The Chi-squared test and the Student's t-test were used to compare genotype frequencies and allele frequencies between patients and controls. The Hardy–Weinberg equilibrium (HWE) of each SNP was determined by the Chi-squared test, which compared the actual and expected frequencies of the genotypes in the controls. Genetic associations between SNPs and the risk of stroke were tested through various genetic models which including additive, dominant, and recessive models which using SNPStats webpage (http://bioinfo.iconcologia.net). The effects of the polymorphisms on the risk of stroke were reflected as odds ratios (ORs) with 95% confidence intervals (95% CIs) which were calculated by unconditional logistic regression analyses adjusted for age and gender []. A linkage disequilibrium (LD) analysis was performed by Haploview v4.2 with genotype data. The pattern of LD was analyzed using D’ and evaluated the haplotypes of the candidate SNPs. All of the statistical tests were two-sided, and p-values < 0.05 were statistically significant. […]

Pipeline specifications

Software tools snpStats, Haploview
Application GWAS
Organisms Homo sapiens
Diseases Cerebral Infarction, Stroke
Chemicals Acetaldehyde