Computational protocol: Polymorphism of Nitric Oxide Synthase 1 Affects the Clinical Phenotypes of Ischemic Stroke in Korean Population

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Protocol publication

[…] Hardy–Weinberg equilibrium (HWE) was assessed using a chi-squared test. The HWE is a principle stating that the genetic variation in a population will remain constant from one generation to the next in the absence of disturbing factors. The HWE can be disturbed by several factors including mutations, natural selection, nonrandom mating, and genetic drift. A significant result (p<0.05) means that controls are not in HWE []. SNPAnalyzer-Pro (ISTECH, Goyang, Korea), HelixTree (Golden Helix, Bozeman, United States), and SNPStats (http://bioinfo.iconcologia.net/index.php?module=Snpstats) were used to analyze genetic data. Multiple logistic regression models (codominant 1, codominant 2, dominant, recessive, overdominant, and log-additive) were performed to determine the odds ratios (ORs), 95% confidence intervals (CIs) and p-values, (age and gender were controlled as co-variables). For the statistical power, the required case size in each SNP was calculated using the genetic power calculator (http://pngu.mgh.harvard.edu/~purcell/gpc/cc2.html). The statistical significance level was considered as a p-value below 0.05. […]

Pipeline specifications

Software tools HelixTree, snpStats
Application GWAS
Organisms Homo sapiens
Diseases Cerebral Infarction, Stroke
Chemicals Nitric Oxide