Computational protocol: The Association between NOS3 Gene Polymorphisms and Hypoxic Ischemic Encephalopathy Susceptibility and Symptoms in Chinese Han Population

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Protocol publication

[…] The Hardy-Weinberg equilibrium (HWE) was determined using Haploview 4.1 to examine the genotype distributions of the three SNPs in the NOS3 gene and establish whether or not the given sample comes from a normally distributed population. The strength of the linkage disequilibrium between the three SNPs was determined using D′ and r 2 algorithm testing with the SHEsis online software (http://analysis.bio-x.cn/myAnalysis.php) []. The differences in the genotypic and allelic frequency distributions between the patients with HIE and the control group were estimated with the SPSS software 18.0 using the Pearson chi-square (χ 2) test. Haplotype analysis for the NOS3 gene was performed using the online SNPStats software (http://bioinfo.iconcologia.net/snpstats) []. The associations between the SNPs in the NOS3 gene and the clinical characteristics were also analyzed with SPSS 18.0 using the χ 2 test. To control for possible confounding effects by gender, birth weight, and gestation week, sample stratification was repeated with these factors. Bonferroni correction was applied to avoid a type I error in the multiple tests []. The Genetic Power Calculator was used for the power analysis []. All of the statistical analyses were two-tailed, and the level of statistical significance was adjusted to P < 0.05. […]

Pipeline specifications

Software tools Haploview, snpStats
Application GWAS
Organisms Homo sapiens
Diseases Brain Diseases, Brain Ischemia