Computational protocol: Genetic variants in adiponectin and blood pressure responses to dietary sodium or potassium interventions: a family-based association study

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Protocol publication

[…] Continuous data are presented as mean±s.e. Categorical data are expressed as frequency with percentage. Differences in the repeated measures were analysed by a paired samples t-test. The Mendelian consistency of the SNP genotype data was assessed with PLINK. Haploview software (Broad Institute, Cambridge, MA, USA) was used to test Hardy–Weinberg equilibrium on parental SNP data and estimate the extent of pairwise linkage disequilibrium (LD) between SNPs. LD blocks were defined by the solid spine LD method implemented in Haploview software. The association of single markers with adjusted phenotypes was performed using the family-based association test, and three genetic models (additive, dominant and recessive) were assumed for each SNP analysis. To assess the effect of genetic variants on the trait value, a univariate family-based association test was performed for each allele. This test provides a Z-statistic with its corresponding P-value. In the present study, a positive Z-statistic for an allele or a haplotype indicates a decreased response to the low-sodium intervention and the high-sodium plus potassium supplementation intervention, as well as an increased response to high-sodium intervention and an increase in the basal BP. The false discovery rate method was used to correct for multiple testing. A P-value of 0.05 was used as the threshold for statistical significance in our study. […]

Pipeline specifications

Software tools PLINK, Haploview, FBAT
Application GWAS
Organisms Homo sapiens
Chemicals Nitroprusside, Potassium, Sodium, Sodium Chloride