Computational protocol: Polymorphisms of Renin-Angiotensin-Aldosterone System Gene in Chinese Han Patients with Nonfamilial Atrial Fibrillation

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Protocol publication

[…] Some tSNPs of RAS system gene were selected by using genotype data obtained from the International HapMap Project (http://hapmap.ncbi.nlm.nih.gov) data (released # 27/PhaseII+III Feb 09). To identify common tagging SNPs, these eligible SNPs were entered into the Tagger program implemented in Haploview 4.2 program (http://www.broad.mit.edu/haploview/haploview-downloads). We defined the common variants as those with minor allele frequency (MAF) of more than 5% and set the threshold of 0.8 for LD measure r2. In the end, a total of 10 tSNPs (ACE gene rs8066114, AGT gene rs7539020, rs3789678, rs2478544, rs11568023, rs2478523, rs4762, rs699 and CYP11B2 rs3802230, rs3097) were chosen in our study. [...] The statistical analyses were performed with the Stata statistical package (version 10.0; StataCorp LP, College Station, TX, USA). The quantitative variables were presented as the mean ± SD, which are normally distributed. Measured variables were compared in patients with and without AF and the healthy group by an unpaired Student’s t-test. Hardy-Weinberg Equilibrium (HWE) was tested in the healthy group by the chi-square test. The allele frequency, genotype, haplotype as well as dihaplotype between the groups were examined by unconditional logistic regression analysis with adjustment for age, gender, LVEF, LVEDD, LAD and frequency of hypertension and diabetes. P < 0.05 was considered statistically significant.The pairwise linkage disequilibrium (LD) among the SNPs was examined using Lewontin’s standardized coefficient D’ and LD coefficient r2 [], and haplotype blocks were defined by the method of Gabriel et al. [] in Haploview 4.2 with default settings (the CI for a strong LD was minimal for upper 0.98 and low 0.7 and maximal for a strong recombination of 0.9, and a fraction of strong LD in informative comparisons was at least 0.95). In addition, PHASE 2.1 Bayesian algorithm [] was used to estimate the haplotype frequencies. The HAPLO.STATS package developed by Schaidet al. [] (http://www.mayo.edu/hsr/Sfunc.html) in the software language R was used for the haplotype analysis. Haplotypes with a frequency of less than 0.03 were pooled into a combined group. Diplotype (haplotype dosage, an estimate of the number of copies of the haplotype) was the most probable haplotype pair for each individual. Unconditional logistic regression analyses were conducted to estimate ORs and 95% CIs for participants carrying one to two copies versus zero copy of each common haplotype for the dichotomized diplotypes. […]

Pipeline specifications

Software tools Tagger, Haploview, haplo.stats
Databases International HapMap Project
Application GWAS
Organisms Homo sapiens
Diseases Diabetes Mellitus, Heart Diseases, Hypertension
Chemicals Aldosterone