Computational protocol: A at Single Nucleotide Polymorphism-358 Is Required for G at -420 to Confer the Highest Plasma Resistin in the General Japanese Population

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Protocol publication

[…] In the human population study, values are expressed as the mean±standard deviation. Differences in plasma resistin levels among genotypes were assessed by analysis of variance (ANOVA). Bonferroni's correction was applied to (raw P value ×8). To assess isolated effects of each SNP on plasma resistin, multiple regression analyses involving each SNP, age (year), gender (male = 1, female = 0), and BMI as independent variables, and plasma resistin (ng/ml) as a dependent variable were performed. In these analyses, we assume that the major and minor alleles based on the allele frequency are normal (N), and susceptibility (S) alleles, respectively. Each SNP genotype, N/N, N/S, and S/S, were denoted by two dummy variables (c1, c2)  = (0, 0), (1, 0), and (0, 1), respectively. This first dummy variable estimates the difference between N/S and N/N, and the second between S/S and N/N. These analyses were performed using a commercially available statistical software package (JMP ver. 7, SAS Institute, Cary, NC). Linkage disequilibrium (LD) was assessed using the Haploview software . Frequency and plasma resistin in each haplotype defined by SNP-420 and SNP-358 genotypes were estimated using SNPstats . ANOVA followed by Scheffe as a post-hoc test was used where indicated. Null hypotheses were rejected at P<0.05. […]

Pipeline specifications

Software tools Haploview, snpStats
Application GWAS
Organisms Mus musculus, Homo sapiens
Diseases Diabetes Mellitus