Computational protocol: Pleiotropic Effect of Common Variants at ABO Glycosyltranferase Locus in 9q32 on Plasma Levels of Pancreatic Lipase and Angiotensin Converting Enzyme

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Protocol publication

[…] Under the assumption of the additive effect of minor allele dosage, we carried out linear regression for each SNP from Infinium and Golden Gate Assays on the plasma levels of P-LIP and ACE separately with adjustment by age and gender as covariates, in which the statistical significance of each regression coefficient was evaluated by p value from the Wald test using the PLINK software package . In addition, we carried out linear regression for the P-LIP and ACE levels on the same SNP set by applying an additional adjustment by potential confounders, alcohol intake (for P-LIP) and smoking (for ACE), and then by applying the Box-Cox normalizing transformation. We also carried out regression diagnosis for these analysis (). Finally, we carried out one-way ANCOVA (analysis of covariance) to compare mean levels of genomically-deduced ABO groups (i.e. six categories) in the combined population separately for the P-LIP and ACE, with adjustment for age and gender as well as rs4356 (i.e. the effect of ACE1), in which AA is set as the baseline group in the corner-point parameterization. These standard genetical/statistical analyses were done with the PLINK software package , the EIGENSTRAT software program and the Haploview , in addition to the MASS package and the R statistical environment . […]

Pipeline specifications

Software tools PLINK, Haploview
Application GWAS
Organisms Homo sapiens
Diseases Pancreatic Neoplasms