Computational protocol: TREM-1 SNP rs2234246 regulates TREM-1 protein and mRNA levels and is associated with plasma levels of L-selectin

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Protocol publication

[…] All investigated molecules (intermediate phenotypes) were log transformed in order to normalise their distribution before analyses. The normality of distribution was tested by Kolmogorov-Smirnov test. Hardy-Weinberg equilibrium was tested using the chi-square test. The SNPs-mRNA and soluble TREM-1 levels associations were assessed through linear regression adjusted for age, gender and BMI under three inheritance models (additive, dominant and recessive) and using the minor allele as the reference allele. The association of the most significant SNPs with selectins levels were tested using similar models. Association studies were performed using the Plink Software []. Populations’ characteristics were determined using the SPSS statistical software version 20.0 (SPSS, Inc, Chicago, Illinois). Bonferroni correction was applied in order to adjust the multiplicity of tests and avoid the type 1 error. Cut-offs were 0.05/ number of SNPs for the association of the selected SNPs with soluble TREM-1 levels, 0.05/ number of SNPs/2 for the associations of the significant SNPs with the 2 mRNA levels and 0.05/number of SNPs/number of selectins for the associations of the significant SNPs with the selectins’ levels. […]

Pipeline specifications

Software tools PLINK, SPSS
Applications Miscellaneous, GWAS
Diseases Atherosclerosis