Computational protocol: Role of MMP-1 (-519A/G, -1607 1G/2G), MMP-3 (Lys45Glu), MMP-7 (-181A/G), and MMP-12 (-82A/G) Variants and Plasma MMP Levels on Obesity-Related Phenotypes and Microvascular Reactivity in a Tunisian Population

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Protocol publication

[…] DNA was isolated as previously described []. Allelic discrimination between variants was performed by PCR-RFLP. The PCR reactions (25 μl) contained 100 ng of genomic DNA, 25 μM of each deoxynucleotide triphosphate (dNTP, Biotools Inc.), 50 pmol of each primer, 2.5 mM of MgCl2, and 0.5 units of Taq polymerase (Promega, Madison, WI, USA). Details of primers and PCR-RFLP conditions are reported in . The PCR digestions were repeated in more than 10% of the samples, to assess the reliability of genotyping, and no differences were found (). [...] SPSS® 17.0 software (Chicago, IL, USA) and GraphPad Prism (version 6.04) were used for statistical analyses. Comparisons of quantitative variables were carried out using a t-test or the Mann–Whitney U test as appropriate. Comparison of categorical variables including calculation for deviation from the Hardy–Weinberg equilibrium (HWE) was performed using the chi-square (χ2) test. The evaluation of odds ratios (ORs) and 95% confidence intervals (CIs) was carried out using an unconditional logistic regression model adjusted for age and sex. Haplotypes and linkage disequilibrium (LD) were analyzed with SNPstats (http://bioinfo.iconcologia.net/SNPstats). Results were considered statistically significant if the P value <0.05. The Bonferroni correction (Pc) was applied to adjust for multiple comparisons. […]

Pipeline specifications

Software tools Biotools, snpStats
Applications Population genetic analysis, GWAS