Computational protocol: Molecular insights into the OGG1 gene, a cancer risk modifier in BRCA1 and BRCA2 mutations carriers

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Protocol publication

[…] Pearson's chi-squared test was used to calculate whether differences in the frequency of the SNP among the FBOC groups were significant, .Telomere length (Kb) was adjusted to the age, using the best fit line controls (y= −0.067* age (years) +12.785). The difference between the actual and the predicted value was calculated for each sample.For the comparative analysis we have considered healthy or affected (patients with cancer antecedents) BRCA1 and BRCA2 mutation carriers in a single group BRCA1/2. We performed an independent linear regression analysis, using cancer status as a binary variable to test whether it could affect significantly OGG1 mRNA expression, TL or percentage of short telomeres ().Kolmogorov-Smirnov test was used to evaluate if the data sets were normally distributed. For the comparative analysis (OGG1 mRNA expression, Telomere studies and γH2AX nuclear intensity signal), statistically significant differences were assessed by Mann-Whitney U test for not normal distributions (Figures: , , , ) and complementary, using lineal regression analysis whenever necessary:Regarding the expression studies, lineal regression model including as explanatory variable OGG1 SNP, was run to test whether this variable could affect OGG1 mRNA levels in each FBOC group (BRCA1/2 carriers, BRCAX cases and non-carriers controls).In relation with the TL studies, a linear regression model was created including as explanatory variables age and the SNP among the different genotypes. Then, if significant differences were found, a separate model was created for each of the genotypes: i) Controls (all) ii) BRCA1/2 carriers harboring the variant iii) BRCA1/2 carriers without the variant. Significant differences among the models were tested with F-test (Figure ).For all the analysis, bilateral p values less than p<0.05 where considered significant.Statistical calculations were done by SPSS version 18 (SPSSI« Inc, Chicago, Illinois), the R project for statistical computing, GraphPad Prim 5.03 (San Diego, California), and graphics were performed by GraphPad Prim 5.03 (San Diego, California) […]

Pipeline specifications

Software tools SPSS, The R Project for Statistical Computing
Application Miscellaneous
Diseases Neoplasms, Ovarian Neoplasms