Computational protocol: Oncogene amplification in male breast cancer: analysis by multiplex ligation-dependent probe amplification

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Protocol publication

[…] Statistical calculations were performed using SPSS for Windows v15.0. Correction for multiple comparisons was applied by resetting the 0.05 threshold according to the Holm–Bonferroni method. Differences between gene copy number and clinicopathological characteristics were calculated with ANOVA for continuous variables and with Pearson Chi-square (or Fisher’s exact test when appropriate) for categorical variables. The following clinicopathological features were dichotomized: age (>50 years), tumor size (>2.0 cm), mitotic activity (>8 mitoses/2 mm2), and histological grade (grade 1/2 vs 3). Correlation between number of gene amplification and clinicopathological features were calculated with Spearman’s rho. Unsupervised hierarchical clustering using the statistical program R (www.r-project.org) was performed to identify relevant clusters and co-amplification. We used the maximum distance and Ward’s clustering method and calculated the stability of the clusters with pvclust. Logistic regression analysis was performed to compare gene amplification in male and female breast cancer, taking significant differences in clinicopathological features between the two groups into account. Information regarding prognosis and therapy was requested from the Integral Cancer registration The Netherlands (IKNL). Survival data were available for 101 cases with a mean follow up of 5.7 years. Therefore, survival analysis was based on 5 years survival rates. For univariate survival analysis Kaplan–Meier curves were plotted and analyzed with the log rank test. Multivariate survival analysis was done with Cox regression including the variables that were significant in univariate analysis. […]

Pipeline specifications

Software tools SPSS, Pvclust
Application Miscellaneous
Diseases Breast Neoplasms, Breast Neoplasms, Male