Computational protocol: Plasma proteins as prognostic biomarkers in radiotherapy treated head and neck cancer patients

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Protocol publication

[…] For outcome driven analysis, the Cutoff Finder web application ( was used to find the optimal cut point for each protein by survival analysis using the log-rank test . The patient cohort was divided into a test (n = 56) and a validation (n = 28) cohort by randomization and stratified for HPV/p16, DAHANCA protocol and sex. In the test cohort, proteins for which an optimal cut point could be defined resulting in a log-rank test with a p-value <0.05 were identified. The identified cut points were used as cut off values for dichotomizing each marker, and a combined profile which most significantly separated the groups was tested in the validation cohort. For the non-outcome driven analysis, unsupervised hierarchical clustering was done on log2-transformed baseline protein levels using the SPSS statistics software version 22 implementation (two-step function) of the Balanced Iterative Reducing and Clustering using Hierarchies method (BIRCH) , to identify subsets of patients with similar baseline protein profiles. The proteins with the least influence on the cluster formation were removed systematically until no further changes in the cluster formation was observed. OPN and leptin were left out of the analysis due to a large number of missing values. Expression data were visualised as heat-maps using TreeView (Version 1.1.6r2, Data were centred on the mean of the cluster means for patients. As no clusters could be identified for the controls, these were median centred. Both patients and controls were randomly ordered. […]

Pipeline specifications

Software tools Cutoff Finder, SPSS, TreeViewX, JTreeView
Applications Miscellaneous, Phylogenetics
Organisms Homo sapiens
Diseases Head and Neck Neoplasms, Neoplasms