Figure 1.
Evaluation of the entropy method performance by the area under the ROC curve from simulated datasets, accessing different amplitudes and prevalences of copy number aberrations.
An area under the ROC curve of 1 means a perfect separation between mutated and normal regions, while a value of 0.5 means a random classification.
Figure 2.
Entropy analysis for the GBM data entire genome (A), chromosome 1(B) and chromosome 7 (C).
The segmented copy number values per sample are displayed as a heatmap on the left, with the tumor samples as columns; the entropy values are shown on the right. The gaps on the heatmap indicate genomic regions that lack coverage, such as the p arms of acrocentric chromosomes. The number in A corresponds to the region number in Table 1. Beside each region label, a plus sign indicates an amplification and a minus indicates a deletion. Note that a low-entropy region can be either a amplification or a deletion. The red line in the entropy plot shows the threshold for defining an aberrant region, which is the 0.05 quantile of the bootstrap distribution of the entropy. Peaks that are below the threshold but have no region assigned are normal CNV. The cytoband annotation was retrieved using the UCSC Table Browser.
Table 1.
Amplifications and deletions in the GBM data.
Figure 3.
Interplay between the amplitude, prevalence and entropy in deletions (A) and amplifications (B).
The prevalence measure adopted is the proportion of DNA probes on determined regions that have a log2 ratio above or below the 0.025 and 0.975 quantiles.
Figure 4.
Log2 ratio of copy number of the 58 tumor-normal sample pairs.
The values in the diagonal line correspond to variations similarly observed in tumor and normal tissue. The values in the horizontal line correspond to amplifications (right) and deletions (left) observed only in the tumor samples.