Figure 2.

Computational separation of arm-level and focal SCNAs. (a) Boxplot showing the distribution of copy-number changes for amplified focal (length < 98% of a chromosome arm) and arm-level (length > 98% of a chromosome arm) SCNAs across 178 GBM profiles from TCGA. The black dotted line denotes a typical low-level amplitude threshold used to eliminate artifactual SCNAs, while the green dotted line denotes a typical high-level amplitude threshold used in previous version of GISTIC to eliminate arm-level SCNAs. (b) Histogram showing the frequency of observing SCNAs of a given length across 178 GBM samples. The high frequency of events occupying exactly one chromosome arm led us to distinguish between focal and arm-level SCNAs. (c) Heatmaps showing the total segmented copy-number profile of the TCGA GBM set (leftmost panel), and the results of computationally separating these samples into arm-level profiles (middle panel) and focal profiles (rightmost panel) by summing arm-level and focal SCNAs. In each heatmap, the chromosomes are arranged vertically from top to bottom and samples are arranged from left to right. Red and blue represent gain and loss, respectively.

Mermel et al. Genome Biology 2011 12:R41   doi:10.1186/gb-2011-12-4-r41
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