Figure 3.

Model of a Nonrandom Genetic Landscape in Gliomas: Confirmation by Validation Set

Permutation-based approach described in Figure 2 was applied to the validation set from The Cancer Genome Atlas Pilot Project (TCGA). The association map (A) indicates chromosomal regions (territories) with significant co-occurrence of gene dosage alteration (false-discovery rate [FDR]–corrected P<.05). Red scores denote the significant association of 2 chromosomal gains or 2 chromosomal losses; blue scores, the significant association of a gain and a loss event. The color gradation reflects a score that indicates the significance of cytoband-cytoband associations. The association map shows a consistent pattern of significant associations, which denotes a nonrandom genetic landscape in gliomas. B, Significant associations identified in the discovery set (Figure 2B) that were confirmed in the TCGA validation set. The blue bars and corresponding blue labels indicate chromosome territories with TCGA-confirmed significant associations to other territories (TCGA-validated nonrandom genetic landscape). (See interactive Figure 1 showing significant associations in the discovery and validation sets at http://www.jama.com.)