Fig. 2.

Significant broad and focal copy-number alterations in the glioma genome. (a) Amplifications (red) and deletions (blue), determined by segmentation analysis of normalized signal intensities from 100K SNP arrays (see SI Text), are displayed across the genome (chromosome positions, indicated along the y axis, are proportional to marker density) for 141 gliomas (x axis; diagnosis is displayed on top, and gliomas with low purity are segregated to the right). Broad events near the size of a chromosome arm are the most prominent, including amplifications of chr7 and deletions of chr10 observed among >80% of GBMs. (b) GISTIC analysis of copy-number changes in glioma. The statistical significance of the aberrations identified in a are displayed as FDR q values (9) to account for multiple-hypothesis testing. Chromosome positions are indicated along the y axis with centromere positions indicated by dotted lines. Fifteen broad events (indicated by red bars for amplifications and blue bars for deletions) and 16 focal events (indicated by dashes) surpass the significance threshold (green line). The locations of the peak regions and the known cancer-related genes within those peaks are indicated to the right of each panel. Several broad regions, including chr7 and chr10, contain superimposed focal events, leading to needle-shaped peaks superimposed on highly significant plateaus.