GeneCount identification of DNA copy number heterogeneity within tumors. (a) Frequency histogram (% array probes) of aCGH ratios in a heterogeneous lymphoma, including data for the entire genome. (b) aCGH ratios are plotted against chromosomal location, showing the heterogeneous regions on chromosomes 8, 9, and 17 with a DNA copy number of 3&4 in blue. (c) Frequency histogram (% array probes) of aCGH ratios for two homogeneous DNA regions with a copy number of 3&4 (upper panel) and the heterogeneous region depicted in (b) with a copy number of 3&4 (lower panel). The ratio distributions of copy number 3, 4, and 3&4 were significantly different (p < 0.001, ANOVA). DNA copy numbers estimated by GeneCount from the DI and tumor cell fractions measured by flow cytometry are marked; those in black were consistent with FISH experiments, whereas those in red have not been subjected to FISH measurements in the specific tumors shown. The arrows in (b) point to the locations of the FISH probes. Note that the 3&4 copy number of the heterogeneous region has been confirmed with FISH.