Illustration of the stepwise increase in aCGH ratios with increasing DNA copy number. Frequency histograms (% array probes) of aCGH ratios (left panels) and plot of aCGH ratio versus chromosomal location (right panels) are shown for a lymphoma with a DNA index (DI) of (a) 1.02, (b) 1.94, (c) 1.21, and (d) 1.05, and (e) for normal DNA comparing male and female. The tumor cell fraction, measured by flow cytometry, is indicated for each tumor. DNA copy numbers estimated by GeneCount are marked; those in black were consistent with FISH data, whereas those in red have not been subjected to FISH measurements in the specific tumors shown. The arrows in the right panels point to the locations of the FISH probes. At a DI close to 1 and 2 (a,b,d,e) the ratio distribution shows a major peak at a median log2 value of approximately zero, representing the most frequent DNA copy numbers of 2 and 4, respectively. At a DI of 1.21 (c) the baseline at a log2 ratio of 0 represents a number between 2 and 3 DNA copies. Note the smaller increase in the ratios with increasing DNA copy number at a tumor cell fraction of 70% (d) than of 96% (a). In (e), determination of the dynamic factor, q, as the absolute value of the X-chromosome log2 ratio level is indicated.