Figure 3

Sensitivity of A-CGH to detect the low-level copy number alteration. A. Measurement of X-chromosomal copy number. A-CGH was performed to analyze the copy number of genes in the X-chromosome. Female DNA (XX) was used as the reference DNA. Male DNA (XY), female DNA (XX), and DNA samples containing different number of X-chromosome (XXX, XXXX, XXXXX) were used as test DNA, with an expected ratio of test/reference of 0.5, 1.0, 1.5, 2.0, and 2.5 respectively for X-chromosome. Mean fluorescence ratios (±SEM) of autosomal DNAs (blue diamonds) and X-chromosomal DNAs (red circles) from each experiment are shown. The slope of the regression line is 0.3. B. Visualization of p-values derived from the topological statistics as described in the Methods along the X-chromosome from samples containing different X-chromosomal copy numbers. Each column represents a different experiment; and each row represents the p value for the alteration at a given SW-locus (a sliding window of 40 adjacent clones, details in Methods), ordered by genome map position from Xpter to Xqter. Red represents gain and green loss. The intensity of the color shows the level of significance according to the p-value shown in the color scale.