Principle of bioinformatic analysis of array output. Analysis of hybridization signal intensity for each SNP probe allows for construction of karyograms. In this example, CNAG v.2 software (www.genome.umin.jp/CNAGtop2.html) was used for analysis: colors result from merging of individual signals grouped based on the topographic distribution throughout the genome and correspond to each of the autosomes and the X-chromosome. The hybridization signal intensity plot results in trace colors oscillating around the diploid signal intensity value. In the example shown, multiple areas of hypoploid signal intensity can be distinguished corresponding to several genomic losses. Zooming in on 2 exemplary chromosomes (5 and X, below the whole genome view) demonstrates the copy number determination plot (red dots symbolize hybridization signals of single SNP probes; blue line represents average copy number) as well as heterozygosity tracing depicted using individual green ticks (which merge when the density of heterozygosity calls is high). Areas of deletion are recognizable by the decrease in the hybridization signal intensity (below the diploid line) and corresponding decrease in the expected density of heterozygosity calls. Of note is that residual heterozygosity calls (here in an example of del5q31) correspond to signals derived from nonclonal cells contaminating the sample.