Figure 3

Screen capture of SNP data visualized in the UCSC Human Genome Browser. SNPscan converts a text file that has been generated by CNAT into a WIG file, which can then be visualized on the UCSC Genome Browser. For case NA07055 (shown in Fig. 2), 50 K Xba SNP data from chromosome 2 are displayed. The three custom tracks, arranged in rows, are LOH p value (color coded with more significant p values having a darker color), copy number (in green), and copy number p value (in blue). Note a region of deletion (dashed circle). The genome browser can be viewed for each chromosome at full scale or reduced to any region of interest. Additional tracks that are displayed in this example are chromosome band, gaps, known genes, Ensembl gene predictions, and SNPs. Dozens of additional tracks can be added or removed. Each WIG file that is generated can contain multiple SNP array data sets.