Figure 3

Copy number analysis of 15 marker regions (see Table 2). A: Kaplan Meier estimates of progression free survival according to number of copy-number imbalanced marker regions in QPCR analysis. Stable (0–2 changes); intermediate (3–4 changes), unstable (> 4 changes). B: Copy number alterations (log2 ratios) of candidate regions determined by SNP microarrays (SNPs flanking the marker regions). Tumors in columns, marker regions in rows. Top row indicates patient and tumor ID, bars below refer to tumor characteristics. Non-progressors to the left, progressors to the right; stage T1 tumors in the middle, stage Ta tumors on the flanks. Tumors are further sorted according to their CIS status: Tumors with concomitant CIS in the very center and on the very verges, tumors with later or no CIS in between. Furthermore, the grade of dysplasia (Bergkvist[15]), the actual clinical risk (including previous history)[3] and the used microarray (1 = 50 K, 2 = 10 K) are indicated. Data area: Red: Copy number gain. Blue: Copy number loss. C: Copy number analysis of the same candidate regions by QPCR of 101 tumors, hereof 77 independent tumors. Tumors are sorted in the same way as in B. A survey of the number of altered regions is provided in Additional File 7.