Figure 3.

Qualitative comparison to prior CNAs observed in prostate cancer. (A) Overall summary of copy number across 17 lethal metastatic castration-resistant prostate cancers. Summed segmented log2 copy number ratios (top panel) for all targeted genes across the 17 samples are shown. Genes exhibiting recurrent amplifications or deletions across the cohort will have large positive or negative values, respectively. Regions of copy number gain and loss for all 17 samples are shown in a heat map (bottom panel). Red represents amplification; white, copy number neutral; blue, deletion. Three samples are derived from three different metastatic foci from a man with lethal castrate-resistant prostate cancer: celiac lymph node metastatic site (WA43-27), lung metastatic site (WA43-71), and bladder metastatic site (WA43-44). (B) Focal amplifications of the AR gene and deletions of the PTEN gene in this cohort. AR has the largest positive summed log copy number ratio across the 17 samples, with a total sum of 32.6, whereas PTEN has the largest negative summed log copy number ratio, with a total sum of -17.5. A plot of this sum over the entire chromosome (top) is shown; a large positive peak is present at AR and a large negative peak is present at PTEN. Segmented copy number ratios are represented by boxes, with the area (absolute log2 ratio) and color intensity (log2 ratio; copy number gain in red; loss in blue) of each box proportional to mean copy number across that gene. Missing boxes indicate that the gene is neither amplified nor deleted in that sample.