Fig. 4

Frequency of copy number alteration. A Landscape of copy number alteration across the autosome. The CN-300 cohort is split into quartile groups defined by burden of copy number alteration (%) in index core (red to yellow=quartile1-4). Y-axis=Number of patients with an alteration (above midline=copy number gain; below midline=copy number loss). X-axis=genomic location. Regions of interest are annotated by chromosome followed by genomic location and mapped cytoband. B Stacked bar chart of selected copy number altered segments in the CN-300 cohort index cores. Regions ordered putatively ‘early’ (top) to ‘late’ alterations (bottom). Each bar divides the patients harbouring the specific genomic alteration (total number of patients annotated at the end of each bar) into burden of copy number alteration quartile groups. Regions of interest are represented by chromosome number, genomic location and cytoband (blue=copy number loss, pink=copy number gain). Regions containing known prostate cancer genes of interest are listed as follows: 8:23.4–24 (NXK3.1), 10:89.5–90 (PTEN), 13:48.5–49 (RB1), 17:7.5–8 (TP53), 8:128.5–129 (cMYC), 5:98–98.5 (CHD1). C Density plots demonstrating distribution of burden of copy number (CN) alteration (%) identified in the index core of patients with and without 8p segment deletions (low KS distance). All CN-300 patients harbouring 8:13–13.5 (8p22) and/or 8:11.5–12 (8p23) segment deletions are represented by a blue line versus no 8p22 and 8p23 segment deletion represented by a black line (8p22 deletion N=220, 8p23 deletion N=236). D Density plots demonstrating two regions with a high KS score that are associated with a higher burden of CN alteration (%); 8:128.5–129 (8q24 harbours cMYC) and 5:98–98.5 (5q21 harbours CHD1). All CN-300 patients harbouring 8:128.5–129 (8q24) gain are represented by a red line (N=145) versus no alteration at that segment (black line). All CN-300 patients harbouring 5:98–98.5 (5q21) loss are represented by a blue line (N=79) versus no alteration at that segment (black line)