FIG. 4.

Left and right detectability. The shaded regions in (a) and (b) represent all undetected breakpoints (x,y) from the joining of TMPRSS2 and ERG. (a) Left detected breakpoints resulting from fusion of the TMPRSS2-ERG region. (b.) Right detected breakpoints. In both cases, the fraction of undetectable breakpoints is less than 5% of all possible breakpoints. (c, d) Venn diagrams (to scale) showing the overlap of missed regions with highly conserved repeats. The outermost circle represents the entire length of the corresponding axis. The “Repeat Block” shaded area corresponds to the sum of lengths for all repeat regions that are over 75% conserved, continuous (or with <100 bp between conserved repeats), and >500bp in length. “Uncovered” corresponds to any positions in TMPRSS2 (c) and ERG (d) that may be undetected—i.e., y coordinates that appear in shaded regions in (a) and x coordinates in (b), respectively. In both diagrams, “Uncovered” is completely contained within “Repeat Blocks.”