Breakpoint detection and localization for different sequencing strategies.

The probability P�� of detecting a fusion point and the expected length E(|����|) of a breakpoint region under various clone lengths (L) and number of end-sequenced clones (N). The values of N and L are chosen to reflect current or proposed sequencing platforms, with the last value for the 150 kb clones representing our current status on the MCF7 cell line. P��* and E(|����*|) correspond to the probability for, and expected size of, a breakpoint region in the case when two clones are required to span ��. The small clone lengths (1 kb, 2 kb) and large number of reads represent what one might achieve in a single run with new technologies (under perfect mapping of end sequences). For a comparison of E(|����|) and N for a fixed P�� = .99 over a continuous range of clone lengths, see Figure S6.