Figure 1

Examples showing a 2-break and 3-break. (A) In a 2-break, two breaks produce four breakends, organized into counterpart pairs x, x′ and y, y′, Aberrant repair leads to an inversion/translocation (left) with adjacencies {x, y} and {x′, y′} or a closed loop that is then lost resulting in a deletion (red X, right). In both cases, all adjacencies are closed. This can be detected as counterpart-symmetry for the inversion adjacencies ({x, y}, {x′, y′}, left) and copy-number symmetry for the deletion adjacency ({x, y′}, right), since due to copy number loss Δ(x) = Δ(y′) = −1. (B) In a (k >2)-break, k breaks produce 2k breakends which are aberrantly repaired. Closed loops formed in this process can result in deletions (red X). The resulting adjacencies are open, since for each adjacency A the counterparts of the two breakends in A are not themselves adjacent. For example, x and y are adjacent but x′ and y′ are not. This can be detected using counterpart-asymmetry (e.g. {x, y}, since x′ is adjacent to w′ but w′ ≠ y′) or copy-number asymmetry (e.g. {x′, w′}, since Δ(x′) = 0 while Δ(w′) = −1).