Patient microdeletion breakpoint analysis. Array CGH data for 13 of the 8p23.1 microdeletion cases (seven typical and six atypical) associated with congenital heart defects mapped against the H2 sequence assembly. The microdeletion breakpoints for seven typical microdeletion cases (SD-mediated) map to clusters of SDs located at REPD and REPP. Breakpoints were refined to specific SDs by using a model for expected signal depletion under recombination between specific directly orientated SD pairs (SD19 and SD20/21/25 and SD41) (see Supplemental Section 6). Two types of breakpoints were identified, with three patients mapping to SD19 (highlighted with dashed red box) and four patients mapping within SD20/21/25 (highlighted by the dashed blue box). The latter breakpoints map to the DA core duplicon associated with the inversion polymorphism.
