Figure 2

PCR validation of breakpoints in MCF7. (a) MCF7 clone 69F1 was sequenced and contained a small piece of chromosome 1 (purple rectangle) to chromosome 17 (yellow rectangle). Arrows on each rectangle indicate whether the fragment is oriented as in the reference genome (pointing to right) or inverted (pointing to left). PCR primers were designed to amplify the breakpoint and these primers were used to assay the other clones in the BES cluster with 69F1. Each of the other clones in the cluster are indicated as lines below 69F1, with the end-points of the lines indicating the locations of the mapped ends relative to the ends of 69F1. The heterogeneous PCR results might result from heterogeneity of the MCF7 cells, or the existence of multiple versions of this breakpoint in MCF7 genome. (b) PCR results for the clones presented in panel a. The expected size of the PCR fragment is 600 base pairs. (c) PCR validation of breakpoints in sequenced clone 37E22 from MCF7 and three additional clones in bacterial artificial chromosome end sequence (BES) cluster all fusing nearby locations from chromosomes 1, 3, and 20. Two other clones have the same complex internal organization as 37E22 with four rearrangement breakpoints. However, clone 34J23 contains only one of these breakpoints, suggesting that the rearrangement history of this clone is different from that of the others in the cluster.