Fig. 5

Using the inter-chromosomal interaction mode of the 3D Genome Browser to discover structural variations in cancer cells. An inter-chromosomal translocation event (BCR-ABL fusion) in K562 and KBM7 CML cell lines appears as “inter-chromosomal interactions” on Hi-C maps. Such aberrant patterns are frequently observed in Hi-C maps in cancer cells, because the cancer genome is not available and Hi-C reads are mapped to the reference genome. We also noted that this translocation is reciprocal in KBM7 but not in K562 cells and that the breakpoint in ABL is different in the two cell lines. Such inter-chromosomal interactions are not observed in the karyotypically normal GM12878 cells