Fig. 1

FuSpot Reference Sequence Retrieval. FuSpot reference retrieval is visualized. In this example, the putative fusion breakpoint exists between the rightmost base of the 5′ side of the Chr2 reference and the leftmost base of the 3′ side of the Chr17 reference. In order to perform alignments of reads which may align over the putative breakpoint or reads which may align to the normal sequence of either Chr2 or Chr17, FuSpot will gather references by collecting sequences of a defined length away from the breakpoint for both fusion gene partners. FuSpot will collect genomic sequences (always sequential — blue and yellow) and exonic sequences (potentially fragmented — green and red). Thus a total of 8 reference sequences are retrieved — 4 on either side of the breakpoint