Figure 5.

SummonChimera undetectable integrations. Viral integrations in cancer have been correlated with chromosomal inversion, translocation, and Copy-Number variation events. When integrations occur as illustrated, SummonChimera cannot predict the genetic content. Arrows point from 5’ to 3’ along the reference strand of each organism chromosome (host is blue and virus is red). Segment labels indicate a portion of the host genome. In the Inversion case one of the chimeras will be determined with opposite organism order and strand orientation, thus eluding integration prediction. In case of translocation, the integration can occur between two separate host chromosomes. The two chimeras will be detected on separate chromosomes and no integration would be predicted. Finally, the Copy-number Variation case, if the integration occurs between the duplicated segments the chimeras will be detected in the wrong chromosomal positions and the 3’ chimera will appear to be upstream of the 5’ chimera on the chromosome.