Figure 2.

2J-COL and 2J-NL cases are defined by co-linear and non-linear mapping of the viral-human junctions. (a) The schematic of junction mapping is shown for cases with two junctions (2J-COL, for 2 junction co-linear mapping and 2J-NL, for 2 junction non-linear categories). The relative orientation of the two viral-human junction reads are identified by mapping the human portion of the sequences against the hg19 reference genome. (b) Junction mapping of 2J-COL cases (left panel) and 2J-NL cases (right panel) are shown, with a scheme indicating the co-linear and non-linear coordinate mapping for these categories. The coordinates of the human (junction to chromosome) and viral (junction to junction) NGS reads are indicated, as well as the chromosomal locus of insertion. At least one gene within 500 kb or greater (//) is indicated. In all cases, the human part of the NGS junction reads was mapped against the forward strand of the hg19 reference. The HPV sequences in either plus or minus orientations, relative to the viral episome, are shown as a grey box with (+) or (−). (rr) indicates repetitive regions. (c) Junction mapping of MJ-CL cases are shown. The human/viral breakpoints are shown as well as the chromosome locus of insertion. Black boxes indicate the human portion of the junction reads. (d) Junction mapping of the MJ-SC cases are shown, as in (c).