Sensitive Detection of Viral Transcripts in Human Tumor Transcriptomes
Figure 9
Human-viral phylogeny based on a HOR.
Phylogenetic tree of HOR #16 of the NB1 stage 4 panel. Viral reference sequences are indicated with red branches and associated tip labels (‘Virus’) while human factors are labeled with green branches. Blue branches represent consensus sequences of neuroblastoma reads (‘Sample’). The tree was generated by the maximum likelihood approach PhyML using the multiple sequence alignment of the HOR as input (see Materials and Methods). Distances between nodes are quantified as substitutions per site. As can be derived from the tree, neuroblastoma consensus sequences are tightly clustered in close proximity to the endogenous retrovirus HERVK9I and two human factors, thereby unambiguously indicating the human origin of these neuroblastoma reads. Clusters of other sequences represent well known sequence homologies, as for example between human ABL1/SRC genes and acutely transforming retroviruses.