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. 2019 May;29(5):819–830. doi: 10.1101/gr.242529.118

Figure 3.

Figure 3.

Virome-wide integrations detected in liver and cervical cancer genome data sets. (A) Comparison of the number of integration events identified in a metastatic cervical carcinoma sample by our VIcaller approach (light blue) and the HPV-specific approach of the original study (Liang et al. 2014) (light gray). (B) Sanger sequencing result for one example of the three HPV-18 integrations, newly detected by VIcaller, that existed in the tumor but not in the paired normal tissue. A 16-bp deletion on the human genome was found at the integration breakpoint. (C) Comparison of the number of HBV-human fusion transcripts identified in three HCC cell lines by the VIcaller virome-wide approach (light blue) and the HBV-specific approach described in the original study (light gray) (Lau et al. 2014). (D) Gel images from RT-PCR validation of the six fusion transcripts newly detected by VIcaller. (E) Sanger sequencing result of an example breakpoint of the six newly identified fusion transcripts. (F) Comparison of the number of HBV integration breakpoints identified in 88 HCC samples by our VIcaller virome-wide approach (light blue) and the HBV-specific approach described in the original study (light gray) (Sung et al. 2012). (G) Sequence read alignment of an HBV integration in the HCG2032978 gene, newly identified by VIcaller, which existed in the tumor but not in the paired normal tissue. Seven chimeric and seven split reads at the upstream breakpoint and four chimeric reads at the downstream breakpoint were found for this integration event. The integrated HBV sequence is ∼808 bp in length, starting from 3170 bp to 3182 bp, and then from 1 bp to ∼796 bp on the circular HBV genome. Black and red represent reads mapped to the human (hg19) and HBV (NC_003977.2) reference genomes, respectively. (H) Sequence read alignment of an adeno-associated virus 6 (AAV-6; AF028704.1) integration event detected by VIcaller (sample ID: 55T) that existed in the tumor but not in the paired normal tissue. Eight chimeric and five split reads were found across the two breakpoints. This integration is 212 bp in length, from 54 bp to 266 bp on the AAV-6 genome.