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Table 1 Integration loci detected by ViralFusionSeq

From: Functional variants of human papillomavirus type 16 demonstrate host genome integration and transcriptional alterations corresponding to their unique cancer epidemiology

Sample Mapped human transcript† Gene description Chromosome location HPV transcript breakpoint(s)‡
AAE6 SLC26A2 Solute carrier family 26, member 2 5q32 E1, L1
PDE6A Cyclic GMP- Phosphodiesterase 6A alpha subunit 5q32 E1, L1
EPE6 None
  1. Viral-human fusion transcripts were discovered using ViralFusionSeq’s [61]: clipped-sequence (CS) and read-pair (RP) modules. Detected by at least 1 RP and CS event (†). As detected by CS method (‡). VFS uses two methods to detect viral-human fusion transcripts. The Clipped-Seq (CS) method detects viral fusion transcript breakpoints with a read that maps to both viral and human sequences, while the Read-Pair (RP) analysis detects transcripts with read ends mapped separately to the viral and human genome [61]. We required candidate viral fusion transcripts to be supported by at least 1 CS and 1 RP event in order to improve its stringency [64]. Although RP events were more abundant in our samples, CS analysis provided single-base resolution of viral-human fusion transcript breakpoints. In particular, we identified an average of 1.33 +/− 1.53 CS transcripts in EPE6 and 7.66 +/− 6.66 in AAE6. We detected no RP transcripts in EPE6, while 118.66 +/− 7.23 were found in AAE6 rafts. While one RP transcript was detected in a NIKS control culture, this read was not confirmed by the CS method of VFS and therefore not considered as a valid event