Figure 2

Integration sites can be determined with the DNA-capture-seq datasets. (A) The IGV profile of virus-host chimeric reads in the ACH-2 dataset, mapped to the hg19 reference sequence alone. The human portion of the chimeric reads can be observed together with the 5-nucleotide long repetitive sequence (R) that results from the retroviral integration step at the integration site. (B) The IGV profile of the integrated provirus after alignment to the newly constructed reference sequence. Since the proviral sequence is integrated within the corresponding chromosome in the reference sequence used for alignment, the reads in the IGV profile show the chimeric fragments, including the junctions. (C) The IGV profiles of the human fragments of virus-host chimeric reads obtained from the ACH-2 cell line’s dataset at the integration site (IS) (left). Two major proviruses were shown, and one was a defective provirus. In this case, both clones were found to be integrated in the minus strand of the genome (−). The localization of the chimeric reads along the reference sequence containing the integrated provirus is shown on the right. The same information is shown for J1.1 (D) and J-Lat 9.2 clone (E).