Fig. 2

PCIP-seq applied to ATL. a In ATL100, both ligation-mediated PCR with Illumina sequencing (targeting the 5′ and 3′ LTRs) and PCIP-seq with Nanopore show a single predominant HTLV-1 insertion site. b Reads from both approaches have been mapped to a custom genome where the HLTV-1 provirus has been incorporated into the host genome. The long PCIP-seq Nanopore reads show this provirus has a ~ 3600 bp internal deletion, removing the binding sites of the guides/primers adjacent to the 5′ LTR. c Internal deletion confirmed via long range PCR and Illumina sequencing (gray reads map to a single position, the white reads map to both LTRs). d ATL2 clonality pie charts generated from ligation-mediated PCR with Illumina- and PCIP-seq-based sequencing data. The ATL2 tumor clone contains three proviruses inserted in chr 1, 5, and 16 (green, orange and blue slices respectively) named according to the chromosome inserted into. The provirus on chr1 (green slice) is inserted into a repetitive element (LTR) and short reads generated from host DNA flanking the insertion site by Illumina sequencing map to multiple positions in the genome. Filtering out multi-mapping reads causes an underestimation of the abundance of this insertion site (13.6%, left pie-chart). This can be partially corrected by retaining multi-mapping reads at this position (25.4%, central pie-chart). However, that approach can cause the potentially spurious inflation of other integration sites (red slice 9%). The long PCIP-seq reads can span repetitive elements and produce even coverage for each provirus without correction (right pie chart). e Screen shot from IGV shows representative PCIP-seq reads coming from the three proviruses (named chr 1, chr16, and chr5) and mapped to four distinct regions of the HTLV-1 proviral genome at positions where de novo mutations were observed