Fig. 1

LoVIS-Seq reproduces clonal distribution of entire mouse blood using 25 µl blood. a Diagram showing Anti-HIV-EGFP-WT and control mCherry-H1/H5 vectors having WT, H1, or H5 LTR-index and strategy for VIS assay with LTRi-seq. LTR index sequences are shown in magenta box. b Hu-BLT mouse model: Fetal liver CD34 + cells were separately transduced with either anti-HIV or control vectors and transduced cells were mixed 1:1 for transplant. The mix of transduced cells was transplanted in myeloablated NSG mice with a fetal thymus tissue implant. c Stacked bar plot showing clonal frequencies of VIS in BM of hu-BLT mouse. Clones from mCherry-H1 and EGFP-WT cells were identified by corresponding LTR barcodes. In the stacked bar plot, each band represents a unique VIS (HSPC clone) and thickness of the band shows clonal frequency or abundance of that HSPC clone. Percentage of mCherry + or EGFP + cells within human cell (hCD45 +) population are shown on top of the corresponding stacked bar. d Plot showing Pearson’s r for correlations of mCherry-H1 (red dots) and EGFP-WT (green dots) VIS clonal profiles between unamplified DNA replicates and replicates of MDA-amplified DNA samples for different cell numbers. e Experimental protocol for longitudinal clonal tracking in humanized BLT mice. f Scatter plot showing VIS clonal frequencies between unamplified whole blood DNA and two replicates of MDA-amplified DNA from 25 µl blood at week 19 (r = Pearson’s r, diagonal line is r = 1) for m599 and m598. Clonal frequency of mCherry-H5 (red dots) and EGFP-WT (green dots) VIS clones in unamplified DNA samples (y-axis) and MDA replicates (x-axis)