Figure 3. Repopulation Kinetics of HSPC Clones.

(A) Sequential Expansions of HSPC Clones Over Time. Major clonal kinetics patterns in serial PBC (in animal 95E132) and PBMC and Grans (in animals 2RC003, RQ5427, and RQ3570) were derived using average linkage hierarchical clustering based on clonal frequency profiles over time. The relative frequencies of QVI clones at different time points (shown in months at the top of each chart) appear in a white–black–yellow color scheme, with white denoting zero frequency and yellow the highest frequency (see the numbers at the bottom of each chart). QVIs were grouped into 5 – 8 clusters (denoted by different colored arrows), depending on animal and cell type, using the WGCNA package (Langfelder and Horvath, 2008). All clusters were clearly separable, with a significance level (|Zsummary.qual|) of >10 (Langfelder and Horvath, 2008), except for the cluster-1 in the 2RC003 PBMC data set (only 9 QVI clones). Results showed that different groups of QVI clones, beginning with Cluster 1, expanded sequentially over time. See Fig. S3 for more details. (B) Repopulation of Long-term and Short-term QVI Clones. Long-term (LT-QVIs) and short-term QVI clones (ST-QVIs) were segregated based on the presence of these clones in blood lineages isolated at 116–117 months (95E132), 70–71 months (2RC003), 63–64 months (RQ5427), or 36–37 months (RQ3570) months post-transplant. The relative contribution (y-axis) of LT-QVIs (orange) and ST-QVIs (black) in serial PBC (95E132) or Grans/PBMCs (2RC003, RQ5427, and RQ3570) are shown over time. See Fig. S4 for more details.