Using this approach, we found that 16/27 (59%) of rearrangements could be detected in the bone marrow of donor mice at the time the HSCs were transplanted (Extended Data Fig. 10). Any rearrangements present before transplantation must be clonal (that is, would not have arisen after the transplant). The failure to amplify the remaining 11 rearrangements by PCR does not mean that these are sub-clonal (that is, post-transplant) events. PCR amplification will depend on how much the transplanted HSC was contributing to blood production in the donor animal at the time of the transplant, as well as the sensitivity of each PCR. Therefore, we inferred clonality for the remaining calls by looking at loss of copy number (in the case of deletions, see Fig. 5l) and the number of reads involved in the rearrangement at the breakpoint for copy number-neutral changes.
