Because reversion is a very rare event we wondered how Q3SC transitioned so quickly from ATM−/− to ATM+/− (most likely between P4 and P10; see Figure 2B). Because these iPSC lines were prepared from T cells, we had a unique opportunity to trace individual subject cells during the reprogramming and growth stages in preparing iPSC. Mature T cells have rearranged genomic T cell receptor (TCR) and this rearrangement is unique to individual T cells. Therefore, we PCR-amplified genomic DNA from iPSC from various cell lines or passage numbers to detect rearranged TCRβ variable region using primers validated previously (Assaf et al., 2000). The PCR products were inserted into plasmids, and individual clones were sequenced. Alignment of these sequences from several passages of Q3SC indicates evidence for a varying number of “founder” T cell signatures in early passage that transitioned to a single type of signature in later passages (Figures 3D and S3A). This indicates that each iPSC line (derived from a single colony) was not produced from a single cell but instead included multiple “founder” cells, each presumably derived from
