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 independent reprogramming events. The sequences specific for Q3SC are distinct from those from Q3SA or Q1SA (Figure S3B), indicating that separate lines came from independent mixtures of founders. Q3SC results are summarized by the percentage of each of three major clusters by frequency of aligned TCRβ sequence (Figure 3E). Clusters A and B, present as the majority of detected sequences at P4, disappeared over further passaging. Cluster C expanded from 33% at P4 to 83% at P10 and to 100% at P20. This means that the ATM reversion event could have occurred either in the original T cells or early after reprogramming of iPSC in an individual “clone” of founder cells, which then expanded to overcome the others. Sequencing traces of crude, PCR-amplified DNA from P4 (Figure 2B) had no evidence for reverted c.217_218 delGA. If 33% of the DNA were indeed previously reverted, the mutated allele at c.217_218 delGA should constitute only 33% of the P4 mixed traces in
