To rule out the possibility of cross-contamination, we evaluated large numbers of genomic variations using SNP arrays. Clustering with the Euclidean distance between called SNPs, DNA from both Q3SA and Q3SC are quite similar to DNA prepared from the amplified JHU_Q3 T cells originally used for reprogramming (Q3SA: 699,368 SNPs match JHU_Q3 out of 701,230 called SNPs [99.73%]; Q3SC: 99.85%; Figure 2C). Less closely related is the DNA from the parent CAR3 (71.95%), the unrelated Q1SA iPSC line (55.65%), or its source JHU_Q1 T cells (55.64%). This confirms that Q3SA and Q3SC are iPSC lines made from the same source individual (JHU_Q3), who is related to JHU_CAR3, but not to the source T cells or iPSC prepared from JHU_Q1. Furthermore, on the basis of SNPs, Q3SA and Q3SC are confirmed as male and both Q1SA and CAR3 are confirmed as female, consistent with designated cell sources. SNPs overlapping those recommended for use in cell line identification (Yu et al., 2015) are shown in Table S2. The ATM-expressing Q3SC, then, is not due to cross-contamination of cultures.
