Because Q3SA and Q3SC represent an isogenic pair of iPSC lines from the same individual but with contrasting ATM genotypes (ATM−/− versus ATM+/−, respectively), we examined gene expression differences using RNA sequencing (RNA-seq), evaluating matches at the transcript level. Relatively few mRNAs were significantly different in the isogenic Q3 pair (206, false discovery rate [FDR] ≤ 5%), as contrasted with a much larger number of differences between Q1SA and Q3SC (1,349), even though both contrasts compared ATM−/− with ATM+/− (Figures 4A–4C). This indicates that observed gene expression differences due to variations in genetic backgrounds generally overwhelm any analysis of single-gene, variant-specific differences. Out of the 206 transcripts different in the isogenic pair of cell lines (Table S3), 113 (54.8%) also differed between Q1SA and Q3SC (Figure 4A). On the other hand, a large proportion (601 of 1,349 [44.6%]) of transcripts differing between Q1SA and Q3SC were in common with the Q1SA versus Q3SA comparison (Figure 4B), even though the latter compared two different ATM−/− cell lines. Nayler et al. (2012) identified 7,920 genes as significantly different in A-T iPSC compared
