We then searched for evidence of sequence variation in Q3SC. The karyotype of Q3SC was normal (Figure 2D; 46,XY in all 20 cells counted). SNP data were evaluated for evidence of loss of heterozygosity (LOH). Plots of the B allele frequency over the entire genome (not shown) or over the region of chr11 surrounding the ATM gene (Figure S2A) show no clear evidence for LOH overall but a lack of any heterozygous SNPs within the ATM gene, precluding the ability to assess LOH within the gene itself. However, the presence of SNP heterozygosity flanking ATM in all cell lines argues against a single crossing-over event between alleles, as this would have produced LOH distal from the event. By highlighting the 1,034 SNPs that distinguish Q3SA or Q3SC from source T cells (Figure S2B, colored dots) it is apparent that there is no concentrated genomic region of LOH between these two sublines, but that sequence variation has accumulated throughout the genome. Similar plots of the signal intensity of SNPs (log R ratio, not shown) show little evidence for copy-number variation (CNV)
