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) near the ATM gene. Not all known SNPs are included on the SNP array, so a 3.5 kb region surrounding the c.217_218 delGA site was re-sequenced. Only one SNP, rs2066734, was found to be heterozygous in Q3SA (red dot, Figure 2E). This SNP was homozygous for the major allele in Q3SC (green) and homozygous for the minor allele in CAR3 (blue). By estimating the rate of random SNP LOH using the SNP array data, a Fisher’s exact test indicates that the probability of finding a specific LOH for rs2066734 within ATM but unrelated to the loss of c.217_218 delGA is p = 0.00014. This indicates that the most likely source of reversion was a short gene correction event, including at least ∼1.5 kb upstream of c.217_218 delGA to include rs2066734. This result also confirms that the maternal allele, containing the c.217_218 delGA deletion as well as the minor rs2066734 allele, is lost in Q3SC and is replaced by a copy
