Copy number (CN) variation associated with a telomere crisis. (A) Cell lines with deficiencies for C- and A-NHEJ were driven through a telomere crisis by expression of DN-TERT with clonal selection occurring either pre- or post-crisis. Genomic CN changes of clones are presented as normalized values relative to the parental lines within the limits of +1 gain and −1 loss. Some samples appeared to share common CN breakpoints with other samples of the same genetic background, with an example from LIG4−/− Chr 8q highlighted with a black arrow. (B) Unique and nonunique breaksites were analyzed, revealing an increase in unique sites for LIG3−/−:LIG4−/−, LIG3−/−:NC3, and TP53−/−:LIG3−/− samples relative to WT. (*) P-value <0.002, Mann–Whitney U test. (C) CN segments for which both breaksites were unique were quantified, indicating a prevalence of CN gains relative to losses. (*) P-value <0.03. “All Esc” refers to a pooled analysis of all post-crisis clones. (**) P-value <2 × 10−5, Mann–Whitney U test.
