Extended Data Fig. 5. SV breakpoint localization of FA SCC, sporadic HNSCC, BRCA2^mut, and BRCA1^mut tumors relative to genome replication timing and fragile sites.

a Replication timing of the SV breakpoint loci. Plotted in black is the expected replication timing distribution. Plotted in blue is the observed SV breakpoint localization to early, mid, or late replicating genomic regions. Vertical axis indicates relative abundance and horizontal axis indicates standard deviation from mean replication timing. Kolmogorov-Smirnov (KS) p-values are indicated. n corresponds to the number of breakpoints included in the sample for each analysis. b Binned SV breakpoint counts from the indicated cohorts and SV class, localizing to common and rare fragile sites. SV class highlighted in red indicates a significant association, as determined by indicated p-value of two-tailed z-score test compared to 1000 permutations of fragile site locations. c Binned SV breakpoint counts localizing to “early-replicating fragile sites”. SV class highlighted in red indicates a significant association, as determined by indicated p-value of two-tailed z-score test compared to 1000 permutations of fragile site locations.