Pan-cancer genomic scars of alternative end joining and single-strand annealing

DNA double-strand breaks (DSBs) are among the most cytotoxic lesions encountered by cells and represent a major source of genome instability in cancer. The preferred pathway to repair resected DSBs is high-fidelity homologous recombination (HR), but error-prone annealing-dependent pathways such as single-strand annealing (SSA) and alternative end joining (Alt-EJ) generally act as backup repair mechanisms in HR-deficient contexts. However, the extent to which these pathways are engaged across tumor types and how their activity is coupled with HR deficiency remains unclear. In this work, we systematically characterize putative scars from SSA and Alt-EJ across 2,157 whole-genome-sequenced tumors spanning 17 cancer types, identifying 832 putative SSA-associated and 37,359 putativeAlt-EJ-associated deletions in total. We find that Alt-EJ-associated scars are more frequent in HR-deficient tumors compared with SSA-associated scars; however, prostate adenocarcinoma and hepatocellular carcinoma exhibit elevated SSA-associated deletion burdens despite low HR-deficiency scores. Moreover, our genome-wide analysis reveals that SSA-associated deletions preferentially occur in SINE-rich regions and exhibit pronounced enrichment near transcription start sites in HR-proficient lymphoid lineage tumors. Our results show that SSA- and Alt-EJ-associated genomic scars are not confined to HR-deficient tumors, but are shaped by local genomic and transcriptional context, capturing distinct dimensions of DSB repair activity beyond HR deficiency alone.