Genome-wide analysis links tumor deletion patterns to alternative DNA repair

A genome-wide analysis of 2,157 whole-genome-sequenced tumors across 17 cancer types identified deletion patterns associated with single-strand annealing (SSA) and alternative end joining (Alt-EJ), according to the study abstract. The researchers detected 832 putative SSA-associated deletions and 37,359 putative Alt-EJ-associated deletions, finding that Alt-EJ-associated scars were more frequent in tumors with low homologous-recombination scores.

The analysis assessed two error-prone pathways that generally serve as backup mechanisms when DNA double-strand breaks cannot be repaired through homologous recombination. Deletion patterns are described as “putative” scars, meaning that the genomic analysis was used to infer association with these repair processes rather than directly measuring pathway activity. The study’s purpose was to determine how extensively such patterns occur across tumor types and whether they are linked solely to homologous-recombination deficiency.

Although Alt-EJ-associated deletion burdens were generally higher in homologous-recombination-deficient tumors, the pattern varied by cancer type. Prostate adenocarcinoma and hepatocellular carcinoma had elevated numbers of SSA-associated deletions despite low homologous-recombination-deficiency scores. The researchers also found that SSA-associated deletions were more frequent in SINE-rich genomic regions. Among homologous-recombination-proficient lymphoid lineage tumors, these deletions showed pronounced enrichment near transcription start sites. Together, the reported results suggest that the genomic context of the deletion was associated with different dimensions of DNA-break repair activity beyond homologous-recombination deficiency alone.

The findings are based on the supplied abstract of an open-access BMC Cancer research article; the full study methods and results were not available for independent assessment. The deletions are therefore presented as putative pathway-associated signatures, and the abstract does not establish that the patterns directly quantify repair-pathway engagement. The publisher also states that the accessible article is an early version of peer-reviewed, accepted research, carries a permanent DOI, and may undergo further editorial revision before the final version of record.

Subject of Research: Genome-wide analysis of deletion patterns associated with SSA and alternative end joining across 17 cancer types

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

Article References: Modi, A., Zito, A., & Parmigiani, G. (2026). Pan-cancer genomic scars of alternative end joining and single-strand annealing. BMC Cancer. https://doi.org/10.1186/s12885-026-16895-2

Image Credits: AI Generated

DOI: 10.1186/s12885-026-16895-2

Keywords: cancer genomics, DNA repair, homologous recombination, single-strand annealing, alternative end joining, genome instability, tumor deletions, pan-cancer analysis, Pan-cancer, genomic, scars, alternative