Abstract Somatic structural variations (SVs) are common in cancer. Although a small fraction of SVs in breast and ovarian cancers can be attributed to homologous recombination deficiency, the underlying molecular mechanisms for the vast majority of somatic SVs remain unclear. Here, we focus on the roles of transcription and DNA replication collisions in genomic instability in cancer. Such collisions are unavoidable in cells since both transcription and replication use the same DNA as template. We hypothesized that transcription replication collisions (TRCs), if not properly repaired, would lead to collapsed replication forks and result in SVs. To this end, we studied somatic SVs in 6193 high-coverage whole-genome sequenced primary and metastatic tumors from three independent pan-cancer cohorts. A total of 13 conserved SV signatures, representing independent molecular mechanisms, were deconvoluted from these cohorts using non-negative matrix factorization approach. We detected replicated-strand bias, the expected footprint of transcription-replication collision, in large tandem duplications (TDs) across multiple cohorts. This bias was only observed in expressed genes, consistent with TRCs depending on transcription activity. Large TDs were abundant in female-specific (breast, ovarian and uterus), upper gastric-intestinal tract, and prostate cancers. They were associated with CDK12 mutations and worse patient survival. CDK12 is a cyclin-dependent kinase, a key regulator of transcription elongation and termination. Deleting or suppressing CDK12 using CRISPR-Cas9 in prostate cell lines increased RNA: DNA hybrids (R-loops), promoted TRCs, and ultimately led to large TDs. Finally, we found that cells lacking CDK12 were sensitive to WEE1, CHK1 and ATR inhibitors. In summary, our data suggest that large TDs in cancer form due to impaired TRC repair and can be used as a biomarker for prognosis and treatment. Citation Format: Lixing Yang. A078: Transcription and DNA replication collisions lead to large tandem duplications and expose targetable therapeutic vulnerabilities in CDK12-mutant prostate cancer abstract. In: Proceedings of the AACR Special Conference in Cancer Research: Innovations in Prostate Cancer Research and Treatment; 2026 Jan 20-22; Philadelphia PA. Philadelphia (PA): AACR; Cancer Res 2026;86 (2Suppl): Abstract nr A078.
Lixing Yang (2026) studied this question.