Detection of oncogenic fusions in colorectal cancer using a partner-agnostic next-generation sequencing approach

Gene fusions exist with low prevalence in colorectal cancer (CRC), and the clinical utility of fusion testing in advanced CRC remains unclear. We sought to identify oncogenic fusions in patients with advanced CRC using a fusion partner-agnostic circulating tumor DNA (ctDNA) assay to better understand their clinical relevance.

We performed a retrospective analysis using de-identified data from 18,558 patients with advanced CRC who underwent ctDNA next-generation sequencing with Guardant360^® from 2017 to 2022. These samples were subsequently reanalyzed with a partner-agnostic bioinformatics method to identify both clonal and non-clonal fusions. We analyzed for associations between fusions and MSI-H status, as well prior EGFR-directed therapy signature.

Fusions were identified in 221 (1.3%) of CRC patients analyzed. 193 patients had 258 activating fusions, while 28 patients had fusions of uncertain significance. Among patients with activating fusions, there were 18 clonal fusions (7%) and 240 (93%) subclonal fusions. Clonal fusions were more common in patients with MSI-H status, and subclonal fusions were associated with prior EGFR exposure signature.

Among patients with advanced CRC, partner-agnostic ctDNA fusion detection is possible and improves identification as a blood-based approach by extension of fusion calling partners. Detection of fusions in the ctDNA may provide rationale for potential therapeutic strategies according to clonality as informed by the ctDNA, whereas subclonal fusions may play a role in acquired resistance to EGFR inhibitors in KRAS/NRAS/BRAF^wild-type tumors.