Beyond colonoscopy, faecal DNA mutation screening provides a potential and viable path to early colorectal cancer detection.

Colorectal cancer (CRC) remains a leading cause of cancer-related morbidity and mortality worldwide, with early detection critical for improving clinical outcomes. In Denmark's CRC screening program, nearly 60% of patients undergoing colonoscopy do not have polyps requiring treatment, highlighting the need for more sensitive and less invasive screening methods to improve early detection and reduce unnecessary procedures. In this study, we assessed the potential of two faecal DNA-based methods for detecting CRC-related mutations. Extracted DNA was analysed using next-generation sequencing (NGS) and digital PCR (dPCR). NGS targeted a gene panel covering the most frequently mutated sites in CRC, while dPCR focused on six specific CRC-associated mutations. A common limitation across both methods was the low abundance of human DNA in faecal samples, which reduced the reliability of variant detection. Nevertheless, both NGS and dPCR showed promise, particularly when DNA input was sufficient. Significant associations were observed between mutation counts and clinical diagnosis, with key CRC mutations reliably detected. The findings suggest that, with further implementation, these methods could serve as a less invasive and more cost-effective alternative to colonoscopy, especially for high-risk individuals. However, the sensitivity of both methods was limited in samples with low DNA yield, likely due to inhibitory effects during sample preservation or extraction. While faecal samples may be better suited for gut microbiome profiling, our findings underscore the potential of human DNA-based faecal screening in CRC and highlight the need for optimized extraction protocols to improve diagnostic accuracy, minimize unnecessary procedures, and provide personalized care for high-risk populations.