Beside the well-studied colorectal cancer (CRC) driver mutations in oncogenes and tumorsuppressor genes, most CRCs also display recurrent alterations of specific chromosome arms or entire chromosomes, such as gains of chromosomes 7, 8q, 13, 20 and losses of chromosomes 17p and 18. However, how these specific aneuploidies arise and contribute to oncogenesis remains unresolved, in part due to the challenges associated with the manipulation of specific chromosomes in relevant in vitro human CRC models. We successfully developed strategies for inducing random or chromosome-specific mis-segregation events (referred to as chromosomal instability, CIN). These methods were introduced into healthy and cancerous human colon tissue organoids to study aneuploidy evolution or to correct specific aneuploidies recurrently found in CRC. We observed that after transient induction of random CIN in healthy human colorectal organoids, the deprivation of specific intestinal stem cell niche factors selected for aneuploidies in the surviving cells that are recurrently found in colorectal cancer. Furthermore, by applying a reverse approach in patient-derived colorectal cancer organoids, we reveal a strong dependency on the trisomic state of chr 7 for CRC organoid growth. Our preliminary data suggest that tissue microenvironment and/or architecture can be important factors in shaping the aneuploidy landscape of CRC, and that the resulting aneuploidies support tumour maintenance.

Circulating tumor DNA (ctDNA) is a cancer-specific biomarker that can be detected in blood draws and other liquid biopsies. Quantitative and qualitative ctDNA measurements allow to better determine prognosis and support adjuvant treatment decision-making after initial treatment with curative intent (‘who to treat’); to better predict the type of therapy to which a patient is likely to respond (‘how to treat’); and to better monitor the (lack of) treatment response over time and support decisions regarding treatment adaptation (‘when to treat’). Therefore, minimal invasive longitudinal liquid biopsy ctDNA biomarker testing has great potential to change current clinical practice.

The clinical potential of ctDNA testing is a strong driver of innovative technological developments. The detection of minimal residual disease (MRD) in patients with non-metastatic colon cancer requires a ctDNA assay with high test sensitivity. We recently applied a novel whole genome sequencing (WGS)-based ctDNA test, Labcorp Plasma Detect, to determine the clinical validity of post-surgery MRD detection in stage III colon cancer patients treated with adjuvant chemotherapy.

Accurate monitoring of treatment response is important for treatment decision-making in patients with metastatic colorectal cancer. This clinical application requires a ctDNA assay that is broadly applicable. Based on the fact there is variation in cell-free DNA (cfDNA) fragment length between cfDNA derived from cancer cells versus normal cells we recently developed a tumor agnostic ctDNA test, the DELFI tumor fraction (DELFI-TF) score, to longitudinally determine changes in tumor load.

These studies indicate that liquid biopsy ctDNA testing has strong potential to complement TNM staging and CT imaging. However, the clinical utility of ctDNA testing remains to be demonstrated. Currently clinical trials are being performed to enable implementation of ctDNA testing to guide decision-making for treatment of patients with cancer as standard of care routine molecular diagnostics.

The Netherlands Cancer Institute has successfully integrated Clinical-grade Whole Genome Sequencing (WGS) into its routine practices since 2021. The success of implementing WGS has relied on adhering to a comprehensive protocol. In the WGS implementation study, known as the WIDE study, we developed this protocol and assessed the feasibility and clinical validity of WGS in a cohort of 1,200 patients. The use of fresh-frozen samples herein is necessary for WGS but can be challenging to implement in pathology laboratories accustomed to using formalin-fixed paraffin-embedded samples. This challenge and other considerations to guide uptake of WGS in routine clinical care will be discussed.
Additionally, we examined the feasibility and clinical utility of implementing two years of WGS within our hospital following the conclusion of the study. We will report the clinical utility of WGS based on the identification of actionable biomarkers, the diagnostic utility of WGS for patients with Cancer of Unknown Primary (CUP), and the utility of WGS in identifying hereditary predispositions, which can inform patient management and referrals.