From innovation to standard care: real-world impact of whole genome sequencing in oncology 

Whole genome sequencing (WGS) is rapidly transforming cancer diagnostics. The Netherlands Cancer Institute (NKI) has already integrated this technology into routine clinical care. New research from the Department of Pathology demonstrates that WGS is technically feasible and delivers meaningful clinical impact for patients with solid tumors. 

Molecular diagnostics has been part of oncology for decades, traditionally focusing on specific genes or small gene panels to guide treatment decisions. WGS fundamentally changes that approach. Instead of analyzing selected parts of the DNA, the entire tumor genome is assessed in a single test. As pathologist José van der Berg explains: “Instead of extracting fragments of information from the DNA, we now obtain a complete overview. That gives us deeper insight into the tumor and helps us make more informed decisions.” 

WGS was implemented in 2021 as part of routine care for patients with metastatic, rare, or diagnostically complex tumors, in close collaboration with the Hartwig Medical Foundation. In daily practice, the technique has proven to be both reliable and fast: sequencing can be performed successfully within a timeframe that supports clinical decision-making in the majority of patients, demonstrating that comprehensive genomic profiling can be integrated into standard workflows. 

These results show that WGS makes a tangible difference for patients. The analysis reveals biomarkers that can guide treatment choices, refine diagnoses, or uncover hereditary risk in a substantial proportion of cases. Pathologist Kim Monkhorst emphasizes that the value of WGS goes beyond identifying individual mutations: “We see the difference that broad molecular diagnostics can make in clinical practice. We don’t just look for a mutation: we integrate all genetic information into patient care, from diagnosis to treatment strategy and hereditary risk.” 

Direct impact on diagnosis and treatment 

WGS also provides clinically relevant findings at scale. In 73% of patients, one or more potentially actionable biomarkers could be identified. In 41% of patients, these results directly influenced clinical care, including identifying biomarker-informed reimbursed treatment options, refining or changing diagnoses, or revealing hereditary cancer risk. Importantly, better survival was observed in patients who received WGS before any systemic treatment and who later received biomarker-informed treatment showed better survival compared to those in whom biomarkers were present, but no treatment was given. 

The impact of WGS is particularly evident in patients with cancer of unknown primary (CUP). The origin of the tumor is often difficult to determine in this group, limiting their treatment options. With WGS, the tumor type could be identified in 63% of cases, enabling more precise and personalized treatment strategies. 

According to physician-researcher Jeffrey van Putten, affiliated with the Hartwig Medical Foundation, these results illustrate a broader shift in oncology care: “This study shows what whole genome sequencing can deliver in daily practice. The technique is feasible and fast to implement, and for a significant proportion of patients it provides information that supports treatment decisions.” 

The study marks an important transition: whole genome sequencing is no longer an experimental technique, but an integral part of modern oncology care. By combining genomic and clinical data, the technique improves decision-making for patients today, and builds a foundation for future advances. 

In that sense, WGS represents more than a technological step forward. It reflects a shift towards a more complete understanding of cancer, and towards care that is better informed, more precise, and ultimately more meaningful for patients. 

Research at the NKI is financially supported by KWF Dutch Cancer Society and the AVL Foundation. 

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