Accelerating Cancer Diagnostics: How CKB Powers Automated Genomic Interpretation

About

In the evolving landscape of precision oncology, genomic data has become a cornerstone in guiding cancer treatment decisions. Whole genome sequencing (WGS) provides unparalleled insights into the molecular mechanisms driving cancer, yet the sheer volume of data presents a significant challenge for clinicians and researchers. Efficiently interpreting genomic variants and translating them into actionable treatment options requires advanced bioinformatics tools that streamline analysis and improve decision-making.

Hartwig Medical Foundation, a leading non-profit research organization based in the Netherlands, recognized the need for a scalable and automated solution to enhance variant interpretation. By integrating Genomenon's Cancer Knowledgebase (CKB) into its genomic workflow, Hartwig was able to accelerate diagnostic turnaround times, improve clinical trial matching, and standardize variant classification across multiple hospitals. This case study explores how CKB empowered Hartwig Medical Foundation to optimize precision oncology workflows, leading to more efficient and informed treatment strategies for cancer patients.

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"CKB enables comprehensive and reliable interpretation of any genomic test in a fully automated setting. We can rely on never missing relevant variants and their associated treatment evidence from our molecular tests."  - Korneel Duyvesteyn, Development lead at Hartwig Medical Foundation

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Organization Overview:About Hartwig Medical Foundation

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Hartwig Medical Foundation is a non-profit organization based in the Netherlands, dedicated to improving cancer care through large-scale genomic sequencing and data-driven decision-making.

The foundation was established a decade ago to provide WGS for cancer patients, filling a critical gap in genomic diagnostics at the time. Today, it operates internationally in Spain,Canada, and Australia and collaborates with over 45 hospitals across the Netherlands.

Hartwig’s genomic database consists of more than 7,000 clinically annotated WGS samples, providing a valuable resource for oncology research and clinical decision-making. The foundation’s mission is to integrate comprehensive genomic insights into clinical practice, ensuring that every patient benefits from precision medicine.

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Executive Summary

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Hartwig Medical Foundation’s Vision:
• Enable efficient and comprehensive genomic profiling for precision oncology
• Improve workflow automation in variant interpretation and treatment guidance.
• Standardize genomic decision-making across hospitals to ensure equitable patient care.

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Challenges:
• Managing large-scale genomic data from whole genome sequencing (WGS).
• Identifying actionable variants among thousands of detected variants.
• Keeping up with evolving variant evidence for accurate treatment recommendations.
• Reducing the manual workload involved in variant curation and clinical reporting.
• Ensuring uniformity in variant classification across different hospitals.

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Solution: Implementing CKB Services

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To address these challenges, Hartwig Medical Foundation integrated the Genomenon’s CKB solution into its genomic interpretation pipeline.

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This integration helped with:
• Automated Variant Annotation – CKB enabled rapid and accurate classification of variants, reducing reliance on manual literature review.
• Prioritization of Clinically Significant Variants – Oncologists could focus on variants with the strongest therapeutic relevance.
• Drug Efficacy and Treatment Matching – CKB provides evidence-based insights on the effectiveness of targeted therapies, supporting informed treatment decisions.
• Clinical Trial Matching – The foundation leveraged CKB’s database of ongoing trials, expanding patient access to investigational treatments.
• Standardized Decision-Making Across Institutions – By centralizing variant interpretation, CKB helped reduce variability in clinical genomic assessments.

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“One of the key strengths of CKB is its category variants. In cancer, trials often demand a category of variants rather than specific mutations, and CKB helps us determine what mutations fall into these categories.” - Korneel Duyvesteyn, Development lead at Hartwig Medical Foundation

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Results:
• Enabled completion of manual report reviews on the same day WGS results became available—an advancement from previous workflows that required over 24 hours.
• Improved clinical decision-making through structured annotation of gain-of-function evidence.
• Enhanced patient access to clinical trials.
• Strengthened consistency in variant interpretation across multiple hospitals.
• Increased patient confidence in comprehensive genomic analysis and treatment options.

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Sample Results: Improving Genomic Interpretation with CKB

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Case Example: Tumor Board Decision Support‍

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A patient at Erasmus MC, one of Hartwig’s partner hospitals, presented with a fusion variant detected in their tumor. Because this fusion had a low incidence in Hartwig's database it was assessed to have a low likelihood of being a driver variant. However, after querying CKB, the fusion was annotated with gain-of-function evidence, providing critical insight to the tumor board for evaluating treatment options. This streamlined access to high-confidence evidence reduced the time needed for genomic review, supporting faster and more precise treatment planning.

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Case Example: Clinical Trial Matching for a U.S.-Based Patient‍

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Through a pilot project in the U.S., Hartwig used CKB’s clinical trial database to evaluate therapeutic options for a colorectal cancer patient. The query identified a relevant clinical trial in Boston, which was not previously considered. CKB’s category variant system was instrumental in confirming the eligibility of the variant, as the trial required an inactivating variant in APC, and CKB provided a structured tree to determine variant classification. This capability helped ensure that the patient was not overlooked for experimental treatment opportunities.

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“One of the key strengths of CKB is its category variants. In cancer, trials often demand a category of variants rather than specific mutations, and CKB helps us determine what mutations fall into these categories.” - Korneel Duyvesteyn, Development lead at Hartwig Medical Foundation

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Conclusion

Hartwig Medical Foundation’s adoption of CKB and Genomenon’s services has been extremely valuable in advancing precision oncology in the Netherlands and beyond. By leveraging a robust genomic knowledgebase, Hartwig has streamlined variant interpretation, enhanced clinical decision-making, and improved patient access to cutting-edge treatments. This case study underscores the power of integrating curated genomic intelligence into clinical workflows, setting a precedent for other institutions seeking to enhance their precision medicine capabilities.

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About CKB

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CKB, powered by Genomenon, is the standard in evidence-based interpretation of complex cancer genomic profiles. It is a professionally curated, up-to-date knowledgebase for interpreting complex cancer genomic profiles and connecting variants to available clinical trials and therapies. CKB contains information on gene variants, FDA drug labels, targeted therapies, and clinical trials related to more than 2,000genes. The standardization protocols and sophisticated search capabilities allow users to navigate increasingly complex data and investigate clinically relevant genomic variants to help identify opportunities to advance cancer research, design clinical trials, and determine the best treatment options for every patient.

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About Genomenon

Genomenon is a leading genomic intelligence company dedicated to improving the quality of patients’ lives by uncovering the genomic drivers of genetic disease and cancer.Blending the power of AI with genomic expertise, Genomenon simplifies complex genetic data into actionable insights for patient diagnosis and precision medicine development.The company’s solutions include software, data, and curation and consulting services.

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