Abstract
Next-generation sequencing is revolutionizing precision oncology, but vast amounts of sequence data must be processed and mined to reveal clinically relevant alterations that can inform patient care. The Personalized OncoGenomics (POG) program at BC Cancer utilizes whole genome and transcriptome analysis, providing a comprehensive view of advanced cancer patient tumours. This analysis relies on curated clinical knowledgebases linking cancer variants and their clinical relevance, but the breadth and utility of these can be limited by proprietary access or limited coverage. CIViC (Clinical Interpretation of Variants in Cancer) is an open-access, crowd-sourced knowledgebase of clinically relevant cancer variants that aims to address these limitations, and is one of several sources used for variant interpretation in POG. Based on a retrospective cohort of POG cases, we evaluated the knowledgebase coverage of genes and variants involved in treatment recommendations from the molecular tumour board (MTB). In a preliminary analysis, we found more than 95% of patients had an alteration considered clinically actionable by the MTB, demonstrating the benefit of combined genome and transcriptome analysis. We found that knowledge from CIViC represented nearly 50% of therapeutic evidence reported at the MTB, emphasizing the role of open-access knowledge in precision oncology. Additionally, by prospectively examining the levels and sources of evidence in patient reports, we identified areas where additional knowledgebase curation would most impact alignment with clinical utility, highlighting genome signatures as a critical area for future curation efforts. We also considered the impact of quality of evidence on MTB recommendations and patient treatments.
Published Version
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