Orientation-Aware Structural Variant Queries: Transforming Gene Fusion Analysis in cBioPortal

Customer

Our customer is a leading biotechnology company dedicated to transforming patient care and advancing the fight against cancer through innovative precision medicine and data-driven solutions.

The Challenge

cBioPortal’s existing Onco Query Language (OQL) supported gene fusion analysis but lacked the ability to specify the orientation of genes in fusion events. This limitation made it difficult for researchers to determine whether a gene was upstream or downstream in a fusion, a critical detail for understanding structural variants and identifying potential biomarkers.

How We Solved It

The Hyve collaborated with the customer to enhance the OQL functionality in cBioPortal, delivering:

1. Orientation-Aware Syntax: A new syntax to query gene fusions with directionality. Researchers can now identify upstream and downstream roles or query specific gene-pair orientations.
   • Example: GeneA::GeneB queries fusions where GeneA is upstream and GeneB is downstream.
2. Enhanced Visual Insights: Separate tracks for upstream and downstream gene fusions in the OncoPrint tab provide a clearer overview of fusion patterns across datasets.
3. Custom Structural Variants Table: A summary table with positional information for fusion events, configurable in local cBioPortal instances, to enhance study-level exploration.

The Outcome

These enhancements empower researchers with precise, orientation-specific gene fusion analysis. Key benefits include enabling detailed exploration of gene fusion events and their roles in cancer research. A detailed example is provided in our article, showcasing insights into TMPRSS2 fusions and their implications in targeted therapy development.

By integrating this functionality, our customer—and now the broader cBioPortal community—can uncover critical genomic insights more quickly and with greater accuracy, accelerating innovation in oncology research.

Learn More

For a deeper dive into this feature and its applications, read the full article on our website: Orientation-Aware OQL Filter for Gene Fusion Events.

Interested in custom cBioPortal enhancements? Contact us to explore how we can support your genomic research goals.