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Knowledge bases and software support for variant interpretation in precision oncology.

Florian Borchert1, Andreas Mock2,3, Aurelie Tomczak4,5

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Precision oncology requires robust tools for cancer variant annotation and treatment recommendations. Current knowledge bases and software tools have limitations in data integration and programmatic access, necessitating further development for comprehensive diagnostics.

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Area of Science:

  • Oncology
  • Bioinformatics
  • Medical Informatics

Background:

  • Precision oncology is rapidly advancing, increasing the need for efficient cancer variant annotation and treatment recommendations.
  • Comprehensive cancer panels are widely adopted, highlighting the demand for scalable diagnostic software.
  • Numerous academic knowledge bases exist, but require integration into practical tools for clinical use.

Purpose of the Study:

  • To identify and categorize knowledge bases relevant for cancer variant interpretation in precision oncology.
  • To analyze the programmatic access and integration of these knowledge bases into existing software tools.
  • To assess the current landscape of cancer variant interpretation tools and identify development needs.

Main Methods:

  • Systematic literature review to identify relevant knowledge bases.
  • Survey of medical experts in German university hospitals to gather insights.
  • Categorization of knowledge bases based on the precision oncology diagnostic workflow.
  • Analysis of programmatic access options and software integration.

Main Results:

  • Commonly used knowledge bases offer good programmatic access and are integrated into various software tools.
  • Access options for a broader range of knowledge bases vary, with limitations in clinical classification and therapy recommendations.
  • Databases for variant classification and pathway information often lack standardized interfaces.
  • No single tool currently integrates all identified knowledge bases for comprehensive variant interpretation.

Conclusions:

  • Existing knowledge bases and software tools partially address the needs of precision oncology.
  • Significant gaps remain in standardized access and integration, particularly for clinical variant data and therapy recommendations.
  • Development of specialized, integrated tools is crucial for advancing cancer variant interpretation and molecularly informed treatment decisions.