PhEval

PhEval provides a standardised and empirical framework to evaluate phenotype-driven variant and gene prioritisation algorithms (VGPAs).

Key Features:

• Standardised test corpora: PhEval includes standardised test corpora and test corpus generation tools for open benchmarking and comparison of methods on standardised data sets.
• Controlled configuration: PhEval controls the configuration of evaluated VGPAs to enable transparent, portable, comparable and reproducible benchmarking.
• Real-world patient data: PhEval provides standardised data on patient cohorts from real-world case-reports to address patient data availability issues.

Scientific Applications:

• VGPA benchmarking: PhEval benchmarks and compares rare disease variant and gene prioritisation algorithms.
• Performance assessment: PhEval assesses the efficacy of VGPAs, measuring performance impacted by factors such as ontology structure, annotation completeness, or changes to the underlying algorithm.
• Diagnostic pipeline evaluation: PhEval enables thorough and standardised assessment of tools that are key components of rare disease diagnostic pipelines.

Methodology:

PhEval integrates complex data types such as ontologies, gene-to-phenotype associations, and cross-species data into the evaluation framework.