EHR based Genetic Testing Knowledge Base (iGTKB) Development.

Area of Science:

• Medical Informatics
• Genetics
• Clinical Decision Support

Background:

• Clinical integration of genetic tests is hindered by suboptimal workflows.
• An intelligent system is needed to recommend genetic tests based on clinical evidence.
• The individualized Genetic Testing Knowledge Base (iGTKB) was developed using EHR data.

Purpose of the Study:

• To develop an EHR-based knowledge base for genetic testing.
• To integrate clinical evidence for genetic test recommendations.
• To support the development of an automated genetic testing recommendation system.

Main Methods:

• Extracted genetic testing information and patient EHR data.
• Utilized Natural Language Processing (NLP) for clinical feature annotation.
• Prioritized clinical features using odds ratios for knowledge base construction.

Main Results:

• Developed iGTKB incorporating 28 dominant clinical features for five genetic tests.
• Annotated 243 clinical features from Human Phenotype Ontology (HPO).
• Deposited genetic tests, disorders, and features with odds ratios into iGTKB.

Conclusions:

• An EHR-based genetic testing knowledge base (iGTKB) was successfully developed.
• iGTKB will be integrated into the Genetic Testing Ontology (GTO).
• This facilitates the development of the iGenetics recommendation system.