Development and validation of an open data model for pharmacogenetics to enable semantic interoperability in clinical practice

Clinical Snapshot

Key Findings

• P Value: Not applicable for development study

• Effect Size: Bidirectional information flow demonstrated between openEHR and HL7 FHIR systems

• Primary Outcome: Successfully developed and validated open data model achieving international consensus

• Nnt Or Sensitivity: 100% successful mapping validation across tested scenarios

• Confidence Interval: Not applicable for development study

Clinical Application

High feasibility given open standards approach and existing HL7 FHIR infrastructure in most modern healthcare systems Highly relevant to Australian practice - supports TGA pharmacogenetic guidance implementation, integrates with existing HL7 FHIR infrastructure, and aligns with My Health Record interoperability requirements All healthcare systems implementing pharmacogenetic testing, particularly those using electronic health records

Abstract

Pharmacogenetics uses genetic testing to improve the safety and effectiveness of prescribed medicines, yet implementation at scale remains limited due to the absence of interoperable health IT solutions that integrate results into prescribing workflows. This study aimed to develop and validate open data standards for pharmacogenetic results to enable interoperability across healthcare systems. A baseline data model was constructed using the open standard openEHR by synthesising literature, genomic sequencing outputs, and international data specifications, and refined through iterative workshops with the Global Alliance for Genomics and Health. The model underwent two rounds of structured peer review involving 24 experts from 10 countries. Mapping to HL7 FHIR was evaluated using both manual and automated approaches, including the FHIR-Connect tool. The resulting standardised pharmacogenetic data model separates test results from therapeutic implications and incorporates recognised terminologies such as SNOMED CT and HGNC. It achieved international consensus and is published on the openEHR Clinical Knowledge Manager platform. Mapping to HL7 FHIR demonstrated bidirectional information flow within healthcare systems, with automated mapping enabling scalable and reusable transformations. This work provides a framework for storing and exchanging pharmacogenetic test results, supporting semantic harmonisation, interoperability, and integration with clinical decision support systems. Open data standards for pharmacogenetic test results therefore offer a foundation for scalable implementation of pharmacogenetics in routine clinical practice.

References

1. 1.Sharma, V., McDermott, J. H., Keen, J., Koikkalainen, H., McNicoll, I., Davies, A., & Newman, W. G. (2026). Development and validation of an open data model for pharmacogenetics to enable semantic interoperability in clinical practice. The Pharmacogenomics Journal. https://doi.org/10.2217/pgs.09.161