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Updated: Sep 9, 2025

Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
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Whole Exome Sequencing on FHIR: Towards Adoption in Clinical Practice for Precision Oncology Pipelines

Sara Nuhic1, Patrick Werner1, Daniel Kazdal2

  • 1MOLIT Institute gGmbH, Heilbronn, Germany.

Studies in Health Technology and Informatics
|September 3, 2025
PubMed
Abstract

Insights

This study introduces a Health Level Seven FHIR Implementation Guide to standardize Whole Exome Sequencing (WES) data for personalized cancer treatments. This standardization enhances data interoperability for machine learning and clinical applications.

Area of Science:

  • Genomics
  • Bioinformatics
  • Health Informatics

Background:

  • Whole Exome Sequencing (WES) offers personalized cancer treatments but lacks data standardization, hindering machine-based analysis and interoperability.
  • Existing molecular analysis methods are limited compared to WES.
  • Health Level Seven (HL7) Fast Healthcare Interoperability Resources (FHIR) standard can address interoperability challenges.

Purpose of the Study:

  • To develop a FHIR Implementation Guide (IG) for standardizing Whole Exome Sequencing (WES) data from molecular pathological reports.
  • To ensure syntactic and semantic interoperability for WES data.
  • To facilitate the integration of WES data into clinical practice and data science applications.

Main Methods:

  • A UML-like model was created based on the University Hospital Heidelberg's clinical WES pipeline.
  • An FHIR Implementation Guide (IG) was developed, incorporating work from the HL7 Clinical Genomics Workgroup.
  • The IG was extended to accurately represent and persist molecular pathology report data in FHIR format.

Main Results:

  • A comprehensive FHIR IG is provided, including 7 profiles, 10 ValueSets, 5 CodeSystems, 1 ConceptMap, and 34 example resources.
  • This IG serves as a foundational element for future standardization of WES data.
  • The developed artifacts enable the representation of molecular findings for clinical WES reports.

Conclusions:

  • The presented FHIR IG acts as a blueprint for standardizing Whole Exome Sequencing (WES) data.
  • Standardized WES data improves semantic integrity and enables well-established API access.
  • Future applications, including digital Molecular Tumorboards and data science initiatives, can benefit from this standardized approach.
Keywords:
FHIRHealth Information InteroperabilityPatient Care ManagementPrecision OncologyWhole Exome Sequencing

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