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. 2023 May 19;30(6):1179-1189.
doi: 10.1093/jamia/ocad061.

Creation of a structured molecular genomics report for Germany as a local adaption of HL7's Genomic Reporting Implementation Guide

Caroline Stellmach  1 , Julian Sass  1 , Bernd Auber  2 , Martin Boeker  3 , Thomas Wienker  4 , Andrew J Heidel  5 , Manuela Benary  6 , Simon Schumacher  7 , Stephan Ossowski  8 , Frederick Klauschen  9   10   11 , Yvonne Möller  12 , Rita Schmutzler  13 , Arsenij Ustjanzew  14 , Patrick Werner  15 , Aurelie Tomczak  16 , Thimo Hölter  1 , Sylvia Thun  1
Affiliations

Creation of a structured molecular genomics report for Germany as a local adaption of HL7's Genomic Reporting Implementation Guide

Caroline Stellmach et al. J Am Med Inform Assoc. .

Abstract

Objective: The objective was to develop a dataset definition, information model, and FHIR® specification for key data elements contained in a German molecular genomics (MolGen) report to facilitate genomic and phenotype integration in electronic health records.

Materials and methods: A dedicated expert group participating in the German Medical Informatics Initiative reviewed information contained in MolGen reports, determined the key elements, and formulated a dataset definition. HL7's Genomics Reporting Implementation Guide (IG) was adopted as a basis for the FHIR® specification which was subjected to a public ballot. In addition, elements in the MolGen dataset were mapped to the fields defined in ISO/TS 20428:2017 standard to evaluate compliance.

Results: A core dataset of 76 data elements, clustered into 6 categories was created to represent all key information of German MolGen reports. Based on this, a FHIR specification with 16 profiles, 14 derived from HL7®'s Genomics Reporting IG and 2 additional profiles (of the FamilyMemberHistory and RiskAssessment resources), was developed. Five example resource bundles show how our adaptation of an international standard can be used to model MolGen report data that was requested following oncological or rare disease indications. Furthermore, the map of the MolGen report data elements to the fields defined by the ISO/TC 20428:2017 standard, confirmed the presence of the majority of required fields.

Conclusions: Our report serves as a template for other research initiatives attempting to create a standard format for unstructured genomic report data. Use of standard formats facilitates integration of genomic data into electronic health records for clinical decision support.

Keywords: FHIR®; Fast Healthcare Interoperability Resources; HL7®; Implementation Guide; interoperability; molecular genomics report; sequencing data.

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Conflict of interest statement

ST is vice chair of HL7 Germany. The other authors declare no competing interests.

Figures

None
Graphical abstract
Figure 1.
Figure 1.
Overview of the steps undertaken in the process of developing a FHIR-based molecular genomics report format.
Figure 2.
Figure 2.
General outline of the main informational elements contained in molecular genomics reports issued by MII project partners. The number in brackets indicates the category of the dataset definition where the respective information was assigned: 1: Specimen information, 2: Request, 3: Methods, 4: Results, 5: Interpretation, 6: Miscellaneous.
Figure 3.
Figure 3.
Overview of data elements defined in the logical model of the MII’s MolGen report that can be referenced using the ServiceRequest.supportingInfo extension.
Figure 4.
Figure 4.
Overview of how the FamilyMemberHistory.relationship.snomed element was extended to enable coding of lineage, degree, and relationship using the SNOMED CT® terminology. *SNOMED CT concepts are currently only available for first and second degree blood relatives but have been requested for third and fourth degree relative concepts.
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