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. 2021 Jun:118:103795.
doi: 10.1016/j.jbi.2021.103795. Epub 2021 Apr 28.

Genomic considerations for FHIR®; eMERGE implementation lessons

Mullai Murugan  1 , Lawrence J Babb  2 , Casey Overby Taylor  3 , Luke V Rasmussen  4 , Robert R Freimuth  5 , Eric Venner  6 , Fei Yan  7 , Victoria Yi  7 , Stephen J Granite  3 , Hana Zouk  8 , Samuel J Aronson  9 , Kevin Power  10 , Alex Fedotov  11 , David R Crosslin  12 , David Fasel  13 , Gail P Jarvik  14 , Hakon Hakonarson  15 , Hana Bangash  16 , Iftikhar J Kullo  16 , John J Connolly  15 , Jordan G Nestor  17 , Pedro J Caraballo  18 , WeiQi Wei  19 , Ken Wiley  20 , Heidi L Rehm  21 , Richard A Gibbs  6
Affiliations

Genomic considerations for FHIR®; eMERGE implementation lessons

Mullai Murugan et al. J Biomed Inform. 2021 Jun.

Abstract

Structured representation of clinical genetic results is necessary for advancing precision medicine. The Electronic Medical Records and Genomics (eMERGE) Network's Phase III program initially used a commercially developed XML message format for standardized and structured representation of genetic results for electronic health record (EHR) integration. In a desire to move towards a standard representation, the network created a new standardized format based upon Health Level Seven Fast Healthcare Interoperability Resources (HL7® FHIR®), to represent clinical genomics results. These new standards improve the utility of HL7® FHIR® as an international healthcare interoperability standard for management of genetic data from patients. This work advances the establishment of standards that are being designed for broad adoption in the current health information technology landscape.

Keywords: Clinical decision support; Clinical genomics; Electronic health record (EHR); Genetic test results; HL7® FHIR® standard; Interoperability.

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Conflict of interest statement

Declaration of Competing Interest

The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: [Luke V. Rasmussen has a patent GENERATING DATA IN STANDARDIZED FORMATS AND PROVIDING RECOMMENDATIONS that is no longer being pursued. Samuel J. Aronson, Hana Zouk and Heidi L. Rehm are employed by Mass General Brigham which receives royalties on sales of GeneInsight software. David R. Crosslin is a consultant for UnitedHealth Group. Richard A. Gibbs declares that Baylor College of Medicine receives payments from Baylor Genetics Laboratories, which provides services for genetic testing; Baylor College of Medicine is part owner of Codified Genomics. Eric Venner is a cofounder of Codified Genomics, which provides variant interpretation services. All other authors declare no competing interests.]

Figures

Fig. 1.
Fig. 1.. The eMERGE III Network.
The Network comprised 11 study sites, 2 central sequencing and genotyping facilities (CSGs) and a coordinating center (CC) with samples sent from the study sites to the CSGs. Clinical genetic results were returned to the study sites after sequencing, variant classification and harmonization at the CSGs with raw data and de-identified results being returned to the CC for research. Both the clinical and research data flow is illustrated in this figure[14].
Fig. 2.
Fig. 2.. Methods for specification and pilot projects development.
The two columns represent complementary work streams - the leftmost dedicated to the specification development, and the right on use cases for pilot projects development. The solid arrows represent the stepwise or iterative direction of the respective processes.
Fig. 3.
Fig. 3.. BCM-HGSC & LMM eMERGE Narrative Report Examples.
Reports illustrate the content and structure of a typical positive genetic report generated by each of the CSGs.
Fig. 4.
Fig. 4.. BCM-HGSC general report layout and detailed mapping.
Illustrates the composition and layout of the data concepts within the eMERGE reports with each of the concepts coded by color and more precisely by number. Note: though Fig. 4 is the BCM-HGSC format, BI/LMM also included the same concepts in a slightly modified layout. The numbering also correlates to the concepts in Fig. 5.
Fig. 4.
Fig. 4.. BCM-HGSC general report layout and detailed mapping.
Illustrates the composition and layout of the data concepts within the eMERGE reports with each of the concepts coded by color and more precisely by number. Note: though Fig. 4 is the BCM-HGSC format, BI/LMM also included the same concepts in a slightly modified layout. The numbering also correlates to the concepts in Fig. 5.
Fig. 5.
Fig. 5.. Structural Design of the eMERGE FHIR® Specification.
A color-coded organizational mapping of the FHIR® GR IG resources and profiles for eMERGE, including custom eMERGE extensions in blue (X6, X7). The color and numbering maps back to the report layout and example in Fig. 4 for easier reference. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
Fig. 6.
Fig. 6.. eMERGE III FHIR® Pilot.
FHIR® reports for the eMERGE pilot samples were generated by BCM-HGSC and pushed to NU and JHU’s FHIR® servers. Data was extracted from these FHIR® reports for the NU PGx and JHU Variant Associated Phenotype use cases respectively.
See this image and copyright information in PMC

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