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. 2020 Mar 18:5:13.
doi: 10.1038/s41525-020-0115-6. eCollection 2020.

FHIR Genomics: enabling standardization for precision medicine use cases

Gil Alterovitz  1   2 , Bret Heale  3 , James Jones  1 , David Kreda  4 , Fan Lin  1   5 , Lei Liu  1 , Xin Liu  1 , Kenneth D Mandl  1   6 , David W Poloway  1 , Rachel Ramoni  7 , Alex Wagner  8 , Jeremy L Warner  9
Affiliations

FHIR Genomics: enabling standardization for precision medicine use cases

Gil Alterovitz et al. NPJ Genom Med. .

Abstract

The development of Fast Healthcare Interoperability Resources (FHIR) Genomics, a feasible and efficient method for exchanging complex clinical genomic data and interpretations, is described. FHIR Genomics is a subset of the emerging Health Level 7 FHIR standard and targets data from increasingly available technologies such as next-generation sequencing. Much care and integration of feedback have been taken to ease implementation, facilitate wide-scale interoperability, and enable modern app development toward a complete precision medicine standard. A new use case, the integration of the Variant Interpretation for Cancer Consortium (VICC) "meta-knowledgebase" into a third-party application, is described.

Keywords: Clinical genetics; Data processing; Genomics; Health policy; High-throughput screening.

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Conflict of interest statement

Competing interestsThe authors declare no competing interests.

Figures

Fig. 1
Fig. 1. FHIR Genomics workflow use case.
a A ServiceRequest instance; b a DiagnosticReport instance refers to Observations under “result”; c a MolecularSequence instance carries the reference sequence and variant information; d an Observation instance carries clinical interpretation; e additional Observations can carry further analysis information. Arrows depict the inter-resource pointers.
Fig. 2
Fig. 2. Example of SMART on FHIR application.
a Arrows show API calls integrating clinical and genomic data at the point of care with external information, for example, through the GA4GH streaming standard htsget. b Screenshot of sample application showing associated drugs in the VICC meta-KB for a given variant on a sample patient. Clicking a drug name provides a list of relevant publications, sorted by AMP/ASCO/CAP guideline levels of evidence.
See this image and copyright information in PMC

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