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Genomics in FHIR

The era of precision medicine-- an emerging approach for disease treatment and prevention that takes into account individual variability in genes, environment, and lifestyle for each person-- is upon us.

Precision medicine is fueled by the amazing technological advancements in genomics, making it possible (and feasible) to undertake broad genetic testing on an individual in a clinically useful timeframe. Whereas not so long ago genomics was primarily of concern to bioinformaticists interacting with such artifacts as alignment (e.g., BAM, CRAM) and variant calling (e.g., VCF) data files, we are now seeing tremendous interest across the clinical community for integrating genomics findings and recommendations into the EHR and into the care process. To that end, the HL7 Clinical Genomics Work Group is developing a set of standards for reporting structured genomic data using FHIR.

An individual's genetic data set is large and complex, and therefore requires systems that can manage the size and make sense of the complexity. Unfortunately, due to a lack of widely adopted standards, these systems are often incompatible. A standards-based approach to data exchange that could be adopted to integrate both genetic data and clinical information systems will be crucial to accelerating the integration of precision medicine and to make sense of genetic testing results in a complete clinical context.

The Clinical Genomics Work Group supports the HL7 mission to create and promote its standards by enabling the semantically meaningful exchange of data between parties interested in clinical, personal, and population genomic information and family health history, which are required to support precision medicine. The committee's work products include:

• Genomics Reporting Implementation Guide: Standardizes the reporting of genomic variants, haplotypes, genotypes, variant annotations, and more.

• MolecularDefinition Resource: The MolecularDefinition resource represents molecular entities (e.g., nucleotide or protein sequences) for both clinical and non-clinical use cases, including translational research. The resource is definitional, in that it focuses on discrete, computable, and semantically expressive data structures that reflect the genomic domain. Because the resource focuses on the molecular entities rather than specimen source or annotated knowledge, it supports both patient/participant-specific use cases and population-based data, and both human and non-human data.

• Molecular Definition Implementation Guide for Molecular Data Types is an emerging product that includes profiles for structured representation of the fundamental concepts such as Sequence, Allele, and Variation, Haplotype, and Genotype. This guide is work in progress and will evolve to represent additional concepts.

• GenomicStudy Resource: A resource that aims at delineating relevant information of a genomic study. A genomic study might comprise one or more analyses, each serving a specific purpose. These analyses may vary in method (e.g., karyotyping, CNV, or SNV detection), performer, software, devices used, or regions targeted.

Uses of these FHIR artifacts and other genomic use cases can be found here

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