Introducing HL7 FHIR Genomics Operations: a developer-friendly approach to genomics-EHR integration

Robert H Dolin; Bret S E Heale; Gil Alterovitz; Rohan Gupta; Justin Aronson; Aziz Boxwala; Shaileshbhai R Gothi; David Haines; Arthur Hermann; Tonya Hongsermeier; Ammar Husami; James Jones; Frank Naeymi-Rad; Barbara Rapchak; Chandan Ravishankar; James Shalaby; May Terry; Ning Xie; Powell Zhang; Srikar Chamala

doi:10.1093/jamia/ocac246

Introducing HL7 FHIR Genomics Operations: a developer-friendly approach to genomics-EHR integration

J Am Med Inform Assoc. 2023 Feb 16;30(3):485-493. doi: 10.1093/jamia/ocac246.

Authors

Robert H Dolin¹, Bret S E Heale², Gil Alterovitz^{3

4}, Rohan Gupta⁵, Justin Aronson⁶, Aziz Boxwala¹, Shaileshbhai R Gothi⁷, David Haines⁸, Arthur Hermann⁹, Tonya Hongsermeier¹, Ammar Husami^{10

11}, James Jones¹², Frank Naeymi-Rad⁸, Barbara Rapchak⁸, Chandan Ravishankar⁸, James Shalaby¹, May Terry¹³, Ning Xie¹⁴, Powell Zhang¹⁵, Srikar Chamala^{16

17}

Affiliations

¹ Elimu Informatics, El Cerrito, California, USA.
² Humanized Health Consulting, Salt Lake City, Utah, USA.
³ Brigham and Women's Hospital, Boston, Massachusetts, USA.
⁴ Harvard/MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, Massachusetts, USA.
⁵ Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India.
⁶ Northwestern University, Chicago, Illinois, USA.
⁷ Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida, USA.
⁸ Leap of Faith Technologies, Libertyville, Illinois, USA.
⁹ Department of Health IT Strategy & Policy, Kaiser Permanente, Pasadena, California, USA.
¹⁰ Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.
¹¹ Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.
¹² Computational Health Informatics Program, Boston Children's Hospital, Boston, Massachusetts, USA.
¹³ MITRE Corporation, McLean, Virginia, USA.
¹⁴ Biomedical Cybernetics Laboratory, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.
¹⁵ Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
¹⁶ Keck School of Medicine, Department of Pathology, University of Southern California, Los Angeles, California, USA.
¹⁷ Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California, USA.

Abstract

Objective: Enabling clinicians to formulate individualized clinical management strategies from the sea of molecular data remains a fundamentally important but daunting task. Here, we describe efforts towards a new paradigm in genomics-electronic health record (HER) integration, using a standardized suite of FHIR Genomics Operations that encapsulates the complexity of molecular data so that precision medicine solution developers can focus on building applications.

Materials and methods: FHIR Genomics Operations essentially "wrap" a genomics data repository, presenting a uniform interface to applications. More importantly, operations encapsulate the complexity of data within a repository and normalize redundant data representations-particularly relevant in genomics, where a tremendous amount of raw data exists in often-complex non-FHIR formats.

Results: Fifteen FHIR Genomics Operations have been developed, designed to support a wide range of clinical scenarios, such as variant discovery; clinical trial matching; hereditary condition and pharmacogenomic screening; and variant reanalysis. Operations are being matured through the HL7 balloting process, connectathons, pilots, and the HL7 FHIR Accelerator program.

Discussion: Next-generation sequencing can identify thousands to millions of variants, whose clinical significance can change over time as our knowledge evolves. To manage such a large volume of dynamic and complex data, new models of genomics-EHR integration are needed. Qualitative observations to date suggest that freeing application developers from the need to understand the nuances of genomic data, and instead base applications on standardized APIs can not only accelerate integration but also dramatically expand the applications of Omic data in driving precision care at scale for all.

Keywords: HL7 FHIR; application programming interface; clinical decision support; clinical genomics; electronic health record.

MeSH terms

Electronic Health Records*
Genomics*
Health Level Seven
Time