SMART on FHIR Genomics: Facilitating Standardized Clinico-genomic Apps

Overview

Journal J Am Med Inform Assoc

Publisher Oxford University Press

Specialty Medical Informatics

Date 2015 Jul 23

PMID 26198304

Citations 58

Authors

Gil Alterovitz

Jeremy Warner

Peijin Zhang

Yishen Chen

Mollie Ullman-Cullere

David Kreda

Isaac S Kohane

Affiliations

Soon will be listed here.

Abstract

Background: Supporting clinical decision support for personalized medicine will require linking genome and phenome variants to a patient's electronic health record (EHR), at times on a vast scale. Clinico-genomic data standards will be needed to unify how genomic variant data are accessed from different sequencing systems.

Methods: A specification for the basis of a clinic-genomic standard, building upon the current Health Level Seven International Fast Healthcare Interoperability Resources (FHIR®) standard, was developed. An FHIR application protocol interface (API) layer was attached to proprietary sequencing platforms and EHRs in order to expose gene variant data for presentation to the end-user. Three representative apps based on the SMART platform were built to test end-to-end feasibility, including integration of genomic and clinical data.

Results: Successful design, deployment, and use of the API was demonstrated and adopted by HL7 Clinical Genomics Workgroup. Feasibility was shown through development of three apps by various types of users with background levels and locations.

Conclusion: This prototyping work suggests that an entirely data (and web) standards-based approach could prove both effective and efficient for advancing personalized medicine.

Citing Articles

Machine Learning-Enabled Clinical Information Systems Using Fast Healthcare Interoperability Resources Data Standards: Scoping Review.

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Opportunities and challenges for biomarker discovery using electronic health record data.

Singhal P, Tan A, Drivas T, Johnson K, Ritchie M, Beaulieu-Jones B Trends Mol Med. 2023; 29(9):765-776.

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Ontologizing health systems data at scale: making translational discovery a reality.

Callahan T, Stefanski A, Wyrwa J, Zeng C, Ostropolets A, Banda J NPJ Digit Med. 2023; 6(1):89.

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A cloud-based pipeline for analysis of FHIR and long-read data.

Dunn T, Cosgun E Bioinform Adv. 2023; 3(1):vbac095.

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

Dolin R, Heale B, Alterovitz G, Gupta R, Aronson J, Boxwala A J Am Med Inform Assoc. 2022; 30(3):485-493.

PMID: 36548217 PMC: 9933060. DOI: 10.1093/jamia/ocac246.

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