title: SMART on FHIR Genomics: facilitating standardized clinico-genomic apps.
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.
  
  
  CONCLUSIONS
  This prototyping work suggests that an entirely data (and web) standards-based approach could prove both effective and efficient for advancing personalized medicine.
authors.affiliation: Children's Hospital Informatics Program, Boston, MA Center for Biomedical Informatics, Harvard Medical School, Boston, MA Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA ga@alum.mit.edu.
authors.forename: Gil
authors.initials: G
authors.lastname: Alterovitz
authors.affiliation: Department of Biomedical Informatics, Vanderbilt University, Nashville, TN Department of Medicine, Division of Hematology/Oncology, Vanderbilt University, Nashville, TN.
authors.forename: Jeremy
authors.initials: J
authors.lastname: Warner
authors.affiliation: Department of Computer Science, Carnegie Mellon University, Pittsburgh, PA.
authors.forename: Peijin
authors.initials: P
authors.lastname: Zhang
authors.affiliation: Department of Computer Science, University of Illinois at Urbana-Champaign, Champaign, IL.
authors.forename: Yishen
authors.initials: Y
authors.lastname: Chen
authors.affiliation: Dana-Farber Cancer Institute, Boston, MA.
authors.forename: Mollie
authors.initials: M
authors.lastname: Ullman-Cullere
authors.affiliation: Center for Biomedical Informatics, Harvard Medical School, Boston, MA.
authors.forename: David
authors.initials: D
authors.lastname: Kreda
authors.affiliation: Children's Hospital Informatics Program, Boston, MA Center for Biomedical Informatics, Harvard Medical School, Boston, MA Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA.
authors.forename: Isaac S
authors.initials: IS
authors.lastname: Kohane
mesh_terms: D030541:Databases, Genetic; D057286:Electronic Health Records; D023281:Genomics / Q000592:standards*; D057208:Health Level Seven; D006801:Humans; D033181:Information Dissemination; D020407:Internet; D012984:Software
keywords: EHR; EMR; FHIR; HL7; SMART; clinicogenomics; data sharing; data warehouse; genomics; i2b2; standards