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

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.

vcf2fhir: a utility to convert VCF files into HL7 FHIR format for genomics-EHR integration.

BACKGROUND: VCF formatted files are the lingua franca of next-generation sequencing, whereas HL7 FHIR is emerging as a standard language for electronic health record interoperability. A growing number of FHIR-based clinical genomics applications are emerging. Here, we describe an open source utility for converting variants from VCF format into HL7 FHIR format. RESULTS: vcf2fhir converts VCF variants into a FHIR Genomics Diagnostic Report. Conversion translates each VCF row into a corresponding FHIR-formatted variant in the generated report. In scope are simple variants (SNVs, MNVs, Indels), along with zygosity and phase relationships, for autosomes, sex chromosomes, and mitochondrial DNA. Input parameters include VCF file and genome build ('GRCh37' or 'GRCh38'); and optionally a conversion region that indicates the region(s) to convert, a studied region that lists genomic regions studied by the lab, and a non-callable region that lists studied regions deemed uncallable by the lab. Conversion can be limited to a subset of VCF by supplying genomic coordinates of the conversion region(s). If studied and non-callable regions are also supplied, the output FHIR report will include 'region-studied' observations that detail which portions of the conversion region were studied, and of those studied regions, which portions were deemed uncallable. We illustrate the vcf2fhir utility via two case studies. The first, 'SMART Cancer Navigator', is a web application that offers clinical decision support by linking patient EHR information to cancerous gene variants. The second, 'Precision Genomics Integration Platform', intersects a patient's FHIR-formatted clinical and genomic data with knowledge bases in order to provide on-demand delivery of contextually relevant genomic findings and recommendations to the EHR. CONCLUSIONS: Experience to date shows that the vcf2fhir utility can be effectively woven into clinically useful genomic-EHR integration pipelines. Additional testing will be a critical step towards the clinical validation of this utility, enabling it to be integrated in a variety of real world data flow scenarios. For now, we propose the use of this utility primarily to accelerate FHIR Genomics understanding and to facilitate experimentation with further integration of genomics data into the EHR.

Integration of Postcoordination Content into a Clinical Interface Terminology to Support Administrative Coding.

BACKGROUND: Clinical interface terminologies (CITs) consist of terms designed for clinical documentation and, through mappings to standardized vocabularies, to support secondary uses of patient data, including clinical decision support, quality measurement, and billing for health care services. The latter purpose requires maps to administrative coding systems, such as the International Classification of Diseases, 10th Revision, Clinical Modification (ICD-10-CM), for diagnoses in the United States. OBJECTIVES: The transition from ICD-9-CM to ICD-10-CM posed a challenge to CIT users due to the substantially increased details in ICD-10-CM. To address this, we developed a content layer within a CIT that provides postcoordination prompts for the details required for accurate ICD-10-CM coding. METHODS: We developed content to support prompting for and capture of additional information specified by the user in a single, clinically relevant term that is added to the patient's record, and whose mapping to other coding systems (like Systematized Nomenclature of Medicine-Clinical Terms [SNOMED CT]) reflects the details added during postcoordination. We worked with clinical information system developers to incorporate this into user interfaces, and with end-users to refine the design. RESULTS: While the prompts were designed around the precoordinated elements implicit in ICD-10-CM, irregularities in ICD-10-CM required some additional design measures, such as providing postcoordination options that interpolate gaps in ICD-10-CM to avoid user confusion. The system we describe has been implemented by ∼30,000 health care provider organizations, with content that covers the vast majority of encounter diagnoses. User feedback has been largely positive, though concerns have been raised about expanding postcoordination content beyond that required for ICD-10-CM coding. CONCLUSION: We have demonstrated the design and development of what, to our knowledge, is the first system that uses postcoordination to capture ICD-10-CM-relevant details in a CIT while also reflecting the details added by the user in maps to other vocabularies.

Interface terminologies: bridging the gap between theory and reality for Africa.

In the United States and Europe, electronic health records (EHRs) allow information technology and decision-support to facilitate the activities of clinicians and are considered an important component of health care improvement. However, actual adoption of EHRs by physicians has been slow and the use of decision support has been minimal. Part of the difficulty lies in the challenges that users face in capturing structured clinical information. Reference and administrative terminologies have been in use for many years and provide a critical infrastructure to support reimbursement, decision-support and data analysis. The problem is that physicians do not think and work using reference terminologies. Interface terminologies bridge the gap between information that is in the physician's mind and information that can be interpreted by computer applications. The maps from interface terminologies to appropriate reference terminologies enable advanced functionality in clinical information systems. The conflict between the need for timely adoption of health information technology and the need for standardization is also relevant to the problems faced by health information technology in Africa. The problem of clinicians having to communicate and/or record information in a format that is acceptable to someone else, somewhere else, leaves the true benefits of these systems beyond the reach of most in Africa. There is a growing effort in the United States to produce clinically-relevant interface terminologies mapped to standards. These interface terminologies can be expanded to incorporate the languages and clinical requirements of clinicians in Africa. The adoption of interface terminologies will help bring the value of standard terminology and the resulting benefits of decision-support, data analysis and information retrieval to parts of the world where they are needed most.

Using a terminology server and consumer search phrases to help patients find physicians with particular expertise.

OBJECTIVES: To design and implement a real world application using a terminology server to assist patients and physicians who use common language search terms to find specialist physicians with a particular clinical expertise. METHOD: Terminology servers have been developed to help users encoding of information using complicated structured vocabulary during data entry tasks, such as recording clinical information. We describe a methodology using Personal Health Terminology trade mark and a SNOMED CT-based hierarchical concept server. RESULTS: Construction of a pilot mediated-search engine to assist users who use vernacular speech in querying data which is more technical than vernacular. CONCLUSION: This approach, which combines theoretical and practical requirements, provides a useful example of concept-based searching for physician referrals.

A mediated health search portal for trusted medical content.

The Internet has become an important source of medical information for both patients and providers. However, it is increasingly difficult to properly access and evaluate the information obtained on the Internet. Search engines are frequently used to find information but suffer either from lack of specificity, or cumbersome requirements for use. Mediated search services have been suggested as a possible alternative. This paper describes one such mediated medical information search service called IMO Health Search.

Website to promote early detection of breast cancer: "www.thinkhealth.com".

We developed and studied a Website to promote breast cancer screening and allow women to access personalized risk and screening information. The site also provides a database of risk and screening information with multimedia enhancement, and direct interaction with experts and online communities. The site was studied to measure its effectiveness in motivating screening intentions and behaviors among a group of women subjects.