A Model Information Management Plan for Molecular Pathology Sequence Data Using Standards: From Sequencer to Electronic Health Record

HL7 FHIR-based tools and initiatives to support clinical research: a scoping review

OBJECTIVES

The HL7® fast healthcare interoperability resources (FHIR®) specification has emerged as the leading interoperability standard for the exchange of healthcare data. We conducted a scoping review to identify trends and gaps in the use of FHIR for clinical research.

MATERIALS AND METHODS

We reviewed published literature, federally funded project databases, application websites, and other sources to discover FHIR-based papers, projects, and tools (collectively, "FHIR projects") available to support clinical research activities.

RESULTS

Our search identified 203 different FHIR projects applicable to clinical research. Most were associated with preparations to conduct research, such as data mapping to and from FHIR formats (n = 66, 32.5%) and managing ontologies with FHIR (n = 30, 14.8%), or post-study data activities, such as sharing data using repositories or registries (n = 24, 11.8%), general research data sharing (n = 23, 11.3%), and management of genomic data (n = 21, 10.3%). With the exception of phenotyping (n = 19, 9.4%), fewer FHIR-based projects focused on needs within the clinical research process itself.

DISCUSSION

Funding and usage of FHIR-enabled solutions for research are expanding, but most projects appear focused on establishing data pipelines and linking clinical systems such as electronic health records, patient-facing data systems, and registries, possibly due to the relative newness of FHIR and the incentives for FHIR integration in health information systems. Fewer FHIR projects were associated with research-only activities.

CONCLUSION

The FHIR standard is becoming an essential component of the clinical research enterprise. To develop FHIR's full potential for clinical research, funding and operational stakeholders should address gaps in FHIR-based research tools and methods.

A Model for Design and Implementation of a Laboratory Information-Management System Specific for Molecular Pathology Laboratory Operations

The Molecular Pathology Section, Cleveland Clinic (Cleveland, OH), has undergone enhancement of its testing portfolio and processes. An Excel 2013- and paper-based data-management system was replaced with a commercially available laboratory information-management system (LIMS) software application, a separate bioinformatics platform, customized test-interpretation applications, a dedicated sample-accessioning service, and a results-releasing software application. The customized LIMS solution manages complex workflows, large-scale data packets, and process automation. A customized approach was required because, in a survey of commercially available off-the-shelf software products, none met the diverse and complex needs of this molecular diagnostics service. The project utilized the expertise of clinical laboratorians, pathologists, genetics counselors, bioinformaticians, and systems analysts in partnering with software-engineering consultants to design and implement a solution. Concurrently, Agile software-building best practices were formulated, which may be emulated for scalable and cost-effective laboratory-authored software.

Challenges for developing health-care knowledge in the digital age

Purpose

Health-care knowledge is dispersed among different departments in a health care organization, which makes it difficult at times to provide quality care services to patients. Therefore, this study aims to identify the main challenges in adopting health information technology (HIT).

Design/methodology/approach

This study surveyed 148 stakeholders in 4 key categories [patients, health-care providers, United Arab Emirates (UAE) citizens and foresight experts] to identify the challenges they face in adopting health care technologies. Responses were analyzed using exploratory (EFA) and confirmatory factor analysis (CFA).

Findings

EFA revealed four key latent factors predicting resistance to HIT adoption, namely, organizational strategy (ORGS); technical barriers; readiness for big data and the internet of things (IoT); and orientation (ORI). ORGS accounted for the greatest amount of variance. CFA indicated that readiness for big data and the IoT was only moderately correlated with HIT adoption, but the other three factors were strongly correlated. Specific items relating to cost, the effectiveness and usability of the technology and the organization were strongly correlated with HIT adoption. These results indicate that, in addition to financial considerations, effective HIT adoption requires ensuring that technologies will be easy to implement to ensure their long-term use.

Research limitations/implications

The results indicate that readiness for big data and the IoT-related infrastructure poses a challenge to HIT adoption in the UAE context. Respondents believed that the infrastructure of big data can be helpful in more efficiently storing and sharing health-care information. On the technological side, respondents felt that they may experience a steep learning curve. Regarding ORI, stakeholders expected many more such initiatives from health-care providers to make it more knowledge-specific and proactive.

Practical implications

This study has implications for knowledge management in the health -care sector for information technologies. The HIT can help firms in creating a knowledge eco-system, which is not possible in a dispersed knowledge environment. The utilization of the knowledge base that emerged from the practices and data can help the health care sector to set new standards of information flow and other clinical services such as monitoring the self-health condition. The HIT can further influence the actions of the pharmaceutical and medical device industry.

Originality/value

This paper highlights the challenges in HIT adoption and the most prominent factors. The conceptual model was empirically tested after the collection of primary data from the UAE using stakeholder theory.

Expanding the Scope of The Journal of Molecular Diagnostics to the Informatics Subdivision of the Association for Molecular Pathology

This editorial describes the expanded scope of The Journal of Molecular Diagnostics, to include informatics-based articles.

Evaluation of Commercial Next-Generation Sequencing Bioinformatics Software Solutions

Next-generation sequencing (NGS) diagnostics continue to expand rapidly in clinical medicine. An ever-expanding menu of molecular biomarkers is deemed important for diagnostic, prognostic, and therapeutic assessment in patients. The increasing role of NGS in the clinic is driven mainly by the falling costs of sequencing. However, the data-intensive nature of NGS makes bioinformatic analysis a major challenge to many clinical laboratories. Critically needed NGS bioinformatics personnel are hard to recruit and retain in small- to mid-size clinical laboratories. Also, NGS software often lacks the scalability necessary for expanded clinical laboratory testing volumes. Commercial software solutions aim to bridge the bioinformatics barrier via turnkey informatics solutions tailored specifically for the clinical workplace. Yet, there has been no systematic assessment of these software solutions thus far. This article presents an end-to-end vendor evaluation experience of commercial NGS bioinformatics solutions. Six different commercial vendor solutions were assessed systematically. Key metrics of NGS software evaluation to aid in the robust assessment of software solutions are described. Comprehensive feedback, provided by the TriCore Reference Laboratories molecular pathology team, enabled the final vendor selection. Many key lessons were learned during the software evaluation process, which are described herein. This article aims to provide a detailed road map for small- to mid-size clinical laboratories interested in evaluating commercial bioinformatics solutions available in the marketplace.