Centralized Interactive Phenomics Resource: an integrated online phenomics knowledgebase for health data users.

OBJECTIVE: Development of clinical phenotypes from electronic health records (EHRs) can be resource intensive. Several phenotype libraries have been created to facilitate reuse of definitions. However, these platforms vary in target audience and utility. We describe the development of the Centralized Interactive Phenomics Resource (CIPHER) knowledgebase, a comprehensive public-facing phenotype library, which aims to facilitate clinical and health services research. MATERIALS AND METHODS: The platform was designed to collect and catalog EHR-based computable phenotype algorithms from any healthcare system, scale metadata management, facilitate phenotype discovery, and allow for integration of tools and user workflows. Phenomics experts were engaged in the development and testing of the site. RESULTS: The knowledgebase stores phenotype metadata using the CIPHER standard, and definitions are accessible through complex searching. Phenotypes are contributed to the knowledgebase via webform, allowing metadata validation. Data visualization tools linking to the knowledgebase enhance user interaction with content and accelerate phenotype development. DISCUSSION: The CIPHER knowledgebase was developed in the largest healthcare system in the United States and piloted with external partners. The design of the CIPHER website supports a variety of front-end tools and features to facilitate phenotype development and reuse. Health data users are encouraged to contribute their algorithms to the knowledgebase for wider dissemination to the research community, and to use the platform as a springboard for phenotyping. CONCLUSION: CIPHER is a public resource for all health data users available at https://phenomics.va.ornl.gov/ which facilitates phenotype reuse, development, and dissemination of phenotyping knowledge.

Framework of the Centralized Interactive Phenomics Resource (CIPHER) standard for electronic health data-based phenomics knowledgebase.

The development of phenotypes using electronic health records is a resource-intensive process. Therefore, the cataloging of phenotype algorithm metadata for reuse is critical to accelerate clinical research. The Department of Veterans Affairs (VA) has developed a standard for phenotype metadata collection which is currently used in the VA phenomics knowledgebase library, CIPHER (Centralized Interactive Phenomics Resource), to capture over 5000 phenotypes. The CIPHER standard improves upon existing phenotype library metadata collection by capturing the context of algorithm development, phenotyping method used, and approach to validation. While the standard was iteratively developed with VA phenomics experts, it is applicable to the capture of phenotypes across healthcare systems. We describe the framework of the CIPHER standard for phenotype metadata collection, the rationale for its development, and its current application to the largest healthcare system in the United States.

The VA Research Enterprise: A Platform for National Partnerships Toward Evidence Building and Scientific Innovation.

Background: Within a year of the start of the COVID-19 pandemic, the US Department of Veterans Affairs (VA) was managing about 300 COVID-19-related research projects across roughly 100 facilities, which has since grown to more than 900 projects. This robust set of activities arose from an existing enterprise strategy and aimed at identifying needs for supporting the clinical care mission, more rapidly leveraging resources, and coordinating research across the VA. The VA's efforts to implement an enterprise strategy before March 2020 positioned its research community to dynamically partner with other federal agencies, academic institutions, and industry in addressing a national public health emergency. Observations: The VA research enterprise involves a broad range of functions, scientific and clinical leaders, and organizational resources to enhance the health and care of veterans and the nation. The scope of research activities enables it to support its priorities while also partnering with others who share in mutual commitments to veteran health. Moving toward being the nation's learning health care system, the VA's leadership support, staff, patient volunteers, and partners were key contributors to a national response to COVID-19. Swift action and consistent communication helped address the complexities of the pandemic and strengthened the VA's ability to prepare and mobilize for emergencies and other potential disease outbreaks. Documenting strategies and practices can enhance future opportunities aimed at addressing the most challenging health care needs while also focusing on the primary mission to serve veterans. Conclusions: The COVID-19 pandemic contributed to critical knowledge and lessons that enabled the VA to advance enterprise goals, particularly in the context of its health care system. Sharing these unique processes and experiences will inform current and future partnerships among research, clinical, and public health communities oriented to serve veterans and the nation through scientific innovation.

The US Department of Veterans Affairs Science and Health Initiative to Combat Infectious and Emerging Life-Threatening Diseases (VA SHIELD): A Biorepository Addressing National Health Threats.

Background: The coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has demonstrated the need to share data and biospecimens broadly to optimize clinical outcomes for US military Veterans. Methods: In response, the Veterans Health Administration established VA SHIELD (Science and Health Initiative to Combat Infectious and Emerging Life-threatening Diseases), a comprehensive biorepository of specimens and clinical data from affected Veterans to advance research and public health surveillance and to improve diagnostic and therapeutic capabilities. Results: VA SHIELD now comprises 12 sites collecting de-identified biospecimens from US Veterans affected by SARS-CoV-2. In addition, 2 biorepository sites, a data processing center, and a coordinating center have been established under the direction of the Veterans Affairs Office of Research and Development. Phase 1 of VA SHIELD comprises 34 157 samples. Of these, 83.8% had positive tests for SARS-CoV-2, with the remainder serving as contemporaneous controls. The samples include nasopharyngeal swabs (57.9%), plasma (27.9%), and sera (12.5%). The associated clinical and demographic information available permits the evaluation of biological data in the context of patient demographics, clinical experience and management, vaccinations, and comorbidities. Conclusions: VA SHIELD is representative of US national diversity with a significant potential to impact national healthcare. VA SHIELD will support future projects designed to better understand SARS-CoV-2 and other emergent healthcare crises. To the extent possible, VA SHIELD will facilitate the discovery of diagnostics and therapeutics intended to diminish COVID-19 morbidity and mortality and to reduce the impact of new emerging threats to the health of US Veterans and populations worldwide.

Pharmacoepidemiology, Machine Learning, and COVID-19: An Intent-to-Treat Analysis of Hydroxychloroquine, With or Without Azithromycin, and COVID-19 Outcomes Among Hospitalized US Veterans.

Hydroxychloroquine (HCQ) was proposed as an early therapy for coronavirus disease 2019 (COVID-19) after in vitro studies indicated possible benefit. Previous in vivo observational studies have presented conflicting results, though recent randomized clinical trials have reported no benefit from HCQ among patients hospitalized with COVID-19. We examined the effects of HCQ alone and in combination with azithromycin in a hospitalized population of US veterans with COVID-19, using a propensity score-adjusted survival analysis with imputation of missing data. According to electronic health record data from the US Department of Veterans Affairs health care system, 64,055 US Veterans were tested for the virus that causes COVID-19 between March 1, 2020 and April 30, 2020. Of the 7,193 veterans who tested positive, 2,809 were hospitalized, and 657 individuals were prescribed HCQ within the first 48-hours of hospitalization for the treatment of COVID-19. There was no apparent benefit associated with HCQ receipt, alone or in combination with azithromycin, and there was an increased risk of intubation when HCQ was used in combination with azithromycin (hazard ratio = 1.55; 95% confidence interval: 1.07, 2.24). In conclusion, we assessed the effectiveness of HCQ with or without azithromycin in treatment of patients hospitalized with COVID-19, using a national sample of the US veteran population. Using rigorous study design and analytic methods to reduce confounding and bias, we found no evidence of a survival benefit from the administration of HCQ.

Classifying Adverse Events in the Dental Office.

BACKGROUND: Dentists strive to provide safe and effective oral healthcare. However, some patients may encounter an adverse event (AE) defined as "unnecessary harm due to dental treatment." In this research, we propose and evaluate two systems for categorizing the type and severity of AEs encountered at the dental office. METHODS: Several existing medical AE type and severity classification systems were reviewed and adapted for dentistry. Using data collected in previous work, two initial dental AE type and severity classification systems were developed. Eight independent reviewers performed focused chart reviews, and AEs identified were used to evaluate and modify these newly developed classifications. RESULTS: A total of 958 charts were independently reviewed. Among the reviewed charts, 118 prospective AEs were found and 101 (85.6%) were verified as AEs through a consensus process. At the end of the study, a final AE type classification comprising 12 categories, and an AE severity classification comprising 7 categories emerged. Pain and infection were the most common AE types representing 73% of the cases reviewed (56% and 17%, respectively) and 88% were found to cause temporary, moderate to severe harm to the patient. CONCLUSIONS: Adverse events found during the chart review process were successfully classified using the novel dental AE type and severity classifications. Understanding the type of AEs and their severity are important steps if we are to learn from and prevent patient harm in the dental office.

Adoption of dental innovations: The case of a standardized dental diagnostic terminology.

BACKGROUND: Standardized dental diagnostic terminologies (SDDxTs) were introduced decades ago. Their use has been on the rise, accompanying the adoption of electronic health records (EHRs). One of the most broadly used terminologies is the Dental Diagnostic System (DDS). Our aim was to assess the adoption of SDDxTs by US dental schools by using the Rogers diffusion of innovations framework, focusing on the DDS. METHODS: The authors electronically surveyed clinic deans in all US dental schools (n = 61) to determine use of an EHR and SDDxT, perceived barriers to adoption of an SDDxT, and the effect of implementing an SDDxT on clinical productivity. RESULTS: The response rate was 57%. Of the 35 responses, 91% reported using an EHR to document patient care, with 84% using axiUm; 41% used the DDS. Fifty-four percent of those who did not use an SDDxT had considered adopting the DDS, but 38% had not, citing barriers such as complexity and compatibility. CONCLUSIONS: Adoption of an SDDxT, particularly the DDS, is on the rise. Nevertheless, a large number of institutions are in the Rogers late majority and laggards categories with respect to adoption. Several factors may discourage adoption, including the inability to try out the terminology on a small scale, poor usability within the EHR, the fact that it would be a cultural shift in practice, and a perception of unclear benefits. However, the consolidation of the DDS and American Dental Association terminology efforts stands to encourage adoption. PRACTICAL IMPLICATIONS: The successful adoption of dental innovation depends not only on the intrinsic merit of the innovation, as some useful innovations do not achieve widespread traction. As such, it is important for health care providers to understand how to disseminate their ideas in order to ensure traction and widespread adoption.

The Undiagnosed Diseases Network: Accelerating Discovery about Health and Disease.

Diagnosis at the edges of our knowledge calls upon clinicians to be data driven, cross-disciplinary, and collaborative in unprecedented ways. Exact disease recognition, an element of the concept of precision in medicine, requires new infrastructure that spans geography, institutional boundaries, and the divide between clinical care and research. The National Institutes of Health (NIH) Common Fund supports the Undiagnosed Diseases Network (UDN) as an exemplar of this model of precise diagnosis. Its goals are to forge a strategy to accelerate the diagnosis of rare or previously unrecognized diseases, to improve recommendations for clinical management, and to advance research, especially into disease mechanisms. The network will achieve these objectives by evaluating patients with undiagnosed diseases, fostering a breadth of expert collaborations, determining best practices for translating the strategy into medical centers nationwide, and sharing findings, data, specimens, and approaches with the scientific and medical communities. Building the UDN has already brought insights to human and medical geneticists. The initial focus has been on data sharing, establishing common protocols for institutional review boards and data sharing, creating protocols for referring and evaluating patients, and providing DNA sequencing, metabolomic analysis, and functional studies in model organisms. By extending this precision diagnostic model nationally, we strive to meld clinical and research objectives, improve patient outcomes, and contribute to medical science.

Clinical documentation of dental care in an era of electronic health record use.

BACKGROUND: Although complete and accurate clinical records do not guarantee the provision of excellent dental care, they do provide an opportunity to evaluate the quality of care provided. However, a lack of universally accepted documentation standards, incomplete record-keeping practices, and unfriendly electronic health care record (EHR) user interfaces are factors that have allowed for persistent poor dental patient record keeping. METHODS: Using 2 different methods-a validated survey, and a 2-round Delphi process-involving 2 appropriately different sets of participants, we explored what a dental clinical record should contain and the frequency of update of each clinical entry. RESULTS: For both the closed-ended survey questions and the open-ended Delphi process questions, respondents had a significant degree of agreement on the "clinical entry" components of an adequate clinical record. There was, however, variance on how frequently each of those clinical entries should be updated. SUMMARY: Dental providers agree that complete and accurate record keeping is essential and that items such as histories, examination findings, diagnosis, radiographs, treatment plans, consents, and clinic notes should be documented. There, however, does not seem to be universal agreement how frequently such items should be recorded. CLINICAL IMPLICATIONS: As the dental profession moves towards prevalent use of electronic health care records, the issue of standardization and interoperability becomes ever more pressing. Settling issues of standardization, including record documentation, must begin with guideline-creating dental professional bodies, who need to clearly define and disseminate what these standards should be and everyday dentists who will ultimately ensure that these standards are met and kept.

Honoring Dental Patients' Privacy Rule Right of Access in the Context of Electronic Health Records.

A person's right to access his or her protected health information is a core feature of the U.S. Health Insurance Portability and Accountability Act (HIPAA) Privacy Rule. If the information is stored electronically, covered entities must be able to provide patients with some type of machine-readable, electronic copy of their data. The aim of this study was to understand how academic dental institutions execute the Privacy Rule's right of access in the context of electronic health records (EHRs). A validated electronic survey was distributed to the clinical deans of 62 U.S. dental schools during a two-month period in 2014. The response rate to the survey was 53.2% (N=33). However, three surveys were partially completed, and of the 30 completed surveys, the 24 respondents who reported using axiUm as the EHR at their dental school clinic were the ones on which the results were based (38.7% of total schools at the time). Of the responses analyzed, 86% agreed that clinical modules should be considered part of a patient's dental record, and all agreed that student teaching-related modules should not. Great variability existed among these clinical deans as to whether administrative and financial modules should be considered part of a patient record. When patients request their records, close to 50% of responding schools provide the information exclusively on paper. This study found variation among dental schools in their implementation of the Privacy Rule right of access, and although all the respondents had adopted EHRs, a large number return records in paper format.

How dental team members describe adverse events.

BACKGROUND: Although some patients experience adverse events (AEs) resulting in harm caused by treatments in dentistry, few published reports have detailed how dental providers describe these events. Understanding how dental treatment professionals view AEs is essential to building a safer environment in dental practice. METHODS: The authors interviewed dental professionals and domain experts through focus groups and in-depth interviews and asked them to identify the types of AEs that may occur in dental settings. RESULTS: The initial interview and focus group findings yielded 1,514 items that included both causes and AEs. In total, 632 causes were coded into 1 of the 8 categories of the Eindhoven classification, and 882 AEs were coded into 12 categories of a newly developed dental AE classification. Interrater reliability was moderate among coders. The list was reanalyzed, and duplicate items were removed leaving a total of 747 unique AEs and 540 causes. The most frequently identified AE types were "aspiration and ingestion" at 14% (n = 142), "wrong-site, wrong-procedure, wrong-patient errors" at 13%, "hard-tissue damage" at 13%, and "soft-tissue damage" at 12%. CONCLUSIONS: Dental providers identified a large and diverse list of AEs. These events ranged from "death due to cardiac arrest" to "jaw fatigue from lengthy procedures." PRACTICAL IMPLICATIONS: Identifying threats to patient safety is a key element of improving dental patient safety. An inventory of dental AEs underpins efforts to track, prevent, and mitigate these events.

SMART on FHIR: a standards-based, interoperable apps platform for electronic health records.

OBJECTIVE: In early 2010, Harvard Medical School and Boston Children's Hospital began an interoperability project with the distinctive goal of developing a platform to enable medical applications to be written once and run unmodified across different healthcare IT systems. The project was called Substitutable Medical Applications and Reusable Technologies (SMART). METHODS: We adopted contemporary web standards for application programming interface transport, authorization, and user interface, and standard medical terminologies for coded data. In our initial design, we created our own openly licensed clinical data models to enforce consistency and simplicity. During the second half of 2013, we updated SMART to take advantage of the clinical data models and the application-programming interface described in a new, openly licensed Health Level Seven draft standard called Fast Health Interoperability Resources (FHIR). Signaling our adoption of the emerging FHIR standard, we called the new platform SMART on FHIR. RESULTS: We introduced the SMART on FHIR platform with a demonstration that included several commercial healthcare IT vendors and app developers showcasing prototypes at the Health Information Management Systems Society conference in February 2014. This established the feasibility of SMART on FHIR, while highlighting the need for commonly accepted pragmatic constraints on the base FHIR specification. CONCLUSION: In this paper, we describe the creation of SMART on FHIR, relate the experience of the vendors and developers who built SMART on FHIR prototypes, and discuss some challenges in going from early industry prototyping to industry-wide production use.

The NIH Undiagnosed Diseases Program and Network: Applications to modern medicine.

INTRODUCTION: The inability of some seriously and chronically ill individuals to receive a definitive diagnosis represents an unmet medical need. In 2008, the NIH Undiagnosed Diseases Program (UDP) was established to provide answers to patients with mysterious conditions that long eluded diagnosis and to advance medical knowledge. Patients admitted to the NIH UDP undergo a five-day hospitalization, facilitating highly collaborative clinical evaluations and a detailed, standardized documentation of the individual's phenotype. Bedside and bench investigations are tightly coupled. Genetic studies include commercially available testing, single nucleotide polymorphism microarray analysis, and family exomic sequencing studies. Selected gene variants are evaluated by collaborators using informatics, in vitro cell studies, and functional assays in model systems (fly, zebrafish, worm, or mouse). INSIGHTS FROM THE UDP: In seven years, the UDP received 2954 complete applications and evaluated 863 individuals. Nine vignettes (two unpublished) illustrate the relevance of an undiagnosed diseases program to complex and common disorders, the coincidence of multiple rare single gene disorders in individual patients, newly recognized mechanisms of disease, and the application of precision medicine to patient care. CONCLUSIONS: The UDP provides examples of the benefits expected to accrue with the recent launch of a national Undiagnosed Diseases Network (UDN). The UDN should accelerate rare disease diagnosis and new disease discovery, enhance the likelihood of diagnosing known diseases in patients with uncommon phenotypes, improve management strategies, and advance medical research.

Lessons learned from dental patient safety case reports.

BACKGROUND: Errors are commonplace in health care, including dentistry. It is imperative for dental professionals to intercept errors before they lead to an adverse event and to mitigate their effects when an adverse event occurs. This requires a systematic approach at both the profession level, encapsulated in the Agency for Healthcare Research and Quality's patient safety initiative framework, as well as at the practice level, in which crew resource management is a tested paradigm. Supporting patient safety at both the profession and dental practice levels relies on understanding the types and causes of errors, which have not been well studied. METHODS: The authors performed a retrospective review of dental adverse events reported in the literature. Electronic bibliographic databases were searched, and data were extracted on background characteristics, incident description, case characteristics, clinic setting where adverse event originated, phase of patient care that adverse event was detected, proximal cause, type of patient harm, degree of harm, and recovery actions. RESULTS: The authors identified 182 publications (containing 270 cases) through their search. Delayed treatment, unnecessary treatment, or disease progression after misdiagnosis was the largest type of harm reported. Of the reviewed cases, 24.4% of those patients involved in an adverse event experienced permanent harm. One of every 10 case reports reviewed (11.1%) reported that the adverse event resulted in the death of the affected patient. CONCLUSIONS: Published case reports provide a window into understanding the nature and extent of dental adverse events; however, the overall dearth of publications on adverse events in the dental literature points to the need for more study. PRACTICAL IMPLICATIONS: Siloed and incomplete contributions to dentistry's understanding of adverse events in the dental office are threats to dental patients' safety. Publishing more, and more comprehensive, case reports on adverse events is recommended for dental practitioners.

Attitudes toward and beliefs about the use of a dental diagnostic terminology: A survey of dental care providers in a dental practice.

BACKGROUND: Attitudes and views are critical to the adoption of innovation. Although there have been broadening calls for a standardized dental diagnostic terminology, little is known about the views of private practice dental team members regarding the adoption of such a terminology. METHODS: The authors developed a survey by using validated questions identified through literature review. Domain experts' input allowed for further modifications. The authors administered the final survey electronically to 814 team members at a multioffice practice based in the US Pacific Northwest. RESULTS: Response proportion was 92%. The survey had excellent reliability (Cronbach α coefficient = 0.87). Results suggested that participants showed, in general, positive attitudes and beliefs about using a standardized diagnostic terminology in their practices. Additional written comments by participants highlighted the potential for improved communication with use of the terminology. CONCLUSIONS: Dental care providers and staff in 1 multioffice practice showed positive attitudes about the use of a diagnostic terminology; specifically, they believed it would improve communication between the dentist and patient, as well as among providers, while expressing some concerns about whether using standardized dental diagnostic terms helps clinicians to deliver better dental care. PRACTICAL IMPLICATIONS: As the dental profession is advancing toward the use of standardized diagnostic terminology, successful implementation will require that dental team leaders prepare their teams by gauging their attitude about the use of such a terminology.