Privacy-preserving record linkage across disparate institutions and datasets to enable a learning health system: The national COVID cohort collaborative (N3C) experience

Introduction

Research driven by real-world clinical data is increasingly vital to enabling learning health systems, but integrating such data from across disparate health systems is challenging. As part of the NCATS National COVID Cohort Collaborative (N3C), the N3C Data Enclave was established as a centralized repository of deidentified and harmonized COVID-19 patient data from institutions across the US. However, making this data most useful for research requires linking it with information such as mortality data, images, and viral variants. The objective of this project was to establish privacy-preserving record linkage (PPRL) methods to ensure that patient-level EHR data remains secure and private when governance-approved linkages with other datasets occur.

Methods

Separate agreements and approval processes govern N3C data contribution and data access. The Linkage Honest Broker (LHB), an independent neutral party (the Regenstrief Institute), ensures data linkages are robust and secure by adding an extra layer of separation between protected health information and clinical data. The LHB's PPRL methods (including algorithms, processes, and governance) match patient records using "deidentified tokens," which are hashed combinations of identifier fields that define a match across data repositories without using patients' clear-text identifiers.

Results

These methods enable three linkage functions: Deduplication, Linking Multiple Datasets, and Cohort Discovery. To date, two external repositories have been cross-linked. As of March 1, 2023, 43 sites have signed the LHB Agreement; 35 sites have sent tokens generated for 9 528 998 patients. In this initial cohort, the LHB identified 135 037 matches and 68 596 duplicates.

Conclusion

This large-scale linkage study using deidentified datasets of varying characteristics established secure methods for protecting the privacy of N3C patient data when linked for research purposes. This technology has potential for use with registries for other diseases and conditions.

Leveraging data visualization and a statewide health information exchange to support COVID-19 surveillance and response: Application of public health informatics

Objective

We sought to support public health surveillance and response to coronavirus disease 2019 (COVID-19) through rapid development and implementation of novel visualization applications for data amalgamated across sectors.

Materials and Methods

We developed and implemented population-level dashboards that collate information on individuals tested for and infected with COVID-19, in partnership with state and local public health agencies as well as health systems. The dashboards are deployed on top of a statewide health information exchange. One dashboard enables authorized users working in public health agencies to surveil populations in detail, and a public version provides higher-level situational awareness to inform ongoing pandemic response efforts in communities.

Results

Both dashboards have proved useful informatics resources. For example, the private dashboard enabled detection of a local community outbreak associated with a meat packing plant. The public dashboard provides recent trend analysis to track disease spread and community-level hospitalizations. Combined, the tools were utilized 133 637 times by 74 317 distinct users between June 21 and August 22, 2020. The tools are frequently cited by journalists and featured on social media.

Discussion

Capitalizing on a statewide health information exchange, in partnership with health system and public health leaders, Regenstrief biomedical informatics experts rapidly developed and deployed informatics tools to support surveillance and response to COVID-19.

Conclusions

The application of public health informatics methods and tools in Indiana holds promise for other states and nations. Yet, development of infrastructure and partnerships will require effort and investment after the current pandemic in preparation for the next public health emergency.

The Children's Respiratory and Environmental Workgroup (CREW) birth cohort consortium: design, methods, and study population

BACKGROUND

Single birth cohort studies have been the basis for many discoveries about early life risk factors for childhood asthma but are limited in scope by sample size and characteristics of the local environment and population. The Children's Respiratory and Environmental Workgroup (CREW) was established to integrate multiple established asthma birth cohorts and to investigate asthma phenotypes and associated causal pathways (endotypes), focusing on how they are influenced by interactions between genetics, lifestyle, and environmental exposures during the prenatal period and early childhood.

METHODS AND RESULTS

CREW is funded by the NIH Environmental influences on Child Health Outcomes (ECHO) program, and consists of 12 individual cohorts and three additional scientific centers. The CREW study population is diverse in terms of race, ethnicity, geographical distribution, and year of recruitment. We hypothesize that there are phenotypes in childhood asthma that differ based on clinical characteristics and underlying molecular mechanisms. Furthermore, we propose that asthma endotypes and their defining biomarkers can be identified based on personal and early life environmental risk factors. CREW has three phases: 1) to pool and harmonize existing data from each cohort, 2) to collect new data using standardized procedures, and 3) to enroll new families during the prenatal period to supplement and enrich extant data and enable unified systems approaches for identifying asthma phenotypes and endotypes.

CONCLUSIONS

The overall goal of CREW program is to develop a better understanding of how early life environmental exposures and host factors interact to promote the development of specific asthma endotypes.

The Emerging Role of the Chief Research Informatics Officer in Academic Health Centers

BACKGROUND

The role of the Chief Research Informatics Officer (CRIO) is emerging in academic health centers to address the challenges clinical researchers face in the increasingly digitalized, data-intensive healthcare system. Most current CRIOs are the first officers in their institutions to hold that role. To date there is very little published information about this role and the individuals who serve it.

OBJECTIVE

To increase our understanding of the CRIO role, the leaders who serve it, and the factors associated with their success in their organizations.

METHODS

The Clinical Research Informatics Working Group of the American Medical Informatics Association (AMIA) conducted a national survey of CRIOs in the United States and convened an expert panel of CRIOs to discuss their experience during the 2016 AMIA Annual Symposium.

RESULTS

CRIOs come from diverse academic backgrounds. Most have advance training and extensive experience in biomedical informatics but the majority have been CRIOs for less than three years. CRIOs identify funding, data governance, and advancing data analytics as their major challenges.

CONCLUSION

CRIOs play an important role in helping shape the future of clinical research, innovation, and data analytics in healthcare in their organizations. They share many of the same challenges and see the same opportunities for the future of the field. Better understanding the background and experience of current CRIOs can help define and develop the role in other organizations and enhance their influence in the field of research informatics.

Core informatics competencies for clinical and translational scientists: what do our customers and collaborators need to know?

Since the inception of the Clinical and Translational Science Award (CTSA) program in 2006, leaders in education across CTSA sites have been developing and updating core competencies for Clinical and Translational Science (CTS) trainees. By 2009, 14 competency domains, including biomedical informatics, had been identified and published. Since that time, the evolution of the CTSA program, changes in the practice of CTS, the rapid adoption of electronic health records (EHRs), the growth of biomedical informatics, the explosion of big data, and the realization that some of the competencies had proven to be difficult to apply in practice have made it clear that the competencies should be updated. This paper describes the process undertaken and puts forth a new set of competencies that has been recently endorsed by the Clinical Research Informatics Workgroup of AMIA. In addition to providing context and background for the current version of the competencies, we hope this will serve as a model for revision of competencies over time.

MD-CTS: An integrated terminology reference of clinical and translational medicine

New vocabularies are rapidly evolving in the literature relative to the practice of clinical medicine and translational research. To provide integrated access to new terms, we developed a mobile and desktop online reference—Marshfield Dictionary of Clinical and Translational Science (MD-CTS). It is the first public resource that comprehensively integrates Wiktionary (word definition), BioPortal (ontology), Wiki (image reference), and Medline abstract (word usage) information. MD-CTS is accessible at http://spellchecker.mfldclin.edu/. The website provides a broadened capacity for the wider clinical and translational science community to keep pace with newly emerging scientific vocabulary. An initial evaluation using 63 randomly selected biomedical words suggests that online references generally provided better coverage (73%-95%) than paper-based dictionaries (57–71%).

Genetic data and electronic health records: a discussion of ethical, logistical and technological considerations

Objective

The completion of sequencing the human genome in 2003 has spurred the production and collection of genetic data at ever increasing rates. Genetic data obtained for clinical purposes, as is true for all results of clinical tests, are expected to be included in patients’ medical records. With this explosion of information, questions of what, when, where and how to incorporate genetic data into electronic health records (EHRs) have reached a critical point. In order to answer these questions fully, this paper addresses the ethical, logistical and technological issues involved in incorporating these data into EHRs.

Materials and methods

This paper reviews journal articles, government documents and websites relevant to the ethics, genetics and informatics domains as they pertain to EHRs.

Results and discussion

The authors explore concerns and tasks facing health information technology (HIT) developers at the intersection of ethics, genetics, and technology as applied to EHR development.

Conclusions

By ensuring the efficient and effective incorporation of genetic data into EHRs, HIT developers will play a key role in facilitating the delivery of personalized medicine.

Real time information from bedside monitors as part of a web-based patient record

Traditional paper-based Medical Records, and even most of their digital counterparts, represent historical patient information. On the other hand new generations of Point-of-Care devices can be connected to standard networks and deliver streams of real time data through an Intranet, or even the Internet. Vital signs provided by IP-based devices can then be viewed at remote stations. Merging both worlds, real time and historical, in the pursuit of a comprehensive EPR is the main challenge of the present project. The basic infra-structure is composed of three main components: an existing Web-based EPR viewing station1 (Web-EPR); a fully integrated HIS/PACS system1; and a monitoring network (Siemens Infinity Network 2). Communication between the components was obtained by developing interfaces based on both HL7 and Siemens protocols the later only for waveforms. For the graphical display a web-browser-based application of the streamed signals was developed and integrated into the existing Web-EPR. This addition expanded the Web-EPR capabilities providing means to include real time signals and calculated parameters on the set of information already available. Some extra features of this project include: one-way SMS messaging of the parameters, interactive WAP access and a DICOM compliant storage of signal waveforms.

Internet and healthcare in Brazil: the role of the Working Group for Healthcare (GT Saúde)

This paper introduces the GT Saúde initiative in Brazil. The group is part of the Brazilian Internet project, which goals are to depict how Internet can be useful to the society. The mission of the GT Saúde group is to foster Internet applications on the healthcare area. The main projects currently under development are presented: Multicom-21, using large bandwidth connections on telemedicine; the Unified Health Record, using Internet and smart-cards for a national minimum patient data set; the Brazilian Virtual Hospital, that presents a large amount of useful information and links for healthcare professionals and people in general; the National Healthcare Information Network (RNIS), that uses Internet as a medium for data exchange among the state secretaries and publishing statistics from the national healthcare system (SUS) for general public access; and finally the virtual university proposal, which uses Internet for education and is offering its first course on nutrition. The heterogeneity of the projects is meant and is part of the group's task, which is to cover the subject as widely as possible. Through this 'demonstration' projects the group is trying to prove the usefulness and benefits of using Internet technologies, even (or mainly) on a developing country with an inadequate healthcare situation. In its short existence the GT Saúde group has achieved several of its original goals. The most relevant accomplishments are: putting together different groups, eliciting synergy across the projects and encompassing a broad spectrum of applications (the 'demonstration factor').

Renewing information infrastructure at Hospital das Clínicas

In this paper we describe the process of renewing the Informatics infrastructure of Sao Paulo University Medical School Hospital, a very complex environment. Our proposal consists of a change in the paradigm of Informatics and the use of Information Technology in the hospital. That change aims at making information available to the hospital, its managers, health care workers and patients. The paradigm change is reflected in every aspect of the new infrastructure: human resources, methods, and organizational structure, as we intend to demonstrate in this paper. This process is expected to be concluded by the end of this year, yielding benefits regarding costs, efficiency, and better patient care.

Lossy compression techniques, medical images, and the clinician

There has been increasing interest in the storage and retrieval of medical images in hospitals and clinics here in Brazil and elsewhere. At the Heart Institute of São Paulo, with thousands of image-based procedures performed each month, the pursuit of optimal transmission and storage methods for digital images is a major concern. The use of data-compression techniques can reduce the enormous amount of imaging data to be stored or transmitted across a computer network, so that the efficiency of the computing system is preserved. The techniques for image compression can be categorized as "lossless" or "lossy," with "lossy" techniques being those in which some, supposedly irrelevant information is lost. Lossy techniques are much more efficient than lossless ones, achieving data-compression ratios as high as 100:1.

Hypermedia patient data retrieval and presentation through WWW

WWW can be a helpful tool for PACS and HIS data retrieval and presentation. The use of gateways to access both text and hypermedia databases (images and video) enables fetched data to be presented in virtually any computer system. WWW browsers provide a very friendly interface and require little training to operate. This paper presents a prototype that uses a SQL gateway for accessing relational patient databases. The dataset used here include text data from reports of diagnostic procedures as well as pointers to the corresponding images. Images can be displayed by the browsers' viewers.

Integrating Hospital Information Systems. The challenges and advantages of (re-)starting now

With the new technologies available today, more complex and useful Hospital Information Systems (HIS) can be designed and implemented. These new technologies have allowed that information from different sources and nature such as documents, images and signals be integrated within a single environment. Open standards, reliable networks, powerful hardware and software and lower prices are among the issues that make all this possible. One of the main issues is what to do with old systems that do not adhere to this new HIS concept. At the Heart Institute (InCor), a decision was made towards starting developing a new system called I3S. This paper gives a brief description of that system.

Method to localise myocardial infarction using magnetocardiography: simulation studies

The work presents a method for localising regions of myocardial infarction (MI) using magnetocardiography, which is validated by simulation techniques. We have verified that the first two principal components of magnetocardiographic signals obtained from torso mapping within a normal group are very similar even in experimental measurements. So, if we have the temporal eigenvectors of a normal group, these can be used as an orthonormal basis for estimating the signals of a patient being tested. Analysis of the residual signals using singular value decomposition (SVD) allows the localisation of regions of MI. Comparisons are made with a similar method which uses spatial eigenvectors as its basis. It is shown that our approach is able to localise the equivalent current dipoles which generate MI even when they are not orthogonal to the spatial eigenvectors.