An OHDSI ATLAS Extension to Support Feasibility Requests in a Research Network

Checking the feasibility of real-world data to answer a certain research question is crucial especially in a multi-site research network. In this work we present an extension of the ATLAS user interface for the OMOP common data model that integrates into an existing national feasibility network and thus foster capabilities for future participation in international research studies.

Architecture for a feasibility query portal for distributed COVID-19 Fast Healthcare Interoperability Resources (FHIR) patient data repositories: Design and Implementation Study (Preprint)

Background

An essential step in any medical research project after identifying the research question is to determine if there are sufficient patients available for a study and where to find them. Pursuing digital feasibility queries on available patient data registries has proven to be an excellent way of reusing existing real-world data sources. To support multicentric research, these feasibility queries should be designed and implemented to run across multiple sites and securely access local data. Working across hospitals usually involves working with different data formats and vocabularies. Recently, the Fast Healthcare Interoperability Resources (FHIR) standard was developed by Health Level Seven to address this concern and describe patient data in a standardized format. The Medical Informatics Initiative in Germany has committed to this standard and created data integration centers, which convert existing data into the FHIR format at each hospital. This partially solves the interoperability problem; however, a distributed feasibility query platform for the FHIR standard is still missing.

Objective

This study described the design and implementation of the components involved in creating a cross-hospital feasibility query platform for researchers based on FHIR resources. This effort was part of a large COVID-19 data exchange platform and was designed to be scalable for a broad range of patient data.

Methods

We analyzed and designed the abstract components necessary for a distributed feasibility query. This included a user interface for creating the query, backend with an ontology and terminology service, middleware for query distribution, and FHIR feasibility query execution service.

Results

We implemented the components described in the Methods section. The resulting solution was distributed to 33 German university hospitals. The functionality of the comprehensive network infrastructure was demonstrated using a test data set based on the German Corona Consensus Data Set. A performance test using specifically created synthetic data revealed the applicability of our solution to data sets containing millions of FHIR resources. The solution can be easily deployed across hospitals and supports feasibility queries, combining multiple inclusion and exclusion criteria using standard Health Level Seven query languages such as Clinical Quality Language and FHIR Search. Developing a platform based on multiple microservices allowed us to create an extendable platform and support multiple Health Level Seven query languages and middleware components to allow integration with future directions of the Medical Informatics Initiative.

Conclusions

We designed and implemented a feasibility platform for distributed feasibility queries, which works directly on FHIR-formatted data and distributed it across 33 university hospitals in Germany. We showed that developing a feasibility platform directly on the FHIR standard is feasible.

Enabling External Inquiries to an Existing Patient Registry by Using the Open Source Registry System for Rare Diseases: Demonstration of the System Using the European Society for Immunodeficiencies Registry

BACKGROUND

The German Network on Primary Immunodeficiency Diseases (PID-NET) utilizes the European Society for Immunodeficiencies (ESID) registry as a platform for collecting data. In the context of PID-NET data, we show how registries based on custom software can be made interoperable for better collaborative access to precollected data. The Open Source Registry System for Rare Diseases (Open-Source-Registersystem für Seltene Erkrankungen [OSSE], in German) provides patient organizations, physicians, scientists, and other parties with open source software for the creation of patient registries. In addition, the necessary interoperability between different registries based on the OSSE, as well as existing registries, is supported, which allows those registries to be confederated at both the national and international levels.

OBJECTIVE

Data from the PID-NET registry should be made available in an interoperable manner without losing data sovereignty by extending the existing custom software of the registry using the OSSE registry framework.

METHODS

This paper describes the following: (1) the installation and configuration of the OSSE bridgehead, (2) an approach using a free toolchain to set up the required interfaces to connect a registry with the OSSE bridgehead, and (3) the decentralized search, which allows the formulation of inquiries that are sent to a selected set of registries of interest.

RESULTS

PID-NET uses the established and highly customized ESID registry software. By setting up a so-called OSSE bridgehead, PID-NET data are made interoperable according to a federated approach, and centrally formulated inquiries for data can be received. As the first registry to use the OSSE bridgehead, the authors introduce an approach using a free toolchain to efficiently implement and maintain the required interfaces. Finally, to test and demonstrate the system, two inquiries are realized using the graphical query builder. By establishing and interconnecting an OSSE bridgehead with the underlying ESID registry, confederated queries for data can be received and, if desired, the inquirer can be contacted to further discuss any requirements for cooperation.

CONCLUSIONS

The OSSE offers an infrastructure that provides the possibility of more collaborative and transparent research. The decentralized search functionality includes registries into one search application while still maintaining data sovereignty. The OSSE bridgehead enables any registry software to be integrated into the OSSE network. The proposed toolchain to set up the required interfaces consists of freely available software components that are well documented. The use of the decentralized search is uncomplicated to use and offers a well-structured, yet still improvable, graphical user interface to formulate queries.

Mesenchymal Stem Cell Soluble Mediators and Cystic Fibrosis

Human Mesenchymal stem cells (hMSCs) secrete products (supernatants) that are anti-inflammatory and antimicrobial. We have previously shown that hMSCs decrease inflammation and Pseudomonas aeruginosa infection in the in vivo murine model of Cystic Fibrosis (CF). Cystic Fibrosis (CF) is a genetic disease in which pulmonary infection and inflammation becomes the major cause of morbidity and mortality. Our studies focus on determining how MSCs contribute to improved outcomes in the CF mouse model centering on how the MSCs impact the inflammatory response to pathogenic organisms. We hypothesize that MSCs secrete products that are anti-inflammatory in scenarios of chronic pulmonary infections using the murine model of infection and inflammation with a specific interest in Pseudomonas aeruginosa (gram negative). Further, our studies will identify whether the MSCs are impacting this inflammatory response through the regulation of peroxisome proliferator activator receptor gamma (PPARγ) which aides in decreasing inflammation.

Proof-of-Concept Integration of Heterogeneous Biobank IT Infrastructures into a Hybrid Biobanking Network

Cross-institutional biobank networks hold the promise of supporting medicine by enabling the exchange of associated samples for research purposes. Various initiatives, such as BBMRI-ERIC and German Biobank Node (GBN), aim to interconnect biobanks for enabling the compilation of joint biomaterial collections. However, building software platforms to facilitate such collaboration is challenging due to the heterogeneity of existing biobank IT infrastructures and the necessary efforts for installing and maintaining additional software components. As a remedy, this paper presents the concept of a hybrid network for interconnecting already existing software components commonly found in biobanks and a proof-of-concept implementation of two prototypes involving four biobanks of the German Biobank Node. Here we demonstrate the successful bridging of two IT systems found in many German biobanks - Samply and i2b2.

Questionable dementia: clinical course and predictors of outcome

OBJECTIVE

To evaluate the clinical course and predictors of outcome in outpatients with cognitive impairment who do not meet criteria for dementia at initial evaluation.

DESIGN

Naturalistic longitudinal study.

METHODS

Cognitively impaired patients in a memory disorders clinic who fell between the "normal" and "dementia" categories were defined broadly as "questionable dementia" (QD). Of 127 consecutive QD patients, 75 were followed for a minimum of 1 year (mean 2.5 years, SD 1.7). Baseline neuropsychological testing was conducted in 62 of these 75 QD patients.

RESULTS

At the final follow-up time-point, 41.3% met diagnostic criteria for dementia (27 of 31 patients with dementia had possible or probable Alzheimer's Disease, AD), 44% were rated as not demented, and 14.7% remained as "uncertain" dementia. Increased age was associated with the final diagnosis of dementia, but duration of follow-up, Clinical Dementia Rating, and modified Mini Mental State (mMMS) scores were not predictive. Low scores on the mMMS delayed recall subtest, consistent long-term retrieval on the Selective Reminding Test, category naming for animals, and the WAIS-R digit symbol, picture arrangement, and block design subtests were predictive of the final diagnosis of dementia (all P < or = .01). mMMS delayed recall showed 66.7% sensitivity and 71.4% specificity, the other five neuropsychological subtests together showed 66.7% sensitivity and 66.7% specificity, and the six tests together showed 81% sensitivity and 76.9% specificity. Similar predictive accuracy was obtained for the final diagnosis of AD.

CONCLUSIONS

In QD patients, poor performance on the mMMS delayed recall item may be a useful predictor of the diagnosis of dementia (and AD) on follow-up. Combining a screening instrument like the mMMS with specific neuropsychological tests may provide good predictive accuracy. In QD patients, the observed heterogeneity in diagnostic outcome, with most patients in the "dementia" and "no dementia" categories at follow-up, enhances the feasibility of evaluating early markers with predictive accuracy for dementia and AD.

Questionable dementia: clinical course and predictors of outcome

OBJECTIVE

To evaluate the clinical course and predictors of outcome in outpatients with cognitive impairment who do not meet criteria for dementia at initial evaluation.

DESIGN

Naturalistic longitudinal study.

METHODS

Cognitively impaired patients in a memory disorders clinic who fell between the "normal" and "dementia" categories were defined broadly as "questionable dementia" (QD). Of 127 consecutive QD patients, 75 were followed for a minimum of 1 year (mean 2.5 years, SD 1.7). Baseline neuropsychological testing was conducted in 62 of these 75 QD patients.

RESULTS

At the final follow-up time-point, 41.3% met diagnostic criteria for dementia (27 of 31 patients with dementia had possible or probable Alzheimer's Disease, AD), 44% were rated as not demented, and 14.7% remained as "uncertain" dementia. Increased age was associated with the final diagnosis of dementia, but duration of follow-up, Clinical Dementia Rating, and modified Mini Mental State (mMMS) scores were not predictive. Low scores on the mMMS delayed recall subtest, consistent long-term retrieval on the Selective Reminding Test, category naming for animals, and the WAIS-R digit symbol, picture arrangement, and block design subtests were predictive of the final diagnosis of dementia (all P < or = .01). mMMS delayed recall showed 66.7% sensitivity and 71.4% specificity, the other five neuropsychological subtests together showed 66.7% sensitivity and 66.7% specificity, and the six tests together showed 81% sensitivity and 76.9% specificity. Similar predictive accuracy was obtained for the final diagnosis of AD.

CONCLUSIONS

In QD patients, poor performance on the mMMS delayed recall item may be a useful predictor of the diagnosis of dementia (and AD) on follow-up. Combining a screening instrument like the mMMS with specific neuropsychological tests may provide good predictive accuracy. In QD patients, the observed heterogeneity in diagnostic outcome, with most patients in the "dementia" and "no dementia" categories at follow-up, enhances the feasibility of evaluating early markers with predictive accuracy for dementia and AD.