[The Medical Informatics Initiative at a glance-establishing a health research data infrastructure in Germany]. / Die Medizininformatik-Initiative im Überblick ­ Aufbau einer Gesundheitsforschungsdateninfrastruktur in Deutschland.

The Medical Informatics Initiative (MII) funded by the Federal Ministry of Education and Research (BMBF) 2016-2027 is successfully laying the foundations for data-based medicine in Germany. As part of this funding, 51 new professorships, 21 junior research groups, and various new degree programs have been established to strengthen teaching, training, and continuing education in the field of medical informatics and to improve expertise in medical data sciences. A joint decentralized federated research data infrastructure encompassing the entire university medical center and its partners was created in the form of data integration centers (DIC) at all locations and the German Portal for Medical Research Data (FDPG) as a central access point. A modular core dataset (KDS) was defined and implemented for the secondary use of patient treatment data with consistent use of international standards (e.g., FHIR, SNOMED CT, and LOINC). An officially approved nationwide broad consent was introduced as the legal basis. The first data exports and data use projects have been carried out, embedded in an overarching usage policy and standardized contractual regulations. The further development of the MII health research data infrastructures within the cooperative framework of the Network of University Medicine (NUM) offers an excellent starting point for a German contribution to the upcoming European Health Data Space (EHDS), which opens opportunities for Germany as a medical research location.

[Digital health progress hubs-data integration beyond university hospitals]. / Die digitalen Fortschrittshubs Gesundheit ­ Gemeinsame Datennutzung über die Universitätsmedizin hinaus.

The digital health progress hubs pilot the extensibility of the concepts and solutions of the Medical Informatics Initiative to improve regional healthcare and research. The six funded projects address different diseases, areas in regional healthcare, and methods of cross-institutional data linking and use. Despite the diversity of the scenarios and regional conditions, the technical, regulatory, and organizational challenges and barriers that the progress hubs encounter in the actual implementation of the solutions are often similar. This results in some common approaches to solutions, but also in political demands that go beyond the Health Data Utilization Act, which is considered a welcome improvement by the progress hubs.In this article, we present the digital progress hubs and discuss achievements, challenges, and approaches to solutions that enable the shared use of data from university hospitals and non-academic institutions in the healthcare system and can make a sustainable contribution to improving medical care and research.

A comprehensive method protocol for annotation and integrated functional understanding of lncRNAs.

Long non-coding RNAs (lncRNAs) are of fundamental biological importance; however, their functional role is often unclear or loosely defined as experimental characterization is challenging and bioinformatic methods are limited. We developed a novel integrated method protocol for the annotation and detailed functional characterization of lncRNAs within the genome. It combines annotation, normalization and gene expression with sequence-structure conservation, functional interactome and promoter analysis. Our protocol allows an analysis based on the tissue and biological context, and is powerful in functional characterization of experimental and clinical RNA-Seq datasets including existing lncRNAs. This is demonstrated on the uncharacterized lncRNA GATA6-AS1 in dilated cardiomyopathy.

RIbench: A Proposed Benchmark for the Standardized Evaluation of Indirect Methods for Reference Interval Estimation.

BACKGROUND: Indirect methods leverage real-world data for the estimation of reference intervals. These constitute an active field of research, and several methods have been developed recently. So far, no standardized tool for evaluation and comparison of indirect methods exists. METHODS: We provide RIbench, a benchmarking suite for quantitative evaluation of any existing or novel indirect method. The benchmark contains simulated test sets for 10 biomarkers mimicking routine measurements of a mixed distribution of non-pathological (reference) values and pathological values. The non-pathological distributions represent 4 common distribution types: normal, skewed, heavily skewed, and skewed-and-shifted. To identify strengths and weaknesses of indirect methods, test sets have varying sample sizes and pathological distributions differ in location, extent of overlap, and fraction. For performance evaluation, we use an overall benchmark score and sub-scores derived from absolute z-score deviations between estimated and true reference limits. We illustrate the application of RIbench by evaluating and comparing the Hoffmann method and 4 modern indirect methods -TML (Truncated-Maximum-Likelihood), kosmic, TMC (Truncated-Minimum-Chi-Square), and refineR- against one another and against a nonparametric direct method (n = 120). RESULTS: For the modern indirect methods, pathological fraction and sample size had a strong influence on the results: With a pathological fraction up to 20% and a minimum sample size of 5000, most methods achieved results comparable or superior to the direct method. CONCLUSIONS: We present RIbench, an open-source R-package, for the systematic evaluation of existing and novel indirect methods. RIbench can serve as a tool for enhancement of indirect methods, improving the estimation of reference intervals.

Shift of radiotherapy use during the first wave of the COVID-19 pandemic? An analysis of German inpatient data.

OBJECTIVE: To assess the change in inpatient radiotherapy related to COVID-19 lockdown measures during the first wave of the pandemic in 2020. METHODS: We included cases hospitalized between January 1 and August 31, 2018-2020, with a primary ICD-10 diagnosis of C00-C13, C32 (head and neck cancer, HNC) and C53 (cervical cancer, CC). Data collection was conducted within the Medical Informatics Initiative. Outcomes were fractions and admissions. Controlling for decreasing hospital admissions during holidays, calendar weeks of 2018/2019 were aligned to Easter 2020. A lockdown period (LP; 16/03/2020-02/08/2020) and a return-to-normal period (RNP; 04/05/2020-02/08/2020) were defined. The study sample comprised a control (admission 2018/19) and study cohort (admission 2020). We computed weekly incidence and IR ratios from generalized linear mixed models. RESULTS: We included 9365 (CC: 2040, HNC: 7325) inpatient hospital admissions from 14 German university hospitals. For CC, fractions decreased by 19.97% in 2020 compared to 2018/19 in the LP. In the RNP the reduction was 28.57% (p < 0.001 for both periods). LP fractions for HNC increased by 10.38% (RNP: 9.27%; p < 0.001 for both periods). Admissions for CC decreased in both periods (LP: 10.2%, RNP: 22.14%), whereas for HNC, admissions increased (LP: 2.25%, RNP: 1.96%) in 2020. Within LP, for CC, radiotherapy admissions without brachytherapy were reduced by 23.92%, whereas surgery-related admissions increased by 20.48%. For HNC, admissions with radiotherapy increased by 13.84%, while surgery-related admissions decreased by 11.28% in the same period. CONCLUSION: Related to the COVID-19 lockdown in an inpatient setting, radiotherapy for HNC treatment became a more frequently applied modality, while admissions of CC cases decreased.

A nationwide registry for recurrent urolithiasis in the upper urinary tract - The RECUR study protocol.

BACKGROUND: Urinary stone disease is a widespread disease with tremendous impact on those affected and on societies around the globe. Nevertheless, clinical and health care research in this area seem to lag far behind cardiovascular diseases or cancer. This may be due to the lack of an immediate deadly threat from the disease and therefore less public and professional interest. However, the patients suffer from recurring, sometimes intense pain and often must be treated in hospital. Long-term morbidity includes doubled rates of chronic kidney disease and arterial hypertension after at least one stone-related event. Observational studies, more specifically, registries and other electronic data sets have been proposed as a means of filling critical gaps in evidence. We propose a nationwide digital and fully automated registry as part of the German Ministry for Education and Research (BMBF) call for the "establishment of model registries". METHODS: RECUR builds on the technical infrastructure of Germany's Medical Informatics Initiative. Local data integration centres (DIC) of participating medical universities will collect pseudonymized and harmonized data from respective hospital information systems. In addition to their clinical data, participants will provide patient reported outcomes using a mobile patient app. Scientific data exploration includes queries and analysis of federated data from DICs of eleven participating sites. All primary patient data will remain at the participating sites at all times. With comprehensive data from this longitudinal registry, we will be able to describe the disease burden, to determine and validate risk factors, and to evaluate treatments. Implementation and operation of the RECUR registry will be funded by the BMBF for five years. Subsequently, the registry is to be continued by the German Society of Urology without significant costs for study personnel. DISCUSSION: The proposed registry will substantially improve the structural and procedural framework for patients with recurrent urolithiasis. This includes advanced diagnostic algorithms and treatment pathways. The registry will help us identify those patients who will most benefit from specific interventions to prevent recurrences. The RECUR study protocol and the registry's technical architecture including full digitalization and automation of almost all registry-associated proceedings can be transferred to future registries. TRIAL REGISTRATION: This study is registered at the German Clinical Trial Register (Deutsches Register Klinischer Studien), DRKS-ID DRKS00026923 , date of registration January, 11th 2022.

DQAgui: a graphical user interface for the MIRACUM data quality assessment tool.

BACKGROUND: With the growing impact of observational research studies, there is also a growing focus on data quality (DQ). As opposed to experimental study designs, observational research studies are performed using data mostly collected in a non-research context (secondary use). Depending on the number of data elements to be analyzed, DQ reports of data stored within research networks can grow very large. They might be cumbersome to read and important information could be overseen quickly. To address this issue, a DQ assessment (DQA) tool with a graphical user interface (GUI) was developed and provided as a web application. METHODS: The aim was to provide an easy-to-use interface for users without prior programming knowledge to carry out DQ checks and to present the results in a clearly structured way. This interface serves as a starting point for a more detailed investigation of possible DQ irregularities. A user-centered development process ensured the practical feasibility of the interactive GUI. The interface was implemented in the R programming language and aligned to Kahn et al.'s DQ categories conformance, completeness and plausibility. RESULTS: With DQAgui, an R package with a web-app frontend for DQ assessment was developed. The GUI allows users to perform DQ analyses of tabular data sets and to systematically evaluate the results. During the development of the GUI, additional features were implemented, such as analyzing a subset of the data by defining time periods and restricting the analyses to certain data elements. CONCLUSIONS: As part of the MIRACUM project, DQAgui is now being used at ten German university hospitals for DQ assessment and to provide a central overview of the availability of important data elements in a datamap over 2 years. Future development efforts should focus on design optimization and include a usability evaluation.

A FHIR has been lit on gICS: facilitating the standardised exchange of informed consent in a large network of university medicine.

BACKGROUND: The Federal Ministry of Education and Research of Germany (BMBF) funds a network of university medicines (NUM) to support COVID-19 and pandemic research at national level. The "COVID-19 Data Exchange Platform" (CODEX) as part of NUM establishes a harmonised infrastructure that supports research use of COVID-19 datasets. The broad consent (BC) of the Medical Informatics Initiative (MII) is agreed by all German federal states and forms the legal base for data processing. All 34 participating university hospitals (NUM sites) work upon a harmonised infrastructural as well as legal basis for their data protection-compliant collection and transfer of their research dataset to the central CODEX platform. Each NUM site ensures that the exchanged consent information conforms to the already-balloted HL7 FHIR consent profiles and the interoperability concept of the MII Task Force "Consent Implementation" (TFCI). The Independent Trusted Third-Party (TTP) of the University Medicine Greifswald supports data protection-compliant data processing and provides the consent management solutions gICS. METHODS: Based on a stakeholder dialogue a required set of FHIR-functionalities was identified and technically specified supported by official FHIR experts. Next, a "TTP-FHIR Gateway" for the HL7 FHIR-compliant exchange of consent information using gICS was implemented. A last step included external integration tests and the development of a pre-configured consent template for the BC for the NUM sites. RESULTS: A FHIR-compliant gICS-release and a corresponding consent template for the BC were provided to all NUM sites in June 2021. All FHIR functionalities comply with the already-balloted FHIR consent profiles of the HL7 Working Group Consent Management. The consent template simplifies the technical BC rollout and the corresponding implementation of the TFCI interoperability concept at the NUM sites. CONCLUSIONS: This article shows that a HL7 FHIR-compliant and interoperable nationwide exchange of consent information could be built using of the consent management software gICS and the provided TTP-FHIR Gateway. The initial functional scope of the solution covers the requirements identified in the NUM-CODEX setting. The semantic correctness of these functionalities was validated by project-partners from the Ludwig-Maximilian University in Munich. The production rollout of the solution package to all NUM sites has started successfully.

BiasCorrector: Fast and accurate correction of all types of experimental biases in quantitative DNA methylation data derived by different technologies.

Quantification of DNA methylation in neoplastic cells is crucial both from mechanistic and diagnostic perspectives. However, such measurements are prone to different experimental biases. Polymerase chain reaction (PCR) bias results in an unequal recovery of methylated and unmethylated alleles at the sample preparation step. Post-PCR biases get introduced additionally by the readout processes. Correcting the biases is more practicable than optimising experimental conditions, as demonstrated previously. However, utilisation of our earlier developed algorithm strongly necessitates automation. Here, we present two R packages: rBiasCorrection, the core algorithms to correct biases; and BiasCorrector, its web-based graphical user interface frontend. The software detects and analyses experimental biases in calibration DNA samples at a single base resolution by using cubic polynomial and hyperbolic regression. The correction coefficients from the best regression type are employed to compensate for the bias. Three common technologies-bisulphite pyrosequencing, next-generation sequencing and oligonucleotide microarrays-were used to comprehensively test BiasCorrector. We demonstrate the accuracy of BiasCorrector's performance and reveal technology-specific PCR- and post-PCR biases. BiasCorrector effectively eliminates biases regardless of their nature, locus, the number of interrogated methylation sites and the detection method, thus representing a user-friendly tool for producing accurate epigenetic results.

High-resolution pediatric reference intervals for 15 biochemical analytes described using fractional polynomials.

OBJECTIVES: Assessment of children's laboratory test results requires consideration of the extensive changes that occur during physiological development and result in pronounced sex- and age-specific dynamics in many biochemical analytes. Pediatric reference intervals have to account for these dynamics, but ethical and practical challenges limit the availability of appropriate pediatric reference intervals that cover children from birth to adulthood. We have therefore initiated the multi-center data-driven PEDREF project (Next-Generation Pediatric Reference Intervals) to create pediatric reference intervals using data from laboratory information systems. METHODS: We analyzed laboratory test results from 638,683 patients (217,883-982,548 samples per analyte, a median of 603,745 test results per analyte, and 10,298,067 test results in total) performed during patient care in 13 German centers. Test results from children with repeat measurements were discarded, and we estimated the distribution of physiological test results using a validated statistical approach (kosmic). RESULTS: We report continuous pediatric reference intervals and percentile charts for alanine transaminase, aspartate transaminase, lactate dehydrogenase, alkaline phosphatase, γ-glutamyl-transferase, total protein, albumin, creatinine, urea, sodium, potassium, calcium, chloride, anorganic phosphate, and magnesium. Reference intervals are provided as tables and fractional polynomial functions (i.e., mathematical equations) that can be integrated into laboratory information systems. Additionally, Z-scores and percentiles enable the normalization of test results by age and sex to facilitate their interpretation across age groups. CONCLUSIONS: The provided reference intervals and percentile charts enable precise assessment of laboratory test results in children from birth to adulthood. Our findings highlight the pronounced dynamics in many biochemical analytes in neonates, which require particular consideration in reference intervals to support clinical decision making most effectively.

Evaluation of a clinical decision support system for rare diseases: a qualitative study.

BACKGROUND: Rare Diseases (RDs) are difficult to diagnose. Clinical Decision Support Systems (CDSS) could support the diagnosis for RDs. The Medical Informatics in Research and Medicine (MIRACUM) consortium developed a CDSS for RDs based on distributed clinical data from eight German university hospitals. To support the diagnosis for difficult patient cases, the CDSS uses data from the different hospitals to perform a patient similarity analysis to obtain an indication of a diagnosis. To optimize our CDSS, we conducted a qualitative study to investigate usability and functionality of our designed CDSS. METHODS: We performed a Thinking Aloud Test (TA-Test) with RDs experts working in Rare Diseases Centers (RDCs) at MIRACUM locations which are specialized in diagnosis and treatment of RDs. An instruction sheet with tasks was prepared that the participants should perform with the CDSS during the study. The TA-Test was recorded on audio and video, whereas the resulting transcripts were analysed with a qualitative content analysis, as a ruled-guided fixed procedure to analyse text-based data. Furthermore, a questionnaire was handed out at the end of the study including the System Usability Scale (SUS). RESULTS: A total of eight experts from eight MIRACUM locations with an established RDC were included in the study. Results indicate that more detailed information about patients, such as descriptive attributes or findings, can help the system perform better. The system was rated positively in terms of functionality, such as functions that enable the user to obtain an overview of similar patients or medical history of a patient. However, there is a lack of transparency in the results of the CDSS patient similarity analysis. The study participants often stated that the system should present the user with an overview of exact symptoms, diagnosis, and other characteristics that define two patients as similar. In the usability section, the CDSS received a score of 73.21 points, which is ranked as good usability. CONCLUSIONS: This qualitative study investigated the usability and functionality of a CDSS of RDs. Despite positive feedback about functionality of system, the CDSS still requires some revisions and improvement in transparency of the patient similarity analysis.

Time Tracking of Standard Ultrasound Examinations in Pediatric Hospitals and Pediatric Medical Practices - A Multicenter Study by the Pediatric Section of the German Society of Ultrasound in Medicine (DEGUM).

PURPOSE: Ultrasonography is the primary imaging modality in pediatrics but still lacks sufficient reimbursement in Germany. In this multicenter study, national data for the duration of standard ultrasound in pediatrics were systematically documented in order to specify the actual time required. MATERIALS AND METHODS: N = 10 hospitals (N = 5 university hospitals, N = 5 non-university hospitals) and N = 3 medical practices in Germany recorded the entire process of an ultrasound examination in a special protocol developed by the Pediatric Section of the DEGUM. The duration of each of seven single steps during ultrasonography (from data input to final discussion of the results) of different organ systems was logged. RESULTS: In total, N = 2118 examinations from different organ systems were recorded. N = 10 organ systems were examined frequently (> 30 times). The total duration of an ultrasound examination was statistically significantly longer in hospitals compared to medical practices (median (IQR) 27 min. (18-38) vs. 12 min. (9-17), p < 0.001). The "hands-on" patient time was approximately one half of the total required time in both settings (49.9 % vs. 48.9 %). Ultrasonography of the abdomen and brain lasted longer in university hospitals than in non-university hospitals (p < 0.001, and p = 0.04, respectively). Cooperation and age did not uniformly correlate with the total duration. CONCLUSION: This study provides novel comprehensive national data for the duration of standardized ultrasound examinations of children and adolescents in Germany. These data are essential for a further evaluation of the economic costs and should support better remuneration in the future.

[RECUR - Establishment of An Automated Digital Registry for Patients with Recurrent Stones in the Upper Urinary Tract]. / RECUR ­ Aufbau eines automatisierten digitalen Registers für Patient*innen mit rezidivierenden Steinen des oberen Harntraktes.

Kidney stones, like cardiovascular diseases and diabetes mellitus, affect a large number of people. Patients suffer from acute pain, repeated hospitalizations and associated secondary diseases, such as arterial hypertension and renal insufficiency. This results in considerable costs for the society and its health care system. The recurrence rate is as high as 50%. The registry for RECurrent URolithiasis (RECUR) aims to fill existing evidence gaps. The prospective and longitudinal RECUR registry is funded by the German Ministry of Education and Science (BMBF). It is based on the digital infrastructure of the German Medical Informatics Initiative (MII). RECUR aims to include patients that have suffered from more than one stone occurrence and treated at any one of the ten participating university hospitals of the MIRACUM consortium. The intention is to obtain new information on risk factors and to evaluate different diagnosis and treatment algorithms. Along with the data form the patient's Electronic Health Records (EHR), the RECUR project will also collect Patient Reported Outcomes data from patients with recurrent kidney stones. These data will be collected at participating sites using digital questionnaires via a smartphone app. These data will be merged with medical data from the hospital information systems and saved in the MII research data repositories. The RECUR registry has a model character due to its fully federated, digital approach. This allows the recruitment of many patients, the collection of a wide range of data and their processing with low administrative and personnel costs.

The generic Informed Consent Service gICS®: implementation and benefits of a modular consent software tool to master the challenge of electronic consent management in research.

BACKGROUND: Defining and protecting participants' rights is the aim of several ethical codices and legal regulations. According to these regulations, the Informed Consent (IC) is an inevitable element of research with human subjects. In the era of "big data medicine", aspects of IC become even more relevant since research becomes more complex rendering compliance with legal and ethical regulations increasingly difficult. METHODS: Based on literature research and practical experiences gathered by the Institute for Community Medicine (ICM), University Medicine Greifswald, requirements for digital consent management systems were identified. RESULTS: To address the requirements, the free-of-charge, open-source software "generic Informed Consent Service" (gICS®) was developed by ICM to provide a tool to facilitate and enhance usage of digital ICs for the international research community covering various scenarios. gICS facilitates IC management based on IC modularisation and supports various workflows within research, including (1) electronic depiction of paper-based consents and (2) fully electronic consents. Numerous projects applied gICS and documented over 336,000 ICs and 2400 withdrawals since 2014. DISCUSSION: Since the consent's content is a prerequisite for securing participants' rights, application of gICS is no guarantee for legal compliance. However, gICS supports fine-granular consents and accommodation of differentiated consent states, which can be directly exchanged between systems, allowing automated data processing. CONCLUSION: gICS simplifies and supports sustained IC management as a major key to successfully conduct studies and build trust in research with human subjects. Therefore, interested researchers are invited to use gICS and provide feedback for further improvements.

Integrating Genomics and Clinical Data for Statistical Analysis by Using GEnome MINIng (GEMINI) and Fast Healthcare Interoperability Resources (FHIR): System Design and Implementation.

BACKGROUND: The introduction of next-generation sequencing (NGS) into molecular cancer diagnostics has led to an increase in the data available for the identification and evaluation of driver mutations and for defining personalized cancer treatment regimens. The meaningful combination of omics data, ie, pathogenic gene variants and alterations with other patient data, to understand the full picture of malignancy has been challenging. OBJECTIVE: This study describes the implementation of a system capable of processing, analyzing, and subsequently combining NGS data with other clinical patient data for analysis within and across institutions. METHODS: On the basis of the already existing NGS analysis workflows for the identification of malignant gene variants at the Institute of Pathology of the University Hospital Erlangen, we defined basic requirements on an NGS processing and analysis pipeline and implemented a pipeline based on the GEMINI (GEnome MINIng) open source genetic variation database. For the purpose of validation, this pipeline was applied to data from the 1000 Genomes Project and subsequently to NGS data derived from 206 patients of a local hospital. We further integrated the pipeline into existing structures of data integration centers at the University Hospital Erlangen and combined NGS data with local nongenomic patient-derived data available in Fast Healthcare Interoperability Resources format. RESULTS: Using data from the 1000 Genomes Project and from the patient cohort as input, the implemented system produced the same results as already established methodologies. Further, it satisfied all our identified requirements and was successfully integrated into the existing infrastructure. Finally, we showed in an exemplary analysis how the data could be quickly loaded into and analyzed in KETOS, a web-based analysis platform for statistical analysis and clinical decision support. CONCLUSIONS: This study demonstrates that the GEMINI open source database can be augmented to create an NGS analysis pipeline. The pipeline generates high-quality results consistent with the already established workflows for gene variant annotation and pathological evaluation. We further demonstrate how NGS-derived genomic and other clinical data can be combined for further statistical analysis, thereby providing for data integration using standardized vocabularies and methods. Finally, we demonstrate the feasibility of the pipeline integration into hospital workflows by providing an exemplary integration into the data integration center infrastructure, which is currently being established across Germany.

A Federated Online Search Tool for Biospecimens (Sample Locator): Usability Study.

BACKGROUND: The German Biobank Alliance (GBA) aims to establish a cross-site biobank network. For this endeavor, the so-called Sample Locator, a federated search tool for biospecimens and related data, has been developed, forming the heart of its information technology (IT) infrastructure. OBJECTIVE: To ensure the sustainable use of such a tool, we included researchers as participants in an end user-based usability evaluation. METHODS: To develop a prototype ready for evaluation, we needed input from GBA IT experts. Thus, we conducted a 2-day workshop with 8 GBA IT team members. The focus was on the respective steps of a user-centered design process. With the acquired knowledge, the participants designed low-fidelity mock-ups. The main ideas of these mock-ups were discussed, extracted, and summarized into a comprehensive prototype using Microsoft PowerPoint. Furthermore, we created a questionnaire concerning the usability of the prototype, including the System Usability Scale (SUS), questions on negative and positive aspects, and typical tasks to be fulfilled with the tool. Subsequently, the prototype was pretested on the basis of this questionnaire with researchers who have a biobank background. Based on this preliminary work, the usability analysis was ultimately carried out with researchers and the results were evaluated. RESULTS: Altogether, 27 researchers familiar with sample requests evaluated the prototype. The analysis of the feedback certified a good usability, given that the Sample Locator prototype was seen as intuitive and user-friendly by 74% (20/27) of the participants. The total SUS score by the 25 persons that completed the questionnaire was 80.4, indicating good system usability. Still, the evaluation provided useful advice on optimization potential (eg, offering a help function). CONCLUSIONS: The findings of this usability analysis indicate that the considerations regarding a user-friendly application that have been made in the development process so far strongly coincide with the perception of the study participants. Nevertheless, it was important to engage prospective end users to ensure that the previous development is going in the desired direction and that the Sample Locator will be used in the future. The user comments and suggestions for improvement will be considered in upcoming iterations for refinement.

Interviews with experts in rare diseases for the development of clinical decision support system software - a qualitative study.

BACKGROUND: Patients with rare diseases (RDs) are often diagnosed too late or not at all. Clinical decision support systems (CDSSs) could support the diagnosis in RDs. The MIRACUM (Medical Informatics in Research and Medicine) consortium, which is one of four funded consortia in the German Medical Informatics Initiative, will develop a CDSS for RDs based on distributed clinical data from ten university hospitals. This qualitative study aims to investigate (1) the relevant organizational conditions for the operation of a CDSS for RDs when diagnose patients (e.g. the diagnosis workflow), (2) which data is necessary for decision support, and (3) the appropriate user group for such a CDSS. METHODS: Interviews were carried out with RDs experts. Participants were recruited from staff physicians at the Rare Disease Centers (RDCs) at the MIRACUM locations, which offer diagnosis and treatment of RDs. An interview guide was developed with a category-guided deductive approach. The interviews were recorded on an audio device and then transcribed into written form. We continued data collection until all interviews were completed. Afterwards, data analysis was performed using Mayring's qualitative content analysis approach. RESULTS: A total of seven experts were included in the study. The results show that medical center guides and physicians from RDC B-centers (with a focus on different RDs) are involved in the diagnostic process. Furthermore, interdisciplinary case discussions between physicians are conducted. The experts explained that RDs exist which cannot be fully differentiated, but rather described only by their overall symptoms or findings: diagnosis is dependent on the disease or disease group. At the end of the diagnostic process, most centers prepare a summary of the patient case. Furthermore, the experts considered both physicians and experts from the B-centers to be potential users of a CDSS. The experts also have different experiences with CDSS for RDs. CONCLUSIONS: This qualitative study is a first step towards establishing the requirements for the development of a CDSS for RDs. Further research is necessary to create solutions by also including the experts on RDs.

Integrative Bioinformatic Analyses of Global Transcriptome Data Decipher Novel Molecular Insights into Cardiac Anti-Fibrotic Therapies.

Integrative bioinformatics is an emerging field in the big data era, offering a steadily increasing number of algorithms and analysis tools. However, for researchers in experimental life sciences it is often difficult to follow and properly apply the bioinformatical methods in order to unravel the complexity and systemic effects of omics data. Here, we present an integrative bioinformatics pipeline to decipher crucial biological insights from global transcriptome profiling data to validate innovative therapeutics. It is available as a web application for an interactive and simplified analysis without the need for programming skills or deep bioinformatics background. The approach was applied to an ex vivo cardiac model treated with natural anti-fibrotic compounds and we obtained new mechanistic insights into their anti-fibrotic action and molecular interplay with miRNAs in cardiac fibrosis. Several gene pathways associated with proliferation, extracellular matrix processes and wound healing were altered, and we could identify micro (mi) RNA-21-5p and miRNA-223-3p as key molecular components related to the anti-fibrotic treatment. Importantly, our pipeline is not restricted to a specific cell type or disease and can be broadly applied to better understand the unprecedented level of complexity in big data research.

Next-generation reference intervals for pediatric hematology.

Background Interpreting hematology analytes in children is challenging due to the extensive changes in hematopoiesis that accompany physiological development and lead to pronounced sex- and age-specific dynamics. Continuous percentile charts from birth to adulthood allow accurate consideration of these dynamics. However, the ethical and practical challenges unique to pediatric reference intervals have restricted the creation of such percentile charts, and limitations in current approaches to laboratory test result displays restrict their use when guiding clinical decisions. Methods We employed an improved data-driven approach to create percentile charts from laboratory data collected during patient care in 10 German centers (9,576,910 samples from 358,292 patients, 412,905-1,278,987 samples per analyte). We demonstrate visualization of hematology test results using percentile charts and z-scores (www.pedref.org/hematology) and assess the potential of percentiles and z-scores to support diagnosis of different hematological diseases. Results We created percentile charts for hemoglobin, hematocrit, red cell indices, red cell count, red cell distribution width, white cell count and platelet count in girls and boys from birth to 18 years of age. Comparison of pediatricians evaluating complex clinical scenarios using percentile charts versus conventional/tabular representations shows that percentile charts can enhance physician assessment in selected example cases. Age-specific percentiles and z-scores, compared with absolute test results, improve the identification of children with blood count abnormalities and the discrimination between different hematological diseases. Conclusions The provided reference intervals enable precise assessment of pediatric hematology test results. Representation of test results using percentiles and z-scores facilitates their interpretation and demonstrates the potential of digital approaches to improve clinical decision-making.

Concept to gain trust for a German personal health record system using public cloud and FHIR.

OBJECTIVE: Although a national Personal Health Record (PHR) infrastructure was supposed to have been introduced in Germany by law in 2006 and different providers are entering the market, no system has yet been widely adopted in Germany. There is also little information available on how current technical advancements affect German patients' and physicians' trust in PHR systems. METHODS: Supporting scenarios obtained from clinicians, this study proposes a concept for a German PHR system using a public cloud infrastructure, smartphone access and focusing on trust, privacy, and interoperability. In advance to an eventual implementation, a multi-center questionnaire study has been conducted to predict patients' and physicians' intention to use that system and evaluate their trust in different providers of such a system. RESULTS: Our results show that both patients and physicians are highly likely to use the PHR based on the present concept. Trust in healthcare providers exceeds trust in other institutions like private companies, health insurance companies, or even governmental institutions when offering such a PHR system. CONCLUSIONS: We recommend the implementation of this PHR system. To maximize patients' and physicians' trust in the system, it should be offered to patients by their healthcare provider. Further evaluation regarding its actual adoption and expected improvement in patient outcome based on the scenarios is advisable.