Presence of minimal residual disease (MRD), detected by flow cytometry, is an important prognostic biomarker in the management of B-cell precursor acute lymphoblastic leukemia (BCP-ALL). However,... Show morePresence of minimal residual disease (MRD), detected by flow cytometry, is an important prognostic biomarker in the management of B-cell precursor acute lymphoblastic leukemia (BCP-ALL). However, data-analysis remains mainly expert-dependent. In this study, we designed and validated an Automated Gating & Identification (AGI) tool for MRD analysis in BCP-ALL patients using the two tubes of the EuroFlow 8-color MRD panel. The accuracy, repeatability, and reproducibility of the AGI tool was validated in a multicenter study using bone marrow follow-up samples from 174 BCP-ALL patients, stained with the EuroFlow BCP-ALL MRD panel. In these patients, MRD was assessed both by manual analysis and by AGI tool supported analysis. Comparison of MRD levels obtained between both approaches showed a concordance rate of 83%, with comparable concordances between MRD tubes (tube 1, 2 or both), treatment received (chemotherapy versus targeted therapy) and flow cytometers (FACSCanto versus FACSLyric). After review of discordant cases by additional experts, the concordance increased to 97%. Furthermore, the AGI tool showed excellent intra-expert concordance (100%) and good inter-expert concordance (90%). In addition to MRD levels, also percentages of normal cell populations showed excellent concordance between manual and AGI tool analysis. We conclude that the AGI tool may facilitate MRD analysis using the EuroFlow BCP-ALL MRD protocol and will contribute to a more standardized and objective MRD assessment. However, appropriate training is required for the correct analysis of MRD data. Show less
The European Congenital Heart Surgeons Association (ECHSA) Congenital Database (CD) is the second largest clinical pediatric and congenital cardiac surgical database in the world and the largest... Show moreThe European Congenital Heart Surgeons Association (ECHSA) Congenital Database (CD) is the second largest clinical pediatric and congenital cardiac surgical database in the world and the largest in Europe, where various smaller national or regional databases exist. Despite the dramatic increase in interventional cardiology procedures over recent years, only scattered national or regional databases of such procedures exist in Europe. Most importantly, no congenital cardiac database exists in the world that seamlessly combines both surgical and interventional cardiology data on an international level; therefore, the outcomes of surgical and interventional procedures performed on the same or similar patients cannot easily be tracked, assessed, and analyzed. In order to fill this important gap in our capability to gather and analyze information on our common patients, ECHSA and The Association for European Paediatric and Congenital Cardiology (AEPC) have embarked on a collaborative effort to expand the ECHSA-CD with a new module designed to capture data about interventional cardiology procedures. The purpose of this manuscript is to describe the concept, the structure, and the function of the new AEPC Interventional Cardiology Part of the ECHSA-CD, as well as the potentially valuable synergies provided by the shared interventional and surgical analyses of outcomes of patients. The new AEPC Interventional Cardiology Part of the ECHSA-CD will allow centers to have access to robust surgical and transcatheter outcome data from their own center, as well as robust national and international aggregate outcome data for benchmarking. Each contributing center or department will have access to their own data, as well as aggregate data from the AEPC Interventional Cardiology Part of the ECHSA-CD. The new AEPC Interventional Cardiology Part of the ECHSA-CD will allow cardiology centers to have access to aggregate cardiology data, just as surgical centers already have access to aggregate surgical data. Comparison of surgical and catheter interventional outcomes could potentially strengthen decision processes. A study of the wealth of information collected in the database could potentially also contribute toward improved early and late survival, as well as enhanced quality of life of patients with pediatric and/or congenital heart disease treated with surgery and interventional cardiac catheterization across Europe and the world. Show less
The European Congenital Heart Surgeons Association (ECHSA) Congenital Database (CD) is the second largest clinical pediatric and congenital cardiac surgical database in the world and the largest... Show moreThe European Congenital Heart Surgeons Association (ECHSA) Congenital Database (CD) is the second largest clinical pediatric and congenital cardiac surgical database in the world and the largest in Europe, where various smaller national or regional databases exist. Despite the dramatic increase in interventional cardiology procedures over recent years, only scattered national or regional databases of such procedures exist in Europe. Most importantly, no congenital cardiac database exists in the world that seamlessly combines both surgical and interventional cardiology data on an international level; therefore, the outcomes of surgical and interventional procedures performed on the same or similar patients cannot easily be tracked, assessed, and analyzed. In order to fill this important gap in our capability to gather and analyze information on our common patients, ECHSA and The Association for European Paediatric and Congenital Cardiology (AEPC) have embarked on a collaborative effort to expand the ECHSA-CD with a new module designed to capture data about interventional cardiology procedures. The purpose of this manuscript is to describe the concept, the structure, and the function of the new AEPC Interventional Cardiology Part of the ECHSA-CD, as well as the potentially valuable synergies provided by the shared interventional and surgical analyses of outcomes of patients. The new AEPC Interventional Cardiology Part of the ECHSA-CD will allow centers to have access to robust surgical and transcatheter outcome data from their own center, as well as robust national and international aggregate outcome data for benchmarking. Each contributing center or department will have access to their own data, as well as aggregate data from the AEPC Interventional Cardiology Part of the ECHSA-CD. The new AEPC Interventional Cardiology Part of the ECHSA-CD will allow cardiology centers to have access to aggregate cardiology data, just as surgical centers already have access to aggregate surgical data. Comparison of surgical and catheter interventional outcomes could potentially strengthen decision processes. A study of the wealth of information collected in the database could potentially also contribute toward improved early and late survival, as well as enhanced quality of life of patients with pediatric and/or congenital heart disease treated with surgery and interventional cardiac catheterization across Europe and the world. Show less
Matern, B.M.; Niemann, M.; Nemparis, I.; Schimanski, A.; Peereboom, E.T.M.; Kramer, C.S.M.; ... ; Spierings, E. 2023
The International HLA and Immunogenetics Workshop (IHIW) is a recurring gathering of researchers, technologists and clinicians where participants contribute to collaborative projects with a variety... Show moreThe International HLA and Immunogenetics Workshop (IHIW) is a recurring gathering of researchers, technologists and clinicians where participants contribute to collaborative projects with a variety of goals, and come to consensus on definitions and standards for representing HLA and immunogenic determinants. The collaborative and international nature of these workshops, combined with the multifaceted goals of several specific workshop components, necessitates the collection and curation of a wide assortment of data, as well as an adaptable platform for export and analysis. With the aim of ensuring data quality and creation of reusable datasets, specific standards and nomenclature conventions are continuously being developed, and are an integral part of IHIW. Here we present the 18th IHIW Database, a purpose-built and extensible cloud-based file repository and web application for collecting and analyzing project-specific data. This platform is based on open-source software and uses established HLA data standards and web technologies to facilitate de-centralized data repository ownership, reduce duplicated efforts, and promote continuity for future IHIWs. Show less
Background: Although considering the pathophysiology of post-coarctectomy hypertension, beta-blockers should be effective, experience with labetalol for treatment is limited in the literature.... Show moreBackground: Although considering the pathophysiology of post-coarctectomy hypertension, beta-blockers should be effective, experience with labetalol for treatment is limited in the literature. Methods: Retrospective collection and analysis of data in children aged <= 6 years following coarctectomy in our tertiary care university medical center between January 2009 and June 2018. Results: 96 patients were included, 45 were treated with intravenous labetalol and 51 received no treatment. Median time to maximum dose received (median 1.1 mg/kg/h) was 2.7 h, and median time to the reduction of labetalol dose was 8.3 h. No antihypertensives had to be added. In one child, labetalol was switched to nitroprusside due to bronchoconstriction. Of patients receiving intravenous labetalol, 48% had been switched to oral labetalol at discharge. Conclusions: Intravenous labetalol is a fast, effective, and safe drug to treat hypertension following aortic coarctation repair. Labetalol is easily converted to oral therapy when the continuation of treatment is considered necessary. Show less
Clinic-based headache registries collect data for a wide variety of purposes including delineating disease characteristics, longitudinal natural disease courses, headache management approaches,... Show moreClinic-based headache registries collect data for a wide variety of purposes including delineating disease characteristics, longitudinal natural disease courses, headache management approaches, quality of care, treatment safety and effectiveness, factors that predict treatment response, health care resource utilization, clinician adherence to guidelines, and cost-effectiveness. Registry data are valuable for numerous stakeholders, including individuals with headache disorders and their caregivers, healthcare providers, scientists, healthcare systems, regulatory authorities, pharmaceutical companies, employers, and policymakers. This International Headache Society document may serve as guidance for developing clinic-based headache registries. Use of registry data requires a formal research protocol that includes: 1) research aims; 2) methods for data collection, harmonization, analysis, privacy, and protection; 3) methods for human subject protection; and 4) publication and dissemination plans. Depending upon their objectives, headache registries should include validated headache-specific questionnaires, patient reported outcome measures, data elements that are used consistently across studies (i.e., "common data elements"), and medical record data. Amongst other data types, registries may be linked to healthcare and pharmacy claims data, biospecimens, and neuroimaging data. Headache diagnoses should be made according to the International Classification of Headache Disorders diagnostic criteria. The data from well-designed headache registries can provide wide-ranging and novel insights into the characteristics, burden, and treatment of headache disorders and ultimately lead to improvements in the management of patients with headache. Show less
BackgroundThe accumulation of risk for the development of rheumatoid arthritis (RA) is regarded as a continuum that may start with interacting environmental and genetic factors, proceed with the... Show moreBackgroundThe accumulation of risk for the development of rheumatoid arthritis (RA) is regarded as a continuum that may start with interacting environmental and genetic factors, proceed with the initiation of autoimmunity, and result in the formation of autoantibodies such as anti-citrullinated peptide antibodies (ACPA). In parallel, at-risk individuals may be asymptomatic or experience joint pain (arthralgia) that is itself non-specific or clinically suspicious for evolving RA, even in the absence of overt arthritis. Optimal strategies for the management of people at-risk of RA, both for symptom control and to delay or prevent progression to classifiable disease, remain poorly understood. MethodsTo help address this, groups of stakeholders from academia, clinical rheumatology, industry and patient research partners have collaborated to advance understanding, define and study different phases of the at-risk state. In this current report we describe different European initiatives in the field and the successful effort to build a European Registry of at-risk people to facilitate observational and interventional research. ResultsWe outline similarities and differences between cohorts of at-risk individuals at institutions spanning several countries, and how to best combine them within the new database. Over the past 2 years, besides building the technical infrastructure, we have agreed on a core set of variables that all partners should strive to collect for harmonization purposes. ConclusionWe emphasize to address this process from different angles and touch on the biologic, epidemiologic, analytic, and regulatory aspects of collaborative studies within a meta-database of people at-risk of RA. Show less
Pathogenic variants of the nuclear receptor subfamily 2 group F member 1 gene (NR2F1) are responsible for Bosch-Boonstra-Schaaf optic atrophy syndrome (BBSOAS), an autosomal dominant disorder... Show morePathogenic variants of the nuclear receptor subfamily 2 group F member 1 gene (NR2F1) are responsible for Bosch-Boonstra-Schaaf optic atrophy syndrome (BBSOAS), an autosomal dominant disorder characterized by optic atrophy associated with developmental delay and intellectual disability, but with a clinical presentation which appears to be multifaceted. We created the first public locus-specific database dedicated to NR2F1. All variants and clinical cases reported in the literature, as well as new unpublished cases, were integrated into the database using standard nomenclature to describe both molecular and phenotypic anomalies. We subsequently pursued a comprehensive approach based on computed representation and analysis suggesting a refinement of the BBSOAS clinical description with respect to neurological features and the inclusion of additional signs of hypotonia and feeding difficulties. This database is fully accessible for both clinician and molecular biologists and should prove useful in further refining the clinical synopsis of NR2F1 as new data is recorded. Show less
Sabatini, F.M.; Lenoir, J.; Hattab, T.; Arnst, E.A.; Chytrý, M.; Dengler, J.; ... ; Bruelheide, H. 2021
Motivation: Assessing biodiversity status and trends in plant communities is critical for understanding, quantifying and predicting the effects of global change on ecosystems. Vegetation plots... Show moreMotivation: Assessing biodiversity status and trends in plant communities is critical for understanding, quantifying and predicting the effects of global change on ecosystems. Vegetation plots record the occurrence or abundance of all plant species co-occurring within delimited local areas. This allows species absences to be inferred, information seldom provided by existing global plant datasets. Although many vegetation plots have been recorded, most are not available to the global research community. A recent initiative, called ‘sPlot’, compiled the first global vegetation plot database, and continues to grow and curate it. The sPlot database, however, is extremely unbalanced spatially and environmentally, and is not open-access. Here, we address both these issues by (a) resampling the vegetation plots using several environmental variables as sampling strata and (b) securing permission from data holders of 105 local-to-regional datasets to openly release data. We thus present sPlotOpen, the largest open-access dataset of vegetation plots ever released. sPlotOpen can be used to explore global diversity at the plant community level, as ground truth data in remote sensing applications, or as a baseline for biodiversity monitoring.Main types of variable contained: Vegetation plots (n = 95,104) recording cover or abundance of naturally co-occurring vascular plant species within delimited areas. sPlotOpen contains three partially overlapping resampled datasets (c. 50,000 plots each), to be used as replicates in global analyses. Besides geographical location, date, plot size, biome, elevation, slope, aspect, vegetation type, naturalness, coverage of various vegetation layers, and source dataset, plot-level data also include community- weighted means and variances of 18 plant functional traits from the TRY Plant Trait Database.Spatial location and grain: Global, 0.01–40,000 m2.Time period and grain: 1888–2015, recording dates.Major taxa and level of measurement: 42,677 vascular plant taxa, plot-level records. Software format: Three main matrices (.csv), relationally linked. Show less
The corpus of bioinformatics resources is huge and expanding rapidly, presenting life scientists with a growing challenge in selecting tools that fit the desired purpose. To address this, the... Show moreThe corpus of bioinformatics resources is huge and expanding rapidly, presenting life scientists with a growing challenge in selecting tools that fit the desired purpose. To address this, the European Infrastructure for Biological Information is supporting a systematic approach towards a comprehensive registry of tools and databases for all domains of bioinformatics, provided under a single portal (https://bio.tools). We describe here the practical means by which scientific communities, including individual developers and projects, through major service providers and research infrastructures, can describe their own bioinformatics resources and share these via bio.tools. Show less
Fokkema, I.F.A.C.; Velde, K.J. van der; Slofstra, M.K.; Ruivenkamp, C.A.L.; Vogel, M.J.; Pfundt, R.; ... ; Gijn, M.E. van 2019
Each year diagnostic laboratories in the Netherlands profile thousands of individuals for heritable disease using next-generation sequencing (NGS). This requires pathogenicity classification of... Show moreEach year diagnostic laboratories in the Netherlands profile thousands of individuals for heritable disease using next-generation sequencing (NGS). This requires pathogenicity classification of millions of DNA variants on the standard 5-tier scale. To reduce time spent on data interpretation and increase data quality and reliability, the nine Dutch labs decided to publicly share their classifications. Variant classifications of nearly 100,000 unique variants were catalogued and compared in a centralized MOLGENIS database. Variants classified by more than one center were labeled as "consensus" when classifications agreed, and shared internationally with LOVD and ClinVar. When classifications opposed (LB/B vs. LP/P), they were labeled "conflicting", while other nonconsensus observations were labeled "no consensus". We assessed our classifications using the InterVar software to compare to ACMG 2015 guidelines, showing 99.7% overall consistency with only 0.3% discrepancies. Differences in classifications between Dutch labs or between Dutch labs and ACMG were mainly present in genes with low penetrance or for late onset disorders and highlight limitations of the current 5-tier classification system. The data sharing boosted the quality of DNA diagnostics in Dutch labs, an initiative we hope will be followed internationally. Recently, a positive match with a case from outside our consortium resulted in a more definite disease diagnosis. Show less
The topical focus of research on terrorism has frequently been critiqued for being too narrow, too event-driven and too strongly tied to governments’ counterterrorism policies. This article uses... Show moreThe topical focus of research on terrorism has frequently been critiqued for being too narrow, too event-driven and too strongly tied to governments’ counterterrorism policies. This article uses keyword analysis to assess the degree to which these issues remain present in the literature on terrorism as represented by the 3.442 articles published between 2007 and 2016 in nine of the field’s leading academic journals. Several fluctuations notwithstanding, research on terrorism has retained a strong focus on al-Qaeda, jihadist terrorism more generally, and the geographic areas most strongly associated with this type of terrorist violence. Results also indicate that the field remains event-driven and consistently underemphasizes state terrorism as well as non-jihadist terrorism, such as that perpetrated by right-wing extremists. Show less
Illicit drugs continue to be a profitable area for criminal organizations operating within the EU. Drug use and drug markets can act as facilitators for all types of violence, which could... Show moreIllicit drugs continue to be a profitable area for criminal organizations operating within the EU. Drug use and drug markets can act as facilitators for all types of violence, which could ultimately lead to homicide. Yet, drug-related homicide (DRH) has not been monitored. The development of a drug-related homicide data collection is necessary to study this phenomenon. This report provides a first step towards a European-level DRH monitor. Show less
Illicit drugs continue to be a profitable area for criminal organizations operating within the EU. Drug use and drug markets can act as facilitators for all types of violence, which could... Show moreIllicit drugs continue to be a profitable area for criminal organizations operating within the EU. Drug use and drug markets can act as facilitators for all types of violence, which could ultimately lead to homicide. Yet, drug-related homicide (DRH) has not been monitored. The development of a drug-related homicide data collection is necessary to study this phenomenon. This report provides a first step towards a European-level DRH monitor. Show less
Dunnen, J.T. den; Dalgleish, R.; Maglott, D.R.; Hart, R.K.; Greenblatt, M.S.; McGowan-Jordan, J.; ... ; Human Genome Org HUGO 2016
