Leveraging European infrastructures to access 1 million human genomes by 2022.

Human genomics is undergoing a step change from being a predominantly research-driven activity to one driven through health care as many countries in Europe now have nascent precision medicine programmes. To maximize the value of the genomic data generated, these data will need to be shared between institutions and across countries. In recognition of this challenge, 21 European countries recently signed a declaration to transnationally share data on at least 1 million human genomes by 2022. In this Roadmap, we identify the challenges of data sharing across borders and demonstrate that European research infrastructures are well-positioned to support the rapid implementation of widespread genomic data access.

Author Correction: Leveraging European infrastructures to access 1 million human genomes by 2022.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

COVID-19 Research: Navigating the European General Data Protection Regulation.

Researchers must collaborate globally to rapidly respond to the COVID-19 pandemic. In Europe, the General Data Protection Regulation (GDPR) regulates the processing of personal data, including health data of value to researchers. Even during a pandemic, research still requires a legal basis for the processing of sensitive data, additional justification for its processing, and a basis for any transfer of data outside Europe. The GDPR does provide legal grounds and derogations that can support research addressing a pandemic, if the data processing activities are proportionate to the aim pursued and accompanied by suitable safeguards. During a pandemic, a public interest basis may be more promising for research than a consent basis, given the high standards set out in the GDPR. However, the GDPR leaves many aspects of the public interest basis to be determined by individual Member States, which have not fully or uniformly made use of all options. The consequence is an inconsistent legal patchwork that displays insufficient clarity and impedes joint approaches. The COVID-19 experience provides lessons for national legislatures. Responsiveness to pandemics requires clear and harmonized laws that consider the related practical challenges and support collaborative global research in the public interest.

Purpose definition as a crucial step for determining the legal basis under the GDPR: implications for scientific research.

The General Data Protection Regulation (GDPR) of the European Union, which became applicable in 2018, contains a new accountability principle. Under this principle, controllers (ie parties determining the purposes and the means of the processing of personal data) are responsible for ensuring and demonstrating the overall compliance with the GDPR. However, interpretive uncertainties of the GDPR mean that controllers must exercise considerable judgement in designing and implementing an appropriate compliance strategy, making GDPR compliance both complex and resource-intensive. In this article, we provide conceptual clarity around GDPR compliance with respect to one core aspect of the law: the determination and relevance of the purpose of personal data processing. We derive from the GDPR's text concrete requirements for purpose specification, which we subsequently apply to the area of secondary use of personal data for scientific research. We offer guidance for correctly specifying purposes of data processing under different research scenarios. To illustrate the practical necessity of purpose specification for GDPR compliance, we then show how our proposed approach can enable controllers to meet their compliance obligations, using the example of the overarching GDPR principle of lawfulness to highlight the relevance of purpose specification for the identification of a suitable legal basis.

DS-PACK: Tool assembly for the end-to-end support of controlled access human data sharing.

The EU General Data Protection Regulation (GDPR) requirements have prompted a shift from centralised controlled access genome-phenome archives to federated models for sharing sensitive human data. In a data-sharing federation, a central node facilitates data discovery; meanwhile, distributed nodes are responsible for handling data access requests, concluding agreements with data users and providing secure access to the data. Research institutions that want to become part of such federations often lack the resources to set up the required controlled access processes. The DS-PACK tool assembly is a reusable, open-source middleware solution that semi-automates controlled access processes end-to-end, from data submission to access. Data protection principles are engraved into all components of the DS-PACK assembly. DS-PACK centralises access control management and distributes access control enforcement with support for data access via cloud-based applications. DS-PACK is in production use at the ELIXIR Luxembourg data hosting platform, combined with an operational model including legal facilitation and data stewardship.

Getting your DUCs in a row - standardising the representation of Digital Use Conditions.

Improving patient care and advancing scientific discovery requires responsible sharing of research data, healthcare records, biosamples, and biomedical resources that must also respect applicable use conditions. Defining a standard to structure and manage these use conditions is a complex and challenging task. This is exemplified by a near unlimited range of asset types, a high variability of applicable conditions, and differing applications at the individual or collective level. Furthermore, the specifics and granularity required are likely to vary depending on the ultimate contexts of use. All these factors confound alignment of institutional missions, funding objectives, regulatory and technical requirements to facilitate effective sharing. The presented work highlights the complexity and diversity of the problem, reviews the current state of the art, and emphasises the need for a flexible and adaptable approach. We propose Digital Use Conditions (DUC) as a framework that addresses these needs by leveraging existing standards, striking a balance between expressiveness versus ambiguity, and considering the breadth of applicable information with their context of use.

Acetyl-DL-leucine in cerebellar ataxia ([18F]-FDG-PET study): how does a cerebellar disorder influence cortical sensorimotor networks?

OBJECTIVE: The aim of the study was to deepen our insights into central compensatory processes of brain networks in patients with cerebellar ataxia (CA) before and with treatment with acetyl-DL-leucine (AL) by means of resting-state [18F]-FDG-PET brain imaging. METHODS: Retrospective analyses of [18F]-FDG-PET data in 22 patients with CA (with vestibular and ocular motor disturbances) of different etiologies who were scanned before (PET A) and on AL treatment (PET B). Group subtraction analyses, e.g., for responders and non-responders, comparisons with healthy controls and correlation analyses of regional cerebral glucose metabolism (rCGM) with symptom duration, ataxia (SARA) and quality of life (QoL) scores were calculated. RESULTS: Prior to treatment rCGM was consistently downregulated at the cerebellar level and increased in multisensory cortical areas, e.g., somatosensory, primary and secondary visual (including V5, precuneus), secondary vestibular (temporal gyrus, anterior insula), and premotor/supplementary motor areas. With AL (PET B vs. A) cerebellar hypometabolism was deepened and sensorimotor hypermetabolism increased only in responders with clinical benefit, but not for the non-responders and the whole CA group. A positive correlation of ataxia improvement with rCGM was found in visual and vestibular cortices, a negative correlation in cerebellar and brainstem areas. QoL showed a positive correlation with rCGM in the cerebellum and symptom duration in premotor and somatosensory areas. CONCLUSIONS: Central compensatory processes in CA mainly involve multisensory visual, vestibular, and somatosensory networks as well as premotor/primary motor areas at the cortical level. The enhanced divergence of cortical sensorimotor up- and cerebellar downregulation with AL in responders could reflect amplification of inhibitory cerebellar mechanisms.

Educational Policies Matter: How Schooling Strategies Influence Refugee Adolescents' School Participation in Lower Secondary Education in Germany.

This article investigates the educational participation of refugee adolescents in Germany as a main European destination country of refugee migration. Opportunities and restrictions for school participation vary not only across countries-, but in the case of the Federal Republic of Germany, also within countries. The influence of different regional educational policies on refugees' educational participation and the extent to which they limit or enable individual agency, are however, widely understudied. We thus aim to analyze how different regional educational policies within Germany influence refugee students' educational participation regarding four central indicators: the duration until school enrollment, the type of class attended (newcomer vs. regular class), the type of school attended, and whether they are enrolled in settings appropriate for their age. We rely on a theoretical model which sees educational decisions as the result of rational cost-benefit calculations. The individual educational investments depend on individual motivations and resources within a given opportunity structure. We integrate the legal regulations via the opportunity structures into the theoretical model. Our analyses are based on data from 2,415 adolescents who were interviewed in the "ReGES-Refugees in the German Educational System" study. Our results show significant correlations between different regional educational policies and the four domains of educational participation. These effects remain stable when considering family and individual resources, as well as further control variables that previous research on social and ethnic educational inequality has shown to be relevant. Family and individual resources only partially influence educational participation. This indicates that refugee students and their parents have only limited options for action concerning their educational participation. Thus, our study shows that educational policies in fact matter: the assignment to a federal state plays a significant role in determining the duration until school enrollment, whether one is placed to a grade level age-appropriately, and whether one attends a newcomer class. Most significantly, legal regulations strongly influence refugees' chances of attending a higher school track (Gymnasium). Due to the low permeability of the German education system, this creates path dependencies for the further education and career paths of new immigrant students.

Genomic Characterization of Aureimonas altamirensis C2P003-A Specific Member of the Microbiome of Fraxinus excelsior Trees Tolerant to Ash Dieback.

Some European ash trees show tolerance towards dieback caused by the invasive pathogen Hymenoscyphus fraxineus. The microbiome of these trees harbours a range of specific bacterial groups. One of these groups belonging to the species Aureimonas altamirensis was studied in detail by genome analysis and a plant inoculation trial. The strain group was shown to be phylogenetically distinct from clinical isolates by 16S rRNA analysis and phylogenomics. Genome analysis of a representative strain C2P003 resulted in a large number of unique gene sequences in comparison to other well-studied strains of the species. A functional analysis of the genome revealed features associated with the synthesis of exopolysaccharides, protein secretion and biofilm production as well as genes for stress adaptation, suggesting the ability of C2P003 to effectively colonize ash leaves. The inoculation of ash seedlings with C2P003 showed a significant positive effect on the plant health of the seedlings that were exposed to H. fraxineus infection. This effect was maintained over a period of three years and was accompanied by a significant shift in the bacterial microbiome composition one year after inoculation. Overall, the results indicate that C2P003 may suppress H. fraxineus in or on ash leaves via colonization resistance or indirectly by affecting the microbiome.

Physiological and genomic characterisation of Luteimonas fraxinea sp. nov., a bacterial species associated with trees tolerant to ash dieback.

A group of isolates of the genus Luteimonas was characterised, which represented a specific component of the healthy core microbiome of Fraxinus excelsior in forest districts with a high infection rate of H. fraxineus, the causal agent of ash dieback. Based on phylogenomic and phenotypic analyses, a clear differentiation from related Luteimonas species was shown. Comparisons of the overall genome relatedness indices with the closest phylogenetic neighbours resulted in values below the recommended species cut-off levels. In addition, differences in several physiological and chemotaxonomic traits allowed a clear demarcation from the type strains of closely related species. Conclusively, the strain group was considered to represent a novel species in the genus Luteimonas, for which the name Luteimonas fraxinea sp. nov. is proposed, with strain D4P002T (=DSM 113273T = LMG 32455T) as the type strain. A functional analysis of the genome revealed features particularly associated with attachment, biofilm production and motility, indicating the ability of D4P002T to effectively colonise ash leaves. In nursery trials, ash seedlings inoculated with this strain showed suppression of the pathogen over a period of three years. This effect was accompanied by a significant shift in the bacterial microbiome of the plants. Altogether, the exclusive occurrence in the microbiome of tolerant ash trees, the genetic background and the results of the inoculation experiment suggest that strain D4P002T may suppress the penetration and spreading of H. fraxineus in or on ash leaves via colonisation resistance or trigger a priming effect of plant defences against the pathogen.

Genomic Analysis of the Endophytic Stenotrophomonas Strain 169 Reveals Features Related to Plant-Growth Promotion and Stress Tolerance.

Plant-associated Stenotrophomonas isolates have great potential for plant growth promotion, especially under stress conditions, due to their ability to promote tolerance to abiotic stresses such as salinity or drought. The endophytic strain Stenotrophomonas sp. 169, isolated from a field-grown poplar, increased the growth of inoculated in vitro plants, with a particular effect on root development, and was able to stimulate the rooting of poplar cuttings in the greenhouse. The strain produced high amounts of the plant growth-stimulating hormone auxin under in vitro conditions. The comparison of the 16S rRNA gene sequences and the phylogenetic analysis of the core genomes showed a close relationship to Stenotrophomonas chelatiphaga and a clear separation from Stenotrophomonas maltophilia. Whole genome sequence analysis revealed functional genes potentially associated with attachment and plant colonization, growth promotion, and stress protection. In detail, an extensive set of genes for twitching motility, chemotaxis, flagella biosynthesis, and the ability to form biofilms, which are connected with host plant colonization, could be identified in the genome of strain 169. The production of indole-3-acetic acid and the presence of genes for auxin biosynthesis pathways and the spermidine pathway could explain the ability to promote plant growth. Furthermore, the genome contained genes encoding for features related to the production of different osmoprotective molecules and enzymes mediating the regulation of stress tolerance and the ability of bacteria to quickly adapt to changing environments. Overall, the results of physiological tests and genome analysis demonstrated the capability of endophytic strain 169 to promote plant growth. In contrast to related species, strain 169 can be considered non-pathogenic and suitable for biotechnology applications.

Analyzing Ash Leaf-Colonizing Fungal Communities for Their Biological Control of Hymenoscyphus fraxineus.

The invasive ascomycete Hymenoscyphus fraxineus has been threatening Fraxinus excelsior populations throughout Europe for over two decades. Since the infection and first colonization by the pathogen occurs in leaves, leaf-colonizing microorganisms have been discussed as a barrier and as possible biocontrol agents against the disease. To identify fungal groups with health-supporting potential, we compared the fungal microbiota of compound leaves from susceptible and tolerant ash trees in four ash stands with high H. fraxineus exposure. The fungal communities were analyzed both culture-independently by ITS2 amplicon sequencing and by the taxonomic classification of 1,704 isolates using matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) or sequencing of the entire ITS region. The fungal community structure did not show significant differences depending on the health status. However, for several OTUs and a MALDI group, a significantly higher abundance was found in tolerant ash trees. Thus, the yeast Papiliotrema flavescens was significantly increased and accounted for 12.3% of the mycobiome of tolerant ashes (OTU0003), and it had also a distinctly higher abundance among the isolates. The filamentous ascomycete Sarocladium strictum was increased 24-fold among the isolates of tolerant trees, but its abundance was comparably low. An in vitro screening for the growth inhibition of the pathogen via cocultivation resulted in 28 yeast-like isolates and 79 filamentous fungi with antagonistic activity. A statistical cocultivation test on two H. fraxineus strains confirmed six of the yeast-like isolates that suppressed H. fraxineus significantly, from 39-50%, two of them through a fungicidal effect. The highest inhibition rates among the yeasts were found for three isolates belonging to Aureobasidium pullulans and P. flavescens. The cocultivation test of the filamentous isolates revealed higher effects compared to the yeasts. Four isolates showed significant inhibition of both H. fraxineus strains with a rate of 72-100%, and five further isolates inhibited only one H. fraxineus strain significantly. The most effective isolates were members of the genus Cladosporium. During the next step, in planta tests will be necessary to verify the efficacy of the antagonistic isolates and to assess their suitability as biocontrol agents.

A Comparative Analysis of Ash Leaf-Colonizing Bacterial Communities Identifies Putative Antagonists of Hymenoscyphus fraxineus.

In the last few years, the alarming spread of Hymenoscyphus fraxineus, the causal agent of ash dieback, has resulted in a substantial threat to native ash stands in central and northern Europe. Since leaves and leaf petioles are the primary infection sites, phyllosphere microorganisms are presumed to interact with the pathogen and are discussed as a source of biocontrol agents. We studied compound leaves from susceptible and visible infection-free trees in four ash stands with a high likelihood of infection to assess a possible variation in the bacterial microbiota, depending on the health status of the trees. The bacterial community was analyzed by culture-independent 16S rRNA gene amplicon sequencing and through the isolation and taxonomic classification of 2,589 isolates using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The bacterial community structure did not show significant differences. However, a set of amplicon sequence variants (ASVs) and MALDI groups belonging to Luteimonas, Aureimonas, Pseudomonas, Bacillus, and Paenibacillus were distinctly increased in tolerant trees, which may be associated with the ability of the tree to resist the pathogen. The most obvious differences were observed for Luteimonas, a genus that is also exclusively present in the healthy core microbiome. In a first in vitro screen of antagonists, approximately 11% of total isolates suppressed the growth of H. fraxineus, but a statistical test with two different H. fraxineus strains confirmed only the antagonistic activity of 8% of these isolates. The antagonistic isolates were assigned to Bacillus velezensis, Pantoea vagans, and Pseudomonas caspiana. Overall, our study provides a set of isolates or phylogenetic groups that might be involved in the process that prevents the penetration and spread of H. fraxineus. In the next step, in planta experiments are required with a longer period of exposure to H. fraxineus to evaluate effective isolates or consortia of isolates acting through direct antagonism or competition or indirectly by inducing resistance.

Follow-Up in Aphasia Caused by Acute Stroke in a Prospective, Randomized, Clinical, and Experimental Controlled Noninvasive Study With an iPad-Based App (Neolexon®): Study Protocol of the Lexi Study.

Rationale: Treatment of aphasia is still challenging for clinicians and patients. So far, there is proven evidence for "face-to-face" speech therapy. However, the digital age potentially offers new and complementary strategies that may add to treatment outcome in a cost-effective way. Neolexon® is a commercial tablet-based software for treatment of aphasia, which can be applied with the help of a therapist or as self-training by the patient. Aims and hypothesis: In the Lexi study, we aim to determine whether treatment with Neolexon® is superior to standard therapy in acute post-stroke aphasia. Sample size estimates: A sample size of 180 patients, 90 for each group, will be included with an assumed dropout rate of ~20%. Methods and design: Prospective, randomized, parallel group, open-label, blinded-endpoint clinical, and experimental controlled non-invasive trial (PROBE). Adult German native speakers with acute aphasia after stroke are included. Computer-generated, blocked, and stratified randomization by aphasia severity will assign patients to one of two groups: 4 weeks of either standard logopedic speech therapy or logopedic speech therapy with the app version of Neolexon®. Both groups will be instructed in self-training: the frequency and duration of self-training will be documented. Screening for aphasia will be performed using the Language Screening Test (LAST). The severity of aphasia in general and in subitems will be assessed using the Bielefelder Aphasie Screening (BIAS) and the Aphasia Check List (ACL). Follow-up will be assessed after 3 months. Study outcomes: Based on the consensus in our study team, we considered a 10% mean difference in the change of percentile rank (PR) of BIAS to be a minimal and clinically important difference. The primary endpoint is defined as a significant difference in BIAS comparing the two groups. Differences in quality of life, Beck Depression Inventory (BDI), and modified Ranking Scale (mRS) will be evaluated as secondary outcome parameters. Discussion: This trial will determine whether speech therapy with the use of Neolexon® is superior to standard logopedic therapy. Subgroups with the greatest response to Neolexon® will be described. The trial was prospectively registered on the "EU Clinical Trials Register" (NCT04080817).

Recurrent Stroke in a Young Patient with Embolic Stroke of Undetermined Source and Patent Foramen Ovale: Quo Vadis?

So far, there has been no generally accepted diagnostic and therapeutic algorithm for patients with embolic stroke of undetermined source (ESUS). As recent clinical trials on secondary stroke prevention in ESUS did not support the use of oral anticoagulation and the concept of ESUS comprises heterogeneous subgroups of patients, including a wide age range, concomitant patent foramen ovale (PFO), variable cardiovascular risk factors as well as a variable probability for atrial fibrillation (AF), an individualized clinical approach is needed. In this context, we here present a case of recurrent stroke in a young patient with ESUS and PFO. During treatment according to our Catch-up-ESUS registry study, prolonged cardiac monitoring diagnosed AF, and PFO closure was omitted.

DAISY: A Data Information System for accountability under the General Data Protection Regulation.

BACKGROUND: The new European legislation on data protection, namely, the General Data Protection Regulation (GDPR), has introduced comprehensive requirements for the documentation about the processing of personal data as well as informing the data subjects of its use. GDPR's accountability principle requires institutions, projects, and data hubs to document their data processings and demonstrate compliance with the GDPR. In response to this requirement, we see the emergence of commercial data-mapping tools, and institutions creating GDPR data register with such tools. One shortcoming of this approach is the genericity of tools, and their process-based model not capturing the project-based, collaborative nature of data processing in biomedical research. FINDINGS: We have developed a software tool to allow research institutions to comply with the GDPR accountability requirement and map the sometimes very complex data flows in biomedical research. By analysing the transparency and record-keeping obligations of each GDPR principle, we observe that our tool effectively meets the accountability requirement. CONCLUSIONS: The GDPR is bringing data protection to center stage in research data management, necessitating dedicated tools, personnel, and processes. Our tool, DAISY, is tailored specifically for biomedical research and can help institutions in tackling the documentation challenge brought about by the GDPR. DAISY is made available as a free and open source tool on Github. DAISY is actively being used at the Luxembourg Centre for Systems Biomedicine and the ELIXIR-Luxembourg data hub.

Catch-up-ESUS - follow-up in embolic stroke of undetermined source (ESUS) in a prospective, open-label, observational study: study protocol and initial baseline data.

INTRODUCTION: So far there is no uniform, commonly accepted diagnostic and therapeutic algorithm for patients with embolic stroke of undetermined source (ESUS). Recent clinical trials on secondary stroke prevention in ESUS did not support the use of oral anticoagulation. As ESUS comprises heterogeneous subgroups including a wide age-range, concomitant patent foramen ovale (PFO), and variable probability for atrial fibrillation (AF), an individualised approach is urgently needed. This prospective registry study aims to provide initial data towards an individual, structured diagnostic and therapeutic approach in ESUS patients. METHODS AND ANALYSIS: The open-label, investigator-initiated, prospective, single-centre, observational registry study (Catch-up-ESUS) started in 01/2018. Consecutive ESUS patients ≥18 years who give informed consent are included and will be followed up for 3 years. Stratified by age <60 or ≥60 years, the patients are processed following a standardised diagnostic and treatment algorithm with an interdisciplinary design involving neurologists and cardiologists. Depending on the strata, patients receive a transesophageal echocardiogram; all patients receive an implantable cardiac monitor. Patients <60 years with PFO and without evidence of concomitant AF are planned for PFO closure within 6 months after stroke. The current diagnostic and therapeutic workup of ESUS patients requires improvement by both standardisation and a more individualised approach. Catch-up-ESUS will provide important data with respect to AF detection and PFO closure and will estimate stratified stroke recurrence rates after ESUS. ETHICS AND DISSEMINATION: The study has been approved by the responsible ethics committee at the Ludwig Maximilian University, Munich, Germany (project number 17-685). Catch-Up-ESUS is conducted in accordance with the Declaration of Helsinki. All patients will have to give written informed consent or, if unable to give consent themselves, their legal guardian will have to provide written informed consent for their participation. The first observation period of the registry study is 1 year, followed by the first publication of the results including follow-up of the patients. Further publications will be considered according the predefined individual follow-up dates of the stroke patients up to 36 months. TRIAL REGISTRATION NUMBER: Clinicaltrialsregister.gov registry (NCT03820375).

Effects of transgenic fructan-producing potatoes on the community structure of rhizosphere and phyllosphere bacteria.

The rhizosphere and phyllosphere microbial communities of transgenic potatoes producing fructan were studied in comparison with isogenic controls and conventional varieties in a field release experiment over a period of 3 years. Population densities and 16S rRNA gene-based terminal restriction fragment length polymorphism (T-RFLP) analysis of the rhizosphere bacterial community only displayed the influence of annual and seasonal effects and the influence of field heterogeneity. In contrast, the T-RFLP analysis of the phyllosphere bacteria revealed in two of the 3 years significant differences in the community structure between the transgenic lines producing inulin and the other variants. This effect was studied in more detail through the analysis of bacterial isolates and a 16S rRNA gene clone library obtained from a transgenic line and the control. Both methods revealed a lower genetic diversity in the transgenic line and changes in the abundance of several bacterial groups. The isolates of the transgenic line were dominated by Bacilli, whereas most of the control isolates represented Actinobacteria. The clones were dominated by Proteobacteria, with main differences between both variants in Deltaproteobacteria, Bacilli and Bacteroidetes. However, all in all, the impact of the transgenic lines did not exceed the natural variability of the phyllosphere community structure on potato plants.

Bacterial diversity of soils assessed by DGGE, T-RFLP and SSCP fingerprints of PCR-amplified 16S rRNA gene fragments: do the different methods provide similar results?

Bacterial communities of four arable soils--pelosol, gley, para brown soil, and podsol brown soil--were analysed by fingerprinting of 16S rRNA gene fragments amplified from total DNA of four replicate samples for each soil type. Fingerprints were generated in parallel by denaturing gradient gel electrophoresis (DGGE), terminal restriction fragment length polymorphism (T-RFLP), and single strand conformation polymorphism (SSCP) to test whether these commonly applied techniques are interchangeable. PCR amplicons could be separated with all three methods resulting in complex ribotype patterns. Although the fragments amplified comprised different variable regions and lengths, DGGE, T-RFLP and SSCP analyses led to similar findings: (a) a clustering of fingerprints which correlated with soil physico-chemical properties, (b) little variability between the four replicates of the same soil, (c) the patterns of the two brown soils were more similar to each other than to those of the other two soils, and (d) the fingerprints of the different soil types revealed significant differences in a permutation test, which was recently developed for this purpose.