Recommendations for whole genome sequencing in diagnostics for rare diseases

In 2016, guidelines for diagnostic Next Generation Sequencing (NGS) have been published by EuroGentest in order to assist laboratories in the implementation and accreditation of NGS in a diagnostic setting. These guidelines mainly focused on Whole Exome Sequencing (WES) and targeted (gene panels) sequencing detecting small germline variants (Single Nucleotide Variants (SNVs) and insertions/deletions (indels)). Since then, Whole Genome Sequencing (WGS) has been increasingly introduced in the diagnosis of rare diseases as WGS allows the simultaneous detection of SNVs, Structural Variants (SVs) and other types of variants such as repeat expansions. The use of WGS in diagnostics warrants the re-evaluation and update of previously published guidelines. This work was jointly initiated by EuroGentest and the Horizon2020 project Solve-RD. Statements from the 2016 guidelines have been reviewed in the context of WGS and updated where necessary. The aim of these recommendations is primarily to list the points to consider for clinical (laboratory) geneticists, bioinformaticians, and (non-)geneticists, to provide technical advice, aid clinical decision-making and the reporting of the results

'You want the right amount of oversight' : interviews with data access committee members and experts on genomic data access

Purpose: Genomic data sharing is vital for optimizing the use of public-funded research data. Data access committees (DACs) have been introduced as a core component of governance in controlled access models. However, the tasks, structure, and functionality of DACs often remain unstudied. This article investigates the role and adequacy of DACs in access reviews from the perspective of DAC members and experts. Methods: Twenty semi-structured interviews were conducted with both DAC members engaged in genomic data sharing via controlled-access databases and experts in the field. Results: The respondents indicated that protecting the privacy of data subjects along with recognition of data producers' efforts are the main underlying reasons of access review and the controlled-access model. In reviewing the ethical basis and the scientific aspects of access requests, tools and mechanisms such as consent forms, data access agreements, and guidelines have been used. Nevertheless, DAC members and experts identified shortcomings associated with current approaches that may adversely impact the effectiveness and efficiency of access review. Conclusion: The identified shortcomings of current approaches to access review could be addressed via complementary mechanisms and alternative models of data sharing to facilitate access to data sets in a responsible fashion

First results of the COVID-19 in MS global data sharing initiative suggest anti-CD20 dmts are associated with worse covid-19 outcomes

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Familial autoinflammation with neutrophilic dermatosis reveals a regulatory mechanism of pyrin activation.

Pyrin responds to pathogen signals and loss of cellular homeostasis by forming an inflammasome complex that drives the cleavage and secretion of interleukin-1β (IL-1β). Mutations in the B30.2/SPRY domain cause pathogen-independent activation of pyrin and are responsible for the autoinflammatory disease familial Mediterranean fever (FMF). We studied a family with a dominantly inherited autoinflammatory disease, distinct from FMF, characterized by childhood-onset recurrent episodes of neutrophilic dermatosis, fever, elevated acute-phase reactants, arthralgia, and myalgia/myositis. The disease was caused by a mutation in MEFV, the gene encoding pyrin (S242R). The mutation results in the loss of a 14-3-3 binding motif at phosphorylated S242, which was not perturbed by FMF mutations in the B30.2/SPRY domain. However, loss of both S242 phosphorylation and 14-3-3 binding was observed for bacterial effectors that activate the pyrin inflammasome, such as Clostridium difficile toxin B (TcdB). The S242R mutation thus recapitulated the effect of pathogen sensing, triggering inflammasome activation and IL-1β production. Successful therapy targeting IL-1β has been initiated in one patient, resolving pyrin-associated autoinflammation with neutrophilic dermatosis. This disease provides evidence that a guard-like mechanism of pyrin regulation, originally identified for Nod-like receptors in plant innate immunity, also exists in humans