Highlights 40 candidate genes might be associated with severe COVID-19. Inflammasome (NLRP1) as a possible cause of cytokine storm in COVID-19. IL-18, CCR1, CCR9 and EndoU(coronavirus protein) inhibition as possible treatment for COVID-19. DC-SIGN (Lectin pathway) and MxA expression might explain SARS-CoV-2 latency and reactivation in some cases. Case report as study design for discovering novel monogenic cases(with low minor allele frequency) of severe COVID-19.

Purpose-To introduce the goals of EAV database modeling, to describe the situations where Entity-Attribute-Value (EAV) modeling is a useful alternative to conventional relational methods of database modeling, and to describe the fine points of implementation in production systems.Methods-We analyze the following circumstances: 1) data are sparse and have a large number of applicable attributes, but only a small fraction will apply to a given entity; 2) numerous classes of data need to be represented, each class has a limited number of attributes, but the number of instances of each class is very small. We also consider situations calling for a mixed approach where both conventional and EAV design are used for appropriate data classes.Results and Conclusions-In robust production systems, EAV-modeled databases trade a modest data sub-schema for a complex metadata sub-schema. The need to design the metadata effectively makes EAV design potentially more challenging than conventional design.

Motivation: The Biological Reference Repository (BioR) is a toolkit for annotating variants. BioR stores public and user-specific annotation sources in indexed JSON-encoded flat files (catalogs). The BioR toolkit provides the functionality to combine and retrieve annotation from these catalogs via the command-line interface. Several catalogs from commonly used annotation sources and instructions for creating user-specific catalogs are provided. Commands from the toolkit can be combined with other UNIX commands for advanced annotation processing. We also provide instructions for the development of custom annotation pipelines.Availability and implementation: The package is implemented in Java and makes use of external tools written in Java and Perl. The toolkit can be executed on Mac OS X 10.5 and above or any Linux distribution. The BioR application, quickstart, and user guide documents and many biological examples are available at http://bioinformaticstools.mayo.edu.Contact: Kocher.JeanPierre@mayo.eduSupplementary information: Supplementary data are available at Bioinformatics online.