GENCODE 2021

© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. The GENCODE project annotates human and mouse genes and transcripts supported by experimental data with high accuracy, providing a foundational resource that supports genome biology and clinical genomics. GENCODE annotation processes make use of primary data and bioinformatic tools and analysis generated both within the consortium and externally to support the creation of transcript structures and the determination of their function. Here, we present improvements to our annotation infrastructure, bioinformatics tools, and analysis, and the advances they support in the annotation of the human and mouse genomes including: the completion of first pass manual annotation for the mouse reference genome; targeted improvements to the annotation of genes associated with SARS-CoV-2 infection; collaborative projects to achieve convergence across reference annotation databases for the annotation of human and mouse protein-coding genes; and the first GENCODE manually supervised automated annotation of lncRNAs. Our annotation is accessible via Ensembl, the UCSC Genome Browser and https://www.gencodegenes.org.National Human Genome Research Institute of the National Institutes of Health [U41HG007234]; the content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health; Wellcome Trust [WT108749/Z/15/Z, WT200990/Z/16/Z]; European Molecular Biology Laboratory; Swiss National Science Foundation through the National Center of Competence in Research ‘RNA & Disease’ (to R.J.); Medical Faculty of the University of Bern (to R.J). Funding for open access charge: National Institutes of Health

Integrated care for asthma: matching care to the patient.

The purpose of the present study was to investigate whether criteria associated with assignment of asthma patients between general practice (GP) care alone, integrated care (shared between GP care and hospital clinic) or conventional specialist review could be identified, and whether outcomes for these patients differed over the next 12 months. Seven hundred and sixty four patients with a diagnosis of asthma and previously assigned to either integrated care or clinic care were reviewed after 1 year and reassigned. These patients were then followed for another 12 months and clinical data were collected over this time. After 12 months in clinic care or integrated care, assignment to integrated care was predicted by previous participation in integrated care (OR 2.94), patient preference for integrated care (OR 3.7), no admission (OR 1.56), fewer steroid courses during the previous year (OR 0.88) and nonattendance at review (OR 0.43) in the previous 12 months. Patient discharge to GP care was predicted by higher level of forced expiratory volume in one second (FEV1) (OR 1.49), lower number of GP consultations for troublesome asthma (OR 0.78), and nonattendance for review in the preceding year (OR 2.15). In the following 12 months, the three groups of patients differed significantly in hospital admissions (Discharged = 0.008; Integrated = 0.12; Clinic = 0.31), bronchodilators prescribed (Discharged = 8.5; Integrated = 10.2; Clinic = 13.9), GP consultations (Discharged = 1.3; Integrated = 3.0; Clinic = 4.1) and oral steroid courses (Discharged = 0.62; Integrated = 1.7; Clinic = 2.4). Patients assigned to integrated care, clinic care or discharged to general practice care form three distinct patient populations differing retrospectively and prospectively in morbidity and admission risk. In particular, patients assigned to integrated care fall midway in risk and morbidity between those discharged or those retained in clinic care. These results suggest that integrated care provides general practitioners with a system of management for asthma patients, for whom they do not wish frequent specialist review but who they do not believe can safely be discharged to general practice care only

A comparative genomics multitool for scientific discovery and conservation

© 2020, The Author(s). The Zoonomia Project is investigating the genomics of shared and specialized traits in eutherian mammals. Here we provide genome assemblies for 131 species, of which all but 9 are previously uncharacterized, and describe a whole-genome alignment of 240 species of considerable phylogenetic diversity, comprising representatives from more than 80% of mammalian families. We find that regions of reduced genetic diversity are more abundant in species at a high risk of extinction, discern signals of evolutionary selection at high resolution and provide insights from individual reference genomes. By prioritizing phylogenetic diversity and making data available quickly and without restriction, the Zoonomia Project aims to support biological discovery, medical research and the conservation of biodiversity