Comment

The emergence of the COVID-19 pandemic has spurred a global rush to uncover basic biological mechanisms to inform effective vaccine and drug development. Despite the novelty of the virus, global sequencing efforts have already identified genomic variation across isolates. To enable easy exploration and spatial visualization of the potential implications of SARS-CoV-2 mutations in infection, host immunity and drug development, we have developed COVID-3D (http://biosig.unimelb.edu.au/covid3d/).

The WashU Virus Genome Browser is a web-based portal for efficient visualization of viral ‘omics’ data in the context of a variety of annotation tracks and host infection responses. The browser features both a phylogenetic-tree-based view and a genomic-coordinate, track-based view in which users can analyze the sequence features of viral genomes, sequence diversity among viral strains, genomic sites of diagnostic tests, predicted immunogenic epitopes and a continuously updated repository of publicly available genomic datasets.

The UCSC SARS-CoV-2 Genome Browser (https://genome.ucsc.edu/covid19.html) is an adaptation of our popular genome-browser visualization tool for this virus, containing many annotation tracks and new features, including conservation with similar viruses, immune epitopes, RT–PCR and sequencing primers and CRISPR guides. We invite all investigators to contribute to this resource to accelerate research and development activities globally.

Standardized gene naming is crucial for effective communication about genes, and as genomics becomes increasingly important in health care, the need for a consistent language to refer to human genes becomes ever more essential. Here, we present the current HUGO Gene Nomenclature Committee (HGNC) guidelines for naming not only protein-coding genes but also RNA genes and pseudogenes, and we outline the changes in approach and ethos that have resulted from the discoveries of the past few decades.

Genetic discrimination is one of the most pervasive challenges resulting from research and development in human genetics. To collaboratively study and prevent this ethical issue, we established an international Genetic Discrimination Observatory comprising a network of researchers and stakeholders from more than 19 jurisdictions.

The African Orphan Crops Consortium promotes the strategic, genome-enabled improvement of under-researched crops for biodiversity-based, nutritious food solutions in Africa. The African Plant Breeding Academy empowers the continent’s plant breeders to apply advanced genetic approaches and shared genetic solutions to the task of tailoring the immense diversity of underutilized crops to the needs of Africa’s producers, processors and consumers.

The 11^th International Conference on Rare Diseases and Orphan Drugs (ICORD), South Africa, included the Africa-Rare initiative launch and facilitated multi-stakeholder engagement in the challenges facing, and opportunities for, Africans living with rare diseases. The following ICORD Global Call to Action, developed in collaboration with the International Rare Diseases Research Consortium, synthesizes the outcomes of the deliberations and emphasizes the international collaborative efforts required to address the global effects of rare diseases on public health.

Ancestral and geographical issues underlie the need to develop Africa-specific guidelines for the return of genomics research results in Africa. In this Commentary, we outline the challenges that will inform policies and practices in the future.

A fundamental problem in rare-disease diagnostics is the lack of consensus as to which genes have sufficient evidence to attribute causation. To address this issue, we have created PanelApp (https://panelapp.genomicsengland.co.uk), a publicly available knowledge base of curated virtual gene panels.

A generic framework for providing participant information and implementing a tiered consent process for health genomic research in Africa can help to harness global health benefits from sharing and meta-analysis of African genomic data while simultaneously respecting and upholding the autonomy and individual choices of African research participants.

To increase the utility of Gene Ontology (GO) annotations for interpretation of genome-wide experimental data, we have developed GO-CAM, a structured framework for linking multiple GO annotations into an integrated model of a biological system. We expect that GO-CAM will enable new applications in pathway and network analysis, as well as improve standard GO annotations for traditional GO-based applications.

The Nordic region, comprising primarily Denmark, Estonia, Finland, Iceland, Norway and Sweden, has many of the necessary characteristics for being at the forefront of genome-based precision medicine. These include egalitarian and universal healthcare, expertly curated patient and population registries, biobanks, large population-based prospective cohorts linked to registries and biobanks, and a widely embraced sense of social responsibility that motivates public engagement in biomedical research. However, genome-based precision medicine can be achieved only through coordinated action involving all actors in the healthcare sector. Now is an opportune time to organize scientists in the Nordic region, together with other stakeholders including patient representatives, governments, pharmaceutical companies, academic institutions and funding agencies, to initiate a Nordic Precision Medicine Initiative. We present a roadmap for how this organization can be created. The Initiative should facilitate research, clinical trials and knowledge transfer to meet regional and global health challenges.

Creating large genome/phenome collections can require consortium-scale resources. DNA.Land is a digital biobank that collects genetic data from individuals tested by consumer genomic companies using a fraction of the resources of traditional studies.