MOTIVATION: Genome-wide association studies (GWAS) are a powerful method to detect even weak associations between variants and phenotypes; however, many of the identified associated variants are in non-coding regions, and presumably influence gene expression regulation. Identifying potential drug targets, i.e. causal protein-coding genes, therefore, requires crossing the genetics results with functional data. RESULTS: We present a novel data integration pipeline that analyses GWAS results in the light of experimental epigenetic and cis-regulatory datasets, such as ChIP-Seq, Promoter-Capture Hi-C or eQTL, and presents them in a single report, which can be used for inferring likely causal genes. This pipeline was then fed into an interactive data resource. AVAILABILITY AND IMPLEMENTATION: The analysis code is available at www.github.com/Ensembl/postgap and the interactive data browser at postgwas.opentargets.io.

SUMMARY: The Illumina Infinium EPIC BeadChip is a new high-throughput array for DNA methylation analysis, extending the earlier 450k array by over 400 000 new sites. Previously, a method named eFORGE was developed to provide insights into cell type-specific and cell-composition effects for 450k data. Here, we present a significantly updated and improved version of eFORGE that can analyze both EPIC and 450k array data. New features include analysis of chromatin states, transcription factor motifs and DNase I footprints, providing tools for epigenome-wide association study interpretation and epigenome editing. AVAILABILITY AND IMPLEMENTATION: eFORGE v2.0 is implemented as a web tool available from https://eforge.altiusinstitute.org and https://eforge-tf.altiusinstitute.org/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

BACKGROUND: The Open Targets Platform integrates different data sources in order to facilitate identification of potential therapeutic drug targets to treat human diseases. It currently provides evidence for nearly 2.6 million potential target-disease pairs. G-protein coupled receptors are a drug target class of high interest because of the number of successful drugs being developed against them over many years. Here we describe a systematic approach utilizing the Open Targets Platform data to uncover and prioritize potential new disease indications for the G-protein coupled receptors and their ligands. RESULTS: Utilizing the data available in the Open Targets platform, potential G-protein coupled receptor and endogenous ligand disease association pairs were systematically identified. Intriguing examples such as GPR35 for inflammatory bowel disease and CXCR4 for viral infection are used as illustrations of how a systematic approach can aid in the prioritization of interesting drug discovery hypotheses. Combining evidences for G-protein coupled receptors and their corresponding endogenous peptidergic ligands increases confidence and provides supportive evidence for potential new target-disease hypotheses. Comparing such hypotheses to the global pharma drug discovery pipeline to validate the approach showed that more than 93% of G-protein coupled receptor-disease pairs with a high overall Open Targets score involved receptors with an existing drug discovery program. CONCLUSIONS: The Open Targets gene-disease score can be used to prioritize potential G-protein coupled receptors-indication hypotheses. In addition, availability of multiple different evidence types markedly increases confidence as does combining evidence from known receptor-ligand pairs. Comparing the top-ranked hypotheses to the current global pharma pipeline serves validation of our approach and identifies and prioritizes new therapeutic opportunities.

Bioinformatics learning opportunities are now easily available face to face [1] or online [2]. As a rule of thumb, the former can (and will) trump the latter for its level of interactivity and engagement [3]. Most, if not all, students appreciate having the trainer (and classmates) available and close by. Their questions will get answered on the spot, on a case-by-case basis, with a personal touch. If the students happen to be in Europe (e.g., [4,5]) or North America (e.g., [6, 7]), they are in luck: there is no shortage of opportunities for such engaging encounters. Funding is often available for these students to attend face-to-face training. However, other parts of the globe tend to get neglected when it comes to live (and lively) face-to-face scientific training. Although capacity-strengthening initiatives, such as the Pan African Bioinformatics Network for Human Heredity and Health in Africa (H3ABioNet) Initiative [8], CABANA [9], Asia Pacific BioInformatics Network (APBioNet) [10], attempt to address this inequality, especially in low- and middle-income countries, scalability will always be an issue for face-to-face training. Online courses [11–13], however, allow training at scale, regardless of the trainees’ location. Funding for travel is no longer a hurdle: the only requirement is access to a computer (perhaps a smart phone or tablet) and an internet connection. The course is taken in the comfort and convenience of the trainee’s home, office, a library, or perhaps a coffee place with free Wi-Fi. However, on-demand access can be offset by lack of interactivity. Although online training portals often have chat rooms or other means of interacting with fellow learners or the course provider, discussions initiated this way often have a lag time. Web-based seminars (webinars) offer the best of both worlds: they are run online and therefore at no (or little) cost for trainees, they can be scheduled at a convenient time for the target audience, the geographic distance between the trainer and the trainee is no longer an issue, and they allow for interaction between trainer and trainees at the moment of delivery. Webinars are short and straight to the point; the duration is usually no longer than 60 minutes. Questions are encouraged. Quick polls can be launched at any time for further interaction and getting to know the audience. Hands-on exercises can be provided, and follow-up webinars can be arranged for further discussions. How can you achieve a stress-free and successful live streaming of bioinformatics training, which is interactive and available to everyone everywhere? Here are 10 simple rules that we have developed over the past five years of organising and delivering webinars [14]. Although our 10 simple rules are designed to deliver training on bioinformatics resources and projects, they can be easily applied to other domains. Due to the low cost, short duration, and flexible, potentially global access, webinars can be used to train and/or promote a variety of themes in bioinformatics, computational biology, and computer science. Webinars will shorten the cycle time of your training and give you leeway to broaden your arsenal of content. You will be able to cover examples on protists, bacteria, plants—typically of great interest in low- and middle-income countries [15]—and have time to explore new trends in the application of machine learning, artificial intelligence, and blockchain in life sciences. Despite the possibilities of different contents, please be aware this article is not about selecting a training topic but rather on delivering training using webinars.