Ensembl 2024.

Ensembl (https://www.ensembl.org) is a freely available genomic resource that has produced high-quality annotations, tools, and services for vertebrates and model organisms for more than two decades. In recent years, there has been a dramatic shift in the genomic landscape, with a large increase in the number and phylogenetic breadth of high-quality reference genomes, alongside major advances in the pan-genome representations of higher species. In order to support these efforts and accelerate downstream research, Ensembl continues to focus on scaling for the rapid annotation of new genome assemblies, developing new methods for comparative analysis, and expanding the depth and quality of our genome annotations. This year we have continued our expansion to support global biodiversity research, doubling the number of annotated genomes we support on our Rapid Release site to over 1700, driven by our close collaboration with biodiversity projects such as Darwin Tree of Life. We have also strengthened support for key agricultural species, including the first regulatory builds for farmed animals, and have updated key tools and resources that support the global scientific community, notably the Ensembl Variant Effect Predictor. Ensembl data, software, and tools are freely available.

Predictors of recurrence of cancer-associated venous thromboembolism after discontinuation of anticoagulant therapy: a multicenter cohort study.

BACKGROUND: Data on recurrence after the end of anticoagulation for a first event of cancer-associated venous thromboembolism (VTE) are scarce. OBJECTIVES: Our aim was to assess predictors of VTE recurrence during a 1-year follow-up period. METHODS: This study is an analysis of RIETE, an international, multicenter, prospective cohort study of patients diagnosed with VTE. Patients had to have active cancer at the time of VTE and to have withdrawn from anticoagulation after 3 months of full treatment. Analyses were performed using Fine and Gray models, with death as a competing risk, and multiple imputation of missing data was performed by chained equations. RESULTS: Among 14 318 patients with cancer-associated VTE, 3414 had undergone time-limited anticoagulation for at least 3 months. The cumulative incidence function for recurrent VTE was 10.2% (95% CI, 9.1-11.5) at 1 year. Chronic kidney disease (a subhazard ratio [sHR] of 1.08 for 10-mL/min decrease in glomerular filtration rate; 95% CI, 1.02-1.14); cancer of the lung, brain, stomach, esophagus, liver, or ovary (sHR, 3.56; 95% CI, 1.07-11.80; compared with cancer of the oropharynx, larynx, or melanoma); cancer of the pancreas, the biliary tract, or of unknown origin (sHR, 6.86; 95% CI, 1.89-24.85); inferior vena cava filter (sHR, 3.16; 95% CI, 1.75-5.71); postthrombotic syndrome (sHR, 2.09; 95% CI, 1.06-4.15); and residual pulmonary thrombotic obstruction (sHR, 2.58; 95% CI, 1.38-4.82) were predictive of recurrence. Surgery during the 2 months before VTE was predictive of absence of recurrence (sHR, 0.60; 95% CI, 0.40-0.92). CONCLUSION: One year after anticoagulant cessation for cancer-associated VTE, approximately 10% of patients experienced recurrence. Discontinuing anticoagulant therapy seems safe, mainly in surgery-associated VTE.

Ensembl 2023.

Ensembl (https://www.ensembl.org) has produced high-quality genomic resources for vertebrates and model organisms for more than twenty years. During that time, our resources, services and tools have continually evolved in line with both the publicly available genome data and the downstream research and applications that utilise the Ensembl platform. In recent years we have witnessed a dramatic shift in the genomic landscape. There has been a large increase in the number of high-quality reference genomes through global biodiversity initiatives. In parallel, there have been major advances towards pangenome representations of higher species, where many alternative genome assemblies representing different breeds, cultivars, strains and haplotypes are now available. In order to support these efforts and accelerate downstream research, it is our goal at Ensembl to create high-quality annotations, tools and services for species across the tree of life. Here, we report our resources for popular reference genomes, the dramatic growth of our annotations (including haplotypes from the first human pangenome graphs), updates to the Ensembl Variant Effect Predictor (VEP), interactive protein structure predictions from AlphaFold DB, and the beta release of our new website.

Ensembl 2022.

Ensembl (https://www.ensembl.org) is unique in its flexible infrastructure for access to genomic data and annotation. It has been designed to efficiently deliver annotation at scale for all eukaryotic life, and it also provides deep comprehensive annotation for key species. Genomes representing a greater diversity of species are increasingly being sequenced. In response, we have focussed our recent efforts on expediting the annotation of new assemblies. Here, we report the release of the greatest annual number of newly annotated genomes in the history of Ensembl via our dedicated Ensembl Rapid Release platform (http://rapid.ensembl.org). We have also developed a new method to generate comparative analyses at scale for these assemblies and, for the first time, we have annotated non-vertebrate eukaryotes. Meanwhile, we continually improve, extend and update the annotation for our high-value reference vertebrate genomes and report the details here. We have a range of specific software tools for specific tasks, such as the Ensembl Variant Effect Predictor (VEP) and the newly developed interface for the Variant Recoder. All Ensembl data, software and tools are freely available for download and are accessible programmatically.

Ensembl 2020.

The Ensembl (https://www.ensembl.org) is a system for generating and distributing genome annotation such as genes, variation, regulation and comparative genomics across the vertebrate subphylum and key model organisms. The Ensembl annotation pipeline is capable of integrating experimental and reference data from multiple providers into a single integrated resource. Here, we present 94 newly annotated and re-annotated genomes, bringing the total number of genomes offered by Ensembl to 227. This represents the single largest expansion of the resource since its inception. We also detail our continued efforts to improve human annotation, developments in our epigenome analysis and display, a new tool for imputing causal genes from genome-wide association studies and visualisation of variation within a 3D protein model. Finally, we present information on our new website. Both software and data are made available without restriction via our website, online tools platform and programmatic interfaces (available under an Apache 2.0 license) and data updates made available four times a year.