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Open Targets

@opentargets.org
719 followers 38 following 293 posts

Public-private partnership using human genetics and genomics data for systematic drug target identification and prioritisation. blog.opentargets.org

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Reposted by Open Targets
Saez-Rodriguez Group @saezlab.bsky.social · 07/09/2026
🧵 Introducing Karenina, an open-source framework to evaluate LLMs & agents: doi.org/10.64898/202...
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Open Targets @opentargets.org · 28/09/2026
The Open Targets Platform autumn (26.09) release is out now! 🍂 It's packed with genetics updates, with: 🧬 1.24 million new molecular QTL credible sets 🧬 2 new sources of gene burden data 🧬 Updates from the GWAS Catalog 🧬 Genetic constraint data for X- and Y-linked genes through gnomAD and more!
26.09 release graphic highlights some of the major updates, including 1.24 million more molecular QTL credible sets, from GTEx v10, MAGE, and IBDverse, through the eQTL Catalogue. Genes & Health and BRaVa as new sources of gene burden. 14,690 new studies from the GWAS Catalog. Genetic constraing for X- and Y- linked genes through gnomAD v4.1.1. A Platform metrics page.
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Open Targets @opentargets.org · 12/08/2026
This work, the largest study of its kind, was recently published in Nature and Nature Genetics. Find out more about the origins of the IBDverse on the blog: blog.opentargets.org/origins-of-t...
blog.opentargets.org
Origins of the IBDverse: how a conversation in a carpark became one of the largest gut cell studies
In 2015, Tim Raine and Carl Anderson had the ambitious idea of using single-cell sequencing to gain insights into the genes and cell types causally driving Inflammatory Bowel Disease (IBD), a project ...
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Open Targets @opentargets.org · 12/08/2026
After persuading funding bodies—Open Targets, the @sangerinstitute.bsky.social, and the Crohn’s and Colitis Foundation—that this was worth the gamble, they launched the “IBDverse”, and processed almost 1200 samples from over 600 patients. Nothing on this scale had ever been attempted before.
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Open Targets @opentargets.org · 12/08/2026
Ambitious science can start in the most unglamorous places. In 2015, gastroenterologist Tim Raine and geneticist Carl Anderson had a casual conversation in an underground carpark, which led to the largest single-cell dataset of Inflammatory Bowel Disease (IBD)-relevant tissues
Two men smile at the camera while posing in front of the entrance to an underground car park on a sunny day.
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Open Targets @opentargets.org · 04/08/2026
We talked to Menatallah Ghouraba, Rebecca McIntyre, and Cristina Cotobal Martin to get a behind-the-scenes perspective on the project. The IBDverse was a collaboration between Open Targets, the Wellcome Sanger Institute, and @cuh.nhs.uk Watch the whole story on YouTube: youtu.be/Hy0eqTiZtr0
youtu.be
Building the IBDverse: the science and team behind a landmark study of inflammatory bowel disease
YouTube video by Open Targets
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Open Targets @opentargets.org · 04/08/2026
6 years 646 patients 1193 samples 100 endoscopists 9 lab scientists 3 postdocs 2 PhD students 502 courier runs from Addenbrooke’s Hospital to @sangerinstitute.bsky.social IBDverse is the largest single-cell dataset of Inflammatory Bowel Disease (IBD)—and generating the data for it was no mean feat
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Open Targets @opentargets.org · 28/07/2026
"Being involved with the Open-IBD study has been a fantastic experience. The research team have been welcoming and responsive, not only listening to our suggestions and experiences, but also making tangible changes to the project based on our input."
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Open Targets @opentargets.org · 28/07/2026
The Open-IBD project team present the key role that PPIE has played in their longitudinal study of inflammatory bowel disease (IBD), its impact on the members of the Lived Experience Advisory Panel (quoted here) and the research team.
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Open Targets @opentargets.org · 28/07/2026
Patient and public involvement and engagement (PPIE) has become a fundamental part of scientific research, improving the relevance and quality of the work. But who should you involve in PPIE? At what stage of the project should you involve them, and how?
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Open Targets @opentargets.org · 28/07/2026
"Patients know what it’s like to live with these conditions on a daily basis and the impact it has on our lives. By getting involved, we can help clinicians and researchers understand what really matters to us, so future research and treatments genuinely meet our needs." fg.bmj.com/content/earl...
fg.bmj.com
Patient and public involvement and engagement in research: who, why, when and how to get it right
Patient and public involvement and engagement (PPIE) refers to the different ways those with lived experience, including patients, family, friends and carers, and the public engage with the design, de...
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Open Targets @opentargets.org · 21/07/2026
This provides a starting point to deciphering the mechanisms that underpin MASLD, which could lead to better treatments and diagnosis of patients. Their approach could be applied to similar diseases where access to longitudinal data is challenging www.nature.com/articles/s42...
nature.com
A data-driven framework reconstructs the molecular continuum of human MASLD progression - Nature Metabolism
A trajectory-based molecular framework reveals coordinated temporal shifts in metabolic, inflammatory and fibrogenic mechanisms across the human MASLD spectrum.
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Open Targets @opentargets.org · 21/07/2026
In parallel, they used a histology-based patient ranking to stratify patients into sequential overlapping groups, to capture the continuous trajectory of the disease.
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Open Targets @opentargets.org · 21/07/2026
Using this methodology, the team created a MASLD-related regulatory network that captures both signalling pathway activities and cellular response patterns.
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Open Targets @opentargets.org · 21/07/2026
Published in Nature Metabolism, the study establishes a methodology to integrate multi-modal MASLD patient data, by anchoring changes in gene expression to the histological changes that characterise MASLD progression and are common to all patients
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Open Targets @opentargets.org · 21/07/2026
“We hope our framework will help drive a conceptual shift in how MASLD is studied and understood.” A new study reframes Metabolic dysfunction-Associated Steatotic Liver Disease as a continuous process, better capturing the underlying disease biology www.nature.com/articles/s42...
nature.com
A data-driven framework reconstructs the molecular continuum of human MASLD progression - Nature Metabolism
A trajectory-based molecular framework reveals coordinated temporal shifts in metabolic, inflammatory and fibrogenic mechanisms across the human MASLD spectrum.
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Reposted by Open Targets
Evangelia Petsalaki @epetsalaki.bsky.social · 14/07/2026
Our MASLD paper is finally out @naturemetabolism.bsky.social @ebi.embl.org @opentargets.org ! Fantastic collaboration with Toni Vidal-Puig's group in the IMS, UCam (co-led), Papatheodorou @earlhaminst.bsky.social and other coauthors, led by Ioannis Kamzolas and Thodoris Koutsandreas. Check it out!
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Open Targets @opentargets.org · 14/07/2026
From this, they found 57 genes that could be measured in the blood and used to predict where patients are in the disease trajectory This biomarker panel outperformed current non-invasive diagnostic tests, and could complement and refine existing tests, or pending validation, replace them Congrats!
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Open Targets @opentargets.org · 14/07/2026
Their method anchors changes in gene expression to the histological changes that characterise MASLD progression and are common to all patients. This work reframes MASLD as a continuous process rather than a series of distinct disease stages.
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Open Targets @opentargets.org · 14/07/2026
Previously known as non-alcoholic fatty liver disease, MASLD is one of the leading causes of chronic liver dysfunction worldwide, affecting 1 in 3 adults The team, led by Ioannis Kamzolas and Thodoris Koutsandreas at @ebi.embl.org, established a new methodology to integrate multi-modal patient data
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Open Targets @opentargets.org · 14/07/2026
Out now in Nature Metabolism! 🖥️🧬 An Open Targets project has identified a set of plasma proteins that could be used to diagnose and monitor patients with Metabolic dysfunction-Associated Steatotic Liver Disease (MASLD) www.nature.com/articles/s42...
nature.com
A data-driven framework reconstructs the molecular continuum of human MASLD progression - Nature Metabolism
A trajectory-based molecular framework reveals coordinated temporal shifts in metabolic, inflammatory and fibrogenic mechanisms across the human MASLD spectrum.
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Open Targets @opentargets.org · 07/07/2026
The team used over 1.6 million variants in the Open Targets Platform to generate over 148,000 dose-response-like gene-phenotype relationships. The genes were then ranked for their therapeutic potential, identifying many potential new targets.

Image caption: Overview of the VIDRA framework. 


(a) Data inputs. VIDRA integrates five complementary sources of genetic evidence: expression quantitative trait loci (eQTLs), protein quantitative trait loci, coding GWAS variants, AstraZeneca PheWAS variants, and ClinVar variants, together with gene-level rare variant burden tests. 


(b) Variant effect estimation. Each variant contributes a point to a dose-response model, where y represents disease effect and x represents either QTL effect size or a protein function score. Gene-level burden tests provide anchoring information for loss-of-function effects. Evidence is integrated using a hierarchical Bayesian model to estimate a gene–phenotype slope. 

(c) Outputs. For each gene–phenotype pair, VIDRA produces a posterior slope estimate, a posterior probability quantifying confidence in a non-zero slope, a Therapeutic Potential Score derived from a machine-learning classifier trained on approved drug targets, and a predicted direction of therapeutic modulation inferred from the slope sign. 

(d) Interpretation of slope direction. The VIDRA slope captures the relationship between protein activity and disease risk across the spectrum from loss-of-function (LoF) to gain-of-function (GoF). Positive slopes indicate that increased protein activity is associated with increased disease risk, whereas negative slopes indicate that increased protein activity is protective. Directionality is inferred from the combined genetic evidence and does not require explicit GoF or LoF annotation.
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Open Targets @opentargets.org · 07/07/2026
VIDRA is out now on medRxiv! Variant-Informed Dose-Response Analysis (VIDRA) is a computational framework which infers genetic dose-response relationships by integrating trait-associated variants across a spectrum of allele frequencies and functional consequences. www.medrxiv.org/content/10.6...
medrxiv.org
Genetic dose-response modelling predicts drug mechanisms, dosing, and adverse events
Understanding how changes in gene function affect disease risk is central to drug development. Genetic variants are natural perturbations of gene activity and provide an opportunity to systematically ...
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Open Targets @opentargets.org · 30/06/2026
He studies the genetics of neurodegeneration, specifically autophagy and lysosomal pathways which are disease hallmarks His team uses the rare familial forms of Alzheimer's and Parkinson's as genetic anchors to look at the extremes of the disease Find out more: blog.opentargets.org/spotlight-le...
blog.opentargets.org
Spotlight: Lewis Evans
Lewis Evans is an Open Targets project lead and Senior Staff Scientist at the Wellcome Sanger Institute. He studies the genetics of neurodegeneration. As part of his project NeuroFlux, Lewis interacts...
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Open Targets @opentargets.org · 30/06/2026
He estimates his team has carried out over 100 whole genome CRISPR screens, and to date they estimate that they’ve grown at least 5 billion neurons. “But then, a human brain has about 80 billion cortical neurons, so we’re not quite there yet!”
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Open Targets @opentargets.org · 30/06/2026
“The scale at which we’re doing things, and in such an unbiased way, means that anything could come out of it. You have to be open to a new theory or something completely out of the ordinary happening.” Lewis Evans is @sangerinstitute.bsky.social Senior Staff Scientist and Open Targets project lead
A man gestures at a scientific poster on a wall of posters, pointing something out to the woman standing next to him.
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Open Targets @opentargets.org · 30/06/2026
The Open Targets Platform 26.06 release is out now! ✋ 🔴 Find out about all the updates on the blog: blog.opentargets.org/open-targets...
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Open Targets @opentargets.org · 23/06/2026
Find out more: Find out more: blog.opentargets.org/spotlight-mu...
blog.opentargets.org
Spotlight: Muzlifah Haniffa
"I’m a dermatologist, and my research straddles the disciplines of genomics, immunology, skin, and human development. I want to make a difference to human health, focusing on understanding how the hum...
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Open Targets @opentargets.org · 23/06/2026
“There isn’t anywhere else in the world where you’ve got genomics, computational, clinical, biological, and pharmaceutical expertise all in one group or consortium.” @mhaniffa.bsky.social discusses her experience working with partners across industry and academia as part of her Open Targets project
Next to a photo of Muzlifah Haniffa, Deputy director and head of the cellular genomics prorgamme at the Wellcome Sanger Institute, a quote reads: working through Open Targets has allowed us to partner with exactly the right people, without constraints. This kind of collaboration creates a real sense that we can accelerate progress towards clinical translation—moving faster and more effectively thanks to the breadth of expertise from many different disciplines.
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Open Targets @opentargets.org · 18/06/2026
How do you ensure the stability of a platform with millions of data points updated every release? You start testing patterns In the last release of the Open Targets Platform, we implemented automated end-to-end testing into our development workflow 🧬🖥️ blog.opentargets.org/end-to-end-t...
blog.opentargets.org
Ensuring stability of the Open Targets Platform: the case for automated end-to-end testing
As a platform grows in complexity, maintaining stability becomes increasingly difficult. The Open Targets Frontend Team has introduced automated end-to-end testing to ensure that core user journeys an...
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Reposted by Open Targets
Wellcome Sanger Institute @sangerinstitute.bsky.social · 15/06/2026
New study into Crohn’s disease helps explain why gut inflammation persists, and could help unlock more targeted treatments for patients. Researchers analysed millions of gut cells, uncovering lasting molecular changes and key inflammatory immune cells. 👇 www.sanger.ac.uk/news_item/ce...
sanger.ac.uk
Cellular study maps gene activity changes across more than 50 gut cell types in Crohn’s disease
The latest IBDverse study identifies the genes expressed in Crohn's disease, revealing a lasting 'molecular scar' in the gut lining.
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Open Targets @opentargets.org · 15/06/2026
This work, part of a broader ‘IBDverse’ project in the Anderson lab, was a collaboration between Open Targets, the @sangerinstitute.bsky.social, and @cuh.nhs.uk Congratulations to the team!
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Open Targets @opentargets.org · 15/06/2026
In particular, they found an upregulation of MHC-I driven by interferon, which persists in progenitor cells after visible inflammation heals. They also point to ITGA4+ macrophages as key drivers of inflammation, acting through JAK/STAT signalling and cytokine expression.
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Open Targets @opentargets.org · 15/06/2026
The team led by @krzakmonika.bsky.social, @tobioinformatics.bsky.social, Leland Taylor, and @gastrogrj.bsky.social, uncover genes aberrantly expressed in Crohn’s disease, where expression is specific to given cell types/cellular responses, and that are most likely to have a causal role in disease
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Open Targets @opentargets.org · 15/06/2026
Out now in Nature Genetics! The largest single-cell RNA sequencing dataset of terminal ileal biopsies profiles 1.1 million cells from over 100 Crohn’s disease patients and over 200 healthy controls. Crohn’s disease is a type of inflammatory bowel disease (IBD) www.nature.com/articles/s41...
nature.com
Single-cell RNA sequencing of terminal ileal biopsies identifies signatures of Crohn’s disease pathogenesis - Nature Genetics
IBDverse is a single-cell RNA atlas of terminal ileal biopsies comprising 1.1 million cells from 111 patients with Crohn’s disease and 232 healthy participants. Analysis of the data identifies genes, ...
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Open Targets @opentargets.org · 09/06/2026
Mathew Garnett was one of the first group leaders to receive an Open Targets project award. He discusses how Open Targets projects brings together academic and industry teams in a unique research partnership model. Find out more: blog.opentargets.org/how-open-tar...
blog.opentargets.org
How Open Targets bridges academic science and pharmaceutical expertise
Open Targets’ most successful collaborations are built on strong connections and regular communication between academic and industry partners at every stage of a project’s lifecycle. A decade after it...
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Open Targets @opentargets.org · 09/06/2026
“Open Targets has had the single biggest impact in integrating the @sangerinstitute.bsky.social and @ebi.embl.org science, above and beyond any other initiative I’ve seen in that time." 🤝
22% of active Open Targets projects involve collaborations between EMBL-EBI and the Wellcome Sanger Institute. The accompanying graphic shows shaking hands as if making a business deal, with one hand in EBI green and one in Sanger blue.52% collaborate across academic teams within their institute. The accompanying graphic shows shaking hands, with the sleeves either two shades of EBI green or two shades of Sanger blue. 100% collaborate with Open Targets industry partners. The accompanying graphic shows shaking hands on a yellow background representing that all of them involve industry partners.
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Open Targets @opentargets.org · 03/06/2026
Congratulations to the team at the @sangerinstitute.bsky.social, Open Targets, and Cambridge University Hospitals NHS Foundation Trust!
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Open Targets @opentargets.org · 03/06/2026
These findings help resolve the biology of IBD, and nominate targets for drug development or repurposing. A similar approach could be applied to other complex diseases to nominate effector genes from GWAS loci.
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Open Targets @opentargets.org · 03/06/2026
By mapping eQTLs at three progressively higher resolutions, they found over 84,000 eQTLs in 251 cellular annotations. Notably, many eQTLs were only found at higher resolutions, and cell-type-level eQTLs were more than twice as likely to colocalise with IBD GWAS loci than tissue-level eQTLs.
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Open Targets @opentargets.org · 03/06/2026
To test this hypothesis, they generated the largest collection of single-cell RNA sequencing data from IBD-relevant sites (terminal ileum, rectum, blood), resulting in nearly 2.2 million single-cell transcriptomes from over 400 individuals including 125 with IBD.
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Open Targets @opentargets.org · 03/06/2026
@tobioinformatics.bsky.social @bradleyomics.bsky.social hypothesised that colocalising GWAS signals with cell-type-specific single-cell eQTLs would more readily nominate disease effector genes, since regulators active only in specific cellular contexts are more likely to escape purifying selection
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Open Targets @opentargets.org · 03/06/2026
Genetics are a good starting point for drug development, but while Genome Wide Association Studies have nominated loci for IBD, only a fraction of these have successfully been linked to causal genes with current eQTL discovery methods, which often rely on bulk RNA sequencing of heterogeneous tissues
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Open Targets @opentargets.org · 03/06/2026
We need new drugs for IBD. Currently, 1 in 123 people suffer from Crohn’s, ulcerative colitis or some form of IBD in the UK, but there is no cure, and existing drugs can be ineffective or lose efficacy over time.
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Open Targets @opentargets.org · 03/06/2026
Out now in Nature! Genetic analysis of the largest single-cell dataset of Inflammatory Bowel Disease (IBD)-relevant tissues nominates effector genes and cell types at over half of known IBD loci, including 74 for which this is the first candidate effector gene 🖥️🧬 www.nature.com/articles/s41...
nature.com
Cell-type-resolved genetic variation shapes inflammatory bowel disease risk - Nature
Single-cell mapping of cis-expression quantitative trait loci in inflammatory bowel disease revealed distal, enhancer-enriched variants detected at the cell-type level more frequently co-loc...
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Open Targets @opentargets.org · 01/06/2026
We're at #ESHG2026! Come say hello and find out about current Open Targets projects. See you there!
Under a banner with the ESHG 2026 graphic, a list of presenters, title sessions, and timings.

Gosia Trynka, Chair, S01. Hunting for effector genes from GWAS studies, June 13, 8:30

Chair, C17. In QTLs We Trust: Linking Genotype to Function, June 14, 10:30

Chair, S11. High-throughput perturbation methods to study disease, June 14, 14:00

Chair, S12. Blood as a window: genetic insights into health, aging, and immune function, June 15, 08:30

Tobi Alegbe, Chair, C17. In QTLs We Trust: Linking Genotype to Function, June 14, 10:30Under a banner with the ESHG 2026 graphic, a list of presenters, title sessions, and timings.

Haerin Jang, P16.032.B Single cell eQTL mapping of immune response regulation in systemic lupus erythematosus patients, Poster viewing with authors June 13, 16:00

Yakov Tsepilov, C32.6 Integration of 100,526 public GWAS defines pervasive pleiotropy and informs drug-target selection, June 15, 11:45

Ellen McDonagh, E06.2 Understanding rare diseases with digital twins, June 15, 17:45
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Reposted by Open Targets
Ben Lehner @benlehner.bsky.social · 28/05/2026
Excited to release #OpenSplice - the impact of >500,000 mutations on the alternative splicing of 600 human exons www.biorxiv.org/content/10.6... Led by @gioia-quarantani.bsky.social + funded by @opentargets.org ‬ @sangerinstitute.bsky.social @crg.eu #cshlsymp26 #RNA2026 @rnasociety.bsky.social
biorxiv.org
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Open Targets @opentargets.org · 27/05/2026
OpenSplice is a powerful resource to help interpret disease-causing variants in the clinic. Expanding OpenSplice to cover the entire human transcriptome would also allow the development of highly accurate predictive models Congratulations to the whole team! www.biorxiv.org/content/10.6...
biorxiv.org
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Open Targets @opentargets.org · 27/05/2026
The team, led by @gioia-quarantani.bsky.social in @benlehner.bsky.social's group, found that more than 60% of variants in the study altered exon inclusion. Their data also reveal that the architecture of splicing regulatory elements is surprisingly diverse.
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Open Targets @opentargets.org · 27/05/2026
But prior to this study, we had only evaluated a small fraction of the possible genetic variants that could affect splicing.
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