David Ochoa
@d0choa.bsky.social
Target discovery | Computational Biology | Human Disease Genetics | ML | Cloud computing - @opentargets.org - @ebi.embl.org
🧬 New preprint: "The Human Pleiotropic Map of GWAS Associations and Therapeutic Implications" Why do some genetically supported drug targets succeed in the clinic while others fail? Across 100,526 GWAS, the same evidence flags constrained gene functions rarely safe to modulate.
The Open Targets Platform spring 🌼 release is out — and this one marks the beginning of something we've been building towards for a while.
The needle in the haystack problem: spotting novel drug targets among redundant evidence. Our solution? A time-series novelty metric for Open Targets Platform associations. Thanks to Coté Falaguera & @opentargets.org partners for making this happen.
Open Targets@opentargets.org · 7mo agoOut now in Nature Communications! 🧬🖥️ An Open Targets team developed a metric for the novelty of a target in the context of a disease, according to current available knowledge. This allows drug discovery scientists to easily identify potentially novel targets www.nature.com/articles/s41...
🚀 Announcing the Official @opentargets.org MCP! We've partnered with @anthropic.com to give AI seamless access to high-quality genetic and target-discovery data. Open for the entire community to accelerate therapeutic development. Read more at blog.opentargets.org/official-ope...
Introducing the official Open Targets Platform Model Context Protocol
We have released the first iteration of a dedicated MCP server to bring our systematic target discovery capabilities to Large Language Model (LLM)-based workflows.
blog.opentargets.org
Open Targets@opentargets.org · 7mo agoIntroducing the official Open Targets Platform Model Context Protocol 🧬🖥️ In partnership with @anthropic.com, we’ve created an MCP server making Open Targets Platform data accessible to AI-powered tools and agents Try it out and watch out for future releases: mcp.platform.opentargets.org/mcp
A project many years in the process, we’re pleased to present our work on multi-ancestry meta-analysis across a boatload of traits in the UK Biobank: www.nature.com/articles/s41...
Pan-UK Biobank genome-wide association analyses enhance discovery and resolution of ancestry-enriched effects - Nature Genetics
Genome-wide analyses for 7,266 traits leveraging data from several genetic ancestry groups in UK Biobank identify new associations and enhance resources for interpreting risk variants across diverse p...
nature.com
If you care about regulatory variants don’t miss the E2G extension of the @opentargets.org Platform. There are synergies that only a fully open science allows and this is a good one!
Jesse Engreitz@jengreitz.bsky.social · 11mo agoExcited for a major milestone in our efforts to map enhancers and interpret variants in the human genome: The E2G Portal! e2g.stanford.edu This collates our predictions of enhancer-gene regulatory interactions across >1,600 cell types and tissues. Uses cases 👇 1/
🚨New preprint just dropped 🚨 medrxiv.org/content/10.1101/2025.06.24.25330216 The main output from my PhD is finally public and we’re SUPER excited about the findings! If you’re interested in what we learnt about IBD with a massive 700+ sample sc-eQTL dataset of the gut, read on!
🚀 The Summer ☀️ @opentargets.org Platform release is here! If you thought the last update was big… just wait till you see what’s inside. A quick thread on the highlights 👇
Our new contribution to the quest to find causal GWAS genes! Sam Ghatan from my lab at @nygenome.org led a systematic comparison of eQTLs and CRISPRi+scRNA-seq screens. TL;DR: they provide highly complementary insights, with ortogonal pros and cons. 🧵👇 www.biorxiv.org/content/10.1...
The most famous heuristic in mapping gwas snps to genes is "it's usually the closest gene". But only slightly less well-known is this: consider the colocalized phenotypes. That is, a genetic variant seldom disrupts exactly one phenotype. What else does tugging on that thread do?
Big thanks to the community for the great feedback we are receiving on the spring @opentargets.org Platform release. There are many positive and new ideas for improving our scientific interpretation and products. Feedback is a critical aspect of an open project's lifecycle. Please keep it coming 🧬🖥️
🚀 Big news! We've just published the official guidelines for submitting affinity proteomics data to PRIDE @pride-ebi.bsky.social (supported technologies Olink & SomaScan)! Get ahead of the curve—check them out & start your submissions! 👇 🔗 github.com/PRIDE-Archiv... #Proteomics #Olink #SomaScan
github.com
The @opentargets.org Platform Spring 🌼 release brings a step-change in how we address common disease genetics. We included the results of a large-scale analysis on GWAS and functional genomics studies to inform target selection further 🧬 👩💻 blog.opentargets.org/a-step-chang...
A step-change in common disease genetics in the Open Targets Platform
We identified an opportunity to create a unified resource to seamlessly access human genetic and target discovery information. The Platform now integrates and evaluates gene-disease associations from ...
blog.opentargets.org
From next spring, the Open Targets Platform will incorporate the best of Open Targets Genetics into an integrated drug discovery platform 🧵
What do GWAS and rare variant burden tests discover, and why? Do these studies find the most IMPORTANT genes? If not, how DO they rank genes? Here we present a surprising result: these studies actually test for SPECIFICITY! A 🧵on what this means... (🧪🧬) www.biorxiv.org/content/10.1...
Specificity, length, and luck: How genes are prioritized by rare and common variant association studies
Standard genome-wide association studies (GWAS) and rare variant burden tests are essential tools for identifying trait-relevant genes. Although these methods are conceptually similar, we show by anal...
biorxiv.org
Specificity, length, and luck: How genes are prioritized by rare and common variant association studies https://www.biorxiv.org/content/10.1101/2024.12.12.628073v1
Out now! A look back at all the changes to the Open Targets Platform in the past two years 🖥️🧬 We've focused on adding data and analyses to help build therapeutic hypotheses, from expanding our associations page...
In the upcoming NAR issue, we summarise the last 2 years of updates in the @opentargets.org Platform. One step at a time... academic.oup.com/nar/advance-...
Instarted making a list the other day, with the help of others adding their own faves: github.com/MichelNivard...
GitHub - MichelNivard/awesome-complex-trait-genetics: A list of awesome tools for complex trait genetics.
A list of awesome tools for complex trait genetics. - MichelNivard/awesome-complex-trait-genetics
github.com
Moving day at @opentargets.org It always amazed me the UK ability to appreciate remarkable scientists. The new @ebi.embl.org building couldn’t be named after a more inspirational figure
My group's work dissecting the contribution of common variants to rare neurodevelopmental conditions is now out at nature.com/articles/s41..., led by co-first authors Qinqin Huang (not yet on blue sky) and @emiliewigdor.bsky.social . See below for Emilie's tweetorial.
Examining the role of common variants in rare neurodevelopmental conditions - Nature
Patients with neurodevelopmental conditions without a monogenic diagnosis have a higher polygenic burden than those with a monogenic diagnosis. Non-transmitted common all...
nature.com
Emilie Wigdor@emiliewigdor.bsky.social · 2y ago📣 Big news! Our tag-team effort on common variants in rare neurodevelopmental conditions is now out in Nature 📣 Co-first authoring with the brilliant Qinqin Huang🌟—proof that teamwork does make the dream work. 💪 www.nature.com/articles/s41...
Resharing here a recent X post. In this preprint, we introduce an improved version of NanoSeq, a duplex sequencing protocol with <5 errors per billion bp in single DNA molecules, and use it to study the somatic mutation landscape of oral epithelium in >1000 people. 1/ www.medrxiv.org/content/10.1...
Somatic mutation and selection at epidemiological scale
As we age, many tissues become colonised by microscopic clones carrying somatic driver mutations ([1][1]–[10][2]. Some of these clones represent a first step towards cancer whereas others may contribu...
medrxiv.org
To complete the healing it would be good to start thinking who are we missing here 🦋
Models for predicting the effect of genetic variation have come a long way in the last few years. When it comes to diagnosis and preventative care, how can we make safe and yet efficient use of them? Here are some of our thoughts authors.elsevier.com/c/1k7J9_4GsX...
authors.elsevier.com
Finally, a newly minted program in Therapeutic Genomics: www.paediatrics.ox.ac.uk/Study/therap... Combining expertise across Oxford with global collaborators to harness genomic approaches and technologies to accelerate the development of effective and safe genome-targeted therapies. End 🧵
Therapeutic Genomics Centre, DPhil Programme
paediatrics.ox.ac.uk
Regenxbio $RGNX says gene therapy strengthened boys with Duchenne muscular dystrophy Pivotal study started, top-line data could come early 2026. FDA accelerated approval filing to follow. www.statnews.com/2024/11/18/d... $SRPT
Regenxbio says gene therapy strengthened boys with Duchenne muscular dystrophy
Based on a small trial with positive muscle performance data, Regenxbio is expected to pursue approval of its gene therapy for Duchenne muscular dystrophy.
statnews.com
First day on bsky. A fresh start. A chance to do better, to be kind, to listen other voices. 👋 Hello everyone
