David Ochoa

🚨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!

25.06 Platform Release Q&A | LinkedIn Join our Q&A session about the Open Targets Platform June release. The team will run through the main points of the release, after which they will open the floor to questions. The walkthrough will b...

📅 Join our Q&A drop-in on June 19 at 3pm BST to explore the new features and ask questions:
🔗 www.linkedin.com/events/25-06...

📰 Read more on our blog:
🔗 blog.opentargets.org/open-targets...

Thanks @helenacornu.bsky.social for the infographic!

Every update helps complete the puzzle 🧩 of target discovery.

Huge thanks to our data providers, partners, and the entire Open Targets team for their tireless work 🙏

🥐 We’ve also redesigned the data downloads section — now built on the ML Commons Croissant standard.

Better documentation + improved AI-readiness = easier use for researchers and developers alike.

More highlights from the release:
🧬 New gene burden studies
💊 Expanded pharmacogenetics annotations
🧠 Interacting protein evidence from IntAct, Reactome, SIGNOR, STRING
🔬 First look at our molecular structure viewers!

Over the past 3 months, we’ve added GWAS from:

VA Million Veteran Program

210+ publications
Including the Nature meta-analysis of osteoarthritis (April 2024) 🧠

All integrated + contextualised with existing data + functional genomics.

🧬 One of our big promises with bringing Open Targets Genetics to the Platform was keeping post-GWAS analysis fresh and integrated.

This release brings a 36% increase in GWAS credible sets, thanks to collaboration with the @gwascatalog.bsky.social and enhanced pipelines.

🚀 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

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 ...

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...

We might not get everything right from the first shot. Still, we hope that by providing an open framework and the community's help, we could consolidate our collective understanding of disease-causing genetics. Stay tuned!

The merged product will bring the best of both worlds in a single web application, covering all journeys from identifying the likely causal signals to the prioritising factors relevant to target progression

This update will power our current target identification coverage, as well as the mechanistic interpretation and biological context

The update will include a refreshed post-GWAS analysis covering state-of-the-art data and methodologies, resulting on 2.5M GWAS and molQTL credible sets, colocalisation analysis and L2G predictions

From next spring, the Open Targets Platform will incorporate the best of Open Targets Genetics into an integrated drug discovery platform 🧵

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...

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 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-...

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

Instarted making a list the other day, with the help of others adding their own faves: github.com/MichelNivard...

crispy morning in the genome campus…

plain and simple 👌

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.

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...

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...

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...