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Reposted by David Ochoa

Konrad @konradjk.bsky.social · 20d

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...

www.nature.com

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David Ochoa @d0choa.bsky.social · 20d

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 · 20d

Excited 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 👇

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Reposted by David Ochoa

Tobi Alegbe @tobioinformatics.bsky.social · Jul 8

🚨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!

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David Ochoa @d0choa.bsky.social · Jun 18

📅 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!

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...

www.linkedin.com

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David Ochoa @d0choa.bsky.social · Jun 18

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 🙏

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David Ochoa @d0choa.bsky.social · Jun 18

🥐 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.

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David Ochoa @d0choa.bsky.social · Jun 18

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!

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David Ochoa @d0choa.bsky.social · Jun 18

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.

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David Ochoa @d0choa.bsky.social · Jun 18

🧬 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.

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David Ochoa @d0choa.bsky.social · Jun 18

🚀 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 👇

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Reposted by David Ochoa

Tuuli Lappalainen @tuuliel.bsky.social · May 6

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...

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Reposted by David Ochoa

Eric Fauman (he/him) @ericfauman.bsky.social · Apr 13

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?

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David Ochoa @d0choa.bsky.social · Mar 28

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 🧬🖥️

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Reposted by David Ochoa

Yasset Perez-Riverol @ypriverol.bsky.social · Mar 28

🚀 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

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David Ochoa @d0choa.bsky.social · Mar 20

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

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David Ochoa @d0choa.bsky.social · Dec 17

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!

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David Ochoa @d0choa.bsky.social · Dec 17

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

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David Ochoa @d0choa.bsky.social · Dec 17

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

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David Ochoa @d0choa.bsky.social · Dec 17

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

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David Ochoa @d0choa.bsky.social · Dec 17

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

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Reposted by David Ochoa

Jeff Spence @jeffspence.github.io · Dec 17

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...

www.biorxiv.org

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Reposted by David Ochoa

bioRxiv Genomics @biorxiv-genomic.bsky.social · Dec 16

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

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Reposted by David Ochoa

Open Targets @opentargets.org · Dec 10

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...

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David Ochoa @d0choa.bsky.social · Dec 6

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-...

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Reposted by David Ochoa

Michel Nivard @michelnivard.bsky.social · Dec 2

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

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