🧬 FUMA v2.0.0 is out, updated by Tanya Phung @ CTG Lab New FLAMES module (effector gene prioritization), new QTLs Analysis module, and expanded xQTL datasets in SNP2GENE fuma.ctglab.nl

Exam prep for a research and statistics exam in 2026! sachaepskamp.com/PL2132_games...

I know that Galton called out for sharing data in 1901

🚨 The preprint for our GWAS of Alzheimer’s disease (AD) is out Preprint: medrxiv.org/content/10.1... 🧵

Proud that the third GWAS for Alzheimer's dementia from the PGC-ALZ working group was just posted online! Huge amounts of work, and what a great collaboration! Check out our exciting findings below 👇 @pgcgenetics.bsky.social #ctglab #alzheimer #dementia #GWAS

🚨 The preprint for our GWAS of Alzheimer’s disease (AD) is out Preprint: medrxiv.org/content/10.1... 🧵

Our new paper is out, in which we developed an approach to transform Polygenic Scores (PGSs) into disorder probabilities (i.e., the absolute lifetime disorder risk). Below a thread 👇 open access link: rdcu.be/eIjvC

The US as viewed by latenight comedians in Europe (it’s 20 secs of Dutch, the rest is English. We are so worried about you all we’re specifically trying to reach you through our latenight I guess…)

Technology can change the world in ways that are unimaginable until they happen. Switching on an electric light would have been unimaginable for our medieval ancestors. In their childhood, our grandparents would have struggled to imagine a world connected by smartphones and the Internet.

As we have learned, genes have dose-dependent effects on psychiatric traits. DOSAGE, it turns out, is a key element that helps unravel mechanisms of gene → pathway → cell type → brain region → diagnosis. Here we developed a framework to characterize cellular processes that mediate genetic effects.

I wrote about how genetic risk works in the context of embryo selection and how people often think about it all wrong. A short 🧵:

📣 New paper published in @natcomms.nature.com‬, where we explored sex differences in local genetic correlations, local heritabilities, and magnitude of effect sizes in quantitative traits. link: rdcu.be/ezuZd 1/7

Thanks! This is amazing! So the term 'Manhattan Plot' is not originally a GWAS term at all. Screenshotting the image here from a 1994 book on nuclear physics, for others who may be interested:

🚨New preprint is out! How do genetic effects on complex traits change with age? In this work, we compare different approaches to obtain age-varying genetic effects, and show how design and modeling choices can impact the conclusions we draw. shorturl.at/17snd A thread 🧵👇

A brilliant article on cancer screening by Siddhartha Mukherjee www.newyorker.com/magazine/202...

📣 Latest from the lab: Performance of deep-learning-based approaches to improve polygenic scores www.nature.com/articles/s41... Its thought deep learning will substantially improve PGS but the reality is MANY have tried but no/little gain has been seen so far. Here we report our negative results.

“I would like to cure brain cancer. I think that's not particularly controversial.” Be that as it may, the NIH terminated that scientist's grant. Here's a huge survey of the 2,500 grants that NIH has killed or delayed...so far. Gift link: nyti.ms/43Jz1yJ

Science-integrity project will root out bad medical papers ‘and tell everyone’ Thrilled to announce this new $900,000 project headed by @jamesheathers.bsky.social

#ctglab is hiring! We have #vacancies! 2 PhD & 2 postdoc positions, in #statistical #genetics and/or #bioinformatics - if you like GWAS, method development and linking with biology - check these out 👇 werkenbij.vu.nl/vacatures/tw... werkenbij.vu.nl/vacatures/po... werkenbij.vu.nl/vacatures/po...

Regeneron buys 23andMe out of bankruptcy https://www.ft.com/content/362bcad4-8f4a-42b4-ab86-38821d74352f

Personally I think it's totally defensible for the head of a meteorology department to say, "you can't work here unless you believe in climate change." That department is going to end up with zero conservatives in it but it's not the department that needs to change!

I’m interested in how we can better communicate genetic science, when cool soundbites may confuse more than they clarify. An example: “You share 98.8% of your genes with a chimpanzee!” Is this true? What does it really mean? Let’s unpack this oft-quoted pearl of wisdom in a 🧵 all about sharing. 🧪1/n

Our ability to predict a person's risk of heart disease keeps getting better, even among those previously considered at low risk by traditional clinical criteria @naturemedicine.bsky.social by my team @scripps.edu www.nature.com/articles/s41...

So happy to finally see this paper out in @natcomms.nature.com. rdcu.be/ehQsd “Correcting for volunteer bias in GWAS increases SNP effect sizes and heritability estimates”. A thread on our findings!

Most people haven’t heard of this test, which is available in the US. It accurately predicts Alzheimer’s (not just if there’s a risk, but when). It is modulated by exercise and likely other lifestyle factors. Here’s (almost) everything we know about it erictopol.substack.com/p/the-breakt...

I am so excited to share our review on microglial heterogeneity @natureneuro.bsky.social! It was a fantastic effort by the lab, led by @c9laura72.bsky.social and Alma Mohebiany. We provide a critical view on the plethora of microglial cell states in health and disease. www.nature.com/articles/s41...

CEOs upset about Trump’s tariffs sound like mob bosses shouting “I thought we had a deal!” at the Joker.

Effect of Disclosing a Polygenic Risk Score for Coronary Heart Disease on Adverse Cardiovascular Events www.ahajournals.org/doi/10.1161/...

Interesting: "Linear combinations of independently optimised scores [across populations] consistently outperformed current jointly optimised multi-source methods, while being substantially more computationally efficient" By Oliver Pain www.medrxiv.org/content/10.1...

In every civilization, people end up sorted into levels of socio-economic status (SES). We explore the history, present, and future of scientific research on the complicated relationship between SES and DNA in @naturehumbehav.bsky.social💰🧬🎓 Link: rdcu.be/efacK Thread below 👇🏽

Just found out NIH has officially canceled our grant, a longitudinal study of Alzheimer's disease in Black Americans. I cannot even put into words how angry I am. The truth is they are canceling it because it has Black in the title. That's it, there is no other reason to do this.

Why do journal submission pages look like they’re from 2005

Get in dorks, we're going protesting! STAND UP FOR SCIENCE WITH US ON MARCH 7TH, 2025 WASHINGTON DC AND EVERY STATE CAPITOL Because science is for everyone! Find us at www.standupforscience2025.org #standupforscience2025 #scienceforall #sciencenotsilence

Incredibly proud to see our latest work out in Nature Genetics: www.nature.com/articles/s41... Here we share our FLAMES framework, which predicts the effector genes in GWAS loci with state-of-the-art precision🔥 Special thanks to @daniposthu.bsky.social A full thread describing findings below!

Just out from #ctglab by @mjschipper.bsky.social - our new tool FLAMES 🔥🔥, to identify the most likely causal genes in GWAS loci, using machine learning techniques, thoroughly benchmarked and freely available Paper: rdcu.be/d9iQP Code: github.com/Marijn-Schip...

FLAMES - a new tool to predict effector genes at GWAS loci www.nature.com/articles/s41...

Modern GWAS can identify 1000s of significant hits but it can be hard to turn this into biological insight. What key cellular functions link genetic variation to disease? I'm very excited to present our new work combining associations and Perturb-seq to build interpretable causal graphs! A 🧵

Great interview with Dorret Boomsma, who has recently joined our lab www.geneticsnetworkamsterdam.org/blog/2025/01...

I posted a couple days ago about our new paper on building causal graphs from genetic associations + Perturb-seq. Here I want to expand on the value of using DIRECTIONAL information contained in LoF burden tests.🧵 [work led by @minetoota.bsky.social ] bsky.app/profile/jkpr...

An embarrassment of riches

New study from the @pgcgenetics.bsky.social: Multi-ancestry GWAS of MDD in over half a million cases and 4 million controls. www.cell.com/cell/fulltex...

RIP Aaron Swartz, who took his own life 12 years ago today en.wikipedia.org/wiki/Aaron_S... Reddit, digital rights and making academic knowledge open

This is not a smart man.

www.wnycstudios.org/story/91684-... Love this old radiolab episode including a nice segment with Carl Zimmer

Just out in @naturehumbehav.bsky.social ! We focused on the causes & impact of self-report error in the UK Biobank. We found that reporting error does not occur at random, is not independent of other participation behaviours, and can complicate the interpretation of GWA findings shorturl.at/N4Qc6

New post: My substack is back, finally! I meant to keep this to 1,000 words but I failed. In any case, here's a round up of 5 major medical breakthroughs in 2024.

Anais Thijssen & Jana Hirzinger interview #GENEAmsterdam member Dirk Smit, Assistant Professor electrophysiology and genetics: How does he combine genetics, which is mostly stable over the lifetime with EEG, where the signal changes every millisecond? www.geneticsnetworkamsterdam.org/blog/2024/12...

Some said it couldn’t be done. That it was impossible; ridiculous; absurd. But @tomchivers.bsky.social and I have done it: recorded a whole podcast episode about collider bias. www.thestudiesshowpod.com/p/episode-57...