LightNews
kauralasoo.bsky.social
Kaur Alasoo
@kauralasoo.bsky.social
720 followers 280 following 240 posts
Associate Professor of Bioinformatics at University of Tartu, Estonia. Project lead at eQTL Catalogue. https://kauralasoo.github.io/
kauralasoo.github.io
Posts Media Videos Starter Packs
Reposted by Kaur Alasoo
jeffreypullin.bsky.social
Jeffrey Pullin @jeffreypullin.bsky.social · 14h
I'm very excited to be attending my first #ASHG25 this week! Come find me at poster board 1090F to talk about flexible and efficient eQTL mapping with quasar!
2 9
Reposted by Kaur Alasoo
gonzalobenegas.bsky.social
Gonzalo Benegas @gonzalobenegas.bsky.social · Feb 13
Can DNA sequence models predict mutations affecting human traits?

We introduce TraitGym, a curated benchmark of causal regulatory variants for 113 Mendelian & 83 complex traits, and evaluate functional genomics and DNA language models. Joint work w/ Gökcen Eraslan and @yun-s-song.bsky.social 🧵👇
1 15 28
kauralasoo.bsky.social
Kaur Alasoo @kauralasoo.bsky.social · 6d
Found the abstract! For those also wondering, these metabolites are : dimethylamine,
glutamic acid, lysine, myo-inositol, 1,2-propanediol, serine and succinate.
kauralasoo.bsky.social
Kaur Alasoo @kauralasoo.bsky.social · 6d
Now I'm super excited to learn what these seven new metabolites ares! Unfortunately I won't be able to make it to ASHG this year.
1
Reposted by Kaur Alasoo
stevesphd.bsky.social
Stephen Burgess @stevesphd.bsky.social · 6d
New pre-print: "PCSK9 and breast cancer survival: a Mendelian Randomization study" www.medrxiv.org/content/10.1... led by Janne Pott. Brief thread:
PCSK9 and breast cancer survival: a Mendelian Randomization study
Background: Proprotein convertase subtilisin/kexin type 9 (PCSK9) is well known for its causal effects on the lipid metabolism. A recent study identified an association between rs562556 within PCSK9 a...
www.medrxiv.org
1 2 13
Reposted by Kaur Alasoo
natsuhiko83.bsky.social
Natsuhiko Kumasaka @natsuhiko83.bsky.social · 6d
Excited to share my poster at #ASHG2025 (Board 9173F)! Can’t wait to see everyone next week!
2 10
Reposted by Kaur Alasoo
oncology.ox.ac.uk
University of Oxford Department of Oncology @oncology.ox.ac.uk · 10d
New findings in @natcomms.nature.com demonstrate the impact of allelic variation on monocyte context-specific splicing.

@bpfairfax.bsky.social & colleagues show that many risk polymorphisms lead to differential gene splicing.

➡️Reveals putative mechanisms of diverse disease risk alleles inc. cancer
Genetic determinants of monocyte splicing are enriched for disease susceptibility loci - Nature Communications
Our understanding of variation in monocyte context-specific splicing and transcript usage is limited. Here, the authors find genetic variants that affect gene splicing in monocytes in specific contexts, including several diseases, and in response to stimulants.
www.nature.com
2 4
Reposted by Kaur Alasoo
labwaggoner.bsky.social
Waggoner Lab @labwaggoner.bsky.social · 10d
Trans-eQTL mapping prioritizes USP18 as a negative regulator of interferon response at a #lupus risk locus
www.nature.com/articles/s41... @natcomms.nature.com @unitartupress.bsky.social @kauralasoo.bsky.social
1 3
Reposted by Kaur Alasoo
mspivakov.bsky.social
Mikhail Spivakov @mspivakov.bsky.social · 10d
Many enhancers that drive tissue-specific gene expression are already connected to gene promoters in human pluripotent cells.

In a new preprint, we share some clues about when, how, and why this happens!

www.biorxiv.org/content/10.1...
Poising and connectivity of emergent human developmental enhancers in the transition from naive to primed pluripotency
In primed human pluripotent stem cells (hPSCs) resembling post-implantation epiblast, numerous lineage-specific enhancers assume the poised chromatin state, co-marked by H3K4me1 and Polycomb-associate...
www.biorxiv.org
1 20 55
kauralasoo.bsky.social
Kaur Alasoo @kauralasoo.bsky.social · 10d
We discussed this briefly in the USP18 paper, but went into more detail in our 'MR with proxy exposures' paper:
doi.org/10.1093/gene...
Mendelian randomisation with proxy exposures: challenges and opportunities
Abstract. A key challenge in human genetics is the discovery of modifiable causal risk factors for complex traits and diseases. Mendelian randomisation (MR
doi.org
1
kauralasoo.bsky.social
Kaur Alasoo @kauralasoo.bsky.social · 10d
Yeah, I would be careful with genes that only have trans colocs and no cis colocs. I like to think of trans-eQTL (and -pQTL) effects primarily as proxy readouts of variant effect on cis gene function (e.g. HERC5 expression is proxy readout of variant effect on USP18 function).
1 2
kauralasoo.bsky.social
Kaur Alasoo @kauralasoo.bsky.social · 10d
And it looks like two of the three studies have also released summary statistics! Guess which ones I am going to read first, run colocs on, and include into our future studies?
1
kauralasoo.bsky.social
Kaur Alasoo @kauralasoo.bsky.social · 10d
Worth kleeping in mind that both USP18 and SP110/SP140 have many trans targets. Not obvious that IFI6 is the causal mediator here. Likely lots of horizontal pleiotropy.
1 1
kauralasoo.bsky.social
Kaur Alasoo @kauralasoo.bsky.social · 11d
This is one of the coolest studies that I have seen recently! Thanks for highlighting, @jeffreypullin.bsky.social!

Genes and environment profoundly affect the human virome
1 1 4
kauralasoo.bsky.social
Kaur Alasoo @kauralasoo.bsky.social · 11d
I do think it is likely to be a true trans effect, but the locus seems to have several causal variants with distinct mechanisms (expression and splicing) in high LD with each other. Our full sumstats (8Tb!) are available via the @eqtlcatalogue.bsky.social if someone wants to take a closer look!
1 1
kauralasoo.bsky.social
Kaur Alasoo @kauralasoo.bsky.social · 11d
Thanks, I had missed that GWAS! We expored the SP110/SP140 locus a bit, but ultimately decided not to focus on it, because it had high heterogeneity between cohorts and did not replicate in MAGE.
1 1
kauralasoo.bsky.social
Kaur Alasoo @kauralasoo.bsky.social · 11d
A big shout out to the @finngen.bsky.social team for releasing their FinnGen+MVP+UKBB meta-analysis ahead of publication at the end of last year (mvp-ukbb.finngen.fi). This is an amazing resources that allowed us to replicate our USP18 trans-eQTL and lupus colocalisation in an independent cohort:
1 3
kauralasoo.bsky.social
Kaur Alasoo @kauralasoo.bsky.social · 11d
Happy to share that this work together with @opentargets.org is now out at Nature Communications.
opentargets.org
Open Targets @opentargets.org · 11d
Out now in Nature Comms: the largest trans-eQTL meta-analysis in a single cell type!

An Open Targets team led by Krista Freimann and @kauralasoo.bsky.social analysed 3,734 lymphoblastoid cell line samples across nine cohorts, identifying four robust loci

www.nature.com/articles/s41...
Trans-eQTL mapping prioritises USP18 as a negative regulator of interferon response at a lupus risk locus - Nature Communications | Open Targets
Out now in Nature Comms: the largest trans-eQTL meta-analysis in a single cell type! An Open Targets team led by Krista Freimann and Kaur Alasoo analysed 3,734 lymphoblastoid cell line samples across...
www.linkedin.com
1 5 15
Reposted by Kaur Alasoo
greally.bsky.social
John Greally @greally.bsky.social · 13d
By ‘epigenetic’, you mean what?

a. A non-genetic mechanism for inheritance of a trait or phenotype?
b. Something involving transcription regulation?
c. A modifiable cellular memory?
d. Genetic influences on cell differentiation?

Without specifying which, the press release is uninterpretable.
2 2 10
kauralasoo.bsky.social
Kaur Alasoo @kauralasoo.bsky.social · 16d
And as a badge of honour, I can now say that I have authored a paper that has been rejected from Scientific Reports for lack of novelty!
2
kauralasoo.bsky.social
Kaur Alasoo @kauralasoo.bsky.social · 16d
Perhaps the biggest change is that we have added some practical guidelines for performing MR with proxy exposures. These are summarised on this nice figure prepared by Ida Rahu:
1 1
kauralasoo.bsky.social
Kaur Alasoo @kauralasoo.bsky.social · 16d
It took two more desk rejects, but happy to share that this study has now been publised in @genetics-gsa.bsky.social. In the end, we received very constructive reviews that I think really improved the clarity of the paper. doi.org/10.1093/gene...
kauralasoo.bsky.social
Kaur Alasoo @kauralasoo.bsky.social · Feb 13
I have now spent almost four months to get this paper with @ericfauman.bsky.social desk-rejected from three journals (Genetic Epidemiology, eLife and HGG Advances) and not really sure where to go from here.
www.medrxiv.org/content/10.1...
Mendelian randomisation with proxy exposures: challenges and opportunities
A key challenge in human genetics is the discovery of modifiable causal risk factors for complex traits and diseases. Mendelian randomisation (MR) using molecular traits as exposures is a particularly...
www.medrxiv.org
1 8
kauralasoo.bsky.social
Kaur Alasoo @kauralasoo.bsky.social · 17d
I also like Excalidraw and some people from my team use Canva.
1
Reposted by Kaur Alasoo
jeffbarrett.eu
Jeffrey Barrett @jeffbarrett.eu · 19d
The science is, in fact, clear. Good studies [1] consistently show a weak association between tylenol & autism. Those studies are very careful to say they can't establish whether this is causal. A huge Swedish study used a clever sibling design to address this, and showed zero causal effect [2].
npr.org
NPR @npr.org · 19d
The science on Tylenol and autism isn't clear, despite President Trump's claims. Here's what parents need to know to make their own decisions about acetaminophen.
When it comes to Tylenol, what are parents to do?
The science on Tylenol and autism isn't clear, despite President Trump's claims. Here's what parents need to know to make their own decisions about acetaminophen.
n.pr
2 10 26
Reposted by Kaur Alasoo
skyjase.bsky.social
Jase Gehring @skyjase.bsky.social · 22d
don't release preprints without a Methods section
don't release preprints with a Supplementary Materials section
don't release preprints without data
don't release preprints without code

use preprint servers to share your science, not advertisements
6 16 65