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Ville Karhunen

@vkarhune.bsky.social
325 followers 298 following 1 posts

Assistant Research Professor | Biostatistics, epidemiology and public health vkarhune.github.io

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Reposted by Ville Karhunen
Stephen Burgess @stevesphd.bsky.social · 28/06/2026
New preprint: "Multivariable Mendelian randomization with weak instruments: a comparison of Bayesian and frequentist methods" led by Andrew Grant: arxiv.org/abs/2606.26638. We present a method for multivariable Mendelian randomization (MVMR): MVMR-Pony. Thread follows:
arxiv.org
Multivariable Mendelian randomization with weak instruments: a comparison of Bayesian and frequentist methods
Weak instruments are a well known limitation for valid causal inference in Mendelian randomization studies. In the single exposure setting, weak instrument bias can be mitigated by selecting genetic i...
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Kaur Alasoo @kauralasoo.bsky.social · 18/06/2026
Happy to share that this work led by @mihkeljesse.bsky.social has now been published at PLOS Genetics! journals.plos.org/plosgenetics... A couple of thoughts below.
journals.plos.org
Ultra-fast genetic colocalisation across millions of association signals
Author summary Over 90% of human genetic variants associated with human traits and diseases lie in non-coding regions of the genome, making it difficult to interpret the mechanisms by which these vari...
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Reposted by Ville Karhunen
Jeffrey Pullin @jeffreypullin.bsky.social · 18/05/2026
tinyurl.com/reuxynmc Very excited to see this work I was a small part of published! We analysed two large scale colocalisation datasets: OpenTargets data and an analysis of immune-mediated disease GWAS/immune cell eQTLs seeking to understand the "colocalisation gap". Some highlights:
journals.plos.org
Design and interpretation of eQTL-GWAS colocalisation studies: Lessons from a large-scale evaluation
Author summary Most of the genetic variants associated with complex traits are located outside genes, limiting functional interpretation. Genetic colocalisation helps identify candidate causal genes b...
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Reposted by Ville Karhunen
American Society of Human Genetics (ASHG) @geneticssociety.bsky.social · 16/04/2026
In their recent @ajhgnews.bsky.social Review, @vkarhune.bsky.social, @stevesphd.bsky.social, & co discuss the key considerations and provide advice to produce a higher standard in planning, conducting, reviewing, and interpreting cis-Mendelian randomization studies: bit.ly/48DEz0H #ASHG
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Reposted by Ville Karhunen
Stephen Burgess @stevesphd.bsky.social · 13/04/2026
Our review "Integrating genetic data with biological insight: A practical guide to cis-Mendelian randomization" is now published at @ajhgnews.bsky.social - led by @vkarhune.bsky.social and Benji Woolf with critical insight from Dipender Gill and Pallav Bhatnagar. Thread follows:
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Kaur Alasoo @kauralasoo.bsky.social · 11/04/2026
Great to see this out! It was a pleasure to be one of the reviewers. @vkarhune.bsky.social @stevesphd.bsky.social
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The American Journal of Human Genetics @ajhgnews.bsky.social · 10/04/2026
📣New Review! 📄Integrating genetic data with biological insight: A practical guide to cis-Mendelian randomization 🧑‍🤝‍🧑 @vkarhune.bsky.social @stevesphd.bsky.social & co 👉 bit.ly/4tKkY7r
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Peter Tennant @pwgtennant.bsky.social · 24/02/2026
Fantastic paper by @jeremylabrecque.bsky.social and Katrina Kezios on 'How and when to use causal and associational language'. Nicely explains why I get so frustrated by studies that claim that their aim is to estimate "the association"! www.bmj.com/content/392/...
bmj.com
How and when to use causal and associational language
Deciding which concepts should be described in causal language and which should not Research questions fall into one of three categories: descriptive, predictive, or causal.1 The past decade has seen...
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Stephen Burgess @stevesphd.bsky.social · 19/01/2026
New paper "Variant selection to maximize variance explained in cis-Mendelian randomization" led by @AngZhou3 and published at @HGGAdvances: pubmed.ncbi.nlm.nih.gov/41548043/, with contribution from @vkarhune.bsky.social, Haodong, Janne, Ash, and Eric. Brief thread:
pubmed.ncbi.nlm.nih.gov
Variant selection to maximize variance explained in cis-Mendelian randomization - PubMed
Optimal selection of instrumental variables (IVs) from a single gene region in cis-Mendelian randomization is challenging as variants are highly correlated due to linkage disequilibrium (LD). Using only the lead variant is convenient but may not achieve full statistical power if multiple signals exi …
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Darren Dahly @statsepi.bsky.social · 29/12/2025
‪It has a name now 😜 Many thanks to Ken for agreeing to put his good name to my...artwork. The image is in the public domain (CC 0), but citations to the linked documents are warmly welcomed. ✅ zenodo.org/records/1808... ✅ pubmed.ncbi.nlm.nih.gov/24452418/
Figure 1: The Rothman-Dahly Evidence Pyramid (original version)

An equilateral triangle with a small blue section labelled "Thoughtful, well-conducted studies of any design" at the top, with the remaining space colored red and labelled "The other shit"
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Stephen Burgess @stevesphd.bsky.social · 16/12/2025
New paper: "Alcohol consumption and risk of cancer: a Mendelian randomization analysis of four biobanks and consortium data" out at BMC Medicine: link.springer.com/article/10.1.... Lots of interesting findings! Brief thread:
link.springer.com
Alcohol consumption and risk of cancer: a Mendelian randomization analysis of four biobanks and consortium data - BMC Medicine
Background Alcohol consumption has been linked to cancer risk. Evidence is strongest for seven cancer types: breast, colorectum, oesophagus, liver, mouth, pharynx, and larynx. However, evidence suppor...
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medRxivpreprint @medrxivpreprint.bsky.social · 24/11/2025
Design and interpretation of eQTL-GWAS colocalisation studies: lessons from a large-scale evaluation www.medrxiv.org/content/10.1101/202…
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Stephen Burgess @stevesphd.bsky.social · 08/11/2025
New pre-print: "Systematic comparison of colocalization methods using protein quantitative trait loci" led by @hwang_seongwon at www.biorxiv.org/content/10.1.... Which method does best? Find out!
biorxiv.org
Systematic comparison of colocalization methods using protein quantitative trait loci
Colocalization is frequently performed as a step to triage findings from genetic investigations linking molecular and disease data. However, the reliability and consistency of the various colocalizati...
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Jonathan Pritchard @jkpritch.bsky.social · 07/11/2025
Excited to share our latest work on the factors that determine what genes we find (and don't find!) in GWAS and burden tests. We describe a critical concept that we call *specificity*. Led by Jeff Spence and Hakhamanesh Mostafavi:
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Stephen Burgess @stevesphd.bsky.social · 27/10/2025
New pre-print "Mendelian randomization in a multi-ancestry world: reflections and practical advice" led by @amymariemason.bsky.social on - arxiv.org/abs/2510.17554
arxiv.org
Mendelian randomization in a multi-ancestry world: reflections and practical advice
Many Mendelian randomization (MR) papers have been conducted only in people of European ancestry, limiting transportability of results to the global population. Expanding MR to diverse ancestry groups...
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Janne Pott @pottj.bsky.social · 06/10/2025
📣Preprint alert - a tricky one, as there are no significant results (and we all know null-results are hard to publish) Do PCSK9 levels affect survival in breast cancer patients? We tried to replicate findings in cell lines and mouse model using 3 Mendelian Randomization approaches, but failed.
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Journal of Clinical Epidemiology @jclinepi.bsky.social · 28/09/2025
Developing risk prediction models for type 2 diabetes and assessing the role of circulating metabolic biomarkers in five independent Finnish cohorts with over 22000 individuals - Journal of Clinical Epidemiology www.jclinepi.com/article/S089...
jclinepi.com
Developing risk prediction models for type 2 diabetes and assessing the role of circulating metabolic biomarkers in five independent Finnish cohorts with over 22000 individuals
Type 2 diabetes is a serious public health risk. It is not well known whether large scale omics data could help improve the risk prediction. We combined the use of metabolic variables with modern mode...
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Chris Wallace @chr1sw.bsky.social · 23/09/2025
In modern datasets, very large sample sizes combined with slight differences in information across SNPs (eg die to imputation) can mislead fine mapping algorithms, and in turn colocalisation.
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Jeffrey Pullin @jeffreypullin.bsky.social · 22/07/2025
Very excited to share new work from my PhD on a new software package for eQTL mapping: quasar. The quasar software package is a C++ program designed to provide a flexible and efficient eQTL mapping. www.medrxiv.org/content/10.1...
medrxiv.org
Flexible and efficient count-distribution and mixed-model methods for eQTL mapping with quasar
Identifying genetic variants that affect gene expression, expression quantitative trait loci (eQTLs), is a major focus of modern genomics. Today, various methods exist for eQTL mapping, each using dif...
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Chris Wallace @chr1sw.bsky.social · 18/07/2025
Booking is now open for the MRC #Biostatistics Unit's 22nd Armitage Day! Keynote from Matthew Stephens: “The menagerie of matrix factorization methods” Plus talks by @manuelazucknick.bsky.social, Gibran Hemani and (as yet unnamed!) BSU researchers. onlinesales.admin.cam.ac.uk/conferences-...
onlinesales.admin.cam.ac.uk
22nd Armitage Workshop and Lecture, 23 October 2025 | University of Cambridge
The MRC Biostatistics Unit is delighted to be organising its annual flagship event. The theme of this year’s Armitage Workshop will be: Integration o
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Georg Heinze @georgheinze.bsky.social · 26/06/2025
Published: the paper 'On the uses and abuses of Regression Models: a Call for Reform of Statistical Practice and Teaching' by John Carlin and Margarita Moreno-Betancur in the latest issue of Statistics in Medicine onlinelibrary.wiley.com/doi/10.1002/... (1/8)
onlinelibrary.wiley.com
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Neil Davies @neilmdavies.bsky.social · 18/06/2025
Looking for your next research position? We're recruiting two genetic epidemiologists to work on two projects at the Division of Psychiatry at UCL, part of the growing UCL Human Genomics group.
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Reposted by Ville Karhunen
Jeffrey Pullin @jeffreypullin.bsky.social · 09/06/2025
Very happy that my first PhD paper is now out in PLOS Genetics! journals.plos.org/plosgenetics.... We describe our implementation of variant-specific priors in coloc. We show that using distance to the TSS as information about which variants are causal can improve colocalisation performance, 1/n
journals.plos.org
Variant-specific priors clarify colocalisation analysis
Author summary Evaluating whether two traits, such as disease risk and gene expression, are affected by the same genetic variants is crucial for understanding the molecular mechanisms through which ge...
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Stephen Burgess @stevesphd.bsky.social · 20/05/2025
New paper published at AJE Advances: "The role of estimation in Mendelian randomization: should Mendelian randomization investigations provide estimates?" led by @BarWoolf and myself: academic.oup.com/ajeadvances/.... Brief thread:
academic.oup.com
The role of estimation in Mendelian randomization: should Mendelian randomization investigations provide estimates?
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Stephen Burgess @stevesphd.bsky.social · 12/02/2025
New pre-print led by @hwang_seongwon: "Human genetics suggests differing causal pathways from HMGCR inhibition to coronary artery disease and type 2 diabetes": www.medrxiv.org/content/10.1.... Brief thread follows:
medrxiv.org
Human genetics suggests differing causal pathways from HMGCR inhibition to coronary artery disease and type 2 diabetes
Background: Statins lower low-density lipoprotein cholesterol (LDL-C) and reduce the risk of coronary artery disease (CAD). However, they also increase the risk of type 2 diabetes (T2D). Methods: We c...
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Stephen Burgess @stevesphd.bsky.social · 08/01/2025
Our work on immortal time bias "Illustrating the structures of bias from immortal time using directed acyclic graphs" led by Emma Guoyi Yang @yanggy_hku is out at International Journal of Epidemiology: doi.org/10.1093/ije/.... Brief thread:
doi.org
Illustrating the structures of bias from immortal time using directed acyclic graphs
AbstractBackground. Immortal time is a period of follow-up during which death or the study outcome cannot occur by design. Bias from immortal time has been
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danielpanyard.bsky.social @danielpanyard.bsky.social · 13/12/2024
Dear early career genetic epidemiologists: The IGES Young Investigator Committee is looking for new members! It's a fun group, low time commitment, and great way to network with peers while supporting trainees around the world. Apply here by Dec 31st: www.geneticepi.org/yic_position...
IGES: the International Genetic Epidemiology Society
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MRC Biostatistics Unit @mrc-bsu.bsky.social · 05/12/2024
Become a #PhDStudent at our Unit. An exciting place to start a career in biostatistics research. Find out more about the great projects we have to offer starting in Oct 2025 & apply 👇 www.mrc-bsu.cam.ac.uk/phd-opportun... @cambridgeuni.bsky.social
Photo of BSU PhD students - some standing and some kneeling, all smiling and looking at camera, with building in background.
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Chen-Yang Su, PhD @chenyangsu.bsky.social · 17/11/2024
Interested in Mendelian randomization or GWAS? I thought it could be nice to connect the MR and GWAS community so here is a Starter Pack I'm building! 🧬 #academicsky #genomics #genetics #MR Let me know if you would like to be added or know someone to add. Enjoy and share! go.bsky.app/R19GhDP
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