Ville Karhunen
vkarhune.bsky.social
Ville Karhunen
@vkarhune.bsky.social
Senior Research Associate | Biostatistics, epidemiology and public health

https://vkarhune.github.io/
Reposted by Ville Karhunen
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!
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...
www.biorxiv.org
November 8, 2025 at 3:40 PM
Reposted by Ville Karhunen
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:
How do GWAS and rare variant burden tests rank gene signals?

In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!

🧬🧪🧵

www.nature.com/articles/s41...
Specificity, length and luck drive gene rankings in association studies - Nature
Genetic association tests prioritize candidate genes based on different criteria.
www.nature.com
November 7, 2025 at 4:08 AM
Reposted by Ville Karhunen
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
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...
arxiv.org
October 27, 2025 at 8:43 AM
Reposted by Ville Karhunen
📣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.
PCSK9 and breast cancer survival: a Mendelian Randomization study https://www.medrxiv.org/content/10.1101/2025.10.03.25337270v1
October 6, 2025 at 4:50 PM
Reposted by Ville Karhunen
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...
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...
www.jclinepi.com
September 28, 2025 at 12:42 PM
Reposted by Ville Karhunen
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.
September 23, 2025 at 1:03 PM
Reposted by Ville Karhunen
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...
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...
www.medrxiv.org
July 22, 2025 at 10:15 AM
Reposted by Ville Karhunen
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-...
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
onlinesales.admin.cam.ac.uk
July 18, 2025 at 9:34 AM
Reposted by Ville Karhunen
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
June 26, 2025 at 12:23 PM
Reposted by Ville Karhunen
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.
June 18, 2025 at 12:42 PM
Reposted by Ville Karhunen
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
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...
journals.plos.org
June 9, 2025 at 10:45 AM
Reposted by Ville Karhunen
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:
The role of estimation in Mendelian randomization: should Mendelian randomization investigations provide estimates?
academic.oup.com
May 20, 2025 at 11:24 AM
Reposted by Ville Karhunen
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:
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...
www.medrxiv.org
February 12, 2025 at 11:43 PM
Reposted by Ville Karhunen
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:
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
doi.org
January 8, 2025 at 8:50 AM
Reposted by Ville Karhunen
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...
December 13, 2024 at 7:42 PM
Reposted by Ville Karhunen
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
December 5, 2024 at 12:57 PM
Reposted by Ville Karhunen
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
November 17, 2024 at 7:58 PM