Ville Karhunen
@vkarhune.bsky.social
Assistant Research Professor | Biostatistics, epidemiology and public health
https://vkarhune.github.io/
https://vkarhune.github.io/
Reposted by Ville Karhunen
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:
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 …
pubmed.ncbi.nlm.nih.gov
January 19, 2026 at 12:24 PM
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:
Reposted by Ville Karhunen
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/
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/
December 29, 2025 at 11:19 AM
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/
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/
Reposted by Ville Karhunen
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:
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...
link.springer.com
December 16, 2025 at 9:55 AM
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:
Reposted by Ville Karhunen
Design and interpretation of eQTL-GWAS colocalisation studies: lessons from a large-scale evaluation https://www.medrxiv.org/content/10.1101/2025.11.20.25340664v1
November 24, 2025 at 4:40 AM
Design and interpretation of eQTL-GWAS colocalisation studies: lessons from a large-scale evaluation https://www.medrxiv.org/content/10.1101/2025.11.20.25340664v1
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
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!
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:
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...
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
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:
We describe a critical concept that we call *specificity*.
Led by Jeff Spence and Hakhamanesh Mostafavi:
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
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
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.
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
📣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.
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.
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
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...
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.
A pre-print for Chris Wallace's colocPropTest method for proportional colocalization is available online: www.biorxiv.org/content/10.1... @chr1sw.bsky.social
Variable information across SNPs in GWAS data can cause false rejections of colocalisation which can be resolved by proportional colocalisation tests
Fine-mapping is now a standard post-GWAS analysis, but it has been shown to be potentially inaccurate for large meta-analysis GWAS. We show how this can be caused by variable amounts of statistical in...
www.biorxiv.org
September 23, 2025 at 1:03 PM
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.
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
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...
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-...
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
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-...
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-...
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
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)
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
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.
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
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
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
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:
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
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:
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
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:
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...
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
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...
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...
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
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
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
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
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
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
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
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