Stephen Burgess
@stevesphd.bsky.social
Medical statistician, work with genetic data to disentangle causation from correlation. Author of book on Mendelian randomization.
New paper "Causal inference in Clinical Research: A Primer" at Journal of Periodontal Research - pubmed.ncbi.nlm.nih.gov/42466618/ led by Nasir Bashir plus co-authors Moritz Kebschull and Gustavo Nascimento.
Causal Inference in Clinical Research: A Primer - PubMed
The study of causal relationships is central to scientific inquiry. Understanding what disease is, why it arises, and how it can be treated are a set of fundamentally causal questions. In this article...
pubmed.ncbi.nlm.nih.gov
New paper: Blood Manganese and Risk of Squamous Cell Carcinomas of the Head and Neck published in JAMA Otolaryngology @jamaotolaryngology.com led by Benjamin Clay and Paul Carter, together with Nasir Bashir: jamanetwork.com/journals/jam...
Blood Manganese and Risk of Squamous Cell Carcinomas of the Head and Neck
This cis-mendelian randomization study aims to determine if variations in genetically predicted blood manganese are associated with risk of squamous cell carcinomas of the oral cavity, oropharynx, hyp...
jamanetwork.com
New publication "Comparison of methods for assessing effects of risk factors on disease progression in Mendelian randomization under index event bias" at @ajhgnews.bsky.social: authors.elsevier.com/sd/article/S.... Collaboration between Eli Lilly, Sequoia Genetics, and Cambridge University. Thread:
authors.elsevier.com
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:
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...
arxiv.org
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: https://bit.ly/48DEz0H #ASHG
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:
The American Journal of Human Genetics@ajhgnews.bsky.social · 4mo ago📣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
New pre-print on treatment effect heterogeneity led by Ash Patel: "Efficient semiparametric estimation of marginal treatment effects with genetic instrumental variables" available at arxiv.org/abs/2603.08871. Brief summary:
Efficient semiparametric estimation of marginal treatment effects with genetic instrumental variables
Alcohol misuse is a key target of public health strategies aimed at reducing cardiovascular risk. The effect of excessive alcohol consumption on blood pressure may vary systematically with individuals...
arxiv.org
Great to be involved in this publication: "Phenome-wide study on alcohol consumption provides genetic evidence for a causal association with multiple diseases and biomarkers" led by Nigussie Kassaw - doi.org/10.1016/j.nu....
Redirecting
doi.org
New preprint: "Revising the use of F-tests in weak instrument practice: point estimation and beyond" led by James Lane: papers.ssrn.com/sol3/papers..... The F>10 threshold for avoiding weak instrument bias has almost mythical status. But where does it come from? And does it make sense? In brief:
papers.ssrn.com
New pre-print: "Correcting for effect modification in the doubly-ranked non-linear Mendelian randomization method" led by Ang Zhou available at www.medrxiv.org/content/10.6.... Brief thread:
Correcting for effect modification in the doubly-ranked non-linear Mendelian randomization method
The doubly-ranked non-linear Mendelian randomization method can yield biased estimates when instrument strength varies across individuals due to gene-environment (GxE) interactions. We propose a simpl...
medrxiv.org
LD patterns can make it difficult to select optimal instrumental variables for Mendelian randomization studies. @stevesphd.bsky.social & co of @hggadvances.bsky.social 's latest article evaluate the ability of four selection methods to increase instrument strength: bit.ly/4a0yXih #ASHG
New paper: "Extending the Use of Mendelian Randomisation With Non-Inherited Variants to Assess Socially Transmitted Parental Exposures Under Assortative Mating" published at Genetic Epidemiology and led by Benji Woolf: onlinelibrary.wiley.com/doi/10.1002/.... Brief thread:
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
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
📣📣📣 Excited for our lab's latest preprint, led by Chief Ben-Eghan! www.medrxiv.org/content/10.1... tl;dr We identify protein vQTLs in multiple ancestries then use MVMR to show independent effects of mean & variance on disease, suggesting targeting protein variance could have therapeutic potential.
Happy to have co-authored a technical report published by @Policy_Exchange on University Technical Colleges. My role was limited to the statistical report, not the policy document - although I proof read the latter to ensure our analyses was correctly represented.
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...
biorxiv.org
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
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...
medrxiv.org
Full recording of the PSI webinar by myself and @jack_bowdenjack on instrumental variable methods is available online: psiweb.org/vod/item/efs...
PSI
The community dedicated to leading and promoting the use of statistics within the healthcare industry for the benefit of patients.
psiweb.org
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...
biorxiv.org
New manuscript led by @BarWoolf "A cautionary note on the naive use of general-population biobanks to study pulmonary arterial hypertension" is now published at Euro Respiratory Journal @ERSpublications: pubmed.ncbi.nlm.nih.gov/40967765/. Summary follows:
A cautionary note on the naive use of general-population biobanks to study pulmonary arterial hypertension, with a focus on Mendelian randomization - PubMed
A cautionary note on the naive use of general-population biobanks to study pulmonary arterial hypertension, with a focus on Mendelian randomization
pubmed.ncbi.nlm.nih.gov
New pre-print online: "Context-stratified Mendelian randomization: exploiting regional exposure variation to explore causal effect heterogeneity and non-linearity", arxiv.org/abs/2507.11088. We propose an alternative approach to assess non-linearity in Mendelian randomization.
Context-stratified Mendelian randomization: exploiting regional exposure variation to explore causal effect heterogeneity and non-linearity
Mendelian randomization (MR) uses genetic variants as instrumental variables to make causal claims. Standard MR approaches typically report a single population-averaged estimate, limiting their abilit...
arxiv.org
New paper led by Nasir Bashir "Periodontitis and Systemic Disease: The Impact of Covariate Selection" published at @JDentRes: journals.sagepub.com/doi/10.1177/.... We investigate how disease associations vary with covariate adjustment.
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New publication at @BMJMedicine "Epidemiology: a partnership of technical expertise and clinical insight" co-authored with Debbie Lawlor: bmjmedicine.bmj.com/content/4/1/.... This essay explores how to be an epidemiologist is in today's world. Comments welcome!
Epidemiology: a partnership of technical expertise and clinical insight
Like all medical fields, epidemiology is a discipline that can be practiced effectively only in partnership with others. While data analysis may seem like a solitary pursuit, epidemiological datasets ...
bmjmedicine.bmj.com
New publication at European Journal of Epidemiology: "Search for common genetic variants to allow reliable Mendelian randomization investigations into ketone metabolism" led by Zhu Liduzi (Julie) Jiesisibieke. Link: link.springer.com/article/10.1.... Brief thread:
Search for common genetic variants to allow reliable Mendelian randomization investigations into ketone metabolism - European Journal of Epidemiology
Ketogenic diets are popular among people aiming for weight management. Ketone supplementation has been linked to improved cognitive performance and increased risk of insulin resistance. We aim to iden...
link.springer.com
Krista and I are giving an introduction to Mendelian randomization in Brown 3 starting in a few moments - I will post my slides here after the session #eshg2025
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
New pre-print: "Mendelian Randomization with longitudinal exposure data: simulation study and real data application" led by Janne Pott is online: medrxiv.org/content/10.1.... Brief thread:
Mendelian Randomization with longitudinal exposure data: simulation study and real data application
Background and aim Mendelian Randomization (MR) is a widely used tool to estimate causal effects using genetic variants as instrumental variables. MR is limited to cross-sectional summary statistics o...
medrxiv.org
Our paper "A Principled Framework for Mendelian Randomization in Oral Health Research" led by Nasir Bashir is now online at Journal of Periodontal Research: onlinelibrary.wiley.com/doi/10.1111/.... Brief thread follows!
A Principled Framework for Mendelian Randomization in Oral Health Research
This methodological article provides a clear and accessible overview of Mendelian randomization for oral health researchers, emphasizing the core assumptions needed for credible causal inference. Foc....
onlinelibrary.wiley.com