Luke Pilling

I get contacted multiple times a week by users; it's really exciting to hear about all the cool science🌟

If {ukbrapR} supports your research, please cite it so I can track its impact (this really helps me!)

Pro-tip: Use the {grateful} package to automatically include {ukbrapR} in your bibliography

GitHub - lcpilling/ukbrapR: R package for working in the UK Biobank Research Analysis Platform (RAP) R package for working in the UK Biobank Research Analysis Platform (RAP) - lcpilling/ukbrapR

Still manually merging UK Biobank-linked health data? Faffing with Swiss Army Knife to extract variants or create polygenic scores? 🧬

I built {ukbrapR} so we could spend more time on science and less on data plumbing

If it helps you, please cite! 📊 citation('ukbrapR')

github.com/lcpilling/uk...

If you're looking to build or deepen your knowledge in statistical genetics, the ISG Workshop (June 1–11) covers the full range: biometrics, GWAS, polygenic scores, causal inference, and more. Open to all levels, virtual, and international: www.colorado.edu/ibg/workshop...

Retweets appreciated 🙏

yodr is a small R package with tools for epidemiology and hypothesis testing

Niche R package with epidemiology tools anyone? 📦

Named it {yodr} (phonetically "Yoda") which I cannot believe no-one has done before to be honest!

Main functions are for "tidy" model output (extends {broom} package) and PheWAS. Also functions for extreme p-values, etc

lcpilling.github.io/yodr

The scale of this whole genome analysis conditioning across large biobanks is extraordinary, revealing novel LDL cholesterol biology 🧪

Bravo to @hiwwright.bsky.social, @drghawkes.bsky.social and the teams from Exeter and Geneva 👏

See Harry's post below for a wonderful analysis & results breakdown

Researchers quantify role of reducing obesity in preventing common conditions Researchers have quantified the role of obesity in common long-term conditions, showing for the first time the effect of losing weight in preventing multiple diseases.   Conditions that often occur to...

Massive GEMINI team effort (ex.ac.uk/gemini)

Can't name them all. Key co-authors: Ninon Mounier, Beth Voller, @janemasoli.bsky.social, João Delgado, Frank Dudbridge, @timfrayling.bsky.social, Jack Bowden

Data/code: github.com/GEMINI-multi...

Press release: news.exeter.ac.uk/faculty-of-h...

Heatmap of the difference between full and partial genetic correlations for all 2485 disease pairs after adjustment for the genetics of BMI. Pairwise partial genetic correlation analysis between 71 conditions (i.e., 2485 disease pairs). Condition pairs where there was no significant (FDR correction) genetic correlation before or after adjustment, or the adjustment for BMI genetics was non-significant (FDR corrected), are coloured white. Data shown is the proportion change in genetic correlation between condition pairs after adjustment for BMI genetics (where the change is statistically significant after FDR correction). https://www.nature.com/articles/s43856-025-01347-y/figures/2

My fav figure: shows the difference between full and partial genetic correlations for all 2485 disease pairs after adjustment for the genetics of BMI ⚖️

Blue shows where the genetics are reduced (explained) by BMI e.g., OA~T2D is fully attenuated 📉

Red shows where the genetic links are stronger!

Genetics identifies obesity as a shared risk factor for co-occurring multiple long-term conditions - Communications Medicine Mounier et al., analyse whether obesity, measured by body mass index (BMI) affects the shared genetic risk between 71 long-term health conditions including diabetes, heart disease and arthritis. Healt...

Latest output from the GEMINI (genetics of multiple long-term conditions) team 🧬

We used genetics to subtract the effect of obesity, revealing multiple conditions that 1) share obesity as a common cause or 2) share other causes 🌟 strong implications for intervention 🥼

Paper doi.org/10.1038/s438...

Healthy Ageing and Chronic Disease research at the University of Exeter YouTube video by University of Exeter

Hear about the awesome research into Healthy Ageing and Chronic Disease @exeter.ac.uk

Fantastic overview from the always inspiring @janemasoli.bsky.social

Special mention to @lornah.bsky.social, Chris Scotton, and the 100s of fabulous colleagues behind the science

www.youtube.com/watch?v=kGlY...

I'm seeing relatively little chatter or outcry about what is happening at the MRC, the UK's biomedical research funder.

Before Christmas MRC paused the acceptance of many of its grants, including the standard applicant-led research grant. There has been no public information on what is happening 🧵

Hi - should work fine, it is not dependent on RStudio at all - just the way I use it! Any issues or suggestions let me know (via GitHub ideally!)

Update to my UK Biobank R package {ukbrapR} 🌟

Get imputed variants (load genos or for PGS) using chr:pos not RSIDs (+ MAF, INFO etc). It can also do this for DRAGEN WGS 🐉

Thanks to @harrygreentkd.bsky.social for the help (and pub+pint whilst bug checking!) 🍻

v0.3.10 :: github.com/lcpilling/uk...

As a neuroscientist, here are 8 ways to maximise misery:
1. Check your phone immediately after waking.
Flood your brain with news designed to make you anxious and angry.

Got to say, pretty impressed by the GitHub Copilot coding agent... for repos with my existing code it is fantastic for extending to new analyses that I am interested in doing i.e., it looks at your coding style, data structures, etc and creates a Pull Request for you to review

My 526 GitHub contributions (mostly commits) over the last 12 months. Never on Saturdays, rarely on Sundays, except where I have personal nerd projects apparently

I don't normally do work on Saturdays (though often end up catching up in evenings due to young children etc)

These Saturday GitHub commits were on nerdy personal repos where I annually analyse data about my central heating (Raspberry Pi managed) and my car fuel efficiency 😅 a wild Saturday evening

Why do some individuals defy their polygenic score?

In the largest study of its kind (402k UKB individuals; 7 continuous traits + 3 diseases), we asked: If your phenotype deviates from common-variant polygenic score prediction, what's driving that difference?

www.medrxiv.org/content/10.6...

January @DEMONNetworkUK Biomarkers working group is hosting an Inflammation special with Dr Maura Malpetti and Dr Sofia Michopoulou “Unravelling Inflammation in Dementia: Proteomic and Imaging Insights” 📅 Wed 14th Jan 10.30am GMT. New members welcome - pls message for details.

Bookmarked! 🔖

Opening Presents Eric Cartman GIF ALT: Opening Presents Eric Cartman GIF

Somehow finished my to-do list (well, the urgent stuff) so early Xmas present to myself is a few (uninterrupted? 🤞) days on DNAnexus with the new release of UK Our Future Health data 🤩

🤞 for effective sample size

Great to be back at the @ukbiobank.bsky.social scientific conference 2025 to meet old friends and make new collaborations #UKBSC25

Positive opening remarks from Prof Collins RE growing data linkages (GP data actually incoming? 🤞) and amazing research outputs

Message if you're here and want to chat

(Re)discovered the ability to "mute" words from the feed. I come here for your niche science, health data, and genetics posts ❤️ I do not need anything about cats or certain megalomanic billionaires (though at least your cat pictures were cute)

HUGERA (@hugeraproject.bsky.social) HUGERA is an ERC-funded Project that brings together philosophers, social scientists, and geneticists to study and foster an ethically sound science of human variation. To know more, please visit huge...

Worth following hugeraproject.bsky.social if you are also interesting - they are hosting workshops and seminars to further the conversation!

Really enjoyed a joint meeting earlier between Exeter rare genetics team and @celsoneto.bsky.social and colleagues from the Human Genomics without Racism (HUGERA) project 🧬

Really complex area. Looking forward to considering how to better consider genetic diversity and self-identified ethnicity!

Embryo selection based on polygenic prediction risks reinforcing social inequality The rise of companies offering embryo selection based on genetic testing has triggered heated debate about ethical acceptability, as well as the accuracy and scientific validity of these techniques. W...

There’s a new kid in town!

Companies are now selling IVF and embryo selection based on genetic testing for traits related to health and even intelligence.

We outline methodological and ethical concerns, and warn against risks for social inequality.

With the fantastic @gaiaghirardi.bsky.social

Estimation and mapping of the missing heritability of human phenotypes - Nature WGS data were used from 347,630 individuals with European ancestry in the UK Biobank to obtain high-precision estimates of coding and non-coding rare variant heritability for 34 co...

First time on Bsky and first big announcement!

I am excited to announce that our new study explaining the missing heritability of many phenotypes using WGS data from ~347,000 UK Biobank participants has just been published in @Nature.

Our manuscript is here: www.nature.com/articles/s41....

I find these cases fascinating, where absence of genetic correlation does not imply absence of shared causal variants!

View of the River Exe running through the Quay in sunny Exeter.

Post-doc opportunity in Exeter 🌟 studying genetic modifiers of haemochromatosis 🩸

Closing date 30 Oct!

Come and work with a interdisciplinary team of epidemiologists, clinicians, and statistical geneticists, in a beautiful city in the South West of England ❤️

jobs.exeter.ac.uk/hrpr_webrecr...

Yeah... at the least could use {renv} to make the same package versions available etc

But my code doesn't try to emulate the real data structures particularly - just col names and variable types, so that at least the initial test can be done there, then tested properly online