Mike Weedon
@mnweedon.bsky.social
📤 174
📥 250
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reposted by
Mike Weedon
Kartik Chundru
22 days ago
Please forward this to any you know who could be interested! The incredible
@drghawkes.bsky.social
will be leading a course on analysis of genome sequence data, functional annotation of the genome, and using the very, very exciting AlphaGenome tool
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If you are looking to learn about rare variant WGS analyses, AlphaGenome and lots more, come join us in Exeter next September. It’s going to be a great few days!
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22 days ago
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reposted by
Mike Weedon
Dr Gareth Hawkes
29 days ago
Genomic superstar
@chundru.bsky.social
taking on fake-news genotypes in >900k individuals. He shows allele-level filtering is rarely suffifient, and makes the brave choice to properly tackle chrX! We’ll be providing our filtered AoU WGS plink pgens for all registered users: watch this space
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reposted by
Mike Weedon
Kartik Chundru
about 1 month ago
New paper on everyone’s favourite topic, QC! We show why you should do genotype-level QC on your WGS data
www.biorxiv.org/content/10.1...
Very real quotes about this paper - “The most exciting, mind-blowing paper of the year!” “On a par with Fisher 1918” “I read it every night. Just so beautiful”
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Genotype-level quality control substantially reduces error rates in population-scale whole-genome sequencing
Population-scale whole-genome sequencing data will contain many individual-level genotype errors, even after allele-level quality control (QC). We establish the need for genotype-level QC using UK Bio...
https://www.biorxiv.org/content/10.1101/2025.11.06.686913v1
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reposted by
Mike Weedon
Kartik Chundru
about 1 month ago
Thank you to other co-authors
@carolinefwright.bsky.social
,
@mnweedon.bsky.social
,
@timfrayling.bsky.social
, and
@drarwood.bsky.social
,
@nihrexeterbrc.bsky.social
, biobanks
@ukbiobank.bsky.social
and All of Us, and all of the participants of the studies
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reposted by
Mike Weedon
Luke Sharp
about 1 month ago
Excited to announce the acceptance and publication of our paper titled “Population prevalence, penetrants, and mortality for genetically confirmed MODY” in JCEM:
doi.org/10.1210/clin...
#MODY
#monogenicdiabetes
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Population prevalence, penetrance, and mortality for genetically confirmed MODY
AbstractContext. Diagnosing Maturity-Onset Diabetes of the Young (MODY) is clinically important for treatment and prognosis. However, phenotype-based studi
https://doi.org/10.1210/clinem/dgaf599
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Population prevalence, penetrance, and mortality for genetically confirmed MODY:
academic.oup.com/jcem/article...
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Population prevalence, penetrance, and mortality for genetically confirmed MODY
AbstractContext. Diagnosing Maturity-Onset Diabetes of the Young (MODY) is clinically important for treatment and prognosis. However, phenotype-based studi
https://academic.oup.com/jcem/article/doi/10.1210/clinem/dgaf599/8307687
about 1 month ago
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reposted by
Mike Weedon
Caroline Wright
about 1 month ago
Excellent autumnal away-day by the seaside with the Exeter genomics teams, organised by
@drghawkes.bsky.social
, discussing improvements to our whole genome sequence annotation and burden-testing pipelines - lots more exciting science to come!
@exeter.ac.uk
@nihrexeterbrc.bsky.social
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reposted by
Mike Weedon
Andrea Ganna
about 2 months ago
🎉 New preprint out! "Removing genetic effects on plasma proteins enhances their utility as disease biomarkers" We show that adjusting plasma proteins for genetic effects can make them stronger predictors of disease 👉
doi.org/10.1101/2025...
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reposted by
Mike Weedon
Nature Metabolism
about 2 months ago
RESEARCH | J Murray Leech, KA Patel et al.
@exeter.ac.uk
Polygenic risk for T2D modifies the onset and phenotypic variability of maturity-onset diabetes of the young (MODY) 🧪
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Common genetic variants modify disease risk and clinical presentation in monogenic diabetes - Nature Metabolism
In clinical and population-based cohorts, a strong contribution of polygenic risk for type 2 diabetes (T2D) significantly modifies the onset and phenotypic variability of maturity-onset diabetes of the young (MODY). This polygenic T2D burden may also account for MODY-like individuals without identified monogenic causes.
https://bit.ly/478FVz0
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reposted by
Mike Weedon
James Russ-Silsby
3 months ago
I’m excited to share the 2 newest Neonatal diabetes genes: RNU4ATAC and RNU6ATAC. These genes encode snRNA components of the minor spliceosome and biallelic variants in them cause monogenic autoimmune diabetes. If you are at
#EASD
, come to Matt Johnson’s talk Tuesday @4pm in Milan hall to hear more.
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The minor spliceosome is a master immune regulator
Pathogenic variants in non-coding genes are emerging as critical contributors to human rare diseases. We identified 19 individuals with early-onset diabetes (diagnosed <5 years) and additional clinica...
https://www.medrxiv.org/content/10.1101/2025.09.12.25335567v1
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reposted by
Mike Weedon
Nature Metabolism
3 months ago
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Common genetic variants modify disease risk and clinical presentation in monogenic diabetes
Nature Metabolism, Published online: 09 September 2025; doi:10.1038/s42255-025-01372-0In clinical and population-based cohorts, a strong contribution of polygenic risk for type 2 diabetes (T2D) significantly modifies the onset and phenotypic variability of maturity-onset diabetes of the young (MODY). This polygenic T2D burden may also account for MODY-like individuals without identified monogenic causes.
https://bit.ly/46iUsrF
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reposted by
Mike Weedon
Jacques Murray Leech
3 months ago
Now out in
@natmetabolism.nature.com
! Excited to share our work showing how common genetic changes shape how diabetes presents in MODY (Maturity-Onset Diabetes of the Young). Our findings highlight the growing overlap between monogenic and polygenic forms of diabetes.
www.nature.com/articles/s42...
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Common genetic variants modify disease risk and clinical presentation in monogenic diabetes - Nature Metabolism
In clinical and population-based cohorts, a strong contribution of polygenic risk for type 2 diabetes (T2D) significantly modifies the onset and phenotypic variability of maturity-onset diabetes of th...
https://www.nature.com/articles/s42255-025-01372-0
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reposted by
Mike Weedon
Aparajita Sriram
3 months ago
Our paper is now out on Diabetes!
diabetesjournals.org/diabetes/art...
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Rare Variants in NEUROD1 and PDX1 Are Low-Penetrance Causes of MODY, Whereas Those in APPL1 and WFS1 Are Not Associated With MODY
An accurate genetic diagnosis of maturity-onset diabetes of the young (MODY) is critical for personalized treatment. To avoid misdiagnosis, only genes with
https://diabetesjournals.org/diabetes/article-abstract/doi/10.2337/db25-0442/163164/Rare-Variants-in-NEUROD1-and-PDX1-Are-Low?redirectedFrom=PDF
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reposted by
Mike Weedon
Jacques Murray Leech
4 months ago
New preprint out now! We show polygenic background shapes GCK-MODY clinical presentation. In >1,000 cases, higher polygenic risk increased the chance of exceeding diagnostic diabetes thresholds, highlighting how monogenic & polygenic factors jointly shape disease.
#Genetics
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reposted by
Mike Weedon
Robin Hofmeister
4 months ago
🚨 Our parent-of-origin study is out in Nature! 🧬 Maternal and paternal alleles can have distinct — even opposite — effects on human traits, revealing a hidden layer of genetic architecture that standard GWAS miss. 🔗
www.nature.com/articles/s41...
Highlights below!
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reposted by
Mike Weedon
5 months ago
🚨Big news! Excited to share my first PhD paper!🎉 We validated & improved a T1D risk model using TrialNet data (originally from TEDDY), boosting accuracy 📈
bmcmedicine.biomedcentral.com/articles/10....
Try the web tool 👉
t1dpredictor.diabetesgenes.org
#T1D
#RiskPrediction
#PrecisionMedicine
#TrialNet
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Development and recalibration of a multivariable type 1 diabetes prediction model for type 1 diabetes across multiple screening studies - BMC Medicine
Background Accurate type 1 diabetes prediction is important to facilitate screening for pre-clinical type 1 diabetes to enable potential early disease-modifying interventions and to reduce the risk of...
https://bmcmedicine.biomedcentral.com/articles/10.1186/s12916-025-04225-5
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reposted by
Mike Weedon
The Lancet Diabetes & Endocrinology
5 months ago
New Research: Non-autoimmune, insulin-deficient
#diabetes
in children and young adults in
#Africa
: evidence from the Young-Onset Diabetes in sub-Saharan Africa (YODA) cross-sectional study
thelancet.com/journals/lan...
#T1D
#OpenAccess
#MedSky
#EndoSky
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Non-autoimmune, insulin-deficient diabetes in children and young adults in Africa: evidence from the Young-Onset Diabetes in sub-Saharan Africa (YODA) cross-sectional study
In sub-Saharan Africa, clinically diagnosed type 1 diabetes is heterogeneous, comprising classic autoimmune type 1 diabetes and a novel, non-autoimmune, insulin-deficient diabetes subtype. There is ev...
https://thelancet.com/journals/landia/article/PIIS2213-8587(25)00120-2/fulltext
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reposted by
Mike Weedon
James Russ-Silsby
5 months ago
Really proud of this Exeter–Stanford collaboration identifying bi-allelic variants in PAX4 as a novel cause of transient neonatal diabetes—the first new genetic cause of this subtype described in over a decade. This work expands our understanding of beta cell development. 🔗
doi.org/10.1016/j.mo...
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Complete Loss of PAX4 causes Transient Neonatal Diabetes in Humans
Gene discovery studies in individuals with diabetes diagnosed within 6 months of life (neonatal diabetes, NDM) can provide unique insights into the de…
https://www.sciencedirect.com/science/article/pii/S2212877825001085
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reposted by
Mike Weedon
medRxivpreprint
5 months ago
Population prevalence, penetrance, and mortality for genetically confirmed MODY
https://www.medrxiv.org/content/10.1101/2025.06.30.25330354v1
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reposted by
Mike Weedon
Zoltán Kutalik
5 months ago
Lausanne Comp Bio Symposium 2025 (
cbiosymposium.unil.ch
) 🗓 Abstract deadline 30 June (𝟑 𝐝𝐚𝐲𝐬 𝐭𝐨 𝐠𝐨!!!) 🎤 Oral presentation notifications: 7 July ✅ Early Bird registration deadline: 11 July 💰 Registration fee for non-PI: 150 CHF
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reposted by
Mike Weedon
Luke Sharp
6 months ago
MODY is prevalent in later onset diabetes. Really proud to announce the release of a preprint of our paper assessing MODY in people diagnosed with diabetes later in life!!
#MonogenicDiabetes
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reposted by
Mike Weedon
Anna Gloyn
6 months ago
Out today from
#HectorOrtega
&
#SethASharp
A state of the art review on polygenic risk scores (#PRS) in diabetes. This is your #101 on what we currently know about them and their application to understanding disease heterogeneity & clinical translation. Read for free here -
rdcu.be/eprel
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reposted by
Mike Weedon
Aparajita Sriram
6 months ago
Excited to share the preprint of our paper (my first paper!) looking at limited evidence MODY genes. We use rare variant burden testing and one of the largest MODY cohorts to evaluate the pathogenicity of these genes. This evidence can help inform clinical guidelines in MODY genetic testing!
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reposted by
Mike Weedon
James Fasham
7 months ago
Congratulations
@carolinefwright.bsky.social
for being elected to a fellow of the Academy of Medical Sciences! 🍾!
news.exeter.ac.uk/faculty-of-h...
@nihrexeterbrc.bsky.social
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reposted by
Mike Weedon
Caroline Wright
7 months ago
⬇️ again. I feel the need to re-post this point pretty much every week! Benign variants are not low penetrance.
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reposted by
Mike Weedon
Amber Luckett
8 months ago
Our new paper updating GRS2 with a new tool to easily generate standardised T1DGRS 🧬 Thanks to Seth Sharp,
@annagloyn.bsky.social
, Richard Oram and
@mnweedon.bsky.social
for a great collaboration!
tinyurl.com/4bsaz9hx
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Standardized Measurement of Type 1 Diabetes Polygenic Risk Across Multiancestry Population Cohorts
Amber M. Luckett, Richard A. Oram, Aaron J. Deutsch, Hector I. Ortega, Diane P. Fraser, Kaavya Ashok, Alisa K. Manning, Josep M. Mercader, Manuel A. Rivas,
https://tinyurl.com/4bsaz9hx
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reposted by
Mike Weedon
Caroline Wright
8 months ago
"Remember that it's not only scientists that read your papers" - sage advice from author of a beautiful poem 'Proband', which began life as a response to our DDD NEJM paper, linking genomic science and its patients.
www.consilience-journal.com/issue-17-pro...
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Proband — Consilience
https://www.consilience-journal.com/issue-17-proband
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reposted by
Mike Weedon
James Russ-Silsby
8 months ago
There are fewer than 10 documented genetic causes of Transient Neonatal Diabetes (TNDM) and now PAX4 is one of them! Really proud of this collaborative work done between the Neonatal Diabetes Research Team at Exeter and the Translational Genomics of Diabetes Lab in Stanford.
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reposted by
Mike Weedon
Caroline Wright
8 months ago
Come and work with us - 2 Graduate Research Assistant positions available in genomic medicine, with a particular focus on variant interpretation and data analysis. Part of the Wellcome-funded PARADIGM project, and based in beautiful Exeter UK!
jobs.exeter.ac.uk/hrpr_webrecr...
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reposted by
Mike Weedon
Jeff Spence
9 months ago
A really nice paper by
@drghawkes.bsky.social
et al. argues that rare and common genetic associations converge on the same genes. While this seems at odds with our recent work about how burden tests and GWAS prioritize different genes, our results agree (🧬🧪🧵 1/6)
www.biorxiv.org/content/10.1...
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Whole-genome sequencing analysis of anthropometric traits in 672,976 individuals reveals convergence between rare and common genetic associations
Genetic association studies have mostly focussed on common variants from genotyping arrays or rare protein-coding variants from exome sequencing. Here, we used whole-genome sequence (WGS) data in 672,...
https://www.biorxiv.org/content/10.1101/2025.02.24.639925v1
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reposted by
Mike Weedon
Dr Gareth Hawkes
9 months ago
Excited to be able to announce I’ll be starting a 5-year MRC Career Development Award fellowship next week on the 1st April at the University of Exeter! Lots of work to do on whole genomes, and I’m hoping to keep contributing my small piece!
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reposted by
Mike Weedon
Daniel MacArthur
9 months ago
New preprint! We worked with
@msftresearch.bsky.social
and
@broadinstitute.org
to see whether large language models (LLMs) can be useful to variant scientists in deciding whether genetic variants seen in a patient are responsible for their disease. tl;dr yes they can:
www.biorxiv.org/content/10.1...
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Evidence Aggregator: AI reasoning applied to rare disease diagnostics
Retrieving, reviewing, and synthesizing technical information can be time-consuming and challenging, particularly when requiring specialized expertise, as is the case of variant assessment for rare di...
https://www.biorxiv.org/content/10.1101/2025.03.10.642480v1
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reposted by
Mike Weedon
Caroline Wright
9 months ago
Exciting times for genomics research
@exeter.ac.uk
@nihrexeterbrc.bsky.social
! 🧬 New preprint from the team: using large-scale WGS from
@ukbiobank.bsky.social
and All of Us shows convergence between rare and common genetic associations, with implications for genetic architecture of complex traits.
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reposted by
Mike Weedon
Dr Gareth Hawkes
10 months ago
This was a really fun and exciting project to work on, and hopefully shows we're not near to exhausting population-scale WGS data. A great collaboration led by
@mnweedon.bsky.social
@drarwood.bsky.social
and
@carolinefwright.bsky.social
, with
@chundru.bsky.social
and
@rnbeaumont.bsky.social
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reposted by
Mike Weedon
John Dennis
10 months ago
5-drug precision prescribing for people with type 2 diabetes is here Our model for optimising glucose lowering therapy using low-cost routine clinical features published in the Lancet today Paper:
thelancet.com/journals/lan...
Try the web tool here:
diabetesgenes.org/t2-treatment/
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reposted by
Mike Weedon
University of Exeter
10 months ago
Millions of people with type 2 diabetes could receive better treatment thanks to a new, simple low-cost tool, according to groundbreaking research announced today at the Diabetes UK Professional Conference and published in the Lancet. 1/3
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reposted by
Mike Weedon
Mike Inouye
10 months ago
Exeter doing some great stuff with biobank scale WGS at the moment! Whole-genome sequencing analysis of anthropometric traits in 672,976 individuals reveals convergence between rare and common genetic associations
www.biorxiv.org/content/10.1...
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Whole-genome sequencing analysis of anthropometric traits in 672,976 individuals reveals convergence between rare and common genetic associations
Genetic association studies have mostly focussed on common variants from genotyping arrays or rare protein-coding variants from exome sequencing. Here, we used whole-genome sequence (WGS) data in 672,...
https://www.biorxiv.org/content/10.1101/2025.02.24.639925v1
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Whole-genome sequencing analysis of anthropometric traits in 672,976 individuals reveals convergence between rare and common genetic associations:
tinyurl.com/ye2yhx9t
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https://tinyurl.com/ye2yhx9t
10 months ago
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reposted by
Mike Weedon
Dr Gareth Hawkes
10 months ago
Excited to finally share that our paper looking at the effect of rare non-coding variants using WGS on circulating protein levels in the UKB has been released in Nature Genetics
@naturegenet.bsky.social
! We now analyse the full 3,000 circulating proteins in all 50,000 individuals
rdcu.be/ea16i
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Whole-genome sequencing analysis identifies rare, large-effect noncoding variants and regulatory regions associated with circulating protein levels
Nature Genetics - Rare variant association analysis of plasma proteins using whole-genome sequencing data in 54,306 individuals in the UK Biobank demonstrates that combining both single-variant and...
https://rdcu.be/ea16i
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reposted by
Mike Weedon
Dr Gareth Hawkes
10 months ago
We’re hiring! Looking for a motivated data scientist/bio-informatician to join our team analysing WGS across biobanks via meta analysis, with a focus on T2D and its related traits. Please get in touch if you’re interested!
tinyurl.com/3wdfc2me
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https://tinyurl.com/3wdfc2me
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A great opportunity to join us in Exeter as a Lecturer in Health Data Science:
tinyurl.com/2sy7w2y5
. Please get in touch if you're interested!
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https://tinyurl.com/2sy7w2y5
10 months ago
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reposted by
Mike Weedon
Andrew Wood
10 months ago
Excited to see our paper on medRxiv "Streamlining Large-Scale Genomic Data Management: Insights from the UK Biobank Whole-Genome Sequencing Data". Paper here:
www.medrxiv.org/content/10.1...
. Tools here:
github.com/drarwood/vcf...
.
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Streamlining Large-Scale Genomic Data Management: Insights from the UK Biobank Whole-Genome Sequencing Data
Biobank-scale Whole-Genome Sequencing (WGS) studies are increasingly pivotal in unraveling the genetic bases of diverse health outcomes. However, managing and analyzing these datasets' sheer volume an...
https://www.medrxiv.org/content/10.1101/2025.01.27.25321225v1
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