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alexblakes.bsky.social

@alexblakes.bsky.social
81 followers 122 following 16 posts
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Nicky Whiffin @nickywhiffin.bsky.social · 30/09/2026
Huge thank you to the patients and families who generously gave samples, without whom this work wouldn't have been possible 💙 And to amazing collaborators: Carlo Rinaldi, Dora Markati, Mike Griffiths, Benjamin Cogné, @stefanbarakat.bsky.social, @jeffbarrett.eu, and Stephan Sanders 🙏 End 🧵
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Nicky Whiffin @nickywhiffin.bsky.social · 30/09/2026
Excited to share our new preprint "A cross-tissue splicing signature as a quantitative biomarker for ReNU syndrome" tinyurl.com/RENUsig Led by super⭐ duo @ruebenadawes.bsky.social @alexblakes.bsky.social We show that just 6 alternative 5'splice site events perfectly predict ReNU syndrome 🧬 🧵 1/4
A panel of 4 plots.
Top left: a bar plot of LASSO coefficients for the six 5' splice site events chosen by the model.
Top right: Box plots showing the LASSO predicted probability of case status for controls compared to ReNU cases across whole-blood and lymphocyte cohorts, for training and test samples. P(case) for ReNU samples are significantly greater than controls.
Bottom left: schematics of the six alternative 5' splice site events.
Bottom right: Box plots showing significant changes in expression for two of the implicated genes, STX16 and RPS15A.
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Kartik Chundru @chundru.bsky.social · 08/11/2025
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”
biorxiv.org
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...
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Eloise Beer Wells @eloisewells.bsky.social · 10/12/2025
*A new pre-print on increasing gene expression!* 🧬📈 doi.org/10.64898/202...
doi.org
Modulating splicing in five prime untranslated regions to treat rare haploinsufficient disease
Rare genetic disorders collectively impact over 300 million people worldwide, yet around 95% have no specific treatments. For the many rare disorders caused by haploinsufficiency, effective therapies ...
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James Fasham @jamesfasham.bsky.social · 08/12/2025
Our new study defines a distinct #neurogenetic condition arising from recurrent structural variants at 16p13.3 palindrome. Individuals show progressive ataxia, cognitive decline, and a characteristic MRI pattern with caudate & cerebellar atrophy. #Genomics #RareDisease 🧵1/3
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Nicky Whiffin @nickywhiffin.bsky.social · 08/09/2025
I absolutely love this figure in a second paper led by Adam Jackson, @alexblakes.bsky.social, and Sid Banka (www.medrxiv.org/content/10.1...) of RNU gene diagnoses in @genomicsengland.bsky.social 100k genomes project. (1) showing just how many new diagnoses are found across these genes ❤️ 2/3
Two pie charts. On the left, a small segment of a grey pie chart labelled 'Unsolved NDD (N=7,968, 100%)' is shaded dark. A zoom out from this small segment shows individuals with new "RNU-opathies" in 100KGP (N=118, 1.48%). This has five segments, in order of size: (1) RNU4-2 dominant (N=59, 0.74%), (2) RNU2-2 recessive (N=38, 0.48%), (3) RNU2-2 dominant (N=11, 0.14%), (3) RNU4-2 recessive (N=5, 0.06%), (4) RNU5B-1 dominant (N=5, 0.06%).
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alexblakes.bsky.social @alexblakes.bsky.social · 08/09/2025
The biology here is fascinating too. Really nice to see the clustering of compound het / homozygous variants in the Sm site in your cohort for example.
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alexblakes.bsky.social @alexblakes.bsky.social · 08/09/2025
Congratulations to you and the whole team on this really beautiful work. This is a really important discovery for patients and families affected by rare conditions.
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Reposted by @alexblakes.bsky.social
Ewan Birney @ewanbirney.bsky.social · 08/09/2025
This is ... just brilliant. Another ncRNA gene involved in rare developmental diseases, and these are a meaningful number of new cases - also interesting the dominance/linear/recessive differences
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Reposted by @alexblakes.bsky.social
Christel Depienne @christeldepienne.bsky.social · 05/09/2025
After our study on RNU4-2 and RNU5B-1 published in May (Nava et al, Nature Genetics 2025), I am excited to share our new preprint reporting dominant and recessive variants in RNU2-2 as a frequent cause of developmental and epileptic encephalopathy (DEE). 📄 www.medrxiv.org/content/10.1...
medrxiv.org
Systematic analysis of snRNA genes reveals frequent RNU2-2 variants in dominant and recessive developmental and epileptic encephalopathies
Variants in spliceosomal small nuclear RNA (snRNA) genes RNU4-2 (ReNU syndrome), RNU5B-1 , and RNU2-2 have recently been linked to dominant neurodevelopmental disorders (NDDs), revealing a major, prev...
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Nicky Whiffin @nickywhiffin.bsky.social · 08/09/2025
(2) but even cooler is the flip of frequency between dominant and recessive forms in RNU4-2 and RNU2-2, driven by different signatures of mutation and selection - variants across RNU2-2 tend to be more common, driving a higher comp het frequency. We have a lot to learn from these genes yet!!! 🧬🤓
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Reposted by @alexblakes.bsky.social
Nicky Whiffin @nickywhiffin.bsky.social · 08/09/2025
While I was taking a holiday last week, 2 super exciting preprints dropped, adding to another posted 6 days prior. These papers describe a remarkable role for *recessive* variants in *RNU2-2* causing developmental and epileptic encephalopathy 🧵 by the amazing @christeldepienne.bsky.social 👇 1/3
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alexblakes.bsky.social @alexblakes.bsky.social · 31/08/2025
Congratulations @alextremophile.bsky.social, tremendous to see this online! :)
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Alex Geary @alextremophile.bsky.social · 29/08/2025
I am super proud to present our new manuscript “Using SpliceAI to triage splice-altering variants in 7,220 individuals with rare conditions highlights limitations of the precomputed scores” www.medrxiv.org/content/10.1...
medrxiv.org
Using SpliceAI to triage splice-altering variants in 7,220 individuals with rare conditions highlights limitations of the precomputed scores
Background: SpliceAI is a deep learning algorithm that predicts whether genetic variants are likely to affect splicing. Precomputed spliceAI predictions for all theoretical SNVs and small indels were ...
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Ruby Dawes @ruebenadawes.bsky.social · 29/08/2025
Love when you can build a paper out of a personal bugbear! tl;dr the precomputed SpliceAI scores are great, but proceed with caution!
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Luke Pilling @lcpilling.bsky.social · 29/08/2025
Very exciting to have access to "Our Future Health" data and begin understanding what is available and how to access it Many thanks to the volunteers so far. Still a long way to go - consider signing up if you haven't already! This is a greater primer on the aims www.nature.com/articles/s41...
nature.com
Our Future Health: a unique global resource for discovery and translational research - Nature Medicine
Our Future Health has recruited more than 1 million participants in the UK, with biobanked bloods, making it the largest consented cohort of its type in the world.
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Reposted by @alexblakes.bsky.social
yuyangchen.bsky.social @yuyangchen.bsky.social · 26/08/2025
3/3 I am thrilled to be part of a study establishing the clinical phenotypes of NDD associated with recessive variants in RNU4-2. Thank you to @rociorius.bsky.social, @alexblakes.bsky.social, @cassimons.bsky.social and @nickywhiffin.bsky.social for leading this work! More details: lnkd.in/eTJ5Rapt
lnkd.in
New recessive neurodevelopmental disorder caused by RNU4-2 variants | Nicola Whiffin posted on the topic | LinkedIn
I am excited to share our preprint describing a new **recessive** neurodevelopmental disorder caused by variants in the non-coding snRNA RNU4-2 🎉 https://lnkd.in/dHNDCsDe Led by two super ⭐ s Roci...
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yuyangchen.bsky.social @yuyangchen.bsky.social · 26/08/2025
1st Bluesky post with recent updates: 1/3 It was incredible to attend and speak at the ReNU Hope Conference in Long Island, NY. This was the first time I met the families and the ReNU warriors, sharing many touching stories. I hope to continue advocacy in China where few are currently diagnosed.
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rociorius.bsky.social @rociorius.bsky.social · 19/08/2025
Nuevo diagnóstico ligado a #RNU4-2 🧬: variantes bialélicas causan un #TND recesivo con cambios característicos en sustancia blanca en RM 👉 hay que considerar este gen no codificante en la búsqueda/diagnóstico. tinyurl.com/3j9r56s8 La historia completa la cuenta @alexblakes.bsky.social aqui 🧵👇
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Daniel MacArthur @dgmacarthur.bsky.social · 18/08/2025
New preprint! The outcome of a wonderful collaboration with @nickywhiffin.bsky.social’s team to define a new recessive syndrome associated with inherited variants in RNU4-2, the non-protein-coding gene that keeps on giving.
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Michel Nivard @michelnivard.bsky.social · 18/08/2025
This whole thread describes how 18 months of work on this tiny piece of genome identified 2/3 new syndromes. it’s a very compelling clinical genetics story!
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Greg Findlay @gregfindlay.bsky.social · 18/08/2025
Our latest research is out today on ‪@medrxivpreprint.bsky.social: www.medrxiv.org/content/10.1... Saturation genome editing of BRCA1 across cell types accurately resolves cancer risk. Led by the amazing Phoebe Dace. This one’s packed full of data, so check out the paper. Quick highlights… 🧵 1/n
medrxiv.org
Saturation genome editing of BRCA1 across cell types accurately resolves cancer risk
Germline pathogenic BRCA1 variants predispose women to breast and ovarian cancer. Despite accumulation of functional evidence for variants in BRCA1 , over half of reported single-nucleotide variants (...
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Reposted by @alexblakes.bsky.social
Nicky Whiffin @nickywhiffin.bsky.social · 18/08/2025
Isn't genetics cool??? Within only 145 nucleotides(!) of a non-coding RNA (RNU4-2) - different variants in distinct regions / structures cause three distinct disorders!!! (all discovered within the last 18 months) 🤯🤓🧬❤️
Schematic of the U4 and U6 snRNAs with coloured annotations to note nucleotides linked to different disorders:
- Teal in the T-loop and Stem III for ReNU syndrome (Chen et al. Nature 2024 and Greene et al. Nature Medicine 2024)
- Red for variants causing a recessive NDD in Stem II, the k-turn and Sm protein binding sites (De Jonghe et al. medRxiv 2025 and Rius & Blakes medRxiv 2025)
- Yellow for the central loop and Retinitis pigmentosa (Quinodoz et al. medRxiv 2025)
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Jeffrey Barrett @jeffbarrett.eu · 18/08/2025
Look at the insane speed of discovery around this snippet of DNA. Sometimes the machine of science is amazing. 🤩
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Alex Geary @alextremophile.bsky.social · 18/08/2025
An awesome piece of work by @alexblakes.bsky.social, @rociorius.bsky.social, @nickywhiffin.bsky.social and team! I am super excited to see more emerging from this tiny, but mighty gene, and am overjoyed at the implications this has for the rare disorders community ❤️
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Greg Findlay @gregfindlay.bsky.social · 18/08/2025
We recently performed SGE of RNU4-2 and identified functionally impactful variants underlying a new recessive disease. Today, the team led by @rociorius.bsky.social @alexblakes.bsky.social @cassimons.bsky.social & @nickywhiffin.bsky.social provide in-depth analysis of its clinical presentation. 🧵⬇️
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Nicky Whiffin @nickywhiffin.bsky.social · 18/08/2025
🚨 New preprint led by amazing duo @rociorius.bsky.social and @alexblakes.bsky.social in collaboration with @cassimons.bsky.social, @dgmacarthur.bsky.social and many other amazing folks! ❤️ We describe the clinical phenotype of a recessive NDD associated with biallelic variants in RNU4-2 🧬 See 🧵👇
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alexblakes.bsky.social @alexblakes.bsky.social · 18/08/2025
I learned so much from this work and I hope that and discoveries like this can make a real difference to the lives of people living with #RareConditions. Please do share! 😊 www.medrxiv.org/content/10.1...
medrxiv.org
Biallelic variants in the non-coding RNA gene RNU4-2 cause a recessive neurodevelopmental syndrome with distinct white matter changes
Genetic variants in RNU4-2, which encodes U4, a key non-coding small nuclear RNA (snRNA) component of the major spliceosome, were recently shown to cause a prevalent neurodevelopmental disorder (NDD) ...
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alexblakes.bsky.social @alexblakes.bsky.social · 18/08/2025
Thanks also to the institutions whose incredible resources and platforms have made this work possible, including @ukbiobank.bsky.social, @genomicsengland.bsky.social, @manchester.ac.uk, @ox.ac.uk, as well as our funders including @wellcometrust.bsky.social.
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alexblakes.bsky.social @alexblakes.bsky.social · 18/08/2025
A huge thank you to the patients and families who participated in the study, and clinical teams who contributed and made this work possible. To tag just a few collaborators from my extremely nascent Bluesky account… @christeldepienne.bsky.social @poseypod.bsky.social @anneotation.bsky.social
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alexblakes.bsky.social @alexblakes.bsky.social · 18/08/2025
... and supported by @dgmacarthur.bsky.social, @gregfindlay.bsky.social, Sid Banka (@mft-imrare.bsky.social), and collaborators across the world.🌏
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alexblakes.bsky.social @alexblakes.bsky.social · 18/08/2025
It’s been an absolute pleasure to work with and learn from @rociorius.bsky.social on a truly international collaboration led by @cassimons.bsky.social and @nickywhiffin.bsky.social...
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alexblakes.bsky.social @alexblakes.bsky.social · 18/08/2025
The functional data is incredibly helpful when it comes to variant classification. Scores from the saturation genome editing study separate really nicely between our cases and controls in UK Biobank, for example. But as always there are exceptions and variant interpretation can still be tricky!
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alexblakes.bsky.social @alexblakes.bsky.social · 18/08/2025
Importantly, most of the mutations potentially responsible for this condition fall outside of the #ReNU syndrome critical region – they cluster in other parts of the U4 structure which make contacts with other RNAs and proteins, or within U4 itself.
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alexblakes.bsky.social @alexblakes.bsky.social · 18/08/2025
The headlines? 1) Variants on both copies of #RNU4-2 cause a recessive neurodevelopmental disorder with prominent speech delay 2) One of the hallmarks is distinct white matter changes on MRI 3) It is clinically and genetically distinct from #ReNU syndrome www.medrxiv.org/content/10.1...
medrxiv.org
Biallelic variants in the non-coding RNA gene RNU4-2 cause a recessive neurodevelopmental syndrome with distinct white matter changes
Genetic variants in RNU4-2, which encodes U4, a key non-coding small nuclear RNA (snRNA) component of the major spliceosome, were recently shown to cause a prevalent neurodevelopmental disorder (NDD) ...
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alexblakes.bsky.social @alexblakes.bsky.social · 18/08/2025
Through international collaborations and with the help of clinicians across the world, we have assembled a cohort of patients with this new condition and describe the disorder here for the first time.
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alexblakes.bsky.social @alexblakes.bsky.social · 18/08/2025
Besides clarifying the critical regions of #RNU4-2 linked to #ReNU syndrome, this study found other regions of the gene which are sensitive to mutations, and raised the possibility of a distinct recessive condition related to the same gene.
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alexblakes.bsky.social @alexblakes.bsky.social · 18/08/2025
Following this, @joachimdejonghe.bsky.social and @gregfindlay.bsky.social led a beautiful saturation genome editing study to help clarify the impact of mutations across the full length of #RNU4-2. Here’s the study on @medrxivpreprint.bsky.social: www.medrxiv.org/content/10.1....
medrxiv.org
Saturation genome editing of RNU4-2 reveals distinct dominant and recessive neurodevelopmental disorders
Recently, de novo variants in an 18 nucleotide region in the centre of RNU4-2 were shown to cause ReNU syndrome, a syndromic neurodevelopmental disorder (NDD) that is predicted to affect tens of thous...
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alexblakes.bsky.social @alexblakes.bsky.social · 18/08/2025
Last year @yuyangchen.bsky.social, @nickywhiffin.bsky.social and co. made headlines with the extraordinary discovery of #ReNU syndrome – a dominant condition caused by *de novo* changes in a *non-coding* snRNA gene, #RNU4-2. www.nature.com/articles/s41....
nature.com
De novo variants in the RNU4-2 snRNA cause a frequent neurodevelopmental syndrome - Nature
The non-coding RNA RNU4-2, which is highly expressed in the developing human brain, is identified as a syndromic neurodevelopmental disorder gene, and, using RNA sequencing, 5′ splice-site use is...
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alexblakes.bsky.social @alexblakes.bsky.social · 18/08/2025
I am absolutely delighted to share our work describing a new *recessive* condition caused by variants in #RNU4-2. Yes, that #RNU4-2! tinyurl.com/3j9r56s8 @rociorius.bsky.social @yuyangchen.bsky.social @gregfindlay.bsky.social @dgmacarthur.bsky.social @cassimons.bsky.social @nickywhiffin.bsky.social
medrxiv.org
Biallelic variants in the non-coding RNA gene RNU4-2 cause a recessive neurodevelopmental syndrome with distinct white matter changes
Genetic variants in RNU4-2, which encodes U4, a key non-coding small nuclear RNA (snRNA) component of the major spliceosome, were recently shown to cause a prevalent neurodevelopmental disorder (NDD) ...
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