@TheGenomeLab

Group Leader of the Genome Function Laboratory @TheCrick From 2025, find me over on the other side: https://xitter.cf/t.co/ajOqpCvaUY (he/him)

 London
crick.ac.uk/research/labs/greg-findlay
Joined July 2011
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  • Following294
  • Followers1.2K
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Great to see this out now in @CellGenomics . A few points about what we learned in revisions over on BlueSky: bsky.app/profile/gregfindlay…
Greg Findlay@TheGenomeLab2 Apr 2024
Our latest from @TheCrick, now on @biorxivpreprint: biorxiv.org/content/10.1101/… Michael Herger (@HergerMichael) and Christina Kajba jointly led development of a new prime editing platform for testing large numbers of human genetic variants.

High-throughput screening of human genetic variants by pooled prime editing

Understanding the effects of rare genetic variants remains challenging, both in coding and non-coding regions. While multiplexed assays of variant effect (MAVEs) have enabled scalable functional...

biorxiv.org
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Join us for a PhD! Applications close November 5th. crick.ac.uk/careers-study/va…
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Crick PhD recruitment for fall 2025 is officially open! Please apply to our lab through the Crick application portal if interested. 👇 crick.ac.uk/careers-study/va…
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New from our lab @TheCrick , led by @BetkaRoe. A fun side project that tried to understand what happens when a chaperonin encounters a translating ribosome. biorxiv.org/content/10.1101/…
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Come join us in making agriculture sustainable at @PhytoformLabs! 🌱We are looking for an R&D scientist with a background in Synthetic biology to join our tools & traits team for precision genome editing 🧬. If you think this could be you, please apply! linkedin.com/jobs/view/39723…

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So excited that our paper “De novo variants in the RNU4-2 snRNA cause a frequent neurodevelopmental syndrome” is out today in @Nature nature.com/articles/s41586-0… 🧵 1/16

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′...

nature.com
Yuyang Chen@quenchentin11 Jul 2024
(1/4) I’m delighted to announce that our research on RNU4-2 is now out on @Nature . This is an exciting finding that will bring many diagnoses worldwide. We have updated some new results since the preprint: nature.com/articles/s41586-0…

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′...

nature.com
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We are delighted to announce that Professor Edith Heard has been appointed as our new director and chief executive! Edith, who is currently director-general at @EMBL, will succeed Paul Nurse in leading the Crick from the summer of 2025. 🔗 crick.ac.uk/news/2024-07-09_…
"The Francis Crick Institute has quickly established a global reputation for its work at the frontiers of science. I relish the challenge of building on that work. I also want to pay tribute to Sir Paul Nurse, without whom the Francis Crick Institute would not be the world-leading institution it is today." - Edith Heard

ALT "The Francis Crick Institute has quickly established a global reputation for its work at the frontiers of science. I relish the challenge of building on that work. I also want to pay tribute to Sir Paul Nurse, without whom the Francis Crick Institute would not be the world-leading institution it is today." - Edith Heard

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Want to fully investigate this large dataset beyond classical 2D formats? Go interactively explore the data 👇 vhl-board.onrender.com/
Greg Findlay@TheGenomeLab5 Jul 2024
Replying to @TheGenomeLab
The VHL data can also be searched, visualised, and explored using this awesome SGE visualisation platform made by @ChloeTerwagne: vhl-board.onrender.com/ Chloé’s code is all on GitHub if you’re interested in viewing and sharing your own data like this. (3/n)
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Massive thanks to all authors, but particularly @ChloeTerwagne, Athina Ganner, @LauraCubitt3, @ReidBrewer3, Dong-Kyu Kim & @Eivakine for key inputs to revisions. And, of course, many thanks to reviewers, @nature_genet, and funders @TheCrick @CRUKresearch (7/n)
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Of course, we hope you read the paper and use the data. Do feel free to reach out with questions on anything from protocol tips to variant classifications. (8/n)
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Finally, we’re delighted to see this published back-to-back with a massive SGE analysis of BAP1 led by Andrew Waters, @David_J_Adams and co. @sangerinstitute: nature.com/articles/s41588-0… So many more variants now readily interpretable, and still more on the way! (9/9)

Saturation genome editing of BAP1 functionally classifies somatic and germline variants

Nature Genetics - Saturation genome editing characterizes BAP1 variants and their association with disease presentation. A phenome-wide association analysis in the UK finds that BAP1 variants...

nature.com
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Lots more new analyses and validations in the paper, too. For instance, comparing function scores to SpiceAI and FoldX computational predictions – both of which do reasonably well. (6/n)
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In new experiments, we also characterise novel mechanisms made apparent by SGE. Specifically, we show that a long C-terminus extension leads to LoF via VHL protein destablization and that stop-codon readthrough can impact the degree of functional impairment. See Fig. 6! (5/n)
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The VHL data can also be searched, visualised, and explored using this awesome SGE visualisation platform made by @ChloeTerwagne: vhl-board.onrender.com/ Chloé’s code is all on GitHub if you’re interested in viewing and sharing your own data like this. (3/n)
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Importantly, we now split loss-of-function variants by SGE score into LOF1 (lowest) and LOF2 (depleted, weaker effect). In collaboration w Athina Ganner and Freiburg colleagues, we show how patients with VHL disease can be stratified by ccRCC risk using these categories. (4/n)
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Our work led by @megan_buckley01 on Saturation Genome Editing of VHL is now out in @NatureGenet: nature.com/articles/s41588-0… Many new experiments and analyses to quickly highlight… (1/n)

Saturation genome editing maps the functional spectrum of pathogenic VHL alleles

Nature Genetics - Saturation genome editing characterizes von Hippel–Lindau (VHL) coding variants and their associations with diseases. Function scores for 2,268 VHL single-nucleotide...

nature.com
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Most importantly, all SGE scores and variant classifications are available for download in Supplementary Table 1 and from MAVEdb (mavedb.org/experiments/urn:m…). Given the data’s high precision, we expect this will lead to a steep reduction in VUS reported clinically. (2/n)
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Our DNA Typewriter protocol (written by @LiaoHanna, @JShendure, and myself) is out! Thank you @NatureProtocols for writing/editing this with us and having it as this week’s #FeaturedProtocol :-)
Nature Protocols@NatureProtocols11 Jun 2024
#FeaturedProtocol this week from Jay Shendure on using #DNATypewriter (#primeediting-based method) for tracing insertional events bit.ly/4cegahU
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Happy to share this opportunity to join our team. Please apply if you are interested, or re-post if you are not on the look out for a new job crick.wd3.myworkdayjobs.com/…
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Excited to see our work on the development of a platform for pooled screening of genetic variants using prime editing published on @biorxivpreprint: doi.org/10.1101/2024.04.01.5….
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