iiinova — where your digital self keeps evolving

Do reach out if interested in establishing PETRA in your system. Thanks for reading, and thanks to our generous funders for all their support. 🙏 @crick.ac.uk @erc.europa.eu END/9

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We hope PETRA’s scalability and flexibility make the method attractive to many labs studying a wide range of genes and cell types, with applications to dissecting the logic of gene regulation, discovering beneficial edits for therapies, and generating data to benchmark and refine AI models. 8/9

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Lastly, PETRA can be used to assess the performance of state-of-the-art AI models, such as Borzoi and AlphaGenome. Correlations between PETRA scores and model outputs vary highly across the four genes studied, emphasising the need to generate more data in diverse genomic contexts. 7/9

Correlations between PETRA expression scores and outputs of sequence-to-expression models.

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Comparing variant sets between primary T cells and Jurkats reveals highly correlated effects for VAV1, but much less so for IL2RA. 6/9

Correlation of expression scores between Jurkats and primary T cells.

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We define TF motifs that modulate expression and engineer alleles with 2+ motifs via combinatorial PE. Expression effects are largely additive. For example, some alleles with multiple MYBL2 motifs express >10-fold more IL2RA RNA. Conversely, CTCF motifs can effectively silence target genes. 5/9

Map of combinatorial MYBL2 and EGR1 motif insertions to IL2RA with expression scores for all possible combinations.

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Scoring of random 6-mer insertions in large libraries is highly reproducible, with dozens of variants having relatively large effects (over 2-fold). Effects of insertions across different genes are largely context dependent, reflecting e.g. transcription factor (TF) binding site creation. 4/9

Variants from the initial screen were re-tested in a smaller library for validation, confirming strong effects.

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PETRA affords high scalability and flexibility, as no pre-engineering or elaborate assay optimisation is required. We demonstrate PETRA across four loci in Jurkat cells and two loci in primary T cells, scoring over 14,000 engineered sequences in total. Highlights of our Results are as follows: 3/9

PETRA enables expression effects to be read out via amplicon sequencing of edited loci.

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PETRA leverages prime editing to test variants installed downstream of target genes' transcription start sites. This allows RNA-level effects to be quantified in multiplex via amplicon sequencing of DNA and RNA, akin to the strategy of STARR-seq but with the big advantage of endogenous editing. 2/9

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The Francis Crick Institute @crick.ac.uk · 06/11/2025

Our latest story is now on bioRxiv. We present PETRA, a new method for deciphering how sequence variants impact gene regulation at scale. www.biorxiv.org/content/10.1... This work was led by Magdalena Armas Reyes, a @crick.ac.uk PhD student until very recently. Congrats, Dr. Armas! 🧵 1/9

biorxiv.org

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Reposted by Greg Findlay

We each carry around six million variations in our DNA. Henry Scowcroft explores how scientists like @gregfindlay.bsky.social and @carovinuesa.bsky.social are helping unravel the effects of these variants, where even a small change can have a big impact on our lives. www.crick.ac.uk/news/2025-10...

Variants: the typos turning loss into hope

Across the 3 billion ‘letters’ of our DNA, we each carry around 6 million variations. Researchers are unravelling their effects on our lives.

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Reposted by Greg Findlay

The Francis Crick Institute @crick.ac.uk · 30/10/2025

Just a few weeks left to apply for our clinical PhD programme. We're looking for clinicians who are passionate about research to join the 3-year fully funded programme. Learn more and see what positions are available ⬇️ www.crick.ac.uk/careers-and-...

Doctoral clinical fellows

The Crick's clinical PhD programme.

048

Reposted by Greg Findlay

Nicky Whiffin @nickywhiffin.bsky.social · 16/10/2025

Planning your afternoon poster session at #ashg25? Come say hello! This is an amalgamation of our two recent preprints - working with @gregfindlay.bsky.social , @cassimons.bsky.social , @dgmacarthur.bsky.social and many others to study variation across RNU4-2 and describe a new recessive NDD 🧬

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And lastly, come chat with me about Phoebe Dace's latest work on performing saturation genome editing of BRCA1 across cell types at poster 9004T, Thursday 2:30-4:30pm. Or come by just to say hi!

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michaelherger.bsky.social @michaelherger.bsky.social · 15/10/2025

On Friday, @chloeterwagne.bsky.social will present: “A scalable framework to link rare human variants to disease phenotypes using pooled prime editing” Friday Oct 17th at 1:40pm, Rm205ABC You can also catch up with Chloé at her poster, 5002T, Thursday 2:30-4:30

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Reposted by Greg Findlay

Excited to be presenting our work on "Saturation mutagenesis of 37 human splicing factor genes using pooled prime editing" later today at #ASHG2025 during the Platform Session "RNA Functions Beyond Coding Sequences" (1:30-2:30PM, Room 205ABC).

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Tomorrow, October 16 at 2:00 pm, @magdaarmas.bsky.social presents a new method: "Modulating gene expression in human cells via high-throughput prime editing of regulatory elements" [Rm210AB]

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Greg Findlay @gregfindlay.bsky.social · 09/10/2025

Hello Boston! The lab is delighted to be at #ASHG25🧬 Check out our talks over the next few days - all unpublished stories. Kicking things off is @michaelherger.bsky.social presenting "Saturation mutagenesis of 37 human splicing factor genes with pooled prime editing". Today @2pm, Rm205abc Also 👇

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We're recruiting early career Group Leaders this autumn! I cannot think of a better place to build a lab. Come join us! 👇

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Greg Findlay @gregfindlay.bsky.social · 01/10/2025

This year the lab is also participating in the Crick's Future Leaders in Biomedical Sciences scholarship programme, which has opened for candidates of Black or mixed Black heritage. www.crick.ac.uk/careers-and-...

Future Leaders in Biomedical Sciences: How to Apply

How to apply for a Future Leaders in Biomedical Sciences Scholarship. Open to candidates of Black or mixed Black heritage only.

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Greg Findlay @gregfindlay.bsky.social · 01/10/2025

🚨 Applications to the Crick PhD programme are now open! We are pleased to be recruiting this year. 👇 www.crick.ac.uk/careers-stud...

Findlay Lab | Developing novel genome editing methods to test human genetic variants at scale

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Reposted by Greg Findlay

The Francis Crick Institute @crick.ac.uk · 01/10/2025

We're looking for clinicians who are passionate about research to join our 3-year fully funded clinical PhD programme. 🔬🩺 Apply by 14 November 2025. 👇 www.crick.ac.uk/careers-stud...

Doctoral clinical fellows

The Crick's clinical PhD programme.

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Greg Findlay @gregfindlay.bsky.social · 08/09/2025

We now have an open post-doc position in the lab: crick.wd3.myworkdayjobs.com/External/job... Please apply if you have a background in functional genomics or a related field and are eager to develop methods to map variant effects at scale.

crick.wd3.myworkdayjobs.com

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Greg Findlay @gregfindlay.bsky.social · 04/09/2025

Hugely thankful for this 🙏. We will do our best to make the most of it. @erc.europa.eu!

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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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This story is the PhD work of Phoebe Dace, who has done remarkably well to bring this all together. Congrats, Phoebe! 👏 Thanks to the lab, Nicole, @lcubes.bsky.social @chloeterwagne.bsky.social and Megan), our great collaborators, and @crick.ac.uk & @cancerresearchuk.org for vital funding. 🙏 END/16

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Rather than confounding clinical interpretation, having data from multiple models is clearly preferable. A path forward to more precisely calibrating the risk caused by individual variants is to integrate functional evidence from multiple experimental data sets generated at scale. 15/n

A Sankey plot of functional evidence derived for BRCA1 variants using SGE across cell lines

In summary, this work reveals the extent to which variant effects can be contingent upon the cell model used. As quality functional data from a single cell line often tips the balance of evidence in favour of pathogenicity or benignity, this is critical to recognise. 14/n

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We’ve opted to release all function scores now (see Supplementary Tables). While this data hasn't yet been peer reviewed, we hope sharing now speeds up others' research and allows performance to be assessed across diverse cohorts. Please reach out with questions regarding specific variants. 13/n

Finally, we used gold-standard sets of variants to calibrate the strength of evidence provided by scores from each cell line individually and produced ACMG/AMP-style evidence codes, which we anticipate will improve BRCA1 variant classification. 12/n

Mapping function score for BRCA1 variants to evidence codes to support clinical classification.

Phoebe also took care to test p.R1699Q in both lines, a variant known to confer intermediate breast cancer risk (pubmed.ncbi.nlm.nih.gov/22889855/). Indeed, p.R1699Q scored discordantly between HAP1 and HMEC, as did all 7 other variants tested thought to cause intermediate cancer risk. 11/n

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@mariazanti.bsky.social‬ and @kmichailidou.bsky.social addressed this by estimating breast cancer risk from case-control data. Variants causing loss-of-function ONLY in HAP1 moderately increased risk (OR=3.3). Yet variants that were loss-of-function in BOTH lines highly increased risk (OR>10). 10/n

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All evidence points to variants scoring discordantly between lines as being hypomorphic in cells (i.e. leading to reduced BRCA1 function but not a null allele). Might such variants also cause intermediate cancer risk? 9/n

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Importantly, both the HAP1 and HMEC SGE assays perform well for predicting which BRCA1 variants are pathogenic. Looking at a set of 420 pathogenic and benign variants in ClinVar, it was the HAP1-based assay that performed better overall, with near-perfect accuracy. 8/n

ROC-AUC cruves for prediction of pathogenic BRCA1 variants using SGE data

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To better understand why variants act differently between lines, Phoebe performed more SGE using PARP inhibition and a knock-out HMEC line to reveal context-specific effects. Many variants initially scoring discordantly between HAP1 and HMEC can be reconciled in specific contexts. 7/n

Comparison of SGE function scores in HMECs with and without PARP inhibitor treatment.

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Comparing how variants impact function across cell lines has proven quite interesting. Nearly half of variants leading to loss-of-function in HAP1 do not have the same effect when introduced to HMECs. Variants with discordant effects are typically missense and splice. Here's an example... 6/n

function scores for BRCA1 variants in exons 11 and 12, measured in HAP1 cells and HMEC cells

She also engineered a new SGE assay in human mammary epithelial cells (HMECs). 5/n

schematic of a new SGE assay in human mammary epithelial cells

distribution of function scores for variants in BRCA1 tested in HMECs

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In each of these key studies, effects of variants were measured in only a single cell line. This is what makes Phoebe’s new work so impressive. She not only tested over 4,000 new BRCA1 variants in our optimised HAP1 system… 4/n

effects of variants measured across the BRCA1 gene

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Since, SGE studies of other tumour suppressors have also yielded valuable data, changing how patients with rare variants are managed clinically. Work from the labs of @davidjadams.bsky.social (BAP1, RAD51C), Shyam Sharan (BRCA2), Fergus Couch (BRCA2), Thorsten Stiewe (TP53) and ours (VHL). 3/n

In @jshendure.bsky.social lab in 2018, we performed saturation genome editing (SGE) to test 3,893 genetic variants in BRCA1. SGE is a CRISPR method to engineer variants in lab-grown human cells. This work showed that SGE could be used to identify variants that cause high cancer risk in people. 2/n

A sequence-function map of variants in BRCA1 produced in 2018 using saturation genome editing.

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