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

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

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

@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

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

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

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

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

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

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

We're hiring again! Now looking for a postdoctoral fellow to join us on our mission to improve methods for testing human variants at scale. 🔎🧬🧪

Many potential projects to tackle, all in the top-tier research environment of the @crick.ac.uk.

crick.wd3.myworkdayjobs.com/External/job...

Huge congratulations to Magdalena Armas @magdaarmas.bsky.social (PhD Student @crick.ac.uk) for winning the Silver Award at the STEM for Britain competition!