@allydunham.bsky.social
New 🧬✂️ pre-print! We show that paired prime editing can efficiently generate large deletions — even >1 Mb — with high precision and at scale. We use this to perform the first pooled prime deletion screen across the human genome.
🔗 biorxiv.org/content/10.1...
A short thread (by Juliane Weller)👇
Accompanied by a less polished nextflow pipeline to handle multiple samples and pre-processing - github.com/allydunham/d.... Configurably downsample, merge and trim reads before quantification plus FastQC, SeqKit Stats and a quanitification QC plot. Inspired by the github.com/cancerit/QUA....
13.10.2025 14:35 — 👍 0 🔁 0 💬 0 📌 0I have more features planned to support my work, for instance multiple constructs in one library, combinations of sub-libraries and a region type expecting variants to a base sequence, but issues and pull-requests with other bugs and suggestions are very welcome too.
13.10.2025 14:35 — 👍 0 🔁 0 💬 1 📌 0Simulated tests and benchmarks and our datasets suggest the tool is generally accurate and robust as well as pretty quick. Feels like a state that could be useful more widely so a good time to share, although I do expect more bugs to come out with wider usage!
13.10.2025 14:35 — 👍 0 🔁 0 💬 1 📌 0Currently position in reads, flanking patterns and full alignment can be used to extract regions and extact matching, hamming distance and (bounded) Levenshtein used to compare to your library. This lets you nicely balance match accuracy with speed for your design.
13.10.2025 14:35 — 👍 2 🔁 0 💬 1 📌 0It takes in (paired) fastq/a files, a JSON expected read structure, an optional expected combinations TSV and a strategy for extracting and matching variable regions and outputs count tables against your library.
13.10.2025 14:35 — 👍 0 🔁 0 💬 1 📌 0
We've been screening across many DNA construct structures with variable number/size of interesting regions - e.g. spacer, extension and barcode for prime editing. There wasn't a widely used tool to process these complex structured reads so I ended up developing github.com/allydunham/d....
13.10.2025 14:35 — 👍 6 🔁 3 💬 1 📌 0MPRAbase (mprabase.ucsf.edu) , a customized database for massively parallel reporter assays (MPRAs) to easily find and download MPRA data. Amazing work by Jingjing Zhao, Fotis Baltoumas, Georgios Pavlopoulos, @vagar.bsky.social, ilias Georgakopoulos-Soares & others.
genome.cshlp.org/content/earl...
We're hiring to expand on the work to understand the human genome by engineering it!
lnkd.in/da-gitNc
Enhancer scrambling strategy
We are happy to share our enhancer scramble story, a strategy to create hundreds of stochastic deletions, inversions, and duplications within mammalian gene regulatory regions and associate these new architectures with gene expression levels 🧵
www.biorxiv.org/content/10.1...
