Sokirniy, Ivan, Inam, Haider, Tomaszkiewicz, Marta, Reynolds, Joshua, McCandlish, David, Pritchard, Justin (September 2024) A side-by-side comparison of variant function measurements using deep mutational scanning and base editing. bioRxiv. ISSN 2692-8205 (Submitted)
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10.1101.2024.06.30.601444.pdf - Submitted Version Available under License Creative Commons Attribution Non-commercial No Derivatives. Download (3MB) | Preview |
Abstract
Variant annotation is a crucial objective in mammalian functional genomics. Deep Mutational Scanning (DMS) is a well-established method for annotating human gene variants, but CRISPR base editing (BE) is emerging as an alternative. However, questions remain about how well high-throughput base editing measurements can annotate variant function and the extent of downstream experimental validation required. This study presents the first direct comparison of DMS and BE in the same lab and cell line. Results indicate that focusing on the most likely edits and highest efficiency sgRNAs enhances the agreement between a “gold standard” DMS dataset and a BE screen. A simple filter for sgRNAs making single edits in their window could sufficiently annotate a large proportion of variants directly from sgRNA sequencing of large pools. When multi-edit guides are unavoidable, directly measuring the variants created in the pool, rather than sgRNA abundance, can recover high-quality variant annotation measurements in multiplexed pools. Taken together, our data show a surprising degree of correlation between base editor data and gold standard deep mutational scanning.
| Item Type: | Paper |
|---|---|
| Subjects: | bioinformatics bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification bioinformatics > genomics and proteomics > genetics & nucleic acid processing bioinformatics > genomics and proteomics bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > mutations |
| CSHL Authors: | |
| Communities: | CSHL labs > McCandlish lab |
| SWORD Depositor: | CSHL Elements |
| Depositing User: | CSHL Elements |
| Date: | 26 September 2024 |
| Date Deposited: | 21 Oct 2024 15:36 |
| Last Modified: | 21 Oct 2024 15:36 |
| PMCID: | PMC11244880 |
| Related URLs: | |
| URI: | https://repository.cshl.edu/id/eprint/41712 |
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