A side-by-side comparison of variant function measurements using deep mutational scanning and base editing

Sokirniy, Ivan, Inam, Haider, Tomaszkiewicz, Marta, Reynolds, Joshua, McCandlish, David, Pritchard, Justin (July 2025) A side-by-side comparison of variant function measurements using deep mutational scanning and base editing. Nucleic Acids Research (NAR), 53 (14). ISSN 0305-1048 (Public Dataset)

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URL: https://www.ncbi.nlm.nih.gov/pubmed/40744495

DOI: 10.1093/nar/gkaf738

Abstract

Variant annotation is a crucial objective in mammalian functional genomics. Deep mutational scanning (DMS) using saturation libraries of complementary DNAs (cDNAs) 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 BE measurements can annotate variant function and the extent of downstream experimental validation required. This study is the first direct comparison of cDNA DMS and BE in the same lab and cell line. We focus on how well short guide RNA (sgRNA) depletion or enrichment is explained by the predicted edits within the editing "window" defined by the sgRNA. The most likely predicted edits enhance 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 edits in medium-sized validation pools can recover high-quality variant annotation data. Our data show a surprisingly high degree of correlation between base editor data and gold standard DMS. We suggest that the main variable measured in base editor screens is the desired base edits.

Item Type:	Paper
Subjects:	bioinformatics bioinformatics > genomics and proteomics
CSHL Authors:	McCandlish, David
Communities:	CSHL labs > McCandlish lab
SWORD Depositor:	CSHL Elements
Depositing User:	CSHL Elements
Date:	19 July 2025
Date Deposited:	01 Aug 2025 17:37
Last Modified:	01 Aug 2025 17:37
Related URLs:	Publisher
Dataset ID:	SRA: PRJNA1218278 10.6084/m9.figshare.29497922 10.6084/m9.figshare.29565386 10.6084/m9.figshare.29497925 10.6084/ m9.figshare.29525993
URI:	https://repository.cshl.edu/id/eprint/41922

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