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Nucleic Acids Res. 2014 Dec 16;42(22):e168. doi: 10.1093/nar/gku936. Epub 2014 Oct 9.

Easy quantitative assessment of genome editing by sequence trace decomposition.

Author information

1
Division of Gene Regulation, Netherlands Cancer Institute, Plesmanlaan 121, 1016 HM Amsterdam, the Netherlands.
2
Division of Gene Regulation, Netherlands Cancer Institute, Plesmanlaan 121, 1016 HM Amsterdam, the Netherlands b.v.steensel@nki.nl.

Abstract

The efficacy and the mutation spectrum of genome editing methods can vary substantially depending on the targeted sequence. A simple, quick assay to accurately characterize and quantify the induced mutations is therefore needed. Here we present TIDE, a method for this purpose that requires only a pair of PCR reactions and two standard capillary sequencing runs. The sequence traces are then analyzed by a specially developed decomposition algorithm that identifies the major induced mutations in the projected editing site and accurately determines their frequency in a cell population. This method is cost-effective and quick, and it provides much more detailed information than current enzyme-based assays. An interactive web tool for automated decomposition of the sequence traces is available. TIDE greatly facilitates the testing and rational design of genome editing strategies.

PMID:
25300484
PMCID:
PMC4267669
DOI:
10.1093/nar/gku936
[Indexed for MEDLINE]
Free PMC Article

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