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Easy quantitative assessment of genome editing by sequence trace decomposition.

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.

SUBMITTER: Brinkman EK

PROVIDER: S-EPMC4267669 | biostudies-literature | 2014 Dec

REPOSITORIES: biostudies-literature

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Easy quantitative assessment of genome editing by sequence trace decomposition.

Brinkman Eva K EK Chen Tao T Amendola Mario M van Steensel Bas B

Nucleic acids research 20141009 22

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 th ...[more]

PMID: 25300484

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