Easy quantitative assessment of genome editing by sequence trace decomposition

EK Brinkman, T Chen, M Amendola… - Nucleic acids …, 2014 - academic.oup.com
EK Brinkman, T Chen, M Amendola, B Van Steensel
Nucleic acids research, 2014academic.oup.com
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 …
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.
Oxford University Press