title: 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.
authors.affiliation: Division of Gene Regulation, Netherlands Cancer Institute, Plesmanlaan 121, 1016 HM Amsterdam, the Netherlands.
authors.forename: Eva K
authors.initials: EK
authors.lastname: Brinkman
authors.affiliation: Division of Gene Regulation, Netherlands Cancer Institute, Plesmanlaan 121, 1016 HM Amsterdam, the Netherlands.
authors.forename: Tao
authors.initials: T
authors.lastname: Chen
authors.affiliation: Division of Gene Regulation, Netherlands Cancer Institute, Plesmanlaan 121, 1016 HM Amsterdam, the Netherlands.
authors.forename: Mario
authors.initials: M
authors.lastname: Amendola
authors.affiliation: Division of Gene Regulation, Netherlands Cancer Institute, Plesmanlaan 121, 1016 HM Amsterdam, the Netherlands b.v.steensel@nki.nl.
authors.forename: Bas
authors.initials: B
authors.lastname: van Steensel
mesh_terms: D000465:Algorithms; D064113:CRISPR-Cas Systems; D002478:Cells, Cultured; D004252:DNA Mutational Analysis / Q000379:methods*; D023281:Genomics / Q000379:methods; D006801:Humans; D054643:INDEL Mutation; D020014:K562 Cells; D016296:Mutagenesis; D016133:Polymerase Chain Reaction; D012984:Software