Easy Quantitative Assessment of Genome Editing by Sequence Trace Decomposition

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

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • CRISPR-Cas Systems
  • Cells, Cultured
  • DNA Mutational Analysis / methods*
  • Genomics / methods
  • Humans
  • INDEL Mutation*
  • K562 Cells
  • Mutagenesis
  • Polymerase Chain Reaction
  • Software