Rapid Quantitative Evaluation of CRISPR Genome Editing by TIDE and TIDER

Methods Mol Biol. 2019;1961:29-44. doi: 10.1007/978-1-4939-9170-9_3.

Abstract

Current genome editing tools enable targeted mutagenesis of selected DNA sequences in many species. However, the efficiency and the type of introduced mutations by the genome editing method are largely dependent on the target site. As a consequence, the outcome of the editing operation is difficult to predict. Therefore, a quick assay to quantify the frequency of mutations is vital for a proper assessment of genome editing actions. We developed two methods that are rapid, cost-effective, and readily applicable: (1) TIDE, which can accurately identify and quantify insertions and deletions (indels) that arise after introduction of double strand breaks (DSBs); (2) TIDER, which is suited for template-mediated editing events including point mutations. Both methods only require a set of PCR reactions and standard Sanger sequencing runs. The sequence traces are analyzed by the TIDE or TIDER algorithm (available at https://tide.nki.nl or https://deskgen.com ). The routine is easy, fast, and provides much more detailed information than current enzyme-based assays. TIDE and TIDER accelerate testing and designing of DSB-based genome editing strategies.

Keywords: Algorithm; CRISPR-Cas; DNA mutational analysis/methods; Genome editing; Indel mutation; Mutagenesis; Sanger sequencing; Web tool.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Clustered Regularly Interspaced Short Palindromic Repeats / genetics*
  • DNA Breaks, Double-Stranded
  • Gene Editing / methods*
  • INDEL Mutation / genetics
  • Mutagenesis
  • Mutation / genetics
  • Point Mutation / genetics