Easy quantitative assessment of genome editing by sequence trace decomposition.

Eva K Brinkman,Mario Amendola,Bas Van Steensel,Tao Chen

doi:10.1093/nar/gku936

Eva K Brinkman, Mario Amendola + Show 2 more

Open Access

https://doi.org/10.1093/nar/gku936

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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.

Highlights

Genome editing tools, such as TAL effector nucleases, zinc finger nucleases and RNA-guided endonucleases (RGENs), enable targeted mutagenesis of a selected DNA sequence in genomes of many species [1,2]
In the first step of TIDE, a stretch of about 500–1500 bp around the editing site is polymerase chain reaction (PCR) amplified from genomic DNA isolated from the cell pool that was treated with the targeted nuclease
In the DNA sample from the cells expressing the targeted nuclease, the sequence trace after the break site consists of a mixture of signals derived from unmodified DNA and sequences that are each shifted by a different number of nucleotides due to insertions and deletions (Figure 1a)

Summary

Introduction

Genome editing tools, such as TAL effector nucleases, zinc finger nucleases and RNA-guided endonucleases (RGENs), enable targeted mutagenesis of a selected DNA sequence in genomes of many species [1,2] In each of these methods, introduction of an endonuclease with programmable sequence specificity into a pool of cells leads to a precisely defined DNA double-strand break (DSB), which, when repaired by non-homologous end-joining, results in a mixture of unaltered and mutated DNA. Used assays to verify the efficacy of programmable nucleases are the enzymatic Surveyor and T7 endonuclease I cleavage assays [7,8], which detect small sequence changes These methods are, semi-quantitative and suffer from high background signals when sequence polymorphisms are present. Highthroughput sequencing around the induced break site [9] is a powerful alternative, but is expensive and usually takes several weeks in most research environments

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