Easy quantitative assessment of genome editing by sequence trace decomposition

By E. Brinkman, Tao Chen, Mario Amendola, B. van Steensel. Nucleic Acids Research, 2014

2,165 citations recorded by the source corpus.

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.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/055277c5b235228474242c3562c4cad2e02627a7

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In Molecular Biology

1. E. Jeng
2. Michael C. Bassik
3. D. Morgens
4. Amy Li
5. Gaelen T. Hess
6. Kyuho Han

Citations in the corpus

• Selenium Utilization by GPX4 Is Required to Prevent Hydroperoxide-Induced Ferroptosis. (2017, neutral): “…LLC https://www.flowjo.com/solutions/ flowjo/downloads ImageJ NIH https://imagej.nih.gov/ij/download.html TIDE: Tracking of Indels by DEcomposition Brinkman et al., 2014 https://tide.nki.nl/ Wave XFe Analyzer 2.2.0 Seahorse Bioscience…”
• Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9 (2016, neutral): “Cells were divided into small molecule and no-selection conditions, cell counts were taken at each passage to determine population doublings, and pellets were collected at day 0 and day 14 of 6-thioguanine treatment for analysis of indels using the TIDE web portal 29 .”
• Synergistic drug combinations for cancer identified in a CRISPR screen for pairwise genetic interactions (2017, positive): “To assess indel frequency, TIDE was used to compare the sequence trace files from the test sample containing the targeting sgRNA to a control sample containing safe harbor sgRNAs and quantify the distribution of indels in the test sample 48 .”