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EditR: A novel base editing quantification software using Sanger sequencing

Mitchell G. Kluesner, Derek A. Nedveck, Walker S. Lahr, John R. Garbe, Juan E. Abrahante, Beau R. Webber, Branden S. Moriarity
doi: https://doi.org/10.1101/213496
Mitchell G. Kluesner
1Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA.
2Department of Pediatrics, University of Minnesota, Minneapolis, MN, 55455, USA.
3Center for Genome Engineering, University of Minnesota, Minneapolis, MN, 55455, USA.
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Derek A. Nedveck
4University of Minnesota, Minneapolis, MN, 55455, USA. Department of Plant Biology, University of Minnesota, Minneapolis, MN, 55455, USA.
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Walker S. Lahr
1Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA.
2Department of Pediatrics, University of Minnesota, Minneapolis, MN, 55455, USA.
3Center for Genome Engineering, University of Minnesota, Minneapolis, MN, 55455, USA.
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John R. Garbe
5Genomics Center, University of Minnesota, Minneapolis, MN, 55455, USA.
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Juan E. Abrahante
6University of Minnesota Informatics Institute, Minneapolis, MN 55455.
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Beau R. Webber
1Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA.
2Department of Pediatrics, University of Minnesota, Minneapolis, MN, 55455, USA.
3Center for Genome Engineering, University of Minnesota, Minneapolis, MN, 55455, USA.
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Branden S. Moriarity
1Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA.
2Department of Pediatrics, University of Minnesota, Minneapolis, MN, 55455, USA.
3Center for Genome Engineering, University of Minnesota, Minneapolis, MN, 55455, USA.
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  • For correspondence: mori0164@umn.edu
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ABSTRACT

CRISPR/Cas9-Cytidine deaminase fusion enzymes - termed Base Editors – allow targeted editing of genomic deoxcytidine to deoxthymidine (C→T) without the need for double stranded break induction. Base editors represent a paradigm-shift in gene editing technology, due to their unprecedented efficiency to mediate targeted, single-base conversion; however, current analysis of base editing outcomes rely on methods that are either imprecise or expensive and time consuming. To overcome these limitations, we developed a simple, cost effective, and accurate program to measure base editing efficiency from fluorescence-based Sanger sequencing, termed EditR. We provide EditR as a free online tool or downloadable desktop application requiring a single Sanger sequencing file and guide RNA sequence (baseeditr.com). EditR is more accurate than enzymatic assays, and provides added insight to the position, type and efficiency of base editing. Collectively, we demonstrate that EditR is a robust, inexpensive tool that will facilitate the broad application of base editing technology, thereby fostering further innovation in this burgeoning field.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted November 05, 2017.
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EditR: A novel base editing quantification software using Sanger sequencing
Mitchell G. Kluesner, Derek A. Nedveck, Walker S. Lahr, John R. Garbe, Juan E. Abrahante, Beau R. Webber, Branden S. Moriarity
bioRxiv 213496; doi: https://doi.org/10.1101/213496
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EditR: A novel base editing quantification software using Sanger sequencing
Mitchell G. Kluesner, Derek A. Nedveck, Walker S. Lahr, John R. Garbe, Juan E. Abrahante, Beau R. Webber, Branden S. Moriarity
bioRxiv 213496; doi: https://doi.org/10.1101/213496

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