The DOI matches its Crossref record; 19 of the 19 references it cites were found in a registry or an index.
Inference of CRISPR Edits from Sanger Trace Data
Abstract
Efficient and precise genome editing requires a fast, quantitative, and inexpensive assay to assess genotype following editing. Here, we present ICE (Inference of CRISPR Edits), which enables robust analysis of CRISPR edits using Sanger data. ICE proposes potential outcomes for editing with guide RNAs, and then determines which are supported by the data via regression. The ICE algorithm is robust and reproducible, and it can be used to analyze CRISPR experiments within days after transfection. We also confirm that ICE produces accurate estimates of editing outcomes across a variety of benchmarks, and within the context of other existing Sanger analysis tools. The ICE tool is free to use and open source, and offers several improvements over current analysis tools, such as batch analysis and support for a variety of editing conditions. It is available online at ice.synthego.com, and the source code is available at github.com/synthego-open/ice.
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Cites
Genome engineering using the CRISPR-Cas9 system
Ran, F. A., Hsu, P. D., Wright, J., Agarwala, V., Scott, D. A., & Zhang, F. (2013) · Nature Protocols · doi:10.1038/nprot.2013.143 · Cited by 11,133
Easy quantitative assessment of genome editing by sequence trace decomposition
Brinkman, E. K., Chen, T., Amendola, M., & van Steensel, B. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku936 · Cited by 2,390
CRISPResso2 provides accurate and rapid genome editing sequence analysis
Clement, K., Rees, H., Canver, M. C., Gehrke, J. M., Farouni, R., Hsu, J. Y., Cole, M. A., Liu, D. R., Joung, J. K., Bauer, D. E., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0032-3 · Cited by 1,660
Enhanced homology-directed human genome engineering by controlled timing of CRISPR/Cas9 delivery
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EditR: A Method to Quantify Base Editing from Sanger Sequencing
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Efficient ablation of genes in human hematopoietic stem and effector cells using CRISPR/Cas9
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Targeted genome editing in human cells with zinc finger nucleases constructed via modular assembly
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DNA Repair Profiling Reveals Nonrandom Outcomes at Cas9-Mediated Breaks
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A Survey of Validation Strategies for CRISPR-Cas9 Editing
Sentmanat, M. F., Peters, S. T., Florian, C. P., Connelly, J. P., & Pruett-Miller, S. M. (2018) · Scientific Reports · doi:10.1038/s41598-018-19441-8 · Cited by 341
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Self-citationLoss of epigenetic information as a cause of mammalian aging
Yang, J.-H., Hayano, M., Griffin, P. T., Amorim, J. A., Bonkowski, M. S., Apostolides, J. K., Salfati, E. L., Blanchette, M., Munding, E. M., Bhakta, M., et al. (2023) · Cell · doi:10.1016/j.cell.2022.12.027 · Cited by 643
Self-citationUnbiased detection of CRISPR off-targets in vivo using DISCOVER-Seq
Wienert, B., Wyman, S. K., Richardson, C. D., Yeh, C. D., Akcakaya, P., Porritt, M. J., Morlock, M., Vu, J. T., Kazane, K. R., Watry, H. L., et al. (2019) · Science · doi:10.1126/science.aav9023 · Cited by 434
Astrocytic interleukin-3 programs microglia and limits Alzheimer’s disease
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Michels, B. E., Mosa, M. H., Streibl, B. I., Zhan, T., Menche, C., Abou-El-Ardat, K., Darvishi, T., Członka, E., Wagner, S., Winter, J., et al. (2020) · Cell Stem Cell · doi:10.1016/j.stem.2020.04.003 · Cited by 222
Metadata
- Authors
- Conant, D., Hsiau, T., Rossi, N., Oki, J., Maures, T., Waite, K., Yang, J., Joshi, S., Kelso, R., Holden, K., Enzmann, B. L., & Stoner, R.
- Venue
- The CRISPR Journal
- Publisher
- SAGE Publications
- Published
- 2022-02-01
- Volume
- 5
- Issue
- 1
- Pages
- 123-130
- ISSN
- 2573-1599 (ISSN-L)
- 2573-1602
- OpenAlex
- W4210762403
- Cited by
- 804
- References
- 19
- FWCI
- 39.01
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- journals.sagepub.com/page/policies/text-and-data-mining-license (tdm)
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- Conant, D., Hsiau, T., Rossi, N., Oki, J., Maures, T., Waite, K., Yang, J., Joshi, S., Kelso, R., Holden, K., Enzmann, B. L., & Stoner, R. (2022). Inference of CRISPR Edits from Sanger Trace Data. The CRISPR Journal. https://doi.org/10.1089/crispr.2021.0113
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