Accurate analysis of genuine CRISPR editing events with ampliCan
Open accessPublished version of a preprint
Abstract
We present ampliCan, an analysis tool for genome editing that unites highly precise quantification and visualization of genuine genome editing events. ampliCan features nuclease-optimized alignments, filtering of experimental artifacts, event-specific normalization, and off-target read detection and quantifies insertions, deletions, HDR repair, as well as targeted base editing. It is scalable to thousands of amplicon sequencing–based experiments from any genome editing experiment, including CRISPR. It enables automated integration of controls and accounts for biases at every step of the analysis. We benchmarked ampliCan on both real and simulated data sets against other leading tools, demonstrating that it outperformed all in the face of common confounding factors.
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The top predicted off-target cut sites in coding regions by CHOPCHOP and COSMID were verified to be intact by Sanger sequencing.
“The top predicted off-target cut sites in coding regions by CHOPCHOP78 and COSMID79 were verified to be intact by Sanger sequencing.”
From The APOE-R136S mutation protects against APOE4-driven tau pathology, neurodegeneration, and neuroinflammation (2023) · cites this paper as [78]
The Abstract describes ampliCan as a tool for analyzing high-throughput amplicon sequencing, and the Methods discuss filtering reads that may come from off-target amplification. Our copy does not report Sanger sequencing of predicted coding-region off-target sites or verify that those sites were intact (searched: Sanger, COSMID, and off-target-site verification). (LLM, conf=0.76)
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References 14 · Cited by 84
Research works printed but not linked: 10
- Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA, 2013 Multiplex genome engineering using CRISPR/Cas systems. Science 339: 819– 823. 10.1126/science.1231143 23287718 PMC3795411 · DOI · Paper page
- Courtney DG, Moore JE, Atkinson SD, Maurizi E, Allen EHA, Pedrioli DML, McLean WHI, Nesbit MA, Moore CBT. 2016 CRISPR/Cas9 DNA cleavage at SNP-derived PAM enables both in vitro and in vivo KRT12 mutation-specific targeting. Gene Ther 23: 108– 112. 10.1038/gt.2015.82 26289666 PMC4705418 · DOI
- Gagnon JA, Valen E, Thyme SB, Huang P, Akhmetova L, Pauli A, Montague TG, Zimmerman S, Richter C, Schier AF. 2014 Efficient mutagenesis by Cas9 protein-mediated oligonucleotide insertion and large-scale assessment of single-guide RNAs. PLoS One 9: e98186 10.1371/journal.pone.0098186 24873830 PMC4038517 · DOI
- Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E. 2012 A programmable dual-RNA–guided DNA endonuclease in adaptive bacterial immunity. Science 337: 816– 821. 10.1126/science.1225829 22745249 PMC6286148 · DOI · Paper page
- Labun K, Montague TG, Gagnon JA, Thyme SB, Valen E. 2016 CHOPCHOP v2: a web tool for the next generation of CRISPR genome engineering. Nucleic Acids Res 44: W272– W276. 10.1093/nar/gkw398 27185894 PMC4987937 · DOI
- Lackner DH, Carré A, Guzzardo PM, Banning C, Mangena R, Henley T, Oberndorfer S, Gapp BV, Nijman SMB, Brummelkamp TR, 2015 A generic strategy for CRISPR-Cas9-mediated gene tagging. Nat Commun 6: 10237 10.1038/ncomms10237 26674669 PMC4703899 · DOI
- Lawrence M, Huber W, Pagès H, Aboyoun P, Carlson M, Gentleman R, Morgan MT, Carey VJ. 2013 Software for computing and annotating genomic ranges. PLoS Comput Biol 9: e1003118 10.1371/journal.pcbi.1003118 23950696 PMC3738458 · DOI
- Lindsay H, Burger A, Biyong B, Felker A, Hess C, Zaugg J, Chiavacci E, Anders C, Jinek M, Mosimann C, 2016 CrispRVariants charts the mutation spectrum of genome engineering experiments. Nat Biotechnol 34: 701– 702. 10.1038/nbt.3628 27404876 · DOI
- Montague TG, Cruz JM, Gagnon JA, Church GM, Valen E. 2014 CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing. Nucleic Acids Res 42: W401– W407. 10.1093/nar/gku410 24861617 PMC4086086 · DOI
- Yin T, Cook D, Lawrence M. 2012 ggbio: an R package for extending the grammar of graphics for genomic data. Genome Biol 13: R77 10.1186/gb-2012-13-8-r77 22937822 PMC4053745 · DOI
- Authors
- Labun, K., Guo, X., Chavez, A., Church, G., Gagnon, J. A., & Valen, E.
- Affiliations
- University of Bergen (NO)
- Harvard University (US)
- Columbia University (US)
- University of Utah (US)
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2019-03-08
- Volume
- 29
- Issue
- 5
- Pages
- 843-847
- ISSN
- 1088-9051 (ISSN-L)
- 1549-5469
- PMC
- PMC6499316
- OpenAlex
- W2950564381
- Cited by
- 84
- References
- 14
- Citations by year
- 2026: 9 · 2025: 12 · 2024: 17 · 2023: 11 · 2022: 7 · 2021: 12 · 2020: 6 · 2019: 9 · 2018: 1
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Genome Research (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- NORA - Norwegian Open Research Archives (submittedVersion, cc-by)
- HighWire Press Open Archive (submittedVersion)
- Funders
- Bergen Research Foundation
- Norwegian Research Council (#250049)
- University of Bergen
- American Cancer Society
- University of Utah
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- CRISPR gene editing, amplicon sequencing, bioinformatics software
- MeSH terms
- Gene Editing, Software, Sequence Alignment, High-Throughput Nucleotide Sequencing, Mutation Rate, DNA End-Joining Repair, Recombinational DNA Repair, Clustered Regularly Interspaced Short Palindromic Repeats, CRISPR-Cas Systems
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