CRISPR-Analytics (CRISPR-A): A platform for precise analytics and simulations for gene editing

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• dc.contributor.author Sanvicente García, Marta
• dc.contributor.author García Valiente, Albert
• dc.contributor.author Jouide, Socayna
• dc.contributor.author Jaraba-Wallace, Jessica
• dc.contributor.author Bautista, Eric
• dc.contributor.author Escobosa Olmo, Marc
• dc.contributor.author Sánchez-Mejías, Avencia
• dc.contributor.author Güell Cargol, Marc, 1982-
• dc.date.accessioned 2023-10-06T06:03:38Z
• dc.date.available 2023-10-06T06:03:38Z
• dc.date.issued 2023
• dc.description.abstract Gene editing characterization with currently available tools does not always give precise relative proportions among the different types of gene edits present in an edited bulk of cells. We have developed CRISPR-Analytics, CRISPR-A, which is a comprehensive and versatile genome editing web application tool and a nextflow pipeline to give support to gene editing experimental design and analysis. CRISPR-A provides a robust gene editing analysis pipeline composed of data analysis tools and simulation. It achieves higher accuracy than current tools and expands the functionality. The analysis includes mock-based noise correction, spike-in calibrated amplification bias reduction, and advanced interactive graphics. This expanded robustness makes this tool ideal for analyzing highly sensitive cases such as clinical samples or experiments with low editing efficiencies. It also provides an assessment of experimental design through the simulation of gene editing results. Therefore, CRISPR-A is ideal to support multiple kinds of experiments such as double-stranded DNA break-based engineering, base editing (BE), primer editing (PE), and homology-directed repair (HDR), without the need of specifying the used experimental approach.
• dc.description.sponsorship This work was supported by the European Commission (European Union Horizon 2020 grant 825825 to MG), Ramón y Cajal program (grant RYC-2015-17734 to MG), Fundación Ramón Areces (grant “Advanced gene editing technologies to restore LAMA2 on merosin-deficient congenital muscular dystrophy type 1A” to MG) and Ministerio de Ciencia e Innovación de España (Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020 «Advanced methodologies for precise and efficient gene delivery» grant PID2020-118597RB-I00 to MG). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
• dc.format.mimetype application/pdf
• dc.identifier.citation Sanvicente-García M, García-Valiente A, Jouide S, Jaraba-Wallace J, Bautista E, Escobosa M, Sánchez-Mejías A, Güell M. CRISPR-Analytics (CRISPR-A): A platform for precise analytics and simulations for gene editing. PLoS Comput Biol. 2023 May 30;19(5):e1011137. DOI: 10.1371/journal.pcbi.1011137
• dc.identifier.doi http://dx.doi.org/10.1371/journal.pcbi.1011137
• dc.identifier.issn 1553-734X
• dc.identifier.uri http://hdl.handle.net/10230/58054
• dc.language.iso eng
• dc.publisher Public Library of Science (PLoS)
• dc.relation.ispartof PLoS Comput Biol. 2023 May 30;19(5):e1011137
• dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/825825
• dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/PID2020-118597RB-I00
• dc.rights © 2023 Sanvicente-García et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by/4.0/
• dc.subject.keyword CRISPR
• dc.subject.keyword Sequence alignment
• dc.subject.keyword Genomics
• dc.subject.keyword Nucleotides
• dc.subject.keyword Nucleotide sequencing
• dc.subject.keyword Simulation and modeling
• dc.subject.keyword Microhomology-mediated end joining
• dc.subject.keyword Polymerase chain reaction
• dc.title CRISPR-Analytics (CRISPR-A): A platform for precise analytics and simulations for gene editing
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion