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. eCollection 2023 May.

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.

MeSH terms

  • CRISPR-Cas Systems* / genetics
  • Clustered Regularly Interspaced Short Palindromic Repeats / genetics
  • DNA Breaks, Double-Stranded
  • Gene Editing* / methods
  • Recombinational DNA Repair

Grants and funding

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.