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

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.

KMAP: Kmer Manifold Approximation and Projection for visualizing DNA sequences

“…Furthermore, in our analysis of the gene editing data of the AAVS1 locus, KMAP identified four distinct editing patterns. Remarkably, these patterns correspond to the top 4 patterns reported in the original publication (Sanvicente-García et al, 2023), reinforcing KMAP’s capability to discern and visualize complex genetic patterns.…”

“…We use KMAP to detect editing patterns from gene editing data of the Adeno-Associated Virus Site 1 (AAVS1) locus. Sanvicente-García et al (2023) used a previously described (Doench et al, 2016; Mali et al, 2013) guide RNA with a 20nt protospacer that targeted the genomic location (chr19:55,115,752-55,115,771; GRCh38/hg38) on the human genome. The Streptococcus pyogenes Cas9 (SpCas9) protein will make a double stranded break (DSB) at three nucleotides upstream of the PAM, after that the broken DNAs are ligated by non-homologous end joining (NHEJ), which leads to different DNA editing results (mainly random small indels).…”

Synergic homology directed recombination by PRDM9 meiotic factor

“…Data coming from miSeq was analyzed using the CRISPR-A nextflow pipeline (Sanvicente-García et al 2022). CRISPR-A template-based edits search is based on CIGAR as well as indels search.…”