Bioinformatics in gene editing

In the context of gene editing, NGS bioinformatics is crucial to study the precision of genome modification techniques like CRISPR/Cas9, ZFN, TALEN, and DdCBE. Focused on unraveling both on-target efficacy and off-target effects, NGS bioinformatics provides researchers with a comprehensive understanding of the precision and potential unintended consequences of genomic alterations.

On-Target Profiling: NGS bioinformatics allows for in-depth analysis of on-target modifications, offering insights into the efficiency and accuracy of gene editing events. Through high-throughput sequencing, researchers can quantify the frequency and types of modifications at the intended genomic loci, enabling optimization of editing protocols and ensuring the desired genetic changes are achieved with precision.

Off-Target Detection: One of the primary challenges in gene editing is the potential for off-target effects—unintended modifications at genomic sites resembling the target sequence. NGS bioinformatics excels in identifying these off-target events, providing a nuanced view of the genomic landscape to assess specificity. Whether employing CRISPR/Cas9, ZFN, TALEN, or DdCBE, the ability to detect and characterize off-target effects is crucial for refining editing strategies and minimizing the risk of unintended genetic alterations.

Technology-Specific Analysis: NGS bioinformatics adapts seamlessly to the diverse array of gene editing tools, including the revolutionary CRISPR/Cas9, the precision of ZFN and TALEN, and the base-editing capabilities of DdCBE. By tailoring analysis pipelines to each technology, researchers gain insights specific to the strengths and limitations of the employed editing tool, facilitating continuous refinement and innovation in gene editing methodologies.

A selection of our papers:

Silva-Pinheiro P, et al. (2022) A library of base editors for the precise ablation of all protein-coding genes in the mouse mitochondrial genome. Nat Biomed Eng doing: 10.1038/s41551-022-00968-1

Silva-Pinheiro P, et al. (2022) In vivo mitochondrial base editing via adeno-associated viral delivery to mouse post-mitotic tissue. Nat commun 18(1):750 dot: 10.1038/s41467-022-28358-w

Gammage PA, et al. (2018) Genome editing in mitochondria corrects a pathogenic mtDNA mutation in vivo. Nat Med 24(11):1691-1695 doi: 10.1038/s41591-018-0165-9

Gammage PA, et al. (2016) Near-complete elimination of mutant mtDNA by iterative or dynamic dose-controlled treatment with mtZFNs. Nucleic Acids Res 44(16):7804-16 dot 10.1093/nar/gkw676