Evaluation of CRISPR Genome Editing: Tool Quantifies Potential Hereditary Mistakes

Scientists from IDC Herzliya and Bar-Ilan University established a unique software device to evaluate possible CRISPR-induced errors.

CRISPR modern technology enables researchers to edit genomes by modifying DNA series and hence changing gene features. Its many possible applications include fixing genetic defects, dealing with and preventing the spread of conditions, and bettering plants.

Genome editing tools, such as the CRISPR-Cas9 technology, can be programmed to make incredibly distinct modifications to the intended target on a chromosome where a specific gene or functional element lies. Nonetheless, one possible problem is that CRISPR editing and enhancing might cause other unplanned genomic modifications. These are referred to as off-target activities. When targeting various sites in the genome, the off-target activity can bring about translocations, uncommon rearrangement of chromosomes, and various other unintentional genomic adjustments.

Managing off-target editing activity is just one of the main obstacles in making CRISPR-Cas9 innovation accurate and appropriate in medical practice. Existing measurement assays and data evaluation methods for measuring off-target activity do not supply statistical assessment, are not sensitive enough in dividing signal from noise in experiments with small editing rates, and require troublesome initiatives to address the detection of translocations.

On May 24th issue of the journal Nature Communications, a report by the multidisciplinary group of researchers from the Interdisciplinary Facility Herzliya and Bar-Ilan University was published.The report explained the development of a brand-new software tool to spot, analyze and measure off-target editing activity, including damaging translocation events that can cause cancer cells. The software program is based upon input extracted from a standard measurement assay, involving multiplexed PCR amplification as well as Next-Generation Sequencing (NGS).

Referred to as CRISPECTOR, the device evaluates next-generation sequencing data acquired from CRISPR-Cas9 experiments and uses statistical modeling to identify and measure editing activity. CRISPECTOR correctly determines off-target activity at every questioned locus. It, even more, enables much better false-negative rates in sites with weak yet significant, off-target activity. Notably, among the new features of CRISPECTOR is its capability to detect unfavorable translocation events occurring in a editing experiment.

” In genome editing, specifically for medical applications, it is critical to recognize low-level off-target activity and damaging translocation incidents. In the context of gene treatment, even a small amount of cells, when transplanted into a patient in the context of gene treatment, can have detrimental consequences in terms of cancer pathogenesis. As part of treatment protocols, it is as a result vital to detect these potential incidents beforehand,” claims Dr. Ayal Hendel, of Bar-Ilan University’s Mina and Everard Goodman Faculty of Life Sciences. Dr. Hendel led the research with Prof. Zohar Yakhini, of the Arazi School of Computer Science at Interdisciplinary Center (IDC) Herzliya. “CRISPECTOR gives a reliable technique to define and measure possible CRISPR-induced errors, consequently dramatically improving the safety of future professional use of genome editing.” Hendel’s group used CRISPR-Cas9 technology to edit genes present in stem cells relevant to blood and immune system disorders. While analyzing the data, they realized the shortcomings of the existing tools for measuring off-target activity and, of spaces that should be connected to improve applicability. This experience brought about the collaboration with Prof Yakhini’s leading computational biology as well as bioinformatics team.

Prof. Zohar Yakhini, of IDC Herzliya and the Technion, adds that “in experiments using deep sequencing techniques that have high levels of background noise, low levels of true off-target activity can be lost under the noise. The need for a measurement method and related data analysis able to see beyond the noise and detect adverse translocation events happening in an editing experiment is evident to genome editing researchers and specialists. CRISPECTOR is a tool that can sort through the background noise to determine and quantify the true off-target signal. Furthermore, CRISPECTOR can likewise determine a larger range of genomic aberrations by utilizing statistical modeling and mindful data analysis. By characterizing and also evaluating prospective CRISPR-induced errors, our approaches will support the more secure medical use genome editing therapeutic approaches.”

Originally published Scitechdaily.com. Read the original article here.

Reference: “CRISPECTOR provides accurate estimation of genome editing translocation and off-target activity from comparative NGS data” by Ido Amit, Ortal Iancu, Alona Levy-Jurgenson, Gavin Kurgan, Matthew S. McNeill, Garrett R. Rettig, Daniel Allen, Dor Breier, Nimrod Ben Haim, Yu Wang, Leon Anavy, Ayal Hendel and Zohar Yakhini, 24 May 2021, Nature Communications.
DOI: 10.1038/s41467-021-22417-4