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DECODR: CRISPR app reveal unwanted mutations

Researchers from ChristianaCare’s Gene Editing Institute have developed a new tool – DECODR – which reveals unwanted mutations at sites of CRISPR gene repair.


In recent years, CRISPR-directed gene editing has established itself as a technically viable platform for genetic modifications. The CRISPR-Cas9 system enables a variety of targeted edits to be introduced into specific regions of the genome. Unfortunately, the pathways involved in this response are not independent and the interplay results in unwanted changes being introduced. Due to its unpredictable nature of edited outcomes, many have raised concerns about advancing CRISPR-directed gene-editing programs toward clinical application.  As a result, there has been a demand to develop and refine analytical tools to provide an accurate detailed global view of the products of such genetic modifications.

Targeted deep sequencing is considered the most comprehensive method to obtain accurate information about relevant indels. However, this approach is costly and the turnaround time prevents simple high-throughput implementation. Several analytical tools, including TIDE, ICE and CRISP-ID have been developed and enable important and useful indel analyses. However, common limitations impede detailed or difficult indel analyses.


In this study, published in The CRISPR Journal, researchers present DECODR – Deconvolution of Complex DNA Repair. This tool can detect indels formed from single or multi-guided CRISPR experiments without a limit on indel size. In addition, it utilises a unique algorithm that allows accurate uncovering of indel identities, including those of inserted bases.

This article presents evidence that the DECODR app can essentially produce the same data as deep sequencing processes in much less time and at a fraction of the cost. This tool was also designed to be scaled to evaluate insertions and deletions executed by CRISPR regardless of size. This means that it can evolve as researchers develop the capacity to attempt more complex repairs.

DECODR is currently only intended as a research tool, not in the clinical evaluation of individual patients. It is also available online as a free version that researchers can use to evaluate the outcomes of their CRISPR gene editing experiments.

Image credit: By vectorjuice – freepik

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