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How did this new software originate, and what does it do?

Scientists and collaborators at the ChristianaCare Gene Editing Institute developed this tool to fill in the gaps in analysis that existed in the sequencing field. Our interdisciplinary team built DECODR for the express purpose of providing detailed, accurate Sanger sequencing analysis with an easy-to-use interface. DECODR is an acronym for Deconvolution of Complex DNA Repair.

Is there really a need for another tool? What is it that DECODR does that others don’t?

There were no tools available at the time that could break down the types of edits at the level of precision that we needed for our research. That’s why we developed DECODR. DECODR can detect indels of any size, formed from single- or multi-guide CRISPR experiments. We utilize a novel proposal generation and determination algorithm that allows accurate uncovering of indel identities, including those of inserted bases. This greater accuracy of genetic content determination allows users to be best informed about the exact genetic changes their CRISPR edits are creating.

What does the DECODR output look like?

There are only three pieces of data that are necessary to run a DECODR analysis: the CRISPR guide RNA sequence, the unedited DNA sequence, and a Sanger sequencing file of edited DNA.  DECODR can perform both bulk analysis of entire populations of edited cells, as well as clonally expanded populations. From there, just press “submit,” and the DECODR algorithm handles the actual work of data deconvolution “to the letter,” as shown above, without any indel size cutoffs or complexity limitations.

Source: Christiana Care Gene Editing Institute logo

What does your lab specialize in?

The Gene Editing Institute is a worldwide leader in CRISPR gene editing technology and the only institute of its kind based within a community healthcare system. The Institute takes a patient-first approach in all its research to improve the lives of people with life-threatening disease. Since 2015, it has been involved in several groundbreaking firsts in the field, including the development of the first CRISPR gene editing tool to allow DNA repairs outside the human cell that will rapidly speed therapies to patients and a unique version of CRISPR called ExACT that reduces the number of off-target edits to other areas of the genome, which is vital for further research and patient applications. Its researchers are currently using DECODR every day in their development of a patient trial for lung cancer using CRISPR.

How can researchers try DECODR?

DECODR is available online at decodr.org as a free version that researchers can immediately use to evaluate the outcomes of their CRISPR gene editing experiments. A feature-rich commercial version of DECODR is available that provides a wider range of options.

 

To learn more, please read our paper in The CRISPR Journal or contact the Institute at: decodr@geneeditinginstitute.com

www.liebertpub.com/doi/10.1089/crispr.2020.0022