Wednesday, September 10, 2014

Paper: More details about what sequence features make a CRISPR target highly "cuttable".

This was interesting for several nice reasons.  First, my interpretation is that this suggests that while most CRISPR targets have some level of acceptable targeting by Cas9/sgRNA, there is a subset of sites that are *very* susceptible.  Therefore, if you want to make a null allele in a gene it's a good idea to score all the possible sites first with this sort of algorithm.

Rational design of highly active sgRNAs for CRISPR-Cas9-mediated gene inactivation.  Doench et al, Nat Biotechnol. 2014 Sep 3. doi: 10.1038/nbt.3026. [Epub ahead of print].

Second, they of course have made their scoring algorithm available as a web tool:

I took a crack at it with a small DNA sequence from mouse that I know has a decent CRISPR target.  Interestingly, my pre-validated target had a lousy score (~0.05 on a scale from 0 to 1)  despite my knowledge that it works pretty well in my hands.  I take this to mean that of course, no scoring algorithm is perfect, but also that most targets actually fall into the so-so category of activity.   This jibes with data in this paper somewhat and I won't jump to conclusions based on my N=1!   I'd be interested to hear other people's results from running their targets through this algorithm.

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