Monday, December 15, 2014

COSMID, a tool to find #CRISPR off-targets including indels (usually not found w/other tools).

From Georgia Tech comes a new web tool, COSMID, for finding CRISPR off-targets (OTs).  But, this one definitely adds something new to the already busy realm of OT-finding tools: the ability to find OTs with small insertions or deletions relative to the target, not just base-pair mismatches.   Like "mismatched" OTs, off-target cleavage can occur at "indel-OTs" as well; see Lin et al, Nucl. Acids Res.42(11): 7473-7485.    

COSMID is described in a new publication by T.J. Cradick, et al.  COSMID: A Web-based Tool for Identifying and Validating CRISPR/Cas Off-target Sites, Molecular Therapy—Nucleic Acids (2014) 3, e214.    I've only used it briefly so far but it has a nice interface that allows the user to search for OTs with a user-specified max number of mismatches in combination with single-base insertions and/or deletions.  It also can perform PCR primer design for the OTs with the primers optimized for Surveyor-style mutation screening.    Thanks go to T.J. and colleagues for the nice addition to the CRISPR off-target screening toolkit.

Alas, this already raises a new caveat about my previous post reviewing off-targets in mice: I'm pretty sure that most or all of those citations did not look at indel OTs, only mismatch OTs.    !

No comments:

Post a Comment