COSMID: A Web-based Tool for Identifying and Validating CRISPR/Cas Off-target Sites

Abstract

Precise genome editing using engineered nucleases can significantly facilitate biological studies and disease treatment. In particular, clustered regularly interspaced short palindromic repeats (CRISPR) with CRISPR-associated (Cas) proteins are a potentially powerful tool for modifying a genome by targeted cleavage of DNA sequences complementary to designed guide strand RNAs. Although CRISPR/Cas systems can have on-target cleavage rates close to the transfection rates, they may also have relatively high off-target cleavage at similar genomic sites that contain one or more base pair mismatches, and insertions or deletions relative to the guide strand. We have developed a bioinformatics-based tool, COSMID (CRISPR Off-target Sites with Mismatches, Insertions, and Deletions) that searches genomes for potential off-target sites (http://crispr.bme.gatech.edu). Based on the user-supplied guide strand and input parameters, COSMID identifies potential off-target sites with the specified number of mismatched bases and insertions or deletions when compared with the guide strand. For each site, amplification primers optimal for the chosen application are also given as output. This ranked-list of potential off-target sites assists the choice and evaluation of intended target sites, thus helping the design of CRISPR/Cas systems with minimal off-target effects, as well as the identification and quantification of CRISPR/Cas induced off-target cleavage in cells.

Figure 1

COSMID design, search steps and characteristics. (a) COSMID input consists of the guide sequence, type of PAM, allowed number of mismatches, insertions and deletions, genome of interest, and primer design parameters. (b) A flow chart showing the COSMID software design and the major steps in performing the search. (c) The search strings with insertions and deletions in the first six possible positions are shown. Alternate deletions of repeated bases are synonymous. (d) COSMID output in HMTL showing the genomic sites matching the user-supplied criteria in comparison to guide strand R-01 with chromosomal location. Scoring of the mismatches is provided for ranking, as are PCR primers and reference sequence. The right primers, in silico link, amplicon, and digest sizes are provided in the output, but not shown here. Links are provided to each location in the UCSC genome browser, and to the output file as a spreadsheet for further manipulation and primer ordering. (e) Run times were measured for COSMID using variations of guide strands R-01 and R-30, with and without a 5′G, using standard (NGG) or relaxed PAM (NRG). All runs included sites matching the guide strand with three or less mismatches without indels. More matching loci “hits” were identified by allowing single-base insertions or deletions together with ≤2 base mismatches. Allowing primer design increased the run times in proportion to the number of hits.

Figure 2

Comparison of COSMID with other available tools in predicting off-target sites for guide strand R-01. (a) On- and off-target cleavage rates for guide strand R-01. Marked differences are seen in the cleavage rates at off-target sites with identical sequences, but different chromosomal locations, such as OT8 and OT9 (purple), OT6 and OT7 (green stripes), and OT1–OT5 (blue). The R-01 on-target indel rate is shown to the right (red pattern). (b–d) Comparison of COSMID with other available tools in predicting off-target sites for guide strand R-01. (b) Comparison of RO1 off-target sites that contain two mismatches. The cleavage rates at R-01 on-target site and off-target sites OT1–OT10 are listed by decreasing T7EI activity. OT3 and OT9 had activities below T7E1 detection limit. Sites with matching sequences (outside first base) have their names in bold with colors matching that shown in a. Annotated genes corresponding to the sites are listed. Off-target analysis was performed with different online search tools. If the genomic sites with measurable T7E1 activity (shown in a) were identified by a specific tool (such as Cas OFFinder), their rankings in its output (if sortable) are shown. Sites not in the output of that tool are indicated by a dash in a grey box. (c) Comparison of search results for off-target sites that contain deletions or insertions, in which sequence-verified off-target sites with insertions or deletions, which can also be modeled as loci with four mismatches or alternate PAM considered. (d) The sequence-verified off-target sites with insertions or deletions that cannot be modeled as four mismatches or alternate PAM can only be predicted by COSMID.