2017
DOI: 10.1038/nbt.3804
|View full text |Cite
|
Sign up to set email alerts
|

GuideScan software for improved single and paired CRISPR guide RNA design

Abstract: We present GuideScan software for the design of CRISPR guide RNA libraries that can be used to edit coding and noncoding genomic regions. GuideScan produces high-density sets of gRNAs for single- and paired-gRNA genome-wide screens. We also show that by using a trie data structure GuideScan designs gRNAs that are more specific than those designed by existing tools.

Help me understand this report

Search citation statements

Order By: Relevance

Paper Sections

Select...
2
1
1
1

Citation Types

1
201
0
1

Year Published

2017
2017
2020
2020

Publication Types

Select...
10

Relationship

1
9

Authors

Journals

citations
Cited by 218 publications
(203 citation statements)
references
References 25 publications
1
201
0
1
Order By: Relevance
“…Even though the number of reads on target was sufficient for analyzing the repeats in this experimental setup, there was a high background of reads derived from off‐target Cas9 activity or by unspecific pulldown of SMRTbell molecules not cleaved by Cas9. Computational gRNA design tools that allows for selection of gRNAs with minimal off‐targets sites (Heigwer, Kerr, & Boutros, ; Naito, Hino, Bono, & Ui‐Tei, ; Perez et al., ) could result in a more sensitive assay. Also, it would be interesting to evaluate high‐fidelity Cas9 enzymes that have proven to decrease off‐target effects while retaining on‐target activity (Kleinstiver et al., ).…”
Section: Discussionmentioning
confidence: 99%
“…Even though the number of reads on target was sufficient for analyzing the repeats in this experimental setup, there was a high background of reads derived from off‐target Cas9 activity or by unspecific pulldown of SMRTbell molecules not cleaved by Cas9. Computational gRNA design tools that allows for selection of gRNAs with minimal off‐targets sites (Heigwer, Kerr, & Boutros, ; Naito, Hino, Bono, & Ui‐Tei, ; Perez et al., ) could result in a more sensitive assay. Also, it would be interesting to evaluate high‐fidelity Cas9 enzymes that have proven to decrease off‐target effects while retaining on‐target activity (Kleinstiver et al., ).…”
Section: Discussionmentioning
confidence: 99%
“…For this purpose we used one of the available bioinformatics tool (see section 2.3.1) that provides a list of potential target sites with a score indicating the faithfulness (i.e., on-target activity) and the predicted number of off-target sites. Other software, which uses different algorithms, e.g., Cas-OFFinder [39] and GuideScan [40], is also available for the design of gRNAs. (For a more complete list, see [41]).…”
Section: Discussionmentioning
confidence: 99%
“…Overall, off-targets can be minimized by iterating a process of: 1) selecting specific sgRNAs (Doench et al, 2016; Perez et al, 2017; Scott and Zhang, 2017), 2) employing optimized Cas9 variants and delivery methods, 3) detecting mutations with unbiased genome-wide methods, and 4) validating off-target edits with sensitive targeted sequencing.…”
Section: Figurementioning
confidence: 99%