Cas9-chromatin binding information enables more accurate CRISPR off-target prediction

Ritambhara Singh, Cem Kuscu, Aaron Quinlan, Yanjun Qi, Mazhar Adli*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

116 Scopus citations


The CRISPR system has become a powerful biological tool with a wide range of applications. However, improving targeting specificity and accurately predicting potential off-targets remains a significant goal. Here, we introduce a web-based CRISPR/Cas9 Off-target Prediction and Identification Tool (CROPIT) that performs improved off-target binding and cleavage site predictions. Unlike existing prediction programs that solely use DNA sequence information; CROP-IT integrates whole genome level biological information from existing Cas9 binding and cleavage data sets. Utilizing whole-genome chromatin state information from 125 human cell types further enhances its computational prediction power. Comparative analyses on experimentally validated datasets show that CROP-IT outperforms existing computational algorithms in predicting both Cas9 binding as well as cleavage sites. With a user-friendly webinterface, CROP-IT outputs scored and ranked list of potential off-targets that enables improved guide RNA design and more accurate prediction of Cas9 binding or cleavage sites.

Original languageEnglish (US)
Article numbere118
JournalNucleic acids research
Issue number18
StatePublished - Oct 15 2015
Externally publishedYes

ASJC Scopus subject areas

  • Genetics


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