Whole genome analysis of CRISPR Cas9 sgRNA off-target homologies via an efficient computational algorithm

Dec 9, 2017BMC genomics

Fast computer analysis of unintended DNA targets for CRISPR Cas9 gene editing guides

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Abstract

Of the 1,876,775 designed sgRNAs for human mRNA genes, only two were free of off-target homology.

Mathematical analysis shows that potential off-target homologies for sgRNAs are inevitable in large genomes like that of humans.
A new computational algorithm was developed to efficiently design sgRNAs and search for off-target homologies across the entire genome.
The algorithm utilizes a dynamically constructed sequence-indexed database and a simplified sequence alignment method.
Results confirmed that it is nearly impossible for sgRNAs to avoid potential off-target sites.
Future efforts in CRISPR Cas9 technology should aim to reduce or eliminate off-target activity.

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BACKGROUND: The beauty and power of the genome editing mechanism, CRISPR Cas9 endonuclease system, lies in the fact that it is RNA-programmable such that Cas9 can be guided to any genomic loci complementary to a 20-nt RNA, single guide RNA (sgRNA), to cleave double stranded DNA, allowing the introduction of wanted mutations. Unfortunately, it has been reported repeatedly that the sgRNA can also guide Cas9 to off-target sites where the DNA sequence is homologous to sgRNA.

RESULTS: Using human genome and Streptococcus pyogenes Cas9 (SpCas9) as an example, this article mathematically analyzed the probabilities of off-target homologies of sgRNAs and discovered that for large genome size such as human genome, potential off-target homologies are inevitable for sgRNA selection. A highly efficient computationl algorithm was developed for whole genome sgRNA design and off-target homology searches. By means of a dynamically constructed sequence-indexed database and a simplified sequence alignment method, this algorithm achieves very high efficiency while guaranteeing the identification of all existing potential off-target homologies. Via this algorithm, 1,876,775 sgRNAs were designed for the 19,153 human mRNA genes and only two sgRNAs were found to be free of off-target homology.

CONCLUSIONS: By means of the novel and efficient sgRNA homology search algorithm introduced in this article, genome wide sgRNA design and off-target analysis were conducted and the results confirmed the mathematical analysis that for a sgRNA sequence, it is almost impossible to escape potential off-target homologies. Future innovations on the CRISPR Cas9 gene editing technology need to focus on how to eliminate the Cas9 off-target activity.

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Whole genome analysis of CRISPR Cas9 sgRNA off-target homologies via an efficient computational algorithm

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