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Nat Methods. 2017 Jun;14(6):607-614. doi: 10.1038/nmeth.4278. Epub 2017 May 1.

CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPR-Cas9 nuclease off-targets.

Tsai SQ1,2,3,4, Nguyen NT1,2,3, Malagon-Lopez J1,2,3,4,5, Topkar VV1,2,3, Aryee MJ1,2,3,4,5, Joung JK1,2,3,4.

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Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts, USA.
Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, USA.
Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts, USA.
Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA.
Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.


Sensitive detection of off-target effects is important for translating CRISPR-Cas9 nucleases into human therapeutics. In vitro biochemical methods for finding off-targets offer the potential advantages of greater reproducibility and scalability while avoiding limitations associated with strategies that require the culture and manipulation of living cells. Here we describe circularization for in vitro reporting of cleavage effects by sequencing (CIRCLE-seq), a highly sensitive, sequencing-efficient in vitro screening strategy that outperforms existing cell-based or biochemical approaches for identifying CRISPR-Cas9 genome-wide off-target mutations. In contrast to previously described in vitro methods, we show that CIRCLE-seq can be practiced using widely accessible next-generation sequencing technology and does not require reference genome sequences. Importantly, CIRCLE-seq can be used to identify off-target mutations associated with cell-type-specific single-nucleotide polymorphisms, demonstrating the feasibility and importance of generating personalized specificity profiles. CIRCLE-seq provides an accessible, rapid, and comprehensive method for identifying genome-wide off-target mutations of CRISPR-Cas9.

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