Research ArticleGENETICS

SpCas9 activity prediction by DeepSpCas9, a deep learning–based model with high generalization performance

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Science Advances  06 Nov 2019:
Vol. 5, no. 11, eaax9249
DOI: 10.1126/sciadv.aax9249


We evaluated SpCas9 activities at 12,832 target sequences using a high-throughput approach based on a human cell library containing single-guide RNA–encoding and target sequence pairs. Deep learning–based training on this large dataset of SpCas9-induced indel frequencies led to the development of a SpCas9 activity–predicting model named DeepSpCas9. When tested against independently generated datasets (our own and those published by other groups), DeepSpCas9 showed high generalization performance. DeepSpCas9 is available at

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