Research ArticleGENETICS

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

See allHide authors and affiliations

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

This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial license, which permits use, distribution, and reproduction in any medium, so long as the resultant use is not for commercial advantage and provided the original work is properly cited.

View Full Text

Stay Connected to Science Advances