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

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...

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Autores principales: Kim, Hui Kwon, Kim, Younggwang, Lee, Sungtae, Min, Seonwoo, Bae, Jung Yoon, Choi, Jae Woo, Park, Jinman, Jung, Dongmin, Yoon, Sungroh, Kim, Hyongbum Henry
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Association for the Advancement of Science 2019
Materias:
Research Articles
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6834390/
https://www.ncbi.nlm.nih.gov/pubmed/31723604
http://dx.doi.org/10.1126/sciadv.aax9249
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author Kim, Hui Kwon
Kim, Younggwang
Lee, Sungtae
Min, Seonwoo
Bae, Jung Yoon
Choi, Jae Woo
Park, Jinman
Jung, Dongmin
Yoon, Sungroh
Kim, Hyongbum Henry
author_facet Kim, Hui Kwon
Kim, Younggwang
Lee, Sungtae
Min, Seonwoo
Bae, Jung Yoon
Choi, Jae Woo
Park, Jinman
Jung, Dongmin
Yoon, Sungroh
Kim, Hyongbum Henry
author_sort Kim, Hui Kwon
collection PubMed
description 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 http://deepcrispr.info/DeepSpCas9.
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spelling pubmed-68343902019-11-13 SpCas9 activity prediction by DeepSpCas9, a deep learning–based model with high generalization performance Kim, Hui Kwon Kim, Younggwang Lee, Sungtae Min, Seonwoo Bae, Jung Yoon Choi, Jae Woo Park, Jinman Jung, Dongmin Yoon, Sungroh Kim, Hyongbum Henry Sci Adv Research Articles 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 http://deepcrispr.info/DeepSpCas9. American Association for the Advancement of Science 2019-11-06 /pmc/articles/PMC6834390/ /pubmed/31723604 http://dx.doi.org/10.1126/sciadv.aax9249 Text en Copyright © 2019 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC). http://creativecommons.org/licenses/by-nc/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial license (http://creativecommons.org/licenses/by-nc/4.0/) , 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.
spellingShingle Research Articles
Kim, Hui Kwon
Kim, Younggwang
Lee, Sungtae
Min, Seonwoo
Bae, Jung Yoon
Choi, Jae Woo
Park, Jinman
Jung, Dongmin
Yoon, Sungroh
Kim, Hyongbum Henry
SpCas9 activity prediction by DeepSpCas9, a deep learning–based model with high generalization performance
title SpCas9 activity prediction by DeepSpCas9, a deep learning–based model with high generalization performance
title_full SpCas9 activity prediction by DeepSpCas9, a deep learning–based model with high generalization performance
title_fullStr SpCas9 activity prediction by DeepSpCas9, a deep learning–based model with high generalization performance
title_full_unstemmed SpCas9 activity prediction by DeepSpCas9, a deep learning–based model with high generalization performance
title_short SpCas9 activity prediction by DeepSpCas9, a deep learning–based model with high generalization performance
title_sort spcas9 activity prediction by deepspcas9, a deep learning–based model with high generalization performance
topic Research Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6834390/
https://www.ncbi.nlm.nih.gov/pubmed/31723604
http://dx.doi.org/10.1126/sciadv.aax9249
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