Journal
NATURE
Volume 563, Issue 7733, Pages 646-+Publisher
NATURE PUBLISHING GROUP
DOI: 10.1038/s41586-018-0686-x
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Funding
- NSF Graduate Research Fellowship
- NWO Rubicon Fellowship
- HHMI [DARPA HR0011-17-2-0049, NIHRM1 HG009490, R01 EB022376, R35 GM118062]
- Human Frontier Science Program [1K01DK101684]
- NWO
- American Cancer Society
- Brigham Research Institute
- Harvard Stem Cell Institute
- [1R01HG008363]
- [1R01HG008754]
- [1R01HG010372]
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Following Cas9 cleavage, DNA repair without a donor template is generally considered stochastic, heterogeneous and impractical beyond gene disruption. Here, we show that template-free Cas9 editing is predictable and capable of precise repair to a predicted genotype, enabling correction of disease-associated mutations in humans. We constructed a library of 2,000 Cas9 guide RNAs paired with DNA target sites and trained inDelphi, a machine learning model that predicts genotypes and frequencies of 1-to 60-base-pair deletions and 1-base-pair insertions with high accuracy (r = 0.87) in five human and mouse cell lines. inDelphi predicts that 5-11% of Cas9 guide RNAs targeting the human genome are 'precise-50', yielding a single genotype comprising greater than or equal to 50% of all major editing products. We experimentally confirmed precise-50 insertions and deletions in 195 human disease-relevant alleles, including correction in primary patient-derived fibroblasts of pathogenic alleles to wild-type genotype for Hermansky-Pudlak syndrome and Menkes disease. This study establishes an approach for precise, template-free genome editing.
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