Predictable and precise template-free CRISPR editing of pathogenic variants

Max W. Shen, Mandana Arbab, Jonathan Y. Hsu, Daniel Worstell, Sannie J. Culbertson, Olga Krabbe, Christopher A. Cassa, David R. Liu (), David K. Gifford () and Richard I. Sherwood ()
Additional contact information
Max W. Shen: Massachusetts Institute of Technology
Mandana Arbab: Broad Institute of Harvard and MIT
Jonathan Y. Hsu: Massachusetts Institute of Technology
Daniel Worstell: Brigham and Women’s Hospital and Harvard Medical School
Sannie J. Culbertson: Brigham and Women’s Hospital and Harvard Medical School
Olga Krabbe: Brigham and Women’s Hospital and Harvard Medical School
Christopher A. Cassa: Brigham and Women’s Hospital and Harvard Medical School
David R. Liu: Broad Institute of Harvard and MIT
David K. Gifford: Massachusetts Institute of Technology
Richard I. Sherwood: Brigham and Women’s Hospital and Harvard Medical School

Nature, 2018, vol. 563, issue 7733, 646-651

Abstract: Abstract 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.

Keywords: Production Editor; Hermansky-Pudlak Syndrome (HPS1); Low-density Lipoprotein Receptor (LDLR); Microhomology-mediated End Joining (MMEJ); gRNA Expression Plasmid (search for similar items in EconPapers)
Date: 2018
References: Add references at CitEc
Citations: View citations in EconPapers (15)

Downloads: (external link)
https://www.nature.com/articles/s41586-018-0686-x Abstract (text/html)
Access to the full text of the articles in this series is restricted.

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:nature:v:563:y:2018:i:7733:d:10.1038_s41586-018-0686-x

Ordering information: This journal article can be ordered from
https://www.nature.com/

DOI: 10.1038/s41586-018-0686-x

Access Statistics for this article

Nature is currently edited by Magdalena Skipper

More articles in Nature from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().