@article{deb56019a30e49e999fb2d993837cb5b,
title = "Large dataset enables prediction of repair after CRISPR–Cas9 editing in primary T cells",
abstract = "Understanding of repair outcomes after Cas9-induced DNA cleavage is still limited, especially in primary human cells. We sequence repair outcomes at 1,656 on-target genomic sites in primary human T cells and use these data to train a machine learning model, which we have called CRISPR Repair Outcome (SPROUT). SPROUT accurately predicts the length, probability and sequence of nucleotide insertions and deletions, and will facilitate design of SpCas9 guide RNAs in therapeutically important primary human cells.",
author = "Leenay, {Ryan T.} and Amirali Aghazadeh and Joseph Hiatt and David Tse and Roth, {Theodore L.} and Ryan Apathy and Eric Shifrut and Hultquist, {Judd F.} and Nevan Krogan and Zhenqin Wu and Giana Cirolia and Hera Canaj and Leonetti, {Manuel D.} and Alexander Marson and May, {Andrew P.} and James Zou",
note = "Funding Information: A.M. is a co-founder of Spotlight Therapeutics. A.M. has served as an advisor to Juno Therapeutics, is a member of the scientific advisory board at PACT Pharma and an is advisor to Sonoma Biotherapeutics. The Marson laboratory has received sponsored research support from Juno Therapeutics, Epinomics, Sanofi and a gift from Gilead. A.M. and T.L.R. are co-founders of Arsenal Biosciences and T.L.R. is chief scientific officer of the company. Funding Information: This work was supported by the Chan–Zuckerberg Biohub. J.Z. was supported by a Chan–Zuckerberg Investigator grant and by National Science Foundation grant CRII 1657155. A.M. was supported by National Iinstitutes of Health (NIH)/NIDA Avenir New Innovator Award (DP2DA042423), NIH/NIGMS funding for the HIV Accessory and Regulatory Complexes (HARC) Center (P50 GM082250; to A.M. and N.J.K.) and gifts from J. Aronov, B. Bakar, K. Jordan, F. Caufield and D. Wolkoff. A.M. holds a Career Award for Medical Scientists from the Burroughs Wellcome Fund, has received funding from the Innovative Genomics Institute (IGI) and the Parker Institute for Cancer Immunotherapy (PICI) and is an investigator at the Chan–Zuckerberg Biohub. A.A. was supported by NIH grant 7R01HG008164-04 and the Stanford data science initiative. J.H. was supported by the UCSF Medical Scientist Training Program. We would like to thank N. Neff and R. Sit for assistance collecting sequence data and A. Sellas for laboratory support. We also thank J. Palacios for statistical discussions. Publisher Copyright: {\textcopyright} 2019, The Author(s), under exclusive licence to Springer Nature America, Inc.",
year = "2019",
month = sep,
day = "1",
doi = "10.1038/s41587-019-0203-2",
language = "English (US)",
volume = "37",
pages = "1034--1037",
journal = "Nature Biotechnology",
issn = "1087-0156",
publisher = "Nature Publishing Group",
number = "9",
}