Large dataset enables prediction of repair after CRISPR–Cas9 editing in primary T cells

Ryan T. Leenay; Amirali Aghazadeh; Joseph Hiatt; David Tse; Theodore L. Roth; Ryan Apathy; Eric Shifrut; Judd F. Hultquist; Nevan Krogan; Zhenqin Wu; Giana Cirolia; Hera Canaj; Manuel D. Leonetti; Alexander Marson; Andrew P. May; James Zou

doi:https://doi.org/10.1038/s41587-019-0203-2

Large dataset enables prediction of repair after CRISPR–Cas9 editing in primary T cells

Ryan T. Leenay, Amirali Aghazadeh, Joseph Hiatt, David Tse, Theodore L. Roth, Ryan Apathy, Eric Shifrut, Judd F. Hultquist, Nevan Krogan, Zhenqin Wu, Giana Cirolia, Hera Canaj, Manuel D. Leonetti, Alexander Marson, Andrew P. May, James Zou

Research output: Contribution to journal › Article › peer-review

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.

Original language	English
Pages (from-to)	1034-1037
Number of pages	4
Journal	Nature biotechnology
Volume	37
Issue number	9
DOIs	https://doi.org/10.1038/s41587-019-0203-2
State	Published - 1 Sep 2019
Externally published	Yes

All Science Journal Classification (ASJC) codes

Applied Microbiology and Biotechnology
Bioengineering
Molecular Medicine
Biotechnology
Biomedical Engineering

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https://doi.org/10.1038/s41587-019-0203-2

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Leenay, R. T., Aghazadeh, A., Hiatt, J., Tse, D., Roth, T. L., Apathy, R., Shifrut, E., Hultquist, J. F., Krogan, N., Wu, Z., Cirolia, G., Canaj, H., Leonetti, M. D., Marson, A., May, A. P., & Zou, J. (2019). Large dataset enables prediction of repair after CRISPR–Cas9 editing in primary T cells. Nature biotechnology, 37(9), 1034-1037. https://doi.org/10.1038/s41587-019-0203-2

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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",

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AU - Leenay, Ryan T.

AU - Aghazadeh, Amirali

AU - Hiatt, Joseph

AU - Tse, David

AU - Roth, Theodore L.

AU - Apathy, Ryan

AU - Shifrut, Eric

AU - Hultquist, Judd F.

AU - Krogan, Nevan

AU - Wu, Zhenqin

AU - Cirolia, Giana

AU - Canaj, Hera

AU - Leonetti, Manuel D.

AU - Marson, Alexander

AU - May, Andrew P.

AU - Zou, James

PY - 2019/9/1

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N2 - 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.

AB - 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.

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SN - 1087-0156

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EP - 1037

JO - Nature biotechnology

JF - Nature biotechnology

IS - 9

ER -

Large dataset enables prediction of repair after CRISPR–Cas9 editing in primary T cells

Abstract

All Science Journal Classification (ASJC) codes

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