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

Nat Biotechnol. 2019 Sep;37(9):1034-1037. doi: 10.1038/s41587-019-0203-2. Epub 2019 Jul 29.


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • CRISPR-Cas Systems*
  • Cell Line
  • Gene Editing / methods*
  • Gene Expression Regulation
  • Genome
  • Genomics
  • Humans
  • Induced Pluripotent Stem Cells / physiology
  • RNA, Guide / genetics*
  • T-Lymphocytes / physiology*


  • RNA, Guide