Quantifying on- and off-target genome editing

Ayal Hendel, Eli J. Fine, Gang Bao, Matthew H. Porteus

Research output: Contribution to journalReview articlepeer-review

110 Scopus citations


Genome editing with engineered nucleases is a rapidly growing field thanks to transformative technologies that allow researchers to precisely alter genomes for numerous applications including basic research, biotechnology, and human gene therapy. While the ability to make precise and controlled changes at specified sites throughout the genome has grown tremendously in recent years, we still lack a comprehensive and standardized battery of assays for measuring the different genome editing outcomes created at endogenous genomic loci. Here we review the existing assays for quantifying on- and off-target genome editing and describe their utility in advancing the technology. We also highlight unmet assay needs for quantifying on- and off-target genome editing outcomes and discuss their importance for the genome editing field.

Original languageEnglish
Pages (from-to)132-140
Number of pages9
JournalTrends in Biotechnology
Issue number2
StatePublished - 1 Feb 2015
Externally publishedYes

Bibliographical note

Funding Information:
This work was supported by the National Institutes of Health as a Nanomedicine Development Center Award (PN2EY018244 to G.B. and M.H.P.). A.H. was supported in part by the Fund-A-Fellow postdoctoral fellowship research grant award from the Myotonic Dystrophy Foundation (MDF) and the Dean's postdoctoral fellowship award at the Stanford School of Medicine. E.J.F. was supported by the National Science Foundation Graduate Research Fellowship (DGE-1148903). M.H.P. is supported as the Laurie Kraus Lacob Faculty Scholar in Pediatric Translational Research. The authors thank Niraj Punjya for his assistance in generating the figures for this review. They apologize for omitting many relevant citations due to space limitations.

Publisher Copyright:
© 2014 Elsevier Ltd.


  • CRISPR/Cas9
  • Gene editing
  • Gene targeting
  • Homologous recombination
  • Nonhomologous end-joining
  • RNA-guided endonucleases
  • TALENs
  • ZFNs


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