Tracking CRISPR’s Footprints

  • Lin Lin
  • Yonglun LuoEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1961)


The programmable clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) and CRISPR-Cas9-derived gene editing and manipulation tools have revolutionized biomedical research over the past few years. One important category of assisting technologies in CRISPR gene editing is methods used for detecting and quantifying indels (deletions or insertions). These indels are caused by the repair of CRISPR-Cas9-introduced DNA double-stranded breaks (DBSs), known as CRISPR’s DNA cleavage footprints. In addition, CRISPR-Cas9 can also leave footprints to the DNA without introducing DSBs, known as CRISPR’s DNA-binding footprints. The indel tracking methods have contributed greatly to the improvement of CRISPR-Cas9 activity and specificity. Here, we review and discuss strategies developed over that past few years to track the CRISPR’s footprints, their advantages, and limitations.

Key words

CRISPR Cas9 Indels DSB Indel frequency Off-target 



L.L. is supported by grants from the Lundbeck Foundation. Y.L is supported by BGI-Shenzhen, BGI-Qingdao, and grants from the Shenzhen Sanming Medical Project. We thank the whole team of Lars Bolund Institute of Regenerative Medicine (LBI), BGI, for their work and assistance on the CRISPR technologies, and especially Jun Wang from LBI for assistance with preparing Fig. 1. Y.L. is also supported by the Guangdong Provincial Key Laboratory of Genome Read and Write (No. 2017B030301011).

Disclaimer Statement: The views expressed in this article are the personal views of the author and may not be understood or quoted as being made on behalf of or reflecting the position of the Lars Bolund Institute of Regenerative Medicine, BGI, or one of its working parties.


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© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of BiomedicineAarhus UniversityAarhusDenmark
  2. 2.BGI-ShenzhenShenzhenChina
  3. 3.Guangdong Provincial Key Laboratory of Genome Read and WriteShenzhenChina
  4. 4.BGI-QingdaoQingdaoChina

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