CHANGE-seq: a rapid, high-throughput method to define genome-wide activity of CRISPR-Cas genome editors (SJ-18-0041)

St. Jude Reference #SJ-18-0041


CRISPR-Cas nucleases are a transformative genome editing technology that has become broadly adopted for research and is being studied as a basis for future therapeutics. While genome editing holds tremendous promise for improving treatment of cancer, sickle cell disease and other conditions, it remains challenging to screen for highly specific targets. Factors that affect unintended off-target activity remain largely unknown.

Scientists at St. Jude Children’s Research Hospital have developed a new research tool helps define unintended off-target effects of CRISPR genome editing, making the process safer and more easy to use, sensitive and high-throughput method to define sites of unintended double stranded breaks in DNA caused by genome editors like the CRISPR-Cas9 technique. They called the method Circularization for High-throughput Analysis of Nuclease Genome-wide Effects by Sequencing (CHANGE-seq). The work appears as an advance online publication June 15th in Nature Biotechnology.

This method could be used to rapidly evaluate the specificity of CRISPR-Cas nucleases for therapeutics, or for any application where it would be beneficial to define the genome-wide activity in vitro. It can be used to evaluate the relative specificity of different targets against the same gene or genetic element, various nucleases, and formulations, and/or to rapidly generate patient-specific profiles of genome-wide activity. 

Advantages over existing technology:

  1. Reduces the DNA input requirements by approximately 5-fold
  2. Reduces processing time by approximately 12 hours, eliminating 8 enzymatic or purification steps.
  3. Eliminates the requirement for physical shearing of genomic DNA by sonication.
  4. Eliminates possibility of shearing-associated DNA damage confounding results.
  5. Improves scalability, enabling testing of more targets, formulations, or sources of genomic DNA.


genome editing, gene editing, genome engineering, CRISPR, CRISPR-Cas, Cas9, Cpf1, base editing, CHANGE-seq, CIRCLE-seq, genome-wide activity, engineered nucleases, Tn5, tagmentation, off-target effects

Granted patents or published applications

Issued US Patent 10,920,272; and another pending

Related scientific references

Lazzarotto, C.R., Malinin, N.L., Li, Y. et al. CHANGE-seq reveals genetic and epigenetic effects on CRISPR–Cas9 genome-wide activity. Nat Biotechnol (2020).

Also, a broader story about the article here:

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