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Related Experiment Video

Updated: Dec 5, 2025

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High throughput single-cell detection of multiplex CRISPR-edited gene modifications.

Elisa Ten Hacken1,2, Kendell Clement3,4,5, Shuqiang Li3,6

  • 1Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.

Genome Biology
|October 21, 2020
PubMed
Summary

This study uses droplet-based technology with CRISPR-Cas9 gene editing to analyze cancer mutations in single cells. The approach accurately identifies mutation combinations and gene editing effects in chronic lymphocytic leukemia models.

Keywords:
CRISPR-Cas9GeneticsGenome editingLoss-of-functionMutationSingle cellchronic lymphocytic leukemia

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Area of Science:

  • Genomics
  • Molecular Biology
  • Cancer Research

Background:

  • CRISPR-Cas9 gene editing is crucial for understanding cancer-driving mutations.
  • Analyzing gene edits in thousands of single cells requires advanced technologies.

Purpose of the Study:

  • To apply droplet-based technology for analyzing CRISPR-Cas9 edits in single cells.
  • To investigate functional impacts of somatic mutations in human cancers, specifically chronic lymphocytic leukemia.

Main Methods:

  • Utilized droplet-based technology for single-cell analysis.
  • Employed CRISPR-Cas9 gene editing in engineered Ba/F3 cells carrying cancer mutations.
  • Quantified Cas9 edits, mutational co-occurrences, and zygosity at single-cell resolution.

Main Results:

  • Successfully analyzed gene edits and mutations in thousands of single cells.
  • Reliably quantified mutational co-occurrences and zygosity status.
  • Demonstrated the capability to assess single and multiplexed loss-of-function mutations.

Conclusions:

  • Droplet-based CRISPR-Cas9 analysis provides high-resolution insights into cancer mutation impacts.
  • This method enables precise characterization of gene editing outcomes in complex cellular models.
  • The technology advances functional genomics for cancer research.