CRISPR/Cas9-Based Chemogenomic Profiling in Mammalian Cells

  • Dominic HoepfnerEmail author
  • Gregory McAllister
  • Gregory R. Hoffman
Part of the Methods in Molecular Biology book series (MIMB, volume 1888)


Chemogenomic profiling is a powerful and unbiased approach to elucidate pharmacological targets and the mechanism of bioactive compounds. It is based on identifying cellular hypersensitivity and resistance caused by individual gene modulations with genome-wide coverage. Due to the requirement of bar-coded, genome-wide deletion collections, high-resolution experiments of this nature have historically been limited to fungal systems. Pooled RNAi reagents have enabled similar attempts in mammalian cells but efforts have been hampered by significant off-target effects and experimental noise. The CRISPR/Cas9 system for the first time enables precise DNA editing at defined loci in a genome-wide fashion. Here we present the detailed protocol that leverages the CRISPR/Cas9 system for chemogenomic profiling and target identification of diverse chemical probes.

Key words

CRISPR Cas9 Chemogenomic profiling Target identification Gene editing Genetics Genomics Haploinsufficiency Resistance NAMPT Signal peptidase 



We thank Nadire Ramadan Cochran, David Estoppey, Malini Varadarajan, and Claudia Agarinis for their help setting up the described protocols and careful proofreading of the manuscript.


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Copyright information

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

Authors and Affiliations

  • Dominic Hoepfner
    • 1
    Email author
  • Gregory McAllister
    • 2
  • Gregory R. Hoffman
    • 2
  1. 1.Novartis Institutes for BioMedical Research, Novartis Pharma AGBaselSwitzerland
  2. 2.Novartis Institutes for BioMedical ResearchCambridgeUSA

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