Identification of Drug Resistance Mechanisms Using Genome-Wide CRISPR-Cas9 Screens

Methods Mol Biol. 2022;2535:141-156. doi: 10.1007/978-1-0716-2513-2_12.


CRISPR-Cas9 genome editing provides a means for simple and scalable production of gene knockouts in mammalian cell lines. The development of guide RNA (gRNA) libraries targeting tens of thousands of genes has allowed researchers to produce pools of cells, each containing a single gene knockout for use in genetic screens. In addition to assessing the effect of gene knockout on cell proliferation, CRISPR-Cas9 genetic screens can be used to assess gene-drug interactions. Here, we outline a protocol for performing positive and negative selection genome-wide CRISPR-Cas9 screens for identifying gene knockouts that cause drug resistance and hypersensitivity. This protocol is designed for the use of the TKOv3 library in human cell lines, but can be readily adapted for different libraries.

Keywords: CRISPR-Cas9; Chemogenomics; Drug resistance; Functional genomics.

MeSH terms

  • Animals
  • CRISPR-Cas Systems* / genetics
  • Drug Resistance
  • Gene Editing / methods
  • Gene Knockout Techniques
  • Humans
  • Mammals / genetics
  • RNA, Guide, Kinetoplastida* / genetics


  • RNA, Guide