Clonogenic assay of cells in vitro

Nat Protoc. 2006;1(5):2315-9. doi: 10.1038/nprot.2006.339.


Clonogenic assay or colony formation assay is an in vitro cell survival assay based on the ability of a single cell to grow into a colony. The colony is defined to consist of at least 50 cells. The assay essentially tests every cell in the population for its ability to undergo "unlimited" division. Clonogenic assay is the method of choice to determine cell reproductive death after treatment with ionizing radiation, but can also be used to determine the effectiveness of other cytotoxic agents. Only a fraction of seeded cells retains the capacity to produce colonies. Before or after treatment, cells are seeded out in appropriate dilutions to form colonies in 1-3 weeks. Colonies are fixed with glutaraldehyde (6.0% v/v), stained with crystal violet (0.5% w/v) and counted using a stereomicroscope. A method for the analysis of radiation dose-survival curves is included.

MeSH terms

  • Cell Culture Techniques
  • Cell Proliferation / drug effects
  • Cell Proliferation / radiation effects*
  • Colony-Forming Units Assay / methods*
  • Humans
  • Radiation Dosage