Archives of Toxicology

, Volume 92, Issue 12, pp 3585–3595 | Cite as

Whole genome sequencing analysis of small and large colony mutants from the mouse lymphoma assay

  • Xiaoqing Guo
  • Bohu Pan
  • Ji-Eun Seo
  • Ying Chen
  • Jian Yan
  • Nan Mei
  • Tao ChenEmail author
Genotoxicity and Carcinogenicity


The Thymidine kinase (Tk) gene forward mutation assay, known as the mouse lymphoma assay (MLA), has been widely used for evaluating the genotoxicity of chemical agents. A striking morphological feature of Tk mutant colonies is the bimodal distribution of their sizes, with cells from the large colonies growing at a normal rate and cells from the small colonies growing at a slower rate than normal. To understand the molecular distinction for the different growth rates, we performed whole genome sequencing (WGS) analysis of the large and small colony mutants generated from the MLA. Three large colony and three small colony mutants generated from cells treated with 4-nitroquinoline 1-oxide (4-NQO) or the vehicle control were selected for analysis. The WGS data were analyzed for loss of heterozygosity (LOH) and chromosome copy number along chromosome 11, where the Tk gene is located. Although there were LOH alterations in both large and small colony mutants, copy number changes near Tk locus were found only in small colony mutants produced by the vehicle control and 4-NQO treatments. The chromosome copy number in the regions near the Tk locus increased from two to three or four in the spontaneous small colony mutants and decreased from two to one in the 4-NQO-induced small colony mutants. These results suggest that chromosome damage was repaired differently in the large and small colony mutants, resulting in significant chromosome alterations in the small colony mutants, but not in the large colony mutants. Thus, chromosome alterations near the Tk locus may play a major role in the inhibition of cell growth in the Tk small colony mutants.


Whole genome sequencing Mouse lymphoma assay Chromosome copy number variation Loss of heterozygosity DNA damage Small colony Tk mutants Large colony Tk mutants 



BP and JES were supported by appointments to the Postgraduate Research Program at the National Center for Toxicological Research (NCTR) administered by the Oak Ridge Institute for Science Education through an interagency agreement between the U.S. Department of Energy and the U.S. Food and Drug Administration (FDA).

Compliance with ethical standards

Conflict of interest

There was no conflict of interest declared.

Supplementary material

204_2018_2318_MOESM1_ESM.docx (587 kb)
Supplementary material 1 (DOCX 587 KB)


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Copyright information

© This is a U.S. government work and its text is not subject to copyright protection in the United States; however, its text may be subject to foreign copyright protection 2018

Authors and Affiliations

  • Xiaoqing Guo
    • 1
  • Bohu Pan
    • 2
  • Ji-Eun Seo
    • 1
  • Ying Chen
    • 1
  • Jian Yan
    • 1
  • Nan Mei
    • 1
  • Tao Chen
    • 1
    Email author
  1. 1.Division of Genetic and Molecular ToxicologyNational Center for Toxicological ResearchJeffersonUSA
  2. 2.Division of Bioinformatics and BiostatisticsNational Center for Toxicological ResearchJeffersonUSA

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