Whole Genome Sequencing of the Mutamouse Model Reveals Strain- and Colony-Level Variation, and Genomic Features of the Transgene Integration Site
- DOI
- Language of the publication
- English
- Date
- 2019-09-24
- Type
- Article
- Author(s)
- Meier, Matthew J.
- Beal, Marc A.
- Schoenrock, Andrew
- Yauk, Carole L.
- Marchetti, Francesco
- Publisher
- Nature Research
Abstract
The MutaMouse transgenic rodent model is widely used for assessing in vivo mutagenicity. Here, we report the characterization of MutaMouse’s whole genome sequence and its genetic variants compared to the C57BL/6 reference genome. High coverage (>50X) next-generation sequencing (NGS) of whole genomes from multiple MutaMouse animals from the Health Canada (HC) colony showed ~5 million SNVs per genome, ~20% of which are putatively novel. Sequencing of two animals from a geographically separated colony at Covance indicated that, over the course of 23 years, each colony accumulated 47,847 (HC) and 17,677 (Covance) non-parental homozygous single nucleotide variants. We found no novel nonsense or missense mutations that impair the MutaMouse response to genotoxic agents. Pairing sequencing data with array comparative genomic hybridization (aCGH) improved the accuracy and resolution of copy number variants (CNVs) calls and identified 300 genomic regions with CNVs. We also used long-read sequence technology (PacBio) to show that the transgene integration site involved a large deletion event with multiple inversions and rearrangements near a retrotransposon. The MutaMouse genome gives important genetic context to studies using this model, offers insight on the mechanisms of structural variant formation, and contributes a framework to analyze aCGH results alongside NGS data.
Plain language summary
The MutaMouse transgenic rodent is a widely used animal model that is routinely used for assessing whether a substance in the environment is capable of inducing mutations (changes in DNA sequence) that can result in cancer and other diseases. The MutaMouse contains a bacterial gene that is used to investigate the induction of mutations in any tissue in the body. Health Canada has lead the development of a test guideline for the Organization for the Economic Co-Operation and Development that describes how to use transgenic rodents for regulatory testing. In this study, Health Canada sequenced the entire genome (all the DNA in the organism) of the MutaMouse to determine whether there are mutations in MutaMouse that may have an impact on the results of chemical testing. Out of the ~3 billion sites that compose the entire genome, the analysis identified approximately 5 million sites in the MutaMouse genome that are different from the average mouse genome, with ~20% of them that are potentially specific to MutaMouse (i.e., not present in other types of mice). None of the genetic variations represented by those 5 million sites are expected to influence toxicology testing using the MutaMouse because they occur almost exclusively in regions of the genome that do not result in the formation of proteins that are responsible for the activity in any cell in the body. Moreover, the analysis provided a detailed description of the point in the genome whether the bacteria gene was inserted during the creation of the MutaMouse model and showed that this insertion did not disrupt important genes. Overall, the results confirm that the MutaMouse is a good model for use in genetic toxicology and will help designing and interpreting the data obtained from their utilization.
Subject
- Health,
- Health and safety