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Reference genomes for BALB/c Nude and NOD/SCID mouse models
Emanuel Schmid-Siegert1, Mengting Qin2, Huan Tian2
1JSR Life Sciences, NGS-AI CH Division Route de la Corniche 3, 1066 Epalinges, Switzerland.
Abstract:
Mouse xenograft models play a vital role in tumor studies for research as well as for screening of drugs for the pharmaceutical industry. In particular, models with compromised immunity are favorable to increase the success of transplantation, such as, e.g. NOD/SCID and BALB/c Nude strains. The genomic sequence and alterations of many of these models still remain elusive and might hamper a model's further optimization or proper adapted usage. This can be in respect to treatments (e.g. NOD/SCID sensitivity to radiation), experiments or analysis of derived sequencing data of such models. Here we present the genome assemblies for the NOD/SCID and BALB/c Nude strains to overcome this short-coming for the future and improve our understanding of these models in the process. We highlight as well first insights into observed genomic differences for these models compared to the C57BL/6 reference genome. Genome assemblies for both are close to full-chromosome representations and provided with liftover annotations from the GRCm39 reference genome.
Insights
Researchers have sequenced the genomes of NOD/SCID and BALB/c Nude mice, crucial for tumor research and drug screening. This provides a foundational resource to improve the understanding and application of these immunocompromised models in biomedical studies.
Area of Science:
- Immunology
- Genomics
- Pharmacology
Background:
- Mouse xenograft models are essential for cancer research and drug development.
- Immunocompromised strains like NOD/SCID and BALB/c Nude facilitate successful tumor transplantation.
- Limited genomic data for these models hinders their optimization and application.
Purpose of the Study:
- To provide high-quality genome assemblies for NOD/SCID and BALB/c Nude mouse strains.
- To enhance the utility and understanding of these immunocompromised models in research.
- To identify genomic differences compared to the C57BL/6 reference genome.
Main Methods:
- Whole-genome sequencing of NOD/SCID and BALB/c Nude mice.
- De novo genome assembly to achieve near full-chromosome representation.
- Liftover annotation using the GRCm39 reference genome.
Main Results:
- Near complete genome assemblies for NOD/SCID and BALB/c Nude strains were generated.
- Initial analysis revealed genomic variations between these models and the C57BL/6 reference.
- The assemblies are annotated and ready for comparative genomic studies.
Conclusions:
- The presented genome assemblies address a critical knowledge gap for NOD/SCID and BALB/c Nude mice.
- These genomic resources will facilitate improved experimental design and data interpretation in xenograft studies.
- Understanding strain-specific genomic alterations is vital for advancing cancer research and drug discovery.
