The Updated Mouse Universal Genotyping Array Bioinformatic Pipeline Improves Genetic QC in Laboratory Mice

Blanchard, M. W.; Sigmon, J. S.; Brennan, J.; Ahulamibe, C.; Allen, M. E.; Baric, R. S.; Bell, T. A.; Farrington, J.; Ciavatta, D.; Cruz Cisneros, M.; Drushal, M.; Ferris, M. T.; Fry, R.; Gaines, C.; Gu, B.; Heise, M. T.; Hodges, R. A.; Kafri, T.; Lynch, R.; Magnuson, T.; Miller, D.; Murphy, C. E. Y.; Nguyen, D. T.; Noll, K. E.; Proulx, M.; Sassetti, C.; Shaw, G. D.; Simon, J. M.; Smith, C.; Styblo, M.; Tarantino, L.; Woo, J.; Pardo-Manuel de Villena, F.

doi:10.1101/2024.02.29.582794

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bioRxiv · 10.1101/2024.02.29.582794

The Updated Mouse Universal Genotyping Array Bioinformatic Pipeline Improves Genetic QC in Laboratory Mice

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Abstract

The MiniMUGA genotyping array is a popular tool for genetic QC of laboratory mice and genotyping of samples from most types of experimental crosses involving laboratory strains, particularly for reduced complexity crosses. The content of the production version of the MiniMUGA array is fixed; however, there is the opportunity to improve arrays performance and the associated reports usefulness by leveraging thousands of samples genotyped since the initial description of MiniMUGA in 2020. Here we report our efforts to update and improve marker annotation, increase the number and the reliability of the consensus genotypes for inbred strains and increase the number of constructs that can reliably be detected with MiniMUGA. In addition, we have implemented key changes in the informatics pipeline to identify and quantify the contribution of specific genetic backgrounds to the makeup of a given sample, remove arbitrary thresholds, include the Y Chromosome and mitochondrial genome in the ideogram, and improve robust detection of the presence of commercially available substrains based on diagnostic alleles. Finally, we have made changes to the layout of the report, to simplify the interpretation and completeness of the analysis and added a table summarizing the ideogram. We believe that these changes will be of general interest to the mouse research community and will be instrumental in our goal of improving the rigor and reproducibility of mouse-based biomedical research.

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Blanchard, M. W., Sigmon, J. S., Brennan, J., Ahulamibe, C., Allen, M. E., Baric, R. S., Bell, T. A., Farrington, J., Ciavatta, D., Cruz Cisneros, M., Drushal, M., Ferris, M. T., Fry, R., Gaines, C., Gu, B., Heise, M. T., Hodges, R. A., Kafri, T., Lynch, R., Magnuson, T., Miller, D., Murphy, C. E. Y., Nguyen, D. T., Noll, K. E., Proulx, M., Sassetti, C., Shaw, G. D., Simon, J. M., Smith, C., Styblo, M., Tarantino, L., Woo, J., Pardo-Manuel de Villena, F.. 2024-03-03. The Updated Mouse Universal Genotyping Array Bioinformatic Pipeline Improves Genetic QC in Laboratory Mice. https://doi.org/10.1101/2024.02.29.582794

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