1. The updated mouse universal genotyping array bioinformatic pipeline improves genetic QC in laboratory mice.
- Author
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Blanchard MW, Sigmon JS, Brennan J, Ahulamibe C, Allen ME, Ardery S, Baric RS, Bell TA, Farrington J, Ciavatta D, Cruz Cisneros MC, Drushal M, Ferris MT, Fry RC, Gaines C, Gu B, Heise MT, Hock P, Hodges RA, Hulgin M, Kafri T, Lynch RM, Magnuson T, Miller DR, Murphy CEY, Nguyen DT, Noll KE, Proulx MK, Sassetti CM, Schoenrock SA, Shaw GD, Simon JM, Smith CM, Styblo M, Tarantino LM, Woo J, and Pardo Manuel de Villena F
- Subjects
- Animals, Mice, Genotype, Quality Control, Alleles, Reproducibility of Results, Oligonucleotide Array Sequence Analysis methods, Genotyping Techniques methods, Genotyping Techniques standards, Computational Biology methods
- Abstract
The MiniMUGA genotyping array is a popular tool for genetic quality control of laboratory mice and genotyping samples from most 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 the array's performance and the associated report's usefulness by leveraging thousands of samples genotyped since the initial description of MiniMUGA. Here, we report our efforts to update and improve marker annotation, increase the number and the reliability of the consensus genotypes for classical inbred strains and substrains, and increase the number of constructs reliably 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 updated the layout of the report to simplify the interpretation and completeness of the analysis and added a section summarizing the ideogram in table format. 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., Competing Interests: Conflicts of interest The authors have no conflict of interest to declare. None of the authors have a financial relationship with Neogen Inc. apart from the service contracts listed above., (© The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America.)
- Published
- 2024
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