The updated mouse universal genotyping array bioinformatic pipeline improves genetic QC in laboratory mice

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 fixe...

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Published in:	G3 : genes - genomes - genetics Vol. 14; no. 10
Main Authors:	Blanchard, Matthew W, Sigmon, John Sebastian, Brennan, Jennifer, Ahulamibe, Chidima, Allen, Michelle E, Ardery, Sam, Baric, Ralph S, Bell, Timothy A, Farrington, Joseph, Ciavatta, Dominic, Cruz Cisneros, Marta C, Drushal, Madison, Ferris, Martin T, Fry, Rebecca C, Gaines, Christiann, Gu, Bin, Heise, Mark T, Hock, Pablo, Hodges, Richard Austin, Hulgin, Mia, Kafri, Tal, Lynch, Rachel M, Magnuson, Terry, Miller, Darla R, Murphy, Caroline E Y, Nguyen, David Truong, Noll, Kelsey E, Proulx, Megan K, Sassetti, Christopher M, Schoenrock, Sarah A, Shaw, Ginger D, Simon, Jeremy M, Smith, Clare M, Styblo, Miroslav, Tarantino, Lisa M, Woo, Joyce, Pardo Manuel de Villena, Fernando
Format:	Journal Article
Language:	English
Published:	US Oxford University Press 07-10-2024
Subjects:	Alleles Animals Computational Biology - methods Genotype Genotyping Techniques - methods Genotyping Techniques - standards Mice Oligonucleotide Array Sequence Analysis - methods Quality Control Reproducibility of Results Software and Data Resources diagnostic SNPs genetic QC substrains chromosomal sex genetic background genetic constructs inbred strains microarrays
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Summary:	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.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 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.
ISSN:	2160-1836 2160-1836
DOI:	10.1093/g3journal/jkae193