The updated mouse universal genotyping array bioinformatic pipeline improves genetic QC in laboratory mice
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.
Authors
- Jeremy M. Simon (ORCID: https://orcid.org/0000-0003-3906-1663)
- Marta C Cruz Cisneros (ORCID: https://orcid.org/0000-0002-2785-3498)
- Bin Gu (ORCID: https://orcid.org/0000-0002-6846-5563)
- Matthew W Blanchard (ORCID: https://orcid.org/0000-0003-3977-2115)
- Miroslav Stýblo (ORCID: https://orcid.org/0000-0001-6764-1900)
- Terry Magnuson (ORCID: https://orcid.org/0000-0002-0792-835X)
- Joseph Farrington (ORCID: https://orcid.org/0000-0003-4156-3419)
- Dominic J. Ciavatta (ORCID: https://orcid.org/0000-0003-2571-8679)
- Ralph Steven Baric (ORCID: https://orcid.org/0000-0001-6827-8701)
- Fernando Pardo‐Manuel de Villena (ORCID: https://orcid.org/0000-0002-5738-5795)
- Mark T. Heise (ORCID: https://orcid.org/0000-0001-5829-8477)
- Lisa M. Tarantino (ORCID: https://orcid.org/0000-0001-9984-2600)
- Pablo Hock
- Jennifer Brennan
- Timothy A. Bell (ORCID: https://orcid.org/0000-0002-9546-6334)
- Megan K. Proulx (ORCID: https://orcid.org/0000-0002-9524-8302)
- Martin T. Ferris (ORCID: https://orcid.org/0000-0003-1241-6268)
- Tal Kafri (ORCID: https://orcid.org/0000-0002-9386-921X)
- Christiann H. Gaines
- Kelsey E. Noll (ORCID: https://orcid.org/0000-0002-3977-0083)
- Ginger D. Shaw (ORCID: https://orcid.org/0000-0003-2590-4973)
- Christopher M. Sassetti (ORCID: https://orcid.org/0000-0001-6178-4329)
- Clare M. Smith (ORCID: https://orcid.org/0000-0003-2601-0955)
- Darla R. Miller (ORCID: https://orcid.org/0000-0002-0781-7254)
- John Sebastian Sigmon (ORCID: https://orcid.org/0000-0003-1635-3882)
- Rebecca C. Fry (ORCID: https://orcid.org/0000-0003-0899-9018)
- Caroline E Y Murphy (ORCID: https://orcid.org/0000-0001-9886-3178)
- Michelle E Allen (ORCID: https://orcid.org/0000-0001-7177-5063)
- Joyce Woo (ORCID: https://orcid.org/0000-0001-6958-4903)
- Sarah A. Schoenrock (ORCID: https://orcid.org/0000-0001-7345-444X)
- Rachel Lynch (ORCID: https://orcid.org/0000-0001-8164-0744)
- Madison Drushal
- Chidima Ahulamibe
- Mia Hulgin
- Sam Ardery
- Richard Austin Hodges
- David Truong Nguyen
Institutions
- University of North Carolina at Chapel Hill (US)
- University of Massachusetts Chan Medical School (US)
- Duke University (US)
- UNC Lineberger Comprehensive Cancer Center
- The Ohio State University (US)
Publication Details
- Journal
- G3 Genes Genomes Genetics
- Published
- 2024-09-13
- DOI
- https://doi.org/10.1093/g3journal/jkae193
- Citations
- 4
- Primary Topic
- Genetic Mapping and Diversity in Plants and Animals
- Type
- article
- Field-Weighted Citation Impact
- 2.20
Funders
- National Institutes of Health
- National Institute on Drug Abuse