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Cited by 214Genetic Mapping and Diversity in Plants and AnimalsGenetic and phenotypic traits in livestockGenetic diversity and population structure

The Mouse Universal Genotyping Array: From Substrains to Subspecies

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Morgan, Andrew P, Fu, Chen-Ping, Kao, Chia-Yu, Welsh, Catherine E, Didion, John P, Yadgary, Liran, Hyacinth, Leeanna, Ferris, Martin T +15 more·2016·G3 Genes|Genomes|Genetics
DOI 10.1534/g3.115.022087PMC PMC4751547
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Abstract

Genotyping microarrays are an important resource for genetic mapping, population genetics, and monitoring of the genetic integrity of laboratory stocks. We have developed the third generation of the Mouse Universal Genotyping Array (MUGA) series, GigaMUGA, a 143,259-probe Illumina Infinium II array for the house mouse (Mus musculus). The bulk of the content of GigaMUGA is optimized for genetic mapping in the Collaborative Cross and Diversity Outbred populations, and for substrain-level identification of laboratory mice. In addition to 141,090 single nucleotide polymorphism probes, GigaMUGA contains 2006 probes for copy number concentrated in structurally polymorphic regions of the mouse genome. The performance of the array is characterized in a set of 500 high-quality reference samples spanning laboratory inbred strains, recombinant inbred lines, outbred stocks, and wild-caught mice. GigaMUGA is highly informative across a wide range of genetically diverse samples, from laboratory substrains to other Mus species. In addition to describing the content and performance of the array, we provide detailed probe-level annotation and recommendations for quality control.

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  • The GigaMUGA contains 143,259 genetic markers specifically designed for genetic mapping in the DO mouse population.

    “The GigaMUGA contains 143,259 genetic markers that were speci cally designed for genetic mapping in the DO mouse population [19,33].”

    From Identification of Genetic Variants Regulating the Abundance of Clinically Relevant Plasma Proteins using the Diversity Outbred Mouse Model (2021) · cites this paper as [19]

    The Abstract identifies GigaMUGA as a 143,259-probe array and says the bulk of its content is optimized for genetic mapping in the Collaborative Cross and Diversity Outbred populations. It does not say all 143,259 markers were specifically designed for mapping in the DO; the Abstract and Results and Discussion describe probes serving other purposes, including copy-number detection and studies of wild mice. (LLM, conf=0.90)

    Experimental — accuracy not yet measured

  • GigaMUGA scoring for 143,259 probes showed high performance in a set of 500 high-quality reference samples spanning laboratory inbred strains, recombinant inbred lines, outbred stocks, and wild-caught mice.

    “The robustness, simplicity and curated content of the third generation of this genotyping array (GigaMUGA) scoring for 143,259 probes showed high performance in a set of 500 high-quality reference samples spanning laboratory inbred strains, recombinant inbred lines, outbred stocks, and wild-caught mice [67].”

    From Genetic Insights into the Economic Toll of Cell Line Misidentification: A Comprehensive Review (2026) · cites this paper as [67]

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Authors
Morgan, A. P., Fu, C.-P., Kao, C.-Y., Welsh, C. E., Didion, J. P., Yadgary, L., Hyacinth, L., Ferris, M. T., Bell, T. A., Miller, D. R., Giusti-Rodriguez, P., Nonneman, R. J., Cook, K. D., Whitmire, J. K., Gralinski, L. E., Keller, M., Attie, A. D., Churchill, G. A., Petkov, P., Sullivan, P. F., Brennan, J. R., McMillan, L., & Pardo-Manuel de Villena, F.
Affiliations
  • University of North Carolina at Chapel Hill (US)
  • Rhodes College (US)
  • Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
  • University of Wisconsin–Madison (US)
  • Jackson Laboratory (US)
ORCID
Venue
G3 Genes|Genomes|Genetics
Publisher
Oxford University Press (OUP)
Published
2016-02-01
Volume
6
Issue
2
Pages
263-279
ISSN
2160-1836 (ISSN-L)
DOI
10.1534/g3.115.022087
PMC
PMC4751547
OpenAlex
W2221387489
Cited by
214
References
2
Citations by year
2026: 8 · 2025: 17 · 2024: 20 · 2023: 28 · 2022: 24 · 2021: 27 · 2020: 25 · 2019: 20 · 2018: 15 · 2017: 17 · 2016: 9 · 2015: 2
FWCI
9.85
Type
journal article
Language
en
Open access
Licence
Locations
  • G3 Genes Genomes Genetics (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Carolina Digital Repository (University of North Carolina at Chapel Hill) (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • The Mouseion at the JAXlibrary (Jackson Laboratory) (submittedVersion)
  • UNC Libraries
Funders
  • University of North Carolina
  • National Institutes of Health (U42OD010924)
  • National Institute of Mental Health (F30MH103925)
  • National Human Genome Research Institute (P50HG006582)
  • National Institute of General Medical Sciences (T32GM067553, R01GM070683)
  • National Institute of Allergy and Infectious Diseases (U19AI100625)
  • National Institute of Diabetes and Digestive and Kidney Diseases (R01DK101573)
  • Eunice Kennedy Shriver National Institute of Child Health and Human Development (R01HD065024)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
Keywords
house mouse, Mus musculus, single nucleotide polymorphisms, copy number variation, gene mapping, Collaborative Cross, inbred strains, recombinant inbred lines, probe annotation, quality control
MeSH terms
Alleles, Animals, Chromosome Mapping, Genetics, Population, Genotype, Mice, Inbred Strains, Phylogeny, Genome, Gene Dosage, Computational Biology, Oligonucleotide Array Sequence Analysis, Polymorphism, Single Nucleotide, Genomics, Mice

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