ArticleGenetics2020
Content and Performance of the MiniMUGA Genotyping Array: A New Tool To Improve Rigor and Reproducibility in Mouse Research.
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Article in Genetics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 72 papers.
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72citing papers in PubMed
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72 citing papers in PubMed, 107 citations in OpenAlex.
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- Trans-regulation of heterochromatin underlies genetic variation in 3D genome contacts in mouse embryonic stem cells.Genome biology · 2026Article
- Non-Mendelian inheritance of DNA methylation patterns in mice.Nature genetics · 2026Article
- Genetic mapping in collaborative cross mouse strains identifies loci that affect initial sensitivity to cocaine.Psychopharmacology · 2026Article
- Improve genetic quality control to increase rigor and reproducibility of mouse research.Science (New York, N.Y.) · 2026Article
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- Substrain-specific behavioral variation in female C57BL/6 and C57BL/10 mice.Frontiers in behavioral neuroscience · 2026Article
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- Low-coverage whole-genome sequencing facilitates accurate and cost-effective haplotype reconstruction in complex mouse crosses.Mammalian genome : official journal of the International Mammalian Genome Society · 2025Article
- Cohousing or cross-fostering followed by cohousing does not normalize the microbiomes of genetically distinct adult mice.Cell reports · 2025Article
- The Validation of Antibodies Suitable for Flow Cytometric Analysis and Immunopeptidomics of Peptide-MHC Complexes in the Outbred Swiss Albino Mouse Strain.Methods and protocols · 2025Article
- Differential neuronal functions of LNX1 and LNX2 revealed by behavioural analysis in single and double knockout mice.Behavioral and brain functions : BBF · 2025Article
12 more citing papers are in PubMed but not listed here.
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Authors and funding
69 authors at 9 institutions in 1 country.
John Sebastian Sigmon *Department of Computer Science, University of North Carolina, Chapel Hill, North Carolina 27599.
Matthew W Blanchard *Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599.ORCID 0000-0003-3977-2115
Ralph S BaricDepartment of Epidemiology, Gillings School of Public Health, University of North Carolina, Chapel Hill, North Carolina 27599.
Timothy A BellDepartment of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599.
Jennifer BrennanMutant Mouse Resource and Research Center, University of North Carolina, Chapel Hill, North Carolina 27599.
Gudrun A BrockmannHumbolt University of Berlin, Berlin, Germany 10117.ORCID 0000-0002-4387-2947
A Wesley BurksDepartment of Pediatrics, University of North Carolina, Chapel Hill, North Carolina 27599.
J Mauro CalabreseDepartment of Pharmacology, University of North Carolina, Chapel Hill, North Carolina 27599.
Kathleen M CaronDepartment of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599.
Richard E CheneyDepartment of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599.
Dominic CiavattaDepartment of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599.
Frank ConlonDepartment of Biology, University of North Carolina, Chapel Hill, North Carolina 27599.
David B DarrLineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599.
James FaberDepartment of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599.
Craig FranklinDepartment of Veterinary Pathobiology, University of Missouri, Columbia, Missouri 65211.
Timothy R GershonDepartment of Neurology, University of North Carolina, Chapel Hill, North Carolina 27599.
Lisa GralinskiDepartment of Epidemiology, Gillings School of Public Health, University of North Carolina, Chapel Hill, North Carolina 27599.
Bin GuDepartment of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599.
Christiann H GainesDepartment of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599.
Robert S HaganDivision of Pulmonary Diseases and Critical Care Medicine, University of North Carolina, Chapel Hill, North Carolina 27599.ORCID 0000-0002-1504-0086
Ernest G HeimsathLineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599.
Mark T HeiseDepartment of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599.
Pablo HockDepartment of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599.
Folami IderaabdullahDepartment of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599.
J Charles JennetteDepartment of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, North Carolina 27599.
Tal KafriDepartment of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina 27599.
Anwica KashfeenDepartment of Computer Science, University of North Carolina, Chapel Hill, North Carolina 27599.
Mike KulisDepartment of Pediatrics, University of North Carolina, Chapel Hill, North Carolina 27599.
Vivek KumarThe Jackson Laboratory, Bar Harbor, Maine 04609.
Colton LinnertzDepartment of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599.
Alessandra Livraghi-ButricoMarsico Lung Institute/UNC Cystic Fibrosis Center, University of North Carolina, Chapel Hill, North Carolina 27599.
K C Kent LloydDepartment of Surgery, University of California Davis, Davis, California 95616.
Cathleen LutzThe Jackson Laboratory, Bar Harbor, Maine 04609.ORCID 0000-0003-2969-8193
Rachel M LynchDepartment of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599.ORCID 0000-0001-8164-0744
Terry MagnusonDepartment of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599.ORCID 0000-0002-0792-835X
Glenn K MatsushimaDepartment of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina 27599.
Rachel McMullanDepartment of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599.
Darla R MillerDepartment of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599.ORCID 0000-0002-0781-7254
Karen L MohlkeDepartment of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599.
Sheryl S MoyDepartment of Psychiatry, University of North Carolina, Chapel Hill, North Carolina 27599.
Caroline E Y MurphyDepartment of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599.ORCID 0000-0001-0986-3178
Maya NajarianDepartment of Computer Science, University of North Carolina, Chapel Hill, North Carolina 27599.
Lori O'BrienDepartment of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599.
Abraham A PalmerUniversity of California San Diego, La Jolla, California 92093.ORCID 0000-0003-3634-0747
Benjamin D PhilpotDepartment of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599.
Scott H RandellDepartment of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599.
Laura ReinholdtThe Jackson Laboratory, Bar Harbor, Maine 04609.ORCID 0000-0003-4054-4048
Yuyu RenUniversity of California San Diego, La Jolla, California 92093.
Steve RockwoodThe Jackson Laboratory, Bar Harbor, Maine 04609.
Allison R RogalaDepartment of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, North Carolina 27599.
Avani SaraswatulaDepartment of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599.
Christopher M SassettiDepartment of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts 01655.
Jonathan C SchislerDepartment of Pharmacology, University of North Carolina, Chapel Hill, North Carolina 27599.ORCID 0000-0001-7382-2783
Sarah A SchoenrockDepartment of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599.
Ginger D ShawDepartment of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599.
John R ShorterDepartment of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599.ORCID 0000-0003-4732-5526
Clare M SmithDepartment of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts 01655.
Celine L St PierreUniversity of California San Diego, La Jolla, California 92093.ORCID 0000-0001-5465-6601
Lisa M TarantinoDepartment of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599.
David W ThreadgillUniversity of California San Diego, La Jolla, California 92093.
William ValdarDepartment of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599.ORCID 0000-0002-2419-0430
Barbara J VilenDepartment of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina 27599.
Keegan WardwellThe Jackson Laboratory, Bar Harbor, Maine 04609.
Jason K WhitmireDepartment of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599.
Lucy WilliamsDepartment of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599.
Mark J ZylkaDepartment of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599.
Martin T FerrisDepartment of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599 fernando_pardo-manuel@med.unc.edu.ORCID 0000-0003-1241-6268
Leonard McMillanDepartment of Computer Science, University of North Carolina, Chapel Hill, North Carolina 27599.
Fernando Pardo Manuel de VillenaDepartment of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599.ORCID 0000-0002-5738-5795
University of North Carolina at Chapel Hill · USJackson Laboratory · USUNC Lineberger Comprehensive Cancer CenterUniversity of California, San Diego · USUniversity of Massachusetts Chan Medical School · USLung Institute · USTexas A&M University · USUniversity of California, Davis · USUniversity of Missouri · US
Funding
Virology Research Program (Program 4)P30CA016086 · NCI · UNIV OF NORTH CAROLINA CHAPEL HILL · PI Deborah F. Tate · 1985 to 2026
$201.5MUnlocking Zika Virus Immune Control and Pathogenesis with the Collaborative CrossU19AI100625 · NIAID · UNIV OF NORTH CAROLINA CHAPEL HILL · PI PARDO-MANUEL DE VILLENA, FERNANDO · 2012 to 2021
$36.6MUNC-CH CENTER FOR ENVIRONMENTAL HEALTH &SUSCEPTIBILITYP30ES010126 · NIEHS · UNIV OF NORTH CAROLINA CHAPEL HILL · PI Hazel B Nichols · 2001 to 2026
$36.3MUCD Mutant Mouse Regional Resource CenterU42OD012210 · OD · UNIVERSITY OF CALIFORNIA AT DAVIS · PI KC KENT LLOYD · 2012 to 2026
$29.2MVector CoreP30DK065988 · NIDDK · UNIV OF NORTH CAROLINA CHAPEL HILL · PI Scott H Randell · 2004 to 2026
$26.5MProject 5: Circadian RhythmsP50DA039841 · NIDA · JACKSON LABORATORY · PI Lisa M Tarantino · 2016 to 2026
$26.2MTranslation of Knowledge on the Pathogenesis of ANCA Disease into NovelP01DK058335 · NIDDK · UNIV OF NORTH CAROLINA CHAPEL HILL · PI NACHMAN, PATRICK H · 2000 to 2019
$25.9MThe Mutant Mouse Resource and Research Center at the University of Missouri - ResourceU42OD010918 · OD · UNIVERSITY OF MISSOURI-COLUMBIA · PI Bret Daniel Ulery · 2012 to 2026
$25.1MResource Section - Core 001U42OD010924 · OD · UNIV OF NORTH CAROLINA CHAPEL HILL · PI TERRY R MAGNUSON · 2012 to 2026
$24.5MThe UNC Chapel Hill Superfund Research Program (UNC-SRP)P42ES031007 · NIEHS · UNIV OF NORTH CAROLINA CHAPEL HILL · PI Kathleen M Gray · 2020 to 2026
$22.2MThe Mutant Mouse Resource and Research Center at The Jackson LaboratoryU42OD010921 · OD · JACKSON LABORATORY · PI Cathleen M Lutz · 2012 to 2026
$21.4MMUTANT MOUSE RESOURCE AND RESEARCH CENTER: ANIMAL EMBRYONIC STEM CELLSU42RR014821 · NCRR · UNIVERSITY OF MISSOURI-COLUMBIA · PI CRITSER, JOHN K. · 2000 to 2011
$15.8MNCI NIH HHS P30 CA016086NCRR NIH HHS U42 RR014821NHGRI NIH HHS U24 HG010100NHLBI NIH HHS K08 HL143271NHLBI NIH HHS R01 HL128119NHLBI NIH HHS R01 HL155986NHLBI NIH HHS R37 HL065619NIAID NIH HHS P01 AI059443NIAID NIH HHS P01 AI132130NIAID NIH HHS R01 AI138337NIAID NIH HHS R01 AI143894NIAID NIH HHS R21 AI117575NIAID NIH HHS U19 AI100625NIA NIH HHS R01 AG066710NIDA NIH HHS P50 DA039841NIDDK NIH HHS P01 DK058335NIDDK NIH HHS P30 DK065988NIDDK NIH HHS R01 DK058702NIEHS NIH HHS K22 ES023849NIEHS NIH HHS P30 ES010126NIEHS NIH HHS P42 ES031007NIEHS NIH HHS R01 ES029925NIEHS NIH HHS R01 ES032643NIGMS NIH HHS F32 GM085999NIGMS NIH HHS R01 GM061728NIGMS NIH HHS R01 GM121806NIGMS NIH HHS R01 GM134531NIH HHS U42 OD010918NIH HHS U42 OD010921NIH HHS U42 OD010924NIH HHS U42 OD012210NIMH NIH HHS R01 MH100241
Abstract
The laboratory mouse is the most widely used animal model for biomedical research, due in part to its well-annotated genome, wealth of genetic resources, and the ability to precisely manipulate its genome. Despite the importance of genetics for mouse research, genetic quality control (QC) is not standardized, in part due to the lack of cost-effective, informative, and robust platforms. Genotyping arrays are standard tools for mouse research and remain an attractive alternative even in the era of high-throughput whole-genome sequencing. Here, we describe the content and performance of a new iteration of the Mouse Universal Genotyping Array (MUGA), MiniMUGA, an array-based genetic QC platform with over 11,000 probes. In addition to robust discrimination between most classical and wild-derived laboratory strains, MiniMUGA was designed to contain features not available in other platforms: (1) chromosomal sex determination, (2) discrimination between substrains from multiple commercial vendors, (3) diagnostic SNPs for popular laboratory strains, (4) detection of constructs used in genetically engineered mice, and (5) an easy-to-interpret report summarizing these results. In-depth annotation of all probes should facilitate custom analyses by individual researchers. To determine the performance of MiniMUGA, we genotyped 6899 samples from a wide variety of genetic backgrounds. The performance of MiniMUGA compares favorably with three previous iterations of the MUGA family of arrays, both in discrimination capabilities and robustness. We have generated publicly available consensus genotypes for 241 inbred strains including classical, wild-derived, and recombinant inbred lines. Here, we also report the detection of a substantial number of
Indexed as
AnimalsFemaleGenome-Wide Association StudyGenotypeGenotyping TechniquesMaleMiceMice, Inbred C57BLOligonucleotide Array Sequence AnalysisPolymorphism, GeneticReproducibility of ResultsSex Determination Processeschromosomal sexdiagnostic SNPsgenetic backgroundgenetic constructsgenetic QCsubstrains
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