title: The Mouse Universal Genotyping Array: From Substrains to Subspecies.
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.
authors.affiliation: Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599 Lineberger Comprehensive Cancer Center and Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599.
authors.forename: Andrew P
authors.identifier: http://orcid.org/0000-0003-1942-4543
authors.initials: AP
authors.lastname: Morgan
authors.affiliation: Department of Computer Science, University of North Carolina, Chapel Hill, North Carolina 27599.
authors.forename: Chen-Ping
authors.initials: CP
authors.lastname: Fu
authors.affiliation: Department of Computer Science, University of North Carolina, Chapel Hill, North Carolina 27599.
authors.forename: Chia-Yu
authors.initials: CY
authors.lastname: Kao
authors.affiliation: Department of Mathematics and Computer Science, Rhodes College, Memphis, Tennessee 38112.
authors.forename: Catherine E
authors.initials: CE
authors.lastname: Welsh
authors.affiliation: Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599 Lineberger Comprehensive Cancer Center and Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599.
authors.forename: John P
authors.initials: JP
authors.lastname: Didion
authors.affiliation: Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599 Lineberger Comprehensive Cancer Center and Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599.
authors.forename: Liran
authors.initials: L
authors.lastname: Yadgary
authors.affiliation: Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599 Lineberger Comprehensive Cancer Center and Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599.
authors.forename: Leeanna
authors.initials: L
authors.lastname: Hyacinth
authors.affiliation: Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599 Lineberger Comprehensive Cancer Center and Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599.
authors.forename: Martin T
authors.initials: MT
authors.lastname: Ferris
authors.affiliation: Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599 Lineberger Comprehensive Cancer Center and Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599.
authors.forename: Timothy A
authors.initials: TA
authors.lastname: Bell
authors.affiliation: Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599 Lineberger Comprehensive Cancer Center and Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599.
authors.forename: Darla R
authors.initials: DR
authors.lastname: Miller
authors.affiliation: Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599 Lineberger Comprehensive Cancer Center and Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599.
authors.forename: Paola
authors.initials: P
authors.lastname: Giusti-Rodriguez
authors.affiliation: Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599 Lineberger Comprehensive Cancer Center and Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599.
authors.forename: Randal J
authors.initials: RJ
authors.lastname: Nonneman
authors.affiliation: Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599 Lineberger Comprehensive Cancer Center and Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599.
authors.forename: Kevin D
authors.initials: KD
authors.lastname: Cook
authors.affiliation: Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599 Lineberger Comprehensive Cancer Center and Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599.
authors.forename: Jason K
authors.initials: JK
authors.lastname: Whitmire
authors.affiliation: Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina 27599 Lineberger Comprehensive Cancer Center and Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599.
authors.forename: Lisa E
authors.initials: LE
authors.lastname: Gralinski
authors.affiliation: Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706.
authors.forename: Mark
authors.initials: M
authors.lastname: Keller
authors.affiliation: Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706.
authors.forename: Alan D
authors.initials: AD
authors.lastname: Attie
authors.affiliation: The Jackson Laboratory, Bar Harbor, Maine 04609.
authors.forename: Gary A
authors.initials: GA
authors.lastname: Churchill
authors.affiliation: The Jackson Laboratory, Bar Harbor, Maine 04609.
authors.forename: Petko
authors.initials: P
authors.lastname: Petkov
authors.affiliation: Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599 Lineberger Comprehensive Cancer Center and Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599 Department of Psychiatry, University of North Carolina, Chapel Hill, North Carolina 27599.
authors.forename: Patrick F
authors.initials: PF
authors.lastname: Sullivan
authors.affiliation: Mutant Mouse Resource and Research Center, University of North Carolina, Chapel Hill, North Carolina 27599.
authors.forename: Jennifer R
authors.initials: JR
authors.lastname: Brennan
authors.affiliation: Department of Computer Science, University of North Carolina, Chapel Hill, North Carolina 27599.
authors.forename: Leonard
authors.initials: L
authors.lastname: McMillan
authors.affiliation: Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599 Lineberger Comprehensive Cancer Center and Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599 fernando@med.unc.edu.
authors.forename: Fernando
authors.initials: F
authors.lastname: Pardo-Manuel de Villena
mesh_terms: D000483:Alleles; D000818:Animals; D002874:Chromosome Mapping / Q000379:methods; D019295:Computational Biology / Q000379:methods; D018628:Gene Dosage; D005828:Genetics, Population; D016678:Genome; D023281:Genomics / Q000379:methods; D005838:Genotype; D051379:Mice; D008815:Mice, Inbred Strains; D020411:Oligonucleotide Array Sequence Analysis; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide
keywords: genetic mapping; inbred strains; microarrays