RT Journal Article
SR Electronic
T1 The Mouse Universal Genotyping Array: From Substrains to Subspecies
JF G3: Genes|Genomes|Genetics
FD Genetics Society of America
SP 263
OP 279
DO 10.1534/g3.115.022087
VO 6
IS 2
A1 Morgan, Andrew P.
A1 Fu, Chen-Ping
A1 Kao, Chia-Yu
A1 Welsh, Catherine E.
A1 Didion, John P.
A1 Yadgary, Liran
A1 Hyacinth, Leeanna
A1 Ferris, Martin T.
A1 Bell, Timothy A.
A1 Miller, Darla R.
A1 Giusti-Rodriguez, Paola
A1 Nonneman, Randal J.
A1 Cook, Kevin D.
A1 Whitmire, Jason K.
A1 Gralinski, Lisa E.
A1 Keller, Mark
A1 Attie, Alan D.
A1 Churchill, Gary A.
A1 Petkov, Petko
A1 Sullivan, Patrick F.
A1 Brennan, Jennifer R.
A1 McMillan, Leonard
A1 Pardo-Manuel de Villena, Fernando
YR 2016
UL http://www.g3journal.org/content/6/2/263.abstract
AB 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.