Mouse Universal Genotyping Arrays

The Mouse Universal Genotyping Arrays (MUGA) are a series of SNP genotyping arrays for the house mouse (Mus musculus) on the Illumina Infinium platform. Their content is optimized for genetic mapping in the Collaborative Cross and Diversity Outbred populations; for discriminating haplotypes from common laboratory strains and substrains; and for evaluating the ancestry of wild-caught mice. The MUGA arrays were designed at the University of North Carolina at Chapel Hill, manufactured by Illumina, and distributed by Neogen Inc.

MUGA

(1st generation; 7,851 markers)

The first MUGA array was designed to support the breeding efforts of the Collaborative Cross. All markers were biallelic SNPs chosen for high allele frequency among founder strains and low mutual information. It was optimized for discrimination between CC founder haplotypes and detection of heterozygous segments.

Collaborative Cross Consortium (2012) Genetics 190:389–401.
Welsh CE et al. (2012) Mamm Genome 23:706–712.

MegaMUGA

(2nd generation; 77,808 markers)

MegaMUGA expanded MUGA with ~60,000 additional SNPs optimized for discrimination among CC/DO haplotypes and added ancestry-informative markers for wild mice. It also included Y chromosome, mitochondrial, and engineered construct probes.

Discontinued mid-2015

Rogala AR et al. (2014) Mamm Genome 25:95–108.
Morgan AP, Welsh CE (2015) Mamm Genome 29:521–539.

GigaMUGA

(3rd generation; 143,259 markers)

GigaMUGA carries forward high-quality probes from MegaMUGA and adds ~70,000 SNPs. It improves coverage of laboratory strains, wild-derived strains, CC/DO populations, and adds ~2,000 CNV probes.

Morgan AP et al. (2015) G3 (preprint available via giga.pdf)

Preprint (PDF)

Annotation files

Array	Files	Notes
MUGA	probes (mm9) clusters	Reference clusters derived from Diversity Outbred mice (2,425 samples).
MegaMUGA	probes (mm9) clusters	Reference clusters from 500 DO mice across multiple batches.
GigaMUGA	probes (mm10) clusters	Broad strain coverage including CC, DO, lab and wild mice.

Technical notes

Illumina Infinium uses two-color encoding; SNP design minimizes two-bead probes when possible.
Alleles may be on plus or minus strand; reported alleles may not match dbSNP orientation.

Additional resources

We provide an R package (argyle) for analyzing Illumina genotyping arrays: GitHub repository.

Morgan AP (2015) argyle: an R package for Illumina genotyping arrays (preprint).