< platform. Their content is optimized for genetic mapping in the Collaborative Cross and Diveristy 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 by investigators at the University of North Carolina at Chapel Hill, manufactured by Illumina and distributed on a service basis by [Neogen Inc](http://www.neogen.com/Genomics/).
#### MUGA
*(1st generation; 7,851 markers)*
The first MUGA array was designed to support the breeding efforts of the Collaborative Cross. All markers were designed as biallelic SNPs. SNPs were chosen on to have high allele frequency among the CC founder strains and low mutual information. Consequently MUGA was optimized for discrimination between CC founder haplotypes (in the homozygous state) and for detection of heterozygous segments. MUGA was used extensively to accelerate inbreeding in the CC and for QTL mapping in the DO.
> Collaborative Cross Consortium (2012) The genome architecture of the Collaborative Cross mouse genetic reference population. *Genetics* **190**: 389-401. doi:[10.1534/genetics.111.132639](http://dx.doi.org/10.1534/genetics.111.132639)<br />
> Welsh CE, *et al*. (2012) Status and access to the Collaborative Cross population. *Mamm Genome* **23**: 706-712. doi:[10.1007/s00335-012-9410-6](http://dx.doi.org/10.1007/s00335-012-9410-6)
#### MegaMUGA
*(2nd generation; 77,808 markers)*
MegaMUGA was a superset of MUGA but added a further 60,000 SNPs chosen with an optimization scheme which maximized discrimination between the 36 possible haplotype states in CC or DO mice. It also included approximately 14,000 SNPs chosen to be informative for ancestry in wild-caught mice. Coverage of the Y chromosome and mitochondria was greatly improved. Finally, non-SNP probes for a set of common engineered constructs was included to facilitate quality control of knockout and transgenic mice. MegaMUGA was used extensively for management of the CC population; for QTL mapping in the DO and other laboratory crosses; for characterizing wild mouse populations; and for verifying the genetic background of stocks deposited in the [Mutant Mouse Resource and Research Center](https://www.med.unc.edu/mmrrc).
<span class="alert-danger">Discontinued mid-2015</span>.
> Rogala AR, *et al.* (2014) The Collaborative Cross as a resource for modeling human disease: CC011/Unc, a new mouse model for spontaneous colitis. *Mamm Genome* **25**: 95-108. doi:[10.1007/s00335-013-9499-2](http://dx.doi.org/10.1007/s00335-013-9499-2)<br />
> Morgan AP, Welsh CE (2015) Informatics resources for the Collaborative Cross and related mouse populations. *Mamm Genome* **29**: 521-539. doi:[10.1007/s00335-015-9581-z](http://dx.doi.org/10.1007/s00335-015-9581-z)
#### GigaMUGA
*(3rd generation; 143,259 markers)*
GigaMUGA carries forward the highest-quality subset of probes from MegaMUGA and adds an additional 70,000 SNPs. Compared to MegaMUGA, GigaMUGA has improved coverage of alleles in common laboratory strains and nearly doubles the information content for wild-caught mice. A set of 2,000 copy-number probes, tiled across regions of the genome associated with recurrent structural variation, provide the opportunity to assay common CNVs in diverse populations.
GigaMUGA is described in detail in the reference below, which also serves as a general reference for the MUGA series.
> Morgan AP, Fu CP, Kao CY *et al.* (2015) The Mouse Universal Genotyping Array: from substrains to subspecies. *G3*, in press. [preprint](giga.pdf) 
## Annotation files
Array | Files | Notes
------|-------|-------
MUGA | [probes (mm9)](snps.muga.Rdata) <br />[clusters](clusters.muga.Rdata)  | Reference clusters derived from a set of 2,425 Diversity Outbred mice (1309 male, 1116 female) genotyped across multiple batches.
MegaMUGA | [probes (mm9)](snps.megamuga.Rdata) <br />[clusters](clusters.megamuga.Rdata)  | Reference clusters derived from a set of 500 Diversity Outbred mice (250 male, 250 female) genotyped across multiple batches.
GigaMUGA | [probes (mm10)](snps.gigamuga.Rdata) <br />[clusters](clusters.gigamuga.Rdata)  | Reference clusters derived from a set of 500 mice spanning classical inbred strains; wild-derived strains; the Collaborative Cross and Diversity Outbred populations; and common laboratory stocks. These samples were processed in 7 batches but genotype-calling was performed on all batches jointly.
## Technical notes
* The Illumina Infinium chemistry uses two color channels, encoding two nucleotides in each channel. This means that [A/G] and [C/T] SNPs (ie. transitions) can be assayed with a single bead, while transversions require two beads. In the probe annotations below, "sequence A" is the probe sequence for the first bead (always present) and "sequence B" is the probe sequence for the second bead (empty for one-bead probes.) The MUGA arrays were designed to minimize usage fo two-bead probes when possible.
* Alleles may be on the plus or minus strand in the reference genome, so the reported alleles at a given position may not match exactly those reported in, for instance, dbSNP.
## Additional resources
We have developed an add-on package (dubbed `argyle`) for the `R` statistical computing environment to facilitate analysis of data from GigaMUGA and other Illumina arrays. The package is available [on Github](https://github.com/andrewparkermorgan/argyle) and is described in a manuscript currently under review.
> Morgan AP (2015) `argyle`: and `R` package for Illumina genotyping arrays. In review. [preprint](argyle.pdf) 
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