Genotyping microarrays are an important resource for genetic mapping, population genetics and monitoring of the genetic integrity of laboratory stocks
The third generation of the Mouse Universal Genotyping Array (MUGA) series has been developed, GigaMUGA, a 143K-probe array on the Illumina Infinium II platform. The content of GigaMUGA is optimized for substrain-level identification of laboratory mice and for genetic mapping in the Collaborative Cross and Diversity Outbred populations. In addition to 141K SNP probes, GigaMUGA contains 2K copy-number probes and more than 100 presence-absence probes for transgenes and other engineered constructs. GigaMUGA is highly informative across a wide range of genetically-diverse samples, from laboratory substrains to other species in the Mus genus. In addition to an in-depth description of the design and performance of the array, we provide genotypes for 500 reference samples (including 61 inbred strains and 115 F1 hybrids), detailed probe-level annotations and recommendations for quality control.
Tools for analysis and quality control of genotypes from the MUGA arrays are implemented in a new open-source software package, argyle. argyle is an add-on package for the R statistical computing environment.
Links to papers and associated stuff:
GigaMUGA paper: http://dx.doi.org/10.1534/g3.115.022087
argyle paper: http://dx.doi.org/10.1534/g3.115.023739
argyle download: https://github.com/andrewparkermorgan/argyle
GigaMUGA genotypes on Dryad: http://dx.doi.org/10.5061/dryad.2p7ns
Annotation files for the three different MUGA platform arrays: http://csbio.unc.edu/MUGA