Mouse Diversity Genotyping Array



The Mouse Diversity Genotyping Array (MDA) is a custom Affymetrix array designed by Drs. Fernando Pardo-Manuel de Villena and Gary Churchill. The MDA includes 623,124 probes designed to detect single nucleotide polymorphisms (SNPs) and 916,269 invariant genomic probes that are targeted to functional elements and known segmental duplications in the mouse genome.

The MDA has been applied to assay genetic diversity of thousands of mouse strains, strain panels, outbred and wild-caught mice.


FTP Data Download

Raw and processed MDA data from 1902 samples are available as download as CEL files and as an SQLite database.
Download Sample List (csv)
Link to Data (ftp site) cannot connect to FTP site

MDA Probe Browser

The MDA probe browser provides a visualization of raw probe intensity data in genomic region of interest.
View Probe Intensity Data – bad link 404 not found

Mouse Phylogeny Viewer

MDA data were used generate genome-wide haplotype blocks structure of 198 mouse strains. (Wang et at., 2012)
Mouse Phylogeny Browser (UNC SysGen site)

Haplotype Reconstruction

MDA data were used to reconstruct the haplotypes of recombinant inbred strains (AXB/BXA, LXS and BXD) and chromosome substitution strains (B6.A, B6.PWD and B6.MSM).  We provide an interactive tool for viewing and data download. (Simecek et al., unpubl.)
View Haplotype Reconstructions – bad link (site not found)

Mouse GWAS

MDA genotyping of the Mouse Hybrid Diversity Panel improves the resolution of association mapping. (Rau et al., 2015)
Mouse GWAS Results (UCLA site) – bad link



Rau CD, Parks B, Wang Y, Eskin E, Simecek P, Churchill GA, Lusis AJ

Liu EY, Morgan AP, Chesler EJ, Wang W, Churchill GA, Pardo-Manuel de Villena F
Genetics. 2014 Feb 27. doi: 10.1534/genetics.114.161653
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