Journal: G3: Genes|Genomes|Genetics

Article Title: The Mouse Universal Genotyping Array: From Substrains to Subspecies

doi: 10.1534/g3.115.022087

Figure Lengend Snippet: Quality checks for GigaMUGA arrays. Distribution of per-array mean (A) and standard deviation (B) of total hybridization intensity d (see Materials and Methods ). (C) Examples of the distribution of d within single arrays. From left to right: a high-quality array (an inbred C3H/HeJ mouse), with approximately symmetric distribution and mean near 1.0; a failed array (a Diversity Outbred mouse), with right-skewed distribution; and a high-quality array for a genetically divergent individual (species Mus spretus ), whose distribution is a mixture of a symmetric component and a spike near zero. (D) Cumulative distribution of Kolmogorov-Smirnov statistic ( K ) for departure from the expected N ( 0.97 , 0.42 ) distribution of d . (E) Count of missing calls vs. heterozygous calls for reference samples, by sample group (see Table S1 ).

Article Snippet: 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 ).

Techniques: Standard Deviation, Hybridization

Journal: G3: Genes|Genomes|Genetics

Article Title: The Mouse Universal Genotyping Array: From Substrains to Subspecies

doi: 10.1534/g3.115.022087

Figure Lengend Snippet: Phylogenetic information content of the GigaMUGA array. (A) Diagnostic alleles (blue, M. m. domesticus ; red, M. m. musculus ; green, M. m. castaneus ) are shown as hash marks in a region of chromosome 16 where CAST/EiJ (top) has mixed ancestry. Pure representatives of each subspecies are shown for comparison. Smoothed ancestry blocks inferred using genotypes from the Mouse Diversity Array ( Yang et al. 2011 ) are underlaid. (B) First two PCs from principal components analysis (PCA) of 20 wild M. musculus specimens at a randomly chosen subset of 3000 diagnostic markers (1000 per subspecies) on the autosomes. Individuals are colored according to their subspecies of origin, using the color scheme of panel A. (C) Phylogenetic tree constructed from 83 markers in the male-specific region of the Y chromosome in 67 male samples. Samples are colored according to their nominal subspecies or species of origin: blue, red and green as in panel A; maroon, M. m. molossinus (a M. m. musculus and M. m. castaneus hybrid); and gray, Mus spretus . See Materials and Methods for details of tree construction. Filled dots, wild-caught samples; open dots, inbred strains. (D) Phylogenetic tree for the same 67 male samples as in (C) but constructed from 32 mitochondrial markers.

Article Snippet: 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 ).

Techniques: Diagnostic Assay, Construct

Journal: G3: Genes|Genomes|Genetics

Article Title: The Mouse Universal Genotyping Array: From Substrains to Subspecies

doi: 10.1534/g3.115.022087

Figure Lengend Snippet: Genomic distribution of GigaMUGA probes. (A) Marker density across the autosomes and X-chromosome, plotted in 500-kb bins. Fill color indicates probe type. Individual markers are shown for the Y-chromosome and mitochondrial genome in the insets at right. (B) Relative representation of markers in all but the largest two classes (“haplotype discrimination” and “recombination hotspot”). (C) Distribution of marker density, in markers per Mb, for probes targeting biallelic SNPs (see Materials and Methods ). Dot indicates median, dark bar 25 th − 75 th percentile, light bar 10 th − 90 th percentile. (D) Distribution of physical distance between adjacent marker pairs. (E) Distribution of genetic distance between adjacent marker pairs, calculated by linear interpolation on the genetic map of Liu et al. (2014) .

Article Snippet: 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 ).

Techniques: Marker