Array CGH profiles. (A) Normalized genome-wide DNA copy number profiles of mouse strain DBA/2J using FVB/N genomic DNA as a reference. BACs are ordered by position on the genome starting with Chromosome 1 and ending with Chromosome X. Vertical bars indicate chromosome boundaries. Each array (MouseArray 3.1) contained 2069 BAC clones, 1848 of which have been mapped onto the draft sequence of the mouse genome (October 2003 freeze). We highlighted in red data points corresponding to a number of the 75 polymorphic clones, which in this individual showed |log₂ratio| > 0.25. (B,C) Normalized DNA copy number profiles of Chromosomes 13 and 17 after hybridization with SPRET/Glasgow and C57BL/6J genomic DNA, respectively, using FVB/N genomic DNA as a reference. Note the high-level DNA copy number polymorphism on the proximal arm of Chromosome 13 showing a gain (log ratio ∼ 1) spanning three overlapping BAC clones. The proximal part of Chromosome 17 shows ²a lower-level DNA copy number polymorphism (log₂ratio ∼ 0.5) encompassing one BAC clone.

Copy number differences among mouse strains compared to FVB/N for BACs mapping to multiple sites by FISH. We display the average log₂ratio computed over all individuals from each mouse strain or species.

Array CGH mapping of interspecific backcrosses. (A,B,C) Genome-wide DNA copy number profiles of three different individuals from the cross (NIH × SPRET/Glasgow) F₁ × NIH using NIH genomic DNA as a reference. We normalized these ratios relative to the ratios from the hybridization of the (NIH × SPRET/Glasgow) F₁ parent versus NIH as a reference, in order to minimize fluctuation in ratios due to technical sources. Note the small deviations in copy number ratio around zero (average log₂ratio < 0.2). The panels on the right show the smoothed genome-wide DNA copy number profiles and microsatellite mapping data for ∼100 markers across the genome for each of the different mice. Blue indicates regions determined to be homozygous and red regions heterozygous for NIH by microsatellite mapping. We confirmed these observations by carrying out two more hybridizations. First, we repeated the hybridizations for all three mice and found all previously observed ratio changes, and second, we did a dye-swap experiment, which resulted in the expected inversion of the ratio changes (data not shown). Microsatellite mapping agrees with the observed subtle changes in the log₂ratio and indicates that relative increases in the log ratio are regions homozygous for NIH, while regions of the genome that exhibit a relative decrease in the log₂ratio correspond to regions heterozygous for NIH. (D) Genome-wide DNA copy number profile (left) and smoothed genome-wide DNA copy number profile (right) of the (NIH × SPRET/Glasgow) F₁ parent using NIH as a reference. Note the absence of subtle copy number deviations as observed in A,B,C.

Agglomerative hierarchical clustering of 74 regions of sequence variation. We used a Euclidian metric and Ward method to cluster both samples and clones. For overlapping BACs in contigs, we used the one clone from the contig for which the greatest number of observations met the threshold (clone denoted by an asterisk). Note that all mice cluster in two separate branches according to species in agreement with accepted phylogeny. Within the M. spretus cluster, all SPRET/Ei mice cluster together and are more closely related to one another than to the outbred SPRET/Glasgow mice. In the M. musculus branch, all individual mice from each of the strains cluster together. Furthermore, FVB/N and NIH are closest to each other in the clustering dendrogram, which again agrees with the strain phylogeny.

Cytogenetic mapping of a multisite BAC. Distribution of hybridization signals on C57BL/6J metaphase spreads from clones RP23-110E20 (red) and RP23-106H14 (green), marker for Chromosome 9. RP23-110E20 was selected from the RP23 library by an STS that mapped to 21.6 Mb on Chromosome 9. We observed hybridization signals at two sites on Chromosome 9 in addition to regions on Chromosomes 5, 7, 12 (2 loci), 14, and 17. Note that at least four out of a total of eight hybridization loci showing hybridization with RP23-110E20 are located in the proximal 1/3 of the corresponding chromosomes. The arrows indicate the positions of the RP23-110E20 hybridization signals.