We have conducted a genome-wide analysis of spontaneous copy number variation (CNV) in the laboratory mouse. We used high resolution microarrays to identify 38 CNVs between 14 colonies of the C57BL/6 strain spanning ~967 generations of inbreeding, and examined these loci in 12 additional strains. It is clear from our results that many CNVs arise through a highly non-random process: 18 of 38 were the product of recurrent mutation, and rates of change vary roughly four orders of magnitude across different loci. These recurrent CNVs are distributed throughout the genome, affect 43 genes, and fluctuate in copy number over mere hundreds of generations, observations that raise questions about their contribution to natural variation. Keywords: Representational oligonucleotide microarray analysis, comparative genomic hybridization, DNA copy number variation, structural variation, inbred mice, spontaneous mutation rate
Overall design
We performed ROMA for both liver and tail DNA from a single pedigreed mouse from each of 13 different C57BL/6 substrains. For each substrain we performed at least 3 independent dye-swap experiments against the C57BL/6J reference strain, and we performed at least 1 dye-swap experiment against a third strain. We then used ROMA to assess relative DNA copy number at each locus in 13 additional inbred strains for which we analyzed at least two individuals with at least 1 dye-swap experiment per individual These included four unpedigreed individuals from the C57BL/6Crl substrain, as well as two individuals from each of 12 inbred strains. We also performed ROMA on tail DNA from 6 different C57BL/6 families comprising 12 parental individuals and 41 progeny. We verified CNVs using a custom-designed tiling array (see related submission). We performed three types of replicates: biological replicates involved either separate individuals from the same inbred strain or separate tissues from the same individual (numbers signify individuals, L=Liver, T=Tail); ROMA replicates entailed independently-constructed genomic representations from the same DNA sample, and are indicated in the experiment title (rep1, rep2, etc.); hybridization replicates entailed independent labeling and hybridization of the same genomic representation from the same DNA sample, and are indicated in the experiment title (hyb1, hyb2, etc.)
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