Nature Genetics
37, 532 - 536 (2005)
Published online: 24 April 2005; | doi:10.1038/ng1551
Complex haplotypes, copy number polymorphisms and coding variation in two recently divergent mouse strainsDavid J Adams1, 4, Emmanouil T Dermitzakis1, 2, 4, Tony Cox1, James Smith1, Rob Davies1, Ruby Banerjee1, James Bonfield1, James C Mullikin3, Yeun Jun Chung1, Jane Rogers1
& Allan Bradley11
The Wellcome Trust Sanger Institute, Hinxton, Cambs, CB10 1SA, UK. 2
Department of Genetic Medicine and Development. University of Geneva Medical School, 1211 Geneva, Switzerland. 3
National Human Genome Research Institute, Bethesda, Maryland 20892-8004, USA. 4
These authors contributed equally to this work.
Correspondence should be addressed to Allan Bradley abradley@sanger.ac.ukInbred mouse strains provide the foundation for mouse genetics. By selecting for phenotypic features of interest, inbreeding drives genomic evolution and eliminates individual variation, while fixing certain sets of alleles that are responsible for the trait characteristics of the strain. Mouse strains 129Sv (129S5) and C57BL/6J, two of the most widely used inbred lines, diverged from common ancestors within the last century1,
2,
3,
4,
5, yet very little is known about the genomic differences between them. By comparative genomic hybridization and sequence analysis of 129S5 short insert libraries, we identified substantial structural variation, a complex fine-scale haplotype pattern with a continuous distribution of diversity blocks, and extensive nucleotide variation, including nonsynonymous coding SNPs and stop codons. Collectively, these genomic changes denote the level and direction of allele fixation that has occurred during inbreeding and provide a basis for defining what makes these mouse strains unique.
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