As the most powerful model organism in biomedical research, the mouse was the second mammal to be sequenced as part of the Human Genome Project. A high-quality draft of the mouse genome was produced and analyzed in 2002 by the Mouse Genome Sequencing Consortium, including the Broad Institute, Washington University, and the Sanger Institute. The genome sequence allows genetic studies, such as identification of disease mutations, on an unprecedented scale. Initial analysis of the differences and similarities between the mouse and human genomes suggested that as much as 5% of the human genome might be highly conserved between mammals based on function — considerably more than the ~1% of the genome known to contain protein coding genes. This finding has sparked the current search for all the highly conserved, potentially functional elements across mammalian genomes. The Mouse Genome Sequencing Consortium has now produced a high-quality finished genome of the mouse of similar quality to the human genome.
In addition, the Broad Institute has been generating a map of single-nucleotide polymorphisms (SNPs) among mouse strains. The initial set contains ~340,000 SNPs and has been used to characterize the haplotype structure of the laboratory mouse. The current goal is a dense haplotype map (20 kb resolution) of 48 mouse strains, as well as an in-depth characterization of variation within 15 mouse strains. This latter work is being carried out in collaboration with Perlegen Science.