Happy little mouse HapMap

Kelly Frazer and colleagues from Perlegen Sciences in California, in association with National Institute of Environmental Health Sciences (NIEHS), have resequenced the genomes of four wild-derived and 11 classical inbred mouse strains to create a comprehensive resource of DNA variation.

The team identified 8.27 million high-quality single nucleotide polymorphisms (SNPs) across the genome, and have generated a genome-wide haplotype map containing 40,898 segments.

For the classical strains, the researchers have found the genetic contributions of the Mus musculus subspecies to be 68 per cent M. m. domesticus, six per cent M. m. musculus, three per cent M. m. castaneus and 10 per cent M. m. molossinus. The remaining 13 per cent are of unknown ancestral origin, the authors say.

The mouse HapMap was published online in the July 29 issue of Nature.

"These data allow researchers to compare the genetic makeup of one mouse strain to another, and perform the necessary genetic analyses to determine why some individuals might be more susceptible to disease than another," the director of the NIEHS, Dr David Schwartz, said.

"This puts us one step closer to understanding individual susceptibility to environmental toxins in humans. We also hope that pharmaceutical companies developing new treatments for environmental diseases will find these data and this paper as a valuable resource."

Much of the project was conducted through a contract between a national toxicology program at NIEHS and Perlegen Sciences.

The Perlegen scientists used C57BL/6J - the first mouse strain to undergo DNA sequencing - as their standard reference to conduct the re-sequencing on the four wild-derived and eleven classical mouse strains.

The data are publicly available on the National Center for Biotechnology Information website and at a website developed by Perlegen which allows researchers to download SNPs, genotypes, and LR-PCR primer pairs, which are currently mapped to NCBI Build 36.

See: http://dx.doi.org/10.1038/nature06067