Population genetics of Mus domesticus wild mice-sc-2010-08-13
Population genetics of Mus domesticus wild mice
The aim of the project is to understand population genetics of Mus domesticus wild mice. We caught ~100 Mus domesticus wild mice in Ambert, Massif Central, France. We genotyped 50 unrelated samples using the Mouse Diversity Array (Yang H et al, Nature Methods, 2009) and ran the APT (Affymetrix Power Tool) to call alleles. In order to validate these genotyping results and gain insight into the degree of diversity, we want to sequence a genome of a Mus domesticus wild mice at about 10x coverage. We strongly encourage researchers to contact us if there is any queries about referencing or publishing analysis based on pre-publication data. This data is part of a pre-publication release. For information on use of the data and the data release policy please see: http://www.sanger.ac.uk/resources/mouse/genomes/datarelease.html
It is known that wild mouse populations carry a huge amount of genetic variation not present in laboratory strains. For example, it has been shown that the classical inbred mice contain less than half the variation segregating in three so-called wild derived inbred strains of mice. Characterisation of the currently unknown genetic variation present in wild mice is critical to for several reasons: 1) It may be desirable to use mice caught in the wild directly, for genetic association studies. It has been shown that the pattern of LD decay in house mice is very similar to that in human populations, providing resolution on the order of one or a few genes. However, to fully utilise this resource, we require a deep catalogue of mouse genetic variation and a detailed haplotype map, along the lines previously established for human association studies. With this data it will be possible to design a genotyping chip for the wild mouse populations. 2) As previously successfully applied in humans, the haplotype framework will allow estimation of fine-scale recombination rates, and identification of "blocks" of high LD, throughout the mouse genome. In turn, the same haplotype framework can be used in conjunction with knowledge of LD and recombination rates to impute those variants typed in the HapMap but not present on a given genotyping platform, adding power to association mapping. We strongly encourage researchers to contact us if there is any queries about referencing or publishing analysis based on pre-publication data. This data is part of a pre-publication release. For information on use of the data and the data release policy please see: http://www.sanger.ac.uk/resources/mouse/genomes/datarelease.html