Advanced integrated mouse YAC map including BAC framework

Functional characterization of the mouse genome requires the availability o f a comprehensive physical map to obtain molecular access to chromosomal re gions of interest. Positional cloning remains a crucial way of linking phen otype with particular genes. A key step and frequent stumbling block in pos itional cloning is making a contig of a genetically defined candidate regio n. The most efficient first step is isolating YAC (Yeast Artificial Chromos ome) clones. A robust, detailed YAC contig map is thus an important tool. E mploying Interspersed Repetitive Sequence (IRS)-PCR genomics, we have gener ated an advanced second-generation YAC contig map of the mouse genome that doubles both the depth of clones and the density of markers available. In a ddition to the primarily YAC-based map, we located 1942 BAC (Bacterial Arti ficial Chromosome) clones. This allows us to present for the first time a d ense framework of BACs spanning the genome of the mouse, which, for instanc e, can serve as a nucleus for genomic sequencing. Four lar.-e-insert mouse YAC libraries from three different strains are included in Our data, and ou r analysis incorporates the data of Hunter et al. and Nusbaum et al. There is a total of 20,205 markers on the final map, 12,033 from our own data, an d a total of 56,093 YACs, of which 44,401 are positive for more than one ma rker.