DOE Human Genome Program Contractor-Grantee Workshop VIII
February 27-March 2, 2000  Santa Fe, NM

50. Rapid Construction of Mouse Sequence-Ready Maps Using a Homology-Driven Approach

Lisa Stubbs, Joomyeong Kim, Laurie Gordon, Hummy Badri, Mari Christensen, Matt Groza, Chi Ha, Sha Hammond, Michelle Vargas, and Eddy Wehri

DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 and Genome Division, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore CA 94550

stubbs5@llnl.gov

We have developed a rapid and efficient "homology-driven" strategy for assembling mouse BAC clone contigs for comparative sequencing, and are using this approach to generate large contigs spanning all mouse regions related to gene-containing segments of human chromosome 19. The strategy uses overgo probes designed from matches detected between human genomic DNA sequence and mouse ESTs or other cDNA fragments in pooled hybridization against gridded mouse BACs. The overgoes are chosen with 50-100 kb spacing and hybridized in pools corresponding to position of the homologous sequence in the human chromosome. The human map is used as a model for assembly of corresponding mouse contigs, and contig assembly, clone integrity, and overlap are verified by restriction fingerprinting, completed at a depth that permits the creation of a detailed restriction map of the mouse contig. This strategy has been used to assemble maps of more than 15 Mb of mouse DNA as of the date of this submission (12/99), and we expect to complete maps of all chromosome 19-related regions within 2-3 months. The maps we have generated provide an important source of clones for directed comparative sequencing, and reagents for basic studies of genome evolution and for analysis of mouse mutations.

Supported by the US DOE, OBER under contract W-7405-ENG-36.