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

49. Progress in Mapping the Mouse Genome

Cliff S. Han, Linda J. Meincke, Larry L. Deaven, and Norman A. Doggett

Bioscience Division and DOE Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, NM 87545

chan@telomere.lanl.gov

The mouse genome is the second major target for sequencing by the JGI. The initial focus is on regions of biological interest and regions of synteny to human chromosome 5, 16, and 19. The mapping group at LANL is now focusing on mouse genome targets syntenic to human chromosome 16 for BAC map construction. The probes for this effort are derived from STSs and cDNA sequences.

1) STS mapping: We utilyze the sequences from STSs located on mouse chromosomes syntenic to human chromosome 16. These STSs come from various map sources. To date, 960 overgos generated from STSs have been screened against a 5X portion of the RPCI-23 mouse library and 2403 BACs identified. Overgos from 833 STSs were located to at least one BAC.

2) cDNA mapping: We use two approaches to find cDNAs in the region syntenic to human chromosome 16: 1) BLAST against mouse unigene database with unigene sequences from human chromosome 16 that are masked with repeatmasker. 2) BLAST against mouse unigene database with genomic sequences of human chromosome 16 that are masked with repeatmasker. A total 600 cDNA sequences were found after the two BLAST searches. Overgos from 96 of the cDNAs have been screened against the RPCI-23 library. 570 BACs were hit by 94 overgos. Average hit per overgo probe is 12. The first eighty six mouse BAC clones have been sent to the sequence queue.

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