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

53. Toward Completion of a Human Chromosome 5 BAC Map and a Mouse Syntenic BAC Map

Steve Lowry, Ze Peng, Duncan Scott, Yiwen Zhu, Mei Wang, Roya Hosseini, Michele Bakis, Joel Martin, Ingrid Plajzer-Frick, Jeff Shreve, Le-Thu Nguyen, and Jan-Fang Cheng

Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720

jcheng@mhgc.lbl.gov

Physical mapping of BACs on human chromosome 5 is in a final stage. The current map consists of 7,618 BAC clones anchored to the chromosome by 2,954 STSs. The distribution of STSs is not even across the chromosome. Approximately 50% of the STSs were derived from 1/3 of the chromosome at the end of the q arm where the average size of contigs is greater than 1 Mb. Most BACs were isolated as single colonies. Restriction maps and FISH maps were constructed for all contigs and are available on the web. The maps are updated regularly.

To date, 1,702 BACs have been selected for sequencing. These BACs contain a total restriction fragment length of 163.5 Mb or approximately 90% of the euchromatin portion of the 190 Mb chromo-some. In an independent experiment, we tested the degree of coverage provided by our map by probing the mapped clones with 796 new STSs (580 ESTs, 216 randomly derived). We found 88% of the STSs were contained by the mapped clones. Both restriction map length and STS analysis indicate that the selected BAC tiling path covers approximately 88-90% of the chromosome.

Sequence already generated for our mapped clones is enabling us to expand contigs by detecting overlaps between BACs that were undetected by restriction fragment analysis and STS content mapping. BAC end sequences in the TIGR database also enable extension of contigs.

The clone map and sequence information for human chromosome 5 are being used to isolate syntenic mouse BACs. Several large contigs have been built using mouse ESTs that were identified by high sequence similarity to human chromosome 5 sequences. To streamline the identification of syntenic mouse ESTs, we have generated a web interface to facilitate (1) blasting of GenBank databases with batches of masked sequences, (2) parsing of output based on length and level of similarity, and (3) reduction of background matches by identifying successive exons in the genomic sequence.